Comparative Metagenomic Analysis of Soil Microbial Communities across Three Hexachlorocyclohexane Contamination Levels

Abstract

This paper presents the characterization of the microbial community responsible for the in-situ bioremediation of hexachlorocyclohexane (HCH). Microbial community structure and function was analyzed using 16S rRNA amplicon and shotgun metagenomic sequencing methods for three sets of soil samples. The three samples were collected from a HCH-dumpsite (450 mg HCH/g soil) and comprised of a HCH/soil ratio of 0.45, 0.0007, and 0.00003, respectively. Certain bacterial; (Chromohalobacter, Marinimicrobium, Idiomarina, Salinosphaera, Halomonas, Sphingopyxis, Novosphingobium, Sphingomonas and Pseudomonas), archaeal; (Halobacterium, Haloarcula and Halorhabdus) and fungal (Fusarium) genera were found to be more abundant in the soil sample from the HCH-dumpsite. Consistent with the phylogenetic shift, the dumpsite also exhibited a relatively higher abundance of genes coding for chemotaxis/motility, chloroaromatic and HCH degradation (lin genes). Reassembly of a draft pangenome of Chromohalobacter salaxigenes sp. (∼8X coverage) and 3 plasmids (pISP3, pISP4 and pLB1; 13X coverage) containing lin genes/clusters also provides an evidence for the horizontal transfer of HCH catabolism genes.

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics

“…1). For instance, chemical contaminated environment such as hexachlorocyclohexane (HCH) dumpsite has been found to be dominated by Sphingomonads and Pseudomonads [11,12]. Similarly, soil microcosms are dominantly characterized by Rhodanobacter, Burkholderia, Acidobacteria [13].…”

“…With the availability of sequenced bacterial genomes, comparative genomics has emerged to be indispensable in elucidating evolutionary forces active across genera or species; however it remains incompetent to demonstrate results at the population level of in situ cohorts in an environment [1][2][3][4][5][6][7][8][9][10][11]. The problem can be resolved to some extent by using genomics and metagenomics data together delineating the pan-genome dynamics of a community distinctly elucidating environment specific lifestyles adopted by bacteria ( Fig.…”

Carl Woese: from Biophysics to Evolutionary Microbiology

“…In past 10-15 years Indian research in microbial cultivation and taxonomy has made good progress and till date we have described more than 300 novel taxa in International Journal of Systematic and Evolutionary Microbiology from different niches (http://www.bacterio.cict.fr) [8,9,29,30,37]. In the past few years there have been studies on microbial diversity of diverse habitats including the Western Ghats [45], psychrophilic habitat of Pangong Lake, Antarctic and Arctic soil and sediments [6,7,42], effluent treatment plant and pesticide contaminated dumpsite [3,35,39,41] marine sediment [43] and human gut [9,20,25]. Some laboratories have also focused their attention on SSU rRNA gene sequences and developed a phylogenetic framework, detected species specific signature sequences and designed improved PCR-primers using bioinformatic tools to improve the taxonomic resolution and environmental detection of related microorganisms [13,16,28,33].…”

Cloning of merA Gene from Methylotenera Mobilis for Mercury Biotransformation

“…S4). The merA gene product has the capability to convert the dangerous methyl mercury and other organic mercury derivatives to ionic mercury; which can then be reduced to Hg° [23,24].…”