Acidobacteria: Comparison
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Acidobacteria is a phylum of bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.

  • acidobacteria
  • phylum
  • physiologically

1. Description

Members of this phylum are physiologically diverse, and can be found in a variety of environments including soil, decomposing wood,[1] hot springs, oceans, caves, and metal-contaminated soils.[2] The members of this phylum are particularly abundant in soil habitats representing up to 52% of the total bacterial community.[3] Environmental factors such as pH and nutrients have been seen to drive Acidobacteria dynamics.[4][5][6] Many Acidobacteria are acidophilic, including the first described member of the phylum, Acidobacterium capsulatum.[7]

Other notable species are Holophaga foetida,[8] Geothrix fermentans,[9] Acanthopleuribacter pedis[10] and Bryobacter aggregatus.[11] 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.[12] However, these bacteria may be an important contributor to ecosystems, since they are particularly abundant within soils.[13] Members of subdivisions 1, 4, and 6 are found to be particularly abundant in soils.[14]

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.[15]

Members of subdivision 1 have been found to dominate in low pH conditions.[4][16] 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,[17] potentially due to cell specialization and enzyme stability.[4]

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.[12]

The majority of Acidobacteria are considered aerobes.[18][19] There are some Acidobacteria that are considered anaerobes within subdivision 8[9] and subdivision 23.[20] 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.[19]

Members of the Acidobacteria phylum have been considered oligotrophic bacteria due to high abundances in low organic carbon environments.[4] However, the variation in this phylum may indicate that they may not have the same ecological strategy.[4]

2. History

The first species, Acidobacterium capsulatum, of this phylum was discovered in 1991.[21] However, Acidobacteria were not recognized as a novel division until 1997,[7] and were not recognized as a phylum until 2012.[22] First genome was sequenced in 2007.[23]

3. Metabolism

3.1. Carbon

Some members of subdivision 1 are able to use D-glucose, D-xylose, and lactose as carbon sources,[4] but are unable to use fucose or sorbose.[24] Members of subdivision 1 also contain enzymes such as galactosidases used in the breakdown of sugars.[4] Members of subdivision 4 have been found to use chitin as a carbon source.[4][25][26]

3.2. Nitrogen

There has been no clear evidence that Acidobacteria are involved in nitrogen-cycle processes such as nitrification, denitrification, or nitrogen fixation.[4] However, Geothrix fermantans was shown to be able to reduce nitrate and contained the norB gene.[4] The NorB gene was also identified in Koribacter verstailis and Solibacter usitatus.[4][27] In addition, the presence of the nirA gene has been observed in members of subdivision 1.[4] Additionally, to date, all genomes have been described to directly uptake ammonium via ammonium channel transporter family genes.[4][19] Acidobacteria can use both inorganic and organic nitrogen as their nitrogen sources.

4. Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[28] and the National Center for Biotechnology Information (NCBI).[29]

Phylogeny of Acidobacteria using 16S rRNA (LTP release 132[30])

Phylogeny of Acidobacteria using 16S rRNA (LTP release 132[30])
 
 
Vicinamibacteria
 

Luteitalea

 
 

Vicinamibacter

 
 
Holophagae
Acanthopleuribacteraceae

Acanthopleuribacter

 
Holophagaceae
 

Geothrix

 
 

Holophaga

 
 
 
 
Acidobacteriia
Bryobacteraceae
 

Bryobacter

 
 

Paludibaculum

 
 
 

Acidobacteriaceae

 
 
 

Phylogeny of Acidobacteria (Annotree v1.2.0,[31][32] GTDB 05-RS95[33][34])
 
 

Holophagaceae

 
 
"Aminicenantia"
 

"Aminicenantaceae"

 
 

"Saccharicenantaceae"

 
 
 
 

Thermoanaerobaculaceae

 
 
 

Vicinamibacteraceae

 
 
Blastocatellia
 

"Chloracidobacteriaceae"

 
 

Pyrinomonadaceae

 
 
Acidobacteria
Bryobacterales

Bryobacteraceae

 
Acidobacteriales
 

"Korobacteraceae"

 
 

Acidobacteriaceae

 
 
 
 
 
 
 
 

Phylogeny of Acidobacteria (Annotree v1.2.0,[31][32] GTDB 05-RS95[33][34])

  • 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
        • Genus Acanthopleuribacter 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"
      • Family "Chloracidobacteriaceae"
        • Genus Chloracidobacterium Tank & Bryant 2015
    • 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
  • 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
        • Genus Acanthopleuribacter 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"
      • Family "Chloracidobacteriaceae"
        • Genus Chloracidobacterium Tank & Bryant 2015
    • 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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