Metagenomic Analysis of Forest and Farm Soils
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Date
2011
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UAS, Dharwad
Abstract
Metagenomics is an emerging field of science mainly aims at studying the
activity of uncultured microorganisms through the nucleotide sequences. Standard
culture techniques allow only 1% of microorganisms to grow in defined laboratory
conditions. Thus, culture dependent study of microbial diversity unravels only part of
the microbial populations present in the environment. The present study was done to
analyze the soil microbial diversity between forest and farm soils through the
metagenomic approach.
The success of any metagenomic study depends on the method of DNA
extraction. So considering the significance and need, method was optimized for
extraction of microbial community DNA from forest and farm soils. Extracted DNA
was purified with the aid of chemical flocculation using FeCl3 as chemical flocculent.
Purity of DNA was confirmed by effective PCR amplification using 16S rDNA
primers. The purified DNA from respective soil was PCR amplified using DGGE
specific 16S rDNA primers. The amplified PCR products were then separated on
DGGE gel to analyze fingerprinting pattern in each soil types. Soil microbial diversity
analyses of fingerprints were done by using NTSYS software. DGGE analysis was
shown that forest soil microbial community shares more similarity with organic
farming soil microbial communities. The sequence based metagenomics approach was
used to know the microbial community composition. This was done by constructing
PCR based 16S rDNA library of metagenome of each soil using T/A cloning method.
About 17 clones of each soil were randomly selected from respective 16S rDNA
library and sequenced. Blast analyses of each clone form respective soil were done in
RDP database to know the taxonomic affiliation of each clone. Further the processed
51 sequences were then submitted to NCBI database. Blast results obtained shown
that majority of the microbial communities in forest and farm soil contained
uncultured microorganisms.
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Keywords
Plant Biotechnology