Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov.

Lajudie, Philippe de; Willems, Anne; Nick, Giselle; Moreira, F. M. S.; Molouba, Flore; Hoste, Bart; Torck, U; Neyra, Marc; Collins, Matthew D.; Lindström, Kristina; Dreyfus, B; Gillis, M.

doi:10.1099/00207713-48-2-369

Cited by 209 publications

(122 citation statements)

References 38 publications

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“…A polyphasic approach has been suggested to accurately define taxonomic groups among rhizobia (de Lajudie et al, 1998). Of the available methods, 16S rRNA gene sequencing is the most reliable for genus identification.…”

Section: Resultsmentioning

confidence: 99%

“…All these species share more than 97 % sequence similarity among their 16S rRNA genes (de Lajudie et al, 1998) and their definition relies mainly on the genetic and phenotypic grouping results, including DNA-DNA hybridization. Strains SDW014 T , SDW018 T and SDW052 representing the candidate species I, II and III, respectively, were chosen for determination of DNA base composition and for DNA-DNA hybridization with the type strains of Mesorhizobium and Agrobacterium species.…”

Section: Dna Base Composition and Dna-dna Hybridizationmentioning

confidence: 99%

“…It has been shown that different plants in the same geographical region can share the same rhizobial group for nodulation; examples are Mesorhizobium tianshanense (Chen et al, 1995), Mesorhizobium plurifarium (de Lajudie et al, 1998) and Rhizobium hainanense . Conversely, the same plant species may associate with different rhizobial species; for example, soybean is nodulated by Bradyrhizobium japonicum, Bradyrhizobium liaoningense (Xu et al, 1995), Mesorhizobium tianshanense (Chen et al, 1995), Sinorhizobium fredii and Sinorhizobium xinjiangense (Chen et al, 1988;Peng et al, 2002) in different regions of China.…”

Section: Introductionmentioning

confidence: 99%

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Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China

Gao

Turner

Kan

et al. 2004

International Journal of Systematic and Evolutionary Microbiology

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Ninety-five rhizobial strains isolated from Astragalus adsurgens growing in the northern regions of China were classified into three main groups, candidate species I, II and III, based on a polyphasic approach. Comparative analysis of full-length 16S rRNA gene sequences of representative strains showed that candidate species I and II were Mesorhizobium, while candidate species III, which consisted of non-nodulating strains, was closely related to Agrobacterium tumefaciens. The phylogenetic relationships of the three candidate species and some related strains were also confirmed by the sequencing of glnA genes, which were used as an alternative chromosomal marker. The DNA–DNA relatedness was between 11·3 and 47·1 % among representative strains of candidate species I and II and the type strains of defined Mesorhizobium species. Candidate III had DNA relatedness of between 4·3 and 25·2 % with type strains of Agrobacterium tumefaciens and Agrobacterium rubi. Two novel species are proposed to accommodate candidate species I and II, Mesorhizobium septentrionale sp. nov. (type strain, SDW014T=CCBAU 11014T=HAMBI 2582T) and Mesorhizobium temperatum sp. nov. (type strain, SDW018T=CCBAU 11018T=HAMBI 2583T), respectively. At least two distinct nodA sequences were identified among the strains. The numerically dominant nodA sequence type was most similar to that from the Mesorhizobium tianshanense type strain and was identified in strains belonging to the two novel species as well as other, as yet, undefined genome types. Host range studies indicate that the different nodA sequences correlate with different host ranges. Further comparative studies with the defined Agrobacterium species are needed to clarify the taxonomic identity of candidate species III.

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Section: Resultsmentioning

confidence: 99%

Section: Dna Base Composition and Dna-dna Hybridizationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China

Gao

Turner

Kan

et al. 2004

International Journal of Systematic and Evolutionary Microbiology

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“…However, reliance cannot be placed on any particular sequence comparison, Classifications, gene transfer and bacterial taxonomy because analyses give differing results depending on the algorithm chosen and particularly on the selection of included sequences. This is shown by comparison of inferred phylogenies in recent reports (Amarger et al, 1997 ;Chen et al, 1997 ;de Lajudie et al, 1994de Lajudie et al, , 1998a Nour et al, 1994 ; Rome et al, 1996 ;Tan et al, 1997 ;van Berkum et al, 1998 ;Wang et al, 1998 ;Willems & Collins, 1993). The reasons given by de Lajudie et al (1998b) for proposing the new genus were the unsettled state of Agrobacterium nomenclature and the evidence of heterogeneity (in phylogenetic terms) in Rhizobium, which implied to them the need for the creation of a new genus separate from Agrobacterium and Rhizobium.…”

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confidence: 94%

Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy.

Young¹

2001

International Journal of Systematic and Evolutionary Microbiology

165

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Following the publication of the Approved Lists, there has been a tendency to regard all subsequent revisions of classification as providing improved nomenclature, to be accepted without question. This takes no account of the fact that such revisions may be based on one of three alternative concepts, phenetic, phylogenetic or polyphasic classification, sometimes leading to different, valid, but incompatible nomenclature, or that some investigations are based only on subsets of relevant taxa and on limited data, leading to incomplete and sometimes confusing revisions of nomenclature. The polyphasic approach to classification has widespread support, although there appears to be a tendency to allow comparative sequence analyses of 16S rDNA to determine classification contrary to the indications of other data. In some cases, classification is based solely on 16S rDNA data. Examples are considered. Consideration is given to the criteria by which taxa are circumscribed, particularly at the level of genus and species. It is suggested that there is a need for reconciliation of the criteria by which taxa at these levels are circumscribed. Recent studies demonstrating the widespread occurrence of horizontal gene transfer suggest that there is a need for caution in monophyletic interpretations, especially when these are based on the analysis of single sequences. Keywords : phenetic, phylogenetic, polyphasic, bacterial systematics IntroductionAlthough Staley & Krieg (1984) wrote that ' bacterial classifications are devised for microbiologists, not for the entities being classified ', bacteriologists do not necessarily agree about the aims of classification. The several systems of bacterial classification that are in vogue at present are incompatible, sometimes leading to different classifications and to different schemes of bacterial nomenclature. Unless the principles underlying different classifications are understood, these different applications of names cause bewilderment. The thrust of this article is to show that no one system of classification is supreme, each offering a different perspective on evolutionary processes and serving different purposes in systematics. One problem that particularly besets discussions on bacterial taxonomy is that some terms derived elsewhere and often in the distant past are poorly defined or are used in different ways by different writers. For example, see the history of the usage of ' polyphasic ' described below. Ambiguity and lack of precision of usage are real causes of confusion. In attempting to maintain simplicity without confusion, terms are referred to Cowan (1978) and Lincoln et al. (1998) unless further explanation is felt necessary. Terms used here are not inconsistent with Tindall (1997).In 1980, the Approved Lists (Skerman et al., 1980) recorded 1792 validly published species names in 290 genera (6n2 species per genus) (Euze! by, 1997). One expectation of modern systematics has been that the increasing numbers of methods and sophisticated tools for analysis would form co...

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“…A possibility would be to classify them as different types within a single species, as for R. tropici (Martinez-Romero et al, 1991) and M . plurifarium (de Lajudie et al, 1998). However, for the moment, we prefer to propose only the most distinct group (group 1) as a new species within the genus Mesor h izo b iurn, Mesorh izob iurn amorphae.…”

Section: Hybridization Of Nifh Gene Locimentioning

confidence: 99%

Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov.

Wang

Berkum

Sui

et al. 1999

International Journal of Systematic and Evolutionary Microbiology

188

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Fifty-five Chinese isolates from nodules of Amorpha fruticosa were characterized and compared with the type strains of the species and genera of bacteria which form nitrogen-f ixing symbioses with leguminous host plants. A polyphasic approach, which included RFLP of PCR-amplif ied 165 rRNA genes, multilocus enzyme electrophoresis (MLEE), DNA-DNA hybridization, 165 rRNA gene sequencing, electrophoretic plasmid profiles, cross-nodulation and a phenotypic study, was used in the comparative analysis. The isolates originated from several different sites in China and they varied in their phenotypic and genetic characteristics. The majority of the isolates had moderate to slow growth rates, produced acid on YMA and harboured a 930 kb symbiotic plasmid (pSym). Five different RFLP patterns were identified among the 16s rRNA genes of all the isolates. Isolates grouped by PCR-RFLP of the 165 rRNA genes were also separated into groups by variation in MLEE profiles and by DNA-DNA hybridization. A representative isolate from each of these DNA homology groups had a separate position in a phylogenetic tree as determined from sequencing analysis of the 165 rRNA genes. A new species, Mesorhizobium amorphae, is proposed for the majority of the isolates, which belonged to a moderately slow-to slow-growing, acid-producing group based upon their distinct phylogenetic position, their unique electrophoretic type, their low DNA homology with reference strains representing the species within the genus Mesorhizobium and their distinct phenotypic features. Strain ACCC 19665 was chosen as the type strain for M. amorphae sp. nov.

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Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov.

Cited by 209 publications

References 38 publications

Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China

Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China

Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy.

Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov.

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