Handbook for Rhizobia

Somasegaran, Padma; Hoben, Heinz J.

doi:10.1007/978-1-4613-8375-8

Cited by 797 publications

(459 citation statements)

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“…Rhizobial isolates nodulating chickpea were obtained from two soil samples collected in Portugal using trap plants (Somasegaran & Hoben, 1994). Five isolates were selected for further study: C-1-Coimbra, C-27b-Coimbra, V-15b-Viseu, V-18-Viseu and V-20-Viseu.…”

Section: Methodsmentioning

confidence: 99%

dnaJ is a useful phylogenetic marker for alphaproteobacteria

Alexandre

Laranjo

Young

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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In the past, bacterial phylogeny relied almost exclusively on 16S rRNA gene sequence analysis. More recently, multilocus sequence analysis has been used to infer organismal phylogenies. In this study, the dnaJ chaperone gene was investigated as a marker for phylogeny studies in alphaproteobacteria. Preliminary analysis of G+C contents and G+C3s contents (the G+C content of the synonymous third codon position) showed no clear evidence of horizontal transfer of this gene in proteobacteria. dnaJ-based phylogenies were then analysed at three taxonomic levels: the Proteobacteria, the Alphaproteobacteria and the genus Mesorhizobium. Dendrograms based on DnaJ and 16S rRNA gene sequences revealed the same topology described previously for the Proteobacteria. These results indicate that the DnaJ phylogenetic signal is able to reproduce the accepted relationships among the five classes of the Proteobacteria. At a lower taxonomic level, using 20 alphaproteobacteria, the 16S rRNA gene-based phylogeny is distinct from the one based on DnaJ sequence analysis. Although the same clusters are generated, only the topology of the DnaJ tree is consistent with broader phylogenies from recent studies based on concatenated alignments of multiple core genes. For example, the DnaJ tree shows the two clusters within the Rhizobiales as closely related, as expected, while the 16S rRNA gene-based phylogeny shows them as distantly related. In order to evaluate the phylogenetic performance of dnaJ at the genus level, a multilocus analysis based on five housekeeping genes (atpD, gapA, gyrB, recA and rplB) was performed for ten Mesorhizobium species. In contrast to the 16S rRNA gene, the DnaJ sequence analysis generated a tree similar to the multilocus dendrogram. For identification of chickpea mesorhizobium isolates, a dnaJ nucleotide sequence-based tree was used. Despite different topologies, 16S rRNA gene-and dnaJ-based trees led to the same species identification. This study suggests that the dnaJ gene is a good phylogenetic marker, particularly for the class Alphaproteobacteria, since its phylogeny is consistent with phylogenies based on multilocus approaches. INTRODUCTIONThe phylum Proteobacteria is composed of five classes, the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria and Epsilonproteobacteria (Garrity et al., 2005;Stackebrandt et al., 1988). By the end of 2008, more than 380 complete genomes of proteobacteria were available in public databases (http://www. ncbi.nlm.nih.gov/genomes/lproks.cgi). Alphaproteobacteria exhibit an enormous diversity in their morphological and metabolic characteristics and the class is presently recognized solely as a clade in the 16S rRNA gene-based phylogeny (Stackebrandt et al., 1988). Based on 16S rRNA gene trees, the Alphaproteobacteria has been divided into seven orders: Caulobacterales, Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Parvularculales (Kersters et al., 2006). The Alphaproteobacteria includes important bacteria tha...

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Section: Methodsmentioning

confidence: 99%

dnaJ is a useful phylogenetic marker for alphaproteobacteria

Alexandre

Laranjo

Young

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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“…Rhizobium spp. are gram-negative soil bacteria that have a profound scientific and agronomic significance due to their ability to establish nitrogen-fixing symbiosis with leguminous plants, which is of major importance to the maintenance of soil fertility (Somasegaran, 1994). For this reason and taking into consideration the importance of legumes in animal and human consumption, some attention has been given to the effects that heavy metals exert on Rhizobium isolates as free-living organisms or symbiotically associated with legumes (Ibekwe, 2010).…”

Section: Introductionmentioning

confidence: 99%

Characterization of Rhizobium Isolates and their Potential PGPR Characteristics of different Rhizosphere Soils of Telangana Region

Manasa¹,

Reddy²,

Triveni³

et al. 2017

Int.J.Curr.Microbiol.App.Sci

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“…The biochemical analysis showed that all strains grew on YMA+Congo Red with colonies ranging from pink to transparent in color. Furthermore, none of the strains fermented glucose in MacConkey medium, fermented neither lactose nor glucose and was a hydrogen sulfide producer in Kligler medium, and tested catalase positive and were acid producers, reinforcing that the isolated strains were Rhizobium (Somasegaran;Hoben, 1994).…”

Section: Resultsmentioning

confidence: 91%

“…Single colonies were purified by repeatedly streaking on YMA plates. After 2 days of purification, single colonies were individually analyzed by Gramstaining, morpho-cultural (growth rate, color, elevation, edges and slime production), and biochemical (growth in YMA+Congo Red, MacConkey and Kligler medium; catalase production; and production of acid or base) characterization (Somasegaran;Hoben, 1994). Cultural analyses were performed by testing growth at different pH values (4, 5, and 9), NaCl concentrations (0.1, 1 and 2%) and temperature (10, 35, 40 °C) in YMA medium at 30 °C (Bécquer;Prévost;Prieto, 2000;Kulkarni;Nautiyal, 2000).…”

Section: Sample Preparation and Bacterial Isolationmentioning

confidence: 99%

Genetic and phenotypic diversity of Rhizobium isolates from Southern Ecuador

et al. 2017

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Rhizobium-legume symbioses play relevant roles in agriculture but have not been well studied in Ecuador. The aim of this study was to characterize the genetic and phenotypic diversity of Rhizobium isolates associated with Phaseolus vulgaris from southern Ecuador. Morphocultural characterization, biochemical tests and physiological analyses were conducted to authenticate and determine the diversity of bacteria Rhizobium-like isolates. The genetic diversity of the isolates was determined by molecular techniques, which consisted of bacteria DNA extraction and amplification and sequencing of the 16S rRNA gene. The nodulation parameters and nitrogen fixation for P. vulgaris under greenhouse conditions were also assessed to determine the phenotypic diversity among isolates. Furthermore, bacteria indole-acetic-acid production was evaluated by the colorimetric method. Morpho-cultural and biochemical characteristic assessments demonstrated that Rhizobium-like bacteria was associated with the P. vulgaris nodules. The diversity among the isolates, as determined by physiological analyses, revealed the potential of several isolates to grow at different pH values, salinity conditions and temperatures. Partial sequencing of the 16S rRNA gene identified the Rhizobium genus in every sampling site. From a total of 20 aligned sequences, nine species of Rhizobium were identified. Nodule formation and biomass, as well as nitrogen fixation, showed an increase in plant phenotypic parameters, which could be influenced by IAA production, especially for the strains R. mesoamericanum NAM1 and R. leguminosarum bv. viciae COL6. These results demonstrated the efficiency of native symbiotic diazotrophic strains inoculants for legume production. This work can serve as the basis for additional studies of native Rhizobium strains and to help spread the use of biofertilizers in Ecuadorian fields.Index terms: Phaseolus vulgaris; diazotrophic bacteria; 16S rRNA gene; nodulation; indole acetic acid. RESUMOA simbiose Rhizobium-leguminosa desempenha um relevante papel na agricultura, entretanto não tem recebido suficiente atenção de estudos científicos no Equador. O objetivo deste artigo foi caracterizar a diversidade genética e fenotípica de isolados de Rhizobium associados com Phaseolus vulgaris do sul do Equador. A caracterização morfo-cultural, testes bioquímicos e análises fisiológicas foram realizados para autenticar e determinar a diversidade de isolados de bactérias Rhizobium. A diversidade genética foi determinada por por técnicas moleculares consistindo na extração de DNA genômico bacteriano, amplificação e sequenciamento parcial do gene 16SrRNA; e parâmetros de nodulação e fixação de nitrogênio de P. vulgaris sobre condições de estufa foram testados para determinar a diversidade fenotípica entre os isolados. Além disso, a produção de ácido indolacético foi avaliada por um método colorimétrico. A análise fisiológica da diversidade entre os isolados revelou o potencial de crescimento de diversos isolados em diferentes níveis de pH, sa...

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Handbook for Rhizobia

Cited by 797 publications

References 0 publications

dnaJ is a useful phylogenetic marker for alphaproteobacteria

dnaJ is a useful phylogenetic marker for alphaproteobacteria

Characterization of Rhizobium Isolates and their Potential PGPR Characteristics of different Rhizosphere Soils of Telangana Region

Genetic and phenotypic diversity of Rhizobium isolates from Southern Ecuador

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