Biology:Acidobacteria

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Short description: Phylum of bacteria

Acidobacteria
Acidobacterium.jpg
Acidobacterium
Scientific classification
Domain:
Bacteria
Phylum:
Acidobacteria

Thrash and Coates 2012[1]
Class
  • Acidobacteriia
  • "Aminicenantia"
  • Blastocatellia
  • "Fischerbacteria"
  • "Guanabacteria"
  • Holophagae
  • Thermoanaerobaculia
  • Vicinamibacteria
Synonyms
  • Acidobacteraeota Oren et al. 2015
  • "Acidobacteriota" Whitman et al. 2018
  • ?"Aminicenantes" Rinke et al. 2013
  • ?"Fischerbacteria" Anantharaman et al. 2016

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 Bryobacter aggregatus.[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 Solibacter usitatus.[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])
 
 
Vicinamibacteria
 

Luteitalea

 
 

Vicinamibacter

 
 
Holophagae
Acanthopleuribacteraceae

Acanthopleuribacter

 
Holophagaceae
 

Geothrix

 
 

Holophaga

 
 
 
 
Acidobacteriia
Bryobacteraceae
 

Bryobacter

 
 

Paludibaculum

 
 
 

Acidobacteriaceae

 
 
 
Phylogeny of Acidobacteria (Annotree v1.2.0,[34][35] GTDB 05-RS95[36][37])
 
 

Holophagaceae

 
 
"Aminicenantia"
 

"Aminicenantaceae"

 
 

"Saccharicenantaceae"

 
 
 
 

Thermoanaerobaculaceae

 
 
 

Vicinamibacteraceae

 
 
Blastocatellia
 

"Chloracidobacteriaceae"

 
 

Pyrinomonadaceae

 
 
Acidobacteria
Bryobacterales

Bryobacteraceae

 
Acidobacteriales
 

"Korobacteraceae"

 
 

Acidobacteriaceae

 
 
 
 
 
 
 
 
  • Class "Fischerbacteria" (RIF25)
  • Class "Guanabacteria" Tschoeke et al. 2020
    • Genus "Candidatus Guanabacterium" Tschoeke et al. 2020
  • Class Holophagae Fukunaga et al. 2008
    • Order Thermotomaculales Dedysh & Yilmaz 2018 (Acidobacteria subdivision 10)
      • Family Thermotomaculaceae Dedysh & Yilmaz 2018
        • Genus Thermotomaculum Izumi et al. 2017
    • Order Acanthopleuribacterales 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
        • Genus Holophaga Liesack et al. 1995
  • Class "Aminicenantia" (OP8)
    • Order "Aminicenantales" Kadnikov et al. 2019
      • Family "Saccharicenantaceae" Kadnikov et al. 2019
        • Genus "Candidatus Saccharicenans" corrig. Kadnikov et al. 2019
      • Family "Aminicenantaceae"
        • Genus "Candidatus Aminicenans" Rinke et al. 2013
  • Class Thermoanaerobaculia Dedysh & Yilmaz 2018 (Acidobacteria subdivision 23)
    • Order Thermoanaerobaculales Dedysh & Yilmaz 2018
      • Family Thermoanaerobaculaceae Dedysh & Yilmaz 2018
        • Genus Thermoanaerobaculum Losey et al. 2013
  • Class Vicinamibacteria Dedysh & Yilmaz 2018 (Acidobacteria subdivision 6)
    • Order Vicinamibacterales Dedysh & Yilmaz 2018
      • Family Vicinamibacteraceae Huber & Overmann 2018
        • Genus "Luteitalea" Vieira et al. 2017
        • Genus "Vicinamibacter" Huber et al. 2013
  • Class Blastocatellia Pascual et al. 2016 (Acidobacteria subdivision 4)
    • Order "Chloracidobacteriales"
    • Order Blastocatellales Pascual et al. 2016
  • Class Acidobacteriia Thrash & Coates 2012
    • Order "Acidoferrales" Epihov et al. 2021
      • Family "Acidoferraceae" Epihov et al. 2021
    • Order Bryobacterales Dedysh & Yilmaz 2018
      • Family Bryobacteraceae Dedysh et al. 2016
        • Genus Bryobacter Kulichevskaya et al. 2010
        • Genus Paludibaculum Kulichevskaya et al. 2014
        • Genus "Candidatus Solibacter" Ward et al. 2009
        • Genus "Candidatus Sulfopaludibacter" Hausmann et al. 2018
    • Order Acidobacteriales Cavalier-Smith 2002
      • Family "Korobacteraceae"
        • Genus "Candidatus Korobacter" corrig. Ward et al. 2009
        • Genus "Candidatus Sulfotelmatobacter" Hausmann et al. 2018
      • Family Acidobacteriaceae Thrash & Coates 2012

References

  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. PMID 17337544. 
  3. ↑ 3.0 3.1 3.2 Quaiser A 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. ↑ Tláskal, Vojtěch; Baldrian, Petr (2021-06-17). "Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition". Frontiers in Microbiology 12: 685303. doi:10.3389/fmicb.2021.685303. ISSN 1664-302X. 
  6. ↑ Whitman WB, ed (2015). "Acidobacteria phyl. nov.". Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons. pp. 1–5. doi:10.1002/9781118960608.pbm00001. ISBN 9781118960608. 
  7. ↑ Dunbar, John; Barns, Susan M.; Ticknor, Lawrence O.; Kuske, Cheryl R. (2002). "Empirical and Theoretical Bacterial Diversity in Four Arizona Soils". Applied and Environmental Microbiology (American Society for Microbiology) 68 (6): 3035–3045. doi:10.1128/AEM.68.6.3035-3045.2002. OCLC 679526952. PMID 12039765. 
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 Kielak, Anna M.; Barreto, Cristine C.; Kowalchuk, George A.; van Veen, Johannes A.; Kuramae, Eiko E. (2016-05-31). "The Ecology of Acidobacteria: Moving beyond Genes and Genomes". Frontiers in Microbiology 7: 744. doi:10.3389/fmicb.2016.00744. ISSN 1664-302X. PMID 27303369. 
  9. ↑ Jones, Ryan T; Robeson, Michael S; Lauber, Christian L; Hamady, Micah; Knight, Rob; Fierer, Noah (2009-01-08). "A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses". The ISME Journal 3 (4): 442–453. doi:10.1038/ismej.2008.127. ISSN 1751-7362. PMID 19129864. 
  10. ↑ Fierer, Noah; Bradford, Mark A.; Jackson, Robert B. (June 2007). "Toward an Ecological Classification of Soil Bacteria". Ecology 88 (6): 1354–1364. doi:10.1890/05-1839. ISSN 0012-9658. PMID 17601128. 
  11. ↑ 11.0 11.1 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. doi:10.1128/AEM.63.9.3614-3621.1997. PMID 9293013. 
  12. ↑ 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. 
  13. ↑ 13.0 13.1 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. 
  14. ↑ 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. 
  15. ↑ 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. 
  16. ↑ 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. PMID 17293520. 
  17. ↑ 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. PMID 16517615. 
  18. ↑ Salter, Susannah J.; Cox, Michael J.; Turek, Elena M.; Calus, Szymon T.; Cookson, William O.; Moffatt, Miriam F.; Turner, Paul; Parkhill, Julian et al. (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. PMID 25387460. 
  19. ↑ Sait, M.; Davis, K. E. R.; Janssen, P. H. (2006-03-01). "Effect of pH on Isolation and Distribution of Members of Subdivision 1 of the Phylum Acidobacteria Occurring in Soil". Applied and Environmental Microbiology 72 (3): 1852–1857. doi:10.1128/aem.72.3.1852-1857.2006. ISSN 0099-2240. PMID 16517631. 
  20. ↑ Kleinsteuber, Sabine; Müller, Frank-Dietrich; Chatzinotas, Antonis; Wendt-Potthoff, Katrin; Harms, Hauke (January 2008). "Diversity and in situ quantification of Acidobacteria subdivision 1 in an acidic mining lake". FEMS Microbiology Ecology 63 (1): 107–117. doi:10.1111/j.1574-6941.2007.00402.x. ISSN 0168-6496. PMID 18028401. 
  21. ↑ Eichorst, Stephanie A. Kuske, Cheryl R. Schmidt, Thomas M.. Influence of Plant Polymers on the Distribution and Cultivation of Bacteria in the Phylum Acidobacteria ▿ †. American Society for Microbiology (ASM). OCLC 744821434. 
  22. ↑ 22.0 22.1 22.2 Eichorst, Stephanie A. Trojan, Daniela. Roux, Simon. Herbold, Craig. Rattei, Thomas. Woebken, Dagmar.. Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments.. OCLC 1051354840. 
  23. ↑ Losey, N. A.; Stevenson, B. S.; Busse, H.-J.; Damste, J. S. S.; Rijpstra, W. I. C.; Rudd, S.; Lawson, P. A. (2013-06-14). "Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first cultivated member of Acidobacteria subdivision 23, isolated from a hot spring". International Journal of Systematic and Evolutionary Microbiology 63 (Pt 11): 4149–4157. doi:10.1099/ijs.0.051425-0. ISSN 1466-5026. PMID 23771620. 
  24. ↑ 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. 
  25. ↑ Euzeby JP. "Taxa above the rank of class - Acidobacteria". http://www.bacterio.net/-aboveclass.html#acidobacteria. 
  26. ↑ Ward, Naomi L.; Challacombe, Jean F.; Janssen, Peter H.; Henrissat, Bernard; Coutinho, Pedro M.; Wu, Martin; Xie, Gary; Haft, Daniel H. et al. (2009-02-05). "Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils". Applied and Environmental Microbiology 75 (7): 2046–2056. doi:10.1128/aem.02294-08. ISSN 0099-2240. PMID 19201974. 
  27. ↑ Li, Zijie; Gao, Yahui; Nakanishi, Hideki; Gao, Xiaodong; Cai, Li (2013-11-12). "Biosynthesis of rare hexoses using microorganisms and related enzymes". Beilstein Journal of Organic Chemistry 9: 2434–2445. doi:10.3762/bjoc.9.281. ISSN 1860-5397. PMID 24367410. 
  28. ↑ Huber, K. J.; Wust, P. K.; Rohde, M.; Overmann, J.; Foesel, B. U. (2014-02-26). "Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil". International Journal of Systematic and Evolutionary Microbiology 64 (Pt 6): 1866–1875. doi:10.1099/ijs.0.060236-0. ISSN 1466-5026. PMID 24573163. 
  29. ↑ Foesel, Bärbel U.; Rohde, Manfred; Overmann, Jörg (March 2013). "Blastocatella fastidiosa gen. nov., sp. nov., isolated from semiarid savanna soil – The first described species of Acidobacteria subdivision 4". Systematic and Applied Microbiology 36 (2): 82–89. doi:10.1016/j.syapm.2012.11.002. ISSN 0723-2020. PMID 23266188. 
  30. ↑ Coates, J. D.; Ellis, D. J.; Gaw, C. V.; Lovley, D. R. (1999-10-01). "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. ISSN 0020-7713. PMID 10555343. 
  31. ↑ "Acidobacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN). https://lpsn.dsmz.de/phylum/acidobacteria. 
  32. ↑ Sayers. "Acidobacteria". National Center for Biotechnology Information (NCBI) taxonomy database. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=57723&lvl=3&lin=f&keep=1&srchmode=1&unlock. 
  33. ↑ "16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database. https://itol.embl.de/tree/37201229170412631528207598. Retrieved 2015-08-20. 
  34. ↑ "AnnoTree v1.2.0". http://annotree.uwaterloo.ca/app/. 
  35. ↑ Mendler, K; Chen, H; Parks, DH; Hug, LA; Doxey, AC (2019). "AnnoTree: visualization and exploration of a functionally annotated microbial tree of life". Nucleic Acids Research 47 (9): 4442–4448. doi:10.1093/nar/gkz246. PMID 31081040. PMC 6511854. https://academic.oup.com/nar/article/47/9/4442/5432638. 
  36. ↑ "GTDB release 05-RS95". https://gtdb.ecogenomic.org/about#4%7C. 
  37. ↑ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea.". Nature Biotechnology 38 (9): 1079–1086. doi:10.1038/s41587-020-0501-8. PMID 32341564. https://www.researchgate.net/publication/340954053. 

External links

Wikidata ☰ Q41579 entry




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