Comparative genomics and metabolic profiling of the genus Lysobacter

Abstract

BackgroundLysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To better understand their ecology and interactions with other (micro)organisms, five Lysobacter strains representing the four species L. enzymogenes, L. capsici, L. gummosus and L. antibioticus were subjected to genomics and metabolomics analyses.ResultsComparative genomics revealed a diverse genome content among the Lysobacter species with a core genome of 2,891 and a pangenome of 10,028 coding sequences. Genes encoding type I, II, III, IV, V secretion systems and type IV pili were highly conserved in all five genomes, whereas type VI secretion systems were only found in L. enzymogenes and L. gummosus. Genes encoding components of the flagellar apparatus were absent in the two sequenced L. antibioticus strains. The genomes contained a large number of genes encoding extracellular enzymes including chitinases, glucanases and peptidases. Various nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) gene clusters encoding putative bioactive metabolites were identified but only few of these clusters were shared between the different species. Metabolic profiling by imaging mass spectrometry complemented, in part, the in silico genome analyses and allowed visualisation of the spatial distribution patterns of several secondary metabolites produced by or induced in Lysobacter species during interactions with the soil-borne fungus Rhizoctonia solani.ConclusionsOur work shows that mining the genomes of Lysobacter species in combination with metabolic profiling provides novel insights into the genomic and metabolic potential of this widely distributed but understudied and versatile bacterial genus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2191-z) contains supplementary material, which is available to authorized users.

The impact of the omics era on the knowledge and use ofLysobacterspecies to control phytopathogenic micro-organisms

“…A high number of orthologues (2891) is shared by the complete genomes of bacterial strains with biocontrol activities belonging to the L. antibioticus , L. capsici , L. enyzmogenes and L. gummosus species (de Bruijn et al . ). Comparison of the genomes of the biocontrol agent L. capsici AZ78, the plant pathogen X. campestris pv.…”

“…sequenced genomes indeed encompass several genes encoding chitinases such as chiA, belonging to glycosyl hydrolase family 18, which includes most of the chitinases produced by bacteria (de Bruijn et al . ; Puopolo et al . ).…”

“…Indeed, the sequenced genomes revealed the presence of a large number of genes encoding α ‐lytic proteases, β ‐lytic proteases, endopeptidases and metalloendopeptidases (de Bruijn et al . ; Puopolo et al . ).…”

Complete genome sequence and expression profile of the commercial lytic enzyme producerLysobacter enzymogenesM497-1

“…Over 40 species within the genus Lysobacter have been registered in the NCBI taxonomy database, and recently, the complete genomes of 4 species ( L. antibioticus, L. capsici, L. enzymogenes , and L. gummosus ) have been sequenced 37 . The genome sequence data are very useful to elucidate the intragenus as well as intraspecies genomic diversity.…”

The fish egg microbiome : diversity and activity against the oomycete pathogen Saprolegnia

“…10 ml of TSB supplemented with 0.2% (w/v) colloidal chitin (Hsu and Lockwood, 1975;de Bruijn et al, 2015) and 1.2% agar was poured on top of the solidified TSA. The cell suspension of each Frondihabitans isolate was spot-inoculated at three different places of the plate.…”