Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia.
University of Carthage, Faculty of Sciences of Bizerte, Tunis, Tunisia.
Int J Syst Evol Microbiol. 2024 Sep;74(9). doi: 10.1099/ijsem.0.006515.
Three bacterial strains, 1AS14I, 1AS12I and 6AS6, isolated from root nodules of , were characterized using a polyphasic approach. Phylogenetic analysis based on sequences placed all three strains within the complex. Further phylogeny, based on 1 756 bp sequences of four concatenated housekeeping genes (, , and ), revealed their distinction from known rhizobia species of the complex (Rlc), forming a distinct clade. The closest related species, identified as , with a sequence identity of 96.4% based on concatenated --- sequences. The type strain, 1AS14I, showed average nucleotide identity (ANI) values of 94.9, 94.3 and 94.1% and DNA-DNA hybridization values of 56.1, 57.4 and 60.0% with the type strains of closest known species: , and respectively. Phylogenomic analyses using 81 up-to-date bacteria core genes and the Type (Strain) Genome Server pipeline further supported the uniqueness of strains 1AS14I, 1AS12I and 6AS6. The relatedness of the novel strains to NCBI unclassified sp. (396 genomes) and metagenome-derived genomes showed ANI values from 76.7 to 94.8% with a species-level cut-off of 96%, suggesting that strains 1AS14I, 1AS12I and 6AS6 are a distinct lineage. Additionally, differentiation of strains 1AS14I, 1AS12I and 6AS6 from their closest phylogenetic neighbours was achieved using phenotypic, physiological and fatty acid content analyses. Based on the genomic, phenotypic and biochemical data, we propose the establishment of a novel rhizobial species, sp. nov., with strain 1AS14I designated as the type strain (=DSM 113914=LMG 33206). This study contributes to the understanding of microbial diversity in nitrogen-fixing symbioses, specifically within ecosystems in Tunisia.
从 中分离得到的三株细菌，1AS14I、1AS12I 和 6AS6，采用多相方法进行了表征。基于 序列的系统发育分析将这三株菌都归入 复合体。进一步基于 4 个串联看家基因（ 、 、 和 ）的 1756bp 序列的系统发育分析显示，它们与 复合体中已知的根瘤菌物种（Rlc）不同，形成一个独特的分支。最接近的相关物种被鉴定为 ，基于串联 --- 序列的同源性为 96.4%。模式菌株 1AS14I 与最接近的已知种的模式菌株的平均核苷酸同一性（ANI）值分别为 94.9、94.3 和 94.1%，DNA-DNA 杂交值分别为 56.1、57.4 和 60.0%： 、 和 。使用 81 个最新的细菌核心基因和 Type (Strain) Genome Server 管道进行的基因组系统发育分析进一步支持了菌株 1AS14I、1AS12I 和 6AS6 的独特性。新型菌株与 NCBI 未分类的 sp.（396 个基因组）和宏基因组衍生的基因组的相关性显示，ANI 值从 76.7%到 94.8%，种水平的截断值为 96%，表明菌株 1AS14I、1AS12I 和 6AS6 是一个独特的谱系。此外，通过表型、生理和脂肪酸含量分析，菌株 1AS14I、1AS12I 和 6AS6 与其最接近的系统发育邻居之间的分化得以实现。基于基因组、表型和生化数据，我们建议建立一个新的根瘤菌物种， sp. nov.，以菌株 1AS14I 为模式菌株（=DSM 113914=LMG 33206）。本研究有助于了解固氮共生体中的微生物多样性，特别是突尼斯的 生态系统中的微生物多样性。
