Acidobacteria

Abstract

Acidobacteria are one of the globally distributed and highly diverse phyla of the domain Bacteria. These microorganisms inhabit a wide variety of terrestrial and aquatic habitats and are particularly abundant in acidic soils, peatlands and mineral iron‐rich environments. Owing to the difficulties in cultivating Acidobacteria, the taxonomically described diversity within this phylum remains limited. All characterised representatives are Gram‐negative, nonspore‐forming bacteria that display a variety of cell morphologies. Most characterised acidobacteria are chemoheterotrophs, although photoheterotrophic members have also been described. Cells of these bacteria contain a number of characteristic lipids, which may be responsible for their environmental adaptations. Genomes of acidobacteria are up to 10 Mbp in size and encode a wide repertoire of carbohydrate‐active enzymes involved in breakdown, utilisation and biosynthesis of diverse carbohydrates. Their functional role in the environment includes the decomposition of various biopolymers and participation in the global cycling of carbon, iron and hydrogen.

Key Concepts

  • Acidobacteria are one of the major bacterial groups in soils and peatlands.
  • Not all members of Acidobacteria are acidophiles; some subgroups within this phylum display preferences for neutral or slightly alkaline environments.
  • Representatives of this phylum can be cultured using modified techniques.
  • Mesophilic acidobacteria possess large genomes, which encode a wide repertoire of carbohydrate‐active enzymes.
  • Acidobacteria utilise a broad range of complex carbon substrates and have the potential to participate in the cycling of plant‐, fungal‐ and insect‐derived organic matter.
  • Owing to their slow growth rates, acidobacteria become particularly important in the econiches where fast‐acting degraders are absent or numerically insignificant.
  • Some ecologically important groups of acidobacteria are characterised by the presence of a quite unique membrane‐spanning lipid, iso‐diabolic acid, which is composed of two condensed iso‐C15 fatty acids.
  • In some acidobacteria, ether membrane lipids occur and they are suspected producers of the omnipresent bacterial tetraether lipids.

Keywords: Acidobacteria; soils; peatlands; difficult‐to‐culture bacteria; chemoheterotrophs; photoheterotrophs; unique lipids; biopolymer degraders

Figure 1. (a) Mini colonies produced by Granulicella paludicola OB1010T at the stage of isolation. Bar, 2 mm. (b) Development of depressions in the gellan‐solidified medium during colony growth of Bryocella elongata SN10T. Bar, 5 mm. (c–e) Examples of cell morphologies of acidobacteria: Granulicella rosea TPO1014T (c), Acidobacteriaceae bacterium CCO287 (d), Paludibaculum fermentans P105T (e). Bar, 5 µm (applies to c–e).
Figure 2. The current taxonomic structure of the phylum Acidobacteria and physiological characteristics of taxonomically described representatives. SD, subdivision. The names given in parentheses remain to be validly published. Two additional representatives of the classes Acidobacteriia and ‘Bryobacteria’ with determined genome sequences, ‘Candidatus Koribacter versatilis’ and ‘Candidatus Solibacter usitatus’, are not included in this diagram because no detailed information regarding their physiology is currently available.
Figure 3. Structures of some lipids characteristic for Acidobacteria: 1iso‐diabolic acid, 2iso‐diabolic acid with an additional methyl group, 3 and 4iso‐diabolic acid ether bound to a glycerol moiety, 5 – other monoethers synthesised by acidobacteria, 6 and 7 – tetraesters, 8 and 9 – diester/diethers, 10 and 11 – structurally related ‘orphan’ branched tetraethers which are widespread in terrestrial habitats, 12 and 13 – bacteriohopanepolyol derivatives, 14 – derivatives of bacteriochlorophyll c with straight‐chain esterifying alcohols and 15 – the uncommon carotenoid echinenone produced by Chl. thermophilum.
Figure 4. Specific detection of cells of peat‐inhabiting acidobacteria (indicated by white arrows) attached to semidecomposed organic material. Epifluorescent micrograph of in situ hybridisation with Acidobacteria‐specific Cy3‐labeled probe HoAc1402 (a) and the corresponding phase‐contrast image (b) are shown.
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Further Reading

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Dedysh, Svetlana N, and Sinninghe Damsté, Jaap S(Jan 2018) Acidobacteria. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0027685]