title: 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.
authors.affiliation: Department of Zoology, University of Delhi, Delhi, India.
authors.forename: Naseer
authors.initials: N
authors.lastname: Sangwan
authors.forename: Pushp
authors.initials: P
authors.lastname: Lata
authors.forename: Vatsala
authors.initials: V
authors.lastname: Dwivedi
authors.forename: Amit
authors.initials: A
authors.lastname: Singh
authors.forename: Neha
authors.initials: N
authors.lastname: Niharika
authors.forename: Jasvinder
authors.initials: J
authors.lastname: Kaur
authors.forename: Shailly
authors.initials: S
authors.lastname: Anand
authors.forename: Jaya
authors.initials: J
authors.lastname: Malhotra
authors.forename: Swati
authors.initials: S
authors.lastname: Jindal
authors.forename: Aeshna
authors.initials: A
authors.lastname: Nigam
authors.forename: Devi
authors.initials: D
authors.lastname: Lal
authors.forename: Ankita
authors.initials: A
authors.lastname: Dua
authors.forename: Anjali
authors.initials: A
authors.lastname: Saxena
authors.forename: Nidhi
authors.initials: N
authors.lastname: Garg
authors.forename: Mansi
authors.initials: M
authors.lastname: Verma
authors.forename: Jaspreet
authors.initials: J
authors.lastname: Kaur
authors.forename: Udita
authors.initials: U
authors.lastname: Mukherjee
authors.forename: Jack A
authors.initials: JA
authors.lastname: Gilbert
authors.forename: Scot E
authors.initials: SE
authors.lastname: Dowd
authors.forename: Rajagopal
authors.initials: R
authors.lastname: Raman
authors.forename: Paramjit
authors.initials: P
authors.lastname: Khurana
authors.forename: Jitendra P
authors.initials: JP
authors.lastname: Khurana
authors.forename: Rup
authors.initials: R
authors.lastname: Lal
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics; D001673:Biodegradation, Environmental; D002633:Chemotaxis / Q000235:genetics; D005670:Fusarium / Q000235:genetics* / Q000378:metabolism; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D001556:Hexachlorocyclohexane / Q000378:metabolism*; D008190:Lyases / Q000235:genetics; D056186:Metagenomics; D059013:Microbial Consortia / Q000235:genetics*; D010957:Plasmids / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000145:classification / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D012336:RNA, Ribosomal, 16S; D012989:Soil Pollutants; D001556:Hexachlorocyclohexane; D008190:Lyases; C071445:linA protein, Pseudomonas paucimobilis