Acidobacteria

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Acidobacteria
Acidobacterium.jpg
Acidobacterium
Scientific classification
Domain: Bacteria
Phylum: Acidobacteria
Thrash and Coates 2012[1]
Class

Acidobacteria
Blastocatellia
Holophagae

Acidobacteria is a phylum of bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.[2][3][4]

Description[edit]

Members of this phylum are physiologically diverse, and can be found in a variety of environments including soil, hot springs, oceans, caves, and metal-contaminated soils.[5] Many Acidobacteria are acidophilic, including the first described member of the phylum, Acidobacterium capsulatum.[6]

Other notable species are Holophaga foetida,[7] Geothrix fermentans,[8] Acanthopleuribacter pedis[9] and Bryobacter aggregatus.[10] 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.[3] However, these bacteria may be an important contributor to ecosystems, since they are particularly abundant within soils.[11]

As well as their natural soil habitat, unclassified subdivision 2 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.[12]

The G+C content of Acidobacteria genomes are consistent within their subdivisions - above 60% for group V fragments and roughly 10% lower for group III fragments.[3]

History[edit]

The first species, Acidobacterium capsulatum, of this phylum was discovered in 1991.[13] However, Acidobacteria were not recognized as a novel division until 1997,[6] and were not recognized as a phylum until 2012.[14]

Phylogeny[edit]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[15][16] and the phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project.[17]

Holophagae
Acanthopleuribacteraceae

Acanthopleuribacter pedis Fukunaga et al. 2008

Holophagaceae

Geothrix fermentans Coates et al. 1999

Holophaga foetida Liesack et al. 1995

"Solibacteres"

Bryobacter aggregatus Kulichevskaya et al. 2010

Paludibaculum fermentans Kulichevskaya et al. 2014

Acidobacteriaceae

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.)

"Granulicella" mallensis Männistö et al. 2012

Terriglobus

T. aquaticus Baik et al. 2013

T. roseus Eichorst et al. 2007 (type sp.)

T. saanensis Männistö et al. 2011

T. tenax Whang et al. 2014

Granulicella

G. cerasi Yamada et al. 2014

G. paludicola Pankratov and Dedysh 2010 (type sp.)

G. pectinivorans Pankratov and Dedysh 2010

G. sapmiensis Männistö et al. 2012

G. aggregans Pankratov and Dedysh 2010

G. tundricola Männistö et al. 2012

G. arctica Männistö et al. 2012

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[edit]

  1. ^ "Validation List no. 143". Int. J. Syst. Evol. Microbiol. 62: 1–4. 2012. doi:10.1099/ijs.0.68147-0. 
  2. ^ 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 1892891Freely accessible. PMID 17337544. 
  3. ^ a b c 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. 
  4. ^ 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. 
  5. ^ Thrash JC, Coates JD (2015). "Acidobacteria phyl. nov.". In Whitman WB. Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons. doi:10.1002/9781118960608.pbm00001. 
  6. ^ a b 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 168668Freely accessible. PMID 9293013. 
  7. ^ 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. 
  8. ^ 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. 
  9. ^ 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. 
  10. ^ 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. 
  11. ^ 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 1855589Freely accessible. PMID 17293520. 
  12. ^ Salter, Susannah J.; Cox, Michael J.; Turek, Elena M.; Calus, Szymon T.; Cookson, William O.; Moffatt, Miriam F.; Turner, Paul; Parkhill, Julian; Loman, Nicholas J. (2014-01-01). "Reagent and laboratory contamination can critically impact sequence-based microbiome analyses". BMC Biology. 12: 87. doi:10.1186/s12915-014-0087-z. ISSN 1741-7007. PMC 4228153Freely accessible. PMID 25387460. 
  13. ^ 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. 
  14. ^ Euzeby JP. "Taxa above the rank of class - Acidobacteria". LPSN. Retrieved 26 November 2017. 
  15. ^ See the List of Prokaryotic names with Standing in Nomenclature. Data extracted from J.P. Euzéby. "Acidobacteria". Archived from the original on 2013-01-27. Retrieved 2016-09-09. 
  16. ^ See the NCBI webpage on Chlorobi Data extracted from Sayers; et al. "NCBI Taxonomy Browser". National Center for Biotechnology Information. Retrieved 2016-09-09. 
  17. ^ See the All-Species Living Tree Project [1]. Data extracted from the "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-09-09. 

External links[edit]