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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 9

Strains of sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands Open Access

Abstract

The taxonomic status of two previously characterized strains (58S1 and S23321) isolated from contrasting habitats in Canada and Japan was verified by genomic and phenotypic analyses. Phylogenetic analyses of five and 27 concatenated protein-encoding core gene sequences placed both strains in a highly supported lineage distinct from named species in the genus with as the closest relative. Average nucleotide identity values of genome sequences between the test and reference strains were between 84.5 and 94.2 %, which is below the threshold value for bacterial species circumscription. The complete genomes of strains 58S1 and S23321 consist of single chromosomes of 7.30 and 7.23 Mbp, respectively, and do not have symbiosis islands. The genomes of both strains have a G+C content of 64.3 mol%. Present in the genome of these strains is a photosynthesis gene cluster (PGC) containing key photosynthesis genes. A tRNA gene and its partial tandem duplication were found at the boundaries of the PGC region in both strains, which is likely the hallmark of genomic island insertion. Key nitrogen-fixation genes were detected in the genomes of both strains, but nodulation and type III secretion system genes were not found. Sequence analysis of the nitrogen fixation gene, , placed 58S1 and S23321 in a novel lineage distinct from described species. Data for phenotypic tests, including growth characteristics and carbon source utilization, supported the sequence-based analyses. Based on the data presented here, a novel species with the name sp. nov. is proposed with 58S1 (=LMG 31545=HAMBI 3725) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bradyrhizobium cosmicum , complete genome sequence , genomic island and photosynthesis gene cluster
Funding
This study was supported by the:
  • Japan Society for the Promotion of Science (Award JSPS KAKENHI 18H02112)
    • Principle Award Recipient: Kiwamu Minamisawa
  • Agriculture and Agri-Food Canada (Award J-002272)
    • Principle Award Recipient: Eden S. P. Bromfield
© 2020 Her Majesty the Queen, in right of Canada, represented by the Minister of Agriculture and Agri-Food
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2020-08-17
2024-04-24
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Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands
Int J Syst Evol Microbiol 70, 5063 (2020); https://doi.org/10.1099/ijsem.0.004380
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