Bacteria

Bacterium
Escherichia coli E. coli cell with bacterial fimbriae (pili). EM, cell width 0.75 micron. (CC) Photo: Manu Forero
Scientific classification
Domain: Bacteria
Subgroups
Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae

Bacteria (singular: bacterium) are a major group of living organisms. The term "bacteria" (singular: bacterium) has variously applied to all prokaryotes or to a major group of them, otherwise called the eubacteria, depending on ideas about their relationships. Here, bacteria is used specifically to refer to the eubacteria. Another major group of bacteria (in the broadest, non-taxonomic sense) are the Archaea. The study of bacteria is known as bacteriology, a subfield of microbiology.

Bacteria are the most abundant of all organisms. They are ubiquitous in soil, water, and as symbionts of other organisms. Many pathogens are bacteria. Most are minute, usually only 0.5-5.0 μm in their longest dimension, although giant bacteria like Thiomargarita namibiensis and Epulopiscium fishelsoni may grow past 0.5 mm in size. They generally have cell walls, like plant and fungal cells, but bacterial cell walls are normally made out of peptidoglycan instead of cellulose (as in plants) or chitin (as in fungi and arthropods), and are not homologous with eukaryotic cell walls. Many move around using flagella, which are different in structure from the flagella of eukaryotes.

History

Bacteria were first observed by the Dutch scientist Anton van Leeuwenhoek in 1674, using a single-lens microscope of his own design. He called them "animalcules" and published his observations in a long series of letters to the Royal Society. The name bacterium was introduced much later, by Christian Gottfried Ehrenberg in 1828, and is derived from the Greek word βακτήριον -α , bacterion -a , meaning "small staff".

Louis Pasteur demonstrated in 1859 that the fermentation process is caused by the growth of microorganisms, and that this growth is not due to spontaneous generation. (Yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungi.) Along with his contemporary, Robert Koch, Pasteur was an early advocate of the germ theory of disease. Robert Koch was a pioneer in medical microbiology and worked on cholera, anthrax and tuberculosis. In his research into tuberculosis, Koch finally proved the germ theory, for which he was awarded a Nobel Prize in 1905. In Koch's postulates, he set out criteria to test if an organism is the cause of a disease; these postulates are still used today.

Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available. In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum—the spirochete that causes syphilis—into compounds that selectively killed the pathogen. Ehrlich had been awarded a 1908 Nobel Prize for his work on immunology, and pioneered the use of stains to detect and identify bacteria, with his work being the basis of the Gram stain and the Ziehl-Neelsen stain.

A major step forward in the study of bacteria was the recognition in 1977 by Carl Woese that archaea have a separate line of evolutionary descent from bacteria. This new phylogenetic taxonomy was based on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains as part of the three-domain system.

Cellular structure

As prokaryotes (organisms without a cell nucleus) all bacteria have a relatively simple cell structure lacking a cell nucleus and organelles such as mitochondria and chloroplasts. Most bacteria are relatively small and possess distinctive cell and colony morphologies (shapes) as described below.

The most important bacterial structural characteristic is the cell wall. Bacteria can be divided into two groups (Gram positive and Gram negative) based on differences in cell wall structure as revealed by Gram staining. Gram positive bacteria possess a cell wall containing a thick peptidoglycan (called Murein in older sources) layer and teichoic acids while Gram negative bacteria have an outer, lipopolysaccharide-containing membrane and a thin peptidoglycan layer located in the periplasm (the region between the outer and cytoplasmic membranes).

Many bacteria contain other extracellular structures such as flagella and fimbriae which are used for motility (movement), attachment, and conjugation respectively. Some bacteria also contain capsules or slime layers that also facilitate bacterial attachment to surfaces and biofilm formation. Bacteria contain relatively few intracellular structures compared to eukaryotes but do contain a tightly supercoiled chromosome, ribosomes, and several other species-specific structures such as intracellular membranes, nutrient storage structures, gas vesicles, and magnetosomes.

Some bacteria are capable of forming endospores which allows them to survive extreme environmental and chemical stresses. This property is restricted to specific Gram positive organisms such as Bacillus and Clostridium.

Metabolism

Main article: Microbial metabolism

In contrast to higher organisms, bacteria exhibit an extremely wide variety of metabolic types. In fact, it is widely accepted that eukaryotic metabolism is largely a derivative of bacterial metabolism with mitochondria having descended from a lineage within the α-Proteobacteria and chloroplasts from the Cyanobacteria by ancient endosymbiotic events.

Bacterial metabolism can be divided broadly on the basis of the kind of energy used for growth, electron donors and electron acceptors and by the source of carbon used. Most bacteria are heterotrophic; using organic carbon compounds as both carbon and energy sources. In aerobic organisms, oxygen is used as the terminal electron acceptor. In anaerobic organisms other inorganic compounds, such as nitrate, sulfate or carbon dioxide as terminal electron acceptors leading to the environmentally important processes of denitrification, sulfate reduction and acetogenesis, respectively. Non-respiratory anaerobes use fermentation to generate energy and reducing power, secreting metabolic by-products (such as ethanol in brewing) as waste. Facultative anaerobes can switch between fermentation and different terminal electron acceptors depending on the environmental conditions in which they find themselves. As an alternative to heterotrophy many bacteria are autotrophic, fixing carbon dioxide into cell mass.

Energy metabolism of bacteria is either based on phototrophy or chemotrophy, i. e. the use of either light or exergonic chemical reactions for fueling life processes. Lithotrophic bacteria use inorganic electron donors for respiration (chemolithotrophs) or biosynthesis and carbon dioxide fixation (photolithotrophs), opposed by organotrophs which need organic compounds as electron donors for biosynthetic reactions (and mostly as well as carbon sources). Common inorganic electron donors are hydrogen, carbon monoxide, ammonia (leading to nitrification), ferrous iron, other reduced metal ions or even elemental iron and several reduced sulphur compounds. Additionally, methane metabolism, although formally counted as organotrophic, is actually more related to lithotrophic metabolic pathways. In both aerobic phototrophy and chemolithotrophy oxygen is used as a terminal electron acceptor, while under anaerobic conditions inorganic compounds (see above) are used instead. Most photolithotrophic and chemolithotrophic organisms are autotrophic, meaning that they obtain cellular carbon by fixation of carbon dioxide, whereas photoorganotrophic and chemoorganotrophic organisms are heterotrophic.

In addition to carbon, some organisms also fix nitrogen gas (nitrogen fixation). This environmentally important trait can be found in bacteria of nearly all the metabolic types listed above but is not universal.

The distribution of metabolic traits within a group of organisms has traditionally been used to define their taxonomy, although these traits often do not correspond with genetic techniques (see groups and identification below).

Growth and reproduction

All bacteria reproduce through asexual reproduction (one parent) binary fission, which results in cell division. Two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that facilitate the dispersal of the newly-formed daughter cells. Examples include fruiting body formation by Myxococcus and arial hyphae formation by Streptomyces, or budding. Budding is resulted of a 'bud' of a cell growing from another cell, and then finally breaking away.

In the laboratory, bacteria are usually grown using two methods, solid and liquid. Solid growth media such as agar plates are used to isolate pure cultures of a bacterial strain. When quantitation of growth or large volumes of cells are required liquid growth media are generally used. Growth in liquid media, with stirring, most often occurs as an even cell suspension making the cultures easier to divide and transfer compared to solid media, although the isolation of individual cells from liquid media is extremely difficult. In both liquid and solid media there exist a finite amount of nutrients, which allows for the study of the bacterial cell cycle. These limitations can be avoided by the use of a chemostat, which maintains a bacterial culture under steady-state conditions by the continuous addition of nutrients and the removal of waste products and cells. Large chemostats are often used for industrial-scale microbial processes.

Most techniques commonly used to grow bacteria are designed to optimise the amount of cells produced, the amount of time needed to produce them, and the cost to produce them. In a bacterium's natural environment nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This constant limitation of nutrients has led the evolution of many different growth strategies in different types of organisms (see R/K selection theory). Some possess the ability to grow extremely rapidly when nutrients become available, such as the formation of algal (and cyanobacterial) blooms that often occur in lakes during the summer. Other organisms have devised more specialized strategies to make them more successful in a harsh environment, such as the production of antibiotics by Streptomyces; often at the expense of a slower growth rate. In a natural environment, many organisms live in communities (e.g. biofilms) which may allow for increased supply of nutrients and protection of environmental stresses. In some bacterial communities, individuals can send chemical messages to other members to encourage them to kill themselves, speculatively so that a fraction of a population under stress sacrifices itself to provide nutrients for the survival of the group; to protect against spread of bacterial viruses infecting the group; and/or, to preserve the group's genetic integrity. Often these relationships are essential for growth of a particular organism or group of organisms (syntrophy). These evolutionary tactics to overcome nutrient limitation must be accounted for in an industrial/laboratory bacterial growth experiment. For instance bacteria that tend to agglutinate may need more vigorous stirring to break apart any large bacterial masses. The main growth attribute that must be understood for controlled growth is that bacteria have defined growth phases.

A controlled bacterial growth will follow three distinct phases. Nearly all cultures start from taking a relatively old stock of bacteria and diluting them in to fresh media; these cells need to adapt to the nutrient rich environment. The first phase of growth is the lag phase, a period of slow growth most often attributed to the need for cells to adapt to fast growth. The lag phase has high biosynthesis rates; enzymes needed to metabolise a variety of substrates are produced. The second phase of growth is the logarithmic phase (log phase), also known as the exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the growth rate (k). The time it takes the cells to double during the log phase is known as the generation time (g). During the log phase, nutrients are metabolised at maximum speed until they are all gone. The final phase of growth is the stationary phase. This phase of growth is caused by depleted nutrients. The cells begin to shut down their metabolic activity, as well as break-down their own non-essential proteins. The stationary phase is a transition from rapid growth to dormancy. Without positive signals from the environment transcription of many non-essential genes are no longer promoted to conserve ATP.

Genetic variation

Bacteria, as asexual organisms, inherit an identical copy of their parent's genes (i.e. are clonal). All bacteria, however, have the ability to evolve and change their genetic material, either through mutation or genetic recombination. Mutation occurs as a result of errors made during the replication of a gene and is most often gradual. It occurs naturally and as a result of the presence of mutagens. Mutation rates can vary among different species of bacteria, but is usually in the range of 10^-5 to 10^-7 mutations per gene per generation. Some bacteria can increase the rate of mutation during DNA replication as a response to stress.

Asexual reproduction does not afford an organism many opportunities to evolve its genome. Certain types of bacteria are also capable of exchanging genetic information through bacterial conjugation. The genetic material transferred may be either chromosomal or from a plasmid. In conjugation one bacterium, referred to as the F+ type, transfers genetic material to another (F- type) through a mating bridge. The F factor is the plasmid that contains genes coding for autonomous replication, pilli formation, and conjugal transfer functions. If the plasmid has integrated into the chromosome then it is referred to as a "high frequency recombination" strain (Hfr). Conjugation increases the genetic variability of bacterial populations and facilitates the emergences of antibiotic resistance. This is often thought of as a primitive form of sexual reproduction; however, since gametes (n) are not uniting to form a zygote (2n), this cannot be considered sexual reproduction. The ability to transfer DNA is not ubiquitous in the bacterial kingdom, so most bacteria also rely on other transfer methods to diversify their DNA. The most frequent genetic changes in bacterial genomes come from random mutation. Bacteria can also undergo genetic recombination. Many bacteria can take-up exogenous environmental DNA from closely related genera in a process called transformation. In the process of transduction, a virus can alter the DNA of a bacterium by becoming lysogenic and introducing foreign DNA into the host chromosome, which can then be transcribed and replicated. The generic term for gene acquisition from the environment is horizontal gene transfer.

Because of their ability to quickly grow, and the relative ease with which they can be manipulated, bacteria have historically been the workhorses for the fields of molecular biology, genetics and biochemistry. By making mutations in bacteria and examining the resulting phenotypes, scientists have been able to determine the function of many different genes and enzymes. Lessons learned from bacteria can then be applied to more complex organisms which are often more difficult to study.

Movement

(PD) Photo: Eric Erbe; Christopher Pooley
E. coli bacteria magnified 10,000 times.

Motile bacteria can move about, using flagella, bacterial gliding, or changes of buoyancy. A unique group of bacteria, the spirochaetes, have structures similar to flagella, called axial filaments, between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves.

Bacterial flagella are arranged in many different ways. Bacteria can have a single polar flagellum at one end of a cell, clusters of many flagella at one end or flagella scattered all over the cell, as with peritrichous. Many bacteria (such as E.coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and introduces an important element of randomness in their forward movement. (See external links below for link to videos.)

Motile bacteria are attracted or repelled by certain stimuli, behaviors called taxes - for instance, chemotaxis, phototaxis, mechanotaxis, and magnetotaxis. In one peculiar group, the myxobacteria, individual bacteria attract to form swarms and may differentiate to form fruiting bodies. The myxobacteria move only when on solid surfaces, unlike E. coli which is motile in liquid or solid media.

Groups and identification

Historically, bacteria as originally studied by botanists were classified in the same way as plants, that is, mainly by shape. Bacteria come in a variety of different cell morphologies (shapes), including bacillus (rod-shape), coccus (spherical), spirillum (helical), and vibrio (curved bacillus). However, because of their small size bacteria are relatively uniform in shape and therefore classification based on morphology was unsuccessful. The first formal classification scheme was developed following the development of the Gram stain by Hans Christian Gram which separates bacteria based on the structural characteristics of their cell walls. This scheme included:

• Gracilicutes - Gram negative staining bacteria with a second cell membrane
• Firmicutes - Gram positive staining bacteria with a thick peptidoglycan wall
• Mollicutes - Gram negative staining bacteria with no cell wall or second membrane
• Mendosicutes - atypically staining strains now known to belong to the Archaea

Further developments (essentially) based on this scheme included comparisons of bacteria based on differences in cellular metabolism as determined by a wide variety of specific tests. Bacteria were also classified based on differences in cellular chemical compounds such as fatty acids, pigments, and quinones for example. While these schemes allowed for the differentiation between bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. It was not until the utilization of genome-based techniques such as %guanine+cytosine ratio determination, genome-genome hybridization and gene sequencing (in particular the rRNA gene) that microbial taxonomy developed (or at least is developing) into a stable, accurate classification system. It should be noted, however, that due to the existence numerous historical classification schemes and our current poor understanding of microbial diversity, bacterial taxonomy remains a changing and expanding field.

Benefits and dangers

Bacteria are both harmful and useful to the environment and animals, including humans. The role of bacteria in disease and infection is important. Some bacteria act as pathogens and cause tetanus, typhoid fever, pneumonia, syphilis, cholera, food-borne illness, leprosy, and tuberculosis(TB). Sepsis, a systemic infectious syndrome characterized by shock and massive vasodilation, or localized infection, can be caused by bacteria such as Streptococcus, Staphylococcus, or many gram-negative bacteria. Some bacterial infections can spread throughout the host's body and become systemic. In plants, bacteria cause leaf spot, fireblight, and wilts. The mode of infection includes contact, air, food, water, and insect-borne microorganisms. The hosts infected with the pathogens may be treated with antibiotics, which can be classified as bacteriocidal and bacteriostatic, which at concentrations that can be reached in bodily fluids either kill bacteria or hamper their growth, respectively. Antiseptic measures may be taken to prevent infection by bacteria, for example, by swabbing skin with alcohol prior to piercing the skin with the needle of a syringe. Sterilization of surgical and dental instruments is done to make them sterile or pathogen-free to prevent contamination and infection by bacteria. Sanitizers and disinfectants are used to kill bacteria or other pathogens to prevent contamination and risk of infection.

In soil, microorganisms which reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking) help in the transformation of molecular dinitrogen gas as their source of nitrogen, converting it to nitrogenous compounds in a process known as nitrogen fixation. This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts in humans and other organisms. For example, the presence of the gut flora in the large intestine can help prevent the growth of potentially harmful microbes.

The ability of bacteria to degrade a variety of organic compounds is remarkable. Highly specialized groups of microorganisms play important roles in the mineralization of specific classes of organic compounds. For example, the decomposition of cellulose, which is one of the most abundant constituents of plant tissues, is mainly brought about by aerobic bacteria that belong to the genus Cytophaga. This ability has also been utilized by humans in industry, waste processing, and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills. Some beaches in Prince William Sound were fertilized in an attempt to facilitate the growth of such bacteria after the infamous 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil.

Bacteria, often in combination with yeasts and molds, are used in the preparation of fermented foods such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine, and yogurt. Using biotechnology techniques, bacteria can be bioengineered for the production of therapeutic drugs, such as insulin, or for the bioremediation of toxic wastes.

"Friendly bacteria" is a term used to refer to those bacteria that offer some benefit to human hosts, such as Lactobacillus species, which convert milk protein to lactic acid in the gut. The presence of such bacterial colonies also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion). Other bacteria that are helpful inside the body are many strains of E. coli, which are harmless in healthy individuals and provide Vitamin K.

Sources

• Some text in this entry was merged with the Nupedia article entitled Bacteria, written by Nagina Parmar; reviewed and approved by the Biology group (editor: Gaytha Langlois, lead reviewer: Gaytha Langlois, lead copyeditors: Ruth Ifcher and Jan Hogle)