BACTERIA

singular bacterium, any of a group of microscopic organisms that are prokaryotic, i.e., that lack a membrane-bound nucleus and organelles. They are unicellular (one-celled) and may have spherical (coccus), rodlike (bacillus), or curved (vibrio, spirillum, or spirochete) bodies. Bacteria can be found in all natural environments, often in extremely large numbers. As a group, they display exceedingly diverse metabolic capabilities and use almost any organic compound, and even some inorganic salts, as a food source. Some bacteria cause disease in humans, animals, or plants, but most are harmless or beneficial ecological agents whose metabolic activities sustain higher life-forms. Without bacteria, soil would not be fertile, and dead organic material would decay much more slowly. Some bacteria are widely used in the preparation of foods, chemicals, and antibiotics. In a sense, bacteria are the dominant living creatures on Earth, having been present for perhaps three-quarters of Earth history and having adapted to almost all available ecological habitats. Studies of the relationships among different groups of bacteria continue to yield new insights into the origin of life on Earth and the directions of evolution. Bacteria are classified as the prokaryotic kingdom Monera; all bacterial cells, and only bacterial cells, are prokaryotic in nature. Prokaryotic cells are fundamentally different from the eukaryotic cells that constitute all other forms of lifenamely, plants, animals, fungi, and protists (protozoa and algae). Prokaryotic cells are defined by a much simpler design than is found in eukaryotic cells, most apparent in their lack of any intracellular organelles, a feature characteristically found in all eukaryotic cells. Organelles are discrete membrane-enclosed structures floating in the cytoplasm and include the nucleus, where genetic information is retained, copied, and expressed; the mitochondria and chloroplasts, where chemical or light energy is converted into energy; the lysosome, where ingested proteins are digested and other nutrients are made available; and the endoplasmic reticulum and Golgi complex, where the proteins that will be released from the cell are assembled, modified, and exported. All the activities performed by organelles also take place in bacteria, but they are not carried out by specialized structures. Prokaryotic and eukaryotic cells also differ in many other ways, including lipid composition, structure of key metabolic enzymes, responses to antibiotics and toxins, and the mechanism of expression of the genetic information. In most eukaryotic organisms, genes are much larger than they need to be to impart information for the synthesis of proteins. Substantial portions of the ribonucleic acid (RNA) copy of the genetic information (deoxyribonucleic acid, or DNA) are discarded, and the remaining messenger RNA (mRNA) is substantially modified before it is copied for protein synthesis. In contrast, bacterial mRNAs are exact copies of their gene and are not modified. In keeping with their simpler cell design, bacterial cells are usually much smaller than eukaryotic cells. The combination of small size, simple design, and broad metabolic capabilities allows bacteria to grow and divide very rapidly and to inhabit and flourish in almost any type of environment. It has become clear from studies of bacterial genes that bacteria are not simply primitive cells or precursors to higher organisms. In fact, bacteria have been divided into two major phylogenetic kingdoms, Eubacteria and Archaebacteria, based on such differences as chemistry and physiology. All remaining living organisms are eukaryotes. It can be said that members of these two prokaryotic kingdoms are as different from one another as they are from eukaryotic cells; these differences are manifested in almost all observable characteristics, including metabolic pathways, identity of lipids, cell surface structures, and gene sequences. The present article treats primarily the morphology, genetics, and ecology of bacteria. For more information on the metabolism of bacteria and other living organisms, see metabolism. Additional reading Comprehensive surveys are presented in John G. Holt (ed.), Bergey's Manual of Systematic Bacteriology, 4 vol. (198489), a reference and sourcebook accepted as standard throughout the world for classification of bacteria and related microorganisms; Thomas D. Brock and Michael T. Madigan, Biology of Microorganisms, 6th ed. (1991), an advanced textbook covering all general characteristics of microorganisms: morphology, physiology, biochemistry, ecological role, and classification; Albert G. Moat and John W. Foster, Microbial Physiology, 2nd ed. (1988), a massive reference work; and Bernard D. Davis et al., Microbiology, 4th ed. (1990), a comprehensive textbook covering bacteriology, immunology, and virology as related to medical aspects of microbiology.Thomas D. Brock, The Emergence of Bacterial Genetics (1990), describes the historical development of bacterial genetics and molecular biology. Wesley A. Volk et al., Essentials of Medical Microbiology, 4th ed. (1991), presents the basic medical aspects of bacteriology, immunology, and virology. Mortimer P. Starr et al. (eds.), The Prokaryotes: A Handbook on Habitats, Isolation, and Identification of Bacteria, 2 vol. (1981), comprehensively describes the types of bacteria, especially the conditions for their isolation and identification. Clive Edwards (ed.), Microbiology of Extreme Environments (1990), assembles a series of studies of microorganisms that live in extreme environments, with an emphasis on their applications in technology and ecology.State-of-the-art research in all aspects of microbiology is reflected in the 20 to 30 review articles appearing each year in the Annual Review of Microbiology. Among articles of special interest are the following from Microbiological Reviews (quarterly): Carl R. Woese, Bacterial Evolution, 51(2):221271 (1987), a seminal review of the use of nucleic acid sequences for bacterial taxonomy and of some implications of this analysis; G. Wchtershuser, Before Enzymes and Templates: Theory of Surface Metabolism, 52(4):452484 (1988), discussing the metabolic activities of the earliest forms of life; and S. Krawiec and M. Riley, Organization of the Bacterial Chromosome, 54(4):502539 (1990), on the structure and genetic arrangement of bacterial chromosomes. Genetic and physiological properties of bacteria that are symbionts or pathogens of plants are examined in Plant-Microbe Interactions: Molecular and Genetic Perspectives (irregular). Robert J. Kadner Biosynthesis, nutrition, and growth Factors affecting bacterial growth Nutritional requirements Bacteria differ dramatically with respect to the conditions that allow their optimal growth. In terms of nutritional needs, all cells require carbon, nitrogen, sulfur, phosphorus, numerous inorganic salts (potassium, magnesium, sodium, calcium, and iron), and a large number of other elements called micronutrients (e.g., zinc, copper, manganese, selenium, tungsten, and molybdenum). Carbon is the element required in greatest amount, since hydrogen and oxygen can be obtained from water that must be present as a prerequisite for growth. Also required is a source of energy to fuel the metabolism of the bacterium. One means of organizing bacteria is based on these fundamental nutritional needs: the carbon source and the energy source. There are two sources for carbon, inorganic compounds and organic compounds. Bacteria that use the inorganic compound carbon dioxide (CO2) as their source of carbon are called autotrophs. Bacteria that require an organic source of carbon, such as sugars, proteins, fats, or amino acids, are called heterotrophs. Many heterotrophs, such as E. coli or P. aeruginosa, synthesize all their cellular constituents from such simple sugars as glucose because they are able to use all necessary biosynthetic pathways. Other heterotrophs have lost some of these biosynthetic pathways and require particular amino acids, nitrogenous bases, or vitamins intact in their environments for growth. In addition to carbon, bacteria also need energy. There are three basic sources of carbon and energy: light, inorganic compounds, and organic compounds. Phototrophic bacteria use photosynthesis to generate cellular energy in the form of adenosine triphosphate (ATP) from light energy. Chemotrophs use chemicals (organic and inorganic compounds) as their energy source. Chemolithotrophs obtain their energy from reactions with inorganic salts, as described below. (The term lithotroph comes from the Greek word lithos for stone, which indicates their ability to grow without an organic food supply.) Chemoheterotrophs use organic compounds as their source of carbon and energy; the organic compounds utilized as the energy source may also be the carbon source. In all cases, cellular energy is generated by means of electron-transfer reactions, in which electrons move from an organic or inorganic donor molecule to an acceptor via a pathway that conserves the energy released during the transfer of electrons by trapping it in a form the cell can use for its chemical or physical workthat is, ATP. The metabolic processes that break down (oxidize) an organic molecule and generate energy are called catabolic reactions; those that synthesize all the molecules the cell needs to be able to grow are called anabolic reactions. Many bacteria can use a large number of compounds as carbon and energy sources; others are highly restricted in their metabolic capabilities. Carbohydrates are a common energy source, but a substantial number of chemoheterotrophic bacterial species are unable to use them and depend on amino acids, fats, or other simple compounds. Phosphate is often the factor that limits microbial growth in many environments, particularly in water; the extent of algae blooms in lakes can be directly related to the introduction of phosphate from runoff of agricultural fertilizers or other phosphate-containing materials. Most bacteria can convert sulfate or sulfide to the organic form needed for protein synthesis. The capability of a living organism to incorporate nitrogen from ammonia is widespread in nature, and chemotrophic bacteria differ in their ability to convert other forms of nitrogen, such as nitrate in the soil or dinitrogen gas (N2) in the atmosphere, into cell material. A particularly important nutrient of bacteria is iron, an abundant element in the Earth's crust. Iron is a component of heme proteins intrinsic to hemoglobin in red blood cells and many other proteins involved in electron transfer reactions. It is needed for the growth of almost all organisms. In aerobic environments at neutral pH values, ferrous (+II) iron is oxidized in the presence of oxygen to the ferric (+III) state, which is virtually insoluble in water and unable to enter cells. Many bacteria synthesize and secrete chemicals of low molecular weight, called siderophores, which bind very tightly to iron and can make it soluble in water. These bacteria then take up these iron-siderophore complexes very effectively and remove the iron for their synthetic tasks. The ability to acquire iron in this way is particularly important to pathogenic bacteria, which must compete with their host for iron. In anaerobic environments, iron can exist in the more soluble ferrous state and is readily used by bacteria. Some bacteria are obligate parasites and grow only within a living host cell. Rickettsia and Chlamydia, for example, grow in eukaryotic cells, and Bdellovibrio requires a bacterial cell as host. Treponema pallidum is difficult, if not impossible, to grow in culture, perhaps because it needs the low oxygen tension and low oxidation-reduction level provided by the presence of animal cells, rather than any specific nutrient. It might be expected that bacteria with multiple nutritional needs might not thrive living free in nature but must grow as animal or plant parasites or in some rich source of nutrients, such as milk. Many bacteria from natural environments exist in a consortium with other bacteria and are difficult to isolate and culture separately from the other members of that partnership. Physical requirements The physical requirements optimal for or permissive of bacterial growth also vary dramatically for different bacterial types. As a group, bacteria display the widest variation of all organisms in their ability to inhabit different environments. Some of the most prominent factors are described here. Biosynthesis, nutrition, and growth Biotypes The fact that pathogenic bacteria are constantly battling their host's immune system might account for the bewildering number of different strains or types of bacteria that belong to the same species but are distinguishable by immunological tests. Microbiologists often identify bacteria by the presence of specific molecules on their cell surfaces, which are detected with specific antibodies. Antibodies are serum proteins that bind very tightly to foreign invaders (antigens) in an immune reaction aimed at removing or destroying the antigens. Antibodies have remarkable specificity, and the substitution of even one amino acid in a protein might prevent that protein from being recognized by an antibody. In the case of E. coli, there are hundreds of different strains (called serovars, for serological variants), which differ from one another solely in the antigenic identity of their lipopolysaccharide, flagella, or capsule. Similarly, there are hundreds of types of Salmonella enteritidis, differing only in the nature of their lipopolysaccharide sugars chains. Different serovars of these enteric bacteria are often found to be associated with the ability to inhabit different host animals or to cause different diseases. Formation of these numerous serovars reflects the ability of bacteria to respond effectively to the intense pressure from the immune system and other factors to fight off the bacteria. Evolution of bacteria Bacteria have existed from very early in the history of life on Earth. They have been detected as fossils in rocks dating from at least the Devonian Period (408 to 360 million years ago), and there are convincing arguments that bacteria have been present since the middle of the Precambrian, 3 billion years ago. Bacteria have to have been widespread on Earth at least since the middle Proterozoic Era, about 1.5 billion years ago, when oxygen appeared in the atmosphere; the cyanobacteria were responsible for this dramatic global occurrence. They have thus had plenty of time to adapt to their environments and to have given rise to numerous descendant forms. The nature of the original predecessor involved in the origin of life is subject to considerable speculation. It has been suggested that the original cell might have used RNA as original genetic material, since investigations have shown that RNA molecules can have some catalytic functions, including cleavage of specific RNA sequences. The eubacteria and archaebacteria diverged from their common precursor very early in this time period. The two types of bacteria tend to inhabit different types of environments and to be able to give rise to new species at very different rates. Archaebacteria generally prefer high-temperature niches. One major branch of the archaebacterial tree consists only of thermophilic species, and many of the methanogens in another major branch can grow at high temperatures. In contrast, no major eubacterial branch consists solely of thermophiles. The thermophilic archaebacteria can grow at much higher temperatures (80 to 110 C) than can any of the thermophilic eubacteria (no hotter than 80 C). Perhaps the archaebacterial line developed when the Earth was hotter. Another prominent difference is that eubacteria have readily adapted to aerobic conditions, whereas the majority of archaebacteria are obligate anaerobes and no obligately aerobic archaebacteria have been described. No archaebacteria are obligately photosynthetic. Perhaps the archaebacteria are a more primitive type of organism with an impaired genetic response to changing environmental conditions: the rate of divergence of rRNA sequences appears to be slower in them. A limited ability to adapt to new situations could restrict the archaebacteria to harsher environments, where there is less competition from other life-forms. How do organisms evolve or adapt to changing environments? It is clear that mutations, which are changes in the sequence of bases in the DNA, occur constantly in all organisms. The changes in DNA sequence might result in changes in the amino acid sequence of the protein that is encoded by that stretch of DNA; the resultant altered protein might be either better-suited or less well-suited for function under the prevailing conditions. Although many base changes have no effect on the fitness of the cell, if the base change enhances the growth of that cell even by a small degree, then the mutant form would be able to increase its relative numbers in the population. If the base change retards the growth of the cell, however, then the mutant form would be outgrown by the other cells and lost. The ability to transfer genetic information among organisms is a factor that allows more facile adaptation to changes in environment. Exchange of DNA is an essential part of the life cycle of higher eukaryotic organisms and can occur in all eukaryotes. Genetic exchange also occurs throughout the eubacterial world. Although the amount of DNA transferred is relatively small, this transfer can occur between very distantly related organisms, allowing each to acquire some of the traits of the other. Genes carried on plasmids can even find their way onto the bacterial chromosome and thus become a stable part of the bacterium's inheritance. Organisms usually possess mobile genetic elements, often called transposons, which can rearrange the order and presence of any genes on the chromosome; these may play a role in helping to accelerate the pace of evolution. A clear example of the rapid evolution of bacteria is immediately available. Before the 1940s, antibiotics were not used in medical practice, and the majority of bacteria were characteristically sensitive to antibiotics. Since the time when these drugs became widely used, however, the bacterial resistance to one or more antibiotics has increased to the point that some previously widely effective antibiotics are no longer efficacious against certain bacterial types. Most examples of antibiotic resistance in pathogenic bacteria are not the result of a mutation that alters the protein that the antibiotic attacks, although this mechanism can occur in laboratory experiments. Instead, antibiotic resistance in nature usually involves the production by the bacterium of enzymes that alter the antibiotic, rendering it inactive. The major factor in the spread of antibiotic resistance is transmissible plasmids, which carry the genes for the drug-inactivating enzymes from one bacterial species to another. Although the original source of the gene for these enzymes is not known, mobile genetic elements (transposons) may have played a role in their appearance and may also allow their transfer to other bacterial types.