Eubacteria

The Eubacteria, also called just "bacteria," are one of the three main domains of life, along with the Archaea and the Eukarya. Eubacteria are prokaryotic, meaning their cells do not have defined, membrane-limited nuclei. As a group they display an impressive range of biochemical diversity, and their numerous members are found in every habitat on Earth. Eubacteria are responsible for many human diseases, but also help maintain health and form vital parts of all of Earth's ecosystems.

Structure

Like archeans, eubacteria are prokaryotes, meaning their cells do not have nuclei in which their DNA is stored. This distinguishes both groups from the eukaryotes, whose DNA is contained in a nucleus. Despite this structural resemblance, the Eubacteria are not closely related to the Archaea, as shown by analysis of their RNA (see below).

Eubacteria are enclosed by a cell wall. The wall is made of cross-linked chains of peptidoglycan, a polymer that combines both amino acid and sugar chains. The network structure gives the wall the strength it needs to maintain its size and shape in the face of changing chemical and osmotic differences outside the cell. Penicillin and related antibiotics prevent bacterial cell growth by inactivating an enzyme that builds the cell wall. Penicillin-resistant bacteria contain an enzyme that chemically modifies penicillin, making it ineffective.

Some types of bacteria have an additional layer outside the cell wall. This layer is made from lipopolysaccharide (LPS), a combination of lipids and sugars. There are several consequences to possessing this outer layer. Of least import to the bacteria but significant for researchers, this layer prevents them from retaining a particular dye (called Gram stain) that is used to classify bacteria. Bacteria that have this LPS layer are called Gram-negative, in contrast to Gram-positive bacteria, which do not have an outer LPS layer and which do retain the stain. Of more importance to both the bacteria and the organisms they infect is that one portion of the LPS layer, called endotoxin, is particularly toxic to humans and other mammals. Endotoxin is partly to blame for the damage done by infection from Salmonella and other Gram-negative species.

Within the cell wall is the plasma membrane, which, like the eukaryotic plasma membrane, is a phospholipid bilayer studded with proteins. Embedded in the membrane and extending to the outside may be flagella, which are whiplike protein filaments. Powered by molecular motors at their base, these spin rapidly, propelling the bacterium through its environment.

Within the plasma membrane is the bacterial cytoplasm. Unlike eukaryotes, bacteria do not have any membrane-bound organelles, such as mitochondria or chloroplasts. In fact, these two organelles are believed to have evolved from eubacteria that took up residence inside an ancestral eukaryote.

Bacterial cells take on one of several common shapes, which until recently were used as a basis of classification. Bacilli are rod shaped; cocci are spherical; and spirilli are spiral or wavyshaped. After division, bacterial cells may remain linked, and these form a variety of other shapes, from clusters to filaments to tight coils.

Metabolism

Despite the lack of internal compartmentalization, bacterial metabolism is complex, and is far more diverse than eukaryotic metabolism. Within the Eubacteria there are species that perform virtually every biochemical reaction known (and much bacterial chemistry remains to be discovered). Most of the vitamins humans require in our diet can be synthesized by bacteria, including the vitamin K humans absorb from the Escherichia coli (E. coli ) bacteria in our large intestines.

The broadest and most significant metabolic distinction among the Eubacteria is based on the source of energy they use to power their metabolism. Like humans, many bacteria are heterotrophs, consuming organic (carbon-containing) high-energy compounds made by other organisms. Other bacteria are chemolithotrophs, which use inorganic high-energy compounds, such as hydrogen gas, ammonia, or hydrogen sulfide. Still others are phototrophs, using sunlight to turn simple low-energy compounds into high-energy ones, which they then consume internally.

For all organisms, extraction of energy from high-energy compounds requires a chemical reaction in which electrons move from atoms that bind them loosely to atoms that bind them tightly. The difference in binding energy is the profit available for powering other cell processes. In almost all eukaryotes, the ultimate electron acceptor is oxygen, and water and carbon dioxide are the final waste products. Some bacteria use oxygen for this purpose as well. Others use sulfur (forming hydrogen sulfide, which has a strong odor), carbon (forming flammable methane, common in swamps), and a variety of other compounds.

Bacteria that use oxygen are called aerobes. Those that do not are called anaerobes. This distinction is not absolute, however, since many organisms can switch between the two modes of metabolism, and others can tolerate the presence of oxygen even if they do not use it. Some bacteria die in oxygen, however, including members of the Gram positive Clostridium genus. Clostridium botulinum produces botulinum toxin, the deadliest substance known. C. tetani produces tetanus toxin, responsible for tetanus and "lockjaw," while other Clostridium species cause gangrene.

Life Cycle

When provided with adequate nutrients at a suitable temperature and pH,E. coli bacteria can double in number within 20 minutes. This is faster than most species grow, and faster than E. coli grows under natural conditions. Regardless of the rate, the growth of a bacterium involves synthesizing double the quantity of all its parts, including membrane, proteins, ribosomes , and DNA. Separation of daughter cells, called binary fission, is accomplished by creating a wall between the two halves. The new cells may eventually separate, or may remain joined.

When environmental conditions are harsh, some species (including members of the genus Clostridium ) can form a special resistive structure within themselves called an endospore. The endospore contains DNA, ribosomes, and other structures needed for life, but is metabolically inactive. It has a protective outer coat and very low water content, which help it survive heating, freezing, radiation, and chemical attack. Endospores are known to have survived for several thousand years, and may be capable of surviving for much longer, possibly millions of years. When exposed to the right conditions (presence of warmth and nutrients), the endospore quickly undergoes conversion back into an active bacterial cell.

DNA

Most eubacteria have DNA that is present in a single large circular chromosome. In addition, there may be numerous much smaller circles, called plasmids . Plasmids usually carry one or a few genes. These often are for specialized functions, such as metabolism of a particular nutrient or antibiotic.

Despite the absence of a nucleus, the chromosome is usually confined to a small region of the cell, called the nucleoid , and is attached to the inner membrane. The bacterial genome is smaller than that of a eukaryote. For example, E. coli has only 4.6 million base pairs of DNA, versus three billion in humans. As in eukaryotes, the DNA is tightly coiled to fit it into the cell. Unlike eukaryotes, however, the DNA is not attached to histone proteins.

Much of what we know about DNA replication has come from study of bacteria, particularly E. coli, and the details of this process are discussed elsewhere in this encyclopedia. Unlike eukaryotic replication, prokaryotic replication begins at a single point, and proceeds around the circle in both directions. The result is two circular chromosomes, which are separated during cell division. Plasmids replicate by a similar process.

Gene Transfer

While bacteria do not have sex like multicellular organisms, there are several processes by which they obtain new genes: conjugation , transformation, and transduction. Conjugation can occur between two appropriate bacterial strains when one (or both) extends hairlike projections called pili to contact the other. The chromosome, or part of one, may be transferred from one bacterium to the other. In addition, plasmids can be exchanged through these pili. Some bacteria can take up DNA from the environment, a process called transformation. The DNA can then be incorporated into the host chromosome.

Some bacterial viruses, called phages, can carry out transduction. With some phages, the virus temporarily integrates into the host chromosome. When it releases itself, it may carry some part of the host DNA with it. When it goes on to infect another cell, this extra DNA may be left behind in the next round of integration and release. Other phages, called generalized transducers, package fragments of the chromosome into the phage instead of their own genome . When the transducing phage infects a new cell, they inject bacterial DNA. These phages lack their own genome and are unable to replicate in the new cell. The inserted bacterial DNA may recombine (join in with) the host bacterial chromosome.

Gene Regulation and Protein Synthesis

Gene expression in many bacteria is regulated through the existence of operons. An operon is a cluster of genes whose protein products have related functions. For instance, the lac operon includes one gene that transports lactose sugar into the cell and another that breaks it into two parts. These genes are under the control of the same promoter , and so are transcribed and translated into protein at the same time. RNA polymerase can only reach the promoter if a repressor is not blocking it; the lac repressor is dislodged by lactose. In this way, the bacterium uses its resources to make lactose-digesting enzymes only when lactose is available.

Other genes are expressed constantly at low levels; their protein products are required for "housekeeping" functions such as membrane synthesis and DNA repair. One such enzyme is DNA gyrase, which relieves strain in the double helix during replication and repair. DNA gyrase is the target for the antibiotic ciproflaxin (sold under the name Cipro), effective against Bacillus anthracis, the cause of anthrax. Since eukaryotes do not have this type of DNA gyrase, they are not harmed by the action of this antibiotic.

As in eukaryotes, translation (protein synthesis) occurs on the ribosome. Without a nucleus to exclude it, the ribosome can attach to the messenger RNA even while the RNA is still attached to the DNA. Multiple ribosomes can attach to the same mRNA, making multiple copies of the same protein.

The ribosomes of eubacteria are similar in structure to those in eukaryotes and archaea, but differ in molecular detail. This has two important consequences. First, sequencing ribosomal RNA molecules is a useful tool for understanding the evolutionary diversification of the Eubacteria. Organisms with more similar sequences are presumed to be more closely related. The same tool has been used to show that Archaea and Eubacteria are not closely related, despite their outward similarities. Indeed, Archaea are more closely related to eukaryotes (including humans) than they are to Eubacteria.

Second, the differences between bacterial and eukaryotic ribosomes can be exploited in designing antibacterial therapies. Various unique parts of the bacterial ribosome are the targets for numerous antibiotics, including streptomycin, tetracycline, and erythromycin.

see also Archaea; Cell, Eukaryotic; Chromosome, Prokaryotic; Conjugation; Escherichia Coli ; Operon; Plasmid; Transduction; Transformation.

Richard Robinson

Bibliography

Madigan, Michael T., John M. Martinko, and Jack Parker. Brock Biology of Micro-organisms, 9th ed. Upper Saddle River, NJ: Prentice Hall, 2000.

Margulis, Lynn, and Karlene Schwartz. Five Kingdoms, 3rd ed. New York: W. H.Freeman, 1998.

Eubacteria

Bacteria are microscopic organisms that comprise the domain Eubacteria. A domain is the highest grouping of organisms, superseding the level of kingdom in the classical Linnaean system of biological classification. There are three domains, two of which, Eubacteria and Archaea, are composed entirely of prokaryotic organisms; the third domain, Eucarya, encompasses all other (eukaryotic ) life forms, including the single-cell and multicellular protists, as well as animals, green plants, and fungi. Unlike eukaryotic cells, prokaryotic cells lack nuclei and other organelles , and tend to be less complex.

Eubacteria are differentiated from archaea primarily based on chemical composition of cellular constituents. For example, bacterial cell walls are composed of peptidoglycan (though there are examples of bacteria that lack cell walls) while archaeal cell walls are composed of a protein -carbohydrate molecule called pseudopeptidoglycan or other molecules. Bacterial cell membranes are composed of fatty acids joined to glycerol by ester bonds (COOC), while archaeal membranes are composed of isoprenoids rather than glycerol, linked to fatty acids by ether bonds (COC). In addition, the archaea have a more complex ribonucleic acid (RNA) polymerase than bacteria.

Life Cycle

Reproduction in bacteria involves duplicating the genetic material and dividing the cell into two daughter cells, a process known as binary fission. Under very favorable conditions, certain bacterial cells can divide as often as once every twenty minutes. Some bacteria, such as Clostridium and Bacillus species, possess the ability to form a resting state, or "spore," when unfavorable conditions are encountered. These spores are very resistant to heat, drying, radiation, and toxic chemicals. Bacterial spores have reportedly been reawakened from a 250-million-year-old salt crystal that existed before the time of the dinosaurs. Sterilization techniques used in medicine must overcome these resistant properties.

Size and Shape

Prokaryotes range in size from 0.2 micrometers to more than 50 micrometers, although the average prokaryote is around 1 to 3 micrometers in size. Eukaryotic cells are approximately one order of magnitude larger, ranging in size from 5 to 20 micrometers in diameter, with an average size of 20 micrometers.

The bacteria come in a number of distinct shapes as well. Common shapes include spherical (coccus), cylindrical (rod), and spiral forms (spirilla). While bacteria are generally regarded as unicellular organisms, there are also examples of bacteria that exist as multicellular colonies, aggregates, or filaments. In addition, bacteria can aggregate on surfaces. Called biofilms, these assemblages can consist of a single species or communities of microorganisms that can participate in metabolic cooperation.

Origin of Bacteria

It is not known whether the ancestor of bacteria originated on Earth or elsewhere. Some scientists believe that a life form existed extraterrestrially in the Martian meteorite ALH84001. Whether primitive life originated on Earth or elsewhere, current consensus is that bacteria were present on Earth 3.8 billion years ago.

Diversity

Bacteria show an incredible range of metabolic diversity. Some bacteria can get their energy from light (these are referred to as phototrophic organisms), organic compounds (organotrophic), or inorganic compounds such as hydrogen (H₂), sulfur compounds (H₂S), inorganic nitrogen compounds or ferrous iron compounds (chemolithotrophic). Some bacteria can make all of their organic compounds by fixing carbon (autotrophic), while others need to break down organic compounds to provide a carbon source (heterotrophic). Many bacteria are capable of fixing atmospheric nitrogen as a nitrogen source, in addition to organic and inorganic sources of nitrogen. Because of this metabolic diversity, bacteria play an important role in biogeochemical cycles such as the carbon, nitrogen, and phosphorous cycles.

This metabolic diversity also permits them to occupy a wide range of habitats. Bacteria can thrive in extremes of temperature, pH , salt, pressure, or toxic substances. Some bacteria can survive these conditions by spore formation, while other bacteria are able to multiply under extreme conditions. The most primitive bacteria extant today are theromophiles, leading to the consensus view that life arose under extreme conditions. Within and between these extremes, bacteria are found in marine, aquatic, terrestrial and subterranean environments. There are bacteria that are obligate aerobes and some that are obligate anaerobes , and many that fall somewhere in between.

In recent years, highly conserved genes such as the gene coding for the small subunit ribosomal RNA have been used as principal taxonomic characters. As bacteria evolve over time the sequence of this molecule changes, allowing taxonomic relationships between bacteria to be discerned.

Many divisions exist within the Bacteria. An example of this diversity is the subdivision α-proteobacteria, whose members are more diverse from each other than are plants from animals. More recently, full genome sequencing has revealed that genes can move between cells and even between species. Thus, bacterial genomes are in constant flux driven by gene acquisition from other species as well as evolutionary forces. The known bacterial tree of life is remarkable, but as 99 percent of bacterial life remains uncultured, this tree will undoubtedly expand greatly over time.

Associations

While most bacteria are free living at some point of their life cycles, many bacteria are capable of living in close associations with other organisms, including eukaryotes. Some of these so-called symbiotic associations are so highly evolved as to be obligate, while other associations are facultative, meaning the symbiotic partners can live apart from each other. In some symbioses, the eukaryotic host provides a highly specialized structure within which the bacteria reside, such as the nitrogen-fixing root nodules found on leguminous plants, such as clover, or the rumen possessed by some herbivorous mammals. Looser symbiotic associations exist where the host provides no specialized structure for the symbiotic bacteria. Organisms that populate the root zone of plants can provide growth benefits; these bacteria are in turn making use of plant products exuded though the roots.

There are also bacteria that are very harmful or even fatal to eukaryotic hosts. An example of this is Yersinia pestis, causative agent of the bubonic plague. Not all associations between bacteria and their eukaryotic hosts have such a drastic result. Many bacteria exist in relatively benign associations with their hosts, such as the Escherichia coli bacteria in the human large intestine. Some resident bacteria can become pathogenic under certain circumstances. These opportunistic pathogens can cause serious infection in hosts whose defenses are compromised by age or previous illness.

Some association can be very intimate, occurring on the intracellular level. It is generally accepted that the eukaryotic chloroplasts and mitochondria arose from associations between bacteria and other cells. These organelles are similar in size to bacteria and contain remnants of bacterial genomes.

see also Archaea; Bacterial Diseases; Bacterial Genetics; Biogeochemical Cycles; Cell Wall; Chloroplast; Extreme Communities; Mitochondrion; Nitrogen Fixation; Symbiosis

Marisa K. Chelius, Angela D. Kent, Anthony C. Yannarell, and Eric W. Triplett

Bibliography

Friedmann, E. I., J. Wierzchos, C. Ascaso, and Michael Winklhofer. "Chains of Magnetite Crystals in the Meteorite ALH84001: Evidence Of Biological Origin." Proc. Natl. Acad. Sci. USA 98, no. 5 (2001): 2176–2181.

Madigan, M. T., J. T. Martinko, and J. Parker. Brock Biology of Microorganisms, 9th ed. Upper Saddle River, NJ: Prentice Hall, 2000.

Perry, J. J., and J. T. Staley. Microbiology: Dynamics and Diversity. Philadelphia, PA: W. B. Saunders, Co., 1997.

Vreeland, R. H., W. D. Rosenzweig, and D. W. Powers. "Isolation of a 250-Million-Year-Old Halotolerant Bacterium from a Primary Salt Crystal." Nature 407 (2000): 897–900.

Eubacteria

Eubacteria (more commonly known as bacteria) are prokaryotic microorganisms that can be found almost everywhere on Earth. They are usually single cells but can also be found in chains, filaments , or multicellular clusters. Most are about 1 micron (1 µm), or one millionth of a meter in length, although some of the largest can be up to half a millimeter (500 µm). They come in a variety of shapes such as rods, filaments, spirals, vibrio (comma-shaped), and cocci (ball-shaped). Some have stalks that can be used for attachment. Many of them can move by gliding or by rotating small, projecting filaments called flagella . They lack the complex intracellular motility and mitosis found in eukaryotic cells.

Cellular Structure

Bacterial cells are fairly simple in structure when compared to the eukaryotic cells of fungi, protists , plants, and animals. As seen with an electron microscope, the majority of bacterial cell volume is filled with ribosomes, the sites of protein synthesis. Some bacteria, such as those that are photosynthetic, contain many internal membranes where metabolic processes take place. They contain no internal organelles , such as mitochondria and chloroplasts . Like archaea, bacteria have a prokaryotic cell organization: their deoxyribonucleic acid (DNA) is loosely gathered into a nucleoid and is not surrounded by a nuclear membrane, like that found in Eukaryotes. The DNA usually occurs as a single long circular strand, but some bacteria have linear chromosomes or divide their genetic material into several DNA molecules. Although they are different from the chromosomes of Eukaryotes, the large circular or linear prokaryotic DNA molecules are often termed chromosomes as well. Bacteria can also have smaller circles of DNA called plasmids, which usually carry a small number of genes used for specific metabolic functions—for example, to allow bacteria to metabolize certain compounds. Plasmids can easily be passed from cell to cell, allowing bacteria to rapidly pick up new metabolic functions, and are the basis for many advances in genetic engineering.

Like all living cells, bacteria are surrounded by lipid membranes. Most bacteria also have cell walls made up of a peptidoglycan called murein. The peptidoglycan layer is made up of a single kind of molecule from covalently linked sugar derivatives and amino acids. This molecule surrounds the bacterial cell like chain mail armor. Together with the osmotic pressure, the wall gives cells rigidity and shape. The cell wall structure and the presence or absence of a second lipid membrane surrounding the murein layer determine how bacteria react in a procedure called the Gram stain. Gram-positive organisms, which take up Gram stain, have a single membrane and a very thick outer peptidoglycan layer. Gram-negative organisms do not take up the stain and have two membranes in between which is a thin layer of peptidoglycan.

Distribution and Ecological Roles

Although bacteria may appear simple, they excel in the diversity and complexity of their metabolic capabilities and they are able to survive in many places. Bacteria are found everywhere on Earth where life is able to exist. They are plentiful in soils, bodies of water, on ice and snow, and are even found deep within Earth's crust. They often take advantage of living in and on other organisms in symbiotic relationships and can be found inhabiting the intestinal tracts and surfaces of animals, including humans. For the most part, the bacteria in and around us bring us more benefit than harm. Sometimes however, bacteria can be pathogenic, or disease causing. This can happen for a number of reasons, such as when the host has a compromised immune system or when a bacterium acquires genes that make it grow more aggressively or secrete toxins into its host environment.

Oxygen-producing photosynthesis, which is so familiar in plants, is actually a bacterial invention. Many bacteria are photosynthetic and use light energy to turn CO₂ from the atmosphere into cell material. Among these only the cyanobacteria produce oxygen during photosynthesis. Plastids, the photosynthetic organelles found in plants and algae, evolved from cyanobacteria through a process called endosymbiosis, in which cyanobacteria lived inside the cells of other organisms that were the ancestors of green algae. Mitochondria, found in most eukaryotic cells, also evolved from nonphoto-synthetic respiring bacteria in this way.

Bacteria are crucial for the cycling of elements necessary for all life. Through various processes, which we generally call decomposition, bacteria break down the cell materials of dead organisms into simpler carbon-, phosphorus-, sulfur-, and nitrogen-containing nutrients that can be used again by other organisms for growth. Without bacteria to recycle these essential nutrients, they would remain within the dead organisms or sediments and would thus be unavailable for use by other organisms.

see also Archaea; Biogeochemical Cycles; Cyanobacteria; Decomposers; Endosymbiosis; Evolution of Plants; Nitrogen Fixation.

J. Peter Gogarten

Lorraine Olendzenski

Bibliography

Needham, Cynthia, Mahlon Hoagland, Kenneth McPherson, and Bert Dodson. Intimate Strangers: Unseen Life on Earth. Washington, DC: ASM Press, 2000.

Schlegel, H. G. General Microbiology, 7th ed., tr. M. Kogut. Cambridge: Cambridge University Press, 1993.

Eubacteria

The Eubacteria are the largest and most diverse taxonomic group of bacteria . Some scientists regard the Eubacteria group as an artificial assemblage, merely a group of convenience rather than a natural grouping. Other scientists regard eubacteria as comprising their own kingdom. Another recent classification holds Eubacteria and Archaebacteria as domains or major groupings, classified above the kingdom level. The Eubacteria are all easily stained, rod-shaped or spherical bacteria. They are generally unicellular, but a small number of multicellular forms do occur. They can be motile or nonmotile and the motile forms are frequently characterized by the presence of numerous flagellae. Many of the ecologically important bacteria responsible for the fixation of nitrogen, such as Azotobacter and Rhizobium, are found in this group.

The cell walls of all of these species are relatively thick and unchanging, thus shape is generally constant within groups found in the Eubacteria. Thick cell walls are an evolutionary adaptation that allows survival in extreme situations where thinner walled bacteria would dry out. Some of the bacteria are gram positive while others are gram negative. One commonality that can be found within the group is that they all reproduce by transverse binary fission, although not all bacteria that reproduce in this manner are members of this group.

Eubacteria are often classified according to the manner in which they gain energy. Photoautotrophic Eubacteria manufacture their own energy through photosynthesis . Cyanobacteria, often called blue-green algae , are common photoautotrophic Eubacteria that are found in ponds and wetlands. Although not true algae, Cyanobacteria grow in chain-like colonies and contain chloroplasts as do aquatic algae. Cyanobacteria fossils are among the oldest-known fossils on Earth, some more than 3.5 billion years old.

Heterotrphic Eubacteria depend upon organic molecules to provide a source of energy. Heterotrophic Eubacteria are among the most abundant and diverse bacteria on Earth, and include bacteria that live as parasites , decomposers of organic material (saprophytes), as well as many pathogens (diseasecausing bacteria). Chemoautotrophic Eubacteria bacteria obtain their own energy by the oxidation of inorganic molecules. Chemoautotrophic bacteria are responsible for releasing the sulfur resulting in a sulfur taste of freshwater near many beaches (such as in Florida), and for supplying nitrogen in a form able to be used by plants.

See also Autotrophic bacteria; Heterotrophic bacteria; Nitrogen cycle in microorganisms; Oxidation-reduction reaction; Photosynthetic microorganisms

Eubacteria The taxonomic domain that contains the single kingdom Bacteria, comprising the true bacteria. There are 11 main groups: purple (photosynthetic); gram positive; cyanobacteria; green non-sulphur; spirochaetes; flavobacteria; green sulphur, Planctomyces; Chlamydiales; Deinococci; and Thermatogales. The only feature common to all bacteria is their prokaryotic cellular organization. The majority of bacteria are single-celled, and most have a rigid cell wall. Cell division usually occurs by binary fission; mitosis never occurs. Bacteria are almost universal in distribution and may live as saprotrophs, parasites, symbionts, pathogens, etc. They have many important roles in nature, e.g. as agents of decay and mineralization, and in the recycling of elements (such as nitrogen) in the biosphere. Bacteria are also important to humans, e.g. as causal agents of certain diseases, as agents of spoilage of food and other commodities, and as useful agents in the industrial production of commodities such as vinegar, antibiotics, and many types of dairy products. The oldest fossils known are of bacteria, from rocks in S. Africa that are apparently 3200 million years old. These must have been heterotrophic bacteria, feeding off organic molecules dissolved in the oceans of that time. The first photosynthetic bacteria, of anaerobic type, appeared a little later, about 3000 Ma ago.