Ensifer glycinis sp. nov., a rhizobial species associated with species of the genus Glycine

Yan, Hui; Yan, Jun; Sui, Xin; Wang, En Tao; Chen, Wen Xin; Chen, Wen Feng

doi:10.1099/ijsem.0.001120

Cited by 26 publications

(11 citation statements)

References 35 publications

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“…The description is as provided by Yan et al . 2016 [59]. S. glycinis can be differentiated from other species of the genus Sinorhizobium based on OGRI calculations (ANI and isDDH).…”

Section: Resultsmentioning

confidence: 99%

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

Kuzmanović

Fagorzi

Mengoni

et al. 2021

Preprint

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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.

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“…The description is as provided by Yan et al . 2016 [59]. S. glycinis can be differentiated from other species of the genus Sinorhizobium based on OGRI calculations (ANI and isDDH).…”

Section: Resultsmentioning

confidence: 99%

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

Kuzmanović

Fagorzi

Mengoni

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…) and E. glycinis (Yan et al . ) have been confirmed to be soybean's nitrogen‐fixing microsymbionts in China. In our current study, besides the six known Bradyrhizobium species and one known Sinorhizobium/Ensifer species, we found another two unidentified Bradyrhizobium species and one novel Ensifer species, i.e., E. shofinae sp.…”

Section: Discussionmentioning

confidence: 99%

“…) and E. glycinis (Yan et al . ). Soil pH and salinity have been found to be related to the ecological distribution of soybean‐nodulating rhizobial species (Giongo et al .…”

Section: Introductionmentioning

confidence: 97%

Rhizobial biogeography and inoculation application to soybean in four regions across China

Yang

Chen

Wang³

et al. 2018

J Appl Microbiol

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“…The description is as provided by Yan et al . 2016 [63]. S. glycinis can be differentiated from other species of the genus Sinorhizobium based on OGRI calculations (ANI and dDDH).…”

Section: Description Of Sinorhizobium Glycinis Comb Novmentioning

confidence: 99%

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

Kuzmanović

Fagorzi

Mengoni

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

137

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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.

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Ensifer glycinis sp. nov., a rhizobial species associated with species of the genus Glycine

Cited by 26 publications

References 35 publications

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

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

Rhizobial biogeography and inoculation application to soybean in four regions across China

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

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