Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 496962
Title Comparative genomics and metabolic profiling of the genus Lysobacter
Author(s) Bruijn, Irene de; Cheng, Xu; Jager, Victor de; Expósito, Ruth Gómez; Watrous, Jeramie; Patel, Nrupali; Postma, Joeke; Dorrestein, P.C.; Kobayashi, Donald; Raaijmakers, Jos M.
Source BMC Genomics 16 (2015)1. - ISSN 1471-2164 - 16 p.
DOI https://doi.org/10.1186/s12864-015-2191-z
Department(s) Laboratory of Phytopathology
EPS
PPO/PRI Biointeractions and Plant Health
PRI Bioint Entomology & Disease Management
PE&RC
Publication type Refereed Article in a scientific journal
Publication year 2015
Keyword(s) Comparative genomics - Lysobacter - Mass spectrometry imaging - Microbial interactions - Nonribosomal peptide synthesis
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.

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