title: Exploring the genomic traits of fungus-feeding bacterial genus Collimonas.
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.
authors.affiliation: Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands. c.song@nioo.knaw.nl.
authors.forename: Chunxu
authors.initials: C
authors.lastname: Song
authors.affiliation: Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands. r.schmidt@nioo.knaw.nl.
authors.forename: Ruth
authors.initials: R
authors.lastname: Schmidt
authors.affiliation: Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands. v.dejager@nioo.knaw.nl.
authors.forename: Victor
authors.initials: V
authors.lastname: de Jager
authors.affiliation: Laboratory of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG&MUG, Kladki 24, Gdansk, 80-822, Poland. dorota.krzyzanowska@biotech.ug.edu.pl.
authors.forename: Dorota
authors.initials: D
authors.lastname: Krzyzanowska
authors.affiliation: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands. esmer.jongedijk@wur.nl.
authors.forename: Esmer
authors.initials: E
authors.lastname: Jongedijk
authors.affiliation: Business Unit Bioscience, Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands. katarina.cankar@wur.nl.
authors.forename: Katarina
authors.initials: K
authors.lastname: Cankar
authors.affiliation: Business Unit Bioscience, Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands. jules.beekwilder@wur.nl.
authors.forename: Jules
authors.initials: J
authors.lastname: Beekwilder
authors.affiliation: Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands. anouk_v_veen@hotmail.com.
authors.forename: Anouk
authors.initials: A
authors.lastname: van Veen
authors.affiliation: Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands. w.deboer@nioo.knaw.nl.
authors.forename: Wietse
authors.initials: W
authors.lastname: de Boer
authors.affiliation: Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands. h.vanveen@nioo.knaw.nl.
authors.forename: Johannes A
authors.initials: JA
authors.lastname: van Veen
authors.affiliation: Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands. p.garbeva@nioo.knaw.nl.
authors.forename: Paolina
authors.initials: P
authors.lastname: Garbeva
mesh_terms: D058947:Bacterial Secretion Systems / Q000235:genetics; D001435:Bacteriophages; D020562:Betaproteobacteria / Q000235:genetics* / Q000378:metabolism / Q000821:virology; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics; D005658:Fungi; D023061:Gene Order; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics / Q000379:methods; D055442:Metabolome; D055432:Metabolomics; D056265:Microbial Interactions; D005810:Multigene Family; D010802:Phylogeny; D019655:Quantitative Trait, Heritable; D064210:Secondary Metabolism; D015398:Signal Transduction
chemical_list: D058947:Bacterial Secretion Systems