Genomic analysis provides novel insights into diversification and taxonomy ofAllorhizobium vitis(i.e.Agrobacterium vitis)

Abstract

Allorhizobium vitis (formerly named Agrobacterium vitis or Agrobacterium biovar 3) is the primary causative agent of crown gall disease of grapevine worldwide. Whole-genome sequence comparisons and phylogenomic analysis of various All. vitis strains clearly indicated that All. vitis is not a single species, but represents a species complex composed of at least four genomic species. Thus, we amended the description of All. vitis which now refers to a restricted group of strains within the All. vitis complex (i.e. All. vitis sensu stricto) and proposed a description of a novel species All. ampelinum sp. nov. The type strain of All. vitis sensu stricto remains the existing type strain of All. vitis, K309T (= NCPPB 3554T =HAMBI 1817T = ATCC 49767T = CIP 105853T = ICMP 10752T = IFO 15140T = JCM 21033T = LMG 8750T = NBRC 15140T). The type strain of All. ampelinum sp. nov. is S4T (= DSM 112012T = ATCCBAA-846T). This genome-based classification was supported by differentiation of strains based on a MALDI-TOF MS analysis. We also identified gene clusters specific for All. vitis species complex, All. vitis sensu stricto and All. ampelinum, and attempted to predict their function and their role in ecological diversification of these clades, some of which were experimentally validated. Functions of All. vitis species complex-specific genes convergently indicate a role in adaptation to different stresses, including exposure to aromatic compounds. Similarly, All vitis sensu stricto-specific genes also confer the ability to degrade 4-hydroxyphenylacetate and a putative compound related to gentisic acid, while All. ampelinum-specific genes have putative functions related to polyamine metabolism and nickel assimilation. This suggests that these species have differentiated ecologies, each relying on specialized nutrient consumption or toxic compound degradation to adapt to their respective niche. Moreover, our genome-based analysis indicated that Allorhizobium and the “R. aggregatum complex” represent separate genera of the family Rhizobiaceae.

Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation

“…The “ Rhizobium aggregatum complex” was initially identified as a sister taxon of the genus Agrobacterium [26], with subsequent work demonstrating that it is instead located on a clade neighbouring the genus Allorhizobium [12]. Moreover, the latter study suggested that “ R. aggregatum complex” includes members of the genus Ciceribacter and that it may represent a novel genus on the basis of phylogenetic and multiple OGRI data, although the authors advised that further investigation was required [12]. It was recently suggested that the “ R. aggregatum complex” be split into two genera [27].…”

“…The core genome phylogeny was obtained using the GET_HOMOLOGUES software package version 10032020 [10] and the GET_PHYLOMARKERS software package Version 2.2.8_18Nov2018 [11], as described previously [12]. As a result, a set of 170 non-recombining single-copy core marker genes was selected ( Dataset S2 ), and a concatenation of their codon-based alignments was used as input for IQ-Tree ModelFinder, with which a search for the best sequence evolution model was conducted.…”