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Comparative genomics of bacteria from the genusCollimonas: linking (dis)similarities in gene content to phenotypic variation and conservation

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Abstract

Collimonas

is a genus of soil bacteria comprising three recognized species:C. fungivorans,C. pratensisandC. arenae. Collimonads share the ability to degrade chitin (chitinolysis), feed on living fungal hyphae (mycophagy), and dissolve minerals (weathering), but vary in their inhibition of fungi (fungistasis). To better understand this phenotypic variability, we analysed the genomic content of four strains representing threeCollimonasspecies (Ter14, Ter6, Ter91 and Ter10) by hybridization to a microarray based on reference strainC. fungivoransTer331. The analysis revealed genes unique to strain Ter331 (e.g. those on the extrachromosomal element pTer331) and genes present in some but not all of the tested strains. Among the latter were several candidates that may contribute to fungistasis, including genes for the production and secretion of antifungals. We hypothesize that differential possession of these genes underlies the specialization ofCollimonasstrains towards different fungal hosts. We identified a set of 136 genes that were common in all testedCollimonasstrains, but absent from the genomes of three other members of the familyOxalobacteraceae. Predicted products of these ‘Collimonascore’ genes include lytic, secreted enzymes such as chitinases, peptidases, nucleases and phosphatases with a putative role in mycophagy and weathering.

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