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Abstract

Four bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soils of legumes native to Canada were previously identified as a novel lineage consisting of symbiovars (sv.) glycinearum and septentrionale. Our purpose was to verify the taxonomic status of these strains using phylogenetic, genomic and phenotypic analyses. Multiple phylogenetic analyses including analysis of 51 full-length ribosome protein subunit () gene sequences confirmed placement of the novel strains in a highly supported lineage distinct from named species with USDA 6 as the closest relative. The results of genomic and phylogenomic analyses based on digital DNA–DNA hybridization and genome distance phylogeny showed that novel strains in comparisons with type strains of closest relatives were below the established threshold (70 %) for species delineation. Moreover, the novel strains were divided into two subspecies clusters based on the established threshold of 79 %. The genomes of strains 144S4, 323S2, 1S5 and 38S5 have sizes of 11 399 526, 11 474 152, 10580853 and 10 530 141 bp with DNA G+C contents of 63.1, 63.0, 63.4 and 63.3 mol%, respectively. These strains possess symbiosis islands harbouring key nodulation, nitrogen-fixation and type III secretion system genes as well as abundant insertion sequences and between two and four putative plasmids. Strains 144S4 and 323S2 (sv. glycinearum) are effective with regard to nitrogen fixation in symbiotic association with soybeans whereas strains 1S5 and 38S5 (sv. septentrionale) are ineffective. Data for morphological, physiological and symbiotic characteristics complement the sequence-based results. The data presented here support the description of a new species and two new subspecies for which the names sp. nov. subsp. subsp. nov. (sv. glycinearum) and sp. nov. subsp. subsp. nov. (sv. septentrionale) are proposed with strain 144S4 (=LMG 31552=HAMBI 3722) as the species type strain and type strain of subsp. subsp. nov., and strain 38S5 (=LMG 31556=HAMBI 3721) as the type strain of subsp. subsp. nov.

Funding
This study was supported by the:
  • New Energy and Industrial Technology Development Organization (Award JPNP18016)
    • Principle Award Recipient: ApplicableNot
  • Agriculture and Agri-Food Canada (Award J-002272)
    • Principle Award Recipient: NotApplicable
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License
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2022-10-19
2024-02-27
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