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Acidobacteria

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Acidobacteria
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{{Taxobox| name = Acidobacteria| image = Acidobacterium.jpg| image_caption = Acidobacterium| domain = Bacteria| phylum = Acidobacteria
YEAR = 2012 DOI = 10.1099/IJS.0.68147-0 VOLUME = 62 PAGES = 1–4, | subdivision_ranks = Class| subdivision = AcidobacteriaBlastocatelliaHolophagae}}Acidobacteria is a phylum of bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.JOURNAL, Barns SM, Cain EC, Sommerville L, Kuske CR, Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum, Appl. Environ. Microbiol., 73, 9, 3113–6, 2007, 17337544, 10.1128/AEM.02012-06, 1892891, JOURNAL, Quaiser A, Ochsenreiter T, Lanz C, Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics, Mol. Microbiol., 50, 2, 563–75, 2003, 14617179, 10.1046/j.1365-2958.2003.03707.x, etal, RAPPE > FIRST1 = M. S. FIRST2 = S. J., The Uncultured Microbial Majority, Annual Review of Microbiology, 57, 369–394, 2003, 14527284, 10.1146/annurev.micro.57.030502.090759,

Description

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.BOOK, Bergey's Manual of Systematics of Archaea and Bacteria, 1–5, Acidobacteria phyl. nov., 2015, 10.1002/9781118960608.pbm00001, Thrash JC, Coates JD, Whitman WB, John Wiley & Sons, 9781118960608, The members of this phylum are particularly abundant in soil habitats representing up to 52% of the total bacterial community.BOOK,weblink Empirical and Theoretical Bacterial Diversity in Four Arizona Soils, Dunbar, John Barns, Susan M. Ticknor, Lawrence O. Kuske, Cheryl R., American Society for Microbiology, 679526952, Environmental factors such as pH and nutrients have been seen to drive Acidobacteria dynamics.JOURNAL, 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,weblink Frontiers in Microbiology, 7, 10.3389/fmicb.2016.00744, 1664-302X, JOURNAL, 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,weblink The ISME Journal, 3, 4, 442–453, 10.1038/ismej.2008.127, 1751-7362, JOURNAL, Fierer, Noah, Bradford, Mark A., Jackson, Robert B., June 2007, TOWARD AN ECOLOGICAL CLASSIFICATION OF SOIL BACTERIA,weblink Ecology, 88, 6, 1354–1364, 10.1890/05-1839, 0012-9658, Many Acidobacteria are acidophilic, including the first described member of the phylum, Acidobacterium capsulatum.JOURNAL, Kuske CR, Barns SM, Busch JD, 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, 1 September 1997, 9293013, 168668, Other notable species are Holophaga foetida,JOURNAL, Liesack, Werner, Bak, Friedhelm, Kreft, Jan-Ulrich, Stackebrandt, E., Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds, Archives of Microbiology, 30 June 1994, 162, 1–2, 85–90, 10.1007/BF00264378, 8085918, Geothrix fermentans,JOURNAL, Coates, J. D., Ellis, D. J., Gaw, C. V., Lovley, D. R., Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer, International Journal of Systematic Bacteriology, 1 October 1999, 49, 4, 1615–1622, 10.1099/00207713-49-4-1615, 10555343, Acanthopleuribacter pedisJOURNAL, Fukunaga, Y, Kurahashi, M, Yanagi, K, Yokota, A, Harayama, S, 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, November 2008, 58, Pt 11, 2597–2601, 10.1099/ijs.0.65589-0, 18984699, and Bryobacter aggregatus.JOURNAL, Kulichevskaya, IS, Suzina, NE, Liesack, W, Dedysh, SN, 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, February 2010, 60, Pt 2, 301–6, 10.1099/ijs.0.013250-0, 19651730, 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. However, these bacteria may be an important contributor to ecosystems, since they are particularly abundant within soils.JOURNAL, Eichorst SA, Breznak JA, Schmidt TM, Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria, Appl. Environ. Microbiol., 73, 8, 2708–17, 2007, 17293520, 10.1128/AEM.02140-06, 1855589, Members of subdivisions 1,4,and 6 are found to be particularly abundant in soils.JOURNAL, Janssen, P. H., 2006-03-01, Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes,weblink Applied and Environmental Microbiology, 72, 3, 1719–1728, 10.1128/aem.72.3.1719-1728.2006, 0099-2240, 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.JOURNAL, 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, 10.1186/s12915-014-0087-z, 1741-7007, 4228153, 25387460, Members of subdivision 1 have been found to dominate in low pH conditions.JOURNAL, 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,weblink Applied and Environmental Microbiology, 72, 3, 1852–1857, 10.1128/aem.72.3.1852-1857.2006, 0099-2240, 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,JOURNAL, 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,weblink FEMS Microbiology Ecology, 63, 1, 107–117, 10.1111/j.1574-6941.2007.00402.x, 0168-6496, potentially due to cell specialization and enzyme stability.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.The majority of Acidobacteria are considered aerobes.BOOK,weblink Influence of Plant Polymers on the Distribution and Cultivation of Bacteria in the Phylum Acidobacteria ▿ †, Eichorst, Stephanie A. Kuske, Cheryl R. Schmidt, Thomas M., American Society for Microbiology (ASM), 744821434, BOOK,weblink Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments., Eichorst, Stephanie A. Trojan, Daniela. Roux, Simon. Herbold, Craig. Rattei, Thomas. Woebken, Dagmar., 1051354840, There are some Acidobacteria that are considered anaerobes within subdivision 8JOURNAL, 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, 10.1099/00207713-49-4-1615, 10555343, and subdivision 23.JOURNAL, 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,weblink INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 63, Pt 11, 4149–4157, 10.1099/ijs.0.051425-0, 1466-5026, 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.Members of the Acidobacteria phylum have been considered oligotrophic bacteria due to high abundances in low organic carbon environments. However, the variation in this phylum may indicate that they may not have the same ecological strategy.

History

The first species, Acidobacterium capsulatum, of this phylum was discovered in 1991.JOURNAL, Kishimoto, Noriaki, Kosako, Yoshimasa, Tano, Tatsuo, Acidobacterium capsulatum gen. nov., sp. nov.: An acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment, Current Microbiology, 31 December 1990, 22, 1, 1–7, 10.1007/BF02106205, However, Acidobacteria were not recognized as a novel division until 1997, and were not recognized as a phylum until 2012.WEB,weblink Taxa above the rank of class - Acidobacteria, LPSN, Euzeby JP, 26 November 2017,

Metabolism

Carbon

Some members of subdivision 1 are able to use D-glucose, D-xylose, and lactose as carbon sources, but are unable to use Fucose or Sorbose.JOURNAL, Li, Zijie, Gao, Yahui, Nakanishi, Hideki, Gao, Xiaodong, Cai, Li, 2013-11-12, Biosynthesis of rare hexoses using microorganisms and related enzymes,weblink Beilstein Journal of Organic Chemistry, 9, 2434–2445, 10.3762/bjoc.9.281, 1860-5397, Members of subdivision 1 also contain enzymes such as Galactosidases used in the breakdown of sugars. Members of subdivision 4 have been found to use chitin as a carbon source.JOURNAL, 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,weblink INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 64, Pt 6, 1866–1875, 10.1099/ijs.0.060236-0, 1466-5026, JOURNAL, 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,weblink Systematic and Applied Microbiology, 36, 2, 82–89, 10.1016/j.syapm.2012.11.002, 0723-2020,

Nitrogen

There has been no clear evidence that Acidobacteria are involved in N-cycle processes such as nitrification, denitrification, or nitrogen fixation. However, Geothrix fermantans was shown to be able to reduce nitrate and contained the norB gene. The NorB gene was also identified in Koribacter verstailis and Solibacter usitatus.JOURNAL, 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,weblink International Journal of Systematic Bacteriology, 49, 4, 1615–1622, 10.1099/00207713-49-4-1615, 0020-7713, In addition, the presence of the nirA gene has been observed in members of subdivision 1. Additionally, to date, all genomes have been described to directly uptake ammonium via ammonium channel transporter family genes.BOOK,weblink Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments., Eichorst, Stephanie A. Trojan, Daniela. Roux, Simon. Herbold, Craig. Rattei, Thomas. Woebken, Dagmar., 1051354840, JOURNAL, 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,weblink Frontiers in Microbiology, 7, 10.3389/fmicb.2016.00744, 1664-302X, Acidobacteria can use both inorganic and organic nitrogen as their N sources.

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)See the List of Prokaryotic names with Standing in Nomenclature. Data extracted from WEB, J.P. Euzéby,weblink Acidobacteria, 2016-09-09, yes,weblink" title="web.archive.org/web/20130127030659weblink">weblink 2013-01-27, See the NCBI webpage on Chlorobi Data extracted from WEB, Sayers,weblink NCBI Taxonomy Browser, National Center for Biotechnology Information, 2016-09-09, etal, and the phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project.See the All-Species Living Tree Project weblink. Data extracted from the WEB,weblink 16S rRNA-based LTP release 123 (full tree), Silva Comprehensive Ribosomal RNA Database, 2016-09-09, {{Clade| style=font-size:100%;line-height:80%|1={{clade
|label1=Holophagae
|1={{clade
|label1=Acanthopleuribacteraceae
|1=Acanthopleuribacter pedis Fukunaga et al. 2008
|label2=Holophagaceae
|2={{clade
|1=Geothrix fermentans Coates et al. 1999
|2=Holophaga foetida Liesack et al. 1995
}}
}}
|2={{clade
|label1="Solibacteres"
|1={{clade
|1=Bryobacter aggregatus Kulichevskaya et al. 2010
|2=Paludibaculum fermentans Kulichevskaya et al. 2014
}}
|label2=Acidobacteriaceae
|2={{clade
|1={{clade
|1=Acidobacterium capsulatum Kishimoto et al. 1991
|2={{clade
|1=Telmatobacter bradus Pankratov and Dedysh 2012
|label2=Acidicapsa
|2={{clade
|1=A. borealis Kulichevskaya et al. 2012 (type sp.)
|2=A. ligni Kulichevskaya et al. 2012
}}
}}
}}
|2={{clade
|1={{clade
|1=Bryocella elongata Dedysh et al. 2012
|label2=Edaphobacter
|2={{clade
|1=E. aggregans Koch et al. 2008 emend. Dedysh et al. 2012
|2=E. modestus Koch et al. 2008 (type sp.)
}}
}}
|2={{clade
|1="Granulicella" mallensis Männistö et al. 2012
|2={{clade
|label1=Terriglobus
|1={{clade
|1=T. aquaticus Baik et al. 2013
|2={{clade
|1=T. roseus Eichorst et al. 2007 (type sp.)
|2={{clade
|1=T. saanensis Männistö et al. 2011
|2=T. tenax Whang et al. 2014
}}
}}
}}
|label2=Granulicella
|2={{clade
|1={{clade
|1=G. cerasi Yamada et al. 2014
|2=G. paludicola Pankratov and Dedysh 2010 (type sp.)
}}
|2={{clade
|1=G. pectinivorans Pankratov and Dedysh 2010
|2={{clade
|1=G. sapmiensis Männistö et al. 2012
|2={{clade
|1=G. aggregans Pankratov and Dedysh 2010
|2={{clade
|1=G. tundricola Männistö et al. 2012
|2={{clade
|1=G. arctica Männistö et al. 2012
|2=G. rosea Pankratov and Dedysh 2010
}}
}}
}}
}}
}}
}}
}}
}}
}}
}}
}}
}}
}}Notes:â™  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

{{Reflist|30em}}

External links

{{Extremophile}}{{Bacteria classification}}{{Life on Earth}}{{Taxonbar|from=Q41579}}


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