Bacteriology at UW-Madison
An Introduction to 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 eucaryotic cells such as those that make up, fungi, protista, 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 Eucarya. 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, except 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, indicates that lithotrophic and fermentative modes of metabolism were the first to evolve in early procaryotes. Photosynthesis developed in bacteria a bit later, 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). However, oxygenic photosynthesis also arose in procaryotes, specifically in the cyanobacteria, which existed millions of years before the evolution of green algae and plants. Larger, more complicated eucaryotic 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 structure from eucaryotic cells, 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 contemporary Tree of Life gives rise to three cellular "Domains": Archaea, Bacteria, and Eucarya (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 eucaryotic domain, Eucarya. Between the two procaryotes, Archaea are apparently more closely related to Eucarya than are the Bacteria. Eucarya consists of all eucaryotic 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. 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.
Size and Distribution of Bacteria and Archaea
Most procaryotic cells are very small compared to eucaryotic cells. A typical bacterial cell is about 1 micrometer in diameter or width, while most eucaryotic cells are from 10 to 100 micrometers in diameter. Eucaryotic 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 eucaryotic 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 eucaryotic cells there by 10,000 : 1. About 3,000 distinct species of bacteria and archaea 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 eucaryotes live, but, as well, in many natural environments considered too extreme or inhospitable for eucaryotic cells. Thus, the outer limits of life on Earth (hottest, coldest, driest, etc.) are usually defined by the existence of procaryotes. Where eucaryotes and procaryotes live together, there may be mutualistic associations between the organisms that allow both to survive or flourish. The organelles of eucaryotes (mitochondria and chloroplasts) are thought to be remnants of Bacteria that invaded, or were captured by, primitive eucaryotes in the evolutionary past. Numerous types of eucaryotic cells that exist today are inhabited 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 eucaryotes. 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 Archaea and Bacteria.
The lives of plants and animals are dependent upon the activities of bacterial cells. Bacteria and archaea 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.
Figure 4. Schematic drawing of a typical bacterium.
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 eucaryotic flagella and cilia. 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 cholerae has 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, in some way stabilizes the transfer of DNA between mating bacteria, but the function of the smaller, more numerous common pili is quite different. Common pili (often 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 gonorrhoeae allow 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 (cells which do not retain the crystal violet dye) 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 their 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 and photophosphorylation in procaryotes, analogous to the functions of mitochondria and chloroplasts in eucaryotic cells. The procaryotic plasma membrane is also a permeability barrier, and it contains a variety of different transport systems 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 eucaryotes, 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 eucaryotic and bacterial membrane lipids. The structure of archaeal membranes is thought to be an adaptation to their existence 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. bacteria and archaea may also have an additional proteinaceous coat called an S-layer. Capsules, slime layers, glycocalyx and s-layer 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 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) for protection against engulfment by phagocytic white blood cells or predatory protozoa: (4) as enzymes to mediate specific reactions on the cell surface important in the survival of the procaryote; (5) 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 biological response to a changing 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.
The cytoplasmic constituents of bacteria invariably include the
chromosome and ribosomes. The chromosome is typically one
circular molecule of DNA, more or less free in the cytoplasm,
although intermittently associated with membranes.
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
in the usual semi-conservative fashion before for distribution to
cells. However, the eucaryotic processes of meiosis and mitosis are
in procaryotes. Replication and segregation of procaryotic DNA is
by the plasma membrane.
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 eucaryotes. Procaryotic ribosomes are 70S in size, being composed of 30S and 50S subunits. The 80S ribosomes of eucaryotes 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 eucaryotes, Bacteria and Archaea. Protein synthesis using bacterial 70S ribosomes occurs in eucaryotic mitochondria and chloroplasts, and this is taken as a major line of evidence that these organelles are descended from bacteria.
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 specialized enzyme complexes.
Figure 8. Bacterial colonies growing in a petri dish containing nutrients.
Hans Knoll Institute, Jena, Germany.
Figure 9 (above) The structure of a typical procaryotic cell, in this case, a Gram-negative bacterium, compared with (below) a typical eucaryotic cell (plant cell). The procaryote is about 1 micrometer in diameter and about the size of the eucaryotic chloroplast or mitochondrion. Drawings by Vaike Haas, University of Wisconsin-Madison.
Sequence analysis of macromolecules such as the small subunit ribosomal RNA found in all cells has allowed bacteriologists to classify bacteria into a typical hierarchal scheme based on genetic relatedness. The current edition (2001) of Bergey's Manual of Systematic Bacteriology has established 24 phyla of bacteria, systematically ordered into class, order, family, genus and species. For example, E. coli is in the Domain Bacteria, Phylum Proteobacteria, Class Gamma Proteobacteria, Order Enterobacteriales, Family Enterobacteriaceae, Genus Escherichia, Species E. coli. You can download Bergey's 400-page taxonomic outline of the procaryotes at Bergey's Manual of Systematic Bacteriology 2nd ed (2001), or you can back in to a taxonomic outline of bacteria in Wikipedia by looking up the scientific name of any well-known bacterium and viewing the right-hand frame, Scientific classification.
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 1). The phylogenetic tree indicates that Archaea are more closely related to Eucarya than are Bacteria. This relatedness seems most evident in the similarities between transcription and translation in the Archaea and the Eucarya. However, it is also evident that the Bacteria have evolved into chloroplasts and mitochondria, so that these eucaryotic organelles derive their lineage from this group of procaryotes. Perhaps the biological success of eucaryotic cells springs from the evolutionary merger of the two procaryotic life forms.Table 1. Phenotypic properties of Bacteria and Archaea compared with Eucarya.
|Number of chromosomes||>1||1||1|
|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|
|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||+||-||+|
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 9th ed, 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.
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.
The sciences of genomics and bioinformatics have led to a radical
reclassification of procaryotes based on comparative analysis of
organismal DNA. Genomics
involves the study of all of the nucleotide sequences, including
structural genes, regulatory sequences, and noncoding DNA segments, in
the chromosomes of an organism. To date over 200 bacterial genomes have
been sequenced. We have seen how highly conserved genetic sequences,
such as those that encode for the small subunit ribosomal RNAs (16S
rRNA) of an
organism, can be analyzed to specifically relate two organisms. So can
the identification of certain genes provide information about
specific properties of an organism, and analysis of specific nucleotide
sequences may be used to indicate identity and degrees of genetic
relatedness among organisms.
The newest editions of Bergey's Manual are adapted to the new phylogenetic classification. This has resulted in the formation of several new taxa of bacteria and archaea at every hierarchical level. Occasionally, organisms thought to be more or less distantly related become unified; but more likely, organisms thought to be closely-related due to similar phenotypic properties are found to be genetically distinct and warrant separation into a new taxa.
Metagenomics. Sequencing of
16S rRNA genes obtained from environmental samples
produces a broad profile of microbial diversity and reveals that the
majority of microbes present have been missed by reliance on
cultivation-based methods. This observation has given rise to the field
of metagenomics. Metagenomics
(also called environmental genomics) is the application of modern
genomics techniques to the
study of communities of microorganisms directly in their natural
environments, bypassing the need for isolation and lab cultivation of
individual species. Metagenomics provides a means to identify and
quantify microbes from environmental samples based on the presence of
distinctive genes. This enables studies of organisms that are not
easily cultured in the laboratory, as well as studies of organisms in
their natural environment.
"Shotgun" metagenomics is capable of sequencing nearly complete
microbial genomes directly from the environment. Because the collection
of DNA from an environment is largely uncontrolled, the most abundant
organisms in a sample are most highly represented in the resulting
sequence data. To achieve the high coverage needed to fully resolve the
genomes of underrepresented community members, large samples, often
prohibitively so, may be needed. However, the random nature of shotgun
sequencing ensures that many of these organisms will be represented by
at least some small sequence segments. Due to the limitations of
microbial isolation methods, the majority of these organisms would go
unnoticed using traditional culturing techniques.
Shotgun sequencing and screens of clone libraries reveal genes
in environmental samples. This provides information both on which
organisms are present and what metabolic processes are possible in the
community. This can be helpful in understanding the ecology of a
community, particularly if multiple samples are compared to one other.
Genetic Exchange in BacteriaAlthough 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 fundamental processes: conjugation, transduction and transformation. Conjugation requires cell-to-cell contact for DNA to be transferred from a donor to a 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 as vectors. The genetic systems of the Archaea are poorly characterized at this point, although the entire genome of Methanosarcina has been sequenced which opens up the possibilities for genetic analysis of the group.
Evolution of Bacteria and ArchaeaFor 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 in the neighborhood of 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.
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.
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 (e.g. photoautotrophs) or from the oxidation of inorganic compounds (e.g. 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 (plus H2 and H2O). 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 lithoautotrophs or 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; methanogenic archaea strip electrons off of H2 as a source of energy and add them 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 photosynthetic metabolism not seen in eucaryotes, 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 employs a light-driven non photosynthetic means of energy generation based on the use of a chromophore called bacteriorhodopsin.
Adaptations to Environmental Conditions
Most procaryotes, whether they have been cultured and studied in the
laboratory, or observed growing in their natural habitats, seem to be
highly adapted to their specific environment by means of their
macromolecular structure and/or their physiologic (metabolic)
capabilities. The nutritional quality of the environment determines
whether a particular organism will be present, but so do various
physical parameters such as the availability of light and O2,
as well as the pH, temperature and salinity of the environment. As
examples, the range of procaryotic responses to oxygen and temperature
are discussed below.
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
of warm-blooded animals (37 degrees) are called mesophiles;
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.
growing procaryotic cells can be found in supercooled environments (ice
does not form) as low as -20 degrees and superheated environments
does not form) as high as 120 degrees. Archaea have been detected
thermal vents on the ocean floor where the temperature is as high as
The biomass of procaryotic cells in the biosphere, their metabolic diversity, and their persistence in all habitats that support life, ensures that these microbe will 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.
Some bacteria are parasites of plants or animals, meaning
they grow at the expense of their eucaryotic host and may damage, harm,
or even kill it in the process. Such bacteria that cause disease in
or animals are pathogens. Human diseases caused by bacterial
include tuberculosis, whooping cough, diphtheria, tetanus, gonorrhea,
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)
to colonize and invade their host; (2) ability to resist or withstand
antibacterial defenses of the host; (3) ability to produce various
substances that damage the host. Plant diseases, likewise, may be
by bacterial pathogens. More than 200 species of bacteria are
with plant diseases, but a very small handful of genera are involved.
Figure 14. Borrelia burgdorferi. This spirochete is the bacterial parasite that causes Lyme disease. CDC.
Bacteria and other procaryotes are used in industry in a number of ways that generally exploit their natural metabolic capabilities. They are used in manufacture of foods and production of antibiotics, probiotics, drugs, vaccines, starter cultures, insecticides, enzymes, fuels and solvents. In addition, with genetic engineering technology, bacteria can be programmed to make various substances used in food science, agriculture and medicine. The genetic systems of bacteria are the foundation of the biotechnology industry discussed below.
In the foods industry, lactic acid bacteria such as Lactobacillus, Lactococcus and Streptococcus are used in the manufacture of dairy products such as cheeses, including cottage cheese and cream cheese, cultured butter, sour cream, buttermilk, yogurt and kefir. Lactic acid bacteria and acetic acid bacteria are used in pickling processes such as olives, cucumber pickles and sauerkraut. Bacterial fermentations are used in processing of teas, coffee, cocoa, soy sauce, sausages and an amazing variety of foods in our everyday lives.
Figure 15a. Lactococcus lactis, the bacterium that makes Wisconsin famous as the #1 producer of Ceddar cheese in the U.S. The bacterium is needed in cheese production for fermentation of milk sugar (lactose) to lactic acid, the formation of flavor and aroma compounds, and the development of texture in the ripened cheese.
Figure 15b. Lactococcus lactis is responsible for the production of many varieties of cheese, including Cheddar, Monterey Jack, Gouda, Edam, Muenster, Feta, Blue, Gorgonzola, Brie, Camembert, Havarti, and Colby, a Wisconsin original. Other dairy products, such as cultured butter, cottage cheese, cream cheese, sour cream, kefir and buttermilk also use the bacterium in their manufacture.
In the pharmaceutical industry, bacteria are used to produce
vaccines, and medically-useful enzymes. Most antibiotics are made by
that live in soil. Actinomycetes such as Streptomyces produce
erythromycin, streptomycin, rifamycin and ivermectin. Bacillus
and Paenibacillus 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.
BiotechnologyThe biotechnology industry uses bacterial cells for the production of biological substances that are useful to human existence, including fuels, foods, medicines, hormones, enzymes, proteins, and nucleic acids. The possibilities of biotechnology are endless considering the gene reservoirs and genetic capabilities among the procaryotic forms of life. Pasteur said it best, "Never underestimate the power of the microbe."
Figure 16. 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".
The polymerase chain reaction (PCR), a mainstay of the biotechnology industry because it allows duplication of genes starting with a single molecule of DNA, is based on the use of the DNA polymerase enzyme derived from Thermus aquaticus.