Acidobacteriota Explained

Acidobacteriota is a phylum of Gram-negative bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.[1] [2] [3]

Description

Members of this phylum are physiologically diverse, and can be found in a variety of environments including soil, decomposing wood,[4] 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 Acidobacteriota dynamics.[7] [8] [9] Many Acidobacteriota are acidophilic, including the first described member of the phylum, Acidobacterium capsulatum.[10]

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, yet, progress is still quite slow. These new methods have only allowed approximately 30% of subdivisions to have species documented.

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,[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.[2] 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 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.[17]

Members of subdivision 1 have been found to dominate in low pH conditions.[18] [7] 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,[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.[2]

The majority of Acidobacteriota are considered aerobes.[20] [21] There are some Acidobacteriota that are considered anaerobes within subdivision 8[12] and subdivision 23.[22] 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.[21]

Members of the Acidobacteriota 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]

History

The first species, Acidobacterium capsulatum, of this phylum was discovered in 1991.[23] However, Acidobacteriota were not recognized as a distinct clade until 1997,[10] and were not recognized as a phylum until 2012.[24] First genome was sequenced in 2006.[25]

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.

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.

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.

Metabolism

Carbon

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]

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.

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.

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. 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.[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] 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 and National Center for Biotechnology Information.[30]

See also

External links

Notes and References

  1. 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. 2007ApEnM..73.3113B .
  2. 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. 25162803 . etal.
  3. Rappe . M. S.. Giovannoni . S. J.. The Uncultured Microbial Majority. Annual Review of Microbiology. 57. 369–394. 2003. 14527284. 10.1146/annurev.micro.57.030502.090759.
  4. 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. 34220772 . 10.3389/fmicb.2021.685303 . 8247643. 1664-302X. free.
  5. 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 .
  6. Empirical and Theoretical Bacterial Diversity in Four Arizona Soils. Dunbar, John. Barns, Susan M.. Ticknor, Lawrence O.. Kuske, Cheryl R.. Applied and Environmental Microbiology. 2002. 68. 6. 3035–3045. American Society for Microbiology. 10.1128/AEM.68.6.3035-3045.2002. 12039765. 123964. 2002ApEnM..68.3035D . 679526952.
  7. 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. 10.3389/fmicb.2016.00744. 27303369. 1664-302X. 4885859. free.
  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. 10.1038/ismej.2008.127. 19129864. 1751-7362. 2997719. 2009ISMEJ...3..442J .
  9. Fierer. Noah. Bradford. Mark A.. Jackson. Robert B.. 7687418. June 2007. Ecology. 88. 6. 1354–1364. 10.1890/05-1839. 17601128. 0012-9658. Toward an Ecological Classification of Soil Bacteria. 2007Ecol...88.1354F .
  10. 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. 10.1128/AEM.63.9.3614-3621.1997 . 9293013 . 168668 . 1997ApEnM..63.3614K .
  11. 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. 1994ArMic.162...85L . 23516245.
  12. 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. free.
  13. 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. free.
  14. 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.
  15. 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. 2007ApEnM..73.2708E .
  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. 10.1128/aem.72.3.1719-1728.2006. 16517615. 0099-2240. 1393246. 2006ApEnM..72.1719J .
  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. 10.1186/s12915-014-0087-z. 1741-7007. 4228153 . 25387460 . free .
  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. 10.1128/aem.72.3.1852-1857.2006. 16517631. 1393200. 2006ApEnM..72.1852S . 0099-2240.
  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. 10.1111/j.1574-6941.2007.00402.x. 18028401. 2008FEMME..63..107K . 0168-6496. free.
  20. Book: 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). 744821434.
  21. Book: 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.. 1051354840.
  22. Losey. N. A.. Stevenson. B. S.. Busse. H.-J.. Damste. J. S. S.. Rijpstra. W. I. C.. Rudd. S.. Lawson. P. A.. 32574193. 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. 10.1099/ijs.0.051425-0. 23771620. 1466-5026.
  23. 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. 20636659.
  24. Web site: Taxa above the rank of class - Acidobacteria . LPSN . Euzeby JP . 26 November 2017.
  25. Web site: Genome List - Genome - NCBI . 2022-06-19 . www.ncbi.nlm.nih.gov.
  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. 10.3762/bjoc.9.281. 24367410. 1860-5397. free. 3869271.
  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. 10.1099/ijs.0.060236-0. 24573163. 1466-5026. 10033/344212. free.
  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. 10.1016/j.syapm.2012.11.002. 23266188. 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. 10.1099/00207713-49-4-1615. 10555343. 0020-7713. free.
  30. Web site: Sayers. Acidobacteriota . 2021-03-20 . National Center for Biotechnology Information (NCBI) taxonomy database . etal.
  31. Dedysh SN, ((Yilmaz P.)) . Refining the taxonomic structure of the phylum Acidobacteria . Int J Syst Evol Microbiol . 2018 . 68 . 12 . 3796–3806 . 10.1099/ijsem.0.003062 . 30325293. 53502177 . free .
  32. Web site: The LTP . 20 November 2023.
  33. Web site: LTP_all tree in newick format. 20 November 2023.
  34. Web site: LTP_08_2023 Release Notes. 20 November 2023.
  35. Web site: GTDB release 08-RS214 . Genome Taxonomy Database. 10 May 2023.
  36. Web site: bac120_r214.sp_label . Genome Taxonomy Database. 10 May 2023.
  37. Web site: Taxon History . Genome Taxonomy Database. 10 May 2023.

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