Exploring the genomic traits of fungus-feeding bacterial genus Collimonas

BMC Genomics

Research Article

Jules Beekwilder¹  Katarina Cankar¹  Dorota Krzyzanowska²  Esmer Jongedijk³  Chunxu Song⁴  Johannes A. van Veen⁴  Wietse de Boer⁴  Paolina Garbeva⁴  Ruth Schmidt⁴  Anouk van Veen⁴  Victor de Jager⁴ 

[1] Business Unit Bioscience, Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands;Laboratory of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG&MUG, Kladki 24, 80-822, Gdansk, Poland;Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands;Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands;

关键词: Comparative genomics;    Collimonas;    Secondary metabolites;    Terpenes;   

DOI  :  10.1186/s12864-015-2289-3

 received in 2015-07-08, accepted in 2015-12-11,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundCollimonas 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.ResultsIn 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.ConclusionsOverall 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.

【 授权许可】

CC BY   
© Song et al. 2015