Analysis of Genetic Determinants Involved in Multiresistance in Clinical Strains Isolated from Renal Transplantation Recipients in Guangzhou, China
Lei Shi1), Yali Kou1), Lin Li1) and Shin-ichi Miyoshi2)
1) College of Food and Biological Engineering, South China University of Technology
2) Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
(Received October 30, 2006)
(Accepted December 25, 2006)
In the present study, we examined the antibiotic sensitivity of 19 bacterial strains [5 coagulase-negative Staphylococcus, 2 methicillin-resistant Staphylococcus aureus (S. aureus), 2 Enterococcus faecium (E. faecium), 5 Escherichia coli (E. coli), 3 Cedecea sp., 1 Klebsiella pneumoniae (K. pneumoniae), and 1 Burkholderia cepacia (B. cepacia)], which were isolated from renal transplantation patients using the Kirby-Bauer method. We also investigated the production of β-lactamase and extended-spectrum β-lactamase (ESBL), and the presence of the integrase gene (intI1) and resistance gene cassette. Among the 19 strains tested, all displayed severe multiresistance, and 12 strains produced β-lactamase, in which 6 strains were ESBL positive. Eleven strains were revealed to possess the class 1 integron; however, neither class 2 nor 3 was detected. Additionally, 3 drug resistance genes, aadA2, dfrA17, and aadA5, were found in some strains. The results indicate that the horizontal transfer of the β-lactamase gene and/or the class 1 integron may contribute significantly to the spread of multiresistant bacteria among renal transplantation patients.
Key words renal transplantation, multiresistance, β-lactamase, integron
Rabu, 20 Februari 2008
Selasa, 19 Februari 2008
Gene Cassette PCR: Sequence-Independent Recovery of Entire Genes from Environmental DNA
Gene Cassette PCR: Sequence-Independent Recovery of Entire Genes from Environmental DNA
H. W. Stokes,1,* Andrew J. Holmes,1,2 Blair S. Nield,1 Marita P. Holley,1,2 K. M. Helena Nevalainen,1 Bridget C. Mabbutt,3 and Michael R. Gillings1,2
Department of Biological Sciences,1 Key Centre for Biodiversity and Bioresources,2 and Department of Chemistry,3 Macquarie University, Sydney, New South Wales 2109, Australia
Received 24 May 2001/Accepted 20 August 2001
The vast majority of bacteria in the environment have yet to be cultured. Consequently, a major proportion of both genetic diversity within known gene families and an unknown number of novel gene families reside in these uncultured organisms. Isolation of these genes is limited by lack of sequence information. Where such sequence data exist, PCR directed at conserved sequence motifs recovers only partial genes. Here we outline a strategy for recovering complete open reading frames from environmental DNA samples. PCR assays were designed to target the 59-base element family of recombination sites that flank gene cassettes associated with integrons. Using such assays, diverse gene cassettes could be amplified from the vast majority of environmental DNA samples tested. These gene cassettes contained complete open reading frames, the majority of which were associated with ribosome binding sites. Novel genes with clear homologies to phosphotransferase, DNA glycosylase, methyl transferase, and thiotransferase genes were identified. However, the majority of amplified gene cassettes contained open reading frames with no identifiable homologues in databases. Accumulation analysis of the gene cassettes amplified from soil samples showed no signs of saturation, and soil samples taken at 1-m intervals along transects demonstrated different amplification profiles. Taken together, the genetic novelty, steep accumulation curves, and spatial heterogeneity of genes recovered show that this method taps into a vast pool of unexploited genetic diversity. The success of this approach indicates that mobile gene cassettes and, by inference, integrons are widespread in natural environments and are likely to contribute significantly to bacterial diversity.
from : http://aem.asm.org
H. W. Stokes,1,* Andrew J. Holmes,1,2 Blair S. Nield,1 Marita P. Holley,1,2 K. M. Helena Nevalainen,1 Bridget C. Mabbutt,3 and Michael R. Gillings1,2
Department of Biological Sciences,1 Key Centre for Biodiversity and Bioresources,2 and Department of Chemistry,3 Macquarie University, Sydney, New South Wales 2109, Australia
Received 24 May 2001/Accepted 20 August 2001
The vast majority of bacteria in the environment have yet to be cultured. Consequently, a major proportion of both genetic diversity within known gene families and an unknown number of novel gene families reside in these uncultured organisms. Isolation of these genes is limited by lack of sequence information. Where such sequence data exist, PCR directed at conserved sequence motifs recovers only partial genes. Here we outline a strategy for recovering complete open reading frames from environmental DNA samples. PCR assays were designed to target the 59-base element family of recombination sites that flank gene cassettes associated with integrons. Using such assays, diverse gene cassettes could be amplified from the vast majority of environmental DNA samples tested. These gene cassettes contained complete open reading frames, the majority of which were associated with ribosome binding sites. Novel genes with clear homologies to phosphotransferase, DNA glycosylase, methyl transferase, and thiotransferase genes were identified. However, the majority of amplified gene cassettes contained open reading frames with no identifiable homologues in databases. Accumulation analysis of the gene cassettes amplified from soil samples showed no signs of saturation, and soil samples taken at 1-m intervals along transects demonstrated different amplification profiles. Taken together, the genetic novelty, steep accumulation curves, and spatial heterogeneity of genes recovered show that this method taps into a vast pool of unexploited genetic diversity. The success of this approach indicates that mobile gene cassettes and, by inference, integrons are widespread in natural environments and are likely to contribute significantly to bacterial diversity.
from : http://aem.asm.org
PCR isolation of catechol 2,3-dioxygenase gene fragments from environmental samples and their assembly into functional genes
PCR isolation of catechol 2,3-dioxygenase gene fragments from environmental samples and their assembly into functional genes
Akiko Okuta, Kouhei Ohnishi and Shigeaki Harayama*
Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026, Japan
Received 1 December 1997; revised 9 March 1998; accepted 10 March 1998 Available online 16 June 1998.
A. Nakazawa.
Abstract
A method was developed to isolate central segments of catechol 2,3-dioxygenase (C23O) genes from environmental samples and to insert these C23O gene segments into nahH (the structural gene for C23O encoded by catabolic plasmid NAH7) by replacing the corresponding nahH sequence with the isolated segments. To PCR-amplify the central C23O gene segments, a pair of degenerate primers was designed from amino acid sequences conserved among C23Os. Using these primers, central regions of the C23O genes were amplified from DNA isolated from a mixed culture of phenol-degrading or crude oil-degrading bacteria. Both the 5′ and 3′ regions of nahH were also PCR-amplified by using appropriate primers. These three PCR products, the 5′-nahH and 3′-nahH segments and the central C23O gene segments, were mixed and PCR-amplified again. Since the primers for the amplification of the central C23O gene segments were designed so that the 20 nucleotides at both ends of the segments are identical to the 3′ end of the 5′-nahH segment and the 5′ end of the 3′-nahH segment, respectively, the central C23O gene segments could anneal to both the 5′- and 3′-nahH segments. After the second PCR, hybrid C23O genes in the form of (5′-nahH segment—central C23O gene segment—3′-nahH segment) were amplified to full length. The resulting products were cloned into a vector and used to transform Escherichia coli. This method enabled divergent C23O sequences to be readily isolated, and more than 90% of the hybrid plasmids expressed C23O activity. Thus, the present method is useful to create, without isolating bacteria, a library of functional hybrid genes.
from : http://www.sciencedirect.com
Akiko Okuta, Kouhei Ohnishi and Shigeaki Harayama*
Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026, Japan
Received 1 December 1997; revised 9 March 1998; accepted 10 March 1998 Available online 16 June 1998.
A. Nakazawa.
Abstract
A method was developed to isolate central segments of catechol 2,3-dioxygenase (C23O) genes from environmental samples and to insert these C23O gene segments into nahH (the structural gene for C23O encoded by catabolic plasmid NAH7) by replacing the corresponding nahH sequence with the isolated segments. To PCR-amplify the central C23O gene segments, a pair of degenerate primers was designed from amino acid sequences conserved among C23Os. Using these primers, central regions of the C23O genes were amplified from DNA isolated from a mixed culture of phenol-degrading or crude oil-degrading bacteria. Both the 5′ and 3′ regions of nahH were also PCR-amplified by using appropriate primers. These three PCR products, the 5′-nahH and 3′-nahH segments and the central C23O gene segments, were mixed and PCR-amplified again. Since the primers for the amplification of the central C23O gene segments were designed so that the 20 nucleotides at both ends of the segments are identical to the 3′ end of the 5′-nahH segment and the 5′ end of the 3′-nahH segment, respectively, the central C23O gene segments could anneal to both the 5′- and 3′-nahH segments. After the second PCR, hybrid C23O genes in the form of (5′-nahH segment—central C23O gene segment—3′-nahH segment) were amplified to full length. The resulting products were cloned into a vector and used to transform Escherichia coli. This method enabled divergent C23O sequences to be readily isolated, and more than 90% of the hybrid plasmids expressed C23O activity. Thus, the present method is useful to create, without isolating bacteria, a library of functional hybrid genes.
from : http://www.sciencedirect.com
THE ARIZONA MYCOTA PROJECT
THE ARIZONA MYCOTA PROJECT
Arizona, contrary to what some may think, has more to offer by way of habit than just desert. Rugged mountains, flowing rivers, and expansive forests are also prevalent within the state. These features contribute to a rich diversity of biotic communities. In fact, only a few states, such as California, rival Arizona in this aspect.
In 1990, British mycologist David Hawksworth suggested that only 5% of the Earth's fungal species had been described. Although opinions differ, the Hawksworth estimate is still widely accepted today. The situation is quite similar in Arizona where recent estimates suggest several thousand fungal species that occur in the state have never been recorded. When we consider the diversity of habitats found in Arizona, it is likely that many new records of macrofungi or even new fungal species are awaiting discovery.
Historically, amateur enthusiasts have made numerous contributions to the science of mycology. Recent technological advances, such as GPS units, have enhanced the average citizen's ability to record accurate scientific data, while the advent of digital cameras has greatly improved our ability to capture and transmit images. In the past, it has been proposed that a virtual 'army' of trained mycologist would be needed to truly advance our understanding of the North American fungal flora. However, when considering today's technology and the information that the world wide web has made available to the public, perhaps 'virtual mycologists' can make a significant contribution toward that goal.
The Arizona Mycota Project (AMP) has been created in an attempt to harness this potential resource. This site solicits the help of volunteer contributors, like you, to help advance our knowledge of the Arizona fungal flora (mycota). We encourage persons who have come across interesting fungal finds in the state, to collect specimens and record basic field data OR merely contribute fungal digital images. Specimens of macrofungi sent to AMP will be identified and the field data added to our database. Specimens with significant scientific value will eventually be housed in the University of Arizona's Robert L. Gilbertson Mycological Herbarium. AMP specimens will contribute records of Arizona mycota to the Checklist of Arizona Macrofungi. In addition, AMP images will eventually be linked to the checklist and available for viewing via the World Wide Web.
from : http://www.azfungi.org/amp/
Arizona, contrary to what some may think, has more to offer by way of habit than just desert. Rugged mountains, flowing rivers, and expansive forests are also prevalent within the state. These features contribute to a rich diversity of biotic communities. In fact, only a few states, such as California, rival Arizona in this aspect.
In 1990, British mycologist David Hawksworth suggested that only 5% of the Earth's fungal species had been described. Although opinions differ, the Hawksworth estimate is still widely accepted today. The situation is quite similar in Arizona where recent estimates suggest several thousand fungal species that occur in the state have never been recorded. When we consider the diversity of habitats found in Arizona, it is likely that many new records of macrofungi or even new fungal species are awaiting discovery.
Historically, amateur enthusiasts have made numerous contributions to the science of mycology. Recent technological advances, such as GPS units, have enhanced the average citizen's ability to record accurate scientific data, while the advent of digital cameras has greatly improved our ability to capture and transmit images. In the past, it has been proposed that a virtual 'army' of trained mycologist would be needed to truly advance our understanding of the North American fungal flora. However, when considering today's technology and the information that the world wide web has made available to the public, perhaps 'virtual mycologists' can make a significant contribution toward that goal.
The Arizona Mycota Project (AMP) has been created in an attempt to harness this potential resource. This site solicits the help of volunteer contributors, like you, to help advance our knowledge of the Arizona fungal flora (mycota). We encourage persons who have come across interesting fungal finds in the state, to collect specimens and record basic field data OR merely contribute fungal digital images. Specimens of macrofungi sent to AMP will be identified and the field data added to our database. Specimens with significant scientific value will eventually be housed in the University of Arizona's Robert L. Gilbertson Mycological Herbarium. AMP specimens will contribute records of Arizona mycota to the Checklist of Arizona Macrofungi. In addition, AMP images will eventually be linked to the checklist and available for viewing via the World Wide Web.
from : http://www.azfungi.org/amp/
Effects of the Hot Water Extract and Its Residues of Chlorella Cells on the Growth of Radish Seedlings and the Changes in Soil Microflora
Effects of the Hot Water Extract and Its Residues of Chlorella Cells on the Growth of Radish Seedlings and the Changes in Soil Microflora.
Abstract
The effects of hot water extract and extracted residues of Chlorella cells on the growth of radish seedlings in relation to chages in soil microflora and microbial activity were studied. In particular, actinomycetes spp.isolated from the soil amended with hot water extract of chlorella cells were screened for their productivity of plant growth regulators and antibiotic substances on a plant pathogen, Fusarium oxysporum f.sp.raphani. The hot water extract promoted the growth of 6 species of streptomyces which generally inhabit the soil. The repeated amendment of hot water extract and its residues of chlorella cells to soil promoted the growth of radish seedling and increased the population of actinomycetes and bacteria in soil. The most significant positive correlations were observed between the growth of seedlings and the population of actinomycetes in these soils. Most actinomycetes spp.isolated from the soil amended with hot water extract produced plant growth regulators and also had antagonistic effects on the plant pathogen, Fusarium oxysporum f.sp.raphani. The hot water extract promoted the production of plant growth regulators and the growth of 3 actinomycetes spp.tested. Repeated soil amendment of the hot water extract increased the population of indigenous Fusarium oxysporum f.sp.raphani-antagonists in the soil. These results indicated that the plant growth-promotive effects of the hot water extract and its residues of chlorella cells were due to the increase in the amount of plant growth regulators in soil and the enhancement of soil fungistasis by increasing in the poulation of such profitable actinomycetes in soil.
from : http://ci.nii.ac.jp/naid/110001747407/en/
Abstract
The effects of hot water extract and extracted residues of Chlorella cells on the growth of radish seedlings in relation to chages in soil microflora and microbial activity were studied. In particular, actinomycetes spp.isolated from the soil amended with hot water extract of chlorella cells were screened for their productivity of plant growth regulators and antibiotic substances on a plant pathogen, Fusarium oxysporum f.sp.raphani. The hot water extract promoted the growth of 6 species of streptomyces which generally inhabit the soil. The repeated amendment of hot water extract and its residues of chlorella cells to soil promoted the growth of radish seedling and increased the population of actinomycetes and bacteria in soil. The most significant positive correlations were observed between the growth of seedlings and the population of actinomycetes in these soils. Most actinomycetes spp.isolated from the soil amended with hot water extract produced plant growth regulators and also had antagonistic effects on the plant pathogen, Fusarium oxysporum f.sp.raphani. The hot water extract promoted the production of plant growth regulators and the growth of 3 actinomycetes spp.tested. Repeated soil amendment of the hot water extract increased the population of indigenous Fusarium oxysporum f.sp.raphani-antagonists in the soil. These results indicated that the plant growth-promotive effects of the hot water extract and its residues of chlorella cells were due to the increase in the amount of plant growth regulators in soil and the enhancement of soil fungistasis by increasing in the poulation of such profitable actinomycetes in soil.
from : http://ci.nii.ac.jp/naid/110001747407/en/
Microbial diversity of soil from two hot springs in Uttaranchal Himalaya
Microbial diversity of soil from two hot springs in Uttaranchal Himalaya
Bhavesh Kumar, Pankaj Trivedi, Anil Kumar Mishra, Anita PandeyCorresponding Author Contact Information, E-mail The Corresponding Author and Lok Man S. Palni**
GB Pant Institute of Himalayan Environment and Development, Kosi-Katarmal, Almora, 263 643 Uttaranchal, India
Accepted 13 January 2004. Available online 20 June 2004.
Abstract
Soil samples collected from two hot springs, Soldhar and Ringigad, both located in the Garhwal region of Uttaranchal Himalaya were analysed for their physical, chemical and microbial components. The alkaline pH, total absence of carbon and nitrogen, and high temperature were features common to soil samples from both sites. The Soldhar samples contained higher amounts of Cu, Fe and Mn. Ringigad soil was devoid of Cu, but had much higher phosphate. While the optimum incubation temperature for isolating the maximum microbial counts from soil samples from the two sites was 50°C, microbial growth in broth was also observed when incubated at 80°C. Microscopic examination revealed three types of microbial populations, i.e., bacteria, yeast and filamentous organisms. The soil samples were found to be dominated by spore forming rods. Out of 58 aerobic isolates, 53 were gram positive bacilli. Gram positive anaerobic oval rods were also observed up to 60°C. Soil dilution plates revealed the presence of antagonistic and phosphate solubilizing populations.
Author Keywords: Microbial diversity; Hot springs; Thermophile; Bacilli; Filamentous communities; Uttaranchal Himalaya
from : http://www.sciencedirect.com
Bhavesh Kumar, Pankaj Trivedi, Anil Kumar Mishra, Anita PandeyCorresponding Author Contact Information, E-mail The Corresponding Author and Lok Man S. Palni**
GB Pant Institute of Himalayan Environment and Development, Kosi-Katarmal, Almora, 263 643 Uttaranchal, India
Accepted 13 January 2004. Available online 20 June 2004.
Abstract
Soil samples collected from two hot springs, Soldhar and Ringigad, both located in the Garhwal region of Uttaranchal Himalaya were analysed for their physical, chemical and microbial components. The alkaline pH, total absence of carbon and nitrogen, and high temperature were features common to soil samples from both sites. The Soldhar samples contained higher amounts of Cu, Fe and Mn. Ringigad soil was devoid of Cu, but had much higher phosphate. While the optimum incubation temperature for isolating the maximum microbial counts from soil samples from the two sites was 50°C, microbial growth in broth was also observed when incubated at 80°C. Microscopic examination revealed three types of microbial populations, i.e., bacteria, yeast and filamentous organisms. The soil samples were found to be dominated by spore forming rods. Out of 58 aerobic isolates, 53 were gram positive bacilli. Gram positive anaerobic oval rods were also observed up to 60°C. Soil dilution plates revealed the presence of antagonistic and phosphate solubilizing populations.
Author Keywords: Microbial diversity; Hot springs; Thermophile; Bacilli; Filamentous communities; Uttaranchal Himalaya
from : http://www.sciencedirect.com
Environment, Energy and Forestry
Environment, Energy and Forestry
Taste and Odour
The Guidelines for Canadian Drinking Water Quality 1989 states that drinking water should be inoffensive with respect to both taste and odour. Although taste and odour are not regulated as parameters of health concern, they are perhaps the most important characteristics of drinking water from the point of view of perception. It is next to impossible to convince the public that water is safe to drink if it either tastes or smells bad.
Taste and odour continue to be one of the most difficult issues faced by the water treatment industry. They are a problem, at least intermittently, in most surface water supplies and also in a number of groundwater supplies.
Taste and odour problems may be caused by natural organic matter present in the water, by synthetic chemicals or by some inorganic substances. Some compounds in the first two classes may react with disinfectants such as chlorine to produce tastes and odours that are worse than those in the raw water.
Sources
Taste-causing substances in drinking water are generally inorganic compounds while organic constituents of water are the ones that cause odour problems most frequently -either in themselves or through reaction with disinfectants or oxidation processes.
* Biological Sources
Historically, taste and odour problems in the water treatment industry were associated with algae and decaying vegetation. In addition a class of bacteria known as actinomycetes were linked to taste and odour. The identification of earthy-smelling and musty-smelling compounds were isolated from certain actinomycetes cultures. Many types of algae are common in water supplies and are known as causes of tastes and odours. Both living and dead algae can be responsible for tastes and odours. Although not as common, other bacteria, fungi, zooplankton, nematodes and some amoebae are sometimes responsible for taste and odour.
* Man-Made Sources
Tastes and odours attributed to anthropogenic (man-made) sources can include non-point inputs and municipal and industrial wastewater effluents. Non-point sources may come from direct runoff or from upstream stormwater discharges. This problem can be severe in times of high flow after a prolonged dry or frozen spell, typically in springtime.
* During Treatment
Tastes and odours created during treatment can be caused by either biological activity or the addition of treatment chemicals. The oxidants used in water treatment can remove or reduce tastes and odours but under certain conditions can also cause them.
* In Distribution Systems
There are four sources of tastes and odours in distribution systems:
1. Compounds of biological origin
Tastes and odours of biological origin can be linked to an increase in the number of microorganisms at certain points in the system.
2. Disinfectant residuals and oxidation by-products
Tastes and odours caused by disinfectant residual can be from the residual itself or the reaction on the organic compound.
3. Emissions from pipes and storage facilities
In high concentrations, metals such as lead, copper, zinc and iron can cause tastes on the water as a result of corrosion of the plumbing system.
4. Diffusion of pollutants through synthetic pipes
Some pollutants such as hydrocarbons and phenols may diffuse through plastic piping so care should be given to which way pipes are laid.
* In Household Plumbing
Tastes and odours can be created within ordinary household plumbing. Some examples are metals in high concentrations due to corrosion; hydrogen sulphide forming in hot water tanks; musty odours from inactivity; and odour causing bacteria within certain treatment devices.
Classification and Treatment
It is important to be able to classify an odour that may be detected in drinking water. Classification simplifies odour description, provides a unified terminology, suggests possible sources of odours and may help in choosing the best method of treatment. A taste classification is also required.
The more common descriptors of drinking water odours have been placed in groups. Some of those groups are as follows:
* Group 1 - Earthy/musty/mouldy Most frequently observed;
* May be detected only after addition of chlorine;
* Can be produced by actinomycetes;
* Very low concentrations can lead to complaints.
* Group 2 - Chlorinous High frequency of complaints resulting from chlorination.
* Group 3 - Grass/hay/straw/wood Often associated with algal by-products and sometimes described as decayed vegetation.
* Group 4 - Marshy/swampy/septic/sewage/sulphurous Very offensive;
* May be of natural or anthropogenic origin (sulphur containing compounds).
Treatment
Aeration, filtration, coagulation, oxidation (disinfection), adsorption, and biological treatment are some of the various treatment methods available in assisting in the removal of tastes and odours from the drinking water.
Some of these techniques may be impractical to some situations and can be costly. If oxidation of the water by disinfection and filtering of the water by granular activated carbon (GAC) is not effective in the removal of the tastes and odours, then an alternate source of drinking water should be obtained.
This usually requires construction/ reconstruction of a water well. This frequently involves the installation of additional casing beyond the length (depth) normally required by regulations.
from : http://www.gov.pe.ca/envengfor/index.php3?number=43848&lang=E
Sabtu, 16 Februari 2008
The Science of Composting
While our ancestors realized that compost was helpful for growing plants and improving soil health, they did not know how or why it worked. Our knowledge about the science of composting comes from research conducted during the past 50 years – relatively recent compared to the 2000 plus years that humans have been composting.
Backyard composting speeds up the natural process of decomposition, providing optimum conditions so that organic matter can break down more quickly. As you dig, turn, layer and water your compost pile, you may feel as if you are doing the composting , but the bulk of the work is actually done by numerous types of decomposer organisms.
Microorganisms In A Compost Pile
Microorganisms such as bacteria, fungi, and actinomycetes account for most of the decomposition that takes place in a pile. They are considered chemical decomposers, because they change the chemistry of organic wastes. The larger decomposers, or macroorganisms, in a compost pile include mites, centipedes, sow bugs, snails, millipedes, springtails, spiders, slugs, beetles, ants, flies, nematodes, flatworms, rotifers, and earthworms. They are considered to be physical decomposers because they grind, bite, suck, tear, and chew materials into smaller pieces.
Of all these organisms, aerobic bacteria are the most important decomposers. They are very abundant; there may be millions in a gram of soil or decaying organic matter. You would need 25,000 of them laid end to end on a ruler to make an inch. They are the most nutritionally diverse of all organisms and can eat nearly anything. Bacteria utilize carbon as a source of energy (to keep on eating) and nitrogen to build protein in their bodies (so they can grow and reproduce). They obtain energy by oxidizing organic material, especially the carbon fraction. This oxidation process heats up the compost pile from ambient air temperature. If proper conditions are present, the pile will heat up fairly rapidly (within days) due to bacteria consuming readily decomposable materials.
While bacteria can eat a wide variety of organic compounds, they have difficulty escaping unfavorable environments due to their size and lack of complexity. Changes in oxygen, moisture, temperature, and acidity can make bacteria die or become inactive. Aerobic bacteria need oxygen levels greater than five percent. They are the preferred organisms, because they provide the most rapid and effective composting. They also excrete plant nutrients such as nitrogen, phosphorus, and magnesium. When oxygen levels fall below five percent, the aerobes die and decomposition slows by as much as 90 percent. Anaerobic microorganisms take over and, in the process, produce a lot of useless organic acids and amines (ammonia-like substances) which are smelly, contain unavailable nitrogen and, in some cases, are toxic to plants. In addition, anaerobes produce hydrogen sulfide (aroma-like rotten eggs), cadaverine, and putrescine (other sources of offensive odors).
There are different types of aerobic bacteria that work in composting piles. Their populations will vary according to the pile temperature. Psychrophilic bacteria work in the lowest temperature range. They are most active at 55° F and will work in the pile if the initial pile temperature is less than 70º F. They give off a small amount of heat in comparison to other types of bacteria. The heat they produce is enough however, to help build the pile temperature to the point where another set of bacteria, mesophilic bacteria, start to take over.
Mesophilic bacteria rapidly decompose organic matter, producing acids, carbon dioxide and heat. Their working temperature range is generally between 70º to 100º F. When the pile temperature rises above 100º F, the mesophilic bacteria begin to die off or move to the outer part of the heap. They are replaced by heat-loving thermophilic bacteria.
Thermophilic bacteria thrive at temperatures ranging from 113º to 160º F. Thermophilic bacteria continue the decomposition process, raising the pile temperature 130º to 160º F, where it usually stabilizes. Unless a pile is constantly fed new materials and turned at strategic times, the high range temperatures typically last no more than three to five days. Thermophilic bacteria use up too much of the degradable materials to sustain their population for any length of time. As the thermophilic bacteria decline and the temperature of the pile gradually cools off, the mesophilic bacteria again become dominant. The mesophilic bacteria consume remaining organic material with the help of other organisms.
The drop in compost pile temperature is not a sign that composting is complete, but rather an indication that the compost pile is entering another phase of the composting process. While high temperatures (above 140º F) have the advantage of killing pathogenic organisms and weed seeds, it is unnecessary to achieve those temperatures unless there is a specific concern about killing disease organisms and seeds. (You can greatly reduce the possibility of pathogens in a pile by excluding pet waste, diseased plants, and manure from diseased animals.) Many decomposers are killed or become inactive when pile temperatures rise above 140º F. If the pile temperature exceeds 160º F, you may want to take action and cool the pile by turning it. A number of research projects have shown that soil amended with compost can help fight fungal infestations. If the compost pile temperature goes above 160º F, the composting material may become sterile and lose its disease fighting properties.
While the various types of bacteria are at work, other microorganisms are also contributing to the degradation process. Actinomycetes, a higher-form bacteria similar to fungi and molds, are responsible for the pleasant earthy smell of compost. Grayish in appearance, actinomycetes work in the moderate heat zones of a compost pile. They decompose some of the more resistant materials in the pile such as lignin, cellulose, starches, and proteins. As they reduce materials, they liberate carbon, nitrogen, and ammonia, making nutrients available for higher plants. Actinomycetes occur in large clusters and become most evident during the later stages of decomposition.
Like bacteria and actinomycetes, fungi are also responsible for organic matter decay in a compost pile. Fungi are primitive plants that can be either single celled or many celled and filamentous. They lack a photosynthetic pigment. Their main contribution to a compost pile is to break down cellulose and lignin, after faster acting bacteria make inroads on them. They prefer cooler temperatures (70 to 75º F) and easily digested food sources. As a result, they also tend to take over during the final stage of composting.
Macroorganisms
As mentioned earlier, larger organisms are involved in physically transforming organic material into compost. They are active during the later stages of composting – digging, chewing, sucking, digesting and mixing compostable materials. In addition to mixing materials, they break it into smaller pieces, and transform it into more digestible forms for microorganisms. Their excrement is also digested by bacteria, causing more nutrients to be released.
Micro- and macroorganisms are part of a complex food chain. This food chain consists of organisms classified as either first-, second-, or third-level consumers. The categories are based on what they eat and who eats them. First level consumers become the food for second level consumers, which in turn, are eaten by third level consumers. Soil ecologist Dr. Daniel L. Dindal gives an example of how the food chain works in Ecology of Compost:
“Mites and springtails eat fungi. Tiny feather-winged beetles feed on fungal spores. Nematodes ingest bacteria. Protozoa and rotifers present in water films feed on bacteria and plant particles. Predaceous mites and pseudoscorpions prey upon nematodes, fly larvae, other mites and collembolans. Free-living flatworms ingest gastropods, earthworms, nematodes and rotifers. Third-level consumers such as centipedes, rove beetles, ground beetles, and ants prey on second-level consumers.”
The following is an overview of some of the larger macroorganisms you are likely to find in a compost pile.
Ants - Ants feed on a variety of materials including fungi, seeds, sweets and other insects. They help the composting process by bringing fungi and other organisms into their nests. Ants can make compost richer in phosphorus and potassium by moving minerals around as they work.
Millipedes – Millipedes have wormlike segmented bodies, with each segment having two pairs of walking legs (except the front few segments). Millipedes help break down plant material by eating soft decaying vegetation. They will roll up in a ball when in danger.
Centipedes – Centipedes are flat, segmented worms with one pair of legs in each segment. They are third-level consumers that feed on soil invertebrates, especially insects and spiders.
Sow bugs – Sow bugs have a flat and oval body with distinct segments and ten pairs of legs. They are first-level consumers that feed on rotting woody materials and other decaying vegetation. Pill bugs look similar to sow bugs, but roll up in a ball when disturbed.
Springtails – Springtails are small insects distinguished by their ability to jump when disturbed. They rarely exceed one-quarter inch in length and vary in color from white to blue to black. Springtails are principally fungi feeders, although they also eat molds and chew on decomposing plants.
Flies – Flies are two-wing insects that feed on almost any kind of organic material. They also act as airborne carriers of bacteria, depositing it wherever they land. Although flies are not often a problem associated with compost piles, you can control their numbers by keeping a layer of dry leaves or grass clippings on top of the pile. Also, bury food scraps at least eight to twelve inches deep into the pile. Thermophilic temperatures kill fly larvae. Mites help to keep fly larvae reduced in numbers.
Beetles - Beetles are insects with two pairs of wings. Types commonly found in compost piles include the rove beetle, ground beetle, and feather-winged beetle.The feather-winged beetle feeds on fungal spores. Immature grubs feed on decaying vegetables. Adult rove and ground beetles prey on snails, slugs, and other small animals.
Snails and slugs - Snails and slugs are mollusks that travel in a creeping movement. Snails have a spiral shell with a distinct head and retractable foot. Slugs do not have a shell and are somewhat bullet shaped with antennae on their front section. They feed primarily on living plant material, but they will also attack plant debris. Look for them in finished compost before using it, as they could do damage to your garden if they move in.
Spiders - Spiders are eight-legged creatures and third-level consumers that feed on insects and small invertebrates. They can be very helpful for controlling garden pests.
Earthworms - Earthworms are the most important of the large physical decomposers in a compost pile. Earthworms ingest organic matter and digest it with the help of tiny stones in their gizzards. Their intestinal juices are rich in hormones, enzymes, and other fermenting substances that continue the breakdown process. The worms leave dark, fertile castings behind. A worm can produce its weight in castings each day. These castings are rich in plant nutrients such as nitrogen, calcium, magnesium, and phosphorus that might otherwise be unavailable to plants. Earthworms thrive on compost and contribute greatly to its quality. The presence of earthworms in either compost or soil is evidence of good microbial activity.
Key Factors Affecting The Composting Process
There are certain key environmental factors which affect the speed of composting. The organisms that make compost need food (carbon and nitrogen), air, and water. When provided with a favorable balance, they will produce compost quickly. Other organism factors affecting the speed of composting include surface area/particle size, volume, and temperature.
Food Factor
Organic material provides food for organisms in the form of carbon and nitrogen. As described earlier, bacteria use carbon for energy and protein to grow and reproduce. Carbon and nitrogen levels vary with each organic material. Carbon-rich materials tend to be dry and brown such as leaves, straw, and wood chips. Nitrogen materials tend to be wet and green such as fresh grass clippings and food waste. A tip for estimating an organic material’s carbon/nitrogen content is to remember that fresh, juicy materials are usually higher in nitrogen and will decompose more quickly than older, drier, and woodier tissues that are high in carbon.
A C:N ratio ranging between 25:1 and 30:1 is the optimum combination for rapid decomposition. If ratio is more than 30:1 carbon, heat production drops and decomposition slows. You may have noticed that a pile of leaves or wood chips will sit for a year or more without much apparent decay. When there is too much nitrogen, your pile will likely release the excess as smelly ammonia gas. Too much nitrogen can also cause a rise in the pH level which is toxic to some microorganisms.
The C:N ratio does not need to be exact. Values in Table 1 are calculated on a dry-weight basis. It is difficult to determine an exact C:N ratio without knowing the moisture content of the materials being used. Blending materials to achieve a satisfactory C:N ratio is part of the art of composting. A simple rule of thumb is to develop a volume-based recipe using from one-fourth to one-half high-nitrogen materials.
Table 1 provides estimates of the C:N ratio for selected composting materials.
TABLE 1. Carbon:Nitrogen Ratios
MATERIAL
C:N RATIO
Corn stalks
50-100:1
Fruit waste
35:1
Grass clippings
12-25:1
Hay, green
25:1
Leaves, ash, black elder and elm
21-28:1
Leaves, pine
60-100:1
Leaves, other
30-80:1
Manure, horse and cow
20-25:1
Paper
170-200:1
Sawdust
200-500:1
Seaweed
19:1
Straw
40-100:2
Vegetable waste
12-25:1
Weeds
25:1
Wood chips
500-700:1
Air Factor
Proper aeration is a key environmental factor. Many microorganisms, including aerobic bacteria, need oxygen. They need oxygen to produce energy, grow quickly, and consume more materials. Aeration involves the replacement of oxygen deficient air in a compost pile with fresh air containing oxygen. Natural aeration occurs when air warmed by the composting process rises through the pile, bringing in fresh air from the surroundings. Aeration can also be affected by wind, moisture content, and porosity (spaces between particles in the compost pile). Composting reduces the pile’s porosity and decreases air circulation. Porosity can be negatively affected if large quantities of finely sized materials such as pine needles, grass clippings, or sawdust are used. In addition, air circulation can be impeded if materials become water saturated.
Air movement in the pile can be improved with a few simple techniques. The easiest way to aerate a pile is to regularly turn it with a pitchfork or shovel. Turning will fluff up the pile and increase its porosity. Another option is to add coarse materials such as leaves, straw, or corn stalks. Other options include using a compost aeration tool (available from garden supply companies) or a ventilator stack. Stacks can be made out of perforated plastic pipes, chicken wire wrapped in a circle, or bundles of twigs. Ventilator stacks may be useful for large piles and should stick out the top or sides.
Moisture Factor
Decomposer organisms need water to live. Microbial activity occurs most rapidly in thin water films on the surface of organic materials. Microorganisms can only utilize organic molecules that are dissolved in water. The optimum moisture content for a compost pile should range from 40 to 60 percent. If there is less than 40 percent moisture, bacteria slow down and may become dormant. If there is more than 60 percent, water will force air out of pile pore spaces, suffocating the aerobic bacteria. Anaerobic bacteria will take over, resulting in unpleasant odors.
The ideal percentage of moisture will depend on the organic material’s structure. Straw and corn stalks will need more moisture than leaves, while food waste or grass clippings are not likely to need additional moisture. Since it is difficult to measure moisture, a general rule of thumb is to wet and mix materials so they are about as moist as a wrung-out sponge. Material should feel damp to the touch, with just a drop or two of liquid expelled when squeezed in your hand.
If a compost pile is too dry, it should be watered as the pile is being turned or with a trickling hose. Certain materials such as dead leaves, hay, straw, and sawdust should be gradually moistened until they glisten. These types of materials have a tendency to shed water or adsorb it only on the surface. If a pile is saturated with water, turn it so that materials are restacked. It may also help to add dry, carbon rich material.
Temperature Factor
Temperature is another important factor in the composting process and is related to proper air and moisture levels. As the microorganisms work to decompose the compost, they give off heat which in turn increases pile temperatures. Temperatures between 90º and 140ºF indicate rapid decomposition. Lower temperatures signal a slowing in the composting process. High temperatures greater than 140º F reduce the activity of most organisms.
Outside air temperatures can impact the decomposition process. Warmer outside temperatures in late spring, summer, and early fall stimulate bacteria and speed up decomposition. Low winter temperatures will slow or temporarily stop the composting process. As air temperatures warm up in the spring, microbial activity will resume. During winter months, compost piles can be covered with a tarp to help retain heat longer, but it is not necessary.
Novice composters and people interested in making fast compost may want to track temperatures. The most accurate readings will come from a compost thermometer or temperature probe. Compost thermometers are available from many garden supply companies.
Another method for monitoring temperature is to stick your fist into the pile. You can also place a metal pipe or iron bar in the middle of the pile, periodically pulling it out and feeling it. If the bar or the interior of the pile feels uncomfortably warm or hot during the first few weeks of composting, you’ll know everything is fine. If the temperature inside the pile is the same as the outside, that is an indication that the composting process is slow. You can increase activity by adding nitrogen rich material and turning the pile.
Particle Size Factor
Particle size affects the rate of organic matter breakdown. The more “surface area” available, the easier it is for microorganisms to work, because activity occurs at the interface of particle surfaces and air. Microorganisms are able to digest more, generate more heat, and multiply faster with smaller pieces of material. Although it is not required, reducing materials into smaller pieces will definitely speed decomposition. Organic materials can be chopped, shredded, split, bruised, or punctured to increase their surface area. Don’t “powder” materials, because they will compact and impede air movement in the pile.
For many yard trimmings, cutting materials with a knife, pruning shear, or machete is adequate. An easy way to shred leaves is to mow them before raking. You can collect them at the same time if your mower has a bag attachment.
Another option is to use a lawn trimmer to shred leaves in a garbage can. Several different models of shredders and chippers are available for sale or rental to use in shredding woody materials and leaves. It is a good idea to wear safety goggles when doing any type of shredding or chopping activity. Hands should be kept out of the machine while it is in operation.
Kitchen scraps can be chopped up with a knife. Some ambitious people use meat grinders and blenders to make “garbage soup” from their food scraps and water. They pour the mixture into their heaps.
Volume Factor
Volume is a factor in retaining compost pile heat. In order to become self insulating and retain heat, piles made in the Midwest should ideally be about one cubic yard. The one cubic yard size retains heat and moisture, but is not too large that the material will become unwieldy for turning. Homes located on lakes or in windy areas may want to consider slightly larger piles measuring 4 feet x 4 feet x 4 feet. Smaller compost piles will still decompose material, but they may not heat up as well, and decomposition is likely to take longer.
from : http://web.extension.uiuc.edu/homecompost/science.html
Backyard composting speeds up the natural process of decomposition, providing optimum conditions so that organic matter can break down more quickly. As you dig, turn, layer and water your compost pile, you may feel as if you are doing the composting , but the bulk of the work is actually done by numerous types of decomposer organisms.
Microorganisms In A Compost Pile
Microorganisms such as bacteria, fungi, and actinomycetes account for most of the decomposition that takes place in a pile. They are considered chemical decomposers, because they change the chemistry of organic wastes. The larger decomposers, or macroorganisms, in a compost pile include mites, centipedes, sow bugs, snails, millipedes, springtails, spiders, slugs, beetles, ants, flies, nematodes, flatworms, rotifers, and earthworms. They are considered to be physical decomposers because they grind, bite, suck, tear, and chew materials into smaller pieces.
Of all these organisms, aerobic bacteria are the most important decomposers. They are very abundant; there may be millions in a gram of soil or decaying organic matter. You would need 25,000 of them laid end to end on a ruler to make an inch. They are the most nutritionally diverse of all organisms and can eat nearly anything. Bacteria utilize carbon as a source of energy (to keep on eating) and nitrogen to build protein in their bodies (so they can grow and reproduce). They obtain energy by oxidizing organic material, especially the carbon fraction. This oxidation process heats up the compost pile from ambient air temperature. If proper conditions are present, the pile will heat up fairly rapidly (within days) due to bacteria consuming readily decomposable materials.
While bacteria can eat a wide variety of organic compounds, they have difficulty escaping unfavorable environments due to their size and lack of complexity. Changes in oxygen, moisture, temperature, and acidity can make bacteria die or become inactive. Aerobic bacteria need oxygen levels greater than five percent. They are the preferred organisms, because they provide the most rapid and effective composting. They also excrete plant nutrients such as nitrogen, phosphorus, and magnesium. When oxygen levels fall below five percent, the aerobes die and decomposition slows by as much as 90 percent. Anaerobic microorganisms take over and, in the process, produce a lot of useless organic acids and amines (ammonia-like substances) which are smelly, contain unavailable nitrogen and, in some cases, are toxic to plants. In addition, anaerobes produce hydrogen sulfide (aroma-like rotten eggs), cadaverine, and putrescine (other sources of offensive odors).
There are different types of aerobic bacteria that work in composting piles. Their populations will vary according to the pile temperature. Psychrophilic bacteria work in the lowest temperature range. They are most active at 55° F and will work in the pile if the initial pile temperature is less than 70º F. They give off a small amount of heat in comparison to other types of bacteria. The heat they produce is enough however, to help build the pile temperature to the point where another set of bacteria, mesophilic bacteria, start to take over.
Mesophilic bacteria rapidly decompose organic matter, producing acids, carbon dioxide and heat. Their working temperature range is generally between 70º to 100º F. When the pile temperature rises above 100º F, the mesophilic bacteria begin to die off or move to the outer part of the heap. They are replaced by heat-loving thermophilic bacteria.
Thermophilic bacteria thrive at temperatures ranging from 113º to 160º F. Thermophilic bacteria continue the decomposition process, raising the pile temperature 130º to 160º F, where it usually stabilizes. Unless a pile is constantly fed new materials and turned at strategic times, the high range temperatures typically last no more than three to five days. Thermophilic bacteria use up too much of the degradable materials to sustain their population for any length of time. As the thermophilic bacteria decline and the temperature of the pile gradually cools off, the mesophilic bacteria again become dominant. The mesophilic bacteria consume remaining organic material with the help of other organisms.
The drop in compost pile temperature is not a sign that composting is complete, but rather an indication that the compost pile is entering another phase of the composting process. While high temperatures (above 140º F) have the advantage of killing pathogenic organisms and weed seeds, it is unnecessary to achieve those temperatures unless there is a specific concern about killing disease organisms and seeds. (You can greatly reduce the possibility of pathogens in a pile by excluding pet waste, diseased plants, and manure from diseased animals.) Many decomposers are killed or become inactive when pile temperatures rise above 140º F. If the pile temperature exceeds 160º F, you may want to take action and cool the pile by turning it. A number of research projects have shown that soil amended with compost can help fight fungal infestations. If the compost pile temperature goes above 160º F, the composting material may become sterile and lose its disease fighting properties.
While the various types of bacteria are at work, other microorganisms are also contributing to the degradation process. Actinomycetes, a higher-form bacteria similar to fungi and molds, are responsible for the pleasant earthy smell of compost. Grayish in appearance, actinomycetes work in the moderate heat zones of a compost pile. They decompose some of the more resistant materials in the pile such as lignin, cellulose, starches, and proteins. As they reduce materials, they liberate carbon, nitrogen, and ammonia, making nutrients available for higher plants. Actinomycetes occur in large clusters and become most evident during the later stages of decomposition.
Like bacteria and actinomycetes, fungi are also responsible for organic matter decay in a compost pile. Fungi are primitive plants that can be either single celled or many celled and filamentous. They lack a photosynthetic pigment. Their main contribution to a compost pile is to break down cellulose and lignin, after faster acting bacteria make inroads on them. They prefer cooler temperatures (70 to 75º F) and easily digested food sources. As a result, they also tend to take over during the final stage of composting.
Macroorganisms
As mentioned earlier, larger organisms are involved in physically transforming organic material into compost. They are active during the later stages of composting – digging, chewing, sucking, digesting and mixing compostable materials. In addition to mixing materials, they break it into smaller pieces, and transform it into more digestible forms for microorganisms. Their excrement is also digested by bacteria, causing more nutrients to be released.
Micro- and macroorganisms are part of a complex food chain. This food chain consists of organisms classified as either first-, second-, or third-level consumers. The categories are based on what they eat and who eats them. First level consumers become the food for second level consumers, which in turn, are eaten by third level consumers. Soil ecologist Dr. Daniel L. Dindal gives an example of how the food chain works in Ecology of Compost:
“Mites and springtails eat fungi. Tiny feather-winged beetles feed on fungal spores. Nematodes ingest bacteria. Protozoa and rotifers present in water films feed on bacteria and plant particles. Predaceous mites and pseudoscorpions prey upon nematodes, fly larvae, other mites and collembolans. Free-living flatworms ingest gastropods, earthworms, nematodes and rotifers. Third-level consumers such as centipedes, rove beetles, ground beetles, and ants prey on second-level consumers.”
The following is an overview of some of the larger macroorganisms you are likely to find in a compost pile.
Ants - Ants feed on a variety of materials including fungi, seeds, sweets and other insects. They help the composting process by bringing fungi and other organisms into their nests. Ants can make compost richer in phosphorus and potassium by moving minerals around as they work.
Millipedes – Millipedes have wormlike segmented bodies, with each segment having two pairs of walking legs (except the front few segments). Millipedes help break down plant material by eating soft decaying vegetation. They will roll up in a ball when in danger.
Centipedes – Centipedes are flat, segmented worms with one pair of legs in each segment. They are third-level consumers that feed on soil invertebrates, especially insects and spiders.
Sow bugs – Sow bugs have a flat and oval body with distinct segments and ten pairs of legs. They are first-level consumers that feed on rotting woody materials and other decaying vegetation. Pill bugs look similar to sow bugs, but roll up in a ball when disturbed.
Springtails – Springtails are small insects distinguished by their ability to jump when disturbed. They rarely exceed one-quarter inch in length and vary in color from white to blue to black. Springtails are principally fungi feeders, although they also eat molds and chew on decomposing plants.
Flies – Flies are two-wing insects that feed on almost any kind of organic material. They also act as airborne carriers of bacteria, depositing it wherever they land. Although flies are not often a problem associated with compost piles, you can control their numbers by keeping a layer of dry leaves or grass clippings on top of the pile. Also, bury food scraps at least eight to twelve inches deep into the pile. Thermophilic temperatures kill fly larvae. Mites help to keep fly larvae reduced in numbers.
Beetles - Beetles are insects with two pairs of wings. Types commonly found in compost piles include the rove beetle, ground beetle, and feather-winged beetle.The feather-winged beetle feeds on fungal spores. Immature grubs feed on decaying vegetables. Adult rove and ground beetles prey on snails, slugs, and other small animals.
Snails and slugs - Snails and slugs are mollusks that travel in a creeping movement. Snails have a spiral shell with a distinct head and retractable foot. Slugs do not have a shell and are somewhat bullet shaped with antennae on their front section. They feed primarily on living plant material, but they will also attack plant debris. Look for them in finished compost before using it, as they could do damage to your garden if they move in.
Spiders - Spiders are eight-legged creatures and third-level consumers that feed on insects and small invertebrates. They can be very helpful for controlling garden pests.
Earthworms - Earthworms are the most important of the large physical decomposers in a compost pile. Earthworms ingest organic matter and digest it with the help of tiny stones in their gizzards. Their intestinal juices are rich in hormones, enzymes, and other fermenting substances that continue the breakdown process. The worms leave dark, fertile castings behind. A worm can produce its weight in castings each day. These castings are rich in plant nutrients such as nitrogen, calcium, magnesium, and phosphorus that might otherwise be unavailable to plants. Earthworms thrive on compost and contribute greatly to its quality. The presence of earthworms in either compost or soil is evidence of good microbial activity.
Key Factors Affecting The Composting Process
There are certain key environmental factors which affect the speed of composting. The organisms that make compost need food (carbon and nitrogen), air, and water. When provided with a favorable balance, they will produce compost quickly. Other organism factors affecting the speed of composting include surface area/particle size, volume, and temperature.
Food Factor
Organic material provides food for organisms in the form of carbon and nitrogen. As described earlier, bacteria use carbon for energy and protein to grow and reproduce. Carbon and nitrogen levels vary with each organic material. Carbon-rich materials tend to be dry and brown such as leaves, straw, and wood chips. Nitrogen materials tend to be wet and green such as fresh grass clippings and food waste. A tip for estimating an organic material’s carbon/nitrogen content is to remember that fresh, juicy materials are usually higher in nitrogen and will decompose more quickly than older, drier, and woodier tissues that are high in carbon.
A C:N ratio ranging between 25:1 and 30:1 is the optimum combination for rapid decomposition. If ratio is more than 30:1 carbon, heat production drops and decomposition slows. You may have noticed that a pile of leaves or wood chips will sit for a year or more without much apparent decay. When there is too much nitrogen, your pile will likely release the excess as smelly ammonia gas. Too much nitrogen can also cause a rise in the pH level which is toxic to some microorganisms.
The C:N ratio does not need to be exact. Values in Table 1 are calculated on a dry-weight basis. It is difficult to determine an exact C:N ratio without knowing the moisture content of the materials being used. Blending materials to achieve a satisfactory C:N ratio is part of the art of composting. A simple rule of thumb is to develop a volume-based recipe using from one-fourth to one-half high-nitrogen materials.
Table 1 provides estimates of the C:N ratio for selected composting materials.
TABLE 1. Carbon:Nitrogen Ratios
MATERIAL
C:N RATIO
Corn stalks
50-100:1
Fruit waste
35:1
Grass clippings
12-25:1
Hay, green
25:1
Leaves, ash, black elder and elm
21-28:1
Leaves, pine
60-100:1
Leaves, other
30-80:1
Manure, horse and cow
20-25:1
Paper
170-200:1
Sawdust
200-500:1
Seaweed
19:1
Straw
40-100:2
Vegetable waste
12-25:1
Weeds
25:1
Wood chips
500-700:1
Air Factor
Proper aeration is a key environmental factor. Many microorganisms, including aerobic bacteria, need oxygen. They need oxygen to produce energy, grow quickly, and consume more materials. Aeration involves the replacement of oxygen deficient air in a compost pile with fresh air containing oxygen. Natural aeration occurs when air warmed by the composting process rises through the pile, bringing in fresh air from the surroundings. Aeration can also be affected by wind, moisture content, and porosity (spaces between particles in the compost pile). Composting reduces the pile’s porosity and decreases air circulation. Porosity can be negatively affected if large quantities of finely sized materials such as pine needles, grass clippings, or sawdust are used. In addition, air circulation can be impeded if materials become water saturated.
Air movement in the pile can be improved with a few simple techniques. The easiest way to aerate a pile is to regularly turn it with a pitchfork or shovel. Turning will fluff up the pile and increase its porosity. Another option is to add coarse materials such as leaves, straw, or corn stalks. Other options include using a compost aeration tool (available from garden supply companies) or a ventilator stack. Stacks can be made out of perforated plastic pipes, chicken wire wrapped in a circle, or bundles of twigs. Ventilator stacks may be useful for large piles and should stick out the top or sides.
Moisture Factor
Decomposer organisms need water to live. Microbial activity occurs most rapidly in thin water films on the surface of organic materials. Microorganisms can only utilize organic molecules that are dissolved in water. The optimum moisture content for a compost pile should range from 40 to 60 percent. If there is less than 40 percent moisture, bacteria slow down and may become dormant. If there is more than 60 percent, water will force air out of pile pore spaces, suffocating the aerobic bacteria. Anaerobic bacteria will take over, resulting in unpleasant odors.
The ideal percentage of moisture will depend on the organic material’s structure. Straw and corn stalks will need more moisture than leaves, while food waste or grass clippings are not likely to need additional moisture. Since it is difficult to measure moisture, a general rule of thumb is to wet and mix materials so they are about as moist as a wrung-out sponge. Material should feel damp to the touch, with just a drop or two of liquid expelled when squeezed in your hand.
If a compost pile is too dry, it should be watered as the pile is being turned or with a trickling hose. Certain materials such as dead leaves, hay, straw, and sawdust should be gradually moistened until they glisten. These types of materials have a tendency to shed water or adsorb it only on the surface. If a pile is saturated with water, turn it so that materials are restacked. It may also help to add dry, carbon rich material.
Temperature Factor
Temperature is another important factor in the composting process and is related to proper air and moisture levels. As the microorganisms work to decompose the compost, they give off heat which in turn increases pile temperatures. Temperatures between 90º and 140ºF indicate rapid decomposition. Lower temperatures signal a slowing in the composting process. High temperatures greater than 140º F reduce the activity of most organisms.
Outside air temperatures can impact the decomposition process. Warmer outside temperatures in late spring, summer, and early fall stimulate bacteria and speed up decomposition. Low winter temperatures will slow or temporarily stop the composting process. As air temperatures warm up in the spring, microbial activity will resume. During winter months, compost piles can be covered with a tarp to help retain heat longer, but it is not necessary.
Novice composters and people interested in making fast compost may want to track temperatures. The most accurate readings will come from a compost thermometer or temperature probe. Compost thermometers are available from many garden supply companies.
Another method for monitoring temperature is to stick your fist into the pile. You can also place a metal pipe or iron bar in the middle of the pile, periodically pulling it out and feeling it. If the bar or the interior of the pile feels uncomfortably warm or hot during the first few weeks of composting, you’ll know everything is fine. If the temperature inside the pile is the same as the outside, that is an indication that the composting process is slow. You can increase activity by adding nitrogen rich material and turning the pile.
Particle Size Factor
Particle size affects the rate of organic matter breakdown. The more “surface area” available, the easier it is for microorganisms to work, because activity occurs at the interface of particle surfaces and air. Microorganisms are able to digest more, generate more heat, and multiply faster with smaller pieces of material. Although it is not required, reducing materials into smaller pieces will definitely speed decomposition. Organic materials can be chopped, shredded, split, bruised, or punctured to increase their surface area. Don’t “powder” materials, because they will compact and impede air movement in the pile.
For many yard trimmings, cutting materials with a knife, pruning shear, or machete is adequate. An easy way to shred leaves is to mow them before raking. You can collect them at the same time if your mower has a bag attachment.
Another option is to use a lawn trimmer to shred leaves in a garbage can. Several different models of shredders and chippers are available for sale or rental to use in shredding woody materials and leaves. It is a good idea to wear safety goggles when doing any type of shredding or chopping activity. Hands should be kept out of the machine while it is in operation.
Kitchen scraps can be chopped up with a knife. Some ambitious people use meat grinders and blenders to make “garbage soup” from their food scraps and water. They pour the mixture into their heaps.
Volume Factor
Volume is a factor in retaining compost pile heat. In order to become self insulating and retain heat, piles made in the Midwest should ideally be about one cubic yard. The one cubic yard size retains heat and moisture, but is not too large that the material will become unwieldy for turning. Homes located on lakes or in windy areas may want to consider slightly larger piles measuring 4 feet x 4 feet x 4 feet. Smaller compost piles will still decompose material, but they may not heat up as well, and decomposition is likely to take longer.
from : http://web.extension.uiuc.edu/homecompost/science.html
The Scope of Bacteriology
The Scope of Bacteriology
The Bacteria are a group of single-cell microorganisms with procaryotic cellular configuration. The genetic material (DNA) of procaryotic cells exists unbound in the cytoplasm of the cells. There is no nuclear membrane, which is the definitive characteristic of eukaryotic cells such as those that make up plants and animals. Until recently, bacteria were the only known type of procaryotic cell, and the discipline of biology related to their study is called bacteriology. In the 1980's, with the outbreak of molecular techniques applied to phylogeny of life, another group of procaryotes was defined and informally named "archaebacteria". This group of procaryotes has since been renamed Archaea and has been awarded biological Domain status on the level with Bacteria and Eukarya. The current science of bacteriology includes the study of both Domains of procaryotic cells, but the name "bacteriology" is not likely to change to reflect the inclusion of archaea in the discipline. Actually, many archaea have been studied as intensively and as long as their bacterial counterparts, but with the notion that they were bacteria.
Figure 1. The cyanobacterium Anabaena. American Society for Microbiology. Two (not uncommon) exceptions that procaryotes are unicellular and undifferentiated are seen in Anabaena: 1. The organism lives as a multicellular filament or chain of cells. Procaryotes are considered "unicellular organisms" because all the cells in a filament or colony are of the same type, and any one individual cell can give rise to an exact filament or colony; 2. The predominant photosynthetic (bright yellow-green) cells do differentiate into another type of cell: the obviously large "empty" cells occasionally seen along a filament are differentiated cells in which nitrogen fixation, but not photosynthesis, takes place.
The Origin of Life
When life arose on Earth about 4 billion years ago, the first types of cells to evolve were procaryotic cells. For approximately 2 billion years, procaryotic-type cells were the only form of life on Earth. The oldest known sedimentary rocks, from Greenland, are about 3.8 billion years old. The oldest known fossils are procaryotic cells, 3.5 billion years in age, found in Western Australia and South Africa. The nature of these fossils, and the chemical composition of the rocks in which they are found, indicate that lithotrophic and fermentative modes of metabolism were the first to evolve in early procaryotes. Photosynthesis developed in bacteria at least 3 billion years ago. Anoxygenic photosynthesis (bacterial photosynthesis, which is anaerobic and does not produce O2) preceded oxygenic photosynthesis (plant-type photosynthesis, which yields O2). But oxygenic photosynthesis also arose in procaryotes, specifically in the cyanobacteria, which existed millions of years before the evolution of plants. Larger, more complicated eukaryotic cells did not appear until much later, between 1.5 and 2 billion years ago.
Figure 2. Opalescent Pool in Yellowstone National Park, Wyoming USA. K. Todar. Conditions for life in this environment are similar to Earth over 2 billion years ago. In these types of hot springs, the orange, yellow and brown colors are due to pigmented photosynthetic bacteria which make up the microbial mats. The mats are literally teeming with bacteria. Some of these bacteria such as Synechococcus conduct oxygenic photosynthesis, while others such as Chloroflexus conduct anoxygenic photosynthesis. Other non-photosynthetic bacteria, as well as thermophilic and acidophilic Archaea, are also residents of the hot spring community.
The archaea and bacteria differ fundamentally in their cell structure from eukaryotes, which always contain a membrane-enclosed nucleus, multiple chromosomes, and various other membranous organelles, such as mitochondria, chloroplasts, the golgi apparatus, vacuoles, etc. Unlike plants and animals, archaea and bacteria are unicellular organisms that do not develop or differentiate into multicellular forms. Some bacteria grow in filaments or masses of cells, but each cell in the colony is identical and capable of independent existence. The cells may be adjacent to one another because they did not separate after cell division or because they remained enclosed in a common sheath or slime secreted by the cells, but typically there is no continuity or communication between the cells.
The Universal Tree of Life
On the basis of small subunit ribosomal RNA (ssrRNA) analysis the Woesean tree of life gives rise to three cellular domains of life: Archaea, Bacteria, and Eukarya (Figure 3). Bacteria (formerly known as eubacteria) and Archaea (formerly called archaebacteria) share the procaryotic type of cellular configuration, but otherwise are not related to one another any more closely than they are to the eukaryotic domain, Eukarya. Between the two procaryotes, Archaea are apparently more closely related to Eukarya than are the Bacteria. Eukarya consists of all eukaryotic cell-types, including protista, fungi, plants and animals.
Figure 3. The Universal Tree of Life as derived from sequencing of ssrRNA. N. Pace. Note the three major domains of living organisms: Archaea, Bacteria and Eucarya (Eukarya). The "evolutionary distance" between two organisms is proportional to the measurable distance between the end of a branch to a node to the end of a comparative branch. For example, in Eucarya, humans (Homo) are more closely related to corn (Zea) than to slime molds (Dictyostelium); or in Bacteria, E. coli is more closely related to Agrobacterium than to Thermus.
OFF THE WALL. It is interesting to note several features of phylogeny and evolution that are revealed in the Unrooted Tree.
--Archaea are the least evolved type of cell (they remain closest to the common point of origin). This helps explain why contemporary Archaea are inhabitants of environments that are something like the earth 3.86 billion years ago (hot, salty, acidic, anaerobic, low in organic material, etc.).
--Eucaryotes (Eucarya) are the most evolved type of cell (they move farthest from the common point of origin). However, the eucaryotes do not begin to diversify (branch) until relatively late in evolution, at a time when the Bacteria diversify into oxygenic photosynthesis (Synechococcus) and aerobic respiration (Agrobacterium).
--Mitochondria and the respiratory bacterium, Agrobacterium, are derived from a common ancestor; likewise, chloroplast and the cyanobacterium, Synechococcus, arise from a common origin. This is good evidence for the idea of evolutionary endosymbiosis, i.e., that the origin of eukaryotic mitochondria and chloroplasts is in procaryotic cells that were either captured by, or which invaded, eukaryotic cells, and subsequently entered into a symbiotic association with one cell living inside of the other.
--Diversification in Eucarya is within the Protista (unicellular protozoa, algae, and including fungi). The only multicellular eukaryotes on the Tree are Zea (plants) and Homo (animals). Since the protists, along with the archaea and bacteria, constitute the microbial ("microorganismal") community of the planet, this helps to substantiate the claim the microorganisms are the predominant and most diverse form of life on Earth.
--Humans (Homo) are more closely related to yeast (Saccharomyces) than they are to corn (Zea). There are more genetic differences between E. coli and Bacillus than there are between humans and a paramecium. The protozoan Trichomonas is more closely related to the archaea than it is to the protozoan Trypoanosoma. When the tree branches are amplified there many other similar surprises to biologists.
--Most biology and anthropology students have been presented with fossil and other structural evidence that humans (Homo) emerged a very short time ago on the evolutionary clock. The Tree confirms this evidence on the basis of comparative molecular genetic analysis.
Genomic Timescale of Procaryotic Evolution
Comparison of protein sequences whose genes are common to the genomes of several procaryotes has resulted in a "genomic timescale of procaryotic evolution" and establishes the following dates for some major events in procaryotic evolution (Battistuzzi, et al. MC Evol Biol. 2004; 4: 44). The results are consistent with most other phylogenetic schemes that recognize higher-level groupings of procaryotes.
Table 1. Genomic timescale for some major events in procaryotic evolution
Origin of life: prior to 4.1 billion years ago (Ga)
Origin of methanogenesis: 3.8 - 4.1 Ga
Origin of phototrophy: prior to 3.2 Ga
Divergence of the major groups of Archaea: 3.1 - 4.1 Ga
Origin of anaerobic methanotrophy: after 3.1 Ga
Colonization of land: 2.8 - 3.1 Ga
Divergence of the major groups of Bacteria: 2.5 - 3.2 Ga
Origin of aerobic methanotrophy: 2.5 - 2.8 Ga.
The time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface.
Divergence times for the origin of anaerobic methanotrophy are compatible with carbon isotopic values found in rocks dated 2.8 - 2.6 Ga.
The origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those structures (if biologically produced) would have been made by anoxygenic photosynthesizers.
A well-supported group of three major lineages of Bacteria (Actinobacteria, Deinococcus, and Cyanobacteria), that have been called "Terrabacteria", are associated with an early colonization of land.
Size and Distribution of Bacteria and Archaea
Most procaryotic cells are very small compared to eukaryotic cells. A typical bacterial cell is about 1 micrometer in diameter while most eukaryotic cells are from 10 to 100 micrometers in diameter. Eukaryotic cells have a much greater volume of cytoplasm and a much lower surface : volume ratio than procaryotic cells. A typical procaryotic cell is about the size of a eukaryotic mitochondrion. Since procaryotes are too small to be seen except with the aid of a microscope, it is usually not appreciated that they are the most abundant form of life on the planet, both in terms of biomass and total numbers of species. For example, in the sea, procaryotes make up 90 percent of the total combined weight of all organisms. In a single gram of fertile agricultural soil there may be in excess of 109 bacterial cells, outnumbering all eukaryotic cells there by 10,000 : 1. About 3,000 distinct species of bacteria and archea are recognized, but this number is probably less than one percent of all the species in nature. These unknown procaryotes, far in excess of undiscovered or unstudied plants, are a tremendous reserve of genetic material and genetic information in nature that awaits exploitation.
Procaryotes are found in all of the habitats where eukaryotes live, but, as well, in many natural environments considered too extreme or inhospitable for eukaryotic cells. Thus, the outer limits of life on Earth (hottest, coldest, driest, etc.) are usually defined by the existence of procaryotes. Where eukaryotes and procaryotes live together, there may be mutualistic associations between the organisms that allow both to survive or flourish. The organelles of eukaryotes (mitochondria and chloroplasts) are thought to be remnants of Bacteria that invaded, or were captured by, primitive eukaryotes in the evolutionary past. Numerous types of eukaryotic cells that exist today are inhabitated by endosymbiotic procaryotes.
From a metabolic standpoint, the procaryotes are extraordinarily diverse, and they exhibit several types of metabolism that are rarely or never seen in eukaryotes. For example, the biological processes of nitrogen fixation (conversion of atmospheric nitrogen gas to ammonia) and methanogenesis (production of methane) are metabolically-unique to procaryotes and have an enormous impact on the nitrogen and carbon cycles in nature. Unique mechanisms for energy production and photosynthesis are also seen among the Archea and Bacteria.
The lives of plants and animals are dependent upon the activities of bacterial cells. Bacteria and archea enter into various types of symbiotic relationships with plants and animals that usually benefit both organisms, although a few bacteria are agents of disease.
The metabolic activities of procaryotes in soil habitats have an enormous impact on soil fertility that can affect agricultural practices and crop yields. In the global environment, procaryotes are absolutely essential to drive the cycles of elements that make up living systems, i.e., the carbon, oxygen, nitrogen and sulfur cycles. The origins of the plant cell chloroplast and plant-type (oxygenic) photosynthesis are found in procaryotes. Most of the earth's atmospheric oxygen may have been produced by free-living bacterial cells. The bacteria fix nitrogen and a substantial amount of CO2, as well.
Bacteria or bacterial products (including their genes) can be used to increase crop yield or plant resistance to disease, or to cure or prevent plant disease. Bacterial products include antibiotics to fight infectious disease, as well as components for vaccines used to prevent infectious disease. Because of their simplicity and our relative understanding of their biological processes, the bacteria provide convenient laboratory models for study of the molecular biology, genetics, and physiology of all types of cells, including plant and animal cells.
STRUCTURE AND FUNCTION OF PROCARYOTIC CELLS
Procaryotic cells have three architectural regions (Figure 4): appendages (proteins attached to the cell surface) in the form of flagella and pili; a cell envelope consisting of a capsule, cell wall and plasma membrane; and a cytoplasmic region that contains the cell genome (DNA) and ribosomes and various sorts of inclusions.
Figure 4. Schematic drawing of a typical bacterium.
Surface Structures-Appendages
Flagella are filamentous protein structures attached to the cell surface that provide swimming movement for most motile procaryotic cells. The flagellar filament is rotated by a motor apparatus in the plasma membrane allowing the cell to swim in fluid environments. Bacterial flagella are powered by proton motive force (chemiosmotic potential) established on the bacterial membrane, rather than ATP hydrolysis which powers eukaryotic flagella. Procaryotes are known to exhibit a variety of types of tactic behavior, i.e., the ability to move (swim) in response to environmental stimuli. For example, during chemotaxis a bacterium can sense the quality and quantity of certain chemicals in their environment and swim towards them (if they are useful nutrients) or away from them (if they are harmful substances).
Figure 5.Vibrio choleraehas a single polar flagellum for swimming movement. Electron Micrograph of Vibrio cholerae by Leodotia Pope, Department of Microbiology, University of Texas at Austin.
Fimbriae and Pili are interchangeable terms used to designate short, hair-like structures on the surfaces of procaryotic cells. Fimbriae are shorter and stiffer than flagella, and slightly smaller in diameter. Like flagella, they are composed of protein. A specialized type of pilus the F or sex pilus, mediates the transfer of DNA between mating bacteria, but the function of the smaller, more numerous common pili is quite different. Common pili (almost always called fimbriae) are usually involved in adherence (attachment) of procaryotes to surfaces in nature. In medical situations, they are major determinants of bacterial virulence because they allow pathogens to attach to (colonize) tissues and to resist attack by phagocytic white blood cells.
Figure 6.Fimbriae of Neisseria gonorrhoeaeallow the bacterium to adhere to tissues. Electron micrograph by David M. Phillips, Visuals Unlimited, with permission.
The Cell Envelope
Most procaryotes have a rigid cell wall. The cell wall is an essential structure that protects the delicate cell protoplast from osmotic lysis. The cell wall of Bacteria consists of a polymer of disaccharides cross-linked by short chains of amino acids (peptides). This molecule is a type of peptidoglycan which is called murein. In the Gram-positive bacteria (those that retain the purple crystal violet dye when subjected to the Gram-staining procedure) the cell wall is a thick layer of murein. In the Gram-negative bacteria (which do not retain the crystal violet) the cell wall is relatively thin and is composed of a thin layer of murein surrounded by a membranous structure called the outer membrane. Murein is a substance unique in nature to bacterial cell walls. Also, the outer membrane of Gram-negative bacteria invariably contains a unique component, lipopolysaccharide (LPS or endotoxin), which is toxic to animals. The cell walls of Archaea may be composed of protein, polysaccharides, or peptidgolycan-like molecules, but never do they contain murein. This feature distinguishes the Bacteria from the Archaea.
Although procaryotes lack any intracellular organelles for respiration or photosynthesis, many species possess the physiologic ability to conduct these processes, usually as a function of the plasma membrane. For example, the electron transport system that couples aerobic respiration and ATP synthesis is found in the plasma membrane. The photosynthetic chromophores that harvest light energy for conversion into chemical energy are located in the membrane. Hence, the plasma membrane is the site of oxidative phosphorylation or photophosphorylation in procaryotes, analogous to the functions of mitochondria and chloroplasts in eukaryotic cells. The procaryotic plasma membrane is also a permeability barrier, and it contains a variety of different transportsystems that selectively mediate the passage of substances into and out of the cell.
The membranes of Bacteria are structurally similar to the cell membranes of eukaryotes, except that bacterial membranes consist of saturated or monounsaturated fatty acids (rarely polyunsaturated fatty acids) and do not normally contain sterols. The membranes of Archaea form phospholipid bilayers functionally equivalent to bacterial membranes, but archaeal lipids are saturated, branched, repeating isoprenoid subunits that attach to glycerol via an ether linkage, as opposed to the ester linkage found in glycerides of eukaryotic and bacterial membrane lipids. The structure of archaeal membranes is thought to be an adaptation to their survival in extreme environments.
Most bacteria contain some sort of a polysaccharide layer outside of the cell wall or outer membrane. In a general sense, this layer is called a capsule or glycocalyx. Capsules, slime layers, and glycocalyx are known to mediate attachment of bacterial cells to particular surfaces. Capsules also protect bacteria from engulfment by predatory protozoa or white blood cells (phagocytes) and from attack by antimicrobial agents of plant or animal origin. Capsules in certain soil bacteria protect them from perennial effects of drying or desiccation.
Importance of Surface Components
All of the various surface components of a procaryotic cell are important in its ecology since they mediate the contact of the cell with its environment. The only "sense" that a procaryote has results from its immediate contact with its environment. It must use its surface components to assess the environment and respond in a way that supports its own existence and survival in that environment. The surface properties of a procaryote are determined by the exact molecular composition of its plasma membrane and cell wall, including LPS, and the function of surface structures such as flagella, fimbriae and capsules. Some important ways that procaryotes use their surface components are (1) as permeability barriers that allow selective passage of nutrients and exclusion of harmful substances; (2) as "adhesins" used to attach or adhere to specific surfaces or tissues; (3) as enzymes to mediate specific reactions on the cell surface important in the survival of the procaryote; (4) as "sensing proteins" that can respond to temperature, osmolarity, salinity, light, oxygen, nutrients, etc.,resulting in a signal to the genome of the cell that will cause a beneficial response to the new environment.
Figure 7. The complex surface of Streptococcus pyogenes.Electron micrograph of Streptococcus pyogenes by Maria Fazio and Vincent A. Fischetti, Ph.D. with permission. The Laboratory of Bacterial Pathogenesis and Immunology, Rockefeller University.
Cytoplasmic Constituents
The cytoplasmic constituents of bacteria invariably include the procaryotic chromosome and ribosomes. The chromosome is typically one large circular molecule of DNA, more or less free in the cytoplasm. Procaryotes sometimes possess smaller extrachromosomal pieces of DNA called plasmids. The total DNA content of a cell is referred to as the cell genome. During cell growth and division, the procaryotic chromosome is replicated in the usual semi-conservative fashion before for distribution to progeny cells. However, the eukaryotic processes of meiosis and mitosis are absent in procaryotes. Replication and segregation of procaryotic DNA is coordinated by the membrane, possibly by mesosomes.
The distinct granular appearance of procaryotic cytoplasm is due to the presence and distribution of ribosomes The ribosomes of procaryotes are smaller than cytoplasmic ribosomes of eukaryotes. Procaryotic ribosomes are 70S in size, being composed of 30S and 50S subunits. The 80S ribosomes of eukaryotes are made up of 40S and 60S subunits. Ribosomes are involved in the process of translation (protein synthesis), but some details of their activities differ in eukaryotes, Bacteria and Archaea. Protein synthesis using 70S ribosomes occurs in eukaryotic mitochondria and chloroplasts, and this is taken as a major line of evidence that these organelles are descended from procaryotes.
Often contained in the cytoplasm of procaryotic cells is one or another of some type of inclusion granule. Inclusions are distinct granules that may occupy a substantial part of the cytoplasm. Inclusion granules are usually reserve materials of some sort. For example, carbon and energy reserves may be stored as glycogen (a polymer of glucose) or as polybetahydroxybutyric acid (a type of fat) granules. Polyphosphate inclusions are reserves of PO4 and possibly energy; elemental sulfur (sulfur globules) are stored by some phototrophic and some lithotrophic procaryotes as reserves of energy or electrons. Some inclusion bodies are actually membranous vesicles or intrusions into the cytoplasm which contain photosynthetic pigments or enzymes.
Figure 8. Bacterial colonies growing in a petri dish containing nutrients.
Hans Knoll Institute, Jena, Germany.
TAXONOMY AND CLASSIFICATION OF PROCARYOTES
Haeckel (1866) was the first to create a natural Kingdom for the microorganisms, which had been discovered nearly two centuries before by van Leeuwenhoek. He placed all unicellular (microscopic) organisms in a new kingdom, "Protista", separated from plants (Plantae) and animals (Animalia), which were multicellular (macroscopic) organisms. The development of the electron microscope in the 1950's revealed a fundamental dichotomy among Haeckel's "Protista": some cells contained a membrane-enclosed nucleus, and some cells lacked this intracellular structure. The latter were temporarily shifted to a fourth kingdom, Monera (or Moneres), the procaryotes (also called Procaryotae). Protista remained as a kingdom of unicellular eukaryotic microorganisms. Whittaker refined the system into five kingdoms in 1967, by identifying the Fungi as a separate multicellular eukaryotic kingdom of organisms, distinguished by their absorptive mode of nutrition.
In the 1980's, Woese began phylogenetic analysis of all forms of cellular life based on comparative sequencing of the small subunit ribosomal RNA (ssrRNA) that is contained in all organisms. A new dichotomy was revealed, this time among the procaryotes: their existed two types of procaryotes, as fundamentally unrelated to one another as they are to eukaryotes. Thus, Woese defined the three cellular domains of life as they are displayed in Figure 3 (above): Eucarya, Bacteria and Archaea. Whittaker's Plant, Animal and Fungi kingdoms (all of the multicellular eukaryotes) are at the end of a very small branch of the tree of life, and all other branches lead to microorganisms, either procaryotes (Bacteria and Archaea), or protists (unicellular algae and protozoa).
Although the definitive difference between Woese's Archaea and Bacteria is based on fundamental differences in the nucleotide base sequence in the 16S ribosomal RNA, there are many biochemical and phenotypic differences between the two groups of procaryotes. (Table 2). The phylogenetic tree indicates that Archaea are more closely related to Eukarya than are Bacteria. This relatedness seems most evident in the similarities between transcription and translation in the Archaea and the Eukarya. However, it is also evident that the Bacteria have evolved into chloroplasts and mitochondria, so that these eukaryotic organelles derive their lineage from this group of procaryotes. Perhaps the biological success of eukaryotic cells springs from the evolutionary merger of the two procaryotic life forms.
Figure 9 (above) The structure of a typical procaryotic cell, in this case, a Gram-negative bacterium, compared with (below) a typical eukaryotic cell (plant cell). The procaryote is about 1 micrometer in diameter and about the size of the eukaryotic chloroplast or mitochondrion. Drawings by Vaike Haas, University of Wisconsin-Madison.
Table 2. Phenotypic properties of Bacteria and Archaea compared with Eukarya.
Property Biological Domain
Eukarya Bacteria Archaea
Cell configuration eukaryotic procaryotic procaryotic
Nuclear membrane present absent absent
Number of chromosomes >1 1 1
Chromosome topology linear circular circular
Murein in cell wall - + -
Cell membrane lipids ester-linked glycerides; unbranched; polyunsaturated ester-linked glycerides; unbranched; saturated or monounsaturated ether-linked branched; saturated
Cell membrane sterols present absent absent
Organelles (mitochondria and chloroplasts) present absent absent
Ribosome size 80S (cytoplasmic) 70S 70S
Cytoplasmic streaming + - -
Meiosis and mitosis present absent absent
Transcription and translation coupled - + +
Amino acid initiating protein synthesis methionine N-formyl methionine methionine
Protein synthesis inhibited by streptomycin and chloramphenicol - + -
Protein synthesis inhibited by diphtheria toxin + - +
IDENTIFICATION OF BACTERIA
The criteria used for microscopic identification of procaryotes include cell shape and grouping, Gram-stain reaction, and motility. Bacterial cells almost invariably take one of three forms: rod (bacillus), sphere (coccus), or spiral (spirilla and spirochetes). Rods that are curved are called vibrios. Fixed bacterial cells stain either Gram-positive (purple) or Gram-negative (pink); motility is easily determined by observing living specimens. Bacilli may occur singly or form chains of cells; cocci may form chains (streptococci) or grape-like clusters (staphylococci); spiral shape cells are almost always motile; cocci are almost never motile. This nomenclature ignores the actinomycetes, a prominant group of branched bacteria which occur in the soil. But they are easily recognized by their colonies and their microscopic appearance.
Figure 10. Gram stain of Bacillus anthracis,the cause of anthrax. K. Todar.
Such easily-made microscopic observations, combined with knowing the natural environment of the organism, are important aids to identify the group, if not the exact genus, of a bacterium - providing, of course, that one has an effective key. Such a key is Bergey's Manual of Determinative Bacteriology, the "field guide" to identification of the bacteria. Bergey's Manual describes affiliated groups of Bacteria and Archaea based on a few easily observed microscopic and physiologic characteristics. Further identification requires biochemical tests which will distinguish genera among families and species among genera. Strains within a single species are usually distinguished by genetic or immunological criteria.
A modification of the Bergey's criteria for bacterial identification, without a key, is used to organize the groups of procaryotes for discussion in a companion chapter Major Groups of Prokaryotes
Figure 11. Size and fundamental shapes of procaryotes revealed by three genera of Bacteria (l to r): Staphylococcus(spheres), Lactobacillus(rods), and Aquaspirillum(spirals).
Figure 12. Chains of dividing streptococci.Electron micrograph of Streptococcus pyogenes by Maria Fazio and Vincent A. Fischetti, Ph.D. with permission. The Laboratory of Bacterial Pathogenesis and Immunology, Rockefeller University.
BACTERIAL REPRODUCTION AND GENETICS
Most bacteria reproduce by a relatively simple asexual process called binary fission: each cell increases in size and divides into two cells. During this process there is an orderly increase in cellular structures and components, replication and segregation of the bacterial DNA, and formation of a septum or cross wall which divides the cell into two. The process is evidently coordinated by activites associated with the cell membrane. The DNA molecule is believed to be attached to a point on the membrane where it is replicated. The two DNA molecules remain attached at points side-by-side on the membrane while new membrane material is synthesized between the two points. This draws the DNA molecules in opposite directions while new cell wall and membrane are laid down as a septum between the two chromosomal compartments. When septum formation is complete the cell splits into two progeny cells. The time interval required for a bacterial cell to divide or for a population of cells to double is called the generation time. Generation times for bacterial species growing in nature may be as short as 15 minutes or as long as several days.
Genetic Exchange in Bacteria
Although procaryotes do not undergo sexual reproduction, they are not without the ability to exchange genes and undergo genetic recombination. Bacteria are known to exchange genes in nature by three processes: conjugation, transduction and transformation. Conjugation involves cell-to-cell contact as DNA crosses a sex pilus from donor to recipient. During transduction, a virus transfers the genes between mating bacteria. In transformation, DNA is acquired directly from the environment, having been released from another cell. Genetic recombination can follow the transfer of DNA from one cell to another leading to the emergence of a new genotype (recombinant). It is common for DNA to be transferred as plasmids between mating bacteria. Since bacteria usually develop their genes for drug resistance on plasmids (called resistance transfer factors, or RTFs), they are able to spread drug resistance to other strains and species during genetic exchange processes. The genetic engineering of bacterial cells in the research or biotechnology laboratory is often based on the use of plasmids. The genetic systems of the Archaea are poorly characterized at this point, although the entire genome of Methanosarcina has been sequenced recently which will certainly open up the possibilites for genetic analysis of the group.
Evolution of Bacteria and Archaea
For most procaryotes, mutation is is a major source of variability that allows the species to adapt to new conditions. The mutation rate for most procaryotic genes is approximately 10-8. This means that if a bacterial population doubles from 108 cells to 2 x 108 cells, there is likely to be a mutant present for any given gene. Since procaryotes grow to reach population densities far in excess of 109 cells, such a mutant could develop from a single generation during 15 minutes of growth. The evolution of procaryotes, driven by such darwinian principles of evolution (mutation and selection) is called vertical evolution
However, as a result of the processes of genetic exchange described above, the bacteria and archaea can also undergo a process of horizontal evolution. In this case, genes are transferred laterally from one organism to another, even between members of different Kingdoms, which may allow immediate experimentation with new genetic characteristics in the recipient. Horizontal evolution is being realized to be a significant force in cellular evolution.
The combined effects of fast growth rates, high concentrations of cells, genetic processes of mutation and selection, and the ability to exchange genes, account for the extraordinary rates of adaptation and evolution that can be observed in the procaryotes.
ECOLOGY OF BACTERIA AND ARCHAEA
Bacteria and Archaea are present in all environments that support life. They may be free-living, or living in associations with eukaryotes (plants and animals), and they are found in environments that support no other form of life. Procaryotes have the usual nutritional requirements for growth of cells, but many of the ways that they utilize and transform their nutrients are unique.
Nutritional Types of Organisms
In terms of carbon utilization a cell may be heterotrophic or autotrophic. Heterotrophs obtain their carbon and energy for growth from organic compounds in nature. Autotrophs use C02 as a sole source of carbon for growth and obtain their energy from light (photoautotrophs) or from the oxidation of inorganic compounds (lithoautotrophs).
Most heterotrophic bacteria are saprophytes, meaning that they obtain their nourishment from dead organic matter. In the soil, saprophytic bacteria and fungi are responsible for biodegradation of organic material. Ultimately, organic molecules, no matter how complex, can be degraded to CO2. Probably no naturally-occurring organic substance cannot be degraded by the combined activities of the bacteria and fungi. Hence, most organic matter in nature is converted by heterotrophs to CO2, only to be converted back into organic material by autotrophs that die and nourish heterotrophs to complete the carbon cycle.
Lithotrophic procaryotes have a type of energy-producing metabolism which is unique. Lithotrophs (also called chemoautotrophs) use inorganic compounds as sources of energy, i.e., they oxidize compounds such as H2 or H2S or NH3 to obtain electrons to feed in to an electron transport system and to produce ATP. Lithotrophs are found in soil and aquatic environments wherever their energy source is present. Most lithotrophs are autotrophs so they can grow in the absence of any organic material. Lithotrophic species are found among the Bacteria and the Archaea. Sulfur-oxidizing lithotrophs convert H2S to So and So to SO4. Nitrifying bacteria convert NH3 to NO2 and NO2 to NO3; methanogens strip electrons off of H2 as a source of energy and add electrons to CO2 to form CH4 (methane). Lithotrophs have an obvious impact on the sulfur, nitrogen and carbon cycles in the biosphere.
Photosynthetic bacteria convert light energy into chemical energy for growth. Most phototrophic bacteria are autotrophs so their role in the carbon cycle is analogous to that of plants. The planktonic cyanobacteria are the "grass of the sea" and their form of oxygenic photosynthesis generates a substantial amount of O2 in the biosphere. However, among the photosynthetic bacteria are types of metabolism not seen in eukaryotes, including photoheterotrophy (using light as an energy source while assimilating organic compounds as a source of carbon), anoxygenic photosynthesis, and unique mechanisms of CO2 fixation (autotrophy).
Photosynthesis has not been found to occur among the Archaea, but one archaeal species of employs a light-driven non photosynthetic means of energy generation based on the use of a chromophore called bacteriorhodopsin
Responses to Environmental Conditions
Procaryotes vary widely in their response to O2 (molecular oxygen). Organisms that require O2 for growth are called obligate aerobes; those which are inhibited or killed by O2, and which grow only in its absence, are called obligate anaerobes; organisms which grow either in the presence or absence of O2 are called facultative anaerobes. Whether or not a particular organism can exist in the presence of O2 depends upon the distribution of certain enzymes such as superoxide dismutase and catalase that are required to detoxify lethal oxygen radicals that are always generated by living systems in the presence of O2
Procaryotes also vary widely in their response to temperature. Those that live at very cold temperatures (0 degrees or lower) are called psychrophiles; those which flourish at room temperature (25 degrees) or at the temperature of warm-blooded animals (37 degrees) are called mesophiles; those that live at high temperatures (greater than 45 degrees) are thermophiles. The only limit that seems to be placed on growth of certain procaryotes in nature relative to temperature is whether liquid water exists. Hence growing procaryotic cells can be found in supercooled environments (ice does not form) as low as -20 degrees and superheated environments (steam does not form) as high as 120 degrees. Archaea have been detected around thermal vents on the ocean floor where the temperature is as high as 320 degrees!
Symbiosis
The biomass of procaryotic cells in the biosphere, their metabolic diversity, and their persistence in all habitats that support life, ensures that the procaryotes play a crucial role in the cycles of elements and the functioning of the world ecosystem. However, the procaryotes affect the world ecology in another significant way through their inevitable interactions with insects, plants and animals. Some bacteria are required to associate with insects, animals or plants for the latter to survive. For example, the sex of offspring of certain insects is determined by endosymbiotic bacteria. Ruminant animals (cows, sheep, etc.), whose diet is mainly cellulose (plant material), must have cellulose-digesting bacteria in their intestine to convert the cellulose to a form of carbon that the animal can assimilate. Leguminous plants grow poorly in nitrogen-deprived soils unless they are colonized by nitrogen-fixing bacteria which can supply them with a biologically-useful form of nitrogen.
Bacterial Pathogenicity
Some bacteria are parasites of plants or animals, meaning that they grow at the expense of their eukaryotic host and may damage, harm, or even kill it in the process. Such bacteria that cause disease in plants or animals are pathogens. Human diseases caused by bacterial pathogens include tuberculosis, whooping cough, diphtheria, tetanus, gonorrhea, syphilis, pneumonia, cholera and typhoid fever, to name a few. The bacteria that cause these diseases have special structural or biochemical properties that determine their virulence or pathogenicity. These include: (1) ability to colonize and invade their host; (2) ability to resist or withstand the antibacterial defenses of the host; (3) ability to produce various toxic substances that damage the host. Plant diseases, likewise, may be caused by bacterial pathogens. More than 200 species of bacteria are associated with plant diseases.
Figure 13. Borrelia burgdorferi. This spirochete is the bacterial parasite that causes Lyme disease. CDC.
APPLICATIONS OF BACTERIA IN INDUSTRY AND BIOTECHNOLOGY
Exploitation of Bacteria by Humans
In addition to other ecological roles, procaryotes, especially bacteria, are used industrially in the manufacture of foods, drugs, vaccines, insecticides, enzymes, hormones and other useful biological products. In fact, through genetic engineering of bacteria, these unicellular organisms can be coaxed to produce just about anything that there is a gene for. The genetic systems of bacteria are the foundation of the biotechnology industry.
In the foods industry, lactic acid bacteria such as Lactobacillus and Streptococcus are used the manufacture of dairy products such as yogurt, cheese, buttermilk, sour cream, and butter. Lactic acid fermentations are also used in pickling process. Bacterial fermentations can be used to produce lactic acid, acetic acid, ethanol or acetone. In many parts of the world, various human cultures ferment indigenous plant material using Zymomonas bacteria to produce the regional alcoholic beverage. For example, in Mexico, a Maguey cactus (Agave) is fermented to "cactus beer" or pulque. Pulque can be ingested as is, or distilled into tequila.
In the pharmaceutical industry, bacteria are used to produce antibiotics, vaccines, and medically-useful enzymes. Most antibiotics are made by bacteria that live in soil. Actinomycetes such as Streptomyces produce tetracyclines, erythromycin, streptomycin, rifamycin and ivermectin. Bacillus species produce bacitracin and polymyxin. Bacterial products are used in the manufacture of vaccines for immunization against infectious disease. Vaccines against diphtheria, whooping cough, tetanus, typhoid fever and cholera are made from components of the bacteria that cause the respective diseases. It is significant to note here that the use of antibiotics against infectious disease and the widespread practice of vaccination (immunization) against infectious disease are two twentieth-century developments that have drastically increased the quality of life and the average life expectancy of individuals in developed countries.
Biotechnology
The biotechnology industry uses bacterial cells for the production of human hormones such as insulin and human growth factor (protropin), and human proteins such as interferon, interleukin-2, and tumor necrosis factor. These products are used for the treatment of a variety of diseases ranging from diabetes to tuberculosis and AIDS. Other biotehnological applications of bacteria involve the genetic construction of "super strains" of organisms to perform a particular metabolic task in the environment. For example, bacteria which have been engineered genetically to degrade petroleum products can be used in cleanup efforts of oil spills in seas or on beaches. One area of biotechnology involves improvement of the qualities of plants through genetic engineering. Genes can be introduced into plants by a bacterium Agrobacterium tumefaciens. Using A. tumefaciens, plants have been genetically engineered so that they are resistant to certain pests, herbicides, and diseases. Finally, the polymerase chain reaction (PCR), a mainstay of the biotechnology industry because it allows scientists to duplicate genes starting with a single molecule of DNA, is based on the use of a DNA polymerase enzyme derived from a thermophilic bacterium, Thermus aquaticus.
Thermus aquaticus,the thermophilic bacterium that is the source of taq polymerase.
L wet mount; R electron micrograph. T.D. Brock. Life at High Temperatures.
from :
http://www.bact.wisc.edu/themicrobialworld/bacteriology.html
The Bacteria are a group of single-cell microorganisms with procaryotic cellular configuration. The genetic material (DNA) of procaryotic cells exists unbound in the cytoplasm of the cells. There is no nuclear membrane, which is the definitive characteristic of eukaryotic cells such as those that make up plants and animals. Until recently, bacteria were the only known type of procaryotic cell, and the discipline of biology related to their study is called bacteriology. In the 1980's, with the outbreak of molecular techniques applied to phylogeny of life, another group of procaryotes was defined and informally named "archaebacteria". This group of procaryotes has since been renamed Archaea and has been awarded biological Domain status on the level with Bacteria and Eukarya. The current science of bacteriology includes the study of both Domains of procaryotic cells, but the name "bacteriology" is not likely to change to reflect the inclusion of archaea in the discipline. Actually, many archaea have been studied as intensively and as long as their bacterial counterparts, but with the notion that they were bacteria.
Figure 1. The cyanobacterium Anabaena. American Society for Microbiology. Two (not uncommon) exceptions that procaryotes are unicellular and undifferentiated are seen in Anabaena: 1. The organism lives as a multicellular filament or chain of cells. Procaryotes are considered "unicellular organisms" because all the cells in a filament or colony are of the same type, and any one individual cell can give rise to an exact filament or colony; 2. The predominant photosynthetic (bright yellow-green) cells do differentiate into another type of cell: the obviously large "empty" cells occasionally seen along a filament are differentiated cells in which nitrogen fixation, but not photosynthesis, takes place.
The Origin of Life
When life arose on Earth about 4 billion years ago, the first types of cells to evolve were procaryotic cells. For approximately 2 billion years, procaryotic-type cells were the only form of life on Earth. The oldest known sedimentary rocks, from Greenland, are about 3.8 billion years old. The oldest known fossils are procaryotic cells, 3.5 billion years in age, found in Western Australia and South Africa. The nature of these fossils, and the chemical composition of the rocks in which they are found, indicate that lithotrophic and fermentative modes of metabolism were the first to evolve in early procaryotes. Photosynthesis developed in bacteria at least 3 billion years ago. Anoxygenic photosynthesis (bacterial photosynthesis, which is anaerobic and does not produce O2) preceded oxygenic photosynthesis (plant-type photosynthesis, which yields O2). But oxygenic photosynthesis also arose in procaryotes, specifically in the cyanobacteria, which existed millions of years before the evolution of plants. Larger, more complicated eukaryotic cells did not appear until much later, between 1.5 and 2 billion years ago.
Figure 2. Opalescent Pool in Yellowstone National Park, Wyoming USA. K. Todar. Conditions for life in this environment are similar to Earth over 2 billion years ago. In these types of hot springs, the orange, yellow and brown colors are due to pigmented photosynthetic bacteria which make up the microbial mats. The mats are literally teeming with bacteria. Some of these bacteria such as Synechococcus conduct oxygenic photosynthesis, while others such as Chloroflexus conduct anoxygenic photosynthesis. Other non-photosynthetic bacteria, as well as thermophilic and acidophilic Archaea, are also residents of the hot spring community.
The archaea and bacteria differ fundamentally in their cell structure from eukaryotes, which always contain a membrane-enclosed nucleus, multiple chromosomes, and various other membranous organelles, such as mitochondria, chloroplasts, the golgi apparatus, vacuoles, etc. Unlike plants and animals, archaea and bacteria are unicellular organisms that do not develop or differentiate into multicellular forms. Some bacteria grow in filaments or masses of cells, but each cell in the colony is identical and capable of independent existence. The cells may be adjacent to one another because they did not separate after cell division or because they remained enclosed in a common sheath or slime secreted by the cells, but typically there is no continuity or communication between the cells.
The Universal Tree of Life
On the basis of small subunit ribosomal RNA (ssrRNA) analysis the Woesean tree of life gives rise to three cellular domains of life: Archaea, Bacteria, and Eukarya (Figure 3). Bacteria (formerly known as eubacteria) and Archaea (formerly called archaebacteria) share the procaryotic type of cellular configuration, but otherwise are not related to one another any more closely than they are to the eukaryotic domain, Eukarya. Between the two procaryotes, Archaea are apparently more closely related to Eukarya than are the Bacteria. Eukarya consists of all eukaryotic cell-types, including protista, fungi, plants and animals.
Figure 3. The Universal Tree of Life as derived from sequencing of ssrRNA. N. Pace. Note the three major domains of living organisms: Archaea, Bacteria and Eucarya (Eukarya). The "evolutionary distance" between two organisms is proportional to the measurable distance between the end of a branch to a node to the end of a comparative branch. For example, in Eucarya, humans (Homo) are more closely related to corn (Zea) than to slime molds (Dictyostelium); or in Bacteria, E. coli is more closely related to Agrobacterium than to Thermus.
OFF THE WALL. It is interesting to note several features of phylogeny and evolution that are revealed in the Unrooted Tree.
--Archaea are the least evolved type of cell (they remain closest to the common point of origin). This helps explain why contemporary Archaea are inhabitants of environments that are something like the earth 3.86 billion years ago (hot, salty, acidic, anaerobic, low in organic material, etc.).
--Eucaryotes (Eucarya) are the most evolved type of cell (they move farthest from the common point of origin). However, the eucaryotes do not begin to diversify (branch) until relatively late in evolution, at a time when the Bacteria diversify into oxygenic photosynthesis (Synechococcus) and aerobic respiration (Agrobacterium).
--Mitochondria and the respiratory bacterium, Agrobacterium, are derived from a common ancestor; likewise, chloroplast and the cyanobacterium, Synechococcus, arise from a common origin. This is good evidence for the idea of evolutionary endosymbiosis, i.e., that the origin of eukaryotic mitochondria and chloroplasts is in procaryotic cells that were either captured by, or which invaded, eukaryotic cells, and subsequently entered into a symbiotic association with one cell living inside of the other.
--Diversification in Eucarya is within the Protista (unicellular protozoa, algae, and including fungi). The only multicellular eukaryotes on the Tree are Zea (plants) and Homo (animals). Since the protists, along with the archaea and bacteria, constitute the microbial ("microorganismal") community of the planet, this helps to substantiate the claim the microorganisms are the predominant and most diverse form of life on Earth.
--Humans (Homo) are more closely related to yeast (Saccharomyces) than they are to corn (Zea). There are more genetic differences between E. coli and Bacillus than there are between humans and a paramecium. The protozoan Trichomonas is more closely related to the archaea than it is to the protozoan Trypoanosoma. When the tree branches are amplified there many other similar surprises to biologists.
--Most biology and anthropology students have been presented with fossil and other structural evidence that humans (Homo) emerged a very short time ago on the evolutionary clock. The Tree confirms this evidence on the basis of comparative molecular genetic analysis.
Genomic Timescale of Procaryotic Evolution
Comparison of protein sequences whose genes are common to the genomes of several procaryotes has resulted in a "genomic timescale of procaryotic evolution" and establishes the following dates for some major events in procaryotic evolution (Battistuzzi, et al. MC Evol Biol. 2004; 4: 44). The results are consistent with most other phylogenetic schemes that recognize higher-level groupings of procaryotes.
Table 1. Genomic timescale for some major events in procaryotic evolution
Origin of life: prior to 4.1 billion years ago (Ga)
Origin of methanogenesis: 3.8 - 4.1 Ga
Origin of phototrophy: prior to 3.2 Ga
Divergence of the major groups of Archaea: 3.1 - 4.1 Ga
Origin of anaerobic methanotrophy: after 3.1 Ga
Colonization of land: 2.8 - 3.1 Ga
Divergence of the major groups of Bacteria: 2.5 - 3.2 Ga
Origin of aerobic methanotrophy: 2.5 - 2.8 Ga.
The time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface.
Divergence times for the origin of anaerobic methanotrophy are compatible with carbon isotopic values found in rocks dated 2.8 - 2.6 Ga.
The origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those structures (if biologically produced) would have been made by anoxygenic photosynthesizers.
A well-supported group of three major lineages of Bacteria (Actinobacteria, Deinococcus, and Cyanobacteria), that have been called "Terrabacteria", are associated with an early colonization of land.
Size and Distribution of Bacteria and Archaea
Most procaryotic cells are very small compared to eukaryotic cells. A typical bacterial cell is about 1 micrometer in diameter while most eukaryotic cells are from 10 to 100 micrometers in diameter. Eukaryotic cells have a much greater volume of cytoplasm and a much lower surface : volume ratio than procaryotic cells. A typical procaryotic cell is about the size of a eukaryotic mitochondrion. Since procaryotes are too small to be seen except with the aid of a microscope, it is usually not appreciated that they are the most abundant form of life on the planet, both in terms of biomass and total numbers of species. For example, in the sea, procaryotes make up 90 percent of the total combined weight of all organisms. In a single gram of fertile agricultural soil there may be in excess of 109 bacterial cells, outnumbering all eukaryotic cells there by 10,000 : 1. About 3,000 distinct species of bacteria and archea are recognized, but this number is probably less than one percent of all the species in nature. These unknown procaryotes, far in excess of undiscovered or unstudied plants, are a tremendous reserve of genetic material and genetic information in nature that awaits exploitation.
Procaryotes are found in all of the habitats where eukaryotes live, but, as well, in many natural environments considered too extreme or inhospitable for eukaryotic cells. Thus, the outer limits of life on Earth (hottest, coldest, driest, etc.) are usually defined by the existence of procaryotes. Where eukaryotes and procaryotes live together, there may be mutualistic associations between the organisms that allow both to survive or flourish. The organelles of eukaryotes (mitochondria and chloroplasts) are thought to be remnants of Bacteria that invaded, or were captured by, primitive eukaryotes in the evolutionary past. Numerous types of eukaryotic cells that exist today are inhabitated by endosymbiotic procaryotes.
From a metabolic standpoint, the procaryotes are extraordinarily diverse, and they exhibit several types of metabolism that are rarely or never seen in eukaryotes. For example, the biological processes of nitrogen fixation (conversion of atmospheric nitrogen gas to ammonia) and methanogenesis (production of methane) are metabolically-unique to procaryotes and have an enormous impact on the nitrogen and carbon cycles in nature. Unique mechanisms for energy production and photosynthesis are also seen among the Archea and Bacteria.
The lives of plants and animals are dependent upon the activities of bacterial cells. Bacteria and archea enter into various types of symbiotic relationships with plants and animals that usually benefit both organisms, although a few bacteria are agents of disease.
The metabolic activities of procaryotes in soil habitats have an enormous impact on soil fertility that can affect agricultural practices and crop yields. In the global environment, procaryotes are absolutely essential to drive the cycles of elements that make up living systems, i.e., the carbon, oxygen, nitrogen and sulfur cycles. The origins of the plant cell chloroplast and plant-type (oxygenic) photosynthesis are found in procaryotes. Most of the earth's atmospheric oxygen may have been produced by free-living bacterial cells. The bacteria fix nitrogen and a substantial amount of CO2, as well.
Bacteria or bacterial products (including their genes) can be used to increase crop yield or plant resistance to disease, or to cure or prevent plant disease. Bacterial products include antibiotics to fight infectious disease, as well as components for vaccines used to prevent infectious disease. Because of their simplicity and our relative understanding of their biological processes, the bacteria provide convenient laboratory models for study of the molecular biology, genetics, and physiology of all types of cells, including plant and animal cells.
STRUCTURE AND FUNCTION OF PROCARYOTIC CELLS
Procaryotic cells have three architectural regions (Figure 4): appendages (proteins attached to the cell surface) in the form of flagella and pili; a cell envelope consisting of a capsule, cell wall and plasma membrane; and a cytoplasmic region that contains the cell genome (DNA) and ribosomes and various sorts of inclusions.
Figure 4. Schematic drawing of a typical bacterium.
Surface Structures-Appendages
Flagella are filamentous protein structures attached to the cell surface that provide swimming movement for most motile procaryotic cells. The flagellar filament is rotated by a motor apparatus in the plasma membrane allowing the cell to swim in fluid environments. Bacterial flagella are powered by proton motive force (chemiosmotic potential) established on the bacterial membrane, rather than ATP hydrolysis which powers eukaryotic flagella. Procaryotes are known to exhibit a variety of types of tactic behavior, i.e., the ability to move (swim) in response to environmental stimuli. For example, during chemotaxis a bacterium can sense the quality and quantity of certain chemicals in their environment and swim towards them (if they are useful nutrients) or away from them (if they are harmful substances).
Figure 5.Vibrio choleraehas a single polar flagellum for swimming movement. Electron Micrograph of Vibrio cholerae by Leodotia Pope, Department of Microbiology, University of Texas at Austin.
Fimbriae and Pili are interchangeable terms used to designate short, hair-like structures on the surfaces of procaryotic cells. Fimbriae are shorter and stiffer than flagella, and slightly smaller in diameter. Like flagella, they are composed of protein. A specialized type of pilus the F or sex pilus, mediates the transfer of DNA between mating bacteria, but the function of the smaller, more numerous common pili is quite different. Common pili (almost always called fimbriae) are usually involved in adherence (attachment) of procaryotes to surfaces in nature. In medical situations, they are major determinants of bacterial virulence because they allow pathogens to attach to (colonize) tissues and to resist attack by phagocytic white blood cells.
Figure 6.Fimbriae of Neisseria gonorrhoeaeallow the bacterium to adhere to tissues. Electron micrograph by David M. Phillips, Visuals Unlimited, with permission.
The Cell Envelope
Most procaryotes have a rigid cell wall. The cell wall is an essential structure that protects the delicate cell protoplast from osmotic lysis. The cell wall of Bacteria consists of a polymer of disaccharides cross-linked by short chains of amino acids (peptides). This molecule is a type of peptidoglycan which is called murein. In the Gram-positive bacteria (those that retain the purple crystal violet dye when subjected to the Gram-staining procedure) the cell wall is a thick layer of murein. In the Gram-negative bacteria (which do not retain the crystal violet) the cell wall is relatively thin and is composed of a thin layer of murein surrounded by a membranous structure called the outer membrane. Murein is a substance unique in nature to bacterial cell walls. Also, the outer membrane of Gram-negative bacteria invariably contains a unique component, lipopolysaccharide (LPS or endotoxin), which is toxic to animals. The cell walls of Archaea may be composed of protein, polysaccharides, or peptidgolycan-like molecules, but never do they contain murein. This feature distinguishes the Bacteria from the Archaea.
Although procaryotes lack any intracellular organelles for respiration or photosynthesis, many species possess the physiologic ability to conduct these processes, usually as a function of the plasma membrane. For example, the electron transport system that couples aerobic respiration and ATP synthesis is found in the plasma membrane. The photosynthetic chromophores that harvest light energy for conversion into chemical energy are located in the membrane. Hence, the plasma membrane is the site of oxidative phosphorylation or photophosphorylation in procaryotes, analogous to the functions of mitochondria and chloroplasts in eukaryotic cells. The procaryotic plasma membrane is also a permeability barrier, and it contains a variety of different transportsystems that selectively mediate the passage of substances into and out of the cell.
The membranes of Bacteria are structurally similar to the cell membranes of eukaryotes, except that bacterial membranes consist of saturated or monounsaturated fatty acids (rarely polyunsaturated fatty acids) and do not normally contain sterols. The membranes of Archaea form phospholipid bilayers functionally equivalent to bacterial membranes, but archaeal lipids are saturated, branched, repeating isoprenoid subunits that attach to glycerol via an ether linkage, as opposed to the ester linkage found in glycerides of eukaryotic and bacterial membrane lipids. The structure of archaeal membranes is thought to be an adaptation to their survival in extreme environments.
Most bacteria contain some sort of a polysaccharide layer outside of the cell wall or outer membrane. In a general sense, this layer is called a capsule or glycocalyx. Capsules, slime layers, and glycocalyx are known to mediate attachment of bacterial cells to particular surfaces. Capsules also protect bacteria from engulfment by predatory protozoa or white blood cells (phagocytes) and from attack by antimicrobial agents of plant or animal origin. Capsules in certain soil bacteria protect them from perennial effects of drying or desiccation.
Importance of Surface Components
All of the various surface components of a procaryotic cell are important in its ecology since they mediate the contact of the cell with its environment. The only "sense" that a procaryote has results from its immediate contact with its environment. It must use its surface components to assess the environment and respond in a way that supports its own existence and survival in that environment. The surface properties of a procaryote are determined by the exact molecular composition of its plasma membrane and cell wall, including LPS, and the function of surface structures such as flagella, fimbriae and capsules. Some important ways that procaryotes use their surface components are (1) as permeability barriers that allow selective passage of nutrients and exclusion of harmful substances; (2) as "adhesins" used to attach or adhere to specific surfaces or tissues; (3) as enzymes to mediate specific reactions on the cell surface important in the survival of the procaryote; (4) as "sensing proteins" that can respond to temperature, osmolarity, salinity, light, oxygen, nutrients, etc.,resulting in a signal to the genome of the cell that will cause a beneficial response to the new environment.
Figure 7. The complex surface of Streptococcus pyogenes.Electron micrograph of Streptococcus pyogenes by Maria Fazio and Vincent A. Fischetti, Ph.D. with permission. The Laboratory of Bacterial Pathogenesis and Immunology, Rockefeller University.
Cytoplasmic Constituents
The cytoplasmic constituents of bacteria invariably include the procaryotic chromosome and ribosomes. The chromosome is typically one large circular molecule of DNA, more or less free in the cytoplasm. Procaryotes sometimes possess smaller extrachromosomal pieces of DNA called plasmids. The total DNA content of a cell is referred to as the cell genome. During cell growth and division, the procaryotic chromosome is replicated in the usual semi-conservative fashion before for distribution to progeny cells. However, the eukaryotic processes of meiosis and mitosis are absent in procaryotes. Replication and segregation of procaryotic DNA is coordinated by the membrane, possibly by mesosomes.
The distinct granular appearance of procaryotic cytoplasm is due to the presence and distribution of ribosomes The ribosomes of procaryotes are smaller than cytoplasmic ribosomes of eukaryotes. Procaryotic ribosomes are 70S in size, being composed of 30S and 50S subunits. The 80S ribosomes of eukaryotes are made up of 40S and 60S subunits. Ribosomes are involved in the process of translation (protein synthesis), but some details of their activities differ in eukaryotes, Bacteria and Archaea. Protein synthesis using 70S ribosomes occurs in eukaryotic mitochondria and chloroplasts, and this is taken as a major line of evidence that these organelles are descended from procaryotes.
Often contained in the cytoplasm of procaryotic cells is one or another of some type of inclusion granule. Inclusions are distinct granules that may occupy a substantial part of the cytoplasm. Inclusion granules are usually reserve materials of some sort. For example, carbon and energy reserves may be stored as glycogen (a polymer of glucose) or as polybetahydroxybutyric acid (a type of fat) granules. Polyphosphate inclusions are reserves of PO4 and possibly energy; elemental sulfur (sulfur globules) are stored by some phototrophic and some lithotrophic procaryotes as reserves of energy or electrons. Some inclusion bodies are actually membranous vesicles or intrusions into the cytoplasm which contain photosynthetic pigments or enzymes.
Figure 8. Bacterial colonies growing in a petri dish containing nutrients.
Hans Knoll Institute, Jena, Germany.
TAXONOMY AND CLASSIFICATION OF PROCARYOTES
Haeckel (1866) was the first to create a natural Kingdom for the microorganisms, which had been discovered nearly two centuries before by van Leeuwenhoek. He placed all unicellular (microscopic) organisms in a new kingdom, "Protista", separated from plants (Plantae) and animals (Animalia), which were multicellular (macroscopic) organisms. The development of the electron microscope in the 1950's revealed a fundamental dichotomy among Haeckel's "Protista": some cells contained a membrane-enclosed nucleus, and some cells lacked this intracellular structure. The latter were temporarily shifted to a fourth kingdom, Monera (or Moneres), the procaryotes (also called Procaryotae). Protista remained as a kingdom of unicellular eukaryotic microorganisms. Whittaker refined the system into five kingdoms in 1967, by identifying the Fungi as a separate multicellular eukaryotic kingdom of organisms, distinguished by their absorptive mode of nutrition.
In the 1980's, Woese began phylogenetic analysis of all forms of cellular life based on comparative sequencing of the small subunit ribosomal RNA (ssrRNA) that is contained in all organisms. A new dichotomy was revealed, this time among the procaryotes: their existed two types of procaryotes, as fundamentally unrelated to one another as they are to eukaryotes. Thus, Woese defined the three cellular domains of life as they are displayed in Figure 3 (above): Eucarya, Bacteria and Archaea. Whittaker's Plant, Animal and Fungi kingdoms (all of the multicellular eukaryotes) are at the end of a very small branch of the tree of life, and all other branches lead to microorganisms, either procaryotes (Bacteria and Archaea), or protists (unicellular algae and protozoa).
Although the definitive difference between Woese's Archaea and Bacteria is based on fundamental differences in the nucleotide base sequence in the 16S ribosomal RNA, there are many biochemical and phenotypic differences between the two groups of procaryotes. (Table 2). The phylogenetic tree indicates that Archaea are more closely related to Eukarya than are Bacteria. This relatedness seems most evident in the similarities between transcription and translation in the Archaea and the Eukarya. However, it is also evident that the Bacteria have evolved into chloroplasts and mitochondria, so that these eukaryotic organelles derive their lineage from this group of procaryotes. Perhaps the biological success of eukaryotic cells springs from the evolutionary merger of the two procaryotic life forms.
Figure 9 (above) The structure of a typical procaryotic cell, in this case, a Gram-negative bacterium, compared with (below) a typical eukaryotic cell (plant cell). The procaryote is about 1 micrometer in diameter and about the size of the eukaryotic chloroplast or mitochondrion. Drawings by Vaike Haas, University of Wisconsin-Madison.
Table 2. Phenotypic properties of Bacteria and Archaea compared with Eukarya.
Property Biological Domain
Eukarya Bacteria Archaea
Cell configuration eukaryotic procaryotic procaryotic
Nuclear membrane present absent absent
Number of chromosomes >1 1 1
Chromosome topology linear circular circular
Murein in cell wall - + -
Cell membrane lipids ester-linked glycerides; unbranched; polyunsaturated ester-linked glycerides; unbranched; saturated or monounsaturated ether-linked branched; saturated
Cell membrane sterols present absent absent
Organelles (mitochondria and chloroplasts) present absent absent
Ribosome size 80S (cytoplasmic) 70S 70S
Cytoplasmic streaming + - -
Meiosis and mitosis present absent absent
Transcription and translation coupled - + +
Amino acid initiating protein synthesis methionine N-formyl methionine methionine
Protein synthesis inhibited by streptomycin and chloramphenicol - + -
Protein synthesis inhibited by diphtheria toxin + - +
IDENTIFICATION OF BACTERIA
The criteria used for microscopic identification of procaryotes include cell shape and grouping, Gram-stain reaction, and motility. Bacterial cells almost invariably take one of three forms: rod (bacillus), sphere (coccus), or spiral (spirilla and spirochetes). Rods that are curved are called vibrios. Fixed bacterial cells stain either Gram-positive (purple) or Gram-negative (pink); motility is easily determined by observing living specimens. Bacilli may occur singly or form chains of cells; cocci may form chains (streptococci) or grape-like clusters (staphylococci); spiral shape cells are almost always motile; cocci are almost never motile. This nomenclature ignores the actinomycetes, a prominant group of branched bacteria which occur in the soil. But they are easily recognized by their colonies and their microscopic appearance.
Figure 10. Gram stain of Bacillus anthracis,the cause of anthrax. K. Todar.
Such easily-made microscopic observations, combined with knowing the natural environment of the organism, are important aids to identify the group, if not the exact genus, of a bacterium - providing, of course, that one has an effective key. Such a key is Bergey's Manual of Determinative Bacteriology, the "field guide" to identification of the bacteria. Bergey's Manual describes affiliated groups of Bacteria and Archaea based on a few easily observed microscopic and physiologic characteristics. Further identification requires biochemical tests which will distinguish genera among families and species among genera. Strains within a single species are usually distinguished by genetic or immunological criteria.
A modification of the Bergey's criteria for bacterial identification, without a key, is used to organize the groups of procaryotes for discussion in a companion chapter Major Groups of Prokaryotes
Figure 11. Size and fundamental shapes of procaryotes revealed by three genera of Bacteria (l to r): Staphylococcus(spheres), Lactobacillus(rods), and Aquaspirillum(spirals).
Figure 12. Chains of dividing streptococci.Electron micrograph of Streptococcus pyogenes by Maria Fazio and Vincent A. Fischetti, Ph.D. with permission. The Laboratory of Bacterial Pathogenesis and Immunology, Rockefeller University.
BACTERIAL REPRODUCTION AND GENETICS
Most bacteria reproduce by a relatively simple asexual process called binary fission: each cell increases in size and divides into two cells. During this process there is an orderly increase in cellular structures and components, replication and segregation of the bacterial DNA, and formation of a septum or cross wall which divides the cell into two. The process is evidently coordinated by activites associated with the cell membrane. The DNA molecule is believed to be attached to a point on the membrane where it is replicated. The two DNA molecules remain attached at points side-by-side on the membrane while new membrane material is synthesized between the two points. This draws the DNA molecules in opposite directions while new cell wall and membrane are laid down as a septum between the two chromosomal compartments. When septum formation is complete the cell splits into two progeny cells. The time interval required for a bacterial cell to divide or for a population of cells to double is called the generation time. Generation times for bacterial species growing in nature may be as short as 15 minutes or as long as several days.
Genetic Exchange in Bacteria
Although procaryotes do not undergo sexual reproduction, they are not without the ability to exchange genes and undergo genetic recombination. Bacteria are known to exchange genes in nature by three processes: conjugation, transduction and transformation. Conjugation involves cell-to-cell contact as DNA crosses a sex pilus from donor to recipient. During transduction, a virus transfers the genes between mating bacteria. In transformation, DNA is acquired directly from the environment, having been released from another cell. Genetic recombination can follow the transfer of DNA from one cell to another leading to the emergence of a new genotype (recombinant). It is common for DNA to be transferred as plasmids between mating bacteria. Since bacteria usually develop their genes for drug resistance on plasmids (called resistance transfer factors, or RTFs), they are able to spread drug resistance to other strains and species during genetic exchange processes. The genetic engineering of bacterial cells in the research or biotechnology laboratory is often based on the use of plasmids. The genetic systems of the Archaea are poorly characterized at this point, although the entire genome of Methanosarcina has been sequenced recently which will certainly open up the possibilites for genetic analysis of the group.
Evolution of Bacteria and Archaea
For most procaryotes, mutation is is a major source of variability that allows the species to adapt to new conditions. The mutation rate for most procaryotic genes is approximately 10-8. This means that if a bacterial population doubles from 108 cells to 2 x 108 cells, there is likely to be a mutant present for any given gene. Since procaryotes grow to reach population densities far in excess of 109 cells, such a mutant could develop from a single generation during 15 minutes of growth. The evolution of procaryotes, driven by such darwinian principles of evolution (mutation and selection) is called vertical evolution
However, as a result of the processes of genetic exchange described above, the bacteria and archaea can also undergo a process of horizontal evolution. In this case, genes are transferred laterally from one organism to another, even between members of different Kingdoms, which may allow immediate experimentation with new genetic characteristics in the recipient. Horizontal evolution is being realized to be a significant force in cellular evolution.
The combined effects of fast growth rates, high concentrations of cells, genetic processes of mutation and selection, and the ability to exchange genes, account for the extraordinary rates of adaptation and evolution that can be observed in the procaryotes.
ECOLOGY OF BACTERIA AND ARCHAEA
Bacteria and Archaea are present in all environments that support life. They may be free-living, or living in associations with eukaryotes (plants and animals), and they are found in environments that support no other form of life. Procaryotes have the usual nutritional requirements for growth of cells, but many of the ways that they utilize and transform their nutrients are unique.
Nutritional Types of Organisms
In terms of carbon utilization a cell may be heterotrophic or autotrophic. Heterotrophs obtain their carbon and energy for growth from organic compounds in nature. Autotrophs use C02 as a sole source of carbon for growth and obtain their energy from light (photoautotrophs) or from the oxidation of inorganic compounds (lithoautotrophs).
Most heterotrophic bacteria are saprophytes, meaning that they obtain their nourishment from dead organic matter. In the soil, saprophytic bacteria and fungi are responsible for biodegradation of organic material. Ultimately, organic molecules, no matter how complex, can be degraded to CO2. Probably no naturally-occurring organic substance cannot be degraded by the combined activities of the bacteria and fungi. Hence, most organic matter in nature is converted by heterotrophs to CO2, only to be converted back into organic material by autotrophs that die and nourish heterotrophs to complete the carbon cycle.
Lithotrophic procaryotes have a type of energy-producing metabolism which is unique. Lithotrophs (also called chemoautotrophs) use inorganic compounds as sources of energy, i.e., they oxidize compounds such as H2 or H2S or NH3 to obtain electrons to feed in to an electron transport system and to produce ATP. Lithotrophs are found in soil and aquatic environments wherever their energy source is present. Most lithotrophs are autotrophs so they can grow in the absence of any organic material. Lithotrophic species are found among the Bacteria and the Archaea. Sulfur-oxidizing lithotrophs convert H2S to So and So to SO4. Nitrifying bacteria convert NH3 to NO2 and NO2 to NO3; methanogens strip electrons off of H2 as a source of energy and add electrons to CO2 to form CH4 (methane). Lithotrophs have an obvious impact on the sulfur, nitrogen and carbon cycles in the biosphere.
Photosynthetic bacteria convert light energy into chemical energy for growth. Most phototrophic bacteria are autotrophs so their role in the carbon cycle is analogous to that of plants. The planktonic cyanobacteria are the "grass of the sea" and their form of oxygenic photosynthesis generates a substantial amount of O2 in the biosphere. However, among the photosynthetic bacteria are types of metabolism not seen in eukaryotes, including photoheterotrophy (using light as an energy source while assimilating organic compounds as a source of carbon), anoxygenic photosynthesis, and unique mechanisms of CO2 fixation (autotrophy).
Photosynthesis has not been found to occur among the Archaea, but one archaeal species of employs a light-driven non photosynthetic means of energy generation based on the use of a chromophore called bacteriorhodopsin
Responses to Environmental Conditions
Procaryotes vary widely in their response to O2 (molecular oxygen). Organisms that require O2 for growth are called obligate aerobes; those which are inhibited or killed by O2, and which grow only in its absence, are called obligate anaerobes; organisms which grow either in the presence or absence of O2 are called facultative anaerobes. Whether or not a particular organism can exist in the presence of O2 depends upon the distribution of certain enzymes such as superoxide dismutase and catalase that are required to detoxify lethal oxygen radicals that are always generated by living systems in the presence of O2
Procaryotes also vary widely in their response to temperature. Those that live at very cold temperatures (0 degrees or lower) are called psychrophiles; those which flourish at room temperature (25 degrees) or at the temperature of warm-blooded animals (37 degrees) are called mesophiles; those that live at high temperatures (greater than 45 degrees) are thermophiles. The only limit that seems to be placed on growth of certain procaryotes in nature relative to temperature is whether liquid water exists. Hence growing procaryotic cells can be found in supercooled environments (ice does not form) as low as -20 degrees and superheated environments (steam does not form) as high as 120 degrees. Archaea have been detected around thermal vents on the ocean floor where the temperature is as high as 320 degrees!
Symbiosis
The biomass of procaryotic cells in the biosphere, their metabolic diversity, and their persistence in all habitats that support life, ensures that the procaryotes play a crucial role in the cycles of elements and the functioning of the world ecosystem. However, the procaryotes affect the world ecology in another significant way through their inevitable interactions with insects, plants and animals. Some bacteria are required to associate with insects, animals or plants for the latter to survive. For example, the sex of offspring of certain insects is determined by endosymbiotic bacteria. Ruminant animals (cows, sheep, etc.), whose diet is mainly cellulose (plant material), must have cellulose-digesting bacteria in their intestine to convert the cellulose to a form of carbon that the animal can assimilate. Leguminous plants grow poorly in nitrogen-deprived soils unless they are colonized by nitrogen-fixing bacteria which can supply them with a biologically-useful form of nitrogen.
Bacterial Pathogenicity
Some bacteria are parasites of plants or animals, meaning that they grow at the expense of their eukaryotic host and may damage, harm, or even kill it in the process. Such bacteria that cause disease in plants or animals are pathogens. Human diseases caused by bacterial pathogens include tuberculosis, whooping cough, diphtheria, tetanus, gonorrhea, syphilis, pneumonia, cholera and typhoid fever, to name a few. The bacteria that cause these diseases have special structural or biochemical properties that determine their virulence or pathogenicity. These include: (1) ability to colonize and invade their host; (2) ability to resist or withstand the antibacterial defenses of the host; (3) ability to produce various toxic substances that damage the host. Plant diseases, likewise, may be caused by bacterial pathogens. More than 200 species of bacteria are associated with plant diseases.
Figure 13. Borrelia burgdorferi. This spirochete is the bacterial parasite that causes Lyme disease. CDC.
APPLICATIONS OF BACTERIA IN INDUSTRY AND BIOTECHNOLOGY
Exploitation of Bacteria by Humans
In addition to other ecological roles, procaryotes, especially bacteria, are used industrially in the manufacture of foods, drugs, vaccines, insecticides, enzymes, hormones and other useful biological products. In fact, through genetic engineering of bacteria, these unicellular organisms can be coaxed to produce just about anything that there is a gene for. The genetic systems of bacteria are the foundation of the biotechnology industry.
In the foods industry, lactic acid bacteria such as Lactobacillus and Streptococcus are used the manufacture of dairy products such as yogurt, cheese, buttermilk, sour cream, and butter. Lactic acid fermentations are also used in pickling process. Bacterial fermentations can be used to produce lactic acid, acetic acid, ethanol or acetone. In many parts of the world, various human cultures ferment indigenous plant material using Zymomonas bacteria to produce the regional alcoholic beverage. For example, in Mexico, a Maguey cactus (Agave) is fermented to "cactus beer" or pulque. Pulque can be ingested as is, or distilled into tequila.
In the pharmaceutical industry, bacteria are used to produce antibiotics, vaccines, and medically-useful enzymes. Most antibiotics are made by bacteria that live in soil. Actinomycetes such as Streptomyces produce tetracyclines, erythromycin, streptomycin, rifamycin and ivermectin. Bacillus species produce bacitracin and polymyxin. Bacterial products are used in the manufacture of vaccines for immunization against infectious disease. Vaccines against diphtheria, whooping cough, tetanus, typhoid fever and cholera are made from components of the bacteria that cause the respective diseases. It is significant to note here that the use of antibiotics against infectious disease and the widespread practice of vaccination (immunization) against infectious disease are two twentieth-century developments that have drastically increased the quality of life and the average life expectancy of individuals in developed countries.
Biotechnology
The biotechnology industry uses bacterial cells for the production of human hormones such as insulin and human growth factor (protropin), and human proteins such as interferon, interleukin-2, and tumor necrosis factor. These products are used for the treatment of a variety of diseases ranging from diabetes to tuberculosis and AIDS. Other biotehnological applications of bacteria involve the genetic construction of "super strains" of organisms to perform a particular metabolic task in the environment. For example, bacteria which have been engineered genetically to degrade petroleum products can be used in cleanup efforts of oil spills in seas or on beaches. One area of biotechnology involves improvement of the qualities of plants through genetic engineering. Genes can be introduced into plants by a bacterium Agrobacterium tumefaciens. Using A. tumefaciens, plants have been genetically engineered so that they are resistant to certain pests, herbicides, and diseases. Finally, the polymerase chain reaction (PCR), a mainstay of the biotechnology industry because it allows scientists to duplicate genes starting with a single molecule of DNA, is based on the use of a DNA polymerase enzyme derived from a thermophilic bacterium, Thermus aquaticus.
Thermus aquaticus,the thermophilic bacterium that is the source of taq polymerase.
L wet mount; R electron micrograph. T.D. Brock. Life at High Temperatures.
from :
http://www.bact.wisc.edu/themicrobialworld/bacteriology.html
Major Groups of Prokaryotes
Major Groups of Prokaryotes
Winogradsky's original drawings of Beggiatoa illustrating sulfur inclusions (1887)
Major Groups of Prokaryotes
The prokaryotes consist of millions of genetically-distinct unicellular organisms. What they lack in structural diversity, so well-known among eukaryotes (including the protista), they make up for in their physiological diversity. It is often a particular physiological trait that unifies and distinguishes a particular group of prokaryotes. In Bergey's Manual (Reference 2) the groups of prokaryotes are formed based on easily-observed characteristics such as Gram stain, morphology (rods, cocci, etc), motility, structural features (e.g. spores, filaments, sheaths, appendages, etc.), and on distinguishing physiological features (e.g. anoxygenic photosynthesis, methanogenesis, lithotrophy, etc.). Nowadays, of course, the politically correct way to group organisms, especially prokaryotes, is on a genetic basis, i.e., by comparison of the nucleotide sequences of the small subunit ribosomal RNA that is contained in all cellular organisms.
The ensuing description of prokaryotes may rely on various of these cellular traits in defining "groups", but herein the prokaryotes are placed under trivial headings based on common structural, biochemical or ecological properties. This does not imply close genetic relatedness among all members in a group. Sometimes, all of the members of a group share a close genetic relatedness; in other cases, members of a group are genetically-unrelated, even to an extent that is greater than exists among all members of the Eukaryotic domain. Also herein, some prokaryotes are in more than one group, and some groups consist of both Archaea and Bacteria.
Archaea
On the basis of ssrRNA analysis, the Archaea consist of three phylogenetically-distinct groups: Crenarchaeota, Euryarchaeota and Korarchaeota. However, for the Korarchaeota, only their nucleic acids have been detected, and no organisms have been isolated or cultured. Based on their physiology, the Archaea can be organized into three types: methanogens (prokaryotes that produce methane); extreme halophiles (prokaryotes that live at very high concentrations of salt (NaCl); and extreme (hyper) thermophiles (prokaryotes that live at very high temperatures). Besides the unifying archaeal features that distinguish them from Bacteria (i.e., no murein in cell wall, ester-linked membrane lipids, etc.), these prokaryotes exhibit unique structural or biochemical attributes which adapt them to their particular habitats. The Crenarchaeota consists mainly of hyperthermophilic sulfur-dependent prokaryotes and the Euryarchaeota contains the methanogens and extreme halophiles. ssrRNAs of the Korarchaeota have been obtained from hyperthermophilic environments similar to those inhabitated by Crenarchaeota.
Figure 1. Phylogenetic tree of Archaea.
Methanogens are obligate anaerobes that will not tolerate even brief exposure to air (O2). Anaerobic environments are plentiful, however, and include marine and fresh-water sediments, bogs and deep soils, intestinal tracts of animals, and sewage treatment facilities. Methanogens have an incredible type of metabolism that can use H2 as an energy source and CO2 as a carbon source for growth. In the process of making cell material from H2 and CO2, the methanogens produce methane (CH4) in a unique energy-generating process. The end product (methane gas) accumulates in their environment. Methanogen metabolism created most the natural gas (fossil fuel) reserves that are tapped as energy sources for domestic or industrial use. Methanogens are normal inhabitants of the rumen (fore-stomach) of cows and other ruminant animals. A cow belches about 50 liters of methane a day during the process of eructation (chewing the cud). Methane is a significant greenhouse gas and is accumulating in the atmosphere at an alarming rate. When rain forests are destroyed and replaced by cows, it is "double-hit" on the greenhouse: (1) less CO2 is taken up by removal of the the autotrophic green plants; (2) additional CO2 and CH4 are produced as gases by the combined metabolism of the animal and methanogens. Methanogens represent a microbial system that can be exploited to produce energy from waste materials. Large amounts of methane are produced during industrial sewage treatment processes, but the gas is usually wasted rather than trapped for recycling.
Figure 2. Methanococcus jannischii
Methanococcus jannischii was originally isolated from a sample taken from a "white smoker" chimney at an oceanic depth of 2,600 meters on the East Pacific Rise. It can be grown in a mineral medium containing only H2 and CO2 as sources of energy and carbon for growth within a temperature range of 50 to 86 degrees. Cells are irregular cocci that are motile due to two bundles of polar flagella inserted near the same cellular pole.
Extreme halophiles live in natural environments such as the Dead Sea, the Great Salt Lake, or evaporating ponds of seawater where the salt concentration is very high (as high as 5 molar or 25 percent NaCl). These prokaryotes require salt for growth and will not grow at low salt concentrations. Their cell walls, ribosomes, and enzymes are stabilized by Na+. Halobacterium halobium, the prevalent species in the Great Salt Lake, adapts to the high-salt environment by the development of "purple membrane", actually patches of light-harvesting pigment in the plasma membrane. The pigment is a type of rhodopsin called bacteriorhodopsin which reacts with light in a way that forms a proton gradient on the membrane allowing the synthesis of ATP. This is the only example in nature of non photosynthetic photophosphorylation. These organisms are heterotrophs that normally respire by aerobic means. The high concentration of NaCl in their environment limits the availability of O2 for respiration so they are able to supplement their ATP-producing capacity by converting light energy into ATP using bacteriorhodopsin.
Figure 3. Halobacterium salinarium
Halobacterium salinarium is an extreme halophile that grows at 4 to 5 M NaCl and does not grow below 3 M NaCl. This freeze etched preparation shows the surface structure of the cell membrane and reveals smooth patches of "purple membrane" (bacteriorhodopsin) embedded in the plasma membrane.
The extreme thermophiles come from several distinct phylogenetic lines of Archaea. These organisms require a very high temperature (80 degrees to 105 degrees) for growth. Their membranes and enzymes are unusually stable at high temperatures. Most of these Archaea require elemental sulfur for growth. Some are anaerobes that use sulfur as an electron acceptor for respiration in place of oxygen. Some are lithotrophs that oxidize sulfur as an energy source. Sulfur-oxidizers grow at low pH (less than pH 2) because they acidify their own environment by oxidizing So (sulfur) to SO4 (sulfuric acid). These hyperthermophiles are inhabitants of hot, sulfur-rich environments usually associated with volcanism, such as hot springs, geysers and fumaroles in Yellowstone National Park, and thermal vents ("smokers") and cracks in the ocean floor. Sulfolobus was the first hyperthermophilic Archaean discovered by Thomas D. Brock of the University of Wisconsin in 1970. His discovery, along with that of Thermus aquaticus in Yellowstone National Park, launched the field of hyperthermophile biology. (Thermus aquaticus, source of the enzyme taq polymerase used in the polymerase chain reaction (PCR), is a Bacterium which has an optimum temperature for growth of 70 degrees.) Sulfolobus grows in sulfur-rich, hot acid springs at temperatures as high as 90 degrees and pH values as low as 1. Thermoplasma, also discovered by Brock, is a unique thermophile that is the sole representative of a distinct phylogenetic line of Archaea. Thermoplasma resembles the bacterial mycoplasmas in that it lacks a cell wall. Thermoplasma grows optimally at 55 degrees and pH 2. Interestingly, it has only been found in self-heating coal refuse piles, which are a man-made waste.
Figure 4. Sulfolobus acidocaldarius
(T.D. Brock)
Sulfolobusis an extreme thermophile that has been found in geothermally-heated acid springs, mud pots and surface soils with temperatures from 60 to 95 degrees C, and a pH of 1 to 5. Left: Electron micrograph of a thin section (X85,000). Under the electron microscope the organism appears as irregular spheres which are often lobed. Right: Fluorescent photomicrograph of cells attached to a sulfur crystal. Fimbrial-like appendages have been observed on the cells attached to solid surfaces such as sulfur crystals.
Although the Archaea are often inhabitants of unusual or extreme environments, there may be corresponding species of Bacteria, and even eukaryotes, in these habitats as well. No bacterium can produce methane, but Bacteria are always found in anaerobic habitats in association with methanogens. With regard to acid tolerance, a bacterium, Thiobacillus, has been observed growing at pH near 0. An Alga, Cyanidium, has also been found growing near pH 0. In superheated environments (greater than100 degrees), Archaea seem to have an exclusive hold, but Bacteria have been isolated from boiling hot springs in Yellowstone National Park and other parts of the world. No bacterium grows at the highest salt concentration which supports the growth of the halobacteria, but osmophilic yeasts and fungi can grow at correspondingly low water actvities where sugar is the solute in high concentration.
BACTERIA
Phylogenetic analysis of the Bacteria has demonstrated that eleven distinct groups exist but most groups consist of members that are phenotypically and physiologically unrelated. Below we discuss the major groups of Bacteria based on morphology, physiology, or ecology, and often use informal, but familiar, terms to identify them.
Figure 5. Phylogenetic tree of Bacteria.
Photosynthetic purple and green bacteria. These bacteria conduct anoxygenic photosynthesis, also called bacterial photosynthesis. Bacterial photosynthesis differs from plant-type (oxygenic) photosynthesis in several ways. Bacterial photosynthesis does not produce O2; in fact, it only occurs under anaerobic conditions. Bacterial photosynthesis utilizes chlorophyll other than chlorophyll a, and only one photosystem, photosystem I. The electron donor for bacterial photosynthesis is never H2O but may be H2, H2S of So, or certain organic compounds. The light-absorbing pigments of the purple and green bacteria consist of bacterial chlorophylls and carotenoids. Phycobilins, characteristic of the cyanobacteria, are not found. Many purple and green sulfur bacteria store elemental sulfur as a reserve material that can be further oxidized to SO4 as a photosynthetic electron donor.
The purple and green sulfur bacteria use H2S during photosynthesis in the same manner that cyanobacteria or algae or plants use H2O as an electron donor for autotrophic CO2 reduction (the "dark reaction" of photosynthesis). They can also use organic compounds as electron donors for photosynthesis. For example, Rhodobacter can use light as an energy source while oxidizing succinate or butyrate in order to obtain electrons for CO2 fixation.
The bacterium that became an endosymbiont of eukaryotes and evolved into mitochondria is thought to be a relative of the purple bacteria. This conclusion is based on similar metabolic features of mitochondria and purple nonsulfur bacteria and on comparisons of the base sequences in their 16S rRNAs.
Figure 6. Photomicrographs (phase contrast and and ordinary illumination) of various photosynthetic bacteria (Norbert Pfennig). Magnifications are about X1400. The purple and green bacteria exhibit a full range of prokaryotic morphologies, as these photomicrographs illustrate.
A. Purple sulfur bacteria (L to R): Chromatium vinosum, Thiospirillum jenense, Thiopedia rosea
B. Purple nonsulfur bacteria (L to R): Rhodospirillum rubrum, Rhodobacter sphaeroides, Rhodomicrobium vannielii
C. Green sulfur bacteria (L to R): Chlorobium limicola, Prosthecochloris aestuarii, Pelodictyon clathratiforme
Figure 7 . Green nonsulfur bacterium, Chloroflexus (T.D. Brock). Chloroflexus represents a phylogenetically distinct group of green bacteria, which includes other green nonsulfur bacteria. Chloroflexus is a thermophilic, filamentous gliding bacterium.
Figure 8. Photosynthetic prokaryotes growing in a hot spring run-off channel (T.D. Brock). The white area of the channel is too hot for photosynthetic life, but as the water cools along a gradient, the colored phototrophic bacteria colonize and ultimately construct the colored microbial mats composed of a consortium of photosynthetic microorganisms.
Cyanobacteria. The cyanobacteria deserve special emphasis because of their great ecological importance in the global carbon, oxygen and nitrogen cycles, as well as their evolutionary significance in relationship to plants. Photosynthetic cyanobacteria have chlorophyll a and carotenoids in addition to some unusual accessory pigments named phycobilins. The blue pigment, phycocyanin and the red one, phycoerythrin, absorb wavelengths of light for photosynthesis that are missed by chlorophyll and the carotenoids. Within the cytoplasm of cyanobacteria are numerous layers of membranes, often parallel to one another. These membranes are photosynthetic thylakoids that resemble those found in chloroplasts, which, in fact, correspond in size to the entire cyanobacterial cell. The main storage product of the cyanobacteria is glycogen, and glycogen inclusions may be seen in the cytoplasm of the cells. Cyanobacteria are thought to have given rise to eukaryotic chloroplasts during the evolutionary events of endosymbiosis. In biochemical detail, cyanobacteria are especially similar to the chloroplasts of red algae (Rhodophyta).
Most cyanobacteria have a mucilaginous sheath, or coating, which is often deeply pigmented, particularly in species that occur in terrestrial habitats. The colors of the sheaths in different species include light gold, yellow, brown, red, green, blue, violet, and blue-black. It is these pigments that impart color to individual cells and colonies as well as to "blooms" of cyanobacteria in aquatic environments
Figure 9. Some common cyanobacteria L to R: Oscillatoria, a filamentous species common in fresh water and hot springs; Nostoc, a sheathed communal species; Anabaena, a nitrogen fixing species. The small cell with an opaque surface (third from right) in the anabaena filament is a heterocyst, a specialized cell for nitrogen fixation. The large bright cell in the filament is a type of spore called an akinete; Synechococcus, a unicelluar species in marine habitats and hot springs. Synechococcus is among the most important photosynthetic bacteria in the marine environment, estimated to account for about 25 percent of the primary production that occurs in typical marine habitats.
Although thousands of cyanobacteria have been observed, only about 200 species have been identified as distinct, free-living, nonsymbiotic prokaryotes. Relative to other oxygenic phototrophs, cyanobacteria often grow under fairly extreme environmental conditions such as high temperature and salinity . They are the only oxygenic phototrophs present in many hot springs of the Yellowstone ecosystem, and in frigid lakes and oceans of Antarctica, they form luxuriant mats 2 to 4 centimeters thick in water beneath more than five meters of permanent ice. However, cyanobacteria are absent in acidic waters where their eukaryotic counterparts, the algae, may be abundant.
Layered chalk deposits called stromatolites, which exhibit a continuous geologic record covering 2.7 billion years, are produced when colonies of cyanobacteria bind calcium-rich sediments. Today, stromatolites are formed in only a few places, such as shallow pools in hot dry climates. The abundance of cyanobacteria in the fossil record is evidence of the early development of the cyanobacteria and their important role in elevating the level of free oxygen in the atmosphere of the early Earth.
Cyanobacteria often form filaments and may grow in large masses or "tufts" one meter or more in length. Some are unicellular, a few form branched filaments, and a few form irregular plates or irregular colonies. Cyanobacterial cells usually divide by binary fission, and the resulting progeny cells may separate to form new colonies. In addition, filaments may break into fragments, called hormogonia, which separate and develop into new colonies. As in other filamentous or colonial bacteria, the cells of cyanobacteria may joined by their walls or by mucilaginous sheaths, but each cell is an independent unit of life.
As true Bacteria, cyanobacteria contain peptidoglycan or murein in their cell walls. Most cyanobacteria have a Gram-negative type cell wall that consists of an outer membrane component, even though they show a distant phylogenetic relationship with Gram-positive bacteria. Some of the filamentous cyanobacteria are motile by means gliding or rotating around a longitudinal axis. Short segments (hormogonia) may break off from a cyanobacterial colony and glide away from their parent colony at rates as rapid as 10 micrometers per second. The mechanism for this movement is unexplained but may be connected to the extrusion of slime (mucilage) through small pores in their cell wall, together with contractile waves in one of the surface layers of the wall.
Cyanobacteria are found in most aerobic environments where water and light are available for growth. Mainly they live in fresh water and marine habitats. Those inhabiting the surface layers of water are part of a complex microbial community called plankton. Planktonic cyanobacteria usually contain cytoplasmic inclusions called gas vesicles which are hollow protein structures filled with various gases. The vesicles can be inflated or deflated with gases allowing the organisms maintain buoyancy and to float at certain levels in the water. Thus, the cyanobacteria can regulate their position in the water column to meet their optimal needs for photosynthesis, oxygen, and light-shielding. When numerous cyanobacteria become unable to regulate their gas vesicles properly (for example, because of extreme fluctuations of temperature or oxygen supply), they may float to the surface of a body of water and form visible "blooms". A planktonic species related to Oscillatoria gives rise to the redness (and the name) of the Red Sea.
The cyanobacteria have very few harmful effects on plants or animals. They may be a nuisance if they bloom in large numbers and then die and decay in bodies of fresh water that are used for drinking or recreational purposes. Many cyanobacteria are responsible for the earthy odors and flavors of fresh waters, including drinking waters, due to the production of compounds called geosmins. Some cyanobacteria that form blooms secrete poisonous substances that are toxic for animals that ingest large amounts of the contaminated water.
Many marine cyanobacteria occur in limestone (calcium carbonate) or lime-rich substrates, such as coral algae and the shells of mullosks. Some fresh water species, particularly those that grow in hot springs, often deposit thick layers of lime in their colonies.
Some cyanobacteria can fix nitrogen. In filamentous cyanobacteria, nitrogen fixation often occurs in heterocysts, which are specialized, enlarged cells, usually distributed along the length of a filament or at the end of a filament. Heterocysts have intercellular connections to adjacent vegetative cells, and there is continuous movement of the products of nitrogen fixation moving from heterocysts to vegetative cells, and the products of photosynthesis moving from vegetative cells to heterocysts. Heterocysts are low in phycobilin pigments and have only photosystem I. They lack the oxygen-evolving photosystem II. Furthermore, they are surrounded in a thickened, specialized glycolipid cell wall that slows the rate of diffusion of O2 into the cell. Any O2 that diffuses into the heterocyst is rapidly reduced by hydrogen, a byproduct of N2 fixation, or is expelled through the wall of the heterocyst. The process of nitrogen fixation, specifically the enzyme nitrogenase, only functions in anaerobic conditions so the organism must maintain these oxygen-free compartments in order for N2 fixation to occur.
In addition to the heterocysts, some cyanobacteria form resistant spores called akinetes enlarged cells around which thickened outer walls develop. Akinetes are resistant to heat, freezing and drought (desiccation) and thus allow the cyanobacteria to survive unfavorable environmental conditions. The are functionally analogous to bacterial endospores, but they bear little resemblance and lack the extraordinary resistance properties of endospores.
A few cyanobacteria are symbionts of liverworts, ferns, cycads, flagellated protozoa, and algae, sometimes occurring as endosymbionts of the eukaryotic cells. In the case of the water fern Azolla, the cyanobacterial endophyte (a species of Anabaena) fixes nitrogen that becomes available to the plant . In addition, it is often the case that the photosynthetic partners of lichens are cyanobacteria.
The planktonic cyanobacteria fix an enormous amount of CO2 during photosynthesis, and as "primary producers" they and are the basis of the food chain in marine environments. Their type of photosynthesis, which utilizes photosystem II, generates a substantial amount of oxygen present in the earth's atmosphere. Since many cyanobacteria can fix N2 under certain conditions, they are one of the most significant free-living nitrogen-fixing prokaryotes. Cyanobacteria carried out plant-type (oxygenic) photosynthesis for at least a billion and a half years before the emergence of plants, and cyanobacteria are believed to be the evolutionary forerunners of modern-day plant and algal chloroplasts. A group of phototrophic prokaryotes, called prochlorophytes contain chlorophyll a and b but do not contain phycobilins. Prochlorophytes, therefore, resemble both cyanobacteria (because they are prokaryotic and contain chlorophyll a) and the plant chloroplast (because they contain chlorophyll b instead of phycobilins). Prochloron, the first prochlorophyte discovered, is phenotypically very similar to certain plant chloroplasts and is the leading candidate for the type of bacterium that might have undergone endosymbiotic events that led to the development of the plant chloroplast.
Spirochetes are a phylogenetically distinct group of Bacteria which have a unique cell morphology and mode of motility. Spirochetes are very thin, flexible, spiral-shaped prokaryotes that move by means of structures called axial filaments or endoflagella. The flagellar filaments are contained within a sheath between the cell wall peptidoglycan and an outer membrane. The filaments flex or rotate within their sheath which causes the cells to bend, flex and rotate during movement. Most spirochetes are free living (in muds and sediments), or live in associations with animals (e.g. in the oral cavity or GI tract). A few are pathogens of animals (e.g. leptospirosis in dogs, Syphilis in humans and Lyme Disease in dogs and humans).
Figure 10. Spirochetes: A. Cross section of a spirochete showing the location of endoflagella between the inner membrane and outer sheath; B. Borrelia burgdorferi, the agent of Lyme disease; C. Treponema pallidum, the spirochete that causes syphilis.
Spirilla are Gram-negative aerobic heterotrophic bacteria with a helical or spiral shape. Their metabolism is respiratory and never fermentative. Unlike spirochetes, they have a rigid cell wall and are motile by means of ordinary polar flagella. Spirilla are inhabitants of microaerophilic aquatic environments. Most spirilla require or prefer that oxygen in their environment be present in an amount that is well below atmospheric concentration. Spirillum and Aquaspirillum are inhabitants of fresh water. They frequently contain magnetosomes and exhibit the property of magnetotaxis (movement in relationship to the magnetic field of the earth). Oceanospirillum lives in marine habitats and is able to grow at NaCl concentrations as high as 9 percent. Azospirillum is a nitrogen-fixing bacterium that enters into a mutualistic symbiosis with certain tropical grasses and grain crops. Spirilla are thought to play a significant role in recycling of organic matter, particularly in aquatic environments.
Related to the spirilla is the small vibrioid bacterium, Bdellovibrio, which is a parasite of other Gram-negative bacteria, including E. coli. It preys on other bacteria by entering into the periplasmic space and obtaining nutrients from the cytoplasm of its host cell while undergoing an odd type of reproductive cycle.
Two pathogens of humans are found among the spirilla. Campylobacter jejuni is an important cause of bacterial diarrhea, especially in children. The bacterium is transmitted via contaminated food, usually undercooked poultry or shellfish, or untreated drinking water. Helicobacter pylori is able to colonize the gastric mucosal cells of humans, i.e., the lining of the stomach, and it has been fairly well established as the cause of peptic ulcers.
The Myxobacteria are a group of gliding bacteria that aggregate together to form a multicellular fruiting body in which development and spore formation takes place. They exhibit the most complex behavioral patterns and life cycles of all known prokaryotes. Myxobacteria are inhabitants of the soil. They have a eukaryotic counterpart in nature in the Myxomycetes, or slime molds, and the two types of organisms are an example of parallel or convergent evolution, having adopted similar life styles in the soil environment.
The vegetative cells of myxobacteria are typical Gram-negative rods that glide across a substrate such as a decaying leaf or piece of animal dung, or colonies of other bacteria. They obtain nutrients from the substrate as they glide across it and they secrete a slime track which other myxobacterial cells preferentially follow. If their nutrients become exhausted, the cells signal to one another to aggregate and form a swarm of myxobacteria which eventually differentiate into a multicellular fruiting body that contains myxospores, a type of dormant cell descended from a differentiated vegetative cell. In the case of Stigmatella, the myxospores are packed into secondary structures called cysts, which develop at the tips of the fruiting body (Figure 11). The bright-colored fruiting bodies of myxobacteria, containing millions of cells and spores, can often be seen with the unaided eye on dung pellets and decaying vegetation in the soil.
Figure 11. Stigmatella aurantiaca, a fruiting myxobacterium: L. Life Cycle R. Fruiting Body.
Lithotrophs. Lithotrophy, a type of metabolism that requires inorganic compounds as sources of energy, is established in both the Archaea and the Bacteria. The methanogens utilize H2 as an energy source, and many extreme thermophiles use H2S or elemental sulfur as a source of energy for growth. Lithotrophic Bacteria are typically Gram-negative species that utilize inorganic substrates including H2, NH3, NO2, H2S, S, Fe++, and CO. Ecologically, the most important lithotrophic Bacteria are the nitrifying bacteria, Nitrosomonas and Nitrobacter that together convert NH3 to NO2, and NO2 to NO3, and the colorless sulfur bacteria such as Thiobacillus that oxidizes H2S to S and S to SO4. Most lithotrophic bacteria are autotrophs, and, in some cases, they may play an important role in primary production of organic material in nature. Lithotrophic metabolism does not extend to eukaryotes (unless a nucleated cell harbors lithotrophic endosymbiotic bacteria), and these bacteria are important in the biogeochemical cycles of the elements.
Figure 12. Lithotroph Habitats. A. Stream in Northern Wisconsin near Hayward is a good source of iron bacteria. B. Bacteriologist J.C. Ensign of the University of Wisconsin observing growth of iron bacteria in a run-off channel from the Chocolate Pots along the Gibbon River, in Yellowstone National Park. C. An acid hot spring at the Norris Geyser Basin in Yellowstone is rich in iron and sulfur. D. A black smoker chimney in the deep sea emits iron sulfides at very high temperatures (270 to 380 degrees C).
Pseudomonads and their relatives "Pseudomonads" is a term for bacteria which morphologically and physiologically resemble members of the genus Pseudomonas, a very diverse group of Gram-negative rods with a strictly-respiratory mode of metabolism. Usually the term is reserved for members of the genera Pseudomonas and Xanthomonas, but many other related bacteria share the definitive characterictics of pseudomonads, i.e., Gram-negative bacteria which typically live by aerobic (as opposed to facultative), means. In Bergey's Manual, these bacteria are unified as Gram-negative aerobic rods and cocci. In Woese's Universal Phylogenetic Tree the genera are scattered about among the Purple Bacteria, with some being close relatives of the Enterobacteriaceae. In fact, the morphology and habitat of many pseudomonads sufficiently overlaps with the enterics (below) that microbiologists must quickly learn how to differentiate these two types of Gram-negative motile rods. Pseudomonads move by polar flagella; enterics such as E. coli swim by means of peritrichous flagella. Enterics ferment sugars such as glucose; pseudomonads generally do not ferment sugars. And most pseudomonads have an unusual cytochrome in their respiratory electron transport chain that can be detected in colonies by a colorimetric test called the oxidase test. Pseudomonads are oxidase- positive.
Figure 13. Profile of a Pseudomonad: Gram-negative rods motile by polar flagella. A. Electron micrograph, negative stain. B. Scanning electron micrograph. C. Gram stain.
Most pseudomonads are free-living organisms in soil and water; they play an important role in decomposition, biodegradation, and the C and N cycles. The phrase "no naturally-occurring organic compound cannot be degraded by some microorganism" must have been coined to apply to members of the genus Pseudomonas, known for their ability to degrade hundreds of different organic compounds including insecticides, pesticides, herbicides, plastics, petroleum substances, hydrocarbons and other of the most refractory molecules in nature. However, they are usually unable to degrade biopolymers in their environment, such as cellulose and lignen, and their role in anaerobic decomposition is minimal.
There are about 150 species of Pseudomonas, but, especially among the plant pathogens, there are many strains and biovars among the species. These bacteria are frequently found as part of the normal flora of plants, but they are one of the most important bacterial pathogens of plants, as well. Pseudomonas syringae and Xanthomonas species cause a wide variety of plant diseases as discussed below. One strain of Pseudomonas that lives on the surfaces of plants can act as an "ice nucleus" which causes ice formation and inflicts frost damage on plants at one or two degrees above the conventional freezing temperature of water (0 degrees C). One Pseudomonas species is an important pathogen of humans, Pseudomonas aeruginosa, the quintessential opportunistic pathogen, which is a leading cause of hospital-acquired infections. A few relatives of the pseudomonads are pathogens of animals, i.e., the agents of whooping cough, Bordetella pertussis, Legionaires' pneumonia (Legionella pneumophilia), gonorrhea (Neisseria gonorrhoeae), and bacterial meningitis (Neisseria meningitidis), but most of these bacteria have a normal existence apart from animals - in soil, water, and on the surfaces of plants. The pseudomonads have a lesser predilection for pathogenicity of animals than do the enteric bacteria.
Among the interesting or important relatives of the pseudomonads are Rhizobiumand Bradyrhizobium, species that fix nitrogen in association with leguminous plants, and related Agrobacterium species that cause tumors ("galls") in plants. These bacteria are discussed later in this article because of their special relationships with plants. Relatives of the pseudomonads also include the methanotrophs that can oxidize methane and other one-carbon compounds, the azotobacters, which are very prevalent free-living (nonsymbiotic) nitrogen-fixing bacteria, and the acetobacters that are used in the manufacture of vinegar.
Enterics. Enteric bacteria are Gram-negative rods with facultative anaerobic metabolism that live in the intestinal tracts of animals. This group consists of Escherichia coli and its relatives, the members of the family Enterobacteriaceae. Enteric bacteria are related phenotypically to several other genera of bacteria such as Pseudomonas and Alcaligenes, but are physiologically quite unrelated. Generally, a distinction can be made on the ability to ferment glucose; enteric bacteria all ferment glucose to acid end products while similar Gram-negative bacteria cannot ferment glucose. Because they are consistent members of the normal flora of humans, and because of their medical importance, an extremely large number of enteric bacteria have been isolated and characterized.
Escherichia coli is, of course, the type species of the enterics. E. coli is such a regular inhabitant of the intestine of humans that it is used by public health authorities as an indicator of fecal pollution of drinking water supplies, swimming beaches, foods, etc. E. coli is the most studied of all organisms in biology because of its occurrence, and the ease and speed of growing the bacteria in the laboratory. It has been used in hundreds of thousands of experiments in cell biology, physiology, and genetics, and was among the first cells for which the entire chromosomal DNA base sequence was determined. In spite of the knowledge gained about the molecular biology and physiology of E. coli, surprisingly little is known about its ecology, for example why it consistently associates with humans, how it helps its host, how it harms its host, etc. A few strains of E. coli are pathogenic (one is notorious, strain 0157:H7, that keeps turning up in raw hamburger headed for a fast-food restaurants).Pathogenic strains of E. coli cause intestinal tract infections (usually acute and uncomplicated, except in the very young ) or uncomplicated urinary tract infections.
Figure 14. Left: Escherichia coli cells. Right: E. coli colonies on EMB Agar.
The enteric group also includes some other intestinal pathogens of humans such as Shigella dysenteriae, cause of bacillary dysentery, and Salmonella typhimurium, cause of gastroenteritis. Salmonella typhi, which infects via the intestinal route, causes typhoid fever. Some bacteria that don't have an intestinal habitat resemble E. coli in enough ways to warrant inclusion in the enteric group. This includes Proteus, a common saprophyte of decaying organic matter, Yersinia pestis which causes bubonic plague, and Erwinia, an important pathogen of plants.
Vibrios (which have a curved rod morphology or comma shape) are very common bacteria in aquatic environments. They have structural and metabolic properties that overlap with both the enterics and the pseudomonads. In Bergey's Manual, Vibrionaceae is a family on the level with Enterobacteriaceae. Vibrios are facultative like enterics, but they have polar flagella, are oxidase-positive, and dissimilate sugars in the same manner as the pseudomonads. In aquatic habitats they overlap with the Pseudomonadaceae in their ecology, although pseudomonads favor fresh water and vibrios prefer salt water. The genus Vibrio contains an important pathogen of humans, Vibrio cholerae, the cause of Asiatic cholera. Cholera is an intestinal disease with a pathology related to diarrheal diseases caused by the enteric bacteria.
Five species of marine vibrios exhibit the property of bioluminescence, the ability to emit light of a blue-green color. These bacteria may be found as saprophytes on dead fish or as symbionts of living fish and invertebrates in marine environments. Some grow in special organs of the fish and emit light for the benefit of the fish (to attract prey, or as a mating signal) in return for a protected habitat and supply of nutrients. The reaction leading to light emission, catalyzed by the enzyme luciferase, has been found to be the same in all prokaryotes, and differs from light emission by eukaryotes such as the fire fly. Luciferase diverts electrons from the normal respiratory electron transport chain and causes formation of an excited peroxide that leads to emission of light.
Nitrogen-fixing organisms. This is a diverse group of prokaryotes, reaching into phylogenetically distinct groups of Archaea and Bacteria. Members are unified only on the basis of their metabolic ability to "fix" nitrogen. Nitrogen fixation is the reduction of N2 (atmospheric nitrogen) to NH3 (ammonia). It is a complicated enzymatic process mediated by the enzyme nitrogenase. Nitrogenase is found only in prokaryotes and is second only to RUBP carboxylase (the enzyme responsible for CO2 fixation) as the most abundant enzyme on Earth.
The conversion of nitrogen gas (which constitutes about 80 percent of the atmosphere) to ammonia introduces nitrogen into the biological nitrogen cycle. Living cells obtain their nitrogen in many forms, but usually from ammonia (NH3) or nitrates (NO3), and never from N2. Nitrogenase extracts N2 from the atmosphere and reduces it to NH3 in a reaction that requires substantial reducing power (electrons) and energy (ATP). The NH3 is immediately assimilated into amino acids and proteins by subsequent cellular reactions. Thus, nitrogen from the atmosphere is fixed into living (organic) material.
Although a widespread trait in prokaryotes, nitrogen fixation occurs in only a few select genera. Outstanding among them are the symbiotic bacteria Rhizobium and Bradyrhizobium which form nodules on the roots of legumes. In this symbiosis the bacterium invades the root of the plant and fixes nitrogen which it shares with the plant. The plant provides a favorable habitat for the bacterium and supplies it with nutrients and energy for efficient nitrogen fixation. Rhizobium and Bradyrhizobium are Gram-negative aerobes related to the pseudomonads (above). An unrelated bacterium, an actinomycete (below), enters into a similar type of symbiosis with plants. The actinomycete, Frankia, forms nodules on the roots of several types of trees and shrubs, including alders (Alnus), wax myrtles (Myrica) and mountain lilacs (Ceanothus). They, too, fix nitrogen which they provide to their host in a useful form. This fact allows alder species to be "pioneer plants" (among the first to colonize) in newly-forming nitrogen-deficient soils. Still other bacteria live in regular symbiotic associations with plants on roots or leaves and fix nitrogen for their hosts, but they do not cause tissue hyperplasia or the formation of nodules.
Cyanobacteria are likewise very important in nitrogen fixation. Cyanobacteria provide fixed nitrogen, in addition to fixed carbon, for their symbiotic partners which make up lichens. This enhances the capacity for lichens to colonize bare areas where fixed nitrogen is in short supply. In some parts of Asia, rice can be grown in the same paddies continuously without the addition of fertilizers because of the presence of nitrogen fixing cyanobacteria. The cyanobacteria, especially Anabaena, occur in association with the small floating water fern Azolla, which forms masses on the paddies. Because of the nearly obligate association of Azolla with Anabaena , paddies covered with Azolla remain rich in fixed nitrogen.
In addition to symbiotic nitrogen-fixing bacteria, there are various free-living nitrogen-fixing prokaryotes in both soil and aquatic habitats. Cyanobacteria may be able to fix nitrogen in virtually all habitats that they occupy. Clostridia and some methanogens fix nitrogen in anaerobic soils and sediments, including thermophilic environments. A common soil bacterium, Azotobacter is a vigorous nitrogen fixer, as is Rhodospirillum, a purple sulfur bacterium. Even Klebsiella, an enteric bacterium closely related to E. coli, fixes nitrogen. There is great scientific interest, of course, in knowing how one might move the genes for nitrogen fixation from a prokaryote into a eukaryote such as corn or some other crop plant. The genetically engineered plant might lose its growth requirement for costly ammonium or nitrate fertilizers and grow in nitrogen deficient soils.
Besides nitrogen fixation, bacteria play other essential roles in the processes of the nitrogen cycle. For example, saprophytic bacteria, decompose proteins releasing NH3 in the process of ammoniafication. NH3 is oxidized by lithotrophic Nitrosomonas species to NO2 which is subsequently oxidized by Nitrobacter to NO3. The overall conversion of NH3 to NO3 is called nitrification. NO3 can be assimilated by cells as a source of nitrogen (assimilatory nitrate reduction), or certain bacteria can reduce NO3 during a process called anaerobic respiration, wherein nitrate is used in place of oxygen as a terminal electron acceptor for a process analogous to aerobic respiration. In the case of anaerobic respiration, NO3 is first reduced to NO2, which is subsequently reduced to N2O or N2 or NH3 (all gases). This process is called denitrification and it occurs in anaerobic environments where nitrates are present. If denitrification occurs in crop soils it may not be beneficial to agriculture if it converts utilizable forms of nitrogen (as in nitrate fertilizers) to nitrogen gases that will be lost into the atmosphere. One rationale for tilling the soil is to keep it aerobic in order to discourage denitrification processes in Pseudomonas and Bacillus which are ubiquitous inhabitants.
The pyogenic cocci are spherical bacteria which cause various suppurative (pus-producing) infections in animals. Included are the Gram-positive cocci Staphylococcus aureus, Streptococcus pyogenes and Streptococcus pneumoniae, and the Gram-negative cocci Neisseria gonorrhoeae and N. meningitidis. These bacteria are leading pathogens of humans. It is estimated that they produce at least a third of all the bacterial infections of humans, including strep throat, pneumonia, food poisoning, various skin diseases and severe types of septic shock, gonorrhea and meningitis. Staphylococcus aureus is arguably the most successful of all bacterial pathogens because it has a very wide range of virulence determinants (so it can produce a wide range of infections) and it often occurs as normal flora of humans (on skin, nasal membranes and the GI tract), which ensures that it is readily transmitted from one individual to another. In terms of their phylogeny, physiology and genetics, these genera of bacteria are quite unrelated to one another. They share a common ecology, however, as parasites of humans.
Figure 15. Gallery of pyogenic cocci, Gram stains of clinical specimens (pus), L to R: Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Neisseria gonorrhoeae, Neisseria meningitidis. The large cells with lobed nuclei are neutrophils. Pus is the outcome of the battle between phagocytes (neutrophils) and the invading cocci. As the bacteria are ingested and killed by the neutrophils, the neutrophils eventually lyse (rupture) and release their own components, plus the digested products of bacterial cells, which are the make-up of pus. As a defense against phagocytes the staphylococci and streptococci produce toxins that kill the neutrophils before they are able to ingest the bacteria. This contributes to the pus, and therefore these bacteria are "pyogenic" during their pathogenic invasions.
Two species of Staphylococcus live in association with humans: Staphylococcus epidermidis which lives normally on the skin and mucous membranes, and Staphylococcus aureus which may occur normally at various locales, but in particular on the nasal membranes (nares). S. epidermidis is rarely a pathogen and probably benefits its host by producing acids on the skin that retard the growth of dermatophytic fungi. S. aureus always has the potential to cause disease and so is considered a pathogen. Different strains of S. aureus differ in the range of diseases they can cause, including boils and pimples, wound infections, pneumonia, osteomyelitis, septicemia, food intoxication, and toxic shock syndrome. S. aureus is the leading cause of nosocomial (hospital-acquired) infections by Gram-positive bacteria. Also, it is notoriously resistant to penicillin and many other antibiotics. Recently, a strain of S. aureus has been reported that is resistant to EVERY known antibiotic in clinical usage, which is a grim reminder that the clock is ticking on the lifetime of the usefulness of current antibiotics in treatment of infectious disease.
Streptococcus pyogenes, more specifically the Beta-hemolytic Group A Streptococci, like S. aureus, causes an array of suppurative diseases and toxinoses (diseases due to the production of a bacterial toxin), in addition to some autoimmune or allergic diseases. S. pyogenes is rarely found as normal flora (<1%), but it is the main streptococcal pathogen for man, most often causing tonsillitis or strep throat. Streptococci also invade the skin to cause localized infections and lesions, and produce toxins that cause scarlet fever and toxic shock. Sometimes, as a result of an acute streptococcal infection, anomalous immune responses are started that lead to diseases like rheumatic fever and glomerulonephritis, which are called post-streptococcal sequelae. Unlike the staphylococci, the streptococci have not developed widespread resistance to penicillin and the other beta lactam antibiotics, so that the beta lactams remain drugs of choice for the treatment of acute streptococcal infections.
Streptococcus pneumoniae is the most frequent cause of bacterial pneumonia in humans. It is also a frequent cause of otitis media (infection of the middle ear) and meningitis. The bacterium colonizes the nasopharynx and from there gains access to the lung or to the eustachian tube. If the bacteria descend into the lung they can impede engulfment by alveolar macrophages if they possess a capsule which somehow prevents the engulfment process. Thus, encapsulated strains are able to invade the lung and are virulent (cause disease) and noncapsulated strains, which are readily removed by phagocytes, are nonvirulent.
The Neisseriaceae is a family of Gram-negative bacteria with characteristics of both enterics and pseudomonads. The neisseriae are small, Gram-negative cocci usually seen in pairs with flattened adjacent sides. Most neisseriae are normal flora or harmless commensals of mammals living on mucous membranes. In humans they are common residents of the throat and upper respiratory tract. Two species are primary pathogens of man, Neisseria gonorrhoeae and Neisseria meningitidis.
Neisseria gonorrhoeae is the second leading cause of sexually-transmitted disease in the U.S., causing over three million cases of gonorrhea annually. Sometimes, in females, the disease may be unrecognized or asymptomatic such that an infected mother can give birth and unknowingly transmit the bacterium to the infant during its passage through the birth canal. The bacterium is able to colonize and infect the newborn eye resulting neonatal ophthalmia, which may produce blindness. For this reason (as well as to control Chlamydia which may also be present), an antimicrobial agent is usually added to the neonate eye at the time of birth.
Neisseria meningitidis is one bacterial cause of meningitis, an inflammation of the meninges of the brain and spinal cord. Other bacteria that cause meningitis include Haemophilus influenzae, Staphylococcus aureus and Escherichia coli. Meningococcal meningitis differs from other causes in that it is often responsible for epidemics of meningitis. It occurs most often in children aged 6 to 11 months, but it also occurs in older children and in adults. Meningococcal meningitis can be a rapidly fatal disease, and untreated meningitis has a mortality rate near 50 percent. However, early intervention with antibiotics is highly effective, and with treatment most individuals recover without permanent damage to the nervous system.
Lactic acid bacteria are Gram-positive, nonsporeforming rods and cocci which produce lactic acid as a sole or major end product of fermentation. They are important in the food industry as fermentation organisms in the production of cheese, yogurt, buttermilk, sour cream, pickles, sauerkraut, sausage and other foods. Important genera are Streptococcus and Lactobacillus. Some species are normal flora of the human body (found in the oral cavity, GI tract and vagina); some streptococci are pathogens of humans (see pyogenic cocci above). Certain oral lactic acid bacteria are responsible for the formation of dental plaque and the initiation of dental caries (cavities).
Endospore-forming bacteria produce a unique resting cell called an endospore. They are Gram-positive and usually rod-shaped, but there are exceptions. The two important genera are Bacillus, the members of which are aerobic sporeformers in the soils, and Clostridium, whose species are anaerobic sporeformers of soils, sediments and the intestinal tracts of animals.
Figure 16. Endospore-forming bacilli (phase contrast illumination). Endospores are dehydrated, refractile cells appearing as points of bright light under phase microcsopy. Endospore-forming bacteria are characterized by the location (position) of the endospore in the mother cell (sporangium) before its release. The spore may be central, terminal or subterminal, and the sporangium may or may not be swollen to accomodate the spore.
Figure 17. Anatomy of an endospore, cross section drawing by Viake Haas. Endospores differ from the vegetative cells that form them in a variety of ways. Several new surface layers develop outside the core (cell) wall, including the cortex and spore coat. The cytoplasm is dehydrated and contains only the cell genome and a few ribosomes and enzymes. The endospore is cryptobiotic (exhibits no signs of life) and is remarkably resistant to environmental stress such as heat (boiling), acid, irradiation, chemicals and disinfectants. Some endospores have remained dormant for 25 million years preserved in amber, only to be shaken back into life when extricated and introduced into a favorable environment.
Figure 18. The sequential steps in the process of endospore formation in Bacillus subtilis.
Some sporeformers are pathogens of animals, usually due to the production of powerful toxins. Bacillus anthracis causes anthrax, a disease of domestic animals (cattle, sheep, etc.) which may be transmitted to humans. Clostridium botulinum causes botulism, a form of food poisoning. Clostridium tetani is the agent of tetanus.
Figure 19. Robert Koch's original photomicrographs of Bacillus anthracis. In 1876, Koch established by careful microscopy that the bacterium was always present in the blood of animals that died of anthrax. He took a small amount of blood from such an animal and injected it into a healthy mouse, which subsequently became diseased and died. He took blood from that mouse and injected it into a another healthy mouse. After repeating this several times he was able to recover the original anthrax organism from the dead mouse, demonstrating for the first time that a specific bacterium is the cause of a specific disease. In so doing, he established Koch's Postulates, which still today supply the microbiological standard to demonstrate that a specific microbe is the cause of a specific disease.
In association with the process of sporulation, some Bacillus species form a crystalline protein inclusion called parasporal crystals. The protein crystal and the spore (actually the spore coat) are toxic to lepidopteran insects (certain moths and caterpillars) if ingested. The crystals and spores of Bacillus thuringiensis are marketed as "Bt" a natural insecticide for use on garden or crop plants. Another species of Bacillus, B. cereus, produces an antibiotic that inhibits growth of Phytophthera, a fungus that attacks alfalfa seedling roots causing a "damping off" disease. The bacteria, growing in association with the roots of the seedlings, can protect the plant from disease.
Also, apparently in association with the sporulation process, some Bacillus species produce clinically-useful antibiotics. Bacillus antibiotics such as polymyxin and bacitracin are usually polypeptide molecules that contain unusual amino acids.
Actinomycetes and related bacteria are a large group of Gram-positive bacteria that usually grow by filament formation, or at least show a tendency towards branching and filament formation. Many of the organisms can form resting structures called spores, but they are not the same as endospores. Branched forms superficially resemble molds and are a striking example of convergent evolution of a prokaryote and a eukaryote together in the soil habitat. Actinomycetes such as Streptomyces have a world-wide distribution in soils. They are important in aerobic decomposition of organic compounds and have an important role in biodegradation and the carbon cycle. Products of their metabolism, called geosmins, impart a characteristic earthy odor to soils. Actinomycetes are the main producers of antibiotics in industrial settings, being the source of most tetracyclines, macrolides (e.g. erythromycin), and aminoglycosides (e.g. streptomycin, gentamicin, etc.). Two bacteria in this diverse group are important pathogens of humans: Mycobacterium tuberculosis is the cause of tuberculosis; Corynebacterium diphtheriae is the cause of diphtheria. Also, many nonpathogenic mycobacteria and corynebacteria live in associations with animals.
Figure 20. Schematic diagrams illustrating mycelial growth and spore formation in several genera of actinomycetes.
Rickettsias and chlamydiae are two unrelated groups of Bacteria that are obligate intracellular parasites of eukaryotic cells. Rickettsias cannot grow outside of a host cell because they have leaky membranes and are unable to obtain nutrients in an extracellular habitat. Chlamydiae are unable to produce ATP in amounts required to sustain metabolism outside of a host cell and are, in a sense, energy-parasites.
Rickettsias occur in nature in the gut lining of arthropods (ticks, fleas, lice, etc.). They are transmitted to vertebrates by an arthropod bite and produce such diseases as typhus fever, Rocky Mountain Spotted Fever, Q fever and canine ehrlichiosis. Chlamydiae are tiny bacteria that infect birds and mammals. They may colonize and infect tissues of the eye and urogenital tract in humans. Chlamydia trachomatis causes several important diseases in humans: chlamydia, the most prevalent sexually transmitted disease in the U.S., trachoma, a leading cause of blindness worldwide, and lymphogranuloma venereum.
Figure 21. Mammalian cells infected with rickettsial organisms. L. Bartonella bacilliformis infection of human erythrocytes and blood monoyctyes. R. Ehrlichia canis infection of canine erythrocytes and blood monocytes. The distinct stained intracytoplasmic inclusion body in the monocyte is characteristic of the infection.
Mycoplasmas are a group of bacteria that lack a cell wall. The cells are bounded by a single triple-layered membrane. They may be free-living in soil and sewage, parasitic inhabitants of the mouth and urinary tract of humans, or pathogens in animals and plants. In humans, Mycoplasma pneumoniae causes primary atypical pneumonia ("walking pneumonia").
Mycoplasmas include the smallest known cells, usually about 0.2 - 0.3 micrometers in diameter. Mycoplasmas correspondingly have the smallest known genome of any cell. Their DNA is thought to contain about 650 genes, which is about one-fifth the number found in E. coli and other common bacteria. Mycoplasmas can survive without a cell wall because their cytoplasmic membrane is more stable than that of other prokaryotes. In one group of mycoplasmas, the membrane contains sterols which seem to be responsible for the stability. Also, mycoplasmas tend to inhabit environments of high osmolarity wherein the risk of osmotic shock and lysis of the cells is minimized.
Plant-pathogenic bacteria. Many economically-important diseases of plants are caused by members of the Bacteria. It is estimated that one-eighth of the crops worldwide are lost to diseases caused by bacteria, fungi or insects. Almost all kinds of plants can be affected by bacterial diseases, and many of these diseases can be extremely destructive.
Almost all plant-pathogenic bacteria are Gram-negative bacilli, usually affiliated with the pseudomonads or enterics (above). The symptoms of bacterial disease in plants are described by a number of terms such as spots, blights, soft rots, wilts, and galls. Bacterial spots of various sizes on stems, leaves, flowers and fruits are usually caused by Pseudomonas or Xanthomonas species. Bacteria may cause spots by producing toxins that kill cells at the site of infection. Blights are caused by rapidly developing necrosis (dead, discolored areas) on stems, leaves and flowers. Fire blight in apples and pears, caused by Erwinia amylovora, can kill young trees within a single season. Bacterial soft rots occur most commonly in fleshy vegetables such as potatoes or onions or fleshy fruits such as tomatoes and eggplants. The most destructive soft rots are caused by Erwinia species that attack fruits and vegetables at the post-harvest stage.
Bacterial vascular wilts mainly affect herbaceous plants. The bacteria invade the vessels of the xylem, where they multiply, interfering with the movement of water and inorganic nutrients and resulting in the wilting and the death of the plants. The bacteria commonly degrade portions of the vessel walls and can even cause the vessels to rupture. Once the walls have ruptured, the bacteria then spread to the adjacent parenchyma tissues, where they continue to multiply. In some bacterial wilts, the bacteria ooze to the surface of the stems or leaves through cracks formed over cavities filled with cellular debris, gums, and bacteria. More commonly, however, the bacteria do not reach the surface of the plant until the plant has been killed by the disease. Wilts of alfalfa and bean plants are cause by species of Clavibacter; bacterial wilt of cucurbits, such as squashes and watermelons, are cause by Erwinia tracheiphila; the black rot of crucifers such as cabbage is caused by Xanthomonas campestris. The most economically-important wilt of plants is caused by Pseudomonas solanacearum which affects 44 genera of plants, including such major crops as bananas, peanuts, tomatoes, potatoes, eggplants and tobacco. This disease occurs worldwide in tropical, subtropical, and warm temperate areas.
Mycoplasmas (discussed above) have been identified in more than 200 plant species and associated with more than 50 plant diseases, many with symptoms of yellowing. Among these plant-pathogens are the spiroplasmas (genus Spiroplasma), which are pleomorphic, ovoid or spiral-shaped cells which are motile by means of a rotary or screw-like motion. Intracellular fibrils are thought to be responsible for their movement. The organisms have been isolated from the fluids of vascular plants and from the gut of insects that feed on these fluids. Some have been cultured on artificial media, including Spiroplasma citri, which is isolated from the leaves of citrus plants, where it causes citrus stubborn disease, and from corn plants suffering from corn stunt disease. A number of other mycoplasma-like organisms (sometimes called MLOs) have been detected in diseased plants by electron microscopy, which has been taken as evidence that these organisms may be more involved in plant disease than previously realized.
The causative agent of a common plant disease, termed crown gall, is Agrobacterium tumefaciens. The disease is characterized by large galls or swellings that form on the plant at the site of infection, usually near the soil line. Crown gall is a problem in nurseries, affecting ornamental plants and fruit stock, and it may be a serious disease in grapes. Because of their role in the genetic engineering of plants, the molecular biology of these bacteria is intensively studied.
References
1. Balows, A., H.G. Truper, M. Dworkin, W. Harder, and K.-H. Schleifer (eds.). The Prokaryotes, 2nd ed. Springer-Verlag, New York. 1992. Published in four volumes. The most complete reference on the characteristics of prokaryotes. Includes procedures for the selective isolation and identification of virtually all known prokaryotes.
2. Holt, J.G. (editor-in-chief). Bergey's Manual of Systematic Bacteriology. Volume 1, 1982. Gram-negative bacteria of medical or industrial importance. Volume 2, 1986. Gram-positive bacteria of medical or industrial importance. Volume 3, 1988. Other Gram-negative bacteria, cyanobacteria, Archaea. Volume 4, 1988. Other Gram- positive bacteria. This is the standard authoritative guide to bacterial taxonomy and identification. This the usual place to begin a literature survey or an identification process of a specific bacterial group.
3. Madigan, M.T., J.M. Martinko and J. Parker. Brock Biology of Microorganisms, 8th ed. Prentice-Hall, Inc., Englewood Cliffs, New Jersey. 1997.
4. Raven, P.H., R.F. Evert and S.E. Eichhorn. Biology of Plants, 5th ed. Worth Publishers, New York. 1992.
5. Stanier, R.Y., J.L. Ingraham, M.L. Wheelis, and P.R Painter. The Microbial World, 5th ed. Prentice-Hall, Inc., Englewood Cliffs, New Jersey. 1986.
from : http://fai.unne.edu.ar/biologia/bacterias/Procariotas.htm
Winogradsky's original drawings of Beggiatoa illustrating sulfur inclusions (1887)
Major Groups of Prokaryotes
The prokaryotes consist of millions of genetically-distinct unicellular organisms. What they lack in structural diversity, so well-known among eukaryotes (including the protista), they make up for in their physiological diversity. It is often a particular physiological trait that unifies and distinguishes a particular group of prokaryotes. In Bergey's Manual (Reference 2) the groups of prokaryotes are formed based on easily-observed characteristics such as Gram stain, morphology (rods, cocci, etc), motility, structural features (e.g. spores, filaments, sheaths, appendages, etc.), and on distinguishing physiological features (e.g. anoxygenic photosynthesis, methanogenesis, lithotrophy, etc.). Nowadays, of course, the politically correct way to group organisms, especially prokaryotes, is on a genetic basis, i.e., by comparison of the nucleotide sequences of the small subunit ribosomal RNA that is contained in all cellular organisms.
The ensuing description of prokaryotes may rely on various of these cellular traits in defining "groups", but herein the prokaryotes are placed under trivial headings based on common structural, biochemical or ecological properties. This does not imply close genetic relatedness among all members in a group. Sometimes, all of the members of a group share a close genetic relatedness; in other cases, members of a group are genetically-unrelated, even to an extent that is greater than exists among all members of the Eukaryotic domain. Also herein, some prokaryotes are in more than one group, and some groups consist of both Archaea and Bacteria.
Archaea
On the basis of ssrRNA analysis, the Archaea consist of three phylogenetically-distinct groups: Crenarchaeota, Euryarchaeota and Korarchaeota. However, for the Korarchaeota, only their nucleic acids have been detected, and no organisms have been isolated or cultured. Based on their physiology, the Archaea can be organized into three types: methanogens (prokaryotes that produce methane); extreme halophiles (prokaryotes that live at very high concentrations of salt (NaCl); and extreme (hyper) thermophiles (prokaryotes that live at very high temperatures). Besides the unifying archaeal features that distinguish them from Bacteria (i.e., no murein in cell wall, ester-linked membrane lipids, etc.), these prokaryotes exhibit unique structural or biochemical attributes which adapt them to their particular habitats. The Crenarchaeota consists mainly of hyperthermophilic sulfur-dependent prokaryotes and the Euryarchaeota contains the methanogens and extreme halophiles. ssrRNAs of the Korarchaeota have been obtained from hyperthermophilic environments similar to those inhabitated by Crenarchaeota.
Figure 1. Phylogenetic tree of Archaea.
Methanogens are obligate anaerobes that will not tolerate even brief exposure to air (O2). Anaerobic environments are plentiful, however, and include marine and fresh-water sediments, bogs and deep soils, intestinal tracts of animals, and sewage treatment facilities. Methanogens have an incredible type of metabolism that can use H2 as an energy source and CO2 as a carbon source for growth. In the process of making cell material from H2 and CO2, the methanogens produce methane (CH4) in a unique energy-generating process. The end product (methane gas) accumulates in their environment. Methanogen metabolism created most the natural gas (fossil fuel) reserves that are tapped as energy sources for domestic or industrial use. Methanogens are normal inhabitants of the rumen (fore-stomach) of cows and other ruminant animals. A cow belches about 50 liters of methane a day during the process of eructation (chewing the cud). Methane is a significant greenhouse gas and is accumulating in the atmosphere at an alarming rate. When rain forests are destroyed and replaced by cows, it is "double-hit" on the greenhouse: (1) less CO2 is taken up by removal of the the autotrophic green plants; (2) additional CO2 and CH4 are produced as gases by the combined metabolism of the animal and methanogens. Methanogens represent a microbial system that can be exploited to produce energy from waste materials. Large amounts of methane are produced during industrial sewage treatment processes, but the gas is usually wasted rather than trapped for recycling.
Figure 2. Methanococcus jannischii
Methanococcus jannischii was originally isolated from a sample taken from a "white smoker" chimney at an oceanic depth of 2,600 meters on the East Pacific Rise. It can be grown in a mineral medium containing only H2 and CO2 as sources of energy and carbon for growth within a temperature range of 50 to 86 degrees. Cells are irregular cocci that are motile due to two bundles of polar flagella inserted near the same cellular pole.
Extreme halophiles live in natural environments such as the Dead Sea, the Great Salt Lake, or evaporating ponds of seawater where the salt concentration is very high (as high as 5 molar or 25 percent NaCl). These prokaryotes require salt for growth and will not grow at low salt concentrations. Their cell walls, ribosomes, and enzymes are stabilized by Na+. Halobacterium halobium, the prevalent species in the Great Salt Lake, adapts to the high-salt environment by the development of "purple membrane", actually patches of light-harvesting pigment in the plasma membrane. The pigment is a type of rhodopsin called bacteriorhodopsin which reacts with light in a way that forms a proton gradient on the membrane allowing the synthesis of ATP. This is the only example in nature of non photosynthetic photophosphorylation. These organisms are heterotrophs that normally respire by aerobic means. The high concentration of NaCl in their environment limits the availability of O2 for respiration so they are able to supplement their ATP-producing capacity by converting light energy into ATP using bacteriorhodopsin.
Figure 3. Halobacterium salinarium
Halobacterium salinarium is an extreme halophile that grows at 4 to 5 M NaCl and does not grow below 3 M NaCl. This freeze etched preparation shows the surface structure of the cell membrane and reveals smooth patches of "purple membrane" (bacteriorhodopsin) embedded in the plasma membrane.
The extreme thermophiles come from several distinct phylogenetic lines of Archaea. These organisms require a very high temperature (80 degrees to 105 degrees) for growth. Their membranes and enzymes are unusually stable at high temperatures. Most of these Archaea require elemental sulfur for growth. Some are anaerobes that use sulfur as an electron acceptor for respiration in place of oxygen. Some are lithotrophs that oxidize sulfur as an energy source. Sulfur-oxidizers grow at low pH (less than pH 2) because they acidify their own environment by oxidizing So (sulfur) to SO4 (sulfuric acid). These hyperthermophiles are inhabitants of hot, sulfur-rich environments usually associated with volcanism, such as hot springs, geysers and fumaroles in Yellowstone National Park, and thermal vents ("smokers") and cracks in the ocean floor. Sulfolobus was the first hyperthermophilic Archaean discovered by Thomas D. Brock of the University of Wisconsin in 1970. His discovery, along with that of Thermus aquaticus in Yellowstone National Park, launched the field of hyperthermophile biology. (Thermus aquaticus, source of the enzyme taq polymerase used in the polymerase chain reaction (PCR), is a Bacterium which has an optimum temperature for growth of 70 degrees.) Sulfolobus grows in sulfur-rich, hot acid springs at temperatures as high as 90 degrees and pH values as low as 1. Thermoplasma, also discovered by Brock, is a unique thermophile that is the sole representative of a distinct phylogenetic line of Archaea. Thermoplasma resembles the bacterial mycoplasmas in that it lacks a cell wall. Thermoplasma grows optimally at 55 degrees and pH 2. Interestingly, it has only been found in self-heating coal refuse piles, which are a man-made waste.
Figure 4. Sulfolobus acidocaldarius
(T.D. Brock)
Sulfolobusis an extreme thermophile that has been found in geothermally-heated acid springs, mud pots and surface soils with temperatures from 60 to 95 degrees C, and a pH of 1 to 5. Left: Electron micrograph of a thin section (X85,000). Under the electron microscope the organism appears as irregular spheres which are often lobed. Right: Fluorescent photomicrograph of cells attached to a sulfur crystal. Fimbrial-like appendages have been observed on the cells attached to solid surfaces such as sulfur crystals.
Although the Archaea are often inhabitants of unusual or extreme environments, there may be corresponding species of Bacteria, and even eukaryotes, in these habitats as well. No bacterium can produce methane, but Bacteria are always found in anaerobic habitats in association with methanogens. With regard to acid tolerance, a bacterium, Thiobacillus, has been observed growing at pH near 0. An Alga, Cyanidium, has also been found growing near pH 0. In superheated environments (greater than100 degrees), Archaea seem to have an exclusive hold, but Bacteria have been isolated from boiling hot springs in Yellowstone National Park and other parts of the world. No bacterium grows at the highest salt concentration which supports the growth of the halobacteria, but osmophilic yeasts and fungi can grow at correspondingly low water actvities where sugar is the solute in high concentration.
BACTERIA
Phylogenetic analysis of the Bacteria has demonstrated that eleven distinct groups exist but most groups consist of members that are phenotypically and physiologically unrelated. Below we discuss the major groups of Bacteria based on morphology, physiology, or ecology, and often use informal, but familiar, terms to identify them.
Figure 5. Phylogenetic tree of Bacteria.
Photosynthetic purple and green bacteria. These bacteria conduct anoxygenic photosynthesis, also called bacterial photosynthesis. Bacterial photosynthesis differs from plant-type (oxygenic) photosynthesis in several ways. Bacterial photosynthesis does not produce O2; in fact, it only occurs under anaerobic conditions. Bacterial photosynthesis utilizes chlorophyll other than chlorophyll a, and only one photosystem, photosystem I. The electron donor for bacterial photosynthesis is never H2O but may be H2, H2S of So, or certain organic compounds. The light-absorbing pigments of the purple and green bacteria consist of bacterial chlorophylls and carotenoids. Phycobilins, characteristic of the cyanobacteria, are not found. Many purple and green sulfur bacteria store elemental sulfur as a reserve material that can be further oxidized to SO4 as a photosynthetic electron donor.
The purple and green sulfur bacteria use H2S during photosynthesis in the same manner that cyanobacteria or algae or plants use H2O as an electron donor for autotrophic CO2 reduction (the "dark reaction" of photosynthesis). They can also use organic compounds as electron donors for photosynthesis. For example, Rhodobacter can use light as an energy source while oxidizing succinate or butyrate in order to obtain electrons for CO2 fixation.
The bacterium that became an endosymbiont of eukaryotes and evolved into mitochondria is thought to be a relative of the purple bacteria. This conclusion is based on similar metabolic features of mitochondria and purple nonsulfur bacteria and on comparisons of the base sequences in their 16S rRNAs.
Figure 6. Photomicrographs (phase contrast and and ordinary illumination) of various photosynthetic bacteria (Norbert Pfennig). Magnifications are about X1400. The purple and green bacteria exhibit a full range of prokaryotic morphologies, as these photomicrographs illustrate.
A. Purple sulfur bacteria (L to R): Chromatium vinosum, Thiospirillum jenense, Thiopedia rosea
B. Purple nonsulfur bacteria (L to R): Rhodospirillum rubrum, Rhodobacter sphaeroides, Rhodomicrobium vannielii
C. Green sulfur bacteria (L to R): Chlorobium limicola, Prosthecochloris aestuarii, Pelodictyon clathratiforme
Figure 7 . Green nonsulfur bacterium, Chloroflexus (T.D. Brock). Chloroflexus represents a phylogenetically distinct group of green bacteria, which includes other green nonsulfur bacteria. Chloroflexus is a thermophilic, filamentous gliding bacterium.
Figure 8. Photosynthetic prokaryotes growing in a hot spring run-off channel (T.D. Brock). The white area of the channel is too hot for photosynthetic life, but as the water cools along a gradient, the colored phototrophic bacteria colonize and ultimately construct the colored microbial mats composed of a consortium of photosynthetic microorganisms.
Cyanobacteria. The cyanobacteria deserve special emphasis because of their great ecological importance in the global carbon, oxygen and nitrogen cycles, as well as their evolutionary significance in relationship to plants. Photosynthetic cyanobacteria have chlorophyll a and carotenoids in addition to some unusual accessory pigments named phycobilins. The blue pigment, phycocyanin and the red one, phycoerythrin, absorb wavelengths of light for photosynthesis that are missed by chlorophyll and the carotenoids. Within the cytoplasm of cyanobacteria are numerous layers of membranes, often parallel to one another. These membranes are photosynthetic thylakoids that resemble those found in chloroplasts, which, in fact, correspond in size to the entire cyanobacterial cell. The main storage product of the cyanobacteria is glycogen, and glycogen inclusions may be seen in the cytoplasm of the cells. Cyanobacteria are thought to have given rise to eukaryotic chloroplasts during the evolutionary events of endosymbiosis. In biochemical detail, cyanobacteria are especially similar to the chloroplasts of red algae (Rhodophyta).
Most cyanobacteria have a mucilaginous sheath, or coating, which is often deeply pigmented, particularly in species that occur in terrestrial habitats. The colors of the sheaths in different species include light gold, yellow, brown, red, green, blue, violet, and blue-black. It is these pigments that impart color to individual cells and colonies as well as to "blooms" of cyanobacteria in aquatic environments
Figure 9. Some common cyanobacteria L to R: Oscillatoria, a filamentous species common in fresh water and hot springs; Nostoc, a sheathed communal species; Anabaena, a nitrogen fixing species. The small cell with an opaque surface (third from right) in the anabaena filament is a heterocyst, a specialized cell for nitrogen fixation. The large bright cell in the filament is a type of spore called an akinete; Synechococcus, a unicelluar species in marine habitats and hot springs. Synechococcus is among the most important photosynthetic bacteria in the marine environment, estimated to account for about 25 percent of the primary production that occurs in typical marine habitats.
Although thousands of cyanobacteria have been observed, only about 200 species have been identified as distinct, free-living, nonsymbiotic prokaryotes. Relative to other oxygenic phototrophs, cyanobacteria often grow under fairly extreme environmental conditions such as high temperature and salinity . They are the only oxygenic phototrophs present in many hot springs of the Yellowstone ecosystem, and in frigid lakes and oceans of Antarctica, they form luxuriant mats 2 to 4 centimeters thick in water beneath more than five meters of permanent ice. However, cyanobacteria are absent in acidic waters where their eukaryotic counterparts, the algae, may be abundant.
Layered chalk deposits called stromatolites, which exhibit a continuous geologic record covering 2.7 billion years, are produced when colonies of cyanobacteria bind calcium-rich sediments. Today, stromatolites are formed in only a few places, such as shallow pools in hot dry climates. The abundance of cyanobacteria in the fossil record is evidence of the early development of the cyanobacteria and their important role in elevating the level of free oxygen in the atmosphere of the early Earth.
Cyanobacteria often form filaments and may grow in large masses or "tufts" one meter or more in length. Some are unicellular, a few form branched filaments, and a few form irregular plates or irregular colonies. Cyanobacterial cells usually divide by binary fission, and the resulting progeny cells may separate to form new colonies. In addition, filaments may break into fragments, called hormogonia, which separate and develop into new colonies. As in other filamentous or colonial bacteria, the cells of cyanobacteria may joined by their walls or by mucilaginous sheaths, but each cell is an independent unit of life.
As true Bacteria, cyanobacteria contain peptidoglycan or murein in their cell walls. Most cyanobacteria have a Gram-negative type cell wall that consists of an outer membrane component, even though they show a distant phylogenetic relationship with Gram-positive bacteria. Some of the filamentous cyanobacteria are motile by means gliding or rotating around a longitudinal axis. Short segments (hormogonia) may break off from a cyanobacterial colony and glide away from their parent colony at rates as rapid as 10 micrometers per second. The mechanism for this movement is unexplained but may be connected to the extrusion of slime (mucilage) through small pores in their cell wall, together with contractile waves in one of the surface layers of the wall.
Cyanobacteria are found in most aerobic environments where water and light are available for growth. Mainly they live in fresh water and marine habitats. Those inhabiting the surface layers of water are part of a complex microbial community called plankton. Planktonic cyanobacteria usually contain cytoplasmic inclusions called gas vesicles which are hollow protein structures filled with various gases. The vesicles can be inflated or deflated with gases allowing the organisms maintain buoyancy and to float at certain levels in the water. Thus, the cyanobacteria can regulate their position in the water column to meet their optimal needs for photosynthesis, oxygen, and light-shielding. When numerous cyanobacteria become unable to regulate their gas vesicles properly (for example, because of extreme fluctuations of temperature or oxygen supply), they may float to the surface of a body of water and form visible "blooms". A planktonic species related to Oscillatoria gives rise to the redness (and the name) of the Red Sea.
The cyanobacteria have very few harmful effects on plants or animals. They may be a nuisance if they bloom in large numbers and then die and decay in bodies of fresh water that are used for drinking or recreational purposes. Many cyanobacteria are responsible for the earthy odors and flavors of fresh waters, including drinking waters, due to the production of compounds called geosmins. Some cyanobacteria that form blooms secrete poisonous substances that are toxic for animals that ingest large amounts of the contaminated water.
Many marine cyanobacteria occur in limestone (calcium carbonate) or lime-rich substrates, such as coral algae and the shells of mullosks. Some fresh water species, particularly those that grow in hot springs, often deposit thick layers of lime in their colonies.
Some cyanobacteria can fix nitrogen. In filamentous cyanobacteria, nitrogen fixation often occurs in heterocysts, which are specialized, enlarged cells, usually distributed along the length of a filament or at the end of a filament. Heterocysts have intercellular connections to adjacent vegetative cells, and there is continuous movement of the products of nitrogen fixation moving from heterocysts to vegetative cells, and the products of photosynthesis moving from vegetative cells to heterocysts. Heterocysts are low in phycobilin pigments and have only photosystem I. They lack the oxygen-evolving photosystem II. Furthermore, they are surrounded in a thickened, specialized glycolipid cell wall that slows the rate of diffusion of O2 into the cell. Any O2 that diffuses into the heterocyst is rapidly reduced by hydrogen, a byproduct of N2 fixation, or is expelled through the wall of the heterocyst. The process of nitrogen fixation, specifically the enzyme nitrogenase, only functions in anaerobic conditions so the organism must maintain these oxygen-free compartments in order for N2 fixation to occur.
In addition to the heterocysts, some cyanobacteria form resistant spores called akinetes enlarged cells around which thickened outer walls develop. Akinetes are resistant to heat, freezing and drought (desiccation) and thus allow the cyanobacteria to survive unfavorable environmental conditions. The are functionally analogous to bacterial endospores, but they bear little resemblance and lack the extraordinary resistance properties of endospores.
A few cyanobacteria are symbionts of liverworts, ferns, cycads, flagellated protozoa, and algae, sometimes occurring as endosymbionts of the eukaryotic cells. In the case of the water fern Azolla, the cyanobacterial endophyte (a species of Anabaena) fixes nitrogen that becomes available to the plant . In addition, it is often the case that the photosynthetic partners of lichens are cyanobacteria.
The planktonic cyanobacteria fix an enormous amount of CO2 during photosynthesis, and as "primary producers" they and are the basis of the food chain in marine environments. Their type of photosynthesis, which utilizes photosystem II, generates a substantial amount of oxygen present in the earth's atmosphere. Since many cyanobacteria can fix N2 under certain conditions, they are one of the most significant free-living nitrogen-fixing prokaryotes. Cyanobacteria carried out plant-type (oxygenic) photosynthesis for at least a billion and a half years before the emergence of plants, and cyanobacteria are believed to be the evolutionary forerunners of modern-day plant and algal chloroplasts. A group of phototrophic prokaryotes, called prochlorophytes contain chlorophyll a and b but do not contain phycobilins. Prochlorophytes, therefore, resemble both cyanobacteria (because they are prokaryotic and contain chlorophyll a) and the plant chloroplast (because they contain chlorophyll b instead of phycobilins). Prochloron, the first prochlorophyte discovered, is phenotypically very similar to certain plant chloroplasts and is the leading candidate for the type of bacterium that might have undergone endosymbiotic events that led to the development of the plant chloroplast.
Spirochetes are a phylogenetically distinct group of Bacteria which have a unique cell morphology and mode of motility. Spirochetes are very thin, flexible, spiral-shaped prokaryotes that move by means of structures called axial filaments or endoflagella. The flagellar filaments are contained within a sheath between the cell wall peptidoglycan and an outer membrane. The filaments flex or rotate within their sheath which causes the cells to bend, flex and rotate during movement. Most spirochetes are free living (in muds and sediments), or live in associations with animals (e.g. in the oral cavity or GI tract). A few are pathogens of animals (e.g. leptospirosis in dogs, Syphilis in humans and Lyme Disease in dogs and humans).
Figure 10. Spirochetes: A. Cross section of a spirochete showing the location of endoflagella between the inner membrane and outer sheath; B. Borrelia burgdorferi, the agent of Lyme disease; C. Treponema pallidum, the spirochete that causes syphilis.
Spirilla are Gram-negative aerobic heterotrophic bacteria with a helical or spiral shape. Their metabolism is respiratory and never fermentative. Unlike spirochetes, they have a rigid cell wall and are motile by means of ordinary polar flagella. Spirilla are inhabitants of microaerophilic aquatic environments. Most spirilla require or prefer that oxygen in their environment be present in an amount that is well below atmospheric concentration. Spirillum and Aquaspirillum are inhabitants of fresh water. They frequently contain magnetosomes and exhibit the property of magnetotaxis (movement in relationship to the magnetic field of the earth). Oceanospirillum lives in marine habitats and is able to grow at NaCl concentrations as high as 9 percent. Azospirillum is a nitrogen-fixing bacterium that enters into a mutualistic symbiosis with certain tropical grasses and grain crops. Spirilla are thought to play a significant role in recycling of organic matter, particularly in aquatic environments.
Related to the spirilla is the small vibrioid bacterium, Bdellovibrio, which is a parasite of other Gram-negative bacteria, including E. coli. It preys on other bacteria by entering into the periplasmic space and obtaining nutrients from the cytoplasm of its host cell while undergoing an odd type of reproductive cycle.
Two pathogens of humans are found among the spirilla. Campylobacter jejuni is an important cause of bacterial diarrhea, especially in children. The bacterium is transmitted via contaminated food, usually undercooked poultry or shellfish, or untreated drinking water. Helicobacter pylori is able to colonize the gastric mucosal cells of humans, i.e., the lining of the stomach, and it has been fairly well established as the cause of peptic ulcers.
The Myxobacteria are a group of gliding bacteria that aggregate together to form a multicellular fruiting body in which development and spore formation takes place. They exhibit the most complex behavioral patterns and life cycles of all known prokaryotes. Myxobacteria are inhabitants of the soil. They have a eukaryotic counterpart in nature in the Myxomycetes, or slime molds, and the two types of organisms are an example of parallel or convergent evolution, having adopted similar life styles in the soil environment.
The vegetative cells of myxobacteria are typical Gram-negative rods that glide across a substrate such as a decaying leaf or piece of animal dung, or colonies of other bacteria. They obtain nutrients from the substrate as they glide across it and they secrete a slime track which other myxobacterial cells preferentially follow. If their nutrients become exhausted, the cells signal to one another to aggregate and form a swarm of myxobacteria which eventually differentiate into a multicellular fruiting body that contains myxospores, a type of dormant cell descended from a differentiated vegetative cell. In the case of Stigmatella, the myxospores are packed into secondary structures called cysts, which develop at the tips of the fruiting body (Figure 11). The bright-colored fruiting bodies of myxobacteria, containing millions of cells and spores, can often be seen with the unaided eye on dung pellets and decaying vegetation in the soil.
Figure 11. Stigmatella aurantiaca, a fruiting myxobacterium: L. Life Cycle R. Fruiting Body.
Lithotrophs. Lithotrophy, a type of metabolism that requires inorganic compounds as sources of energy, is established in both the Archaea and the Bacteria. The methanogens utilize H2 as an energy source, and many extreme thermophiles use H2S or elemental sulfur as a source of energy for growth. Lithotrophic Bacteria are typically Gram-negative species that utilize inorganic substrates including H2, NH3, NO2, H2S, S, Fe++, and CO. Ecologically, the most important lithotrophic Bacteria are the nitrifying bacteria, Nitrosomonas and Nitrobacter that together convert NH3 to NO2, and NO2 to NO3, and the colorless sulfur bacteria such as Thiobacillus that oxidizes H2S to S and S to SO4. Most lithotrophic bacteria are autotrophs, and, in some cases, they may play an important role in primary production of organic material in nature. Lithotrophic metabolism does not extend to eukaryotes (unless a nucleated cell harbors lithotrophic endosymbiotic bacteria), and these bacteria are important in the biogeochemical cycles of the elements.
Figure 12. Lithotroph Habitats. A. Stream in Northern Wisconsin near Hayward is a good source of iron bacteria. B. Bacteriologist J.C. Ensign of the University of Wisconsin observing growth of iron bacteria in a run-off channel from the Chocolate Pots along the Gibbon River, in Yellowstone National Park. C. An acid hot spring at the Norris Geyser Basin in Yellowstone is rich in iron and sulfur. D. A black smoker chimney in the deep sea emits iron sulfides at very high temperatures (270 to 380 degrees C).
Pseudomonads and their relatives "Pseudomonads" is a term for bacteria which morphologically and physiologically resemble members of the genus Pseudomonas, a very diverse group of Gram-negative rods with a strictly-respiratory mode of metabolism. Usually the term is reserved for members of the genera Pseudomonas and Xanthomonas, but many other related bacteria share the definitive characterictics of pseudomonads, i.e., Gram-negative bacteria which typically live by aerobic (as opposed to facultative), means. In Bergey's Manual, these bacteria are unified as Gram-negative aerobic rods and cocci. In Woese's Universal Phylogenetic Tree the genera are scattered about among the Purple Bacteria, with some being close relatives of the Enterobacteriaceae. In fact, the morphology and habitat of many pseudomonads sufficiently overlaps with the enterics (below) that microbiologists must quickly learn how to differentiate these two types of Gram-negative motile rods. Pseudomonads move by polar flagella; enterics such as E. coli swim by means of peritrichous flagella. Enterics ferment sugars such as glucose; pseudomonads generally do not ferment sugars. And most pseudomonads have an unusual cytochrome in their respiratory electron transport chain that can be detected in colonies by a colorimetric test called the oxidase test. Pseudomonads are oxidase- positive.
Figure 13. Profile of a Pseudomonad: Gram-negative rods motile by polar flagella. A. Electron micrograph, negative stain. B. Scanning electron micrograph. C. Gram stain.
Most pseudomonads are free-living organisms in soil and water; they play an important role in decomposition, biodegradation, and the C and N cycles. The phrase "no naturally-occurring organic compound cannot be degraded by some microorganism" must have been coined to apply to members of the genus Pseudomonas, known for their ability to degrade hundreds of different organic compounds including insecticides, pesticides, herbicides, plastics, petroleum substances, hydrocarbons and other of the most refractory molecules in nature. However, they are usually unable to degrade biopolymers in their environment, such as cellulose and lignen, and their role in anaerobic decomposition is minimal.
There are about 150 species of Pseudomonas, but, especially among the plant pathogens, there are many strains and biovars among the species. These bacteria are frequently found as part of the normal flora of plants, but they are one of the most important bacterial pathogens of plants, as well. Pseudomonas syringae and Xanthomonas species cause a wide variety of plant diseases as discussed below. One strain of Pseudomonas that lives on the surfaces of plants can act as an "ice nucleus" which causes ice formation and inflicts frost damage on plants at one or two degrees above the conventional freezing temperature of water (0 degrees C). One Pseudomonas species is an important pathogen of humans, Pseudomonas aeruginosa, the quintessential opportunistic pathogen, which is a leading cause of hospital-acquired infections. A few relatives of the pseudomonads are pathogens of animals, i.e., the agents of whooping cough, Bordetella pertussis, Legionaires' pneumonia (Legionella pneumophilia), gonorrhea (Neisseria gonorrhoeae), and bacterial meningitis (Neisseria meningitidis), but most of these bacteria have a normal existence apart from animals - in soil, water, and on the surfaces of plants. The pseudomonads have a lesser predilection for pathogenicity of animals than do the enteric bacteria.
Among the interesting or important relatives of the pseudomonads are Rhizobiumand Bradyrhizobium, species that fix nitrogen in association with leguminous plants, and related Agrobacterium species that cause tumors ("galls") in plants. These bacteria are discussed later in this article because of their special relationships with plants. Relatives of the pseudomonads also include the methanotrophs that can oxidize methane and other one-carbon compounds, the azotobacters, which are very prevalent free-living (nonsymbiotic) nitrogen-fixing bacteria, and the acetobacters that are used in the manufacture of vinegar.
Enterics. Enteric bacteria are Gram-negative rods with facultative anaerobic metabolism that live in the intestinal tracts of animals. This group consists of Escherichia coli and its relatives, the members of the family Enterobacteriaceae. Enteric bacteria are related phenotypically to several other genera of bacteria such as Pseudomonas and Alcaligenes, but are physiologically quite unrelated. Generally, a distinction can be made on the ability to ferment glucose; enteric bacteria all ferment glucose to acid end products while similar Gram-negative bacteria cannot ferment glucose. Because they are consistent members of the normal flora of humans, and because of their medical importance, an extremely large number of enteric bacteria have been isolated and characterized.
Escherichia coli is, of course, the type species of the enterics. E. coli is such a regular inhabitant of the intestine of humans that it is used by public health authorities as an indicator of fecal pollution of drinking water supplies, swimming beaches, foods, etc. E. coli is the most studied of all organisms in biology because of its occurrence, and the ease and speed of growing the bacteria in the laboratory. It has been used in hundreds of thousands of experiments in cell biology, physiology, and genetics, and was among the first cells for which the entire chromosomal DNA base sequence was determined. In spite of the knowledge gained about the molecular biology and physiology of E. coli, surprisingly little is known about its ecology, for example why it consistently associates with humans, how it helps its host, how it harms its host, etc. A few strains of E. coli are pathogenic (one is notorious, strain 0157:H7, that keeps turning up in raw hamburger headed for a fast-food restaurants).Pathogenic strains of E. coli cause intestinal tract infections (usually acute and uncomplicated, except in the very young ) or uncomplicated urinary tract infections.
Figure 14. Left: Escherichia coli cells. Right: E. coli colonies on EMB Agar.
The enteric group also includes some other intestinal pathogens of humans such as Shigella dysenteriae, cause of bacillary dysentery, and Salmonella typhimurium, cause of gastroenteritis. Salmonella typhi, which infects via the intestinal route, causes typhoid fever. Some bacteria that don't have an intestinal habitat resemble E. coli in enough ways to warrant inclusion in the enteric group. This includes Proteus, a common saprophyte of decaying organic matter, Yersinia pestis which causes bubonic plague, and Erwinia, an important pathogen of plants.
Vibrios (which have a curved rod morphology or comma shape) are very common bacteria in aquatic environments. They have structural and metabolic properties that overlap with both the enterics and the pseudomonads. In Bergey's Manual, Vibrionaceae is a family on the level with Enterobacteriaceae. Vibrios are facultative like enterics, but they have polar flagella, are oxidase-positive, and dissimilate sugars in the same manner as the pseudomonads. In aquatic habitats they overlap with the Pseudomonadaceae in their ecology, although pseudomonads favor fresh water and vibrios prefer salt water. The genus Vibrio contains an important pathogen of humans, Vibrio cholerae, the cause of Asiatic cholera. Cholera is an intestinal disease with a pathology related to diarrheal diseases caused by the enteric bacteria.
Five species of marine vibrios exhibit the property of bioluminescence, the ability to emit light of a blue-green color. These bacteria may be found as saprophytes on dead fish or as symbionts of living fish and invertebrates in marine environments. Some grow in special organs of the fish and emit light for the benefit of the fish (to attract prey, or as a mating signal) in return for a protected habitat and supply of nutrients. The reaction leading to light emission, catalyzed by the enzyme luciferase, has been found to be the same in all prokaryotes, and differs from light emission by eukaryotes such as the fire fly. Luciferase diverts electrons from the normal respiratory electron transport chain and causes formation of an excited peroxide that leads to emission of light.
Nitrogen-fixing organisms. This is a diverse group of prokaryotes, reaching into phylogenetically distinct groups of Archaea and Bacteria. Members are unified only on the basis of their metabolic ability to "fix" nitrogen. Nitrogen fixation is the reduction of N2 (atmospheric nitrogen) to NH3 (ammonia). It is a complicated enzymatic process mediated by the enzyme nitrogenase. Nitrogenase is found only in prokaryotes and is second only to RUBP carboxylase (the enzyme responsible for CO2 fixation) as the most abundant enzyme on Earth.
The conversion of nitrogen gas (which constitutes about 80 percent of the atmosphere) to ammonia introduces nitrogen into the biological nitrogen cycle. Living cells obtain their nitrogen in many forms, but usually from ammonia (NH3) or nitrates (NO3), and never from N2. Nitrogenase extracts N2 from the atmosphere and reduces it to NH3 in a reaction that requires substantial reducing power (electrons) and energy (ATP). The NH3 is immediately assimilated into amino acids and proteins by subsequent cellular reactions. Thus, nitrogen from the atmosphere is fixed into living (organic) material.
Although a widespread trait in prokaryotes, nitrogen fixation occurs in only a few select genera. Outstanding among them are the symbiotic bacteria Rhizobium and Bradyrhizobium which form nodules on the roots of legumes. In this symbiosis the bacterium invades the root of the plant and fixes nitrogen which it shares with the plant. The plant provides a favorable habitat for the bacterium and supplies it with nutrients and energy for efficient nitrogen fixation. Rhizobium and Bradyrhizobium are Gram-negative aerobes related to the pseudomonads (above). An unrelated bacterium, an actinomycete (below), enters into a similar type of symbiosis with plants. The actinomycete, Frankia, forms nodules on the roots of several types of trees and shrubs, including alders (Alnus), wax myrtles (Myrica) and mountain lilacs (Ceanothus). They, too, fix nitrogen which they provide to their host in a useful form. This fact allows alder species to be "pioneer plants" (among the first to colonize) in newly-forming nitrogen-deficient soils. Still other bacteria live in regular symbiotic associations with plants on roots or leaves and fix nitrogen for their hosts, but they do not cause tissue hyperplasia or the formation of nodules.
Cyanobacteria are likewise very important in nitrogen fixation. Cyanobacteria provide fixed nitrogen, in addition to fixed carbon, for their symbiotic partners which make up lichens. This enhances the capacity for lichens to colonize bare areas where fixed nitrogen is in short supply. In some parts of Asia, rice can be grown in the same paddies continuously without the addition of fertilizers because of the presence of nitrogen fixing cyanobacteria. The cyanobacteria, especially Anabaena, occur in association with the small floating water fern Azolla, which forms masses on the paddies. Because of the nearly obligate association of Azolla with Anabaena , paddies covered with Azolla remain rich in fixed nitrogen.
In addition to symbiotic nitrogen-fixing bacteria, there are various free-living nitrogen-fixing prokaryotes in both soil and aquatic habitats. Cyanobacteria may be able to fix nitrogen in virtually all habitats that they occupy. Clostridia and some methanogens fix nitrogen in anaerobic soils and sediments, including thermophilic environments. A common soil bacterium, Azotobacter is a vigorous nitrogen fixer, as is Rhodospirillum, a purple sulfur bacterium. Even Klebsiella, an enteric bacterium closely related to E. coli, fixes nitrogen. There is great scientific interest, of course, in knowing how one might move the genes for nitrogen fixation from a prokaryote into a eukaryote such as corn or some other crop plant. The genetically engineered plant might lose its growth requirement for costly ammonium or nitrate fertilizers and grow in nitrogen deficient soils.
Besides nitrogen fixation, bacteria play other essential roles in the processes of the nitrogen cycle. For example, saprophytic bacteria, decompose proteins releasing NH3 in the process of ammoniafication. NH3 is oxidized by lithotrophic Nitrosomonas species to NO2 which is subsequently oxidized by Nitrobacter to NO3. The overall conversion of NH3 to NO3 is called nitrification. NO3 can be assimilated by cells as a source of nitrogen (assimilatory nitrate reduction), or certain bacteria can reduce NO3 during a process called anaerobic respiration, wherein nitrate is used in place of oxygen as a terminal electron acceptor for a process analogous to aerobic respiration. In the case of anaerobic respiration, NO3 is first reduced to NO2, which is subsequently reduced to N2O or N2 or NH3 (all gases). This process is called denitrification and it occurs in anaerobic environments where nitrates are present. If denitrification occurs in crop soils it may not be beneficial to agriculture if it converts utilizable forms of nitrogen (as in nitrate fertilizers) to nitrogen gases that will be lost into the atmosphere. One rationale for tilling the soil is to keep it aerobic in order to discourage denitrification processes in Pseudomonas and Bacillus which are ubiquitous inhabitants.
The pyogenic cocci are spherical bacteria which cause various suppurative (pus-producing) infections in animals. Included are the Gram-positive cocci Staphylococcus aureus, Streptococcus pyogenes and Streptococcus pneumoniae, and the Gram-negative cocci Neisseria gonorrhoeae and N. meningitidis. These bacteria are leading pathogens of humans. It is estimated that they produce at least a third of all the bacterial infections of humans, including strep throat, pneumonia, food poisoning, various skin diseases and severe types of septic shock, gonorrhea and meningitis. Staphylococcus aureus is arguably the most successful of all bacterial pathogens because it has a very wide range of virulence determinants (so it can produce a wide range of infections) and it often occurs as normal flora of humans (on skin, nasal membranes and the GI tract), which ensures that it is readily transmitted from one individual to another. In terms of their phylogeny, physiology and genetics, these genera of bacteria are quite unrelated to one another. They share a common ecology, however, as parasites of humans.
Figure 15. Gallery of pyogenic cocci, Gram stains of clinical specimens (pus), L to R: Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Neisseria gonorrhoeae, Neisseria meningitidis. The large cells with lobed nuclei are neutrophils. Pus is the outcome of the battle between phagocytes (neutrophils) and the invading cocci. As the bacteria are ingested and killed by the neutrophils, the neutrophils eventually lyse (rupture) and release their own components, plus the digested products of bacterial cells, which are the make-up of pus. As a defense against phagocytes the staphylococci and streptococci produce toxins that kill the neutrophils before they are able to ingest the bacteria. This contributes to the pus, and therefore these bacteria are "pyogenic" during their pathogenic invasions.
Two species of Staphylococcus live in association with humans: Staphylococcus epidermidis which lives normally on the skin and mucous membranes, and Staphylococcus aureus which may occur normally at various locales, but in particular on the nasal membranes (nares). S. epidermidis is rarely a pathogen and probably benefits its host by producing acids on the skin that retard the growth of dermatophytic fungi. S. aureus always has the potential to cause disease and so is considered a pathogen. Different strains of S. aureus differ in the range of diseases they can cause, including boils and pimples, wound infections, pneumonia, osteomyelitis, septicemia, food intoxication, and toxic shock syndrome. S. aureus is the leading cause of nosocomial (hospital-acquired) infections by Gram-positive bacteria. Also, it is notoriously resistant to penicillin and many other antibiotics. Recently, a strain of S. aureus has been reported that is resistant to EVERY known antibiotic in clinical usage, which is a grim reminder that the clock is ticking on the lifetime of the usefulness of current antibiotics in treatment of infectious disease.
Streptococcus pyogenes, more specifically the Beta-hemolytic Group A Streptococci, like S. aureus, causes an array of suppurative diseases and toxinoses (diseases due to the production of a bacterial toxin), in addition to some autoimmune or allergic diseases. S. pyogenes is rarely found as normal flora (<1%), but it is the main streptococcal pathogen for man, most often causing tonsillitis or strep throat. Streptococci also invade the skin to cause localized infections and lesions, and produce toxins that cause scarlet fever and toxic shock. Sometimes, as a result of an acute streptococcal infection, anomalous immune responses are started that lead to diseases like rheumatic fever and glomerulonephritis, which are called post-streptococcal sequelae. Unlike the staphylococci, the streptococci have not developed widespread resistance to penicillin and the other beta lactam antibiotics, so that the beta lactams remain drugs of choice for the treatment of acute streptococcal infections.
Streptococcus pneumoniae is the most frequent cause of bacterial pneumonia in humans. It is also a frequent cause of otitis media (infection of the middle ear) and meningitis. The bacterium colonizes the nasopharynx and from there gains access to the lung or to the eustachian tube. If the bacteria descend into the lung they can impede engulfment by alveolar macrophages if they possess a capsule which somehow prevents the engulfment process. Thus, encapsulated strains are able to invade the lung and are virulent (cause disease) and noncapsulated strains, which are readily removed by phagocytes, are nonvirulent.
The Neisseriaceae is a family of Gram-negative bacteria with characteristics of both enterics and pseudomonads. The neisseriae are small, Gram-negative cocci usually seen in pairs with flattened adjacent sides. Most neisseriae are normal flora or harmless commensals of mammals living on mucous membranes. In humans they are common residents of the throat and upper respiratory tract. Two species are primary pathogens of man, Neisseria gonorrhoeae and Neisseria meningitidis.
Neisseria gonorrhoeae is the second leading cause of sexually-transmitted disease in the U.S., causing over three million cases of gonorrhea annually. Sometimes, in females, the disease may be unrecognized or asymptomatic such that an infected mother can give birth and unknowingly transmit the bacterium to the infant during its passage through the birth canal. The bacterium is able to colonize and infect the newborn eye resulting neonatal ophthalmia, which may produce blindness. For this reason (as well as to control Chlamydia which may also be present), an antimicrobial agent is usually added to the neonate eye at the time of birth.
Neisseria meningitidis is one bacterial cause of meningitis, an inflammation of the meninges of the brain and spinal cord. Other bacteria that cause meningitis include Haemophilus influenzae, Staphylococcus aureus and Escherichia coli. Meningococcal meningitis differs from other causes in that it is often responsible for epidemics of meningitis. It occurs most often in children aged 6 to 11 months, but it also occurs in older children and in adults. Meningococcal meningitis can be a rapidly fatal disease, and untreated meningitis has a mortality rate near 50 percent. However, early intervention with antibiotics is highly effective, and with treatment most individuals recover without permanent damage to the nervous system.
Lactic acid bacteria are Gram-positive, nonsporeforming rods and cocci which produce lactic acid as a sole or major end product of fermentation. They are important in the food industry as fermentation organisms in the production of cheese, yogurt, buttermilk, sour cream, pickles, sauerkraut, sausage and other foods. Important genera are Streptococcus and Lactobacillus. Some species are normal flora of the human body (found in the oral cavity, GI tract and vagina); some streptococci are pathogens of humans (see pyogenic cocci above). Certain oral lactic acid bacteria are responsible for the formation of dental plaque and the initiation of dental caries (cavities).
Endospore-forming bacteria produce a unique resting cell called an endospore. They are Gram-positive and usually rod-shaped, but there are exceptions. The two important genera are Bacillus, the members of which are aerobic sporeformers in the soils, and Clostridium, whose species are anaerobic sporeformers of soils, sediments and the intestinal tracts of animals.
Figure 16. Endospore-forming bacilli (phase contrast illumination). Endospores are dehydrated, refractile cells appearing as points of bright light under phase microcsopy. Endospore-forming bacteria are characterized by the location (position) of the endospore in the mother cell (sporangium) before its release. The spore may be central, terminal or subterminal, and the sporangium may or may not be swollen to accomodate the spore.
Figure 17. Anatomy of an endospore, cross section drawing by Viake Haas. Endospores differ from the vegetative cells that form them in a variety of ways. Several new surface layers develop outside the core (cell) wall, including the cortex and spore coat. The cytoplasm is dehydrated and contains only the cell genome and a few ribosomes and enzymes. The endospore is cryptobiotic (exhibits no signs of life) and is remarkably resistant to environmental stress such as heat (boiling), acid, irradiation, chemicals and disinfectants. Some endospores have remained dormant for 25 million years preserved in amber, only to be shaken back into life when extricated and introduced into a favorable environment.
Figure 18. The sequential steps in the process of endospore formation in Bacillus subtilis.
Some sporeformers are pathogens of animals, usually due to the production of powerful toxins. Bacillus anthracis causes anthrax, a disease of domestic animals (cattle, sheep, etc.) which may be transmitted to humans. Clostridium botulinum causes botulism, a form of food poisoning. Clostridium tetani is the agent of tetanus.
Figure 19. Robert Koch's original photomicrographs of Bacillus anthracis. In 1876, Koch established by careful microscopy that the bacterium was always present in the blood of animals that died of anthrax. He took a small amount of blood from such an animal and injected it into a healthy mouse, which subsequently became diseased and died. He took blood from that mouse and injected it into a another healthy mouse. After repeating this several times he was able to recover the original anthrax organism from the dead mouse, demonstrating for the first time that a specific bacterium is the cause of a specific disease. In so doing, he established Koch's Postulates, which still today supply the microbiological standard to demonstrate that a specific microbe is the cause of a specific disease.
In association with the process of sporulation, some Bacillus species form a crystalline protein inclusion called parasporal crystals. The protein crystal and the spore (actually the spore coat) are toxic to lepidopteran insects (certain moths and caterpillars) if ingested. The crystals and spores of Bacillus thuringiensis are marketed as "Bt" a natural insecticide for use on garden or crop plants. Another species of Bacillus, B. cereus, produces an antibiotic that inhibits growth of Phytophthera, a fungus that attacks alfalfa seedling roots causing a "damping off" disease. The bacteria, growing in association with the roots of the seedlings, can protect the plant from disease.
Also, apparently in association with the sporulation process, some Bacillus species produce clinically-useful antibiotics. Bacillus antibiotics such as polymyxin and bacitracin are usually polypeptide molecules that contain unusual amino acids.
Actinomycetes and related bacteria are a large group of Gram-positive bacteria that usually grow by filament formation, or at least show a tendency towards branching and filament formation. Many of the organisms can form resting structures called spores, but they are not the same as endospores. Branched forms superficially resemble molds and are a striking example of convergent evolution of a prokaryote and a eukaryote together in the soil habitat. Actinomycetes such as Streptomyces have a world-wide distribution in soils. They are important in aerobic decomposition of organic compounds and have an important role in biodegradation and the carbon cycle. Products of their metabolism, called geosmins, impart a characteristic earthy odor to soils. Actinomycetes are the main producers of antibiotics in industrial settings, being the source of most tetracyclines, macrolides (e.g. erythromycin), and aminoglycosides (e.g. streptomycin, gentamicin, etc.). Two bacteria in this diverse group are important pathogens of humans: Mycobacterium tuberculosis is the cause of tuberculosis; Corynebacterium diphtheriae is the cause of diphtheria. Also, many nonpathogenic mycobacteria and corynebacteria live in associations with animals.
Figure 20. Schematic diagrams illustrating mycelial growth and spore formation in several genera of actinomycetes.
Rickettsias and chlamydiae are two unrelated groups of Bacteria that are obligate intracellular parasites of eukaryotic cells. Rickettsias cannot grow outside of a host cell because they have leaky membranes and are unable to obtain nutrients in an extracellular habitat. Chlamydiae are unable to produce ATP in amounts required to sustain metabolism outside of a host cell and are, in a sense, energy-parasites.
Rickettsias occur in nature in the gut lining of arthropods (ticks, fleas, lice, etc.). They are transmitted to vertebrates by an arthropod bite and produce such diseases as typhus fever, Rocky Mountain Spotted Fever, Q fever and canine ehrlichiosis. Chlamydiae are tiny bacteria that infect birds and mammals. They may colonize and infect tissues of the eye and urogenital tract in humans. Chlamydia trachomatis causes several important diseases in humans: chlamydia, the most prevalent sexually transmitted disease in the U.S., trachoma, a leading cause of blindness worldwide, and lymphogranuloma venereum.
Figure 21. Mammalian cells infected with rickettsial organisms. L. Bartonella bacilliformis infection of human erythrocytes and blood monoyctyes. R. Ehrlichia canis infection of canine erythrocytes and blood monocytes. The distinct stained intracytoplasmic inclusion body in the monocyte is characteristic of the infection.
Mycoplasmas are a group of bacteria that lack a cell wall. The cells are bounded by a single triple-layered membrane. They may be free-living in soil and sewage, parasitic inhabitants of the mouth and urinary tract of humans, or pathogens in animals and plants. In humans, Mycoplasma pneumoniae causes primary atypical pneumonia ("walking pneumonia").
Mycoplasmas include the smallest known cells, usually about 0.2 - 0.3 micrometers in diameter. Mycoplasmas correspondingly have the smallest known genome of any cell. Their DNA is thought to contain about 650 genes, which is about one-fifth the number found in E. coli and other common bacteria. Mycoplasmas can survive without a cell wall because their cytoplasmic membrane is more stable than that of other prokaryotes. In one group of mycoplasmas, the membrane contains sterols which seem to be responsible for the stability. Also, mycoplasmas tend to inhabit environments of high osmolarity wherein the risk of osmotic shock and lysis of the cells is minimized.
Plant-pathogenic bacteria. Many economically-important diseases of plants are caused by members of the Bacteria. It is estimated that one-eighth of the crops worldwide are lost to diseases caused by bacteria, fungi or insects. Almost all kinds of plants can be affected by bacterial diseases, and many of these diseases can be extremely destructive.
Almost all plant-pathogenic bacteria are Gram-negative bacilli, usually affiliated with the pseudomonads or enterics (above). The symptoms of bacterial disease in plants are described by a number of terms such as spots, blights, soft rots, wilts, and galls. Bacterial spots of various sizes on stems, leaves, flowers and fruits are usually caused by Pseudomonas or Xanthomonas species. Bacteria may cause spots by producing toxins that kill cells at the site of infection. Blights are caused by rapidly developing necrosis (dead, discolored areas) on stems, leaves and flowers. Fire blight in apples and pears, caused by Erwinia amylovora, can kill young trees within a single season. Bacterial soft rots occur most commonly in fleshy vegetables such as potatoes or onions or fleshy fruits such as tomatoes and eggplants. The most destructive soft rots are caused by Erwinia species that attack fruits and vegetables at the post-harvest stage.
Bacterial vascular wilts mainly affect herbaceous plants. The bacteria invade the vessels of the xylem, where they multiply, interfering with the movement of water and inorganic nutrients and resulting in the wilting and the death of the plants. The bacteria commonly degrade portions of the vessel walls and can even cause the vessels to rupture. Once the walls have ruptured, the bacteria then spread to the adjacent parenchyma tissues, where they continue to multiply. In some bacterial wilts, the bacteria ooze to the surface of the stems or leaves through cracks formed over cavities filled with cellular debris, gums, and bacteria. More commonly, however, the bacteria do not reach the surface of the plant until the plant has been killed by the disease. Wilts of alfalfa and bean plants are cause by species of Clavibacter; bacterial wilt of cucurbits, such as squashes and watermelons, are cause by Erwinia tracheiphila; the black rot of crucifers such as cabbage is caused by Xanthomonas campestris. The most economically-important wilt of plants is caused by Pseudomonas solanacearum which affects 44 genera of plants, including such major crops as bananas, peanuts, tomatoes, potatoes, eggplants and tobacco. This disease occurs worldwide in tropical, subtropical, and warm temperate areas.
Mycoplasmas (discussed above) have been identified in more than 200 plant species and associated with more than 50 plant diseases, many with symptoms of yellowing. Among these plant-pathogens are the spiroplasmas (genus Spiroplasma), which are pleomorphic, ovoid or spiral-shaped cells which are motile by means of a rotary or screw-like motion. Intracellular fibrils are thought to be responsible for their movement. The organisms have been isolated from the fluids of vascular plants and from the gut of insects that feed on these fluids. Some have been cultured on artificial media, including Spiroplasma citri, which is isolated from the leaves of citrus plants, where it causes citrus stubborn disease, and from corn plants suffering from corn stunt disease. A number of other mycoplasma-like organisms (sometimes called MLOs) have been detected in diseased plants by electron microscopy, which has been taken as evidence that these organisms may be more involved in plant disease than previously realized.
The causative agent of a common plant disease, termed crown gall, is Agrobacterium tumefaciens. The disease is characterized by large galls or swellings that form on the plant at the site of infection, usually near the soil line. Crown gall is a problem in nurseries, affecting ornamental plants and fruit stock, and it may be a serious disease in grapes. Because of their role in the genetic engineering of plants, the molecular biology of these bacteria is intensively studied.
References
1. Balows, A., H.G. Truper, M. Dworkin, W. Harder, and K.-H. Schleifer (eds.). The Prokaryotes, 2nd ed. Springer-Verlag, New York. 1992. Published in four volumes. The most complete reference on the characteristics of prokaryotes. Includes procedures for the selective isolation and identification of virtually all known prokaryotes.
2. Holt, J.G. (editor-in-chief). Bergey's Manual of Systematic Bacteriology. Volume 1, 1982. Gram-negative bacteria of medical or industrial importance. Volume 2, 1986. Gram-positive bacteria of medical or industrial importance. Volume 3, 1988. Other Gram-negative bacteria, cyanobacteria, Archaea. Volume 4, 1988. Other Gram- positive bacteria. This is the standard authoritative guide to bacterial taxonomy and identification. This the usual place to begin a literature survey or an identification process of a specific bacterial group.
3. Madigan, M.T., J.M. Martinko and J. Parker. Brock Biology of Microorganisms, 8th ed. Prentice-Hall, Inc., Englewood Cliffs, New Jersey. 1997.
4. Raven, P.H., R.F. Evert and S.E. Eichhorn. Biology of Plants, 5th ed. Worth Publishers, New York. 1992.
5. Stanier, R.Y., J.L. Ingraham, M.L. Wheelis, and P.R Painter. The Microbial World, 5th ed. Prentice-Hall, Inc., Englewood Cliffs, New Jersey. 1986.
from : http://fai.unne.edu.ar/biologia/bacterias/Procariotas.htm
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