Metagenomics to assess bacterial diversity in the soil as influenced by organic and chemical inputs
By: Ashwini S P.
Contributor(s): Girija D (Guide).
Material type:
BookPublisher: Vellanikkara Center for Plant Biotechnology and Molecular Biology,College of Horticulture 2016Description: 90 pages.Subject(s): Plant Biotechnology and Molecular BiologyDDC classification: 660.6 Online resources: Click here to access online Dissertation note: MSc Summary: The rhizosphere region of soil is the dwelling place for many microorganisms.The rich microbial activity supports many biological processes in the soil. The abundance
of Plant Growth Promoting Rhizobacteria (PGPR) in rhizosphere assumes natural
significance from agronomic point of view. Knowledge about the total diversity of these
bacterial communities is less understood as the conventional methods for the study of
microbes has their own limitations. It has been estimated that 99 per cent of microbes
cannot be cultured easily. Metagenomics is the culture-independent genomic analysis of
microbes that has been developed to overcome the drawbacks of culture-based analysis of microbial communities.
An attempt was made to analyse the diversity of bacterial community using metagenomic approach in three different rice rhizosphere soils that received organic inputs (ONM), inorganic inputs (I) and soil under integrated management (INM) from
permanent manurial trial plots at RARS, Pattambi. Metagenomic DNA was isolated from the soils by direct lysis method and sequencing of V3 region of 16S rRNA gene was
carried out by using Illumina MiseqTM platform, at SciGenom, Cochin.The diversity of bacterial taxonomic category was assessed at different Operational Taxonomic Unit (OTU) levels using Ribosomal Database Project (RDP) pipeline and MG-RAST. At phylum level, Actinobacteria was the most dominant in all the three soils, and abundance was highest in INM 57.95%) and lowest in INF (25.80%).
Actinomycetes play a major role in organic matter decomposition and their presence is an indicator of soil health. Bacteria under ‘unclassified derived from bacteria’ was highest in INF (33.57%). These bacteria could be novel ones, since no homology was observed with any sequence in database. Acidobacteria was found highest in INF (14.13%) and lowest
in ONM (10.31%). Acidobacteria are metabolically and genetically diverse. Members of Proteobacteria increased in response to chemically recalcitrant substances and were
dominant in INF (14.55%) and lowest in INM (5.62%). Phylum Firmicutes comprised Bacillus and Clostridium and was found highest in ONM (6.76%) and lowest in INM (4.80%).
| Item type | Current location | Collection | Call number | Status | Date due | Barcode |
|---|---|---|---|---|---|---|
Theses
|
KAU Central Library, Thrissur Theses | Reference Book | 660.6 ASH/ME (Browse shelf) | Not For Loan | 173944 |
MSc
The rhizosphere region of soil is the dwelling place for many microorganisms.The rich microbial activity supports many biological processes in the soil. The abundance
of Plant Growth Promoting Rhizobacteria (PGPR) in rhizosphere assumes natural
significance from agronomic point of view. Knowledge about the total diversity of these
bacterial communities is less understood as the conventional methods for the study of
microbes has their own limitations. It has been estimated that 99 per cent of microbes
cannot be cultured easily. Metagenomics is the culture-independent genomic analysis of
microbes that has been developed to overcome the drawbacks of culture-based analysis of microbial communities.
An attempt was made to analyse the diversity of bacterial community using metagenomic approach in three different rice rhizosphere soils that received organic inputs (ONM), inorganic inputs (I) and soil under integrated management (INM) from
permanent manurial trial plots at RARS, Pattambi. Metagenomic DNA was isolated from the soils by direct lysis method and sequencing of V3 region of 16S rRNA gene was
carried out by using Illumina MiseqTM platform, at SciGenom, Cochin.The diversity of bacterial taxonomic category was assessed at different Operational Taxonomic Unit (OTU) levels using Ribosomal Database Project (RDP) pipeline and MG-RAST. At phylum level, Actinobacteria was the most dominant in all the three soils, and abundance was highest in INM 57.95%) and lowest in INF (25.80%).
Actinomycetes play a major role in organic matter decomposition and their presence is an indicator of soil health. Bacteria under ‘unclassified derived from bacteria’ was highest in INF (33.57%). These bacteria could be novel ones, since no homology was observed with any sequence in database. Acidobacteria was found highest in INF (14.13%) and lowest
in ONM (10.31%). Acidobacteria are metabolically and genetically diverse. Members of Proteobacteria increased in response to chemically recalcitrant substances and were
dominant in INF (14.55%) and lowest in INM (5.62%). Phylum Firmicutes comprised Bacillus and Clostridium and was found highest in ONM (6.76%) and lowest in INM (4.80%).
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