DNA Methylation in
            <i>Ensifer</i>
            Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with
            <i>Medicago</i>
            spp.

diCenzo, George C.; Cangioli, Lisa; Nicoud, Quentin; Cheng, Janis H.T.; Blow, Matthew J.; Shapiro, Nicole; Woyke, Tanja; Biondi, Emanuele G.; Alunni, Benoît; Mengoni, Alessio; Mergaert, Peter

doi:10.1128/msystems.01092-21

Cited by 10 publications

(18 citation statements)

References 84 publications

(123 reference statements)

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“…The genome-wide frequency of the pentanucleotide GANTC is higher in all genomes of the symbiotic clade compared to all genomes of the nonsymbiotic clade, with a statistically significant average difference of 60 % (1.70 vs 1.06 GANTC sites per kb, P -value<1×10 −10 using a two-sample t -test) [47]. As the GANTC motif is methylated by the highly conserved cell cycle-regulated methyltransferase CcrM [48, 49], this difference may reflect an important difference in the cell cycle biology of these two clades [47]. Indeed, species of the nonsymbiotic clade ( E.…”

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

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147

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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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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

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147

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“…In the current study, enhanced minerals uptake encourages the availability of nitrogen which enhance vegetative plant growth, including length and biomass of roots, shoots, and number of leaves. We do not test nitrogen fixation by the bacterial strains, however, tested bacterial strains of the genus Bacillus , Pseudomonas , Pontibacter , and Ensifer were previously reported for nitrogen fixation and their role in the promotion of vegetative growth ( Liu et al., 2019 ; Sibponkrung et al., 2020 ; diCenzo et al., 2021 ; Geries and Elsadany, 2021 ). Our tested strains were efficient P solubilizers that may promote P uptake by plants and play their role in cellular division and tissue formation ( Perez-Torres et al., 2008 ; Yu et al., 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Potential of mineral-solubilizing bacteria for physiology and growth promotion of Chenopodium quinoa Willd

et al. 2022

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Nutrient deficiency in wild plant species, including quinoa (Chenopodium quinoa Willd), can be overcome by applying mineral-solubilizing bacteria. Quinoa is a gluten-free, nutritious food crop with unique protein content. The present study aimed to characterize mineral-solubilizing rhizobacterial strains and to evaluate their plant growth-promoting potential in quinoa seedlings. More than sixty rhizobacterial strains were isolated from the quinoa rhizosphere and found eighteen strains to be strong phosphate solubilizers. Most of these bacterial strains showed zinc solubilization, and more than 80% of strains could solubilize manganese. The selected strains were identified as Bacillus altitudinis Cq-3, Pseudomonas flexibilis Cq-32, Bacillus pumilus Cq-35, Pseudomonas furukawaii Cq-40, Pontibacter lucknowensis Cq-48, and Ensifer sp. Cq-51 through 16S rRNA partial gene sequencing. Mainly, these strains showed the production of organic acids, including malic, gluconic, tartaric, ascorbic, lactic, and oxalic acids in insoluble phosphorus amended broth. All strains showed production of gluconic acids, while half of the strains could produce malic, ascorbic, lactic, and oxalic acids. These strains demonstrated the production of indole-3-acetic acid in the presence as well as in the absence of L-tryptophan. The bacterial strains also demonstrated their ability to promote growth and yield attributes, including shoot length, root length, leave numbers, root and shoot dry biomass, spike length, and spikes numbers of quinoa in pots and field trials. Increased physiological attributes, including relative humidity, quantum flux, diffusive resistance, and transpiration rate, were observed due to inoculation with mineral solubilizing bacterial strains under field conditions. P. lucknowensis Cq-48, followed by P. flexibilis Cq-32, and P. furukawaii Cq-40 showed promising results to promote growth, yield, and physiological attributes. The multi-traits characteristics and plant growth-promoting ability in the tested bacterial strains could provide an opportunity for formulating biofertilizers that could promote wild quinoa growth and physiology.

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“…The mechanism of coordination of replication initiation of secondary replicons with that of the chromosome in S. meliloti is still unknown. Transcriptome data [68] and DNA methylation pattern [69] of a S. meliloti wild type strain also suggest an asynchronous replication of the chromosome and the secondary replicons. Stronger upregulation of repC2 (pSymA) than repC1 (pSymB) transcripts during the cell cycle [68] might indicate a threshold-like mechanism contributing to the temporal preference for oriA replication initiation.…”

Section: Discussionmentioning

confidence: 99%

“…In C. crescentus , the interplay of CcrM with GcrA is suggested to mediate methylation state dependent regulation of gene expression [70, 71]. Since in S. meliloti, these two cell cycle regulators are conserved [70, 72] and recognition motifs of the N6-adenosine methyltransferase CcrM were found upstream of cell cycle-regulated genes of the repABC loci on the secondary replicons [69], methylation state dependent regulation of gene expression is hypothesized to also contribute to the integration of these replicons in the cell cycle.…”

Section: Discussionmentioning

confidence: 99%

Engineering aSinorhizobium melilotichassis with monopartite, single replicon genome configuration

Wagner

Döhlemann

Geisel

et al. 2022

Preprint

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While the vast majority of bacterial genomic DNA molecules contain a single origin of replication, some natural isolates and engineered strains were reported to contain chromosomes derived from cointegration events of multiple replicons. We investigated effects of multiple DNA replication origins and terminus regions on spatial DNA organization and spatiotemporal replicon segregation in the alphaproteobacterium Sinorhizobium meliloti. Strains with a bi- and monopartite genome configuration were constructed by Cre/lox-mediated site-specific fusions of the secondary replicons pSymA and pSymB, and of the chromosome, pSymA and pSymB. The design of these strains maintained replichore ratios, GC skew, as well as distribution and orientation of KOPS and coding sequences. Growth of these strains was essentially unaffected, except for high salt conditions. Replication initiation at the three origins as well as key features of spatial organization and spatiotemporal segregation were maintained in the triple-replicon fusion strain. Cell growth was slowed down by deleting, either individually or together, the pSymA- and pSymB-derived replication initiator encoding repC genes with their intrinsic origin of replication from the dual or triple replicon cointegrates, respectively. Replication of the triple cointegrate, characterized by the chromosomal oriC as sole origin and a strongly disbalanced replichore ratio, terminated in the original chromosomal terC region, suggesting a replication trap. Progression of replication of the longer replichore was not blocked but impaired, possibly due to the retained secondary replicon’s terminus regions and reverse alignment of replichore-orienting sequence features following from the deletion of replication origins. Moreover, during the cell cycle of this strain, oriC aberrantly localized and served as replication initiation site in the mid cell area of the cell with the oldest cell pole. Growth deficiency of this strain was attenuated by a suppressor mutation causing amino acid substitution R436H in the cell cycle histidine kinase CckA.

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DNA Methylation in Ensifer Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with Medicago spp.

Abstract: Nitrogen fixation by rhizobia in symbiosis with legumes is economically and ecologically important. The symbiosis can involve a complex bacterial transformation—terminal differentiation—that includes major shifts in the transcriptome and cell cycle.

Cited by 10 publications

References 84 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

Potential of mineral-solubilizing bacteria for physiology and growth promotion of Chenopodium quinoa Willd

Engineering aSinorhizobium melilotichassis with monopartite, single replicon genome configuration

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