Acidobacteria
Acidobacteria | |
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Acidobacterium | |
Scientific classification | |
Domain: | |
Phylum: | Acidobacteria Thrash and Coates 2012[1]
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Class | |
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Synonyms | |
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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[]
Members of this phylum are physiologically diverse, and can be found in a variety of environments including soil, decomposing wood,[5] hot springs, oceans, caves, and metal-contaminated soils.[6] The members of this phylum are particularly abundant in soil habitats representing up to 52% of the total bacterial community.[7] Environmental factors such as pH and nutrients have been seen to drive Acidobacteria dynamics.[8][9][10] Many Acidobacteria are acidophilic, including the first described member of the phylum, Acidobacterium capsulatum.[11]
Other notable species are Holophaga foetida,[12] Geothrix fermentans,[13] Acanthopleuribacter pedis[14] and .[15] 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.[16] Members of subdivisions 1, 4, and 6 are found to be particularly abundant in soils.[17]
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.[18]
Members of subdivision 1 have been found to dominate in low pH conditions.[19][8] Additionally, Acidobacteria from acid mine drainage have been found to be more adapted to acidic pH conditions (pH 2-3) compared to Acidobacteria from soils,[20] potentially due to cell specialization and enzyme stability.[8]
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]
The majority of Acidobacteria are considered aerobes.[21][22] There are some Acidobacteria that are considered anaerobes within subdivision 8[13] and subdivision 23.[23] It has been found that some strains of Acidobacteria originating from soils have the genomic potential to respire oxygen at atmospheric and sub-atmospheric concentrations.[22]
Members of the Acidobacteria phylum have been considered oligotrophic bacteria due to high abundances in low organic carbon environments.[8] However, the variation in this phylum may indicate that they may not have the same ecological strategy.[8]
History[]
The first species, Acidobacterium capsulatum, of this phylum was discovered in 1991.[24] However, Acidobacteria were not recognized as a novel division until 1997,[11] and were not recognized as a phylum until 2012.[25] First genome was sequenced in 2007.[26]
Metabolism[]
Carbon[]
Some members of subdivision 1 are able to use D-glucose, D-xylose, and lactose as carbon sources,[8] but are unable to use fucose or sorbose.[27] Members of subdivision 1 also contain enzymes such as galactosidases used in the breakdown of sugars.[8] Members of subdivision 4 have been found to use chitin as a carbon source.[28][29][8]
Nitrogen[]
There has been no clear evidence that Acidobacteria are involved in nitrogen-cycle processes such as nitrification, denitrification, or nitrogen fixation.[8] However, Geothrix fermantans was shown to be able to reduce nitrate and contained the norB gene.[8] The NorB gene was also identified in Koribacter verstailis and .[30][8] In addition, the presence of the nirA gene has been observed in members of subdivision 1.[8] Additionally, to date, all genomes have been described to directly uptake ammonium via ammonium channel transporter family genes.[22][8] Acidobacteria can use both inorganic and organic nitrogen as their nitrogen sources.
Taxonomy[]
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[31] and the National Center for Biotechnology Information (NCBI).[32]
Phylogeny of Acidobacteria using 16S rRNA (LTP release 132[33]) | |||||||||||||||||||||||||||||||||||||||||||||
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Phylogeny of Acidobacteria (Annotree v1.2.0,[34][35] GTDB 05-RS95[36][37]) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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- Class "" (RIF25)
- Class "" Tschoeke et al. 2020
- Genus "Candidatus " Tschoeke et al. 2020
- Class Fukunaga et al. 2008
- Order Dedysh & Yilmaz 2018 (Acidobacteria subdivision 10)
- Family Dedysh & Yilmaz 2018
- Genus Izumi et al. 2017
- Family Dedysh & Yilmaz 2018
- Order Fukunaga et al. 2008
- Family Fukunaga et al. 2008
- Genus Acanthopleuribacter Fukunaga et al. 2008
- Family Fukunaga et al. 2008
- Order Holophagales Fukunaga et al. 2008
- Family Fukunaga et al. 2008
- Genus Coates et al. 1999
- Genus Liesack et al. 1995
- Family Fukunaga et al. 2008
- Order Dedysh & Yilmaz 2018 (Acidobacteria subdivision 10)
- Class "" (OP8)
- Order "" Kadnikov et al. 2019
- Family "" Kadnikov et al. 2019
- Genus "Candidatus " corrig. Kadnikov et al. 2019
- Family ""
- Genus "Candidatus " Rinke et al. 2013
- Family "" Kadnikov et al. 2019
- Order "" Kadnikov et al. 2019
- Class Dedysh & Yilmaz 2018 (Acidobacteria subdivision 23)
- Order Dedysh & Yilmaz 2018
- Family Dedysh & Yilmaz 2018
- Genus Losey et al. 2013
- Family Dedysh & Yilmaz 2018
- Order Dedysh & Yilmaz 2018
- Class Dedysh & Yilmaz 2018 (Acidobacteria subdivision 6)
- Order Dedysh & Yilmaz 2018
- Family Huber & Overmann 2018
- Genus "" Vieira et al. 2017
- Genus "" Huber et al. 2013
- Family Huber & Overmann 2018
- Order Dedysh & Yilmaz 2018
- Class Blastocatellia Pascual et al. 2016 (Acidobacteria subdivision 4)
- Order ""
- Family ""
- Genus Chloracidobacterium Tank & Bryant 2015
- Family ""
- Order Blastocatellales Pascual et al. 2016
- Family Dedysh & Yilmaz 2018
- Family Wüstet al. 2016
- Family Pascual et al. 2016
- Order ""
- Class Acidobacteriia Thrash & Coates 2012
- Order "" Epihov et al. 2021
- Family "" Epihov et al. 2021
- Genus "Candidatus " Epihov et al. 2021
- Family "" Epihov et al. 2021
- Order Dedysh & Yilmaz 2018
- Family Dedysh et al. 2016
- Genus Kulichevskaya et al. 2010
- Genus Kulichevskaya et al. 2014
- Genus "Candidatus " Ward et al. 2009
- Genus "Candidatus " Hausmann et al. 2018
- Family Dedysh et al. 2016
- Order Acidobacteriales Cavalier-Smith 2002
- Family ""
- Genus "Candidatus " corrig. Ward et al. 2009
- Genus "Candidatus " Hausmann et al. 2018
- Family Acidobacteriaceae Thrash & Coates 2012
- Family ""
- Order "" Epihov et al. 2021
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- ^ 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. S2CID 23516245.
- ^ a b 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.
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- ^ 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.
- ^ Janssen, P. H. (2006-03-01). "Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes". Applied and Environmental Microbiology. 72 (3): 1719–1728. doi:10.1128/aem.72.3.1719-1728.2006. ISSN 0099-2240. PMC 1393246. PMID 16517615.
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External links[]
- Acidobacteria
- Acidophiles