HCHmetagenome
Comparative Metagenomic Analysis to Understand Taxonomic and Functional Fingerprints of HCH (Hexachlorocyclohexane) Degrading Soil Microbial Communities across HCH Gradient.
The development of in-situ bioremediation strategies for hexachlorocyclohexane (HCH) requires a better understanding of its impact on microbial communities. We applied metagenomic and microbiome approaches to study the impact of HCH contamination on microbial diversity by using soil samples across three HCH gradients. Environmental DNA was extracted from soil samples collected from the HCH  dump site (170-450 mg HCH/g soil),  and soils 1 Km (0.7 mg HCH/g soil) and 5 km (0.03 mg HCH/g soil) away from the dump  site was sequenced. Pyrosequencing of DNA yielded 150Mb (approximately 50Mb from each gradient) data. Taxonomic analysis based on the bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) using kingdom specific primer amplification indicated  that highly contaminated soil is enriched for bacterial genera such as Halomonas, Alcanivorax, Sphinogmonas and Pseudomonas whereas Escherichia/Shigella were most abundant in the 0.07 mg HCH (1 Km) site. The results also identified additional taxas such as Marinimicrobium, Idiomarina and Salinosphaera that had never been reported from HCH dumpsite. There was a significant shift in microbial community at the dump site as the bacterial population in the soil with lowest HCH gradient was primarily represented by Salmonella, Acidobacterium, Levilinea, Rubrobacterin. The bacterial community that was over abundant at the dump site appears to have evolved under HCH stress and some of the bacterial genera have acquired key catabolic genes (lin genes) associated with HCH degradation. A comparison of archael and fungal communities across three HCH gradients revealed differences in the structure of both of thesethe archael communities in soils with increasing HCH contamination. Comparative gene centric analysis by two way clustering and statistical approaches showed functional enrichment in dumpsite dataset for genes and pathways involved in transposition mechanisms, chemotaxis and motility, and metabolism of aromatic compounds. Additionally there was an increase in the IS elements, phages and prophages at the dumpsite providing a strong evidence for  lateral gene transfer of catabolic genes especially lin genes a key function that is acquired as a result of HCH stress.  Based upon this study we hypothesize that transposition and conjugation are the favoured mode of genetic recombination in HCH contaminated soil cohorts. The presence of key genera that are associated with HCH degradation at the dump site further reflects that bioaugmentation of the soil is not necessary but biostimulation can be the effective choice for decontamination.
Naseer Sangwan1, Pushp Lata1, Vatsala Dwivedi1, Amit Singh1, Neha Niharika1, Jasvinder Kaur1, Shailly Anand1, Jaya Malhotra1, Swati Jindal1, Aeshna Nigam1, Devi Lal1, Ankita Dua1, Anjali Saxena1, Nidhi Garg1,Mansi Verma1 ,Jaspreet Kaur1, Udita Mukherjee1, Scot E. Dowd, Rajagopal Raman1, Paramjit Khurana3, Jitendra P. Khurana3and Rup Lal1*