Genomic Comparison of Agrobacterium pusense Strains Isolated from Bean Nodules

Aguilar, Alejandro; Peralta, Humberto; Mora, Yolanda; Dı́az, Rosalinda; Vargas-Lagunas, Carmen; Girard, Lourdes; Mora, Jaime

doi:10.3389/fmicb.2016.01720

Cited by 6 publications

(5 citation statements)

References 35 publications

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“…3 ). A similar analysis of a highly-related pair of Agrobacterium strains (CCGM10 and CCGM11) has been published previously [ 10 ]. Strains CCGM10 and CCGM11 differ from each other in one plasmid, which represents an intact phage.…”

Section: Discussionmentioning

confidence: 82%

“…Genomic sequences of seven new seed rhizobial strains were obtained and analyzed in this study. In addition to the genomes of four strains analyzed previously [ 8 , 10 ], sequence analysis of these seed strains expands our view of the species diversity and characteristics of rhizobia found in bean seeds. The findings reported here shed light on the evolution of these microorganisms in this new niche.…”

Section: Discussionmentioning

confidence: 99%

“…High similarity has also been shown among strains of Agrobacterium pusense isolated from root nodules of un-inoculated bean plants; the source of these bacteria is thought to be seeds [ 10 ]. These Agrobacterium strains are closely related to the strain IRBG74, which is currently the only Agrobacterium isolate with a symbiotic plasmid, capable of forming nitrogen-fixing root nodules in Sesbania cannabina [ 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…Strain NRCPB10, originally isolated from root nodules of S. cannabina [21], is capable of nodulating at least eight Sesbania species [19] and has been identified as A. pusense [23]. Strains CNPSo 662 and CNPSo 665 of A.…”

Section: Introductionmentioning

confidence: 99%

“…There are, however, some exceptions, among which A. salinitolerans strains YIC 5082 T and YIC4104 formed effective nodules on Sesbania cannabina, the legume from which they were isolated [19]. Strain NRCPB10, originally isolated from root nodules of S. cannabina [21], is capable of nodulating at least eight Sesbania species [19] and has been identified as A. pusense [23]. Strains CNPSo 662 and CNPSo 665 of A. pusense were isolated from root nodules of common bean and formed nodules on this plant, though ineffective in fixing nitrogen [24].…”

Section: Introductionmentioning

confidence: 99%

Agrobacterium leguminum sp. nov., isolated from nodules of Phaseolus vulgaris in Spain

Castellano‐Hinojosa

Correa‐Galeote

Ramírez-Bahena

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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Two endophytic strains, coded MOVP5T and MOPV6, were isolated from nodules of Phaseolus vulgaris plants grown on agricultural soil in Southeastern Spain, and were characterized through a polyphasic taxonomy approach. Their 16S rRNA gene sequences showed 99.3 and 99.4 %, 98.9 and 99.6 %, and 99.0 and 98.7% similarity to ‘ A. deltaense ’ YIC 4121T, A. radiobacter LGM 140T, and A. pusense NRCPB10T, respectively. Multilocus sequence analysis based on sequences of recA and atpD genes suggested that these two strains could represent a new Agrobacterium species with less than 96.5 % similarity to their closest relatives. PCR amplification of the telA gene, involved in synthesis of protelomerase, confirmed the affiliation of strains MOPV5T and MOPV6 to the genus Agrobacterium . Whole genome average nucleotide identity and digital DNA–DNA hybridization average values were less than 95.1 and 66.7 %, respectively, with respect to its closest related species. Major fatty acids in strain MOPV5T were C18 : 1 ω7c/C18 : 1 ω6c in summed feature 8, C19 : 0 cyclo ω8c, C16 : 0 and C16 : 0 3-OH. Colonies were small to medium, pearl-white coloured on YMA at 28 °C and growth was observed at 10–42 °C, pH 5.0–10.0 and with 0.0–0.5 % (w/v) NaCl. The DNA G+C content was 59.9 mol%. These two strains differ from all other genomovars of Agrobacterium found so far, including those that have not yet given a Latin name. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strain MOPV5T as representing a novel species of Agrobacterium , for which the name Agrobacterium leguminum sp. nov. is proposed. The type strain is MOPV5T (=CECT 30096T=LMG 31779T).

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Ureide metabolism in plant-associated bacteria: purine plant-bacteria interactive scenarios under nitrogen deficiency

Izaguirre‐Mayoral

Lazarovits²,

Baral

2018

Plant Soil

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Background The erratic alterations in climate being experienced in agriculture, such as extended periods of drought or heavy rainfalls, are bringing increasing concerns about nitrogen (N) management. Even in highinput farming systems, unpredictable weather patterns can cause N deficiencies and result in nutrient losses that contribute to major pollution issues in groundwater, lakes, and even the oceans. Our present understanding of the beneficial interactions between N-deficientchallenged plants and plant-associated bacteria (PAB), mainly of the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria, is largely based on

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Genomic Comparison of Agrobacterium pusense Strains Isolated from Bean Nodules

Cited by 6 publications

References 35 publications

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

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

Agrobacterium leguminum sp. nov., isolated from nodules of Phaseolus vulgaris in Spain

Ureide metabolism in plant-associated bacteria: purine plant-bacteria interactive scenarios under nitrogen deficiency

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