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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]

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

Thrash and Coates 2012[1]
Class

Acidobacteria
Blastocatellia
Holophagae

DescriptionEdit

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] The members of this phylum are particularly abundant in soil habitats representing up to 52% of the total bacterial community.[6] Environmental factors such as pH and nutrients have been seen to drive Acidobacteria dynamics.[7][8][9] Many Acidobacteria are acidophilic, including the first described member of the phylum, Acidobacterium capsulatum.[10]

Other notable species are Holophaga foetida,[11] Geothrix fermentans,[12] Acanthopleuribacter pedis[13] and Bryobacter aggregatus.[14] 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.[15] Members of subdivisions 1,4,and 6 are found to be particularly abundant in soils.[16]

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.[17]

Members of subdivision 1 have been found to dominate in low pH conditions.[18][7] 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,[19] potentially due to cell specialization and enzyme stability.[7]

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.[20][21] There are some Acidobacteria that are considered anaerobes within subdivision 8[22] 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.[21]

Members of the Acidobacteria phylum have been considered oligotrophic bacteria due to high abundances in low organic carbon environments.[7] However, the variation in this phylum may indicate that they may not have the same ecological strategy.[7]

HistoryEdit

The first species, Acidobacterium capsulatum, of this phylum was discovered in 1991.[24] However, Acidobacteria were not recognized as a novel division until 1997,[10] and were not recognized as a phylum until 2012.[25]

MetabolismEdit

CarbonEdit

Some members of subdivision 1 are able to use D-glucose, D-xylose, and lactose as carbon sources,[7] but are unable to use fucose or sorbose.[26] Members of subdivision 1 also contain enzymes such as galactosidases used in the breakdown of sugars.[7] Members of subdivision 4 have been found to use chitin as a carbon source.[27][28][7]

NitrogenEdit

There has been no clear evidence that Acidobacteria are involved in nitrogen-cycle processes such as nitrification, denitrification, or nitrogen fixation.[7] However, Geothrix fermantans was shown to be able to reduce nitrate and contained the norB gene.[7] The NorB gene was also identified in Koribacter verstailis and Solibacter usitatus.[29][7] In addition, the presence of the nirA gene has been observed in members of subdivision 1.[7] Additionally, to date, all genomes have been described to directly uptake ammonium via ammonium channel transporter family genes.[21][7] Acidobacteria can use both inorganic and organic nitrogen as their nitrogen sources.

PhylogenyEdit

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[30][31] and the phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project.[32]


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)

ReferencesEdit

  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 1892891. 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 (ed.). Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons. pp. 1–5. doi:10.1002/9781118960608.pbm00001. ISBN 9781118960608.
  6. ^ Dunbar, John Barns, Susan M. Ticknor, Lawrence O. Kuske, Cheryl R. Empirical and Theoretical Bacterial Diversity in Four Arizona Soils. American Society for Microbiology. OCLC 679526952.CS1 maint: multiple names: authors list (link)
  7. ^ a b c d e f g h i j k l m 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. PMC 4885859. PMID 27303369.
  8. ^ 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. PMC 2997719.
  9. ^ 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.
  10. ^ 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 168668. PMID 9293013.
  11. ^ 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.
  12. ^ 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.
  13. ^ 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.
  14. ^ 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.
  15. ^ 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.
  16. ^ 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.
  17. ^ 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 4228153. PMID 25387460.
  18. ^ 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. PMC 1393200. PMID 16517631.
  19. ^ 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.
  20. ^ 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.CS1 maint: multiple names: authors list (link)
  21. ^ a b c 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.CS1 maint: multiple names: authors list (link)
  22. ^ 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.
  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". LPSN. Retrieved 26 November 2017.
  26. ^ 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.
  27. ^ 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.
  28. ^ 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.
  29. ^ 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.
  30. ^ 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.
  31. ^ See the NCBI webpage on Chlorobi Data extracted from Sayers; et al. "NCBI Taxonomy Browser". National Center for Biotechnology Information. Retrieved 2016-09-09.
  32. ^ 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 linksEdit