Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica

Two Gram-negative, aerobic, non-motile, rod-shaped bacterial strains, FH13 T and FH23, representing a novel group of Rhizobium isolated from root nodules of Phaseolus vulgaris in Mexico, were studied by a polyphasic analysis. Phylogeny of 16S rRNA gene sequences revealed them to be members of the genus Rhizobium related most closely to 'Rhizobium anhuiense' CCBAU 23252 (99.7 % similarity), Rhizobium leguminosarum USDA 2370 T (98.6 %), and Rhizobium sophorae CCBAU 03386 T and others (j98.3 %). In sequence analyses of the housekeeping genes recA, glnII and atpD, both strains formed a subclade distinct from all defined species of the genus Rhizobium at sequence similarities of 82.3-94.0 %, demonstrating that they represented a novel genomic species in the genus Rhizobium. Mean levels of DNA-DNA relatedness between the reference strain FH13 T and the type strains of related species varied between 13.0¡2.0 and 52.1¡1.2 %. The DNA G+C content of strain FH13 T was 63.5 mol% (T m ). The major cellular fatty acids were 16 : 0, 17 : 0 anteiso, 18 : 0, summed feature 2 (12 : 0 aldehyde/unknown 10.928) and summed feature 8 (18 : 1v7c). The fatty acid 17 : 1v5c was unique for this strain. Some phenotypic features, such as failure to utilize adonitol, L-arabinose, D-fructose and D-fucose, and ability to utilize D-galacturonic acid and itaconic acid as carbon source, could also be used to distinguish strain FH13 T from the type strains of related species. Based upon these results, a novel species, Rhizobium acidisoli sp. nov., is proposed, with FH13 T (5CCBAU 101094 T 5HAMBI 3626 T 5LMG 28672 T ) as the type strain.

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“…S8). This composition was similar to that of the related species (Rozahon et al, 2014;Zhang et al, 2014).…”

Section: Rhizobium Oryzae Alt505 T (Eu056823)supporting

confidence: 52%

Rhizobium acidisoli sp. nov., isolated from root nodules of Phaseolus vulgaris in acid soils

Román‐Ponce

Zhang

Vásquez-Murrieta

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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“…There are also reports of endophytic rhizobia associated with Arabidopsis , wheat, maize, sugar cane, and rice [6–9]. Strains of endophytic Rhizobium were recently isolated from the tree species Populus euphratica and P. deltoides [10, 11]. …”

Section: Introductionmentioning

confidence: 99%

Genomic studies of nitrogen-fixing rhizobial strains from Phaseolus vulgaris seeds and nodules

et al. 2016

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BackgroundRhizobia are soil bacteria that establish symbiotic relationships with legumes and fix nitrogen in root nodules. We recently reported that several nitrogen-fixing rhizobial strains, belonging to Rhizobium phaseoli, R. trifolii, R. grahamii and Sinorhizobium americanum, were able to colonize Phaseolus vulgaris (common bean) seeds. To gain further insight into the traits that support this ability, we analyzed the genomic sequences and proteomes of R. phaseoli (CCGM1) and S. americanum (CCGM7) strains from seeds and compared them with those of the closely related strains CIAT652 and CFNEI73, respectively, isolated only from nodules.ResultsIn a fine structural study of the S. americanum genomes, the chromosomes, megaplasmids and symbiotic plasmids were highly conserved and syntenic, with the exception of the smaller plasmid, which appeared unrelated. The symbiotic tract of CCGM7 appeared more disperse, possibly due to the action of transposases. The chromosomes of seed strains had less transposases and strain-specific genes. The seed strains CCGM1 and CCGM7 shared about half of their genomes with their closest strains (3353 and 3472 orthologs respectively), but a large fraction of the rest also had homology with other rhizobia. They contained 315 and 204 strain-specific genes, respectively, particularly abundant in the functions of transcription, motility, energy generation and cofactor biosynthesis. The proteomes of seed and nodule strains were obtained and showed a particular profile for each of the strains. About 82 % of the proteins in the comparisons appeared similar. Forty of the most abundant proteins in each strain were identified; these proteins in seed strains were involved in stress responses and coenzyme and cofactor biosynthesis and in the nodule strains mainly in central processes. Only 3 % of the abundant proteins had hypothetical functions.ConclusionsFunctions that were enriched in the genomes and proteomes of seed strains possibly participate in the successful occupancy of the new niche. The genome of the strains had features possibly related to their presence in the seeds. This study helps to understand traits of rhizobia involved in seed adaptation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3053-z) contains supplementary material, which is available to authorized users.

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“…Rhizobia have also been isolated from other tissues of legumes, such as leaves, roots, and stems [2], and from other plants and trees, including Triticum aestivum [3], Zea mays [4], Oryza sativa [5], Arabidopsis thaliana [6], and Populus euphratica [7]. …”

Section: Introductionmentioning

confidence: 99%

Analysis of genome sequence and symbiotic ability of rhizobial strains isolated from seeds of common bean (Phaseolus vulgaris)

et al. 2018

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BackgroundRhizobia are alpha-proteobacteria commonly found in soil and root nodules of legumes. It was recently reported that nitrogen-fixing rhizobia also inhabit legume seeds. In this study, we examined whole-genome sequences of seven strains of rhizobia isolated from seeds of common bean (Phaseolus vulgaris).ResultsRhizobial strains included in this study belonged to three different species, including Rhizobium phaseoli, R. leguminosarum, and R. grahamii. Genome sequence analyses revealed that six of the strains formed three pairs of highly related strains. Both strains comprising a pair shared all but one plasmid. In two out of three pairs, one of the member strains was effective in nodulation and nitrogen fixation, whereas the other was ineffective. The genome of the ineffective strain in each pair lacked several genes responsible for symbiosis, including nod, nif, and fix genes, whereas that of the effective strain harbored the corresponding genes in clusters, suggesting that recombination events provoked gene loss in ineffective strains. Comparisons of genomic sequences between seed strains and nodule strains of the same species showed high conservation of chromosomal sequences and lower conservation of plasmid sequences. Approximately 70% of all genes were shared among the strains of each species. However, paralogs were more abundant in seed strains than in nodule strains. Functional analysis showed that seed strains were particularly enriched in genes involved in the transport and metabolism of amino acids and carbohydrates, biosynthesis of cofactors and in transposons and prophages. Genomes of seed strains harbored several intact prophages, one of which was inserted at exactly the same genomic position in three strains of R. phaseoli and R. leguminosarum. The R. grahamii strain carried a prophage similar to a gene transfer agent (GTA); this represents the first GTA reported for this genus.ConclusionsSeeds represent a niche for bacteria; their access by rhizobia possibly triggered the infection of phages, recombination, loss or gain of plasmids, and loss of symbiosis genes. This process probably represents ongoing evolution that will eventually convert these strains into obligate endophytes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5023-0) contains supplementary material, which is available to authorized users.

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Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica

Cited by 24 publications

References 36 publications

Rhizobium acidisoli sp. nov., isolated from root nodules of Phaseolus vulgaris in acid soils

Rhizobium acidisoli sp. nov., isolated from root nodules of Phaseolus vulgaris in acid soils

Genomic studies of nitrogen-fixing rhizobial strains from Phaseolus vulgaris seeds and nodules

Analysis of genome sequence and symbiotic ability of rhizobial strains isolated from seeds of common bean (Phaseolus vulgaris)

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