Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2289-3) contains supplementary material, which is available to authorized users.
Highlights
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
We identified a cluster of genes encoding T6SS only in C. fungivorans and C. pratensis strains, but not in the C. arenae species
All Collimonas genomes carry large numbers of Genomic Islands pointing to a complex history of gene recombination and horizontal transfer between bacterial relatives
Summary
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). The genus Collimonas comprises soil bacteria with the ability to grow at the expense of living fungal hyphae under nutrient-limited conditions [1,2,3]. Collimonas belongs to the family Oxalobacteraceae, class Betaproteobacteria. The first Collimonas isolates were obtained within the framework of a project searching for a naturally occurring biocontrol agent of fungi pathogenic to marram grass (Ammophilia arenaria) and were determined as being dominant among the cultivable chitinolytic bacteria in the acidic Dutch dune soils [3]. All three species display the ability to feed on fungi (mycophagy), to degrade chitin and to dissolve minerals (weathering) [2].
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