Molecular diversity of Frankia from root nodules of Hippophae salicifolia D.Don found in Sikkim

Khan, Anindita; Myrold, David D.; Misra, Arvind

doi:10.1007/s12088-009-0025-x

Cited by 6 publications

(5 citation statements)

References 11 publications

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“…The strains HsIi10 and HsIi9 of cluster I were closely related to each other while both were distantly related to the other frankial strains of cluster II i.e., HsIi8, HsIi5, HsIi11, HsIi13, HsIi12, HsIi4, HsIi14, and HsIi2. Similarly, an existence of high degree of genetic variation has been recently reported by Khan et al (2009) among the Frankia strains isolated from Hippophae salicifolia found in Sikkim which was based on RFLP analysis of 16S-ITS-23S amplicons.…”

Section: Discussionmentioning

confidence: 60%

“…Recently, Frankia strains isolated from the root nodules of Hippophae salicifolia D. Don found in North Sikkim has been studied but only on the basis of restriction pattern analyses of 16S-ITS-23S amplicon (Khan et al 2009). However, no reports are available that deal with the detailed physiological, biochemical and molecular characterization of Frankia strains isolated from root nodules of Hippophae salicifolia D. Don.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of frankial strains isolated from Hippophae salicifolia D. Don, based on physiological, SDS–PAGE of whole cell proteins and RAPD PCR analyses

Singh

Srivastava

et al. 2009

World J Microbiol Biotechnol

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Different Frankia strains (HsIi2, HsIi4, HsIi5, HsIi8, HsIi9, HsIi10, HsIi11, HsIi12, HsIi13, HsIi14) nodulating Hippophae salicifolia D. Don, were characterized on the basis of physiological, biochemical and molecular attributes. Results suggest that the physiological approaches i.e., nitrogenase activity, glutamine synthetase (GS) activity and ammonia excretion are strain specific. The highest rate of nitrogen fixation and maximum production of ammonia with low GS makes the strain HsIi11, a suitable biofertilizer as compared to other strains. Analysis of total protein pattern (SDS-PAGE) revealed that the most closely related strains HsIi10 and HsIi4 were found to be most distantly related to the most similar strains HsIi14, HsIi5, HsIi13, HsIi11 and HsIi12. RAPD PCR analyses with an arbitrary primer 1253 produced distinct, unique and specific DNA fingerprints for each of the Frankia strain and 100% polymorphism was observed which uncovers the genetic diversity. These approaches might be helpful in rapid identification, in designing the marker for the specific strains as well as in improving nitrogen fixation in agroforestry.

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Section: Discussionmentioning

confidence: 60%

Section: Introductionmentioning

confidence: 99%

Characterization of frankial strains isolated from Hippophae salicifolia D. Don, based on physiological, SDS–PAGE of whole cell proteins and RAPD PCR analyses

Singh

Srivastava

et al. 2009

World J Microbiol Biotechnol

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“…The selected study area ranged in elevation from 2127 to 3150 m above sea level, a difference of 1023 m characterized by craggy configurations of monolithic cliffs, high slopes, with change in the temperature ranging from +25 °C (during summers) to −30 °C (during winters). The collection was done in the month of October as it has been previously mentioned by Varghese and Khan et al that the best growth of Frankia nodules was observable after the monsoon season. Five plants on the hillside and five plants on the riverside were selected on a random basis with care being taken that the underground lateral roots of the plant were at least one meter away from each other.…”

Section: Methodsmentioning

confidence: 99%

“…Similarly, 16S rRNA gene sequences have also been used to discriminate between closely related frankiae . The ITS region between 16S and 23S rRNA has also been used to discriminate between Frankia strains at molecular level . Further, genetic relatedness among the Frankia strains has also been evaluated using nif gene sequences .…”

Section: Introductionmentioning

confidence: 99%

Phylogeny and evolutionary genetics ofFrankiastrains based on 16S rRNA andnifD–K gene sequences

Mishra

Singh

et al. 2015

J. Basic Microbiol.

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16S rRNA and nifD-nifK sequences were used to study the molecular phylogeny and evolutionary genetics of Frankia strains isolated from Hippöphae salicifolia D. Don growing at different altitudes (ecologically classified as riverside and hillside isolates) of the Eastern Himalayan region of North Sikkim, India. Genetic information for the small subunit rRNA (16S rRNA) revealed that the riverside Frankia isolates markedly differed from the hillside isolates suggesting that the riverside isolates are genetically compact. Further, for enhanced resolutions, the partial sequence of nifD (3' end), nifK (5' end) and nifD-K IGS region have been investigated. The sequences obtained, failed to separate riverside isolates and hillside isolates, thus suggesting a possible role of genetic transfer events either from hillside to riverside or vice versa. The evolutionary genetic analyses using evogenomic extrapolations of gene sequence data obtained from 16S rRNA and nifD-K provided differing equations with the pace of evolution being more appropriately, intermediate. Values of recombination frequency (R), nucleotide diversity per site (Pi), and DNA divergence estimates supported the existence of an intermixed zone where spatial isolations occurred in sync with the temporal estimates. J. Basic Microbiol. 2015, 54, 1-9.

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“…Frankia sp. have also been characterized using physiological, biochemical, molecular approaches (Normand et al 1996 ; Singh et al 2010 ) and RFLP-based analyses of 16S-ITS of Frankia (Khan et al 2009 ).…”

Section: Introductionmentioning

confidence: 99%

Deciphering the evolutionary affiliations among bacterial strains (Pseudomonas and Frankia sp.) inhabiting same ecological niche using virtual RFLP and simulation-based approaches

et al. 2016

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To decipher an evolutionary lineage between two different but important bacterial groups, i.e., Pseudomonas strain (γ-Proteobacteria) and Frankia strain (actinobacteria) growing in the same ecological niche in and around of an actinorhizal plant Hippophae salicifolia D. Don, genetic diversity and comparative molecular phylogeny have been investigated using 16S rRNA gene sequences and computer-simulated and virtually directed restriction fragment length polymorphism (RFLP) through 10 restriction enzymes. Bayesian and coalescent analyses on the basis of 16S rRNA gene sequences suggested three major groups with close proximity between Pseudomonas and Frankia isolates. This result has been further validated based on the data observed through similarity coefficient value and computational RFLP. Principal component analysis and Mandel h and k statistical analysis also confirmed and strengthen the findings. Approximately 458 aligned sequence of all the taxa were used to decipher nucleotide diversity, polymorphism and gene flow between these taxa. Thus, our results suggest for a possible co-evolution or a heterologous gene transfer of distantly related microbial forms. Further, our study also advocate for the use of computer aided, virtual RFLP analysis as a cost effective and rapid identification tool.Electronic supplementary materialThe online version of this article (doi:10.1007/s13205-016-0488-5) contains supplementary material, which is available to authorized users.

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Molecular diversity of Frankia from root nodules of Hippophae salicifolia D.Don found in Sikkim

Cited by 6 publications

References 11 publications

Characterization of frankial strains isolated from Hippophae salicifolia D. Don, based on physiological, SDS–PAGE of whole cell proteins and RAPD PCR analyses

Characterization of frankial strains isolated from Hippophae salicifolia D. Don, based on physiological, SDS–PAGE of whole cell proteins and RAPD PCR analyses

Phylogeny and evolutionary genetics ofFrankiastrains based on 16S rRNA andnifD–K gene sequences

Deciphering the evolutionary affiliations among bacterial strains (Pseudomonas and Frankia sp.) inhabiting same ecological niche using virtual RFLP and simulation-based approaches

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