Peteryoungia gen. nov. with four new species combinations and description of Peteryoungia desertarenae sp. nov., and taxonomic revision of the genus Ciceribacter based on phylogenomics of Rhizobiaceae

Rahi, Praveen; Khairnar, Mitesh; Hagir, Ashwini; Narayan, Avinash; Jain, Kunal; Madamwar, Datta; Pansare, Aabeejjeet N.; Shouche, Yogesh S.

doi:10.1007/s00203-021-02349-9

Cited by 57 publications

(23 citation statements)

References 62 publications

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“…All pairwise cpAAI values within this group were > 88%, while all pairwise cpAAI values against the other six “ R. aggregatum complex” species were < 84.7% ( Figure 3 ). These results support the proposal for the genus “ Peteryoungia ” [27], which should also primarily include R. aggregatum , as well as “ A. albertimagni ”, and “ R. glycinendophyticum ” once their names are validly published.…”

Section: Resultssupporting

confidence: 88%

“…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]. It was proposed that R. daejeonense, R. naphthalenivorans , and R. selenitireducens be transferred to the genus Ciceribacter , while R. ipomoeae, Rhizobium rhizophilum, R. rosettiformans, R. wuzhouense , and “ Peteryoungia desertarenae ” be transferred to the novel genus “ Peteryoungia ” [27].…”

Section: Resultsmentioning

confidence: 99%

“…It was recently suggested that the “ R. aggregatum complex” be split into two genera [27]. It was proposed that R. daejeonense, R. naphthalenivorans , and R. selenitireducens be transferred to the genus Ciceribacter , while R. ipomoeae, Rhizobium rhizophilum, R. rosettiformans, R. wuzhouense , and “ Peteryoungia desertarenae ” be transferred to the novel genus “ Peteryoungia ” [27].…”

Section: Resultsmentioning

confidence: 99%

“…All within-group cpAAI values were > 86.5% while all between-group cpAAI values were ≤ 85.4%, providing support for these two clades representing separate genera. However, the bootstrap support for the split of these two clades in the phylogeny is only 80%, and the topology of the tree in this region ( Figure 1 ) differs from the tree reported by Rahi et al ., wherein R. daejeonense, R. naphthalenivorans , and R. selenitireducens were not monophyletic (see Figure 2 of [27]). Overall, the data presented here are not in agreement with the proposal to transfer R. daejeonense, R. naphthalenivorans , and R. selenitireducens to the genus Ciceribacter .…”

Section: Resultsmentioning

confidence: 99%

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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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Section: Resultssupporting

confidence: 88%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

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

Kuzmanović

Fagorzi

Mengoni

et al. 2021

Preprint

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show abstract

“…It was recently suggested that the ‘ R. aggregatum complex’ be split into two genera [30]. It was proposed that R.…”

Section: Resultsmentioning

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

142

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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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Phylogenomic analysis of Citrobacter sp. strain AAK_AS5 and its metabolic capabilities to support nitrogen removal behavior

et al. 2022

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Despite the ubiquity of the genus Citrobacter in clinical, industrial, and environmental scenarios, a large number of Citrobacter strains have not been explored at the genome‐scale level. In this study, accurate taxonomic assignment of strain AAK_AS5 isolated from activated sludge was achieved by in‐silico genomic comparison using Overall Genome‐based Relatedness Indices (ANI(OAT): 97.55%, ANIb:97.28%, and ANIm: 97.83%) that indicated its closest identity to the related strain Citrobacter portucalensis A60T. Results were consistent with a digital DNA–DNA hybridization value of 80% with C. portucalensis A60T which was greater than the species boundary value >70% for delineating closely related bacterial species. Gene mining through Kyoto Encyclopedia of Genes and Genomes (KEGG), and annotation using rapid annotation subsystem technology (RAST) revealed the notable gene contents for nitrogen metabolism and other pathways associated with nitrate/nitrite ammonification (28 genes), ammonia assimilation (22 genes), and denitrification pathways (14 genes). Furthermore, the strain AAK_AS5 also exhibited a high soluble chemical oxygen demand (sCOD), NH4+‐N, and NO3‐‐N removal efficiency of 91.4%, 90%, and 93.6%, respectively thus validating its genetic capability for utilizing both (NH4)2SO4 and KNO3 as the nitrogen source. The study provided deeper insights into the phylogenomics and the genetic potential of Citrobacter, sp. strain AAK AS5 associated with nitrogen metabolism thus signifying the potential application of the isolate for treating nitrogen‐rich wastewaters.

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Peteryoungia gen. nov. with four new species combinations and description of Peteryoungia desertarenae sp. nov., and taxonomic revision of the genus Ciceribacter based on phylogenomics of Rhizobiaceae

Cited by 57 publications

References 62 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

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

Phylogenomic analysis of Citrobacter sp. strain AAK_AS5 and its metabolic capabilities to support nitrogen removal behavior

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