Sustainable Plant Protection, Centre de Cabrils, IRTA-Institute of Agrifood Research and Technology, Cabrils, Spain.
CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME & BIM), Department Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium.
PLoS One. 2024 Nov 19;19(11):e0302954. doi: 10.1371/journal.pone.0302954. eCollection 2024.
Rhizogenic Agrobacterium, the causative agent of hairy root disease (HRD), is known for its high phenotypic and genetic diversity. The taxonomy of rhizogenic agrobacteria has undergone several changes in the past and is still somewhat controversial. While the classification of Agrobacterium strains was initially mainly based on phenotypic properties and the symptoms they induced on plants, more and more genetic information has been used along the years to infer Agrobacterium taxonomy. This has led to the definition of the so-called Agrobacterium tumefaciens species complex (Atsc), which comprises several genomospecies. Interestingly, the rhizogenic Agrobacterium strains are found in several of these genomospecies. Nevertheless, even up until today Agrobacterium strains, and in particular rhizogenic agrobacteria, are prone to misclassification and considerable confusion in literature. In this study, we evaluated different phylogenetic analysis approaches for their use to improve Agrobacterium taxonomy and tried to gain more insight in the classification of strains into this complex genus, with a particular focus on rhizogenic agrobacteria. The genome sequence analysis of 580 assemblies, comprising Agrobacterium, Allorhizobium and Rhizobium strains demonstrated that phylogenies based on single marker genes, such as the commonly used 16S rRNA and recA gene, do not provide sufficient resolution for proper delineation of the different genomospecies within the Atsc. Our results revealed that (in silico) multi-locus sequences analysis (MLSA) in combination with average nucleotide identity (ANIb) at a 94.0% threshold delineates genomospecies accurately and efficiently. Additionally, this latter approach permitted the identification of two new candidate genomospecies.
发根农杆菌是毛根病（HRD）的病原体，以其高表型和遗传多样性而闻名。发根农杆菌的分类在过去经历了几次变化，仍然存在一些争议。虽然最初主要根据表型特性和它们在植物上引起的症状对根癌农杆菌菌株进行分类，但多年来，越来越多的遗传信息被用于推断根癌农杆菌的分类。这导致了所谓的根癌农杆菌物种复合体（Atsc）的定义，其中包括几个基因组种。有趣的是，发根农杆菌菌株存在于其中的几个基因组种中。然而，即使到今天，根癌农杆菌菌株，特别是发根农杆菌，仍然容易被错误分类，并在文献中引起相当大的混乱。在这项研究中，我们评估了不同的系统发育分析方法在改进根癌农杆菌分类中的应用，并试图更深入地了解将菌株分类到这个复杂属中的情况，特别是发根农杆菌。对 580 个组装体的基因组序列分析，包括根癌农杆菌、根瘤菌和根瘤菌菌株，表明基于单个标记基因的系统发育分析，如常用的 16S rRNA 和 recA 基因，不能为 Atsc 内不同基因组种的正确划定提供足够的分辨率。我们的结果表明，（计算机模拟）多位点序列分析（MLSA）结合 94.0%阈值的平均核苷酸同一性（ANIb）能够准确有效地划定基因组种。此外，这种方法还可以识别出两个新的候选基因组种。
