College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China; Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China.
Syst Appl Microbiol. 2022 Sep;45(5):126353. doi: 10.1016/j.syapm.2022.126353. Epub 2022 Aug 12.
Three bacterial strains isolated from a sediment sample collected at a water depth of 4 m from the Huaihe River in China were characterized. Phylogenetic investigation of the 16S rRNA gene and concatenated housekeeping gene sequences assigned the three novel strains in a highly supported lineage distinct from the published Bradyrhizobium species. The sequence similarities of the concatenated housekeeping genes of the three novel strains support their distinctiveness with the type strains of named species. Average nucleotide identity values of the genome sequences (79.9-82.5%) were below the threshold value of 95-96% for bacterial species circumscription. Close relatives to the novel strains are Bradyrhizobium erythrophlei, Bradyrhizobium jicamae, Bradyrhizobium lablabi, Bradyrhizobium mercantei, Bradyrhizobium elkanii and Bradyrhizobium japonicum. The complete genomes of strains S2-20-1, S2-11-2 and S2-11-4 consist of single chromosomes of size 5.55, 5.45 and 5.47 Mb, respectively. These strains lack a symbiosis island, key nodulation and photosystem genes. Based on the data presented here, the three strains represent a novel species for which the name Bradyrhizobium sediminis sp. nov. is proposed for S2-20-1 as the type strain. Those three strains are proposed as novel species in free-living Bradyrhizobium isolates with the smallest genomes so far within the genus Bradyrhizobium. A number of functional differences between the three isolates and other published genomes indicate that the genus Bradyrhizobium is extremely heterogeneous and has roles within the community including non-symbiotic nitrogen fixation.
从中国淮河水深 4 米处采集的沉积物样本中分离出的三株细菌菌株的特性。16S rRNA 基因和连接的看家基因序列的系统发育研究将这三株新菌株分配到一个高度支持的谱系中，与已发表的慢生根瘤菌属物种明显不同。三株新菌株的连接看家基因序列的相似性支持它们与命名种的模式菌株的独特性。基因组序列的平均核苷酸同一性值（79.9-82.5%）低于细菌种划界的 95-96%阈值。与新菌株密切相关的是红斑红假单胞菌、爪哇根瘤菌、豇豆根瘤菌、拉氏根瘤菌、埃尔坎氏根瘤菌和日本根瘤菌。菌株 S2-20-1、S2-11-2 和 S2-11-4 的完整基因组由大小为 5.55、5.45 和 5.47 Mb 的单个染色体组成。这些菌株缺乏共生岛、关键的结瘤和光合作用基因。根据这里提供的数据，这三株菌株代表一个新的物种，建议将 S2-20-1 作为模式菌株命名为 Sediminibacterium sediminis sp. nov.。这三株菌株是游离生活的慢生根瘤菌分离株中提出的新物种，是迄今为止在慢生根瘤菌属中基因组最小的菌株。这三个分离株与其他已发表基因组之间的许多功能差异表明，慢生根瘤菌属是极其异质的，在群落中具有非共生固氮等作用。
