Pseudomonas quebecensis sp. nov., a bacterium isolated from root-zone soil of a native legume, Amphicarpaea bracteata (L.) Fernald, in Quebec, Canada

Author:

Tambong James T.12ORCID,Xu Renlin1,Chi Sylvia I.31,Birugu Isabelle1,Bachelet Sylvia4,Hutter Conrad4,Duceppe Marc-Olivier4,Brière Stephan4

Affiliation:

1. Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada

2. Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada

3. Canadian Blood Services, Ottawa, Ontario, Canada

4. Ottawa Plant Laboratory (Fallowfield), Canadian Food Inspection Agency, Ottawa, Ontario, Canada

Abstract

Four bacterial strains (S1Bt3, S1Bt7, S1Bt30 and S1Bt42T) isolated from soil collected from the rhizosphere of a native legume, Amphicarpaea bracteata, were investigated using a polyphasic approach. Colonies were fluorescent, white-yellowish, circular and convex with regular margins on King’s B medium. Cells were Gram-reaction-negative, aerobic, non-spore-forming rods. Oxidase- and catalase-positive. The optimal growth temperature of the strains was 37 °C. Phylogenetic analysis of the 16S rRNA gene sequences placed the strains within the genus Pseudomonas . Analysis of the 16S rRNA-rpoD-gyrB concatenated sequences clustered the strains and well separated from Pseudomonas rhodesiae CIP 104664T and Pseudomonas grimontii CFM 97-514T with the type strains of the closest species. Phylogenomic analysis of 92 up-to-date bacterial core gene and matrix-assisted laser desorption/ionization-time-of-flight MS biotyper data confirmed the distinct clustering pattern of these four strains. Digital DNA–DNA hybridization (41.7 %–31.2 %) and average nucleotide identity (91.1 %–87.0 %) values relative to closest validly published Pseudomonas species were below the species delineation thresholds of 70 and 96 %, respectively. Fatty acid composition results validated the taxonomic position of the novel strains in the genus Pseudomonas . Phenotypic characteristics from carbon utilization tests differentiated the novel strains from closely related Pseudomonas species. In silico prediction of secondary metabolite biosynthesis gene clusters in the whole-genome sequences of the four strains revealed the presence of 11 clusters involved in the production of siderophore, redox-cofactor, betalactone, terpene, arylpolyene and nonribosomal peptides. Based on phenotypic and genotypic data, strains S1Bt3, S1Bt7, S1Bt30 and S1Bt42T represent a novel species for which the name Pseudomonas quebecensis sp. nov. is proposed. The type strain is S1Bt42T (=DOAB 746T=LMG 32141T=CECT 30251T). The genomic DNA G+C content is 60.95 mol%.

Funder

Agriculture and Agri-Food Canada

Publisher

Microbiology Society

Subject

General Medicine,Ecology, Evolution, Behavior and Systematics,Microbiology

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