J Genomics 2017; 5:36-47. doi:10.7150/jgen.16685 This volume

Research Paper

Metagenomic Analysis of a Complex Community Present in Pond Sediment

Vivek Negi, Rup Lal

Molecular Biology Lab, Department of Zoology, University of Delhi, Delhi-07, India

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Negi V, Lal R. Metagenomic Analysis of a Complex Community Present in Pond Sediment. J Genomics 2017; 5:36-47. doi:10.7150/jgen.16685. Available from https://www.jgenomics.com/v05p0036.htm

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Graphic abstract

The metagenomic profiling of complex communities is gaining immense interest across the scientific community. A complex community present in the pond sediment of a water body located close to a hexachlorocyclohexane (HCH) production site of the Indian Pesticide Limited (IPL) (Chinhat, Lucknow) was selected in an attempt to identify and analyze the unique microbial diversity and functional profile of the site. In this study, we supplement the metagenomic study of pond sediment with a variety of binning approaches along with an in depth functional analysis. Our results improve the understanding of ecology, in terms of community dynamics. The findings are crucial with respect to the mechanisms such as those involving the lin group of genes that are known to be implicated in the HCH degradation pathway or the Type VI secretory system (T6SS) and its effector molecules. Metagenomic studies using the comparative genomics approach involving the isolates from adjacent HCH contaminated soils have contributed significantly towards improving our understanding of unexplored concepts, while simultaneously uncovering the novel mechanisms of microbial ecology.

Keywords: Functional diversity, pond sediment, genomic variation.