title: Diversity and ecology of oxalotrophic bacteria.
abstract: Oxalate is present in environments as diverse as soils or gastrointestinal tracts. This organic acid can be found as free acid or forming metal salts (e.g. calcium, magnesium). Oxalotrophy, the ability to use oxalate as carbon and energy sources, is mainly the result of bacterial catabolism, which can be either aerobic or anaerobic. Although some oxalotrophic bacterial strains are commonly used as probiotics, little is known about the diversity and ecology of this functional group. This review aims at exploring the taxonomic distribution and the phylogenetic diversity of oxalotrophic bacteria across biomes. In silico analyses were conducted using the two key enzymes involved in oxalotrophy: formyl-coenzyme A (CoA) transferase (EC 2.8.3.16) and oxalyl-CoA decarboxylase (EC 4.1.1.8), encoded by the frc and oxc genes, respectively. Our analyses revealed that oxalate-degrading bacteria are restricted to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria and originated from terrestrial, aquatic and clinical environments. Diversity analyses at the protein level suggest that total Oxc diversity is more constrained than Frc diversity and that bacterial oxalotrophic diversity is not yet fully described. Finally, the contribution of oxalotrophic bacteria to ecosystem functioning as well as to the carbon cycle is discussed.
authors.affiliation: Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.|Laboratory of Biogeosciences, Institute of Earth Sciences, University of Lausanne, Geopolis, 1015, Lausanne, Switzerland.
authors.forename: Vincent
authors.initials: V
authors.lastname: Hervé
authors.affiliation: Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.|Vital-IT Group, Swiss Institute of Bioinformatics, Genopode, 1015, Lausanne, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Junier
authors.affiliation: Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
authors.forename: Saskia
authors.initials: S
authors.lastname: Bindschedler
authors.affiliation: Laboratory of Biogeosciences, Institute of Earth Sciences, University of Lausanne, Geopolis, 1015, Lausanne, Switzerland.
authors.forename: Eric
authors.initials: E
authors.lastname: Verrecchia
authors.affiliation: Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland. pilar.junier@unine.ch.
authors.forename: Pilar
authors.initials: P
authors.lastname: Junier
mesh_terms: D039903:Actinobacteria / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D000214:Acyl Coenzyme A / Q000235:genetics / Q000378:metabolism; D000818:Animals; D044822:Biodiversity; D002262:Carboxy-Lyases / Q000235:genetics / Q000378:metabolism; D004463:Ecology; D000068536:Bacillota / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D041981:Gastrointestinal Tract / Q000737:chemistry / Q000382:microbiology; D006801:Humans; D010070:Oxalates / Q000378:metabolism*; D020560:Proteobacteria / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D000214:Acyl Coenzyme A; D010070:Oxalates; D012987:Soil; C106238:formyl-coenzyme A; D002262:Carboxy-Lyases; C059418:oxalyl CoA decarboxylase
keywords: Bacterial diversity; Carbon cycle; Formyl-CoA transferase; Oxalotrophy; Oxalyl-CoA decarboxylase