Comparative studies on the extraction of metagenomic DNA from the saline habitats of Coastal Gujarat and Sambhar Lake, Rajasthan (India) in prospect of molecular diversity and search for novel biocatalysts

Siddhapura, Paresh; Vanparia, S.; Purohit, Megha K.; Singh, Satya P.

doi:10.1016/j.ijbiomac.2010.06.004

Cited by 44 publications

(16 citation statements)

References 31 publications

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“…Incorporation of SDS along with CTAB resulted in higher yield and relatively moderate purity (1.4 to 1.53). Similar results have been reported by several workers (Chen et al, 2010;Siddhapura et al, 2010).…”

Section: Standardization Of Dna Isolation From Soilsupporting

confidence: 93%

Assessment of microbial diversity under arid plants by culture-dependent and culture-independent approaches

Sharma¹,

Singh²,

Sudarsan³

2013

Afr. J. Biotechnol.

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In this work, microbial community structure of two distinct arid plants like ker (Capparis deciduas) and pearl millet (Pennisetum glaucum) was assessed and defined by culture-dependent and cultureindependent approaches on the basis of 16S rRNA and random amplified polymorphic DNA (RAPD) analysis. The average Jaccard's similarity coefficient values for cultivated bacteria that is within ker and pearl millet rhizosphere were 0.701 and 0.707, respectively, for non-rhizosphere of ker and pearl millet 0.739 and 0.762, respectively, and for non-cultivable bacteria under ker (0.519) and under pearl millet (0.534). Both culture-dependent and culture-independent methods indicated that in arid crops, microbial diversity is more influenced by soil type rather than plant type and lower Jaccard value for metagenome showed that whole community harbours more diversity because of different microflora than cultivated only. Salinity and temperature tolerance study of bacteria indicated that ker rhizosphere harbours more salinity and temperature tolerant bacteria.

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Section: Standardization Of Dna Isolation From Soilsupporting

confidence: 93%

Assessment of microbial diversity under arid plants by culture-dependent and culture-independent approaches

Sharma¹,

Singh²,

Sudarsan³

2013

Afr. J. Biotechnol.

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“…The PCR reaction was carried out at gradient of annealing temperatures using Gradient Thermocycler (Eppendorf) [4]. Due to metagenomic nature of the template, varied amplicons were generated using different sets of primers.…”

Section: Amplification Of Alkaline Protease Genesmentioning

confidence: 99%

“…Metagenomic based approaches are used to identify and trap enzymes with novel biocatalytic and antimicrobial activities from the uncultivable components of the microbial communities. Attention on the diversity and phylogeny of uncultivable organisms from the marine environment is being focused as these habitats have apparently shown to have significant diversity [2][3][4].…”

Section: Introductionmentioning

confidence: 99%

A metagenomic alkaline protease from saline habitat: Cloning, over-expression and functional attributes

Purohit

Singh

2013

International Journal of Biological Macromolecules

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“…The presence of humic substances in DNA samples, interfere in enzyme-mediated molecular processes, such as digestion, and amplification and ligation in metagenomic library construction (Paul and Clark 1989 ; Robe 2003 ; Whitehouse and Hottel 2007 ). Since downstream processes in molecular biology demand good quantity of inhibitor-free metagenomic DNA, extraction methods have high significance (Siddhapura et al 2010 ). Numerous DNA extraction methods in vogue had been discussed and practiced for the isolation of DNA from soil (Bruce et al 1992 ; Zhou et al 1996 ; Kuske et al 1998 ; Yeates et al 1998 ; Miller et al 1999 ; Bertrand et al 2005 ; Desai and Madamwar 2007 ).…”

Section: Discussionmentioning

confidence: 99%

High-quality metagenomic DNA from marine sediment samples for genomic studies through a preprocessing approach

et al. 2016

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Recent advances in culture-independent studies of microbes had proved to be more reliable and efficient than the conventional ones. The isolation of good quality and quantity of total community DNA are one of the major hurdles in this endeavour. Shearing of DNA during the extraction process and the co-extraction of inhibitory compounds reduce the quality of the isolated nucleic acids making it unsuitable for the construction of large insert metagenomic libraries. In the present study, a multi-level filtration step was brought in which efficiently isolated total bacterial DNA from three different environment samples. The preprocessing method could efficiently improve the 260/230 ratio of the isolated DNA by 2.3–45 % and decreased the protein contamination by 22.5–34.5 % on saltpan and arctic sediment samples, respectively. The more significant part of the experiment was that the DNA obtained was of high quality with minimal shearing making it most suitable for the construction of large insert genomic libraries. PCR amplification of 16S rRNA gene confirmed that the filtration method was effective in the isolation of high-quality DNA.

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Comparative studies on the extraction of metagenomic DNA from the saline habitats of Coastal Gujarat and Sambhar Lake, Rajasthan (India) in prospect of molecular diversity and search for novel biocatalysts

Cited by 44 publications

References 31 publications

Assessment of microbial diversity under arid plants by culture-dependent and culture-independent approaches

Assessment of microbial diversity under arid plants by culture-dependent and culture-independent approaches

A metagenomic alkaline protease from saline habitat: Cloning, over-expression and functional attributes

High-quality metagenomic DNA from marine sediment samples for genomic studies through a preprocessing approach

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