Du Juan, Liu Yang, Zhu Honghui
Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Building 66, Xianlie Middle Road 100, Guangzhou, 510070, Guangdong Province, People's Republic of China.
Arch Microbiol. 2022 Dec 27;205(1):42. doi: 10.1007/s00203-022-03379-7.
The genus Acidovorax is a genetically heterogeneous species clustering that comprises many environmental and plant-pathogenic taxa. To better understand the evolutionary relationships among the Acidovorax species, 22 available genome sequences of type strains including the genera Acidovorax and Comamonas were used to conduct the genome-based analyses. Three well-supported monophyletic clusters of the Acidovorax species were determined based on the phylogenomic tree reconstructed using core genes, while they were not grouped in the 16S rRNA gene-based phylogenetic tree. The species arrangements of the genus Acidovorax were further confirmed by the comparisons of the digital DNA-DNA hybridization and average nucleotide identity (ANI) values. The ANI, average amino acid identity, and the percentage of conserved proteins values among the inter-clusters were approximately 83, 81, and 61%, respectively, and thus were proposed as practical thresholds for genus delineation. Besides, Acidovorax antarcticus was much closer to members of the genus Comamonas rather than those of the genus Acidovorax based on the genome-based analysis. Taken together, we propose the division of the current genus Acidovorax into the emended genus Acidovorax and the two novel genera Paracidovorax gen. nov., Paenacidovorax gen. nov. and the transfer of Acidovorax antarcticus into the genus Comamonas as Comamonas antarctica comb. nov.
嗜酸菌属是一个基因异质的物种聚类，包含许多环境和植物致病分类群。为了更好地理解嗜酸菌属物种之间的进化关系，利用包括嗜酸菌属和丛毛单胞菌属在内的22个可用模式菌株的基因组序列进行基于基因组的分析。基于使用核心基因重建的系统发育树，确定了嗜酸菌属的三个得到充分支持的单系聚类，而它们在基于16S rRNA基因的系统发育树中并未聚类。通过数字DNA-DNA杂交和平均核苷酸同一性（ANI）值的比较，进一步证实了嗜酸菌属的物种排列。聚类间的ANI、平均氨基酸同一性和保守蛋白百分比值分别约为83%、81%和61%，因此被提议作为属划分的实际阈值。此外，基于基因组分析，南极嗜酸菌与丛毛单胞菌属的成员比与嗜酸菌属的成员关系更密切。综上所述，我们建议将当前的嗜酸菌属划分为修订后的嗜酸菌属以及两个新属，即副嗜酸菌属（Paracidovorax gen. nov.）、类嗜酸菌属（Paenacidovorax gen. nov.），并将南极嗜酸菌转移到丛毛单胞菌属，命名为南极丛毛单胞菌（Comamonas antarctica comb. nov.）。
