Acidobacteriota
Acidobacterium cf. capsulatum
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Acidobacteriota
Thrash and Coates 2021[1]
Type genus
Acidobacterium
Kishimoto et al. 1991
Classes[2]
Synonyms
  • "Acidobacteria" Thrash and Coates 2010[3]
  • "Acidobacteraeota" Oren et al. 2015
  • "Acidobacteriota" Whitman et al. 2018

Acidobacteriota is a phylum of Gram-negative bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.[4][5][6]

Description

Members of this phylum are physiologically diverse, and can be found in a variety of environments including soil, decomposing wood,[7] hot springs, oceans, caves, and metal-contaminated soils.[8] The members of this phylum are particularly abundant in soil habitats representing up to 52% of the total bacterial community.[9] Environmental factors such as pH and nutrients have been seen to drive Acidobacteriota dynamics.[10][11][12] Many Acidobacteriota are acidophilic, including the first described member of the phylum, Acidobacterium capsulatum.[13]

There is much that is unknown about Acidobacteria both in their form and function. Thus, this is a growing field of microbiology. Some of this uncertainty can be attributed to the difficulty with which these bacteria are grown in the laboratory. There has been recent success in propagation by using low concentrations of nutrients in combination with high amounts of CO2,[10] yet, progress is still quite slow. These new methods have only allowed approximately 30% of subdivisions to have species documented.[10]

Additionally, many of the samples sequenced do not have taxonomic names as they have not yet been fully characterized. This area of study is a very current topic, and scientific understanding is expected to grow and change as new information comes to light.

Other notable species are Holophaga foetida,[14] Geothrix fermentans,[15] Acanthopleuribacter pedis[16] and Bryobacter aggregatus.[17] 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.[5] However, these bacteria may be an important contributor to ecosystems, since they are particularly abundant within soils.[18] Members of subdivisions 1, 4, and 6 are found to be particularly abundant in soils.[19]

As well as their natural soil habitat, unclassified subdivision 2 Acidobacteriota have also been identified as a contaminant of DNA extraction kit reagents, which may lead to their erroneous appearance in microbiota or metagenomic datasets.[20]

Members of subdivision 1 have been found to dominate in low pH conditions.[21][10] Additionally, Acidobacteriota from acid mine drainage have been found to be more adapted to acidic pH conditions (pH 2-3) compared to Acidobacteriota from soils,[22] potentially due to cell specialization and enzyme stability.[10]

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.[5]

The majority of Acidobacteriota are considered aerobes.[23][24] There are some Acidobacteriota that are considered anaerobes within subdivision 8[15] and subdivision 23.[25] It has been found that some strains of Acidobacteriota originating from soils have the genomic potential to respire oxygen at atmospheric and sub-atmospheric concentrations.[24]

Members of the Acidobacteriota phylum have been considered oligotrophic bacteria due to high abundances in low organic carbon environments.[10] However, the variation in this phylum may indicate that they may not have the same ecological strategy.[10]

History

The first species, Acidobacterium capsulatum, of this phylum was discovered in 1991.[26] However, Acidobacteriota were not recognized as a distinct clade until 1997,[13] and were not recognized as a phylum until 2012.[27] First genome was sequenced in 2006.[28]

Subdivisions

In an effort to further classify Acidobacteria, 16S rRNA gene regions were sequenced from many different strains. These sequences lead to the formation of subdivisions within the phyla. Today, there are 26 accepted subdivisions recognized in the Ribosomal Database Project.[10]

Much of this variety comes from populations of acidobacteria found in soils contaminated with uranium. Therefore, most of the known species in this phyla are concentrated in a few of the subdivisions, the largest being #1. Most of these microbes are aerobes, and they are all heterotrophic. Subdivision 1 contains 11 of the known genera in addition to the majority of the species that have been able to be cultivated thus far.[10]

Within the 22 known genera, there are 40 conclusive species. The genera are divided amongst subdivisions 3, 4, 8, 10, 23, and 1. As the Acidobateria are a developing area of microbiology, it is hypothesized that these numbers will change drastically with further study.[10]

Metabolism

Carbon

Some members of subdivision 1 are able to use D-glucose, D-xylose, and lactose as carbon sources,[10] but are unable to use fucose or sorbose.[29] Members of subdivision 1 also contain enzymes such as galactosidases used in the breakdown of sugars.[10] Members of subdivision 4 have been found to use chitin as a carbon source.[30][31][10]

Despite the presence of genetic information generally known to encode for carbohydrate processing machinery in various genera of Acidobacteria, several experimental studies have demonstrated the inability to break down various polysaccharides.[10]

Cellulose is the main component of plant cell walls and a seemingly opportune resource for carbon. However, only a single species across all subdivisions has been shown to process it, Telmactobacter bradus from subvision 1. Scientists note that it is much too early in their understanding of the field to draw conclusions about carbon processing in Acidobacteria, but believe that xylan degradation (a polysaccharide primarily found in the secondary cell wall of plants) currently appears to be the most universal carbon breakdown ability.[10]

Researchers believe that an additional factor in the lack of understanding of carbon degradation by acidobacteria may stem from the present limited ability to provide adequate cultivation conditions.[10] To study the natural behavior of these bacteria, they must grow and live in a controlled, observable environment. If such a habitat cannot be provided, recorded data cannot reliably report on the activity of the microbes in question. Therefore, the inconsistencies between genome sequence based predictions and observed carbon processes may be explained by present study methods.

Nitrogen

There has been no clear evidence that Acidobacteriota are involved in nitrogen-cycle processes such as nitrification, denitrification, or nitrogen fixation.[10] However, Geothrix fermantans was shown to be able to reduce nitrate and contained the norB gene.[10] The NorB gene was also identified in Koribacter verstailis and Solibacter usitatus.[32][10] In addition, the presence of the nirA gene has been observed in members of subdivision 1.[10] Additionally, to date, all genomes have been described to directly uptake ammonium via ammonium channel transporter family genes.[24][10] Acidobacteriota can use both inorganic and organic nitrogen as their nitrogen sources.

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature[2] and National Center for Biotechnology Information.[33]

16S rRNA based phylogeny[34] 16S rRNA based LTP_08_2023[35][36][37] 120 single copy marker proteins based GTDB 08-RS214[38][39][40]

Nitrospirota (outgroup)

"Candidatus Aminicenantes"

"Candidatus Fischerbacteria"

Acidobacteriota

Class 1-11

Class 4-3

Thermoanaerobaculia

Class 4-1

Class 1-10

Holophagae

Class 1-6

Vicinamibacteria

Class 6-2

Class 1-4

Class 6-1

Class 1-3

Class 1-2

"Acidobacteriia"

Blastocatellia

Thermoanaerobaculia

Vicinamibacteria

Holophagae

Blastocatellia

Acidobacteria

"Holophagia" Oren, Parte & Garrity 2016

"Fischerbacteria"

"Guanabacteria" Tschoeke et al. 2020[41]

"Aminicenantia"

Thermoanaerobaculia Dedysh and Yilmaz 2018

"Polarisedimenticolia" Flieder et al. 2021

Vicinamibacteria Dedysh and Yilmaz 2018

Blastocatellia Thrash and Coates 2010

"Acidobacteriia" Pascual et al. 2016

See also

References

  1. ↑ Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi:10.1099/ijsem.0.005056. PMID 34694987. S2CID 239887308.
  2. 1 2 Euzéby JP, Parte AC. "Acidobacteriota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved May 6, 2022.
  3. ↑ "Validation List no. 143". Int. J. Syst. Evol. Microbiol. 62: 1–4. 2012. doi:10.1099/ijs.0.68147-0.
  4. ↑ 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. Bibcode:2007ApEnM..73.3113B. doi:10.1128/AEM.02012-06. PMC 1892891. PMID 17337544.
  5. 1 2 3 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. S2CID 25162803.
  6. ↑ 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.
  7. ↑ 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. PMC 8247643. PMID 34220772.
  8. ↑ 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.
  9. ↑ 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. Bibcode:2002ApEnM..68.3035D. doi:10.1128/AEM.68.6.3035-3045.2002. OCLC 679526952. PMC 123964. PMID 12039765.
  10. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 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.
  11. ↑ 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. Bibcode:2009ISMEJ...3..442J. doi:10.1038/ismej.2008.127. ISSN 1751-7362. PMC 2997719. PMID 19129864.
  12. ↑ Fierer, Noah; Bradford, Mark A.; Jackson, Robert B. (June 2007). "Toward an Ecological Classification of Soil Bacteria". Ecology. 88 (6): 1354–1364. Bibcode:2007Ecol...88.1354F. doi:10.1890/05-1839. ISSN 0012-9658. PMID 17601128. S2CID 7687418.
  13. 1 2 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. Bibcode:1997ApEnM..63.3614K. doi:10.1128/AEM.63.9.3614-3621.1997. PMC 168668. PMID 9293013.
  14. ↑ 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. Bibcode:1994ArMic.162...85L. doi:10.1007/BF00264378. PMID 8085918. S2CID 23516245.
  15. 1 2 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.
  16. ↑ 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.
  17. ↑ 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.
  18. ↑ 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. Bibcode:2007ApEnM..73.2708E. doi:10.1128/AEM.02140-06. PMC 1855589. PMID 17293520.
  19. ↑ 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. Bibcode:2006ApEnM..72.1719J. doi:10.1128/aem.72.3.1719-1728.2006. ISSN 0099-2240. PMC 1393246. PMID 16517615.
  20. ↑ 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.
  21. ↑ 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. Bibcode:2006ApEnM..72.1852S. doi:10.1128/aem.72.3.1852-1857.2006. ISSN 0099-2240. PMC 1393200. PMID 16517631.
  22. ↑ 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. Bibcode:2008FEMME..63..107K. doi:10.1111/j.1574-6941.2007.00402.x. ISSN 0168-6496. PMID 18028401.
  23. ↑ 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.{{cite book}}: CS1 maint: multiple names: authors list (link)
  24. 1 2 3 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.{{cite book}}: CS1 maint: multiple names: authors list (link)
  25. ↑ 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. S2CID 32574193.
  26. ↑ 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. S2CID 20636659.
  27. ↑ Euzeby JP. "Taxa above the rank of class - Acidobacteria". LPSN. Retrieved 26 November 2017.
  28. ↑ "Genome List - Genome - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-06-19.
  29. ↑ 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. PMC 3869271. PMID 24367410.
  30. ↑ 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. hdl:10033/344212. ISSN 1466-5026. PMID 24573163.
  31. ↑ 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.
  32. ↑ 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.
  33. ↑ Sayers; et al. "Acidobacteriota". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  34. ↑ Dedysh SN, Yilmaz P. (2018). "Refining the taxonomic structure of the phylum Acidobacteria". Int J Syst Evol Microbiol. 68 (12): 3796–3806. doi:10.1099/ijsem.0.003062. PMID 30325293. S2CID 53502177.
  35. ↑ "The LTP". Retrieved 20 November 2023.
  36. ↑ "LTP_all tree in newick format". Retrieved 20 November 2023.
  37. ↑ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
  38. ↑ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  39. ↑ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  40. ↑ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
  41. ↑ Tschoeke DA, Coutinho FH, Leomil L, Cavalcanti G, Silva BS, Garcia GD, Dos Anjos LC, Nascimento LB, Moreira LS, Otsuki K, Cordeiro RC, Rezende CE, Thompson FL, Thompson CC. (2020). "New bacterial and archaeal lineages discovered in organic rich sediments of a large tropical Bay". Mar Genomics. 54: 100789. Bibcode:2020MarGn..5400789T. doi:10.1016/j.margen.2020.100789. PMID 32563694. S2CID 219971745.
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