Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan.
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada.
Int J Syst Evol Microbiol. 2020 Sep;70(9):5063-5074. doi: 10.1099/ijsem.0.004380.
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.
通过基因组和表型分析，证实了先前从加拿大和日本截然不同生境中分离的两个特征菌株（58S1 和 S23321）的分类地位。5 个和 27 个串联编码核心基因序列的系统发育分析将这两个菌株置于一个与属内命名种明显不同的高度支持的谱系中，其中 是最接近的亲缘关系。测试菌株与参考菌株之间基因组序列的平均核苷酸同一性值在 84.5%至 94.2%之间，低于细菌种划界的阈值。菌株 58S1 和 S23321 的完整基因组分别由 7.30 和 7.23 Mbp 的单个染色体组成，并且没有共生岛。这两个菌株的基因组 G+C 含量均为 64.3 mol%。这些菌株的基因组中存在一个光合作用基因簇（PGC），包含关键的光合作用基因。在两个菌株的 PGC 区域边界处发现了一个 tRNA 基因及其部分串联重复，这可能是基因组岛插入的标志。两个菌株的基因组中都检测到了关键的固氮基因，但没有发现结瘤和 III 型分泌系统基因。氮固定基因 的序列分析将 58S1 和 S23321 置于一个与描述的 种不同的新谱系中。包括生长特性和碳源利用在内的表型测试数据支持基于序列的分析。根据这里提出的数据，建议建立一个新的物种，命名为 sp. nov.，其中 58S1（=LMG 31545=HAMBI 3725）作为模式菌株。
