Ochrobactrum quorumnocens sp. nov., a quorum quenching bacterium from the potato rhizosphere, and comparative genome analysis with related type strains

PLoS One. 2019 Jan 22;14(1):e0210874. doi: 10.1371/journal.pone.0210874. eCollection 2019.

Abstract

Ochrobactrum spp. are ubiquitous bacteria attracting growing attention as important members of microbiomes of plants and nematodes and as a source of enzymes for biotechnology. Strain Ochrobactrum sp. A44T was isolated from the rhizosphere of a field-grown potato in Gelderland, the Netherlands. The strain can interfere with quorum sensing (QS) of Gram-negative bacteria through inactivation of N-acyl homoserine lactones (AHLs) and protect plant tissue against soft rot pathogens, the virulence of which is governed by QS. Phylogenetic analysis based on 16S rRNA gene alone and concatenation of 16S rRNA gene and MLSA genes (groEL and gyrB) revealed that the closest relatives of A44T are O. grignonense OgA9aT, O. thiophenivorans DSM 7216T, O. pseudogrignonense CCUG 30717T, O. pituitosum CCUG 50899T, and O. rhizosphaerae PR17T. Genomes of all six type strains were sequenced, significantly expanding the possibility of genome-based analyses in Ochrobactrum spp. Average nucleotide identity (ANIb) and genome-to-genome distance (GGDC) values for A44T and the related strains were below the single species thresholds (95% and 70%, respectively), with the highest scores obtained for O. pituitosum CCUG 50899T (87.31%; 35.6%), O. rhizosphaerae PR17T (86.80%; 34.3%), and O. grignonense OgA9aT (86.30%; 33.6%). Distinction of A44T from the related type strains was supported by chemotaxonomic and biochemical analyses. Comparative genomics revealed that the core genome for the newly sequenced strains comprises 2731 genes, constituting 50-66% of each individual genome. Through phenotype-to-genotype study, we found that the non-motile strain O. thiophenivorans DSM 7216T lacks a cluster of genes related to flagella formation. Moreover, we explored the genetic background of distinct urease activity among the strains. Here, we propose to establish a novel species Ochrobactrum quorumnocens, with A44T as the type strain (= LMG 30544T = PCM 2957T).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • DNA, Bacterial / genetics
  • DNA, Ribosomal / genetics
  • Flagella / genetics
  • Genome, Bacterial
  • Multigene Family
  • Netherlands
  • Ochrobactrum / classification
  • Ochrobactrum / genetics*
  • Ochrobactrum / physiology
  • Phylogeny
  • Quorum Sensing / genetics
  • Quorum Sensing / physiology
  • RNA, Ribosomal, 16S / genetics
  • Rhizosphere
  • Solanum tuberosum / microbiology*
  • Species Specificity
  • Urease / genetics

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • DNA, Ribosomal
  • RNA, Ribosomal, 16S
  • Urease

Grant support

This study was funded by the National Science Centre, Poland (Narodowe Centrum Nauki, Polska) research grant 2014/13/B/NZ9/02136 to SJ. DK was supported by a personal scholarship START 2017 (START 40.2017) granted by the Foundation for Polish Science (FNP).