Acidobacteria

Acidobacteria
Acidobacterium
Scientific classification
Domain:	Bacteria
Phylum:	Acidobacteria Thrash and Coates 2012[1][2]
Classes, Orders, Families and some Genera
?Candidatus Chloracidobacterium Bryant et al. 2007 ?Candidatus Koribacter Ward et al. 2009 ?Bryobacter Kulichevskaya et al. 2010 ?Thermotomaculum ♠ Izumi et al. 2012 Solibacteres Solibacterales Solibacteraceae Candidatus Solibacter Ward et al. 2009 Holophagae Fukunaga et al. 2008 Acanthopleuribacterales Fukunaga et al. 2008 Acanthopleuribacteraceae Fukunaga et al. 2008 Acanthopleuribacter Fukunaga et al. 2008 Holophagales Fukunaga et al. 2008 Holophagaceae Fukunaga et al. 2008 Geothrix Coates et al. 1999 Holophaga Liesack et al. 1995 Acidobacteria Cavalier-Smith 2002 Acidobacteriales Cavalier-Smith 2002 Acidobacteriaceae Acidicapsa Kulichevskaya et al. 2012 Acidobacterium Kishimoto et al. 1991 Acidopila ♠ Okamura et al. 2011 Blastocatella ♠ Foesel et al. 2012 Bryocella Dedysh et al. 2012 Edaphobacter Koch et al. 2008 Terriglobus Eichorst et al. 2007 Granulicella Pankratov and Dedysh 2010 emend. Männistö et al. 2012 Telmatobacter Pankratov and Dedysh 2012

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 111 by The All-Species Living Tree Project.^[16]

?Candidatus Chloracidobacterium thermophilum Bryant et al. 2007 ?Candidatus Koribacter versatilis Ward et al. 2009 ?Candidatus Solibacter usitatus Ward et al. 2009 ?Thermotomaculum hydrothermale ♠ Izumi et al. 2012 Holophagae Acanthopleuribacter pedis Fukunaga et al. 2008 Holophagaceae Geothrix fermentans Coates et al. 1999 Holophaga foetida Liesack et al. 1995 Bryobacter aggregatus Kulichevskaya et al. 2010 Acidobacteriaceae ?Acidopila rosea ♠ Okamura et al. 2011 ?Blastocatella fastidiosa ♠ Foesel et al. 2012 Acidobacterium capsulatum Kishimoto et al. 1991 Telmatobacter bradus Pankratov and Dedysh 2012 Acidicapsa A. borealis Kulichevskaya et al. 2012 (type sp.) A. ligni Kulichevskaya et al. 2012 Bryocella elongata Dedysh et al. 2012 Edaphobacter E. aggregans Koch et al. 2008 emend. Dedysh et al. 2012 E. modestus Koch et al. 2008 (type sp.) Terriglobus T. roseus Eichorst et al. 2007 (type sp.) T. saanensis Männistö et al. 2011 Granulicella ?G. arctica Männistö et al. 2012 ?G. mallensis Männistö et al. 2012 ?G. sapmiensis Männistö et al. 2012 ?G. tundricola Männistö et al. 2012 G. paludicola Pankratov and Dedysh 2010 (type sp.) G. pectinivorans Pankratov and Dedysh 2010 G. aggregans Pankratov and Dedysh 2010 G. rosea Pankratov and Dedysh 2010

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)

References

1. 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.
2. Validation List no. 143. Int. J. Syst. Evol. Microbiol., 2012, 62, 1-4.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. See the List of Prokaryotic names with Standing in Nomenclature. Data extracted from J.P. Euzéby. "Acidobacteria". Retrieved 2013-03-20.
15. See the NCBI webpage on Chlorobi Data extracted from Sayers; et al. "NCBI Taxonomy Browser". National Center for Biotechnology Information. Retrieved 2013-03-20.
16. See the All-Species Living Tree Project . Data extracted from the "16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.

• 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