Bacterial phyla

Euryarchaeota Nanoarchaeota Crenarchaeota Protozoa Algae Plantae Slime molds Animal Fungus Gram-positive bacteria Chlamydiae Chloroflexi Actinobacteria Planctomycetes Spirochaetes Fusobacteria Cyanobacteria Thermophiles Acidobacteria Proteobacteria
Phylogenetic tree showing the diversity of bacteria, compared to other organisms.[1] Eukaryotes are colored red, archaea green and bacteria blue.

The bacterial phyla are the major lineages (phyla or divisions) of the domain Bacteria.

In the scientific classification established by Carl von Linné,[2] each bacterial strain has to be assigned to a species (binary nomenclature), which is a lower level of a hierarchy of ranks. Currently, the most accepted mega-classification system is under the three-domain system, which is based on molecular phylogeny. In this system bacteria are members of the domain Bacteria[3] and "phylum" is the rank below domain as the rank "kindgom" is disused at present in bacterial taxonomy.[4][nb 1]

In this classification scheme Bacteria is (unofficially)[nb 2] subdivided into over 29 phyla with representatives cultured in a lab.[5][6][7] Many major clades of bacteria that exist but cannot currently be cultured are known solely via [[metagenomics] and are called candidate phyla. If these are included the number of phyla is 52 or higher. Therefore, the number of major phyla has increased from 12 identifiable lineages in 1987, to 52 as of 2003.[8]

Regarding the precise phylogeny at the base of the clade Bacteria, some scientists believe there may be a branching order, whereas other scientists, such as Norman Pace, believe the various Bacterial phyla represent a large hard polytomy (a simultaneous multiple speciation event).[9]

Contents

Molecular phylogenetics

Traditionally, phylogeny were inferred and taxonomy established based on studies of morphology. Recently molecular phylogenetics has been used to allow better elucidation of the evolutionary relationship of the species by analysing their DNA/protein sequences, for example their ribosomal DNA.[10] The lack of easily accessible morphological features, such as those present in animals and plants, hampered early efforts of classification and resulted in erroneous, distored and confusion classification, an examples of which, noted Carl Woese, is Pseudomonas whose etymology ironically matched its taxonomy, namely "false unit".[11]

Initial sub-division

Atomic structure of the 30S ribosomal Subunit from Thermus thermophilus of which 16S makes up part of. Proteins are shown in blue and the single RNA strand in orange.[12]

In 1987, Carl Woese, regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences:[13][11]

The "purple bacteria and relatives" were renamed Proteobacteria.[14]

The low and high CG content gram positive subdivisions were renamed Actinobacteria and Firmicutes divisions, making the number of phyla 12.[15] Until recently, it was believed than only Firmicutes and Actinobacteria were Gram-positive. The candidate phylum TM7 may be Gram positive.[16] Chloroflexi however possess a single bilayer, but stain negative (with some exceptions[17]).[18]

"Green non-sulfur bacteria and relatives" was renamed Chloroflexi.[19]

"Radioresistant micrococci and relatives" are commonly referred to as Deinococcus-Thermus clade,[20], although it has been prosed to call the clade Xenobacteria[21] or Hadobacteria[22] (latter is illegitimate[23]).

New cultured phyla

New species have been cultured since 1987, when Woese's review paper was published, that are sufficiently different to warrant a new phylum, mostly thermophiles and often also chemolithoautotrophs, such as Aquificae, which oxidises hydrogen gas. Other non-thermophiles, such as Acidobacteria, a ubiquitous phyla with divergent physiologies, have been found, some of which are chemolithotrophs, such as Nitrospira (nitrile-oxidising) or Leptospirillum (Fe-oxidising).[8], some proposed phyla however do not appear in LPSN as they were insufficiently described or are awaiting approval or it is debated if they may belong to a pre-existing phyla. An example of this is the genus Caldithrix, consisting of C. palaeochoryensis[24] and C.abyssi,[25] which is considered Deferribacteres,[26], however, it shares only 81% similarity with the other Deferribacteres (Deferribacter species and relatives)[25] and is considered a separate phylum by Rappé and Giovannoni.[8] Additionally the placement of the genus Geovibrio in the phylum Deferribacteres is debated.[27]

Uncultivated and metagenomics

With the advent of methods to analyse environmental DNA (metagenomics), the 16S rRNA of an extremely large number of undiscovered species have been found, showing that there are several whole phyla which have no known cultivable representative and that some phyla lack in culture major subdivisions as is the case for Verrucomicrobia and Chloroflexi.[8] The term Candidatus is used for proposed species for which the lack of information prevents it to be validated, such as where the only evidence is DNA sequence data, even if the whole genome has been sequenced.[28][29] When the species are members of whole phyla it is called a candidate division[30] and in 2003 there were 26 candidate divisions out of 52.[8] A candidate division was defined by in 1998 Hugenholtz and Pace, as a set of 16S ribosomal RNA sequences with less than 85% similarity.[31] Three candidate phyla were known before 1998, prior to the 85% threshold definition by Hugenholtz and Pace:

  • OS-K group (from Octopus spring)
  • Marine Group A (from Pacific ocean)
  • Termite Group 1 (from Termite gut, now Elusimicrobia)

Since then several other cadidate phyla were identified and accepted by Rappé and Giovannoni (2003):[8])

  • OP1, OP3, OP5 (now Caldiserica), OP8, OP9, OP10 (now Armatimonadetes), OP11 (obsidian pool, yellowstone national park)
  • WS2, WS3, WS5, WS6 (Wurtsmith contaminated aquifer)
  • SC3 and SC4 (from arid soil)
  • vadinBE97 (now Lentisphaerae)
  • NC10 (from flooded caves)
  • BRC1 (from bulk soil and rice roots)
  • ABY1 (from sediment)
  • Guyamas1 (from hydrothermal)
  • NKB19 (from activated sludge)
  • SBR1093 (from activated sludge)
  • TM6 and TM7 (Torf, Mittlere Schicht)

Since then a candidate phylum called Poribacteria was discovered, living in symbiosis with sponges and extensively studied.[32] (Note: the divergence of the major bacterial lineages predates sponges)

Other candidate phyla that have been the centre of some studies are TM7,[30] the genomes of organisms of which have even been sequenced (draft),[33] WS6[34] and Marine Group A.[8]

Two species of the candidate division OP10, which is now called Armatimonadetes, where recently cultured: Armatimonas rosea isolated from the rhizoplane of a reed in a lake in Japan[35] and Chthonomonas calidirosea from an isolate from geothermally heated soil at Hell's Gate, Tikitere, New Zealand.[36]

One species, Caldisericum exile, of the candidate division OP5 was cultured, leading to it being named Caldiserica.[37]

Termite Group 1 is now known as Elusimicrobia, after the ultramicrobacterium Elusimicrobium minutum was cultured.[38]

The candidate division VadinBE97 is now known as Lentisphaerae after Lentisphaera araneosa and Victivallis vadensis were cultured.[39]

Despite these lineages not being officially recognised, due to the ever increasing number of sequences belonging to non-existent phyla, ARB-Silva list 57 phyla, not only the 27 phyla with validly accepted species, but also 30 Candidate divisions (BD1-5, BHI80-139, BRC1, CK-1C4-19, EM19, GAL08, GOUTA4, Hyd24-12, JL-ETNP-Z39, Kazan-3B-28, LD1-PA38, MVP-21, NPL-UPA2, OC31, OD1, OP3, OP9, OP10, OP11, RF3, RsaHF231, SM2F11, SR1, TA06, TM6, TM7, WCHB1-60, WS3 and WS6)[40], while Ribosomal Database Project 10, list 29 phyla and 7 candidate divisions (OP10, OP11, OD1, BRC1, SR1, WS3, TM7)[41]

Superphyla

Despite the unclear branching order for most phyla, two groups of phyla have clear clustering and are referred to as superphyla: the FCB group and the PVC group.

The FCB group includes Chlorobi, Bacteroidetes, Fibrobacteres, Gemmatimonadates, Caldithrix and Marine group A.

The PVC group includes Chlamydiae, Lentisphaerae, Planctomycetes, Verrucomicrobia, Poribacteria and OP3.

Overview of phyla

Currently there are 29 phyla accepted by LPSN[7]. There are no fixed rules to the nomenclature of bacterial phyla, it was proposed that the suffix "-bacteria" be used for phyla,[42], but generally the name of the phylum is generally the plural of the type genus, with the exception of the Firmicutes, Cyanobacteria and Proteobacteria, whose names do not stem from a genus name (Actinobacteria instead is from Actinomyces).

Acidobacteria

The Acidobacteria (diderm Gram negative) is most abundant bacterial phylum in many soils, but its members are mostly uncultured. Additionally, they phenotypically diverse and include not only acidophiles, but also many non-acidophiles.[43] Generally its members divide slowly, exhibit slow metabolic rates under low-nutrient conditions and can tolerate well fluctuations in soil hydration.[44]

Actinobacteria

The Actinobacteria is a phylum of monoderm Gram positive bacteria, many of which notable secondary metabolite producers. There are only two phyla of monoderm Gram positive bacteria, the other being the Firmicutes; the actinobacteria generally have higher GC content so are sometimes called "high-CG Gram positive bacteria". Notable genera/species include Streptomyces (antibiotic production), Propionibacterium acnes (odorous skin commensal) and Propionibacterium freudenreichii (holes in Emmental)

Aquificae

The Aquificae (diderm Gram negative) contains only 14 genera (including Aquifex and Hydrogenobacter). The species are hyperthermophiles and chemolithotrophs (sulphur). According to some studies may be one of the most deep branching phyla.

Bacteroidetes

The Bacteroidetes (diderm Gram negative) is a member of the FBC superphylum. Some species are opportunistic pathogens, while other are the most common human gut commensal. Gained notority in the non-scientific comunity with the urban myth as a bacterial weight loss powder.[45]

Caldiserica

This phylum was formerly known as candidate division OP5, Caldisericum exile is the sole representative.

Chlamydiae

The Chlamydiae (diderms, weakly Gram negative) is a phylum of the PVC superphylum. It is composed of only 6 genera of obbligate intracellular pathogens with a complex life cycle. Species include Chlamydia trachomatis (chlamydia infection).

Chlorobi

Chlorobi is a member of the FBC superphylum. It contains only 7 genera of obligately anaerobic photoautotrophic bacteria, known colloquially as Green sulfur bacteria. The reaction centre for photosynthesis in Chlorobi and Chloroflexi (another photosynthetic group) is formed by a structures called the chlorosome as opposed to phycobilisomes of cyanobacteria (another photosynthetic group).[46]

Chloroflexi

Chloroflexi,diverse phylum including thermophiles and halorespirers, known colloquially as Green non-sulfur bacteria.

Chrysiogenetes

Chrysiogenetes, only 3 genera (Chrysiogenes arsenatis, Desulfurispira natronophila, Desulfurispirillum alkaliphilum)

Cyanobacteria

Cyanobacteria, major photosynthetic clade believed to have caused Earth's oxygen atmosphere, also known as the blue-green algae

Deferribacteres

Deferribacteres

Deinococcus-Thermus

Deinococcus-Thermus, Deinococcus radiodurans and Thermus aquaticus are "commonly known" species of this phyla

Dictyoglomi

Dictyoglomi

Elusimicrobia

Elusimicrobia, formerly candidate division Termite Group 1

Fibrobacteres

Fibrobacteres, member of the FBC superphylum.

Firmicutes

Firmicutes, Low-G+C Gram positive species most often spore-forming, in two/three classes: the class Bacilli such as the Bacillus spp. (e.g. B. anthracis, a pathogen, and B. subtilis, biotechnologically useful), lactic acid bacteria (e.g. Lactobacillus casei in yoghurt, Oenococcus oeni in malolactic fermentation, Streptococcus pyogenes, pathogen), the class Clostridia of mostly anaerobic sulphite-reducing saprophytic species, includes the genus Clostridium (e.g. the pathogens C. dificile, C. tetani, C. botulinum and the biotech C. acetobutylicum)

Fusobacteria

Fusobacteria

Gemmatimonadetes

Gemmatimonadetes, member of the FBC superphylum.

Lentisphaerae

Lentisphaerae, formerly clade VadinBE97, member of the PVC superphylum.

Nitrospira

Nitrospira

Planctomycetes

Planctomycetes, member of the PVC superphylum.

Proteobacteria

Proteobacteria, contains most of the "commonly known" species, such as Escherichia coli or Pseudomonas aeruginosa

Spirochaetes

Spirochaetes, notable for compartmentalisation and species include Borrelia burgdorferi, which causes Lyme disease

Synergistetes

The Synergistetesis a phylum whose members are diderm Gram negative, rod-shaped obligate anaerobes, some of which human commanals.[47]

Tenericutes

The Tenericutes includes the class Mollicutes, formerly/debatedly of the phylum Firmicutes (sister clades). Despite their monoderm Gram positive relatives, they lack peptidoglycan and instead possess mycolic acid. Notable genus: Mycoplasma.

Thermodesulfobacteria

The Thermodesulfobacteria is a phylum composed of only three genera in the same family (Thermodesulfobacteriaceae: Caldimicrobium, Thermodesulfatator and Thermodesulfobacterium). The members of the phylum are thermophilic sulphate-reducers.

Thermotogae

The Thermotogae is a phylum of whose members possess an unsual outer membrane called the toga and are hyperthermophilic obligate anaerobic fermenters.

Verrucomicrobia

Verrucomicrobia is a phylum of the PVC superphylum. Like the Planctomycetes species, its members possess a compartmentalised cell plan with a condensed nucleoid and the ribosomes pirellulosome (enclosed by the intracytoplasmic membrane) and paryphoplasm compartment between the intracytoplasmic membrane and cytoplasmic membrane.[48]

Branching order

The branching order of the phyla of bacteria is unclear.[9] Different studies arrive at different results due to different datasets and methods. For example, in studies using 16S and few other sequences Thermotogae and Aquificae appear as the most basal phyla, whereas in several phylogenomic studies, Firmicutes are the most basal.

  • Branching order of bacterial phyla (Woese, 1987)
  • Branching order of bacterial phyla (Rappe and Giovanoni, 2004)
  • Branching order of bacterial phyla after ARB Silva Living Tree
  • Branching order of bacterial phyla (Ciccarelli et al., 2006)
  • Branching order of bacterial phyla (Battistuzzi et al.,2004)
  • Branching order of bacterial phyla (Gupta, 2001)
  • Branching order of bacterial phyla (Cavalier-Smith, 2002)

See also

Footnotes

  1. ^ Past editions of Brock Biology of Microorganisms have referred to the phyla as kingdoms.[5]
  2. ^ For historical reasons, taxa above the rank of class are not covered by the Rules of the Bacteriological Code (1990 Revision),[11][4] consequently there is no "official" nomenclature, but there are several authorities in the field, such as Bergey's Manual of Systematic Bacteriology, which contains a taxonomy outline[6] and the journal International Journal of Systematic Bacteriology/International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM), on which the List of Prokaryotic names with Standing in Nomenclature (LPSN) repository is based.[49]

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  47. ^ PMID 20079831 (PubMed)
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  48. ^ doi:10.1186/1471-2180-9-5
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