Prokaryota
Superregnum: Bacteria
Phylum: Acidobacteria
Classes: Acidobacteriia – Blastocatellia – Holophagae – Thermoanaerobaculia – Vicinamibacteria
Acidobacteria (incertae sedis): Acidobacteria subdivision 2 – Acidobacteria subdivision 13 – Acidobacteria subdivision 22
Name
Acidobacteria Thrash & Coates, 2012
Type order: Acidobacteriales Cavalier-Smith, 2002
Synonyms
Heterotypic
Acidobacteriota
Acidobacterium group
Acidobacteraeota Oren et al., 2015
References
Primary references
Thrash J.C. & Coates J.D. 2011. Phylum XVII. Acidobacteria phyl. nov. pp. 725–735 in Krieg N.R., Staley J.T., Brown D.R., Hedlund B.P., Paster B.J., Ward N.L., Ludwig W. & Whitman W.B. (ed.), Bergey's Manual of Systematic Bacteriology, Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Second ed. Springer. DOI: 10.1007/978-0-387-68572-4_6 Paywall. Reference page.
Euzéby, J. 2012. List of new names and new combinations previously effectively, but not validly, published: Validation List No. 143. International Journal of Systematic Bacteriology 62:1-4. DOI: 10.1099/ijs.0.039487-0 Open access. Reference page.
Additional references
Dedysh, S.N. & Yilmaz, P. 2018. Refining the taxonomic structure of the phylum Acidobacteria. International Journal of Systematic and Evolutionary Microbiology 68:3796–3806. DOI: 10.1099/ijsem.0.003062 Open access Reference page.
Euzéby, J. 2012. List of new names and new combinations previously effectively, but not validly, published: Validation List No. 143. International Journal of Systematic Bacteriology 62:1-4. DOI: 10.1099/ijs.0.039487-0 Open access. Reference page.
Oren, A., da Costa, M.S., Garrity, G.M., Rainey, F.A., Rossello-Mora, R., Schink, B., Sutcliffe, I., Trujillo, M.E., & Whitman, W.B. 2015. Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes. International Journal of Systematic and Evolutionary Microbiology 65(11):4284–4287. DOI: 10.1099/ijsem.0.000664 Open access Reference page.
Whitman, W.B., Oren, A., Chuvochina, M., da Costa, M.S., Garrity, G.M., Rainey, F.A., Rosselló-Móra, R., Schink, B., Sutcliffe, I., Trujillo, M.E., & Ventura, S. 2018. Proposal of the suffix -ota to denote phyla. Addendum to 'Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes'. International Journal of Systematic and Evolutionary Microbiology 68(3):967-969. DOI: 10.1099/ijsem.0.002593 Open access. Reference page.
Links
Acidobacteria – Taxon details on Encyclopedia of Life (EOL).
Global Biodiversity Information Facility. 2019. GBIF Backbone Taxonomy. Checklist dataset. Taxon: Acidobacteria.
Acidobacteria – Taxon details on Integrated Taxonomic Information System (ITIS).
LPSN link : Acidobacteria Thrash and Coates 2012, phyl. nov.
Acidobacteria – Taxon details on National Center for Biotechnology Information (NCBI).
Acidobacteria in the World Register of Marine Species
European Nucleotide Archive
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
List of bacterial orders
List of bacteria genera
References
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