Acidobacteria

Acidobacteria

Acidobacteria
Acidobacterium
Scientific classification
Domain: Bacteria
Phylum: Acidobacteria
Classes, Orders, Families and some Genera

Acidobacteria are a newly devised phylum of Bacteria, whose members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.[1][2][3]

Members of this phylum are physiologically diverse, some being acidophilic, and were first recognized as a novel division in 1997.[4] The first species, Acidobacterium capsulatum, of this phylum was discovered in 1991.[5] Other notable species are Holophaga foetida,[6] Geothrix fermentans,[7] Acanthopleuribacter pedis[8] and Bryobacter aggregatus.[9] 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.[2] However, these bacteria may be an important contributor to ecosystems, since they are particularly abundant within soils.[10]

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.[11]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [12] [13] and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project [14]



?Candidatus Chloracidobacterium thermophilum Bryant et al. 2007


?Candidatus Koribacter versatilis Ward et al. 2009


?Candidatus Solibacter usitatus Ward et al. 2009


?Thermotomaculum hydrothermaleIzumi 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 roseaOkamura et al. 2011


?Blastocatella fastidiosaFoesel 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. ^ 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.  
  2. ^ a b 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.  
  3. ^ Rappe, M. S.; Giovannoni, S. J. (2003). "The Uncultured Microbial Majority". Annual Review of Microbiology 57: 369–394.  
  4. ^ 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.  
  5. ^ 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.  
  6. ^ 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.  
  7. ^ 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.  
  8. ^ 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.  
  9. ^ 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.  
  10. ^ 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.  
  11. ^ 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.  
  12. ^ See the  
  13. ^ See the  
  14. ^ See the  
  • 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.  
  • 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.  

External links

  • Genome PageAcidobacteria bacterium Ellin345
  • Acidobacterium Genome Projects (from Genomes OnLine Database)
  • Science Daily article
  • Scientific American article