Bacterial genome

From Wikipedia, the free encyclopedia

Bacterial genomes are generally smaller and less variant in size among species when compared with genomes of animals and single cell eukaryotes. Bacterial genomes can range in size anywhere from about 130 kbp to over 14 Mbp. A study that included, but was not limited to, 478 bacterial genomes, concluded that as genome size increases, the number of genes increases at a disproportionately slower rate in eukaryotes than in non-eukaryotes. Thus, the proportion of non-coding DNA goes up with genome size more quickly in non-bacteria than in bacteria. This is consistent with the fact that most eukaryotic nuclear DNA is non-gene coding, while the majority of prokaryotic, viral, and organellar genes are coding. Right now, we have genome sequences from 50 different bacterial phyla and 11 different archaeal phyla. Second-generation sequencing has yielded many draft genomes (close to 90% of bacterial genomes in GenBank are currently not complete); third-generation sequencing might eventually yield a complete genome in a few hours. The genome sequences reveal much diversity in bacteria. Analysis of over 2000 Escherichia coli genomes reveals an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Genome sequences show that parasitic bacteria have 500–1200 genes, free-living bacteria have 1500–7500 genes, and archaea have 1500–2700 genes. A striking discovery by Cole et al. described massive amounts of gene decay when comparing Leprosy bacillus to ancestral bacteria. Studies have since shown that several bacteria have smaller genome sizes than their ancestors did. Over the years, researchers have proposed several theories to explain the general trend of bacterial genome decay and the relatively small size of bacterial genomes. Compelling evidence indicates that the apparent degradation of bacterial genomes is owed to a deletional bias.

Methods and techniques

As of 2014, there are over 30,000 sequenced bacterial genomes publicly available and thousands of metagenome projects. Projects such as the Genomic Encyclopedia of Bacteria and Archaea (GEBA) intend to add more genomes.

The single gene comparison is now being supplanted by more general methods. These methods have resulted in novel perspectives on genetic relationships that previously have only been estimated.

A significant achievement in the second decade of bacterial genome sequencing was the production of metagenomic data, which covers all DNA present in a sample. Previously, there were only two metagenomic projects published.

Bacterial genomes

Log-log plot of the total number of annotated proteins in genomes submitted to GenBank as a function of genome size. Based on data from NCBI genome reports.

 

Bacteria possess a compact genome architecture distinct from eukaryotes in two important ways: bacteria show a strong correlation between genome size and number of functional genes in a genome, and those genes are structured into operons. The main reason for the relative density of bacterial genomes compared to eukaryotic genomes (especially multicellular eukaryotes) is the presence of noncoding DNA in the form of intergenic regions and introns. Some notable exceptions include recently formed pathogenic bacteria. This was initially described in a study by Cole et al. in which Mycobacterium leprae was discovered to have a significantly higher percentage of pseudogenes to functional genes (~40%) than its free-living ancestors.

Furthermore, amongst species of bacteria, there is relatively little variation in genome size when compared with the genome sizes of other major groups of life. Genome size is of little relevance when considering the number of functional genes in eukaryotic species. In bacteria, however, the strong correlation between the number of genes and the genome size makes the size of bacterial genomes an interesting topic for research and discussion.

The general trends of bacterial evolution indicate that bacteria started as free-living organisms. Evolutionary paths led some bacteria to become pathogens and symbionts. The lifestyles of bacteria play an integral role in their respective genome sizes. Free-living bacteria have the largest genomes out of the three types of bacteria; however, they have fewer pseudogenes than bacteria that have recently acquired pathogenicity. 

Facultative and recently evolved pathogenic bacteria exhibit a smaller genome size than free-living bacteria, yet they have more pseudogenes than any other form of bacteria. 

Obligate bacterial symbionts or pathogens have the smallest genomes and the fewest pseudogenes of the three groups. The relationship between life-styles of bacteria and genome size raises questions as to the mechanisms of bacterial genome evolution. Researchers have developed several theories to explain the patterns of genome size evolution amongst bacteria.

Genome comparisons and phylogeny

As single-gene comparisons have largely given way to genome comparisons, phylogeny of bacterial genomes have improved in accuracy. The Average Nucleotide Identity method quantifies genetic distance between entire genomes by taking advantage of regions of about 10,000 bp. With enough data from genomes of one genus, algorithms are executed to categorize species. This has been done for the Pseudomonas avellanae species in 2013.

To extract information about bacterial genomes, core- and pan-genome sizes have been assessed for several strains of bacteria. In 2012, the number of core gene families was about 3000. However, by 2015, with an over tenfold increased in available genomes, the pan-genome has increased as well. There is roughly a positive correlation between the number of genomes added and the growth of the pan-genome. On the other hand, the core genome has remain static since 2012. Currently, the E. coli pan-genome is composed of about 90,000 gene families. About one-third of these exist only in a single genome. Many of these, however, are merely gene fragments and the result of calling errors. Still, there are probably over 60,000 unique gene families in E. coli.

Theories of bacterial genome evolution

Bacteria lose a large amount of genes as they transition from free-living or facultatively parasitic life cycles to permanent host-dependent life. Towards the lower end of the scale of bacterial genome size are the mycoplasmas and related bacteria. Early molecular phylogenetic studies revealed that mycoplasmas represented an evolutionary derived state, contrary to prior hypotheses. Furthermore, it is now known that mycoplasmas are just one instance of many of genome shrinkage in obligately host-associated bacteria. Other examples are Rickettsia, Buchnera aphidicola, and Borrelia burgdorferi.

Small genome size in such species is associated with certain particularities, such as rapid evolution of polypeptide sequences and low GC content in the genome. The convergent evolution of these qualities in unrelated bacteria suggests that an obligate association with a host promotes genome reduction.

Given that over 80% of almost all of the fully sequenced bacterial genomes consist of intact ORFs, and that gene length is nearly constant at ~1 kb per gene, it is inferred that small genomes have few metabolic capabilities. While free-living bacteria, such as E. coli, Salmonella species, or Bacillus species, usually have 1500 to 6000 proteins encoded in their DNA, obligately pathogenic bacteria often have as few as 500 to 1000 such proteins.

One candidate explanation is that reduced genomes maintain genes that are necessary for vital processes pertaining to cellular growth and replication, in addition to those genes that are required to survive in the bacteria's ecological niche. However, sequence data contradicts this hypothesis. The set of universal orthologs amongst eubacteria comprises only 15% of each genome. Thus, each lineage has taken a different evolutionary path to reduced size. Because universal cellular processes require over 80 genes, variation in genes imply that the same functions can be achieved by exploitation of nonhomologous genes.

Host-dependent bacteria are able to secure many compounds required for metabolism from the host's cytoplasm or tissue. They can, in turn, discard their own biosynthetic pathways and associated genes. This removal explains many of the specific gene losses. For example, the Rickettsia species, which relies on specific energy substrate from its host, has lost many of its native energy metabolism genes. Similarly, most small genomes have lost their amino acid biosynthesizing genes, as these are found in the host instead. One exception is the Buchnera, an obligate maternally transmitted symbiont of aphids. It retains 54 genes for biosynthesis of crucial amino acids, but no longer has pathways for those amino acids that the host can synthesize. Pathways for nucleotide biosynthesis are gone from many reduced genomes. Those anabolic pathways that evolved through niche adaptation remain in particular genomes.

The hypothesis that unused genes are eventually removed does not explain why many of the removed genes would indeed remain helpful in obligate pathogens. For example, many eliminated genes code for products that are involved in universal cellular processes, including replication, transcription, and translation. Even genes supporting DNA recombination and repair are deleted from every small genome. In addition, small genomes have fewer tRNAs, utilizing one for several amino acids. So, a single codon pairs with multiple codons, which likely yields less-than-optimal translation machinery. It is unknown why obligate intracellular pathogens would benefit by retaining fewer tRNAs and fewer DNA repair enzymes.

Another factor to consider is the change in population that corresponds to an evolution towards an obligately pathogenic life. Such a shift in lifestyle often results in a reduction in the genetic population size of a lineage, since there is a finite number of hosts to occupy. This genetic drift may result in fixation of mutations that inactivate otherwise beneficial genes, or otherwise may decrease the efficiency of gene products. Hence, not will only useless genes be lost (as mutations disrupt them once the bacteria has settled into host dependency), but also beneficial genes may be lost if genetic drift enforces ineffective purifying selection.

The number of universally maintained genes is small and inadequate for independent cellular growth and replication, so that small genome species must achieve such feats by means of varying genes. This is done partly through nonorthologous gene displacement. That is, the role of one gene is replaced by another gene that achieves the same function. Redundancy within the ancestral, larger genome is eliminated. The descendant small genome content depends on the content of chromosomal deletions that occur in the early stages of genome reduction.

The very small genome of M. genitalium possesses dispensable genes. In a study in which single genes of this organism were inactivated using transposon-mediated mutagenesis, at least 129 of its 484 ORGs were not required for growth. A much smaller genome than that of the M. genitalium is therefore feasible.

Doubling time

One theory predicts that bacteria have smaller genomes due to a selective pressure on genome size to ensure faster replication. The theory is based upon the logical premise that smaller bacterial genomes will take less time to replicate. Subsequently, smaller genomes will be selected preferentially due to enhanced fitness. A study done by Mira et al. indicated little to no correlation between genome size and doubling time. The data indicates that selection is not a suitable explanation for the small sizes of bacterial genomes. Still, many researchers believe there is some selective pressure on bacteria to maintain small genome size.

Deletional bias

Selection is but one process involved in evolution. Two other major processes (mutation and genetic drift) can account for the genome sizes of various types of bacteria. A study done by Mira et al. examined the size of insertions and deletions in bacterial pseudogenes. Results indicated that mutational deletions tend to be larger than insertions in bacteria in the absence of gene transfer or gene duplication. Insertions caused by horizontal or lateral gene transfer and gene duplication tend to involve transfer of large amounts of genetic material. Assuming a lack of these processes, genomes will tend to reduce in size in the absence of selective constraint. Evidence of a deletional bias is present in the respective genome sizes of free-living bacteria, facultative and recently derived parasites and obligate parasites and symbionts. 

Free-living bacteria tend to have large population-sizes and are subject to more opportunity for gene transfer. As such, selection can effectively operate on free-living bacteria to remove deleterious sequences resulting in a relatively small number of pseudogenes. Continually, further selective pressure is evident as free-living bacteria must produce all gene-products independent of a host. Given that there is sufficient opportunity for gene transfer to occur and there are selective pressures against even slightly deleterious deletions, it is intuitive that free-living bacteria should have the largest bacterial genomes of all bacteria types. 

Recently-formed parasites undergo severe bottlenecks and can rely on host environments to provide gene products. As such, in recently-formed and facultative parasites, there is an accumulation of pseudogenes and transposable elements due to a lack of selective pressure against deletions. The population bottlenecks reduce gene transfer and as such, deletional bias ensures the reduction of genome size in parasitic bacteria. 

Obligatory parasites and symbionts have the smallest genome sizes due to prolonged effects of deletional bias. Parasites which have evolved to occupy specific niches are not exposed to much selective pressure. As such, genetic drift dominates the evolution of niche-specific bacteria. Extended exposure to deletional bias ensures the removal of most superfluous sequences. Symbionts occur in drastically lower numbers and undergo the most severe bottlenecks of any bacterial type. There is almost no opportunity for gene transfer for endosymbiotic bacteria, and thus genome compaction can be extreme. One of the smallest bacterial genomes ever to be sequenced is that of the endosymbiont Carsonella rudii. At 160 kbp, the genome of Carsonella is one of the most streamlined examples of a genome examined to date.

Genomic reduction

Molecular phylogenetics has revealed that every clade of bacteria with genome sizes under 2 Mb was derived from ancestors with much larger genomes, thus refuting the hypothesis that bacteria evolved by the successive doubling of small-genomed ancestors. Recent studies performed by Nilsson et al. examined the rates of bacterial genome reduction of obligate bacteria. Bacteria were cultured introducing frequent bottlenecks and growing cells in serial passage to reduce gene transfer so as to mimic conditions of endosymbiotic bacteria. The data predicted that bacteria exhibiting a one-day generation time lose as many as 1,000 kbp in as few as 50,000 years (a relatively short evolutionary time period). Furthermore, after deleting genes essential to the methyl-directed DNA mismatch repair (MMR) system, it was shown that bacterial genome size reduction increased in rate by as much as 50 times. These results indicate that genome size reduction can occur relatively rapidly, and loss of certain genes can speed up the process of bacterial genome compaction.

This is not to suggest that all bacterial genomes are reducing in size and complexity. While many types of bacteria have reduced in genome size from an ancestral state, there are still a huge number of bacteria that maintained or increased genome size over ancestral states. Free-living bacteria experience huge population sizes, fast generation times and a relatively high potential for gene transfer. While deletional bias tends to remove unnecessary sequences, selection can operate significantly amongst free-living bacteria resulting in evolution of new genes and processes.

Horizontal gene transfer

Unlike eukaryotes, which evolve mainly through the modification of existing genetic information, bacteria have acquired a large percentage of their genetic diversity by the horizontal transfer of genes. This creates quite dynamic genomes, in which DNA can be introduced into and removed from the chromosome.

Bacteria have more variation in their metabolic properties, cellular structures, and lifestyles than can be accounted for by point mutations alone. For example, none of the phenotypic traits that distinguish E. coli from Salmonella enterica can be attributed to point mutation. On the contrary, evidence suggests that horizontal gene transfer has bolstered the diversification and speciation of many bacteria.

Horizontal gene transfer is often detected via DNA sequence information. DNA segments obtained by this mechanism often reveal a narrow phylogenetic distribution between related species. Furthermore, these regions sometimes display an unexpected level of similarity to genes from taxa that are assumed to be quite divergent.

Although gene comparisons and phylogenetic studies are helpful in investigating horizontal gene transfer, the DNA sequences of genes are even more revelatory of their origin and ancestry within a genome. Bacterial species differ widely in overall GC content, although the genes in any one species' genome are roughly identical with respect to base composition, patterns of codon usage, and frequencies of di- and trinucleotides. As a result, sequences that are newly acquired through lateral transfer can be identified via their characteristics, which remains that of the donor. For example, many of the S. enterica genes that are not present in E. coli have base compositions that differ from the overall 52% GC content of the entire chromosome. Within this species, some lineages have more than a megabase of DNA that is not present in other lineages. The base compositions of these lineage-specific sequences imply that at least half of these sequences were captured through lateral transfer. Furthermore, the regions adjacent to horizontally obtained genes often have remnants of translocatable elements, transfer origins of plasmids, or known attachment sites of phage integrases.

In some species, a large proportion of laterally transferred genes originate from plasmid-, phage-, or transposon-related sequences.

Although sequence-based methods reveal the prevalence of horizontal gene transfer in bacteria, the results tend to be underestimates of the magnitude of this mechanism, since sequences obtained from donors whose sequence characteristics are similar to those of the recipient will avoid detection.

Comparisons of completely sequenced genomes confirm that bacterial chromosomes are amalgams of ancestral and laterally acquired sequences. The hyperthermophilic Eubacteria Aquifex aeolicus and Thermotoga maritima each has many genes that are similar in protein sequence to homologues in thermophilic Archaea. 24% of Thermotoga's 1,877 ORFs and 16% of Aquifex's 1,512 ORFs show high matches to an Archaeal protein, while mesophiles such as E. coli and B. subtilis have far lesser proportions of genes that are most like Archaeal homologues.

Mechanisms of lateral transfer

The genesis of new abilities due to horizontal gene transfer has three requirements. First, there must exist a possible route for the donor DNA to be accepted by the recipient cell. Additionally, the obtained sequence must be integrated with the rest of the genome. Finally, these integrated genes must benefit the recipient bacterial organism. The first two steps can be achieved via three mechanisms: transformation, transduction and conjugation.

Transformation involves the uptake of named DNA from the environment. Through transformation, DNA can be transmitted between distantly related organisms. Some bacterial species, such as Haemophilus influenzae and Neisseria gonorrhoeae, are continuously competent to accept DNA. Other species, such as Bacillus subtilis and Streptococcus pneumoniae, become competent when they enter a particular phase in their lifecycle. 

Transformation in N. gonorrhoeae and H. influenzae is effective only if particular recognition sequences are found in the recipient genomes (5'-GCCGTCTGAA-3' and 5'-AAGTGCGGT-3'. respectively). Although the existence of certain uptake sequences improve transformation capability between related species, many of the inherently competent bacterial species, such as B. subtilis and S. pneumoniae, do not display sequence preference.

New genes may be introduced into bacteria by a bacteriophage that has replicated within a donor through generalized transduction or specialized transduction. The amount of DNA that can be transmitted in one event is constrained by the size of the phage capsid (although the upper limit is about 100 kilobases). While phages are numerous in the environment, the range of microorganisms that can be transduced depends on receptor recognition by the bacteriophage. Transduction does not require both donor and recipient cells to be present simultaneously in time nor space. Phage-encoded proteins both mediate the transfer of DNA into the recipient cytoplasm and assist integration of DNA into the chromosome.

Conjugation involves physical contact between donor and recipient cells and is able to mediate transfers of genes between domains, such as between bacteria and yeast. DNA is transmitted from donor to recipient either by self-transmissible or mobilizable plasmid. Conjugation may mediate the transfer of chromosomal sequences by plasmids that integrate into the chromosome. 

Despite the multitude of mechanisms mediating gene transfer among bacteria, the process's success is not guaranteed unless the received sequence is stably maintained in the recipient. DNA integration can be sustained through one of many processes. One is persistence as an episome, another is homologous recombination, and still another is illegitimate incorporation through lucky double-strand break repair.

Traits introduced through lateral gene transfer

Antimicrobial resistance genes grant an organism the ability to grow its ecological niche, since it can now survive in the presence of previously lethal compounds. As the benefit to a bacterium earned from receiving such genes are time- and space-independent, those sequences that are highly mobile are selected for. Plasmids are quite mobilizable between taxa and are the most frequent way by which bacteria acquire antibiotic resistance genes. 

Adoption of a pathogenic lifestyle often yields a fundamental shift in an organism's ecological niche. The erratic phylogenetic distribution of pathogenic organisms implies that bacterial virulence is a consequence of the presence, or obtainment of, genes that are missing in avirulent forms. Evidence of this includes the discovery of large 'virulence' plasmids in pathogenic Shigella and Yersinia, as well as the ability to bestow pathogenic properties onto E. coli via experimental exposure to genes from other species.

Computer-made form

In April 2019, scientists at ETH Zurich reported the creation of the world's first bacterial genome, named Caulobacter ethensis-2.0, made entirely by a computer, although a related viable form of C. ethensis-2.0 does not yet exist.

Methanogen / Methanotroph

From Wikipedia, the free encyclopedia

Methanogen

Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domain of archaea. They are common in wetlands, where they are responsible for marsh gas, and in the digestive tracts of animals such as ruminants and humans, where they are responsible for the methane content of belching in ruminants and flatulence in humans. In marine sediments the biological production of methane, also termed methanogenesis, is generally confined to where sulfates are depleted, below the top layers. Moreover, methanogenic archaea populations play an indispensable role in anaerobic wastewater treatments. Others are extremophiles, found in environments such as hot springs and submarine hydrothermal vents as well as in the "solid" rock of Earth's crust, kilometers below the surface.

Physical description

Methanogens are coccoid (spherical shaped) or bacilli (rod shaped). There are over 50 described species of methanogens, which do not form a monophyletic group, although all known methanogens belong to Archaea. They are mostly anaerobic organisms that cannot function under aerobic conditions, but recently a species (Candidatus Methanothrix paradoxum) has been identified that can function in anoxic microsites within aerobic environments. They are very sensitive to the presence of oxygen even at trace level. Usually, they cannot sustain oxygen stress for a prolonged time. However, Methanosarcina barkeri is exceptional in possessing a superoxide dismutase (SOD) enzyme, and may survive longer than the others in the presence of O₂. Some methanogens, called hydrogenotrophic, use carbon dioxide (CO₂) as a source of carbon, and hydrogen as a reducing agent.

The reduction of carbon dioxide into methane in the presence of hydrogen can be expressed as follows:

CO₂ + 4 H₂ → CH₄ + 2H₂O

Some of the CO₂ reacts with the hydrogen to produce methane, which creates an electrochemical gradient across the cell membrane, used to generate ATP through chemiosmosis. In contrast, plants and algae use water as their reducing agent.

Methanogens lack peptidoglycan, a polymer that is found in the cell walls of Bacteria but not in those of Archaea. Some methanogens have a cell wall that is composed of pseudopeptidoglycan. Other methanogens do not, but have at least one paracrystalline array (S-layer) made up of proteins that fit together like a jigsaw puzzle.

Extreme living areas

Methanogens play a vital ecological role in anaerobic environments of removing excess hydrogen and fermentation products that have been produced by other forms of anaerobic respiration. Methanogens typically thrive in environments in which all electron acceptors other than CO₂ (such as oxygen, nitrate, ferriciron (Fe(III)), and sulfate) have been depleted. In deep basaltic rocks near the mid ocean ridges, they can obtain their hydrogen from the serpentinisation reaction of olivine as observed in the hydrothermal field of Lost City. 

The thermal breakdown of water and water radiolysis are other possible sources of hydrogen. 

Methanogens are key agents of remineralization of organic carbon in continental margin sediments and other aquatic sediments with high rates of sedimentation and high sediment organic matter. Under the correct conditions of pressure and temperature, biogenic methane can accumulate in massive deposits of methane clathrates, which account for a significant fraction of organic carbon in continental margin sediments and represent a key reservoir of a potent greenhouse gas.

Methanogens have been found in several extreme environments on Earth – buried under kilometres of ice in Greenland and living in hot, dry desert soil. They are known to be the most common archaebacteria in deep subterranean habitats. Live microbes making methane were found in a glacial ice core sample retrieved from about three kilometres under Greenland by researchers from the University of California, Berkeley. They also found a constant metabolism able to repair macromolecular damage, at temperatures of 145 to –40 °C.

Another study has also discovered methanogens in a harsh environment on Earth. Researchers studied dozens of soil and vapour samples from five different desert environments in Utah, Idaho and California in the United States, and in Canada and Chile. Of these, five soil samples and three vapour samples from the vicinity of the Mars Desert Research Station in Utah were found to have signs of viable methanogens.

Some scientists have proposed that the presence of methane in the Martian atmosphere may be indicative of native methanogens on that planet.

Closely related to the methanogens are the anaerobic methane oxidizers, which utilize methane as a substrate in conjunction with the reduction of sulfate and nitrate. Most methanogens are autotrophic producers, but those that oxidize CH₃COO⁻ are classed as chemotroph instead.

Comparative genomics and molecular signatures

Comparative genomic analysis has led to the identification of 31 signature proteins which are specific for methanogens (also known as Methanoarchaeota). Most of these proteins are related to methanogenesis, and they could serve as potential molecular markers for methanogens. Additionally, 10 proteins found in all methanogens which are shared by Archaeoglobus, suggest that these two groups are related. In phylogenetic trees, methanogens are not monophyletic and they are generally split into three clades. Hence, the unique shared presence of large numbers of proteins by all methanogens could be due to lateral gene transfers.

Metabolism

Methane production

Methanogens are known to produce methane from substrates such as H₂/CO₂, acetate, formate, methanol and methylamines in a process called methanogenesis. Different methanogenic reactions are catalyzed by unique sets of enzymes and coenzymes. While reaction mechanism and energetics vary between one reaction and another, all of these reactions contribute to net positive energy production by creating ion concentration gradients that are used to drive ATP synthesis. The overall reaction for H₂/CO₂ methanogenesis is:

${\displaystyle {\ce {CO2 + 4 H2 -> CH4 + 2 H2O}}}$
  (∆G˚’ = -134 kJ/mol CH₄)

Well-studied organisms that produce methane via H2/CO₂ methanogenesis include Methanosarcina barkeri, Methanobacterium thermoautotrophicum, and Methanobacterium wolfei. These organism are typically found in anaerobic environments.

In the earliest stage of H₂/CO₂ methanogenesis, CO₂ binds to methylfuran (MF) and is reduced to formyl-MF. This endergonic reductive process (∆G˚’= +16 kJ/mol) is dependent on the availability of H₂ and is catalyzed by the enzyme formyl-MF dehydrogenase.

${\displaystyle {\ce {CO2 + H2 + MF -> HCO-MF + H2O}}}$

The formyl constituent of formyl-MF is then transferred to the coenzyme tetrahydromethanopterin (H4MPT) and is catalyzed by a soluble enzyme known as formyl transferase. This results in the formation of formyl-H4MPT.

${\displaystyle {\ce {HCO-MF + H4MPT -> HCO-H4MPT + MF}}}$

Formyl-H4MPT is subsequently reduced to methenyl-H4MPT. Methenyl-H4MPT then undergoes a one-step hydrolysis followed by a two-step reduction to methyl-H4MPT. The two-step reversible reduction is assisted by coenzyme F₄₂₀ whose hydride acceptor spontaneously oxidizes. Once oxidized, F₄₂₀’s electron supply is replenished by accepting electrons from H₂. This step is catalyzed by methylene H4MPT dehydrogenase.

${\displaystyle {\ce {HCO-H4MPT + H+ -> CH-H4MPT+ + H2O}}}$ 

(Formyl-H4MPT reduction)

${\displaystyle {\ce {CH-H4MPT+ + F420H2 -> CH2=H4MPT + F420 + H+}}}$

 

(Methenyl-H4MPT hydrolysis)

${\displaystyle {\ce {CH2=H4MPT + H2 -> CH3-H4MPT + H+}}}$ 

(H4MPT reduction)

Next, the methyl group of methyl-M4MPT is transferred to coenzyme M via a methyltransferase-catalyzed reaction.

${\displaystyle {\ce {CH3-H4MPT + HS-CoM -> CH3-S-CoM + H4MPT}}}$

The final step of H₂/CO₂ methanogenic involves methyl-coenzyme M reductase and two coenzymes: N-7 mercaptoheptanoylthreonine phosphate (HS-HTP) and coenzyme F₄₃₀. HS-HTP donates electrons to methyl-coenzyme M allowing the formation of methane and mixed disulfide of HS-CoM.^[24] F₄₃₀, on the other hand, serves as a prosthetic group to the reductase. H₂ donates electrons to the mixed disulfide of HS-CoM and regenerates coenzyme M.

${\displaystyle {\ce {CH3-S-CoM + HS-HTP -> CH4 + CoM-S-S-HTP}}}$ 

  (Formation of methane)

${\displaystyle {\ce {CoM-S-S-HTP + H2 -> HS-CoM + HS-HTP}}}$ 

(Regeneration of coenzyme M)

Wastewater treatment

Methanogens are widely used in anaerobic digestors to treat wastewater as well as aqueous organic pollutants. Industries have selected methanogens for their ability to perform biomethanation during wastewater decomposition thereby rendering the process sustainable and cost-effective.

Bio-decomposition in the anaerobic digester involves a four-staged cooperative action performed by different microorganisms. The first stage is the hydrolysis of insoluble polymerized organic matter by anaerobes such as Streptococcus and Enterobacterium. In the second stage, acidogens breakdown dissolved organic pollutants in wastewater to fatty acids. In the third stage, acetogens convert fatty acids to acetates. In the final stage, methanogens metabolize acetates to gaseous methane. The byproduct methane leaves the aqueous layer and serves as an energy source to power wastewater-processing within the digestor, thus generating a self-sustaining mechanism.

Methanogens also effectively decrease the concentration of organic matter in wastewater run-off. For instance, agricultural wastewater, highly rich in organic material, has been a major cause of aquatic ecosystem degradation. The chemical imbalances can lead to severe ramifications such as eutrophication. Through anaerobic digestion, the purification of wastewater can prevent unexpected blooms in water systems as well as trap methanogenesis within digesters. This allocates biomethane for energy production and prevents a potent greenhouse gas, methane, from being released into the atmosphere. 

The organic components of wastewater vary vastly. Chemical structures of the organic matter select for specific methanogens to perform anaerobic digestion. An example is the members of Methanosaeta genus dominate the digestion of palm oil mill effluent (POME) and brewery waste. Modernizing wastewater treatment systems to incorporate higher diversity of microorganisms to decrease organic content in treatment is under active research in the field of microbiological and chemical engineering. Current new generations of Staged Multi-Phase Anaerobic reactors and Upflow Sludge Bed reactor systems are designed to have innovated features to counter high loading wastewater input, extreme temperature conditions, and possible inhibitory compounds.

Methanotroph

Methanotrophs (sometimes called methanophiles) are prokaryotes that metabolize methane as their only source of carbon and energy. They can be either bacteria or archaea and can grow aerobically or anaerobically, and require single-carbon compounds to survive.

General

Methanotrophs are especially common in or near environments where methane is produced, although also methanotrophs exist that can oxidize atmospheric methane. Their habitats include wetlands, soils, marshes, rice paddies, landfills, aquatic systems (lakes, oceans, streams) and more. They are of special interest to researchers studying global warming, as they play a significant role in the global methane budget, by reducing the amount of methane emitted to the atmosphere.

Methanotrophy is a special case of methylotrophy, using single-carbon compounds that are more reduced than carbon dioxide. Some methylotrophs, however, can also make use of multi-carbon compounds which differentiates them from methanotrophs that are usually fastidious methane and methanol oxidizers. The only facultative methanotrophs isolated to date are members of the genus Methylocella and Methylocystis.

In functional terms, methanotrophs are referred to as methane-oxidizing bacteria, however, methane-oxidizing bacteria encompass other organisms that are not regarded as sole methanotrophs. For this reason methane-oxidizing bacteria have been separated into four subgroups: two methane-assimilating bacteria (MAB) groups, the methanotrophs, and two autotrophic ammonia-oxidizing bacteria (AAOB).

Methanotroph classification

Methantrophs can be either bacteria or archaea. Which methanotroph species is present, is mainly determined by the availability of electron acceptors. Many types of methane oxidizing bacteria (MOB) are known. Differences in the method of formaldehyde fixation and membrane structure divide these bacterial methanotrophs into several groups. These include the Methylococcaceae and Methylocystaceae. Although both are included among the Proteobacteria, they are members of different subclasses. Other methanotroph species are found in the Verrucomicrobiae. Among the methanotrophic archaea, several subgroups are determined.

Aerobic methanotrophs

Under aerobic conditions, methanotrophs combine oxygen and methane to form formaldehyde, which is then incorporated into organic compounds via the serine pathway or the ribulose monophosphate (RuMP) pathway, and [Carbon dioxide], which is released. Type I and type X methanotrophs are part of the Gammaproteobacteria and they use the RuMP pathway to assimilate carbon. Type II methanotrophs are part of the Alphaproteobacteria and utilize the serine pathway of carbon assimilation. They also characteristically have a system of internal membranes within which methane oxidation occurs. No methanotrophic archaea are capable of using oxygen.

Anaerobic methanotrophs

Under anoxic conditions, methanotrophs use different electron acceptors for methane oxidation. This can happen in anoxic habitats such as marine or lake sediments, oxygen minimum zones, anoxic water columns, rice paddies and soils. Some specific methanotrophs can reduce nitrate or nitrite, and couple that to methane oxidation. Investigations in marine environments revealed that methane can be oxidized anaerobically by consortia of methane oxidizing archaea and sulfate-reducing bacteria. This type of Anaerobic oxidation of methane (AOM) mainly occurs in anoxic marine sediments. The exact mechanism behind this is still a topic of debate but the most widely accepted theory is that the archaea use the reversed methanogenesis pathway to produce carbon dioxide and another, unknown substance. This unknown intermediate is then used by the sulfate-reducing bacteria to gain energy from the reduction of sulfate to hydrogen sulfide. The anaerobic methanotrophs are not related to the known aerobic methanotrophs; the closest cultured relative to the anaerobic methanotrophs are the methanogens in the order Methanosarcinales. Metal-oxides, such as manganese and iron, can also be used as terminal electron acceptors by ANME. For this, no consortium is needed. ANME shuttle electrons directly to the abiotic particles, which get reduced chemically. 

In some cases, aerobic methane oxidation can take place in anoxic (no oxygen) environments. Candidatus Methylomirabilis oxyfera belongs to the phylum NC10 bacteria, and can catalyze nitrite reduction through an “intra-aerobic” pathway, in which internally produced oxygen is used to oxidise methane. In clear water lakes, methanotrophs can live in the anoxic water column, but receive oxygen from photosynthetic organisms, that they then directly consume to oxidise methane aerobically.

Special methanotroph species

Methylococcus capsulatus is utilised to produce animal feed from natural gas.

Recently, a new bacterium Candidatus Methylomirabilis oxyfera was identified that can couple the anaerobic oxidation of methane to nitrite reduction without the need for a syntrophic partner. Based on the studies of Ettwig et al., it is believed that M. oxyfera oxidizes methane anaerobically by utilizing the oxygen produced internally from the dismutation of nitric oxide into nitrogen and oxygen gas.

Properties

RuMP pathway in type I methanotrophs

 

Serine pathway in type II methanotrophs

 

Methanotrophs oxidize methane by first initiating reduction of an oxygen atom to H₂O₂ and transformation of methane to CH₃OH using methane monooxygenases (MMOs). Furthermore, two types of MMO have been isolated from methanotrophs: soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO). Cells containing pMMO have demonstrated higher growth capabilities and higher affinity for methane than sMMO containing cells. It is suspected that copper ions may play a key role in both pMMO regulation and the enzyme catalysis, thus limiting pMMO cells to more copper-rich environments than sMMO producing cells.

Bacteria (updated)

From Wikipedia, the free encyclopedia

Bacteria Temporal range: Archean or earlier – present Had'n Archean Proterozoic Pha.
Scanning electron micrograph of Escherichia coli rods
Scientific classification
Domain:	Bacteria Woese, Kandler & Wheelis, 1990
Phyla
Acidobacteria Actinobacteria Aquificae Armatimonadetes Bacteroidetes Caldiserica Chlamydiae Chlorobi Chloroflexi Chrysiogenetes Coprothermobacterota Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Elusimicrobia Fibrobacteres Firmicutes Fusobacteria Gemmatimonadetes Lentisphaerae Nitrospirae Planctomycetes Proteobacteria Spirochaetes Synergistetes Tenericutes Thermodesulfobacteria Thermotogae Verrucomicrobia
Synonyms
Eubacteria Woese & Fox, 1977

Bacteria are a type of biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep portions of Earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.

There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×10³⁰ bacteria on Earth, forming a biomass which exceeds that of all plants and animals. Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Data reported by researchers in October 2012 and published in March 2013 suggested that bacteria thrive in the Mariana Trench, which, with a depth of up to 11 kilometres, is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, "You can find microbes everywhere—they're extremely adaptable to conditions, and survive wherever they are."

The famous notion that bacterial cells in the human body outnumber human cells by a factor of 10:1 has been debunked. There are approximately 39 trillion bacterial cells in the human microbiota as personified by a "reference" 70 kg male 170 cm tall, whereas there are 30 trillion human cells in the body. This means that although they do have the upper hand in actual numbers, it is only by 30%, and not 900%.

The largest number exist in the gut flora, and a large number on the skin. The vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial, particularly in the gut flora. However several species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy, and bubonic plague. The most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year, mostly in sub-Saharan Africa. In developed countries, antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. In industry, bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium, copper and other metals in the mining sector, as well as in biotechnology, and the manufacture of antibiotics and other chemicals.

Once regarded as plants constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that evolved from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.

Etymology

Life timeline

-4500 —

–

-4000 —

–

-3500 —

–

-3000 —

–

-2500 —

–

-2000 —

–

-1500 —

–

-1000 —

–

-500 —

–

0 —

water

Single-celled life

photosynthesis

Eukaryotes

Multicellular life

Arthropods and Molluscs

Plants

Dinosaurs

Mammals

Flowers

Birds

Primates

 

 

 

 

 

 

 

 

 

 

 

←

Earth (−4540)

←

Earliest water

←

Earliest life

←

Earliest oxygen

←

Atmospheric oxygen

←

Oxygen crisis

←

Sexual reproduction

←

Earliest plants

←

Ediacaran biota

←

Cambrian explosion

←

Tetrapoda

←

Earliest apes

Phanerozoic

Proterozoic

Archean

Hadean

Pongola

Huronian

Cryogenian

Andean

Paleozoic

Quaternary

Ice Ages

The word bacteria is the plural of the New Latin bacterium, which is the latinisation of the Greek βακτήριον (bakterion), the diminutive of βακτηρία (bakteria), meaning "staff, cane", because the first ones to be discovered were rod-shaped.

Origin and early evolution

The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago. For about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago.

Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea. This involved the engulfment by proto-eukaryotic cells of alphaproteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya (sometimes in highly reduced form, e.g. in ancient "amitochondrial" protozoa). Later, some eukaryotes that already contained mitochondria also engulfed cyanobacteria-like organisms, leading to the formation of chloroplasts in algae and plants. This is known as primary endosymbiosis.

Morphology

Bacteria display many cell morphologies and arrangements

 

Bacteria display a wide diversity of shapes and sizes, called morphologies. Bacterial cells are about one-tenth the size of eukaryotic cells and are typically 0.5–5.0 micrometres in length. However, a few species are visible to the unaided eye—for example, Thiomargarita namibiensis is up to half a millimetre long and Epulopiscium fishelsoni reaches 0.7 mm. Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses. Some bacteria may be even smaller, but these ultramicrobacteria are not well-studied.

Most bacterial species are either spherical, called cocci (sing. coccus, from Greek kókkos, grain, seed), or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick). Some bacteria, called vibrio, are shaped like slightly curved rods or comma-shaped; others can be spiral-shaped, called spirilla, or tightly coiled, called spirochaetes. A small number of other unusual shapes have been described, such as star-shaped bacteria. This wide variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape predators.

The range of sizes shown by prokaryotes, relative to those of other organisms and biomolecules.

 

Many bacterial species exist simply as single cells, others associate in characteristic patterns: Neisseria form diploids (pairs), Streptococcus form chains, and Staphylococcus group together in "bunch of grapes" clusters. Bacteria can also group to form larger multicellular structures, such as the elongated filaments of Actinobacteria, the aggregates of Myxobacteria, and the complex hyphae of Streptomyces. These multicellular structures are often only seen in certain conditions. For example, when starved of amino acids, Myxobacteria detect surrounding cells in a process known as quorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells. In these fruiting bodies, the bacteria perform separate tasks; for example, about one in ten cells migrate to the top of a fruiting body and differentiate into a specialised dormant state called a myxospore, which is more resistant to drying and other adverse environmental conditions.

Bacteria often attach to surfaces and form dense aggregations called biofilms, and larger formations known as microbial mats. These biofilms and mats can range from a few micrometres in thickness to up to half a metre in depth, and may contain multiple species of bacteria, protists and archaea. Bacteria living in biofilms display a complex arrangement of cells and extracellular components, forming secondary structures, such as microcolonies, through which there are networks of channels to enable better diffusion of nutrients. In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms. Biofilms are also important in medicine, as these structures are often present during chronic bacterial infections or in infections of implanted medical devices, and bacteria protected within biofilms are much harder to kill than individual isolated bacteria.

Cellular structure

Structure and contents of a typical gram-positive bacterial cell (seen by the fact that only one cell membrane is present).

Intracellular structures

The bacterial cell is surrounded by a cell membrane which is made primarily of phospholipids. This membrane encloses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell. Unlike eukaryotic cells, bacteria usually lack large membrane-bound structures in their cytoplasm such as a nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic cells. However, some bacteria have protein-bound organelles in the cytoplasm which compartmentalize aspects of bacterial metabolism, such as the carboxysome. Additionally, bacteria have a multi-component cytoskeleton to control the localisation of proteins and nucleic acids within the cell, and to manage the process of cell division.

Many important biochemical reactions, such as energy generation, occur due to concentration gradients across membranes, creating a potential difference analogous to a battery. The general lack of internal membranes in bacteria means these reactions, such as electron transport, occur across the cell membrane between the cytoplasm and the outside of the cell or periplasm. However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane. These light-gathering complexes may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria.

An electron micrograph of Halothiobacillus neapolitanus cells with carboxysomes inside, with arrows highlighting visible carboxysomes. Scale bars indicate 100 nm.

 

Bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular bacterial chromosome of DNA located in the cytoplasm in an irregularly shaped body called the nucleoid. The nucleoid contains the chromosome with its associated proteins and RNA. Like all other organisms, bacteria contain ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from that of eukaryotes and Archaea.

Some bacteria produce intracellular nutrient storage granules, such as glycogen, polyphosphate, sulfur or polyhydroxyalkanoates. Certain bacterial species, such as the photosynthetic Cyanobacteria, produce internal gas vacuoles which they use to regulate their buoyancy, allowing them to move up or down into water layers with different light intensities and nutrient levels.

Extracellular structures

Around the outside of the cell membrane is the cell wall. Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by peptides containing D-amino acids. Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively. The cell wall of bacteria is also distinct from that of Archaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibiotic penicillin is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.

There are broadly speaking two different types of cell wall in bacteria, that classify bacteria into gram-positive bacteria and gram-negative bacteria. The names originate from the reaction of cells to the Gram stain, a long-standing test for the classification of bacterial species.

Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the gram-negative cell wall, and only the Firmicutes and Actinobacteria (previously known as the low G+C and high G+C gram-positive bacteria, respectively) have the alternative gram-positive arrangement. These differences in structure can produce differences in antibiotic susceptibility; for instance, vancomycin can kill only gram-positive bacteria and is ineffective against gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa. Some bacteria have cell wall structures that are neither classically gram-positive or gram-negative. This includes clinically important bacteria such as Mycobacteria which have a thick peptidoglycan cell wall like a gram-positive bacterium, but also a second outer layer of lipids.

In many bacteria, an S-layer of rigidly arrayed protein molecules covers the outside of the cell. This layer provides chemical and physical protection for the cell surface and can act as a macromolecular diffusion barrier. S-layers have diverse but mostly poorly understood functions, but are known to act as virulence factors in Campylobacter and contain surface enzymes in Bacillus stearothermophilus.

Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface

 

Flagella are rigid protein structures, about 20 nanometres in diameter and up to 20 micrometres in length, that are used for motility. Flagella are driven by the energy released by the transfer of ions down an electrochemical gradient across the cell membrane.

Fimbriae (sometimes called "attachment pili") are fine filaments of protein, usually 2–10 nanometres in diameter and up to several micrometres in length. They are distributed over the surface of the cell, and resemble fine hairs when seen under the electron microscope. Fimbriae are believed to be involved in attachment to solid surfaces or to other cells, and are essential for the virulence of some bacterial pathogens. Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation where they are called conjugation pili or sex pili (see bacterial genetics, below). They can also generate movement where they are called type IV pili.

Glycocalyx is produced by many bacteria to surround their cells, and varies in structural complexity: ranging from a disorganised slime layer of extracellular polymeric substances to a highly structured capsule. These structures can protect cells from engulfment by eukaryotic cells such as macrophages (part of the human immune system). They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.

The assembly of these extracellular structures is dependent on bacterial secretion systems. These transfer proteins from the cytoplasm into the periplasm or into the environment around the cell. Many types of secretion systems are known and these structures are often essential for the virulence of pathogens, so are intensively studied.

Endospores

Bacillus anthracis (stained purple) growing in cerebrospinal fluid

 

Certain genera of gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter, and Heliobacterium, can form highly resistant, dormant structures called endospores. Endospores develop within the cytoplasm of the cell; generally a single endospore develops in each cell. Each endospore contains a core of DNA and ribosomes surrounded by a cortex layer and protected by a multilayer rigid coat composed of peptidoglycan and a variety of proteins.

Endospores show no detectable metabolism and can survive extreme physical and chemical stresses, such as high levels of UV light, gamma radiation, detergents, disinfectants, heat, freezing, pressure, and desiccation. In this dormant state, these organisms may remain viable for millions of years, and endospores even allow bacteria to survive exposure to the vacuum and radiation in space. Endospore-forming bacteria can also cause disease: for example, anthrax can be contracted by the inhalation of Bacillus anthracis endospores, and contamination of deep puncture wounds with Clostridium tetani endospores causes tetanus.

Metabolism

Bacteria exhibit an extremely wide variety of metabolic types. The distribution of metabolic traits within a group of bacteria has traditionally been used to define their taxonomy, but these traits often do not correspond with modern genetic classifications. Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: the source of energy, the electron donors used, and the source of carbon used for growth.

Bacteria either derive energy from light using photosynthesis (called phototrophy), or by breaking down chemical compounds using oxidation (called chemotrophy). Chemotrophs use chemical compounds as a source of energy by transferring electrons from a given electron donor to a terminal electron acceptor in a redox reaction. This reaction releases energy that can be used to drive metabolism. Chemotrophs are further divided by the types of compounds they use to transfer electrons. Bacteria that use inorganic compounds such as hydrogren, carbon monoxide, or ammonia as sources of electrons are called lithotrophs, while those that use organic compounds are called organotrophs. The compounds used to receive electrons are also used to classify bacteria: aerobic organisms use oxygen as the terminal electron acceptor, while anaerobic organisms use other compounds such as nitrate, sulfate, or carbon dioxide.

Many bacteria get their carbon from other organic carbon, called heterotrophy. Others such as cyanobacteria and some purple bacteria are autotrophic, meaning that they obtain cellular carbon by fixing carbon dioxide. In unusual circumstances, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism.

Nutritional types in bacterial metabolism

Nutritional type	Source of energy	Source of carbon	Examples
Phototrophs	Sunlight	Organic compounds (photoheterotrophs) or carbon fixation (photoautotrophs)	Cyanobacteria, Green sulfur bacteria, Chloroflexi, or Purple bacteria
Lithotrophs	Inorganic compounds	Organic compounds (lithoheterotrophs) or carbon fixation (lithoautotrophs)	Thermodesulfobacteria, Hydrogenophilaceae, or Nitrospirae
Organotrophs	Organic compounds	Organic compounds (chemoheterotrophs) or carbon fixation (chemoautotrophs)	Bacillus, Clostridium or Enterobacteriaceae

In many ways, bacterial metabolism provides traits that are useful for ecological stability and for human society. One example is that some bacteria have the ability to fix nitrogen gas using the enzyme nitrogenase. This environmentally important trait can be found in bacteria of most metabolic types listed above. This leads to the ecologically important processes of denitrification, sulfate reduction, and acetogenesis, respectively. Bacterial metabolic processes are also important in biological responses to pollution; for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury (methyl- and dimethylmercury) in the environment. 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.

Growth and reproduction

Many bacteria reproduce through binary fission, which is compared to mitosis and meiosis in this image.

Unlike in multicellular organisms, increases in cell size (cell growth) and reproduction by cell division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction. Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes. In cell division, two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that help disperse the newly formed daughter cells. Examples include fruiting body formation by Myxobacteria and aerial hyphae formation by Streptomyces, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.

A colony of Escherichia coli

 

In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media, such as agar plates, are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms.

Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. However, in natural environments, nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This nutrient limitation has led the evolution of different growth strategies. Some organisms can 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 adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms. In nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and protection from environmental stresses. These relationships can be essential for growth of a particular organism or group of organisms (syntrophy).

Bacterial growth follows four phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth. The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced. The second phase of growth is the logarithmic 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), and the time it takes the cells to double is known as the generation time (g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The third phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair, antioxidant metabolism and nutrient transport. The final phase is the death phase where the bacteria run out of nutrients and die.

Genetics

Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Carsonella ruddii, to 12,200,000 base pairs (12.2 Mbp) in the soil-dwelling bacteria Sorangium cellulosum. There are many exceptions to this, for example some Streptomyces and Borrelia species contain a single linear chromosome, while some Vibrio species contain more than one chromosome. Bacteria can also contain plasmids, small extra-chromosomal DNAs that may contain genes for various useful functions such as antibiotic resistance, metabolic capabilities, or various virulence factors.

Bacteria genomes usually encode a few hundred to a few thousand genes. The genes in bacterial genomes are usually a single continuous stretch of DNA and although several different types of introns do exist in bacteria, these are much rarer than in eukaryotes.

Bacteria, as asexual organisms, inherit an identical copy of the parent's genomes and are clonal. However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations. Mutations come from errors made during the replication of DNA or from exposure to mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria. Genetic changes in bacterial genomes come from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate.

Some bacteria also transfer genetic material between cells. This can occur in three main ways. First, bacteria can take up exogenous DNA from their environment, in a process called transformation. Many bacteria can naturally take up DNA from the environment, while others must be chemically altered in order to induce them to take up DNA. The development of competence in nature is usually associated with stressful environmental conditions, and seems to be an adaptation for facilitating repair of DNA damage in recipient cells. The second way bacteria transfer genetic material is by transduction, when the integration of a bacteriophage introduces foreign DNA into the chromosome. Many types of bacteriophage exist, some simply infect and lyse their host bacteria, while others insert into the bacterial chromosome. Bacteria resist phage infection through restriction modification systems that degrade foreign DNA, and a system that uses CRISPR sequences to retain fragments of the genomes of phage that the bacteria have come into contact with in the past, which allows them to block virus replication through a form of RNA interference. The third method of gene transfer is conjugation, whereby DNA is transferred through direct cell contact. In ordinary circumstances, transduction, conjugation, and transformation involve transfer of DNA between individual bacteria of the same species, but occasionally transfer may occur between individuals of different bacterial species and this may have significant consequences, such as the transfer of antibiotic resistance. In such cases, gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions.

Behaviour

Movement

Transmission electron micrograph of Desulfovibrio vulgaris showing a single flagellum at one end of the cell. Scale bar is 0.5 micrometers long.

 

Many bacteria are motile and can move using a variety of mechanisms. The best studied of these are flagella, long filaments that are turned by a motor at the base to generate propeller-like movement. The bacterial flagellum is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly. The flagellum is a rotating structure driven by a reversible motor at the base that uses the electrochemical gradient across the membrane for power.

The different arrangements of bacterial flagella: A-Monotrichous; B-Lophotrichous; C-Amphitrichous; D-Peritrichous

 

Bacteria can use flagella in different ways to generate different kinds of movement. Many bacteria (such as E. coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and makes their movement a three-dimensional random walk. Bacterial species differ in the number and arrangement of flagella on their surface; some have a single flagellum (monotrichous), a flagellum at each end (amphitrichous), clusters of flagella at the poles of the cell (lophotrichous), while others have flagella distributed over the entire surface of the cell (peritrichous). The flagella of a unique group of bacteria, the spirochaetes, are found between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves.

Two other types of bacterial motion are called twitching motility that relies on a structure called the type IV pilus, and gliding motility, that uses other mechanisms. In twitching motility, the rod-like pilus extends out from the cell, binds some substrate, and then retracts, pulling the cell forward.

Motile bacteria are attracted or repelled by certain stimuli in behaviours called taxes: these include chemotaxis, phototaxis, energy taxis, and magnetotaxis. In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores. The myxobacteria move only when on solid surfaces, unlike E. coli, which is motile in liquid or solid media. 

Several Listeria and Shigella species move inside host cells by usurping the cytoskeleton, which is normally used to move organelles inside the cell. By promoting actin polymerisation at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.

Communication

A few bacteria have chemical systems that generate light. This bioluminescence often occurs in bacteria that live in association with fish, and the light probably serves to attract fish or other large animals.

Bacteria often function as multicellular aggregates known as biofilms, exchanging a variety of molecular signals for inter-cell communication, and engaging in coordinated multicellular behaviour.

The communal benefits of multicellular cooperation include a cellular division of labour, accessing resources that cannot effectively be used by single cells, collectively defending against antagonists, and optimising population survival by differentiating into distinct cell types. For example, bacteria in biofilms can have more than 500 times increased resistance to antibacterial agents than individual "planktonic" bacteria of the same species.

One type of inter-cellular communication by a molecular signal is called quorum sensing, which serves the purpose of determining whether there is a local population density that is sufficiently high that it is productive to invest in processes that are only successful if large numbers of similar organisms behave similarly, as in excreting digestive enzymes or emitting light.

Quorum sensing allows bacteria to coordinate gene expression, and enables them to produce, release and detect autoinducers or pheromones which accumulate with the growth in cell population.

Classification and identification

Streptococcus mutans visualised with a Gram stain

 

Phylogenetic tree showing the diversity of bacteria, compared to other organisms. Eukaryotes are coloured red, archaea green and bacteria blue.

Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components, such as DNA, fatty acids, pigments, antigens and quinones. While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species. Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasises molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridisation, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene. Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology, and Bergey's Manual of Systematic Bacteriology. The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria. 

The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. The archaea and eukaryotes are more closely related to each other than either is to the bacteria. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiology. However, due to the relatively recent introduction of molecular systematics and a rapid increase in the number of genome sequences that are available, bacterial classification remains a changing and expanding field. For example, a few biologists argue that the Archaea and Eukaryotes evolved from gram-positive bacteria.

The identification of bacteria in the laboratory is particularly relevant in medicine, where the correct treatment is determined by the bacterial species causing an infection. Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria. 

The Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls. The thick layers of peptidoglycan in the "gram-positive" cell wall stain purple, while the thin "gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (gram-positive cocci, gram-positive bacilli, gram-negative cocci and gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid-fastness on Ziehl–Neelsen or similar stains. Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology.

Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhoea, while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as blood, urine or spinal fluid, are cultured under conditions designed to grow all possible organisms. Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns (such as aerobic or anaerobic growth), patterns of hemolysis, and staining. 

As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing. However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea; but attempts to estimate the true number of bacterial diversity have ranged from 10⁷ to 10⁹ total species—and even these diverse estimates may be off by many orders of magnitude.

Interactions with other organisms

Overview of bacterial infections and main species involved.

Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiotic associations can be divided into parasitism, mutualism and commensalism. Due to their small size, commensal bacteria are ubiquitous and grow on animals and plants exactly as they will grow on any other surface. However, their growth can be increased by warmth and sweat, and large populations of these organisms in humans are the cause of body odour.

Predators

Some species of bacteria kill and then consume other microorganisms, these species are called predatory bacteria. These include organisms such as Myxococcus xanthus, which forms swarms of cells that kill and digest any bacteria they encounter. Other bacterial predators either attach to their prey in order to digest them and absorb nutrients, such as Vampirovibrio chlorellavorus, or invade another cell and multiply inside the cytosol, such as Daptobacter. These predatory bacteria are thought to have evolved from saprophages that consumed dead microorganisms, through adaptations that allowed them to entrap and kill other organisms.

Mutualists

Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids, such as butyric acid or propionic acid, and produce hydrogen, and methanogenic Archaea that consume hydrogen. The bacteria in this association are unable to consume the organic acids as this reaction produces hydrogen that accumulates in their surroundings. Only the intimate association with the hydrogen-consuming Archaea keeps the hydrogen concentration low enough to allow the bacteria to grow. 

In soil, microorganisms that reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking) carry out nitrogen fixation, converting nitrogen gas to nitrogenous compounds. 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 over 1,000 bacterial species in the normal human gut flora of the intestines can contribute to gut immunity, synthesise vitamins, such as folic acid, vitamin K and biotin, convert sugars to lactic acid (see Lactobacillus), as well as fermenting complex undigestible carbohydrates. The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion) and these beneficial bacteria are consequently sold as probiotic dietary supplements.

Pathogens

Colour-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells

 

If bacteria form a parasitic association with other organisms, they are classed as pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus, typhoid fever, diphtheria, syphilis, cholera, foodborne illness, leprosy and tuberculosis. A pathogenic cause for a known medical disease may only be discovered many years after, as was the case with Helicobacter pylori and peptic ulcer disease. Bacterial diseases are also important in agriculture, with bacteria causing leaf spot, fire blight and wilts in plants, as well as Johne's disease, mastitis, salmonella and anthrax in farm animals. 

Each species of pathogen has a characteristic spectrum of interactions with its human hosts. Some organisms, such as Staphylococcus or Streptococcus, can cause skin infections, pneumonia, meningitis and even overwhelming sepsis, a systemic inflammatory response producing shock, massive vasodilation and death. Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as the Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia, or urinary tract infection and may be involved in coronary heart disease. Finally, some species, such as Pseudomonas aeruginosa, Burkholderia cenocepacia, and Mycobacterium avium, are opportunistic pathogens and cause disease mainly in people suffering from immunosuppression or cystic fibrosis.

Bacterial infections may be treated with antibiotics, which are classified as bacteriocidal if they kill bacteria, or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics and each class inhibits a process that is different in the pathogen from that found in the host. An example of how antibiotics produce selective toxicity are chloramphenicol and puromycin, which inhibit the bacterial ribosome, but not the structurally different eukaryotic ribosome. Antibiotics are used both in treating human disease and in intensive farming to promote animal growth, where they may be contributing to the rapid development of antibiotic resistance in bacterial populations. Infections can be prevented by antiseptic measures such as sterilising the skin prior to piercing it with the needle of a syringe, and by proper care of indwelling catheters. Surgical and dental instruments are also sterilised to prevent contamination by bacteria. Disinfectants such as bleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection.

Significance in technology and industry

Bacteria, often lactic acid bacteria, such as Lactobacillus and Lactococcus, in combination with yeasts and moulds, have been used for thousands of years in the preparation of fermented foods, such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine and yogurt.

The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills. Fertiliser was added to some of the beaches in Prince William Sound in an attempt to promote the growth of these naturally occurring bacteria after the 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic wastes. In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals.

Bacteria can also be used in the place of pesticides in the biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a gram-positive, soil dwelling bacterium. Subspecies of this bacteria are used as a Lepidopteran-specific insecticides under trade names such as Dipel and Thuricide. Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators and most other beneficial insects.

Because of their ability to quickly grow and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields of molecular biology, genetics and biochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists can determine the function of genes, enzymes and metabolic pathways in bacteria, then apply this knowledge to more complex organisms. This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts of enzyme kinetic and gene expression data into mathematical models of entire organisms. This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested. This understanding of bacterial metabolism and genetics allows the use of biotechnology to bioengineer bacteria for the production of therapeutic proteins, such as insulin, growth factors, or antibodies.

Because of their importance for research in general, samples of bacterial strains are isolated and preserved in Biological Resource Centers. This ensures the availability of the strain to scientists worldwide.

History of bacteriology

Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscope.

 

Bacteria were first observed by the Dutch microscopist Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design. He then published his observations in a series of letters to the Royal Society of London. Bacteria were Leeuwenhoek's most remarkable microscopic discovery. They were just at the limit of what his simple lenses could make out and, in one of the most striking hiatuses in the history of science, no one else would see them again for over a century. His observations had also included protozoans which he called animalcules, and his findings were looked at again in the light of the more recent findings of cell theory. 

Christian Gottfried Ehrenberg introduced the word "bacterium" in 1828. In fact, his Bacterium was a genus that contained non-spore-forming rod-shaped bacteria, as opposed to Bacillus, a genus of spore-forming rod-shaped bacteria defined by Ehrenberg in 1835.

Louis Pasteur demonstrated in 1859 that the growth of microorganisms causes the fermentation process, and that this growth is not due to spontaneous generation. (Yeasts and moulds, 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, a pioneer in medical microbiology, worked on cholera, anthrax and tuberculosis. In his research into tuberculosis Koch finally proved the germ theory, for which he received a Nobel Prize in 1905. In Koch's postulates, he set out criteria to test if an organism is the cause of a disease, and these postulates are still used today.

Ferdinand Cohn is said to be a founder of bacteriology, studying bacteria from 1870. Cohn was the first to classify bacteria based on their morphology.

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 spirochaete 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 came in 1977 when Carl Woese recognised that archaea have a separate line of evolutionary descent from bacteria. This new phylogenetic taxonomy depended on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains, as part of the three-domain system.

Computer-made form

In April 2019, scientists at ETH Zurich reported the creation of the world's first bacterial genome, named Caulobacter ethensis-2.0, made entirely by a computer, although a related viable form of C. ethensis-2.0 does not yet exist.