Acidobacteria
| Acidobacteria | |
|---|---|
 | |
| Acidobacterium | |
| Scientific classification | |
| Domain: | Bacteria |
| Phylum: | Acidobacteria Thrash and Coates 2012[1][2] |
| Classes and Orders | |
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Acidobacteria are a newly devised phylum of Bacteria, whose members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.[3][4][5]
Members of this phylum are physiologically diverse, some being acidophilic, and were first recognized as a novel division in 1997.[6] The first species, Acidobacterium capsulatum, of this phylum was discovered in 1991.[7] Other notable species are Holophaga foetida,[8] Geothrix fermentans,[9] Acanthopleuribacter pedis[10] and Bryobacter aggregatus.[11] Since they have only recently been discovered and the large majority have not been cultured, the ecology and metabolism of these bacteria is not well understood.[4] However, these bacteria may be an important contributor to ecosystems, since they are particularly abundant within soils.[12]
As well as their natural soil habitat, unclassified group II Acidobacteria have also been identified as a contaminant of DNA extraction kit reagents, which may lead to their erroneous appearance in microbiota or metagenomic datasets.[13]
Phylogeny
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[14][15] and the phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project.[16]
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Notes:
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN)
Taxonomy
- Genus ?Thermoanaerobaculum Losey et al. 2013
- Species Thermoanaerobaculum aquaticum Losey et al. 2013
- Genus ?"Thermotomaculum" ♠ Izumi et al. 2012
- Species "Thermotomaculum hydrothermale" ♠ Izumi et al. 2012
- Class Blastocatellia ♠ Pascual et al. 2015
- Genus Chloracidobacterium Tank & Bryant 2015 [Candidatus Chloracidobacterium Bryant et al. 2007]
- Species Chloracidobacterium thermophilum Tank & Bryant 2015 [Candidatus Chloracidobacterium thermophilum Bryant et al. 2007]
- Genus Pyrinomonas Crowe et al. 2014
- Species Pyrinomonas methylaliphatogenes Crowe et al. 2014
- Order "Blastocatellales" ♠ Pascual et al. 2015
- Family "Blastocatellaceae" ♠ Pascual et al. 2015
- Genus Blastocatella Foesel et al. 2013 emend. Pascual et al. 2015
- Species Blastocatella fastidiosa Foesel et al. 2013 emend. Pascual et al. 2015
- Genus Aridibacter Huber et al. 2014
- Species A. famidurans Huber et al. 2014
- Species A. kavangonensis Huber et al. 2014
- Genus "Stenotrophobacter" ♠ Pascual et al. 2015
- Species "S. namibiensis" ♠ Pascual et al. 2015
- Species "S. roseus" ♠ Pascual et al. 2015
- Species "S. terrae" ♠ Pascual et al. 2015
- Genus "Tellurimicrobium" ♠ Pascual et al. 2015
- Species "Tellurimicrobium multivorans" ♠ Pascual et al. 2015
- Genus Blastocatella Foesel et al. 2013 emend. Pascual et al. 2015
- Family "Blastocatellaceae" ♠ Pascual et al. 2015
- Genus Chloracidobacterium Tank & Bryant 2015 [Candidatus Chloracidobacterium Bryant et al. 2007]
- Class Holophagae Fukunaga et al. 2008
- Order Acanthopleuribacterales Fukunaga et al. 2008
- Family Acanthopleuribacteraceae Fukunaga et al. 2008
- Genus Acanthopleuribacter Fukunaga et al. 2008
- Species Acanthopleuribacter pedis Fukunaga et al. 2008
- Genus Acanthopleuribacter Fukunaga et al. 2008
- Family Acanthopleuribacteraceae Fukunaga et al. 2008
- Order Holophagales Fukunaga et al. 2008
- Family Holophagaceae Fukunaga et al. 2008
- Genus Geothrix Coates et al. 1999
- Species Geothrix fermentans Coates et al. 1999
- Genus Holophaga Liesack et al. 1995
- Species Holophaga foetida Liesack et al. 1995
- Genus Geothrix Coates et al. 1999
- Family Holophagaceae Fukunaga et al. 2008
- Order Acanthopleuribacterales Fukunaga et al. 2008
- Class Solibacteres
- Genus Bryobacter Kulichevskaya et al. 2010
- Species Bryobacter aggregatus Kulichevskaya et al. 2010
- Genus Paludibaculum Kulichevskaya et al. 2014
- Species Paludibaculum fermentans Kulichevskaya et al. 2014
- Order "Solibacterales"
- Family "Solibacteraceae"
- Genus "Candidatus Solibacter" Ward et al. 2009
- Species "Candidatus Solibacter usitatus" Ward et al. 2009
- Genus "Candidatus Solibacter" Ward et al. 2009
- Family "Solibacteraceae"
- Genus Bryobacter Kulichevskaya et al. 2010
- Class Acidobacteria Cavalier-Smith 2002
- Order Acidobacteriales Cavalier-Smith 2002
- Family Acidobacteriaceae
- Genus Acidicapsa Kulichevskaya et al. 2012
- Species A. borealis Kulichevskaya et al. 2012 (type sp.)
- Species A. ligni Kulichevskaya et al. 2012
- Genus Acidobacterium Kishimoto et al. 1991
- Species Acidobacterium capsulatum Kishimoto et al. 1991
- Genus Acidopila Okamura et al. 2015 ["Acidopila" Okamura et al. 2011]
- Species A. rosea Okamura et al. 2015 ["Acidopila rosea" Okamura et al. 2011]
- Species A. dinghuensis Jiang et al. 2016
- Genus Bryocella Dedysh et al. 2012
- Species Bryocella elongata Dedysh et al. 2012
- Genus Edaphobacter Koch et al. 2008
- Species E. aggregans Koch et al. 2008 emend. Dedysh et al. 2012
- Species E. dinghuensis Jiang et al. 2016
- Species E. modestus Koch et al. 2008 (type sp.)
- Genus "Candidatus Koribacter" Ward et al. 2009
- Species "Candidatus Koribacter versatilis" Ward et al. 2009
- Genus Occallatibacter Foesel et al. 2015
- Species "O. riparius" ♠
- Species O. savannae Foesel et al. 2015
- Genus "Silvibacterium bohemicum" ♠ Llado et al. 2016
- Species "Silvibacterium bohemicum" ♠ Llado et al. 2016
- Genus "Terracidiphilus" ♠ Garcia-Fraile et al. 2016
- Species "Terracidiphilus gabretensis" ♠ Garcia-Fraile et al. 2016
- Genus Terriglobus Eichorst et al. 2007
- Species T. albidus Pascual et al. 2015
- Species T. aquaticus Baik et al. 2013
- Species T. roseus Eichorst et al. 2007 (type sp.)
- Species T. saanensis Männistö et al. 2011
- Species T. tenax Whang et al. 2014
- Genus Granulicella Pankratov and Dedysh 2010 emend. Männistö et al. 2012
- Species G. arctica Männistö et al. 2012
- Species G. cerasi Yamada et al. 2014
- Species G. mallensis Männistö et al. 2012
- Species G. sapmiensis Männistö et al. 2012
- Species G. tundricola Männistö et al. 2012
- Species G. paludicola Pankratov and Dedysh 2010 (type sp.)
- Species G. pectinivorans Pankratov and Dedysh 2010
- Species G. aggregans Pankratov and Dedysh 2010
- Species G. rosea Pankratov and Dedysh 2010
- Genus Telmatobacter Pankratov and Dedysh 2012
- Species Telmatobacter bradus Pankratov and Dedysh 2012
- Genus Acidicapsa Kulichevskaya et al. 2012
- Family Acidobacteriaceae
- Order Acidobacteriales Cavalier-Smith 2002
References
- ↑ Thrash, J. C. & Coates, J. D. (2011). Phylum XVII. Acidobacteria phyl. nov. In Bergey’s Manual of Systematic Bacteriology, 2nd edn, vol. 4, p. 725. Edited by N. R. Krieg, J. T. Staley, D. R. Brown, B. P. Hedlund, B. J. Paster, N. L. Ward, W. Ludwig & W. B. Whitman. New York: Springer.
- ↑ Validation List no. 143. Int. J. Syst. Evol. Microbiol., 2012, 62, 1-4.
- ↑ Barns SM; Cain EC; Sommerville L; Kuske CR (2007). "Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum". Appl. Environ. Microbiol. 73 (9): 3113–6. doi:10.1128/AEM.02012-06. PMC 1892891
. PMID 17337544. - 1 2 Quaiser A; Ochsenreiter T; Lanz C; et al. (2003). "Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics". Mol. Microbiol. 50 (2): 563–75. doi:10.1046/j.1365-2958.2003.03707.x. PMID 14617179.
- ↑ Rappe, M. S.; Giovannoni, S. J. (2003). "The Uncultured Microbial Majority". Annual Review of Microbiology. 57: 369–394. doi:10.1146/annurev.micro.57.030502.090759. PMID 14527284.
- ↑ Kuske CR; Barns SM; Busch JD (1 September 1997). "Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions". Appl. Environ. Microbiol. 63 (9): 3614–21. PMC 168668. PMID 9293013.
- ↑ Kishimoto, Noriaki; Kosako, Yoshimasa; Tano, Tatsuo (31 December 1990). "Acidobacterium capsulatum gen. nov., sp. nov.: An acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment". Current Microbiology. 22 (1): 1–7. doi:10.1007/BF02106205.
- ↑ Liesack, Werner; Bak, Friedhelm; Kreft, Jan-Ulrich; Stackebrandt, E. (30 June 1994). "Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds". Archives of Microbiology. 162 (1–2): 85–90. doi:10.1007/BF00264378. PMID 8085918.
- ↑ Coates, J. D.; Ellis, D. J.; Gaw, C. V.; Lovley, D. R. (1 October 1999). "Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer". International Journal of Systematic Bacteriology. 49 (4): 1615–1622. doi:10.1099/00207713-49-4-1615. PMID 10555343.
- ↑ Fukunaga, Y; Kurahashi, M; Yanagi, K; Yokota, A; Harayama, S (November 2008). "Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum 'Acidobacteria'". International Journal of Systematic and Evolutionary Microbiology. 58 (Pt 11): 2597–2601. doi:10.1099/ijs.0.65589-0. PMID 18984699.
- ↑ Kulichevskaya, IS; Suzina, NE; Liesack, W; Dedysh, SN (February 2010). "Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria". International Journal of Systematic and Evolutionary Microbiology. 60 (Pt 2): 301–6. doi:10.1099/ijs.0.013250-0. PMID 19651730.
- ↑ Eichorst SA; Breznak JA; Schmidt TM (2007). "Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria". Appl. Environ. Microbiol. 73 (8): 2708–17. doi:10.1128/AEM.02140-06. PMC 1855589. PMID 17293520.
- ↑ Salter, S; Cox, M; Turek, E; Calus, S; Cookson, W; Moffatt, M; Turner, P; Parkhill, J; Loman, N; Walker, A (2014). "Reagent contamination can critically impact sequence-based microbiome analyses". bioRxiv. doi:10.1101/007187.
- ↑ See the List of Prokaryotic names with Standing in Nomenclature. Data extracted from J.P. Euzéby. "Acidobacteria". Retrieved 2016-09-09.
- ↑ See the NCBI webpage on Chlorobi Data extracted from Sayers; et al. "NCBI Taxonomy Browser". National Center for Biotechnology Information. Retrieved 2016-09-09.
- ↑ See the All-Species Living Tree Project . Data extracted from the "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-09-09.
- Pankratov, TA; Dedysh, SN (December 2010). "Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs". International Journal of Systematic and Evolutionary Microbiology. 60 (Pt 12): 2951–9. doi:10.1099/ijs.0.021824-0. PMID 20118293.
- Pankratov, T. A.; Kirsanova, L. A.; Kaparullina, E. N.; Kevbrin, V. V.; Dedysh, S. N. (1 April 2011). "Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1993". International Journal of Systematic and Evolutionary Microbiology. 62 (2): 430–437. doi:10.1099/ijs.0.029629-0.
External links
- Acidobacteria bacterium Ellin345 Genome Page
- Acidobacterium Genome Projects (from Genomes OnLine Database)
- Science Daily article
- Scientific American article
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