Ensifer, Phyllobacterium and Rhizobium species occupy nodules of Medicago sativa (alfalfa) and Melilotus alba (sweet clover) grown at a Canadian site without a history of cultivation

Bromfield, E. S. P.; Tambong, James T.; Cloutier, Sylvie; Prévost, Danielle; Laguerre, Gisèle; Berkum, Peter van; Thi, Thu Van Tran; Assabgui, R.; Barran, L. R.

doi:10.1099/mic.0.034058-0

Cited by 50 publications

(69 citation statements)

References 38 publications

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“…Phyllobacterium strains have been identified in different environments (31), mostly as plant-associated bacteria (28,30,47,48). To date, the Phyllobacterium genus contains 10 species, but only two, P. trifolii and P. sophorae, are able to induce effective nodules on their host legumes, Trifolium pratense and Sophora flavescens, respectively (26,27).…”

Section: Discussionmentioning

confidence: 99%

Diverse Bacteria Affiliated with the Genera Microvirga, Phyllobacterium, and Bradyrhizobium Nodulate Lupinus micranthus Growing in Soils of Northern Tunisia

Msaddak

Durán

Rejili

et al. 2017

Appl Environ Microbiol

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The genetic diversity of bacterial populations nodulating Lupinus micranthus in five geographical sites from northern Tunisia was examined. Phylogenetic analyses of 50 isolates based on partial sequences of recA and gyrB grouped strains into seven clusters, five of which belong to the genus Bradyrhizobium (28 isolates), one to Phyllobacterium (2 isolates), and one, remarkably, to Microvirga (20 isolates). The largest Bradyrhizobium cluster (17 isolates) grouped with the B. lupini species, and the other five clusters were close to different recently defined Bradyrhizobium species. Isolates close to Microvirga were obtained from nodules of plants from four of the five sites sampled. We carried out an in-depth phylogenetic study with representatives of the seven clusters using sequences from housekeeping genes (rrs, recA, glnII, gyrB, and dnaK) and obtained consistent results. A phylogeny based on the sequence of the symbiotic gene nodC identified four groups, three formed by Bradyrhizobium isolates and one by the Microvirga and Phyllobacterium isolates. Symbiotic behaviors of the representative strains were tested, and some congruence between symbiovars and symbiotic performance was observed. These data indicate a remarkable diversity of L. micranthus root nodule symbionts in northern Tunisia, including strains from the Bradyrhizobiaceae, Methylobacteriaceae, and Phyllobacteriaceae families, in contrast with those of the rhizobial populations nodulating lupines in the Old World, including L. micranthus from other Mediterranean areas, which are nodulated mostly by Bradyrhizobium strains.IMPORTANCE Lupinus micranthus is a legume broadly distributed in the Mediterranean region and plays an important role in soil fertility and vegetation coverage by fixing nitrogen and solubilizing phosphate in semiarid areas. Direct sowing to extend the distribution of this indigenous legume can contribute to the prevention of soil erosion in pre-Saharan lands of Tunisia. However, rhizobial populations associated with L. micranthus are poorly understood. In this context, the diversity of endosymbionts of this legume was investigated. Most Lupinus species are nodulated by Bradyrhizobium strains. This work showed that about half of the isolates from northern Tunisian soils were in fact Bradyrhizobium symbionts, but the other half were found unexpectedly to be bacteria within the genera Microvirga and Phyllobacterium. These unusual endosymbionts may have a great ecological relevance. Inoculation with the appropriate selected symbiotic

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Section: Discussionmentioning

confidence: 99%

Diverse Bacteria Affiliated with the Genera Microvirga, Phyllobacterium, and Bradyrhizobium Nodulate Lupinus micranthus Growing in Soils of Northern Tunisia

Msaddak

Durán

Rejili

et al. 2017

Appl Environ Microbiol

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“…Numerous studies have reported the isolation and characterization of phages of Rhizobium, including their role in Rhizobium ecology (11,13,19,39,40). Generally, phages have been used for typing Rhizobium strains as indicators of diversity and symbiotic performance (39)(40)(41)(42). They have also been useful as genetic tools to construct linkage maps for the chromosome and to allocate nitrogen fixation and nodulation loci in plasmids (43,44).…”

Section: Discussionmentioning

confidence: 99%

Narrow-Host-Range Bacteriophages That Infect Rhizobium etli Associate with Distinct Genomic Types

Santamaría¹,

Bustos²,

Sepúlveda-Robles

et al. 2014

Appl Environ Microbiol

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bIn this work, we isolated and characterized 14 bacteriophages that infect Rhizobium etli. They were obtained from rhizosphere soil of bean plants from agricultural lands in Mexico using an enrichment method. The host range of these phages was narrow but variable within a collection of 48 R. etli strains. We obtained the complete genome sequence of nine phages. Four phages were resistant to several restriction enzymes and in vivo cloning, probably due to nucleotide modifications. The genome size of the sequenced phages varied from 43 kb to 115 kb, with a median size of ϳ45 to 50 kb. A large proportion of open reading frames of these phage genomes (65 to 70%) consisted of hypothetical and orphan genes. The remainder encoded proteins needed for phage morphogenesis and DNA synthesis and processing, among other functions, and a minor percentage represented genes of bacterial origin. We classified these phages into four genomic types on the basis of their genomic similarity, gene content, and host range. Since there are no reports of similar sequences, we propose that these bacteriophages correspond to novel species. Bacteriophages have an enormous impact on the ecology and evolution of bacteria (1-3). It is well-known that bacteriophages are agents of gene mobilization across bacterial populations and that the majority of bacterial genomes harbor prophages as well as individual genes of phage origin (4-6). Conversely, temperate phages often carry bacterial genes as a result of prophage induction and recombination (7,8). Some reports indicate that phages exist for almost every known bacterial species (9). In the case of symbiotic nitrogen-fixing bacteria, such as Sinorhizobium meliloti (10, 11), Rhizobium leguminosarum (12-14), Mesorhizobium spp. (15), and Bradyrhizobium spp. (16), phages have been isolated and characterized, but no genome sequences have been reported. As a consequence, genomic comparisons have not been made. To date, only the complete genome sequence of phage 16-3 of S. meliloti has been determined (17).Lytic and temperate phages that infect rhizobial species have been isolated from soils and from lysogens induced after UV light treatment or mitomycin C exposure (11). The presence of phageresistant and -sensitive strains of Rhizobium suggests that phages play a substantial role in the selection or elimination of certain genotypes (11,(18)(19)(20). For instance, bacteriophages reduce the population density of susceptible strains of Rhizobium trifolii on the root surface, allowing resistant strains to form nodules (21,22). In field experiments, the persistence of genetically modified rhizobia has been explained in part by their resistance to phages (19).In the completely sequenced genomes of Rhizobium etli strains CFN42 and CIAT652 (23, 24), there are some open reading frames (ORFs) with relatively high degrees of identity to bacteriophage genes, such as DNA integrases, DNA transferases, lysozymes, and the small and large subunits of DNA terminase. In this work, we obtained a collection of 14 R. etli ...

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“…Todos los aislados autóctonos presentaron altos niveles de resistencia intrínseca a los antibió-ticos, particularidad que también fue señalada por Bromfield et al (2010) para especies del género Rhizobium, Ensifer y Phyllobacterium. Según Jordán (1984), la mayor susceptibilidad es característica del género Rhizobium a diferencia de las cepas de crecimiento lento del género Bradyrhizobium, las cuales han mostrado un espectro más amplio de resistencia a los antibióticos en cuanto al número y concentraciones ensayadas.…”

Section: Discussionunclassified

“…Sin embargo, el perfil de restricción incluyó a Rm V en el grupo de S. americanum CFN-Ei 156 (100% similares) y a Rm B en un genotipo diferente con 80% de similaridad a las cepas de referencia de crecimiento rápido R. tropici CiAT 899 y S. americanum CFNEi 156. Estos resultados son apoyados por los encontrados por Bromfield et al (2010), quienes han señalado a Medicago sativa como una leguminosa, cuyos nódulos estaban ocupados por varios genotipos bacterianos, pertenecientes a los géneros Ensifer, Rhizobium y Phyllobacterium, este último considerado como oportunista.…”

Section: Discussionunclassified

Caracterización fenotípica y genotípica de doce rizobios aislados de diversas regiones geográficas de Venezuela

Marquina¹,

González²,

Castro³

2010

RBT

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Phenotypic and genotypic characterization of twelve rhizobial isolates from different regions of Venezuela. Rhizobial taxonomy and systematics have progressed substantially, nevertheless, few studies have been developed on venezuelan species. This study evaluated the phenotypic and genetic variation between 12 venezuelan indigenous rhizobial isolates and 10 international referential strains, by phenotypical traits and DNA molecular markers. in this regard, a PCR-RFLP of the 16S rDNA gene, the presence of large plasmids, metabolic assays in solid media, salinity resistance, pH and temperature growth conditions, and intrinsic antibiotic resistance were assayed. in reference to the phenotypic attributes, we recognized three main groups: A group i, which comprised all the strains metabolizing between 67.5%-90% of the C and N sources. They were also acid-tolerant, as well as acid producers, capable of growing at 40ºC and in high salinity conditions (2-2.5% NaCl). With regard to the antibiotic sensitivity, this group was susceptible to a 30% of the antibiotic assayed. Strains belonging to Group ii exhibited a lower salt tolerance (0.1-1.5%NaCl), as well as a lower acid tolerance, since they grew well at pH values equal or higher than 5.0. This group appeared to be resistant to all of the antibiotics assayed and only metabolized between 52.5%-82.5% of the C and N sources. Group iii was represented by a single bacterial strain: it has a extremely low salt tolerance (0.1% NaCl). This strain grew at a pH equal or higher than 5.6, was susceptible to 50% of the antibiotics assayed and metabolized 72% of the C and N sources. On the basis of a PCR-RFLP of the 16S rDNA, three groups were also obtained. Members of the group A showed a close resemblance to Rhizobium tropici CiAT 899 and Sinorhizobium americanum CFN-Ei 156, while Group B was closely related to Bradyrhizobium spp. Group C, was also represented by only one isolate. The Trebol isolate, was the only one strain able to form nodules and does not appear to be related to any of the referential rhizobial strains, suggesting a possible symbiotic horizontal gene transfer. Finally, in this work, there are evidences of a genetic diversity in the venezuelan rhizobial strains. A different geographical origin is perhaps an important factor affecting the diversity of the indigenous rhizobia in this study. Rev. Biol. Trop. 59 (3): 1017-1036. Epub 2011 September 01.Key words: Rhizobium, Bradyrhizobium, phenotypic characterization, PCR-RFLP, 16S rDNA.Las bacterias denominadas comúnmen-te rizobios presentan varias formas de vida; pueden comportarse como saprófitos en el suelo establecer una asociación simbiótica y formar nódulos con las raíces y tallos de las leguminosas, donde tiene lugar la reducción del nitrógeno atmosférico en amonio, el cual es transportado a la planta y convertido en biomoléculas esenciales, o bien estar presentes como endófito en raíces de diferentes especies vegetales, donde ejercen efectos promotores del crecimiento (Wang et al. 2001).La taxonomía ...

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Ensifer, Phyllobacterium and Rhizobium species occupy nodules of Medicago sativa (alfalfa) and Melilotus alba (sweet clover) grown at a Canadian site without a history of cultivation

Cited by 50 publications

References 38 publications

Diverse Bacteria Affiliated with the Genera Microvirga, Phyllobacterium, and Bradyrhizobium Nodulate Lupinus micranthus Growing in Soils of Northern Tunisia

Diverse Bacteria Affiliated with the Genera Microvirga, Phyllobacterium, and Bradyrhizobium Nodulate Lupinus micranthus Growing in Soils of Northern Tunisia

Narrow-Host-Range Bacteriophages That Infect Rhizobium etli Associate with Distinct Genomic Types

Caracterización fenotípica y genotípica de doce rizobios aislados de diversas regiones geográficas de Venezuela

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