Metagenomics Of Extreme Environments Supplemented With Comparative Genomics
Metagenomic analysis of hexachlorocyclohexane contaminated environments (soil, sediment and water) has been done. We have been able to resolve the taxonomical and functional dynamics of enriched, yet un-cultivated microbial communities using amplicon based and shotgun sequencing data (3.2 Gbp). Using paired end assembled and validated downstream analysis we have reconstructed various genotypes (near complete plasmids and draft genomes) corresponding to their pangenomic abundance. Our future projects (in the pipeline) are targeting the community genomics of hot spring at Manikaran, Himachal Pradesh, India.
Important Papers
- Sangwan, N., Lata, P., Dwivedi, V., Singh, A., Niharika, N., Kaur, J., Anand, S., Malhotra, J., Jindal, S., Nigam, A., Lal, D., Dua, A., Saxena, A., Garg, N., Verma, M., Kaur, J., Mukherjee, U., Gilbert, J.A., Dowd, S.E., Raman, R., Khurana, P., Khurana, J.P., and Lal, R. 2012.Comparative Metagenomic analysis of soil microbial communities across three Hexachlorocyclohexane contamination levels. PLos One : 7,46219
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0046219 - Sangwan, N., Verma, H., Kumar, R., Negi, V., Lax, S., Khurana,P., Khurana, J.P., Gilbert, J. A. and Lal,R. 2013. Reconstructing an ancestral genotype of two hexachlorocyclohexane degrading Sphingobium species using metagenomic sequence data. ISME J. doi:10.1038/ismej.2013.153
http://www.ncbi.nlm.nih.gov/pubmed/24030592. - Verma H., Kumar R., Oldach P., Sangwan N., Khurana J.P., Gilbert J.A., Lal R . 2014. Comparative genomic analysis of nine Sphingobium strains: Insights into their Evolution and Hexachlorocyclohexane (HCH) Degradation Pathway. BMC Genomics .15 :1014.
http://www.biomedcentral.com/1471-2164/15/1014 - Sharma A., Sangwan N., Negi V., Kohli P., Rao D.L.N., Lal R . 2015. Pan-genome dynamics of Pseudomonas gene complements across hexachlorocyclohexane dumpsite. BMC Genomics . 16:313.
http://www.biomedcentral.com/1471-2164/16/313 - Sangwan N., Lambert C., Sharma A., Gupta V., Khurana P., Khurana J.P., Sockett R.E., Gilbert J.A., Lal R . Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes. Environ. Microbiol. Reports DOI: 10.1111/1758-2229.12297.
http://onlinelibrary.wiley.com/doi/10.1111/1758-2229.12297/abstract;jsessionid=A06D0DFD46F2434D496BFC3F85CFB92E.f01t01