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