Acidobacteriota

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]

Acidobacteriota
Acidobacterium cf. capsulatum
Scientific 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

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]

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]

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]

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] GTDB 07-RS207 by Genome Taxonomy Database[35][36][37]
 
 

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

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Holophagae Fukunaga et al. 2008

 
 
 

"Aminicenantia"

 
 
 

"Guanabacteria" Tschoeke et al. 2020[38]

 
 
 

Thermoanaerobaculia Dedysh and Yilmaz 2018

 
 
 

Vicinamibacteria Dedysh and Yilmaz 2018

 
 
 

Blastocatellia Thrash and Coates 2010

 
 

"Acidobacteriia" Pascual et al. 2016

 
 
 
 
 
 
 

See also

References
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  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. doi:10.1128/AEM.02012-06. PMC 1892891. PMID 17337544.
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  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.
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