In the scientific classification established by Carl von Linné, 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 that system, bacteria are members of the domain Bacteria and "phylum" is the rank below domain, since the rank "kingdom" is disused at present in bacterial taxonomy. When bacterial nomenclature was controlled under the Botanical Code, the term division was used, but now that bacterial nomenclature (with the exception of cyanobacteria) is controlled under the Bacteriological Code, the term phylum is preferred.
In this classification scheme, Bacteria is (unofficially) subdivided into 30 phyla with representatives cultured in a lab. Many major clades of bacteria that cannot currently be cultured are known solely and somewhat indirectly through metagenomics, the analysis of bulk samples from the environment. If these possible clades, candidate phyla, 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 30 in 2014, or over 50 including candidate phyla. The total number has been estimated to exceed 1,000 bacterial phyla.
At the base of the clade Bacteria, close to the last universal common ancestor of all living things, some scientists believe there may be a definite branching order, whereas other scientists, such as Norman Pace, believe there was a large hard polytomy, a simultaneous multiple speciation event.
Traditionally, phylogeny was inferred and taxonomy established based on studies of morphology. Recently molecular phylogenetics has been used to allow better elucidation of the evolutionary relationship of species by analysing their DNA and protein sequences, for example their ribosomal DNA. The lack of easily accessible morphological features, such as those present in animals and plants, hampered early efforts of classification and resulted in erroneous, distorted and confused classification, an example of which, noted Carl Woese, is Pseudomonas whose etymology ironically matched its taxonomy, namely "false unit".
- Purple Bacteria and their relatives (later renamed Proteobacteria)
- alpha subdivision (purple non-sulfur bacteria, rhizobacteria, Agrobacterium, Rickettsiae, Nitrobacter)
- beta subdivision (Rhodocyclus, (some) Thiobacillus, Alcaligenes, Spirillum, Nitrosovibrio)
- gamma subdivision (enterics, fluorescent pseudomonads, purple sulfur bacteria, Legionella, (some) Beggiatoa)
- delta subdivision (Sulfur and sulfate reducers (Desulfovibrio), Myxobacteria, Bdellovibrio)
- Gram-positive Eubacteria
- High-G+C species (later renamed Actinobacteria) (Actinomyces, Streptomyces, Arthrobacter, Micrococcus, Bifidobacterium)
- Low-G+C species (later renamed Firmicutes) (Clostridium, Peptococcus, Bacillus, Mycoplasma)
- Photosynthetic species (Heliobacteria)
- Species with Gram-negative walls (Megasphaera, Sporomusa)
- Cyanobacteria and chloroplasts (Aphanocapsa, Oscillatoria, Nostoc, Synechococcus, Gloeobacter, Prochloron)
- Spirochetes and relatives
- Green sulfur bacteria (Chlorobium, Chloroherpeton)
- Bacteroides, Flavobacteria and relatives (later renamed Bacteroidetes
- Planctomyces and relatives (later renamed Planctomycetes)
- Planctomyces group (Planctomyces, Pasteuria [sic])
- Thermophiles (Isocystis pallida)
- Chlamydiae (Chlamydia psittaci, Chlamydia trachomatis)
- Radioresistant micrococci and relatives (now commonly referred to as Deinococcus–Thermus or Thermi)
- Green non-sulfur bacteria and relatives (later renamed Chloroflexi)
- Thermotogae (Thermotoga maritima)
New cultured phyla
New species have been cultured since 1987, when Woese's review paper was published, that are sufficiently different that they warrant a new phylum. Most of these are thermophiles and often also chemolithoautotrophs, such as Aquificae, which oxidises hydrogen gas. Other non-thermophiles, such as Acidobacteria, a ubiquitous phylum with divergent physiologies, have been found, some of which are chemolithotrophs, such as Nitrospira (nitrile-oxidising) or Leptospirillum (Fe-oxidising)., 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 phylum. An example of this is the genus Caldithrix, consisting of C. palaeochoryensis and C. abyssi, which is considered Deferribacteres, however, it shares only 81% similarity with the other Deferribacteres (Deferribacter species and relatives) and is considered a separate phylum by Rappé and Giovannoni. Additionally the placement of the genus Geovibrio in the phylum Deferribacteres is debated.
Uncultivated phyla 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. 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. When the species are members of a whole phylum it is called a candidate division (or candidate phylum) and in 2003 there were 26 candidate phyla out of 52. A candidate phylum was defined by Hugenholtz and Pace in 1998, as a set of 16S ribosomal RNA sequences with less than 85% similarity to already-described phyla. More recently an even lower threshold of 75% was proposed. Three candidate phyla were known before 1998, prior to the 85% threshold definition by Hugenholtz and Pace:
- OS-K group (from Octopus spring, Yellowstone National Park)
- Marine Group A (from Pacific ocean)
- Termite Group 1 (from a Reticulitermes speratus termite gut, now Elusimicrobia)
- OP1, OP3, OP5 (now Caldiserica), OP8, OP9 (now Atribacteria), 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, paddy fields, intertidal zones, etc)
- BRC1 (from bulk soil and rice roots)
- ABY1 (from sediment)
- Guyamas1 (from hydrothermal vents)
- GN01, GN02, GN04 (from a Guerrero Negro hypersaline microbial mat)
- NKB19 (from activated sludge)
- SBR1093 (from activated sludge)
- TM6 and TM7 (Torf, Mittlere Schicht lit. "peat, middle layer")
Since then a candidate phylum called Poribacteria was discovered, living in symbiosis with sponges and extensively studied. (Note: the divergence of the major bacterial lineages predates sponges) Another candidate phylum, called Tectomicrobia, was also found living in symbiosis with sponges. And Nitrospina gracilis, which had long eluded phylogenetic placement, was proposed to belong to a new phylum, Nitrospinae.
Other candidate phyla that have been the center of some studies are TM7, the genomes of organisms of which have even been sequenced (draft), WS6 and Marine Group A.
Two species of the candidate phylum OP10, which is now called Armatimonadetes, where recently cultured: Armatimonas rosea isolated from the rhizoplane of a reed in a lake in Japan and Chthonomonas calidirosea from an isolate from geothermally heated soil at Hell's Gate, Tikitere, New Zealand.
- Candidate phylum ACD58 was renamed Berkelbacteria
- Candidate phylum CD12 (also known as candidate phylum BHI80-139) was renamed Aerophobetes
- Candidate phylum EM19 was renamed Calescamantes
- Candidate phylum GN02 (also known as candidate phylum BD1-5) was renamed Gracilibacteria
- Candidate phylum KSB3 was renamed Modulibacteria
- Candidate phylum NKB19 was renamed Hydrogenedentes
- Candidate phylum OctSpa1-106 was renamed Fervidibacteria
- Candidate phylum OD1 was renamed Parcubacteria
- Candidate phylum OP1 was renamed Acetothermia
- Candidate phylum OP3 was renamed Omnitrophica
- Candidate phylum OP8 was renamed Aminicenantes
- Candidate phylum OP9 (also known as candidate phylum JS1) was renamed Atribacteria
- Candidate phylum OP11 was renamed Microgenomates
- Candidate phylum PER was renamed Perigrinibacteria
- Candidate phylum SAR406 (also known as candidate phylum Marine Group A) was renamed Marinimicrobia
- Candidate phylum SR1 was renamed Absconditabacteria
- Candidate phylum TM6 was renamed Dependentiae
- Candidate phylum TM7 was renamed Saccharibacteria
- Candidate phylum WS3 was renamed Latescibacteria
- Candidate phylum WWE1 was renamed Cloacimonetes
- Candidate phylum WWE3 was renamed Katanobacteria
- Candidate phylum ZB1 was renamed Ignavibacteriae
Despite these lineages not being officially recognised (due to the ever-increasing number of sequences belonging to undescribed phyla) the ARB-Silva database lists 67 phyla, including 37 candidate phyla (Acetothermia, Aerophobetes, Aminicenantes, aquifer1, aquifer2, Atribacteria, Calescamantes, CKC4, Cloacimonetes, GAL08, GOUTA4, Gracilibacteria, Fermentibacteria (Hyd24-12), Hydrogenedentes, JL-ETNP-Z39, Kazan-3B-09, Latescibacteria, LCP-89, LD1-PA38, Marinimicrobia, Microgenomates, OC31, Omnitrophica, Parcubacteria, PAUC34f, RsaHF231, S2R-29, Saccharibacteria, SBYG-2791, SHA-109, SM2F11, SR1, TA06, TM6, WCHB1-60, WD272, and WS6), the Ribosomal Database Project 10, lists 49 phyla, including 20 candidate phyla (Acetothermia, Aminicenantes, Atribacteria, BRC1, Calescamantes, Cloacimonetes, Hydrogenedentes, Ignavibacteriae, Latescibacteria, Marinimicrobia, Microgenomates, Nitrospinae, Omnitrophica, Parcubacteria, Poribacteria, SR1, Saccharibacteria, WPS-1, WPS-2, and ZB3), and NCBI lists 120 phyla, including 90 candidate phyla (AC1, Acetothermia, Aerophobetes, Aminicenantes, Atribacteria, Berkelbacteria, BRC1, CAB-I, Calescamantes, CPR1, CPR2, CPR3, EM 3, Fervidibacteria, GAL15, GN01, GN03, GN04, GN05, GN06, GN07, GN08, GN09, GN10, GN11, GN12, GN13, GN14, GN15, Gracilibacteria, Fermentibacteria (Hyd24-12), Hydrogenedentes, JL-ETNP-Z39, KD3-62, kpj58rc, KSA1, KSA2, KSB1, KSB2, KSB3, KSB4, Latescibacteria, marine group A, Marinimicrobia, Microgenomates, MSBL2, MSBL3, MSBL4, MSBL5, MSBL6, NC10, Nitrospinae, NPL-UPA2, NT-B4, Omnitrophica, OP2, OP4, OP6, OP7, OS-K, Parcubacteria, Peregrinibacteria, Poribacteria, RF3, Saccharibacteria, SAM, SBR1093, Sediment-1, Sediment-2, Sediment-3, Sediment-4, SPAM, SR1, TA06, TG2, TM6, VC2, WOR-1, WOR-3, WPS-1, WPS-2, WS1, WS2, WS4, WS5, WS6, WWE3, WYO, ZB3, and Zixibacteria).
Despite the unclear branching order for most bacterial phyla, several groups of phyla have clear clustering and are referred to as superphyla.
The FCB Group
The FCB group (now called Sphingobacteria) includes Bacteroidetes, the unplaced genus Caldithrix, Chlorobi, candidate phylum Cloacimonetes, Fibrobacteres, Gemmatimonadates, candidate phylum Ignavibacteriae, candidate phylum Latescibacteria, candidate phylum Marinimicrobia, and candidate phylum Zixibacteria.
The PVC Group
The PVC group (now called Planctobacteria) includes Chlamydiae, Lentisphaerae, candidate phylum Omnitrophica, Planctomycetes, candidate phylum Poribacteria, and Verrucomicrobia.
The proposed superphylum, Patescibacteria, includes candidate phyla Gracilibacteria, Microgenomates, Parcubacteria, and Saccharibacteria and possibly Dependentiae. These same candidate phyla, along with candidate phyla Berkelbacteria, CPR2, CPR3, Kazan, Perigrinibacteria, SM2F11, WS6, and WWE3 were more recently proposed to belong to the larger CPR Group. To complicate matters, it has been suggested that several of these phyla are themselves actually superphyla (see the section on cryptic superphyla below).
Proteobacteria as superphylum
It has been proposed that several of the classes of the phylum Proteobacteria are phyla in their own right, which would make Proteobacteria a superphylum. It was recently proposed that the class Epsilonproteobacteria be combined with the order Desulfurellales to create the new phylum Epsilonbacteraeota.
Several candidate phyla (Microgenomates, Omnitrophica, Parcubacteria, and Saccharibacteria) and several accepted phyla (Elusimicrobia, Caldiserica, and Armatimonadetes) have been suggested to actually be superphyla that were incorrectly described as phyla because rules for defining a bacterial phylum are lacking. For example, it is suggested that candidate phylum Microgenomates is actually a superphylum that encompasses 28 subordinate phyla and that phylum Elusimocrobia is actually a superphylum that encompasses 7 subordinate phyla.
Overview of phyla
As of January 2016, there are 30 phyla in the domain "Bacteria" accepted by LPSN. There are no fixed rules to the nomenclature of bacterial phyla. It was proposed that the suffix "-bacteria" be used for phyla, 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).
The Acidobacteria (diderm Gram negative) is the most abundant bacterial phylum in many soils, but its members are mostly uncultured. Additionally, they are phenotypically diverse and include not only acidophiles, but also many non-acidophiles. Generally its members divide slowly, exhibit slow metabolic rates under low-nutrient conditions and can tolerate fluctuations in soil hydration.
The Actinobacteria is a phylum of monoderm Gram positive bacteria, many of which are 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), Cutibacterium acnes (odorous skin commensal) and Propionibacterium freudenreichii (holes in Emmental)
The Aquificae (diderm Gram negative) contains only 14 genera (including Aquifex and Hydrogenobacter). The species are hyperthermophiles and chemolithotrophs (sulphur). According to some studies, this may be one of the most deep branching phyla.
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 bacteria. Gained notoriety in the non-scientific community with the urban myth of a bacterial weight loss powder.
This phylum was formerly known as candidate phylum OP5, Caldisericum exile is the sole representative.
The Chlamydiae (diderms, weakly Gram negative) is a phylum of the PVC superphylum. It is composed of only 6 genera of obligate intracellular pathogens with a complex life cycle. Species include Chlamydia trachomatis (chlamydia infection).
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).
Chloroflexi, a diverse phylum including thermophiles and halorespirers, are known colloquially as Green non-sulfur bacteria.
Chrysiogenetes, only 3 genera (Chrysiogenes arsenatis, Desulfurispira natronophila, Desulfurispirillum alkaliphilum)
Cyanobacteria, major photosynthetic clade believed to have caused Earth's oxygen atmosphere, also known as the blue-green algae
Deinococcus–Thermus, Deinococcus radiodurans and Thermus aquaticus are "commonly known" species of this phylum.
Elusimicrobia, formerly candidate phylum Termite Group 1
Fibrobacteres, member of the FBC superphylum.
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)
Gemmatimonadetes, member of the FBC superphylum.
Lentisphaerae, formerly clade VadinBE97, member of the PVC superphylum.
Planctomycetes, member of the PVC superphylum.
The Tenericutes includes the class Mollicutes, formerly/debatedly of the phylum Firmicutes (sister clades). Despite their monoderm Gram-positive relatives, they lack peptidoglycan. Notable genus: Mycoplasma.
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.
The Thermotogae is a phylum of whose members possess an unusual outer envelope called the toga and are mostly hyperthermophilic obligate anaerobic fermenters.
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.
The branching order of the phyla of bacteria is unclear. 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)
- Past editions of Brock Biology of Microorganisms have referred to the phyla as kingdoms.
- For historical reasons, taxa above the rank of class are not covered by the Rules of the Bacteriological Code (1990 Revision), 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 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.
- Until recently, it was believed than only Firmicutes and Actinobacteria were Gram-positive. However, the candidate phylum TM7 may also be Gram positive. Chloroflexi however possess a single bilayer, but stain negative (with some exceptions).
- Pasteuria is now assigned to phylum Bacilli, not to phylum Planctomycetes.
- It has been proposed to call the clade Xenobacteria or Hadobacteria (the latter is considered an illegitimate name).
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