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The Thermotogae are a phylum of the domain Bacteria. The phylum Thermotogae is composed of Gram-negative
Gram-negative
staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria.[1][2]

Contents

1 Characteristics 2 Taxonomy 3 Molecular signatures 4 Phylogeny 5 Taxonomy 6 References

Characteristics[edit] The name of this phylum is derived from the existence of many of these organisms at high temperatures along with the characteristic sheath structure, or "toga", surrounding the cells of these species.[3] Recently, some Thermotogae existing at moderate temperatures have also been identified.[4] Although Thermotogae species exhibit Gram-negative staining, they are bounded by a single-unit lipid membrane, hence they are monoderm bacteria.[2][5][6] Because of the ability of some Thermotogae species to thrive at high temperatures, they are considered attractive targets for use in industrial processes.[7] The metabolic ability of Thermotogae to utilize different complex-carbohydrates for production of hydrogen gas led to these species being cited as a possible biotechnological source for production of energy alternative to fossil fuels.[8] Taxonomy[edit] This phylum presently consists of a single class (Thermotogae), four orders (Thermotogales, Kosmotogales, Petrotogales, and Mesoaciditogales) and five families (Thermatogaceae, Fervidobacteriaceae, Kosmotogaceae, Petrotogaceae, and Mesoaciditogaceae).[1][2][3][9][10][11][12] It contains a total of 15 genera and 52 species.[13] In the 16S rRNA trees, the Thermotogae have been observed to branch with the Aquificae (another phylum comprising hyperthermophilic organisms) in close proximity to the archaeal-bacterial branch point.[1][3] However, a close relationship of the Thermotogae to the Aquificae, and the deep branching of the latter group of species, is not supported by phylogenetic studies based upon other gene/protein sequences.[2][14][15][16][17] and also by conserved signature indels in several highly conserved universal proteins.[18][19] The Thermotogae have also been scrutinized for their supposedly profuse Lateral gene transfer
Lateral gene transfer
with Archaeal organisms.[20][21] However, recent studies based upon more robust methodologies suggest that incidence of LGT between Thermotogae and other groups including Archaea
Archaea
is not as high as suggested in earlier studies.[22][23][9][24] Molecular signatures[edit] Until recently, no biochemical or molecular markers were known that could distinguish the species from the phylum Thermotogae from all other bacteria.[1] However, a recent comparative genomic study has identified large numbers of conserved signature indels (CSIs) in important proteins that are specific for either all Thermotogae species or a number of its subgroups.[2][9] Many of these CSIs in important housekeeping proteins such as Pol1, RecA, and TrpRS, and ribosomal proteins L4, L7/L12, S8, S9, etc. are uniquely present in different sequenced Thermotogae species providing novel molecular markers for this phylum. These studies also identified CSIs specific for each order and each family.[12] These indels are the premise for the current taxonomic organization of the Thermotogae, and are strongly supported by phylogenomic analyses.[2][9] Additional CSIs have also been found that are specific for Thermotoga, Pseudothermotoga, Fervidobacterium, and Thermosipho. These CSIs are specific for all species within each respective genus, and absent in all other bacteria, thus are specific markers.[2][9] A clade consisting of the deep-branching species Petrotoga mobilis, Kosmotoga olearia, and Thermotogales bacterium mesG1 was also supported by seven CSIs.[9] Additionally, some CSIs that provided evidence of LGT among the Thermotogae and other prokaryotic groups were also reported.[9] The newly discovered molecular markers provide novel means for identification and circumscription of species from the phylum in molecular terms and for future revisions to its taxonomy. Phylogeny[edit] See also: Bacterial taxonomy The phylogeny based on the work of the All-Species Living Tree Project.[25]

Thermotogales

Thermotogaceae

Thermotoga

T. naphthophila

T. petrophila

T. maritima (type sp.)

T. neapolitana

Pseudothermotoga

P. hypogea

P. thermarum

P. subterranea

P. elfii

P. lettingae

Fervidobacteriaceae

Fervidobacterium

F. changbaicum

F. islandicum

F. nodosum (type sp.)

F. gondwanense

F. riparium

Thermosipho

T. activus

T. geolei

T. atlanticus

T. affectus

T. melanesiensis

T. globiformans

T. africanus (type sp.)

T. japonicus

Kosmotogaceae

Kosmotoga arenicorallina

Mesotoga

M. infera

M. prima

Kosmotoga

K. olearia (type sp.)

K. shengliensis

Mesoaciditogaceae

Mesoaciditoga lauensis

Petrotogaceae

Marinitoga

M. hydrogenitolerans

M. litoralis

M. okinawensis

M. piezophila

M. camini (type sp.)

Oceanotoga teriensis

Geotoga

G. petraea (type sp.)

G. subterranea

Defluviitoga tunisiensis

Petrotoga

P. sibirica

P. olearia

P. mexicana

P. mobilis

P. halophila

P. miotherma (type sp.)

Taxonomy[edit] The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[26] and the National Center for Biotechnology Information (NCBI).[27]

Phylum Thermotogae Reysenbach 2002 emend. Bhandari & Gupta 2014 [Thermotogaeota Oren et al. 2015]

Class Thermotogae Reysenbach 2002 [Togobacteria Cavalier-Smith 2002]

Genus Caldotoga ♥ Xue et al. 1999

Species Caldotoga fontana ♥ Xue et al. 1999

Order Thermotogales Reysenbach 2002 emend. Bhandari & Gupta 2014

Family Fervidobacteriaceae Bhandari & Gupta 2014

Genus Fervidobacterium Patel et al. 1985

Species ?F. pennivorans Friedrich and Antranikian 1999 Species F. changbaicum Cai et al. 2007 Species F. gondwanense Andrews and Patel Species F. islandicum Huber et al. 1991 Species F. nodosum Patel et al. 1985 (type sp.) Species F. riparium Podosokorskaya et al. 2011

Genus Thermosipho Huber et al. 1989 emend. Ravot et al. 1996

Species ?T. ferriphilus ♠ Kendall et al. 2002 Species T. activus Podosokorskaya et al. 2014 Species T. affectus Podosokorskaya et al. 2011 Species T. africanus Huber et al. 1989 emend. Ravot et al. 1996 (type sp.) Species T. atlanticus Urios et al. 2004 Species T. geolei L'Haridon et al. 2001 Species T. globiformans Kuwabara et al. 2011 Species T. japonicus Takai and Horikoshi 2000 Species T. melanesiensis Antoine et al. 1997

Family Thermotogaceae Reysenbach 2002 emend. Bhandari & Gupta 2014

Genus Pseudothermotoga Bhandari & Gupta 2014

Species P. elfii (Ravot et al. 1995) Bhandari & Gupta 2014 [ Thermotoga
Thermotoga
elfii Ravot et al. 1995] Species P. hypogea (Fardeau et al. 1997) Bhandari & Gupta 2014 [ Thermotoga
Thermotoga
hypogea Fardeau et al. 1997] Species P. lettingae (Balk, Weijma & Stams 2002) Bhandari & Gupta 2014 [ Thermotoga
Thermotoga
lettingae Balk, Weijma & Stams 2002] Species P. thermarum (Windberger et al. 1992) Bhandari & Gupta 2014 [ Thermotoga
Thermotoga
thermarum Windberger et al. 1992] Species P. subterranea (Jeanthon et al. 2000) Bhandari & Gupta 2014 [ Thermotoga
Thermotoga
subterranea Jeanthon et al. 2000]

Genus ?Thermopallium ♠ Duckworth et al. 1996

Species Thermopallium natronophilum ♠ Duckworth et al. 1996

Genus Thermotoga
Thermotoga
Stetter and Huber 1986

Species ?T. katamachii ♥ Takahata et al. 2000 Species ?T. kuroii ♥ Takahata et al. 2000 Species T. maritima Stetter and Huber 1986 (type sp.) Species T. naphthophila Takahata et al. 2001 Species T. neapolitana Jannasch et al. 1989 Species T. petrophila Takahata et al. 2001

Order Kosmotogales Bhandari & Gupta 2014

Family Kosmotogaceae Bhandari & Gupta 2014

Genus Kosmotoga DiPippo et al. 2009 emend. Nunoura et al. 2010 [Thermococcoides Feng et al. 2010]

Species K. arenicorallina Nunoura et al. 2011 Species K. olearia DiPippo et al. 2009 (type sp.) Species K. pacifica L'Haridon et al. 2016 Species K. shengliensis (Feng et al. 2010) Nunoura et al. 2013 [Thermococcoides shengliensis Feng et al. 2010]

Genus Mesotoga Nesbo et al. 2013

Species M. infera Ben et al. 2013 Species M. prima Nesbo et al. 2013

Order Mesoaciditogales Itoh et al. 2015

Family Mesoaciditogaceae Itoh et al. 2015

Genus Athalassotoga Itoh et al. 2015

Species Athalassotoga saccharophila Itoh et al. 2015

Genus Mesoaciditoga Reysenbach et al. 2013

Species Mesoaciditoga lauensis Reysenbach et al. 2013

Order Petrotogales Bhandari & Gupta 2014

Family Petrotogaceae Bhandari & Gupta 2014

Genus Defluviitoga Ben Hania et al. 2012

Species Defluviitoga tunisiensis Ben Hania et al. 2012

Genus Geotoga Davey et al. 1993

Species G. aestuarianus ♠ Holton et al. 2002 Species G. petraea Davey et al. 1993 (type sp.) Species G. subterranea Davey et al. 1993

Genus Marinitoga Wery et al. 2001

Species M. hydrogenitolerans Postec et al. 2005 Species M. camini Wery et al. 2001 (type sp.) Species M. litoralis Postec et al. 2010 Species M. okinawensis Nunoura et al. 2007 Species M. piezophila Alain et al. 2002

Genus Oceanotoga Jayasinghearachchi and Lal 2011

Species Oceanotoga teriensis Jayasinghearachchi and Lal 2011

Genus Petrotoga Davey et al. 1993

Species P. halophila Miranda-Tello et al. 2007 Species P. mexicana Miranda-Tello et al. 2004 Species P. miotherma Davey et al. 1993 (type sp.) Species P. mobilis Lien et al. 1998 Species P. olearia L'Haridon et al. 2002 Species P. sibirica L'Haridon et al. 2002

Notes: ♠ Strain found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN) ♥ No strains lodged at National Center for Biotechnology Information NCBI and or listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN) References[edit]

^ a b c d Huber R., Hannig M. (2006). "Thermotogales". Prokaryotes. 7: 899–922.  ^ a b c d e f g Gupta, RS (2014) The Phylum Thermotogae. The Prokaryotes 989-1015. Springer Berlin Heidelberg. ^ a b c Reysenbach, A.-L. (2001) Phylum BII. Thermotogae phy. nov. In: Bergey's Manual of Systematic Bacteriology, pp. 369-387. Eds D. R. Boone, R. W. Castenholz. Springer-Verlag: Berlin. ^ Nesbo C.L.; Kumaraswamy R.; Dlutek M.; Doolittle W.F. & Foght J. (2010). "Searching for mesophilic Thermotogales bacteria: "mesotogas" in the wild". Appl Environ Microbiol. 76: 4896–4900. doi:10.1128/AEM.02846-09. PMC 2901743 . PMID 20495053.  ^ Gupta R.S. (1998). "Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes". Microbiol Mol Biol Rev. 62 (4): 1435–1491. PMC 98952 . PMID 9841678.  ^ Gupta R.S. (2011). "Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes". Antonie van Leeuwenhoek. 100: 171–182. doi:10.1007/s10482-011-9616-8. PMC 3133647 . PMID 21717204.  ^ Eriksen N.T.; Riis M.L.; Holm N.K. & Iversen N. (2010). "H(2) synthesis from pentoses and biomass in Thermotoga
Thermotoga
spp". Biotechnol Lett. 33 (2): 293–300. doi:10.1007/s10529-010-0439-x. PMID 20960218.  ^ Conners S.B.; Mongodin E.F.; Johnson M.R.; Montero C.I.; Nelson K.E. & Kelly R.M. (2006). "Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga
Thermotoga
species". FEMS Microbiol Rev. 30 (6): 872–905. doi:10.1111/j.1574-6976.2006.00039.x. PMID 17064285.  ^ a b c d e f g Gupta R.S. & Bhandari V. (2011). "Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups". Antonie Van Leeuwenhoek. 100: 1–34. doi:10.1007/s10482-011-9576-z. PMID 21503713.  ^ Oren A, Garrity GM (2015). "List of new names and new combinations previously effectively, but not validly, published" (PDF). Int. J. Syst. Evol. Microbiol. 65 (7): 2017–2025. doi:10.1099/ijs.0.000317.  ^ Itoh T, Onishi M, Kato S, Iino T, Sakamoto M, Kudo T, Takashina T, Ohkuma M (December 2015). "Athalassotoga saccharophila gen. nov. sp. nov. isolated from an acidic terrestrial hot spring of Japan, and proposal of Mesoaciditogales ord. nov., Mesoaciditogaceae fam. nov. in the phylum Thermotogae". Int. J. Syst. Evol. Microbiol. in press: 1045–1051. doi:10.1099/ijsem.0.000833. PMID 26651491.  ^ a b Bhandari V, Gupta RS (January 2014). "Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations". Antonie Van Leeuwenhoek. 105 (1): 143–168. doi:10.1007/s10482-013-0062-7. PMID 24166034.  ^ Euzeby JP. List of prokaryotic names with standing in nomenclature. http://www.bacterio.cict.fr/t/thermotogales . ^ Klenk H.P.; Meier T.D.; Durovic P.; et al. (1999). "RNA polymerase of Aquifex pyrophilus: Implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria". J Mol Evol. 48 (5): 528–541. Bibcode:1999JMolE..48..528K. doi:10.1007/pl00006496. PMID 10198119.  ^ Gupta R.S. (2000). "The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes". FEMS Microbiol Rev. 24 (4): 367–402. doi:10.1111/j.1574-6976.2000.tb00547.x. PMID 10978543.  ^ Ciccarelli F.D.; Doerks T.; von Mering C.; Creevey C.J.; Snel B. & Bork P. (2006). "Toward automatic reconstruction of a highly resolved tree of life". Science. 311: 1283–1287. Bibcode:2006Sci...311.1283C. doi:10.1126/science.1123061. PMID 16513982.  ^ Di Giulio M. (2003). "The universal ancestor was a thermophile or a hyperthermophile: Tests and further evidence". J Theor Biol. 221 (3): 425–436. doi:10.1006/jtbi.2003.3197. PMID 12642117.  ^ Bhandari V, Naushad HS, Gupta RS (2012). "Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution". Front Cell Infect Microbiol. 2: 98. doi:10.3389/fcimb.2012.00098. PMC 3417386 . PMID 22919687.  ^ Griffiths E. & Gupta R.S. (2004). "Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales". International Microbiology. 7 (1): 41–52. PMID 15179606.  ^ Nelson K.E.; Clayton R.; Gill S.; et al. (1999). "Evidence for lateral gene transfer between Archaea
Archaea
and Bacteria
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from genome sequence of Thermotoga
Thermotoga
maritima". Nature. 399 (6734): 323–329. Bibcode:1999Natur.399..323N. doi:10.1038/20601. PMID 10360571.  ^ Nesbo C.L.; L'Haridon S.; Stetter K.O. & Doolittle W.F. (2001). "Phylogenetic analyses of two "Archaeal" genes in Thermotoga
Thermotoga
maritima reveal multiple transfers between Archaea
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and Bacteria". Mol Biol Evol. 18 (3): 362–375. doi:10.1093/oxfordjournals.molbev.a003812. PMID 11230537.  ^ Ochman H.; Lawrence J.G. & Groisman E.A. (2000). "Lateral gene transfer and the nature of bacterial innovation". Nature. 405 (6784): 299–304. Bibcode:2000Natur.405..299O. doi:10.1038/35012500. PMID 10830951.  ^ Zhaxybayeva O.; Swithers K.S.; Lapierre P.; et al. (2009). "On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales". Proc Natl Acad Sci U S A. 106: 5865–5870. Bibcode:2009PNAS..106.5865Z. doi:10.1073/pnas.0901260106. PMC 2667022 . PMID 19307556.  ^ Kunisawa T (2011). "Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison". Antonie van Leeuwenhoek. 99: 417–422. doi:10.1007/s10482-010-9492-7. PMID 20706870.  ^ "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.  ^ J.P. Euzéby. "Thermotogae". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.  ^ Sayers; et al. "Thermotogae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20. 

v t e

Prokaryotes: Bacteria
Bacteria
classification (phyla and orders)

Domain Archaea Bacteria Eukaryota (Supergroup Plant Hacrobia Heterokont Alveolata Rhizaria Excavata Amoebozoa Opisthokonta

Animal Fungi)

G-/ OM

Terra-/ Glidobacteria (BV1)

Eobacteria

Deinococcus–Thermus

Deinococcales Thermales

Chloroflexi

Anaerolineales Caldilineales Chloroflexales Herpetosiphonales Dehalococcoidales Ktedonobacterales Thermogemmatisporales Thermomicrobiales Sphaerobacterales

other glidobacteria

Thermodesulfobacteria thermophiles

Aquificae Thermotogae

Cyanobacteria

Proteobacteria (BV2)

Alpha

Caulobacterales Kiloniellales Kordiimonadales Magnetococcales Parvularculales Rhizobiales Rhodobacterales Rhodospirillales Rickettsiales Sneathiellales Sphingomonadales

Beta

Burkholderiales Hydrogenophilales Methylophilales Neisseriales Nitrosomonadales Procabacteriales Rhodocyclales

Gamma

Acidithiobacillales Aeromonadales Alteromonadales Cardiobacteriales Chromatiales Enterobacteriales Legionellales Methylococcales Oceanospirillales Orbales Pasteurellales Pseudomonadales Salinisphaerales Thiotrichales Vibrionales Xanthomonadales

Delta

Bdellovibrionales Desulfarculales Desulfobacterales Desulfovibrionales Desulfurellales Desulfuromonadales Myxococcales Syntrophobacterales Syntrophorhabdales

Epsilon

Campylobacterales Nautiliales

Zeta

Mariprofundales

BV4

Spirochaetes

Spirochaetes

Sphingobacteria (FCB group)

Fibrobacteres Chlorobi

Chlorobiales Ignavibacteriales

Bacteroidetes

Bacteroidales Cytophagales Flavobacteriales Sphingobacteriales

Planctobacteria/ (PVC group)

Chlamydiae Lentisphaerae

Lentisphaerales Oligosphaerales Victivallales

Planctomycetes

Phycisphaerales Planctomycetales

Verrucomicrobia

Puniceicoccales Opitutales Chthoniobacterales Verrucomicrobiales

"Poribacteria"

Other GN

Acidobacteria

Acidobacteriales Acanthopleuribacterales Holophagales Solibacterales

Armatimonadetes

Armatimonadales Chthonomonadales Fimbriimonadales

Caldiserica Chrysiogenetes Deferribacteres Dictyoglomi Elusimicrobia Fusobacteria Gemmatimonadetes Nitrospirae Synergistetes

G+/ no OM

Firmicutes (BV3)

Bacilli

Bacillales Lactobacillales

Clostridia

Clostridiales Halanaerobiales Thermoanaerobacteriales Natranaerobiales

Erysipelotrichia

Erysipelotrichiales

Thermolithobacteria

Thermolithobacterales

Tenericutes/ Mollicutes

Mycoplasmatales Entomoplasmatales Anaeroplasmatales Acholeplasmatales Haloplasmatales

Negativicutes

Selenomonadales

Actinobacteria (BV5)

Actinobacteria

Actinomycetales Bifidobacteriales

Acidimicrobiia

Acidimicrobiales

Coriobacteriidae

Coriobacteriales

Nitriliruptoria

Euzebyales Nitriliruptorales

Rubrobacteria

Gaiellales Rubrobacterales Thermoleophilales Solirubrobacterales

Incertae sedis

†Archaeosphaeroides †Eobacterium †Leptotrichites

Source: Bergey's Manual (2001–2012). Alternative views: Wikispecies.

Taxon identifiers

Wd: Q1146853 EoL: 295 EPPO: 1THTGC iNaturalist: 151862 ITIS: 956125

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