Xu Zhenxing, Masuda Yoko, Wang Xueding, Ushijima Natsumi, Shiratori Yutaka, Senoo Keishi, Itoh Hideomi
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido, Japan.
Front Microbiol. 2021 Sep 30;12:737531. doi: 10.3389/fmicb.2021.737531. eCollection 2021.
is a recently proposed order comprising members who originally belonged to the well-known family , which is a key group in terrestrial ecosystems involved in biogeochemical cycles and has been widely investigated in bioelectrochemistry and bioenergy fields. Previous studies have illustrated the taxonomic structure of most members in this group based on genomic phylogeny; however, several members are still in a pendent or chaotic taxonomic status owing to the lack of genome sequences. To address this issue, we performed this taxonomic reassignment using currently available genome sequences, along with the description of two novel paddy soil-isolated strains, designated Red51 and Red69, which are phylogenetically located within this order. Phylogenomic analysis based on 120 ubiquitous single-copy proteins robustly separated the species from other known genera and placed the genus (fam. ) into the family ''; thus, a novel genus is proposed, and the family '' was emended. Moreover, genomic comparisons with similarity indexes, including average amino acid identity (AAI), percentage of conserved protein (POCP), and average nucleotide identity (ANI), showed proper thresholds as genera boundaries in this order with values of 70%, 65%, and 74% for AAI, POCP, and ANI, respectively. Based on this, the three species , , and should be three novel genera, for which the names , , and are proposed, respectively. In addition, the two novel isolated strains phylogenetically belonged to the genus , family , and shared genomic similarity values higher than those of genera boundaries, but lower than those of species boundaries with each other and their neighbors. Taken together with phenotypic and chemotaxonomic characteristics similar to other species, these two strains, Red51 and Red69, represent two novel species in the genus , for which the names sp. nov. and sp. nov. are proposed, respectively.
是最近提出的一个目，其成员最初属于一个著名的家族，该家族是参与生物地球化学循环的陆地生态系统中的关键群体，并且在生物电化学和生物能源领域已得到广泛研究。先前的研究已基于基因组系统发育阐明了该群体中大多数成员的分类结构；然而，由于缺乏基因组序列，仍有几个成员处于悬而未决或混乱的分类地位。为了解决这个问题，我们利用目前可用的基因组序列进行了这种分类重新分配，并描述了两株新分离的水稻土菌株，命名为Red51和Red69，它们在系统发育上属于这个目。基于120个普遍存在的单拷贝蛋白的系统基因组分析有力地将该物种与其他已知属分开，并将属（科）归入科“”；因此，提出了一个新属，并对科“”进行了修订。此外，与相似性指标的基因组比较，包括平均氨基酸同一性（AAI）、保守蛋白百分比（POCP）和平均核苷酸同一性（ANI），显示该目中属界限的适当阈值分别为AAI的70%、POCP的65%和ANI的74%。基于此，三个物种、和应分别为三个新属，分别提出名称、和。此外，这两株新分离菌株在系统发育上属于属、科，并且彼此之间以及与它们的近缘种共享高于属界限但低于种界限的基因组相似性值。结合与其他物种相似的表型和化学分类特征，这两株菌株Red51和Red69代表了属中的两个新物种，分别提出名称新种和新种。
