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).
Highlights
Ochrobactrum spp., together with the closely related Brucella, Agrobacterium, and Rhizobium genera, belong to the class of Alphaproteobacteria [1,2,3]
[30], O. grignonense OgA9aT, obtained from bulk soil in France [5,30], O. rhizosphaerae PR17T, originating from the roots of potato grown in Austria [6], and O. pituitosum CCUG 50899T, isolated from industrial environment in Sweden [31] (Fig 1A; S1 Table)
To obtain higher phylogenetic resolution within this group, we employed Multilocus Sequence Analysis (MLSA) [32] based on the concatenated sequences of 16S rRNA, gyrB, and groEL genes, which suggest that the closest relative of A44T is O. rhizosphaerae PR17T (Fig 1B)
Summary
Ochrobactrum spp., together with the closely related Brucella, Agrobacterium, and Rhizobium genera, belong to the class of Alphaproteobacteria [1,2,3]. The genus is most often associated with O. anthropi [4] and O. intermedium [1], which cause opportunistic infections in humans, the bacteria from the Ochrobactrum spp. genus adapted to a variety of environmental niches and can be found in soil [5], wastewater [6], in association with plants [6,7], and animals [8,9]. Ochrobactrum spp. are of interest as plant beneficial bacteria [16,17]. Scientific data concerning the majority of the strains is limited to information of taxonomic value
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