Acidobacteria

Summary

Acidobacteria
Acidobacterium.jpg
Acidobacterium
Scientific classification
Domain:
Phylum:
Acidobacteria

Thrash and Coates 2012[1]
Class
Synonyms
  • Acidobacteraeota Oren et al. 2015
  • "Acidobacteriota" Whitman et al. 2018
  • ?"Aminicenantes" Rinke et al. 2013
  • ?"Fischerbacteria" Anantharaman et al. 2016

Acidobacteria is a phylum of bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.[2][3][4]

Description

Members of this phylum are physiologically diverse, and can be found in a variety of environments including soil, decomposing wood,[5] hot springs, oceans, caves, and metal-contaminated soils.[6] The members of this phylum are particularly abundant in soil habitats representing up to 52% of the total bacterial community.[7] Environmental factors such as pH and nutrients have been seen to drive Acidobacteria dynamics.[8][9][10] Many Acidobacteria are acidophilic, including the first described member of the phylum, Acidobacterium capsulatum.[11]

Other notable species are Holophaga foetida,[12] Geothrix fermentans,[13] Acanthopleuribacter pedis[14] and Bryobacter aggregatus.[15] 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.[3] However, these bacteria may be an important contributor to ecosystems, since they are particularly abundant within soils.[16] Members of subdivisions 1, 4, and 6 are found to be particularly abundant in soils.[17]

As well as their natural soil habitat, unclassified subdivision 2 Acidobacteria have also been identified as a contaminant of DNA extraction kit reagents, which may lead to their erroneous appearance in microbiota or metagenomic datasets.[18]

Members of subdivision 1 have been found to dominate in low pH conditions.[19][8] Additionally, Acidobacteria from acid mine drainage have been found to be more adapted to acidic pH conditions (pH 2-3) compared to Acidobacteria from soils,[20] potentially due to cell specialization and enzyme stability.[8]

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.[3]

The majority of Acidobacteria are considered aerobes.[21][22] There are some Acidobacteria that are considered anaerobes within subdivision 8[13] and subdivision 23.[23] It has been found that some strains of Acidobacteria originating from soils have the genomic potential to respire oxygen at atmospheric and sub-atmospheric concentrations.[22]

Members of the Acidobacteria phylum have been considered oligotrophic bacteria due to high abundances in low organic carbon environments.[8] However, the variation in this phylum may indicate that they may not have the same ecological strategy.[8]

History

The first species, Acidobacterium capsulatum, of this phylum was discovered in 1991.[24] However, Acidobacteria were not recognized as a novel division until 1997,[11] and were not recognized as a phylum until 2012.[25] First genome was sequenced in 2007.[26]

Metabolism

Carbon

Some members of subdivision 1 are able to use D-glucose, D-xylose, and lactose as carbon sources,[8] but are unable to use fucose or sorbose.[27] Members of subdivision 1 also contain enzymes such as galactosidases used in the breakdown of sugars.[8] Members of subdivision 4 have been found to use chitin as a carbon source.[28][29][8]

Nitrogen

There has been no clear evidence that Acidobacteria are involved in nitrogen-cycle processes such as nitrification, denitrification, or nitrogen fixation.[8] However, Geothrix fermantans was shown to be able to reduce nitrate and contained the norB gene.[8] The NorB gene was also identified in Koribacter verstailis and Solibacter usitatus.[30][8] In addition, the presence of the nirA gene has been observed in members of subdivision 1.[8] Additionally, to date, all genomes have been described to directly uptake ammonium via ammonium channel transporter family genes.[22][8] Acidobacteria can use both inorganic and organic nitrogen as their nitrogen sources.

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[31] and the National Center for Biotechnology Information (NCBI).[32]

Phylogeny of Acidobacteria using 16S rRNA (LTP release 132[33])
Vicinamibacteria

Luteitalea

Vicinamibacter

Holophagae
Acanthopleuribacteraceae

Acanthopleuribacter

Holophagaceae

Geothrix

Holophaga

Acidobacteriia
Bryobacteraceae

Bryobacter

Paludibaculum

Acidobacteriaceae

Phylogeny of Acidobacteria (Annotree v1.2.0,[34][35] GTDB 05-RS95[36][37])

Holophagaceae

"Aminicenantia"

"Aminicenantaceae"

"Saccharicenantaceae"

Thermoanaerobaculaceae

Vicinamibacteraceae

Blastocatellia

"Chloracidobacteriaceae"

Pyrinomonadaceae

Acidobacteria
Bryobacterales

Bryobacteraceae

Acidobacteriales

"Korobacteraceae"

Acidobacteriaceae

  • Class "Fischerbacteria" (RIF25)
  • Class "Guanabacteria" Tschoeke et al. 2020
    • Genus "Candidatus Guanabacterium" Tschoeke et al. 2020
  • Class Holophagae Fukunaga et al. 2008
    • Order Thermotomaculales Dedysh & Yilmaz 2018 (Acidobacteria subdivision 10)
      • Family Thermotomaculaceae Dedysh & Yilmaz 2018
        • Genus Thermotomaculum Izumi et al. 2017
    • Order Acanthopleuribacterales Fukunaga et al. 2008
      • Family Acanthopleuribacteraceae Fukunaga et al. 2008
    • Order Holophagales Fukunaga et al. 2008
      • Family Holophagaceae Fukunaga et al. 2008
        • Genus Geothrix Coates et al. 1999
        • Genus Holophaga Liesack et al. 1995
  • Class "Aminicenantia" (OP8)
    • Order "Aminicenantales" Kadnikov et al. 2019
      • Family "Saccharicenantaceae" Kadnikov et al. 2019
        • Genus "Candidatus Saccharicenans" corrig. Kadnikov et al. 2019
      • Family "Aminicenantaceae"
        • Genus "Candidatus Aminicenans" Rinke et al. 2013
  • Class Thermoanaerobaculia Dedysh & Yilmaz 2018 (Acidobacteria subdivision 23)
    • Order Thermoanaerobaculales Dedysh & Yilmaz 2018
      • Family Thermoanaerobaculaceae Dedysh & Yilmaz 2018
        • Genus Thermoanaerobaculum Losey et al. 2013
  • Class Vicinamibacteria Dedysh & Yilmaz 2018 (Acidobacteria subdivision 6)
    • Order Vicinamibacterales Dedysh & Yilmaz 2018
      • Family Vicinamibacteraceae Huber & Overmann 2018
        • Genus "Luteitalea" Vieira et al. 2017
        • Genus "Vicinamibacter" Huber et al. 2013
  • Class Blastocatellia Pascual et al. 2016 (Acidobacteria subdivision 4)
    • Order "Chloracidobacteriales"
    • Order Blastocatellales Pascual et al. 2016
      • Family Arenimicrobiaceae Dedysh & Yilmaz 2018
      • Family Pyrinomonadaceae Wüstet al. 2016
      • Family Blastocatellaceae Pascual et al. 2016
  • Class Acidobacteriia Thrash & Coates 2012
    • Order "Acidoferrales" Epihov et al. 2021
      • Family "Acidoferraceae" Epihov et al. 2021
        • Genus "Candidatus Acidoferrum" Epihov et al. 2021
    • Order Bryobacterales Dedysh & Yilmaz 2018
      • Family Bryobacteraceae Dedysh et al. 2016
        • Genus Bryobacter Kulichevskaya et al. 2010
        • Genus Paludibaculum Kulichevskaya et al. 2014
        • Genus "Candidatus Solibacter" Ward et al. 2009
        • Genus "Candidatus Sulfopaludibacter" Hausmann et al. 2018
    • Order Acidobacteriales Cavalier-Smith 2002
      • Family "Korobacteraceae"
        • Genus "Candidatus Korobacter" corrig. Ward et al. 2009
        • Genus "Candidatus Sulfotelmatobacter" Hausmann et al. 2018
      • Family Acidobacteriaceae Thrash & Coates 2012

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External links

  • Acidobacteria bacterium Ellin345 Genome Page
  • Acidobacterium Genome Projects (from Genomes OnLine Database)
  • Science Daily article
  • Scientific American article
  • acidoseq, A Python package for studying Acidobacteria