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

Abstract

The alphaproteobacterial family Rhizobiaceae is highly diverse, with 168 species with validly published names classified into 17 genera with validly published names. Most named genera in this family are delineated based on genomic relatedness and phylogenetic relationships, but some historically named genera show inconsistent distribution and phylogenetic breadth. Most problematic is Rhizobium, which is notorious for being highly paraphyletic, as most newly described species in the family being assigned to this genus without consideration for their proximity to existing genera, or the need to create novel genera. In addition, many Rhizobiaceae genera lack synapomorphic traits that would give them biological and ecological significance. We propose a common framework for genus delimitation within the family Rhizobiaceae. We propose that genera in this family should be defined as monophyletic groups in a core-genome gene phylogeny, that are separated from related species using a pairwise core-proteome average amino acid identity (cpAAI) threshold of approximately 86%. We further propose that the presence of additional genomic or phenotypic evidence can justify the division of species into separate genera even if they all share greater than 86% cpAAI. Applying this framework, we propose to reclassify Rhizobium rhizosphaerae and Rhizobium oryzae into the new genus Xaviernesmea gen. nov. Data is also provided to support the recently proposed genus "Peteryoungia", and the reclassifications of Rhizobium yantingense as Endobacterium yantingense comb. nov., Rhizobium petrolearium as Neorhizobium petrolearium comb. nov., Rhizobium arenae as Pararhizobium arenae comb. nov., Rhizobium tarimense as Pseudorhizobium tarimense comb. nov., and Rhizobium azooxidefex as Mycoplana azooxidifex comb. nov. Lastly, we present arguments that the unification of the genera Ensifer and Sinorhizobium in Opinion 84 of the Judicial Commission is no longer justified by current genomic and phenotypic data. We thus argue that the genus Sinorhizobium is not illegitimate and now encompasses 17 species.

Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex

“…However, in our study both the MLSA and WGS phylogeny and ANIb analysis showed that A. albertimagni AOL51 T is more closely related to Allorhizobium , suggesting that “ R. aggregatum complex” is not the best choice. This is in agreement with Kuzmanovic et al [55], who proposed the name “ Peteryoungia ” for strains formerly identified as “ R. aggregatum complex”, and also included A. albertimagni AOL51 T .…”

Two new Rhizobiales species isolated from root nodules of common sainfoin (Onobrychis viciifolia) show different plant colonization strategies

“…The cpAAI between the isolate TH2 and reference Rhizobiaceae spp. were <76 % (Table S4), which was below the threshold of ∼86 % for delimitation of Rhizobiaceae genera proposed recently [60]. This suggested that isolate TH2 represents a new genus and species, described here as Onobrychidicola muellerharveyae gen. nov sp.…”

Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.

“…Branch supports were estimated with 200 Felsenstein bootstrap trees. The 16S tree was rooted using R. leguminosarum USDA 2370 T sequence, whereas the gyrB and MLSA trees were rooted using the sequence from “ A. albertimagni ” AOL15 – a distant relative incorrectly classified in the Agrobacterium genus for which a classification in the newly proposed genus “ Peteryoungia ” was proposed ( Kuzmanović et al, 2021 ).…”