Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 497166
Title Exploring the genomic traits of fungus-feeding bacterial genus Collimonas
Author(s) Song, Chunxu; Schmidt, Ruth; Jager, Victor de; Krzyzanowska, Dorota; Jongedijk, Esmer; Cankar, Katarina; Beekwilder, Jules; Veen, Anouk van; Boer, Wietse de; Veen, Johannes A. van; Garbeva, Paolina
Source BMC Genomics 16 (2015)1. - ISSN 1471-2164
DOI http://dx.doi.org/10.1186/s12864-015-2289-3
Department(s) PE&RC
Laboratory of Plant Physiology
FBR Sustainable Chemistry & Technology
PRI BIOS Applied Metabolic Systems
Publication type Refereed Article in a scientific journal
Publication year 2015
Keyword(s) Collimonas - Comparative genomics - Secondary metabolites - Terpenes
Abstract

Background: Collimonas is a genus belonging to the class of Betaproteobacteria and consists mostly of soil bacteria with the ability to exploit living fungi as food source (mycophagy). Collimonas strains differ in a range of activities, including swimming motility, quorum sensing, extracellular protease activity, siderophore production, and antimicrobial activities. Results: In order to reveal ecological traits possibly related to Collimonas lifestyle and secondary metabolites production, we performed a comparative genomics analysis based on whole-genome sequencing of six strains representing 3 recognized species. The analysis revealed that the core genome represents 43.1 to 52.7 % of the genomes of the six individual strains. These include genes coding for extracellular enzymes (chitinase, peptidase, phospholipase), iron acquisition and type II secretion systems. In the variable genome, differences were found in genes coding for secondary metabolites (e.g. tripropeptin A and volatile terpenes), several unknown orphan polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS), nonribosomal peptide synthetase (NRPS) gene clusters, a new lipopeptide and type III and type VI secretion systems. Potential roles of the latter genes in the interaction with other organisms were investigated. Mutation of a gene involved in tripropeptin A biosynthesis strongly reduced the antibacterial activity against Staphylococcus aureus, while disruption of a gene involved in the biosynthesis of the new lipopeptide had a large effect on the antifungal/oomycetal activities. Conclusions: Overall our results indicated that Collimonas genomes harbour many genes encoding for novel enzymes and secondary metabolites (including terpenes) important for interactions with other organisms and revealed genomic plasticity, which reflect the behaviour, antimicrobial activity and lifestylesof Collimonas spp.

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