In this classification scheme, Bacteria is (unofficially)[Note 2] 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".
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.
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:
TM6 and TM7 (Torf, Mittlere Schichtlit. "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.
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 (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).
The proposed superphylum, Terrabacteria, includes Actinobacteria, Cyanobacteria, Deinococcus–Thermus, Chloroflexi, Firmicutes, and candidate phylum OP10.
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.
As of January 2016[update], 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 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 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.
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).
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.
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.
^ 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).
^ abLapage, S. P.; Sneath PHA; Lessel, E. F.; Skerman VBD; Seeliger HPR; Clark, W. A. (1992). Lapage SP; Sneath PHA; Lessel EF; Skerman VBD; Seeliger HPR; Clark WA (eds.). International Code of Nomenclature of Bacteria, 1990 Revision. Washington (DC): American Society for Microbiology. ISBN978-1-55581-039-9. PMID21089234.
^ abMadigan M (2009). Brock Biology of Microorganisms. San Francisco: Pearson/Benjamin Cummings. ISBN978-0-13-232460-1.
^Stackebrandt; et al. (1988). "Proteobacteria classis nov., a name for the phylogenetic taxon that includes the "purple bacteria and their relatives"". Int. J. Syst. Bacteriol. 38 (3): 321–325. doi:10.1099/00207713-38-3-321.
^Yabe, S.; Aiba, Y.; Sakai, Y.; Hazaka, M.; Yokota, A. (2010). "Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria". International Journal of Systematic and Evolutionary Microbiology. 61 (4): 903–910. doi:10.1099/ijs.0.024877-0. PMID20495028.
^ abStackebrandt, E.; Rainey, F. A.; Ward-Rainey, N. L. (1997). "Proposal for a New Hierarchic Classification System, Actinobacteria classis nov". International Journal of Systematic Bacteriology. 47 (2): 479–491. doi:10.1099/00207713-47-2-479.
^Bergey's Manual of Systematic Bacteriology 1st Ed.
^Cavalier-Smith, T (2002). "The neomuran origin of Archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 1): 7–76. doi:10.1099/00207713-52-1-7. PMID11837318.
^Miroshnichenko ML; et al. (2009). "Caldithrix palaeochoryensis sp. nov., a thermophilic, anaerobic, chemo-organotrophic bacterium from a geothermally heated sediment, and emended description of the genus Caldithrix". International Journal of Systematic and Evolutionary Microbiology. 60 (Pt 9): 2120–3. doi:10.1099/ijs.0.016667-0. PMID19854873.
^ abMiroshnichenko ML; et al. (2003). "Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage". International Journal of Systematic and Evolutionary Microbiology. 53 (Pt 1): 323–9. doi:10.1099/ijs.0.02390-0. PMID12656191.
^Murray, R. G. E.; Schleifer, K. H. (1994). "Taxonomic Notes: A Proposal for Recording the Properties of Putative Taxa of Procaryotes". International Journal of Systematic Bacteriology. 44 (1): 174–6. doi:10.1099/00207713-44-1-174. PMID8123559.
^Tamaki H; et al. (2010). "Armatimonas rosea gen. nov., sp. nov., a Gram-negative, aerobic, chemoheterotrophic bacterium of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10". International Journal of Systematic and Evolutionary Microbiology. 61 (Pt 6): 1442–7. doi:10.1099/ijs.0.025643-0. PMID20622056.
^Lee KCY; et al. (2010). "Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic microorganism of a novel bacterial class, Chthonomonadetes classis. nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10". International Journal of Systematic and Evolutionary Microbiology. 61 (Pt 10): 2482–90. doi:10.1099/ijs.0.027235-0. PMID21097641.
^Mori K; et al. (2009). "Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov". International Journal of Systematic and Evolutionary Microbiology. 59 (Pt 11): 2894–8. doi:10.1099/ijs.0.010033-0. PMID19628600.
^Cho JC; et al. (2004). "Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae". Environmental Microbiology. 6 (6): 611–21. doi:10.1111/j.1462-2920.2004.00614.x. PMID15142250.
^Albertsen M; et al. (2013). "Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes". Nat. Biotechnol. 31 (6): 533–8. doi:10.1038/nbt.2579. PMID23707974.
^Podosokorskaya OA; et al. (2013). "Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria, and a proposal of a novel bacterial phylum Ignavibacteriae". Environ. Microbiol. 15 (6): 1759–71. doi:10.1111/1462-2920.12067. PMID23297868.
^ abBattistuzzi, F. U.; Hedges, S. B. (6 November 2008). "A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land". Molecular Biology and Evolution. 26 (2): 335–343. doi:10.1093/molbev/msn247. PMID18988685.
^Murray, R. G. E. 1984. The higher taxa, or, a place for everything…?, p. 33. In N. R. Krieg and J. G. Holt (ed.), Bergey’s manual of systematic bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore.
^Kielak, A.; Pijl, A. S.; Van Veen, J. A.; Kowalchuk, G. A. (2008). "Phylogenetic diversity of Acidobacteria in a former agricultural soil". The ISME Journal. 3 (3): 378–382. doi:10.1038/ismej.2008.113. PMID19020558.
^Marchandin HLN; et al. (2010). "Phylogeny, diversity and host specialization in the phylum Synergistetes with emphasis on strains and clones of human origin". Research in Microbiology. 161 (2): 91–100. doi:10.1016/j.resmic.2009.12.008. PMID20079831.