Biology:Acidobacteriota

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Short description: Phylum of bacteria

Acidobacteriota
Acidobacterium.jpg
Acidobacterium cf. capsulatum
Scientific classification e
Domain: Bacteria
Phylum: Acidobacteriota
Thrash and Coates 2021[1]
Type genus
Acidobacterium
Kishimoto et al. 1991
Classes[2]
  • "Acidobacteriia"
  • Blastocatellia
  • "Ca. Guanabacteria"
  • Holophagae
  • "Ca. Polarisedimenticolia"
  • Thermoanaerobaculia
  • Vicinamibacteria
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. ↑ "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol 71 (10): 5056. 2021. doi:10.1099/ijsem.0.005056. PMID 34694987. 
  2. ↑ 2.0 2.1 "Acidobacteriota". List of Prokaryotic names with Standing in Nomenclature (LPSN). https://lpsn.dsmz.de/phylum/acidobacteriota. 
  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. doi:10.1128/AEM.02012-06. PMID 17337544. Bibcode: 2007ApEnM..73.3113B. 
  5. ↑ 5.0 5.1 5.2 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. 
  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. PMID 34220772. 
  8. ↑ 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. 
  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. doi:10.1128/AEM.68.6.3035-3045.2002. OCLC 679526952. PMID 12039765. Bibcode: 2002ApEnM..68.3035D. 
  10. ↑ 10.00 10.01 10.02 10.03 10.04 10.05 10.06 10.07 10.08 10.09 10.10 10.11 10.12 10.13 10.14 10.15 10.16 10.17 10.18 10.19 10.20 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. 
  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. doi:10.1038/ismej.2008.127. ISSN 1751-7362. PMID 19129864. Bibcode: 2009ISMEJ...3..442J. 
  12. ↑ 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. Bibcode: 2007Ecol...88.1354F. 
  13. ↑ 13.0 13.1 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. Bibcode: 1997ApEnM..63.3614K. 
  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. doi:10.1007/BF00264378. PMID 8085918. Bibcode: 1994ArMic.162...85L. 
  15. ↑ 15.0 15.1 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. 
  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. doi:10.1128/AEM.02140-06. PMID 17293520. Bibcode: 2007ApEnM..73.2708E. 
  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. doi:10.1128/aem.72.3.1719-1728.2006. ISSN 0099-2240. PMID 16517615. Bibcode: 2006ApEnM..72.1719J. 
  20. ↑ 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. 
  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. doi:10.1128/aem.72.3.1852-1857.2006. ISSN 0099-2240. PMID 16517631. Bibcode: 2006ApEnM..72.1852S. 
  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. doi:10.1111/j.1574-6941.2007.00402.x. ISSN 0168-6496. PMID 18028401. Bibcode: 2008FEMME..63..107K. 
  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. 
  24. ↑ 24.0 24.1 24.2 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. 
  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. 
  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. 
  27. ↑ Euzeby JP. "Taxa above the rank of class - Acidobacteria". http://www.bacterio.net/-aboveclass.html#acidobacteria. 
  28. ↑ "Genome List - Genome - NCBI". https://www.ncbi.nlm.nih.gov/genome/browse#!/prokaryotes/Acidobacteria. 
  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. 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. 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. "Acidobacteriota". 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. 
  34. ↑ "Refining the taxonomic structure of the phylum Acidobacteria". Int J Syst Evol Microbiol 68 (12): 3796–3806. 2018. doi:10.1099/ijsem.0.003062. PMID 30325293. 
  35. ↑ "The LTP". https://imedea.uib-csic.es/mmg/ltp/#LTP. 
  36. ↑ "LTP_all tree in newick format". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_08_2023.ntree. 
  37. ↑ "LTP_08_2023 Release Notes". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_08_2023_release_notes.pdf. 
  38. ↑ "GTDB release 08-RS214". https://gtdb.ecogenomic.org/about#4%7C. 
  39. ↑ "bac120_r214.sp_label". https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/bac120_r214.sp_labels.tree. 
  40. ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/. 
  41. ↑ "New bacterial and archaeal lineages discovered in organic rich sediments of a large tropical Bay". Mar Genomics 54: 100789. 2020. doi:10.1016/j.margen.2020.100789. PMID 32563694. Bibcode: 2020MarGn..5400789T. 

External links

Wikidata ☰ Q73346630 entry



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