Comparative genomics and metabolic profiling of the genus Lysobacter

TitleComparative genomics and metabolic profiling of the genus Lysobacter
Publication TypeJournal Article
Year of Publication2015
Authorsde Bruijn I., Cheng X., de Jager V., Exposito R.G, Watrous J., Patel N., Postma J., Dorrestein PC, Kobayashi D., Raaijmakers J.M
JournalBmc Genomics
Volume16
Date Published2015/11
Type of ArticleArticle
ISBN Number1471-2164
Accession NumberWOS:000365285400005
Keywordsbeta-1,3-glucanase genes; biological-control activity; c3; comparative genomics; damping-off disease; enzymogenes oh11; Lysobacter; lytic protease; maltophilia strain; mass; microbial interactions; Nonribosomal peptide synthesis; outer-membrane vesicles; patch disease; protein families; spectrometry imaging; sugar-beet
Abstract

Background: Lysobacter 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. Results: Comparative 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. Conclusions: Our 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.

DOI10.1186/s12864-015-2191-z
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