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

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).

Taxonomic Organization of the Family Brucellaceae Based on a Phylogenomic Approach

“…The triad anthropi-lupini/cytisi/tritici was generally well resolved in most previous phylogenies, but the position of O. oryzae, O. pecoris, and O. haematophilum was much less consistent. 16S rRNA-based analyses usually branch O. oryzae with O. pseudintermedium and O. gallinifaecis, away from the anthropi/tritici clade, although recA analyses provided results in agreement with our phylogenomic analysis (Scholz et al, 2008a;Huber et al, 2009;Gazolla Volpiano et al, 2019;Krzyżanowska et al, 2019). Similarly, O. pecoris usually branches within or as a sister taxon of Ochrobactrum Clade 2 (see below) in 16S rRNA-based phylogenies, with sometimes a close connection to O. rhizospherae and O. pituitosum (Kämpfer et al, 2011(Kämpfer et al, , 2013Krzyżanowska et al, 2019), while the MLST phylogeny more accurately branched it with the other members of Ochrobactrum Clade 1 (Aujoulat et al, 2014).…”

“…16S rRNA-based analyses usually branch O. oryzae with O. pseudintermedium and O. gallinifaecis, away from the anthropi/tritici clade, although recA analyses provided results in agreement with our phylogenomic analysis (Scholz et al, 2008a;Huber et al, 2009;Gazolla Volpiano et al, 2019;Krzyżanowska et al, 2019). Similarly, O. pecoris usually branches within or as a sister taxon of Ochrobactrum Clade 2 (see below) in 16S rRNA-based phylogenies, with sometimes a close connection to O. rhizospherae and O. pituitosum (Kämpfer et al, 2011(Kämpfer et al, , 2013Krzyżanowska et al, 2019), while the MLST phylogeny more accurately branched it with the other members of Ochrobactrum Clade 1 (Aujoulat et al, 2014). For O. haematophilum, no single-locus or even multi-locus analysis could have resolved its correct position with high support (Scholz et al, 2008a;Aujoulat et al, 2014;Gazolla Volpiano et al, 2019), suggesting that its deep branching at the root of Clade 1 precludes from retrieving enough phylogenetic signal when only few genes are used.…”

“…The most comprehensive analysis of Brucellaceae species to date, that included more than one hundred strains, showed that the use of these single markers results in different tree topologies depending on the locus and the phylogenetic reconstruction algorithm, and with low to very low branching support throughout the topology (Scholz et al, 2008a). Such lack of resolution was confirmed by a number of other studies which each reported a unique tree topology using the same markers (Teyssier et al, 2007;Huber et al, 2009;Kämpfer et al, 2013Chai et al, 2015;Gazolla Volpiano et al, 2019;Krzyżanowska et al, 2019). Nonetheless, a striking common observation of these various studies is that the genus Brucella was consistently embedded within the Ochrobactrum genus diversity, although no definitive conclusion about the taxonomic status of Brucella spp.…”

“…Clade 2 includes Ochrobactrum species gallinifaecis, thiophenivorans, pseudorignonense, quorumnoscens, rhizospherae, grignonense, and pituitosum. These species consistently group together in most 16S rRNA-based phylogenetic analyses, but usually as an internal Ochrobactrum clade and with O. gallinifaecis excluded (Chai et al, 2015;Gazolla Volpiano et al, 2019;Krzyżanowska et al, 2019). On the contrary, recA and multilocus phylogenies usually separated correctly this group from the other Ochrobactrum spp.…”

“…Limited multilocus sequence typing (MLST) or Internal Transcribed Spacer (ITS) region-based analyses were also performed but were hampered by a small set of genes, a small set of species, or poorly supported branching, and still resulted in conflicting results (Zurdo-Pineiro et al, 2007;Aujoulat et al, 2014;Burygin et al, 2019;Gazolla Volpiano et al, 2019;Krzyżanowska et al, 2019). More recently, whole genome phylogenetic studies started to emerge but generally focused on a limited number of isolates of few species and could not provide a comprehensive view of the phylogenetic relationships at the family level or even at the Ochrobactrum genus level (Gazolla Volpiano et al, 2019;Krzyżanowska et al, 2019). Finally, the question of the Brucellaceae positioning among the Rhizobiales order have not been thoroughly investigated to date.…”