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. The most problematic is Rhizobium , which is notorious for being highly paraphyletic, as most newly described species in the family are assigned to this genus without consideration of their proximity to existing genera, or the need to create novel genera. Moreover, 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 , wherein genera are 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 additional genomic or phenotypic evidence can justify division of species into separate genera even if they share greater than 86 % cpAAI. Applying this framework, we propose to reclassify Rhizobium rhizosphaerae and Rhizobium oryzae into Xaviernesmea gen. nov. Data is also provided to support the formation of Peteryoungia aggregata comb. nov., Endobacterium yantingense comb. nov., Neorhizobium petrolearium comb. nov., Pararhizobium arenae comb. nov., Pseudorhizobium tarimense comb. nov. and 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. Despite pairwise cpAAI values for all Ensifer species and all Sinorhizobium species being >86 %, additional genomic and phenotypic data suggest that they significantly differ in their biology and ecology. We therefore propose emended descriptions of Ensifer and Sinorhizobium , which we argue should be considered as separate genera.

New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia

“…In 2020, a study performed phenotypic, genomic, and phylogenetic analyses of the genus Ensifer and suggested that the genus should be separated into two genera, one for the symbiotic clade and the other for the nonsymbiotic clade [ 185 ]. More recently, a publication on the IJSEM suggested the revision of family Rhizobiaceae [ 186 ]. The extensive study suggests a threshold for core-proteome average amino acid identity (cpAAI) of approximately 86% as a new framework for genus delimitation.…”

“…It is noteworthy to mention that cpAAI must not be used as sole information for genus delimitation, and the authors specify “approximately 86%” to provide some flexibility regarding the evolution of each genus. Although not yet updated in the LPSN website as validated names, among the reclassifications based on the study of Kuzmanović and collaborators [ 186 ], there are arguments that the unification of the genera Ensifer and Sinorhizobium is no longer justified, and eight new combinations were suggested, but not all involving rhizobial strains [ 186 ].…”

Two New Rhizobiales Species Isolated from Root Nodules of Common Sainfoin (Onobrychis viciifolia) Show Different Plant Colonization Strategies

“…The core-proteome average amino acid identity (cpAAI) between the isolate TH2 and reference Rhizobiaceae spp. was <76% (Table S4), which was below the threshold of ~86% for delimitation of Rhizobiaceae genera proposed recently ( 37 ). This suggested that isolate TH2 represents a new genus and species, described here as Onobrychidicola muellerharveyae gen. nov. sp.…”

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.…”