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BMC Genomics. 2015 Nov 23;16:991. doi: 10.1186/s12864-015-2191-z.

Comparative genomics and metabolic profiling of the genus Lysobacter.

Author information

1
Department of Microbial Ecology, Netherlands Institute of Ecology, P.O. Box 50, Wageningen, 6700 AB, The Netherlands. i.debruijn@nioo.knaw.nl.
2
Wageningen University and Research Centre, Laboratory of Phytopathology, P.O. Box 8025, Wageningen, 6700 EE, The Netherlands. i.debruijn@nioo.knaw.nl.
3
Wageningen University and Research Centre, Laboratory of Phytopathology, P.O. Box 8025, Wageningen, 6700 EE, The Netherlands. xu.cheng@wur.nl.
4
Department of Microbial Ecology, Netherlands Institute of Ecology, P.O. Box 50, Wageningen, 6700 AB, The Netherlands. v.dejager@nioo.knaw.nl.
5
Department of Microbial Ecology, Netherlands Institute of Ecology, P.O. Box 50, Wageningen, 6700 AB, The Netherlands. R.GomezExposito@nioo.knaw.nl.
6
Wageningen University and Research Centre, Laboratory of Phytopathology, P.O. Box 8025, Wageningen, 6700 EE, The Netherlands. R.GomezExposito@nioo.knaw.nl.
7
Departments of Pharmacology, Chemistry and Biochemistry; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, San Diego, USA. jeramie.watrous@gmail.com.
8
Department of Plant Biology & Pathology, Cook College, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901-8520, USA. npatel@aesop.rutgers.edu.
9
Wageningen University and Research Centre, Plant Research International, PO Box 16, Wageningen, 6700 AA, The Netherlands. joeke.postma@wur.nl.
10
Departments of Pharmacology, Chemistry and Biochemistry; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, San Diego, USA. pdorrestein@ucsd.edu.
11
Department of Plant Biology & Pathology, Cook College, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901-8520, USA. kobayashi@AESOP.Rutgers.edu.
12
Department of Microbial Ecology, Netherlands Institute of Ecology, P.O. Box 50, Wageningen, 6700 AB, The Netherlands. j.raaijmakers@nioo.knaw.nl.

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.

PMID:
26597042
PMCID:
PMC4657364
DOI:
10.1186/s12864-015-2191-z
[Indexed for MEDLINE]
Free PMC Article

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