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

Authors

  • F. Mela,

    1. Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
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    • Present address: VU University Medical Center, Amsterdam, the Netherlands.

  • K. Fritsche,

    1. Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
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  • W. de Boer,

    1. Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
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  • M. van den Berg,

    1. Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
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  • J. A. van Veen,

    1. Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
    2. Institute of Biology, Leiden University, Leiden, the Netherlands
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  • N. N. Maharaj,

    1. Department of Plant Pathology, University of California, Davis, CA 95616, USA
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  • J. H. J. Leveau

    Corresponding author
    1. Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
    2. Department of Plant Pathology, University of California, Davis, CA 95616, USA
      E-mail jleveau@ucdavis.edu; Tel. (+1) 530 752 5046; Fax (+1) 530 752 5674.
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E-mail jleveau@ucdavis.edu; Tel. (+1) 530 752 5046; Fax (+1) 530 752 5674.

Summary

Collimonas is a genus of soil bacteria comprising three recognized species: C. fungivorans, C. pratensis and C. 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 three Collimonas species (Ter14, Ter6, Ter91 and Ter10) by hybridization to a microarray based on reference strain C. fungivorans Ter331. 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 of Collimonas strains towards different fungal hosts. We identified a set of 136 genes that were common in all tested Collimonas strains, but absent from the genomes of three other members of the family Oxalobacteraceae. Predicted products of these ‘Collimonas core’ genes include lytic, secreted enzymes such as chitinases, peptidases, nucleases and phosphatases with a putative role in mycophagy and weathering.

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