Phyllobacterium endophyticum sp. nov., isolated from nodules of Phaseolus vulgaris

Flores-Félix, José-David; Carro, Lorena; Velázquez, Encarna; Valverde, Ángel; Cerda-Castillo, Eugenia; García‐Fraile, Paula; Rivas, Raúl

doi:10.1099/ijs.0.038497-0

Cited by 55 publications

(21 citation statements)

References 22 publications

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“…Total DNA extracted from CCBAU 03422 T according to the method of Chun & Goodfellow (1995) was used for analysis of DNA base composition by the thermal denaturation method (Mandel & Marmur, 1968). The genomic DNA G+C content was 54.1 mol% ( T m ), which is within the range reported for species of the genus Phyllobacterium (Flores-Félix et al , 2013; Mantelin et al , 2006).…”

supporting

confidence: 82%

“…To date, the genus Phyllobacterium contains nine species including the recently described Phyllobacterium loti (Sánchez et al , 2014; ). Of these species, five were isolated from root nodules of legumes, including Phyllobacterium trifolii from Trifolium and Lupinus (Valverde et al , 2005), Phyllobacterium leguminum from Argyrolobium uniflorum and Astragalus algerianus (Mantelin et al , 2006), Phyllobacterium loti from Lotus corniculatus (Sánchez et al , 2014), Phyllobacterium endophyticum from Phaseolus vulgaris (Flores-Félix et al , 2013) and Phyllobacterium ifriqiyense from Astragalus algerianus and Lathyrus numidicus (Mantelin et al , 2006). The other four species were Phyllobacterium catacumbae isolated from Roman catacombs (Jurado et al , 2005), Phyllobacterium brassicacearum and Phyllobacterium bourgognense isolated from rhizoplane of Brassica napus (Mantelin et al , 2006), and Phyllobacterium myrsinacearum (subjective synonym of Phyllobacterium rubiacearum ) isolated form leaf nodules of Ardisia (Mergaert et al , 2002; ).…”

mentioning

confidence: 99%

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Phyllobacterium sophorae sp. nov., a symbiotic bacterium isolated from root nodules of Sophora flavescens

Jiao

Yan

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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Phyllobacterium sophorae sp. nov., a symbiotic bacterium isolated from root nodules of Sophora flavescens Two novel Gram-stain-negative strains (CCBAU 03422 T and CCBAU 03415) isolated from root nodules of Sophora flavescens were classified phylogenetically into the genus Phyllobacterium based on the comparative analysis of 16S rRNA and atpD genes. They showed 99.8 % rRNA gene sequence similarities to Phyllobacterium brassicacearum LMG 22836 T , and strain CCBAU 03422 T showed 91.2 and 88.6 % atpD gene sequence similarities to strains Phyllobacterium endophyticum LMG 26470 T and Phyllobacterium brassicacearum LMG 22836 T , respectively. Strain CCBAU 03422 T contained Q-10 as its major quinone and showed a cellular fatty acid profile, carbon source utilization and other phenotypic characteristics differing from type strains of related species. DNA-DNA relatedness (lower than 48.8 %) further confirmed the differences between the novel strains and the type strains of related species. Strain CCBAU 03422 T could nodulate and fix nitrogen effectively on its original host plant, Sophora flavescens. Based upon the results mentioned above, a novel species named Phyllobacterium sophorae is proposed and the type strain is CCBAU 03422 T (5A-6-3 T 5LMG 27899 T 5HAMBI 3508 T ).The genus Phyllobacterium was originally proposed by Knösel (1962) Table 1). It is obvious that root nodules are the preferred habitats for species of the genus Phyllobacterium more so than leaf nodules (Mergaert & Swings, 2001).In studies on genetic diversity of nodule bacteria from Sophora flavescens, a legume traditionally used as herbal medicine in China, two strains (CCBAU 03422 T and CCBAU 03415) were found to be distinct from the rhizobial species in the genera Mesorhizobium, Ensifer and Rhizobium based on the sequence analysis of the recA (recombinase A)Abbreviations: DDH, DNA-DNA hybridization ; ML, maximum-likelihood.The GenBank/EMBL/DDBJ accession number for the 16S rRNA, atpD, nodC and nifH gene sequences of strain CCBAU 03422 T are KJ685937, KJ685941, KJ685943 and KJ685942, respectively.

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confidence: 82%

mentioning

confidence: 99%

Phyllobacterium sophorae sp. nov., a symbiotic bacterium isolated from root nodules of Sophora flavescens

Jiao

Yan

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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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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“…Fixed nitrogen (NH 4 + ) is provided to plants by bacteroides. It is hypothesized that, in return, the plants deliver organic acids and several carbon and energy sources to the bacteroides as root exudates [24][25][26]. The overall procedure is completely based on saprophytic survival and adherence during chickpea cropping.…”

Section: Introductionmentioning

confidence: 99%

Deciphering the Factors for Nodulation and Symbiosis of Mesorhizobium Associated with Cicer arietinum in Northwest India

et al. 2019

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The compatibility between rhizobia and legumes for nitrogen-fixing nodules and the stages of root hair curling, formation of infection thread, and nodulation initiation have been vitally studied, but the factors for the sustainable root surface colonization and efficient symbiosis within chickpea and rhizobia have been poorly investigated. Hence, we aimed to analyze phenotypic properties and phylogenetic relationships of root-nodule bacteria associated with chickpea (Cicer arietinum) in the north-west Indo Gangetic Plains (NW-IGP) region of Uttar Pradesh, India. In this study, 54 isolates were recovered from five agricultural locations. Strains exhibited high exopolysaccharide production and were capable of survival at 15–42 °C. Assays for phosphate solubilization, catalase, oxidase, Indole acetic acid (IAA) production, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity revealed that all the tested isolates possessed plant growth-promoting potential. Metabolic profiling using Biolog plates indicated that patterns of substrate utilization differed considerably among isolates. A biofilm formation assay showed that isolates displayed a nearly four-fold range in their capacity for biofilm development. Inoculation experiments indicated that all isolates formed nodules on chickpea, but they exhibited more than a two-fold range in symbiotic efficiency. No nodules were observed on four other legumes (Phaseolus vulgaris, Pisum sativum, Lens culinaris, and Vigna mungo). Concatenated sequences from six loci (gap, edD, glnD, gnD, rpoB, and nodC) supported the assignment of all isolates to the species Mesorhizobium ciceri, with strain M. ciceri Ca181 as their closest relative.

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Phyllobacterium endophyticum sp. nov., isolated from nodules of Phaseolus vulgaris

Cited by 55 publications

References 22 publications

Phyllobacterium sophorae sp. nov., a symbiotic bacterium isolated from root nodules of Sophora flavescens

Phyllobacterium sophorae sp. nov., a symbiotic bacterium isolated from root nodules of Sophora flavescens

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

Deciphering the Factors for Nodulation and Symbiosis of Mesorhizobium Associated with Cicer arietinum in Northwest India

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