Phylogeny of nodulation genes and symbiotic properties of Genista tinctoria bradyrhizobia

Kalita, Michał; Stępkowski, Tomasz; Łotocka, Barbara; Małek, Wanda

doi:10.1007/s00203-006-0124-6

Cited by 39 publications

(38 citation statements)

References 35 publications

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“…Notably, nodA clade II comprises bradyrhizobia isolated from other Genisteae species and from serradella species, which corroborates cross-inoculation data (19,28,42). Similar grouping was observed in phylogenies of nodC and nifH genes (17,48,49), giving rise to the new biovar genistearum for Bradyrhizobium strains nodulating Genisteae legumes, which presumably correspond to clade II Bradyrhizobium strains.…”

supporting

confidence: 80%

“…BIOGEOGRAPHIC PATTERN SHOWN BY nod GENE PHYLOGENIES 3255 II) in nod gene trees (19,28). Furthermore we showed that bradyrhizobia of this clade have become established in acid soils of Western Australia and South Africa following their probably accidental introduction with lupine and serradella seeds (42).…”

Section: Vol 73 2007mentioning

confidence: 61%

“…Cross-inoculation studies have shown that lupines share a common rhizobial pool with other legumes in the tribe Genisteae, including the genera Cytisus, Genista, Retama, and Teline (18,19,37,38,47). Additionally, lupines are effectively nodulated by rhizobia isolated from serradella (Ornithopus, a genus that belongs to the more distantly related tribe Loteae) and are ineffectively nodulated by rhizobia isolated from the genera Lotus, Anthyllis, and Phaseolus (8,9,25).…”

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confidence: 99%

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Diversification of Lupine Bradyrhizobium Strains: Evidence from Nodulation Gene Trees

Stępkowski

Hughes

Law³

et al. 2007

Appl Environ Microbiol

119

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Bradyrhizobium strains isolated in Europe from Genisteae and serradella legumes form a distinct lineage, designated clade II, on nodulation gene trees. Clade II bradyrhizobia appear to prevail also in the soils of Western Australia and South Africa following probably accidental introduction with seeds of their lupine and serradella hosts. Given this potential for dispersal, we investigated Bradyrhizobium isolates originating from a range of native New World lupines, based on phylogenetic analyses of nodulation (nodA, nodZ, noeI) and housekeeping (atpD, dnaK, glnII, recA) genes. The housekeeping gene trees revealed considerable diversity among lupine bradyrhizobia, with most isolates placed in the Bradyrhizobium japonicum lineage, while some European strains were closely related to Bradyrhizobium canariense. The nodA gene tree resolved seven strongly supported groups (clades I to VII) that correlated with strain geographical origins and to some extent with major Lupinus clades. All European strains were placed in clade II, whereas only a minority of New World strains was placed in this clade. This work, as well as our previous studies, suggests that clade II diversified predominately in the Old World, possibly in the Mediterranean. Most New World isolates formed subclade III.2, nested in a large "pantropical" clade III, which appears to be New World in origin, although it also includes strains originating from nonlupine legumes. Trees generated using nodZ and noeI gene sequences accorded well with the nodA tree, but evidence is presented that the noeI gene may not be required for nodulation of lupine and that loss of this gene is occurring.

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confidence: 80%

Section: Vol 73 2007mentioning

confidence: 61%

mentioning

confidence: 99%

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Diversification of Lupine Bradyrhizobium Strains: Evidence from Nodulation Gene Trees

Stępkowski

Hughes

Law³

et al. 2007

Appl Environ Microbiol

119

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“…The phylogeny of symbiotic nod genes has been frequently related to symbiotic performances of rhizobial strains (9,42,50,51). Here, a large diversity of nodC sequences was observed within L. micranthus endosymbionts, which clustered into four symbiovars.…”

Section: Discussionmentioning

confidence: 96%

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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“…Symbiotic genes (nif and nod) may have evolutionary histories that are different from those of housekeeping genes in rhizobia, and they have been used to estimate the symbiotic properties of rhizobia (Kalita et al, 2006;Laranjo et al, 2008;van Berkum et al, 2007). Fragments of the nifH (nitrogenase reductase; about 680 bp) and nodA (N-acyltransferase; about 600 bp) genes were amplified from CCBAU 85039 T and sequenced directly, with primers nifH-1 and nifH-2 (Eardly et al, 1992) and nodA-1 and nodA-2 (Haukka et al, 1998), respectively.…”

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confidence: 99%

Rhizobium tibeticum sp. nov., a symbiotic bacterium isolated from Trigonella archiducis-nicolai (Sirj.) Vassilcz.

Hou

Wang

Liu

et al. 2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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Rhizobium tibeticum sp. nov., a symbiotic bacterium isolated from Trigonella archiducisnicolai (Š irj.) Vassilcz. Isolated from root nodules of Trigonella archiducis-nicolai (Š irj.) Vassilcz. grown in Tibet, China, cells of the bacterial strains CCBAU 85039 T and CCBAU 85027 were Gram-negative, aerobic, motile, non-spore-forming rods that formed colonies that were semi-translucent and opalescent on yeast extract-mannitol agar. In numerical taxonomy, SDS-PAGE analysis of whole-cell proteins and DNA-DNA hybridization, the two strains were very similar and were different from reference strains of defined Rhizobium species. In the phylogeny based on 16S rRNA gene sequences, they were most similar to Rhizobium etli CFN 42 T (98.2 % similarity) and R. leguminosarum USDA 2370 T (97.6 %). Sequence analyses of the housekeeping genes recA, atpD and glnII and the 16S-23S rRNA intergenic spacer, phenotypic characteristics and cellular fatty acid profiles strongly suggested that these two strains represented a novel species within Rhizobium. Crossnodulation tests and sequencing of nifH and nodA genes showed that these two strains were symbiotic bacteria that nodulated Trigonella archiducis-nicolai, Medicago lupulina, Medicago sativa, Melilotus officinalis, Phaseolus vulgaris and Trigonella foenum-graecum. Based on the results, the novel species Rhizobium tibeticum sp. nov. is described to accommodate the two strains. The type strain is CCBAU 85039 T (5LMG 24453 T 5CGMCC 1.7071 T ). The DNA G+C content of this strain is 59.7 mol% (T m ).The genus Rhizobium was first described by Frank (1889) to accommodate all symbiotic nitrogen-fixing bacteria associated with legumes. After a series of revisions, some earlier described species have been moved into Bradyrhizobium (Jordan, 1982), Sinorhizobium (de Lajudie et al., 1994) and Mesorhizobium (Jarvis et al., 1997), while many novel species and genera of rhizobia within the Alphaproteobacteria and Betaproteobacteria have been reported (NZ Rhizobia, 2008). The current genus Rhizobium includes about 30 species of fast-growing, acid-producing rhizobia, which can be differentiated from Sinorhizobium species on the basis of 16S rRNA gene sequence-based phylogeny. With the exception of Rhizobium cellulosilyticus (Garcia-Fraile et al., 2007), most of them can induce root nodules on a certain range of legume species.In a survey of rhizobial resources in Tibet, 12 strains of root-nodule bacteria were isolated with yeast mannitol agar (YMA) medium according to the method of Vincent (1970) from root nodules of Trigonella archiducis-nicolai (Širj.) Vassilcz., an ephemeral legume growing in grasslands at altitudes of 3700-4000 m. Six of them were identified as Sinorhizobium meliloti, and six as Rhizobium strains (Hou et al., 2009). Among the Rhizobium strains, CCBAU 85039 T and CCBAU 85027 were classified as a small group by numerical taxonomy, amplified 16S rRNA gene restriction analysis, amplified 16S-23S intergenic spacer restriction analysis and 16S rRNA gene phylogeny (Hou et al., 2009). To...

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Phylogeny of nodulation genes and symbiotic properties of Genista tinctoria bradyrhizobia

Cited by 39 publications

References 35 publications

Diversification of Lupine Bradyrhizobium Strains: Evidence from Nodulation Gene Trees

Diversification of Lupine Bradyrhizobium Strains: Evidence from Nodulation Gene Trees

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

Rhizobium tibeticum sp. nov., a symbiotic bacterium isolated from Trigonella archiducis-nicolai (Sirj.) Vassilcz.

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