Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System.

Tighe, S. W.; Lajudie, Philippe de; Dipietro, K.; Lindström, Kristina; Nick, Giselle; Jarvis, B. D. W.

doi:10.1099/00207713-50-2-787

Cited by 262 publications

(150 citation statements)

References 28 publications

(23 reference statements)

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“…All the BR strains exhibited, in different proportions, C 16 : 0 , C 16 : 1 !5c and summed feature 8 (C 18 : 1 !6c/C 18 : 1 !7c) as major fatty acids; BR 446 T also presented a small amount of C 19 : 0 cyclo !8c (Table S3). These results are consistent with those found in bradyrhizobia (Tighe et al, 2000). It is noteworthy that these strains were different from B. huanghuaihaiense by having larger relative amounts of summed feature 8 and from B. arachidis by lacking C 16 : 1 !5c.…”

supporting

confidence: 82%

Bradyrhizobium stylosanthis sp. nov., comprising nitrogen-fixing symbionts isolated from nodules of the tropical forage legume Stylosanthes spp.

Delamuta

Ribeiro

Simões‐Araújo

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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Bradyrhizobium stylosanthis sp. nov., comprising nitrogen-fixing symbionts isolated from nodules of the tropical forage legume Stylosanthes spp. The introduction of legumes and nitrogen-fixing bacteria in tropical areas under pasture is a key factor for improvement of soil fertility. However, there are still very few studies concerning the symbionts of tropical forage legumes. We performed a polyphasic study with three strains representing the genus Bradyrhizobium (BR 446 T , BR 510 and BR 511) isolated from the tropical perennial forage legume of the genus Stylosanthes. On the basis of 16S rRNA gene sequences, the three strains showed highest similarity with B. huanghuaihaiense, and in the analysis of the intergenic transcribed spacer (ITS) they showed less than 93.4 % similarity to all described species of the genus Bradyrhizobium. Multilocus sequence analysis (MLSA) with three, four or five (dnaK, glnII, gyrB, recA and rpoB) housekeeping genes confirmed that the BR strains belong to a distinct clade, with <96.5 % nucleotide identity with other members of the genus Bradyrhizobium. Average nucleotide identity (ANI) of genome sequences between strain BR 446 T and B. huanghuaihaiense was below the threshold for species circumscription (90.7 %). DNA-DNA hybridization resulted in DT m values over 6.7 C with the most closely related species. Similarities among the BR strains and differences from other species were confirmed by rep-PCR analysis. Interestingly, the BR strains were grouped in the analysis of nifH and nodC genes, but showed higher similarity with B. iriomotense and B. manausense than with B. huanghuaihaiense, indicating a different evolutionary history for nitrogen-fixation genes. Morpho-physiological, genotypic and genomic data supported that these BR strains represent a novel species for which the name Bradyrhizobium stylosanthis sp. nov. isAbbreviations: DDH, DNA-DNA hybridization; ITS, intergenic transcribed spacer; MLSA, multilocus sequence analysis.

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supporting

confidence: 82%

Bradyrhizobium stylosanthis sp. nov., comprising nitrogen-fixing symbionts isolated from nodules of the tropical forage legume Stylosanthes spp.

Delamuta

Ribeiro

Simões‐Araújo

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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“…Fatty acid data (Jarvis et al, 1996) indicate a single cluster of species, representing Agrobacterium, Rhizobium and Sinorhizobium. With the exception of a J. M. Young quantitative difference in a single fatty acid (Tighe et al, 2000), support for Sinorhizobium as distinct from Rhizobium is on the basis of comparative 16S rDNA sequence data alone (de Lajudie et al, 1994(de Lajudie et al, , 1998b.…”

Section: International Journal Of Systematic and Evolutionary Microbimentioning

confidence: 99%

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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“…The cellular fatty acids were extracted, methylated (Dunfield et al, 1999), analysed by gas chromatograph and were identified using Sherlock Microbial Identification System (Tighe et al, 2000). The major cellular fatty acids (>1 %) were summed feature 8 (C 18 : 1 !6c/ C 18 : 1 !7c), C 19 : 0 cyclo !8c, summed feature 2 (C 14 : 0 3-OH/ C 16 : 1 iso/ C 12 : 0 aldehyde), C 16 : 0 , C 18 : 0 and C 17 : 0 cyclo, which were consistent with the related Ensifer species (Table S1).…”

mentioning

confidence: 99%

Ensifer alkalisoli sp. nov. isolated from root nodules of Sesbania cannabina grown in saline–alkaline soils

Yan

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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A group of Sesbania cannabina rhizobia belonging to four recA genotypes of a novel group was further characterized in comparison with the related Ensifer species. They showed 98.2 to 99.9 % similarities among themselves and 92.9 to 93.3 % similarities with the most related strain Ensifer sojae CCBAU 05684 T in multilocus sequence analysis of recA, atpD and glnII. The genome average nucleotide identity values between representative strain YIC4027 T and the type strains of its closely related species were 81.6 to 88.9 %. Identical symbiotic gene (nodA, nodC and nifH) sequences highly similar with those in other Sesbania-nodulating strains (Rhizobium sp. SIN-1, Neorhizobium huautlense S02 T , Ensifer saheli ORS609 T and Rhizobium sp. IRBG74) were detected. The representative strain YIC4027 T could form effective nodules on its original host Sesbania cannabina, but not on Sophora flavescens, Trifolium repens, Glycine max, Glycyrrhiza uralensis, Phaseolus vulgaris or Medicago sativa. The use of lactulose as sole carbon source, possession of C 13 : 0 2-OH, C 13 : 1 at 12-13, C 15 : 1 iso !9c, C 17 : 0 anteiso and C 18 : 0 iso and absence of C 14 : 0 anteiso, C 15 : 0 anteiso and C 18 : 0 3-OH in fatty acids distinguished the strain YIC4027 T from the type strains of its closely related species. Based on all the analyses mentioned above, we propose a novel species Ensifer alkalisoli sp. nov. and designate YIC4027 T (=HAMBI 3655 T =LMG 29286 T ) as the type strain. The genome size of YIC4027 T is 5.97 Mbp, comprising 5588 predicted genes, and the DNA G+C content is 62.2 mol%.

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Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System.

Cited by 262 publications

References 28 publications

Bradyrhizobium stylosanthis sp. nov., comprising nitrogen-fixing symbionts isolated from nodules of the tropical forage legume Stylosanthes spp.

Bradyrhizobium stylosanthis sp. nov., comprising nitrogen-fixing symbionts isolated from nodules of the tropical forage legume Stylosanthes spp.

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

Ensifer alkalisoli sp. nov. isolated from root nodules of Sesbania cannabina grown in saline–alkaline soils

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