Pushp Lata

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

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.

Pontibacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil.

An orange-pigmented bacterial strain, designated LP100(T), was isolated from hexachlorocyclohexane-contaminated soil (Lucknow, India). A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LP100(T) occupied a distinct phylogenetic position in the Pontibacter species cluster, showing highest similarity with Pontibacter lucknowensis DM9(T) (97.4 %). Levels of similarity to strains of other Pontibacter species ranged between 94.0 and 96.8 %. Strain LP100(T) contained MK-7 as the predominant menaquinone and sym-homospermidine was the major polyamine in the cell. The major cellular fatty acids of strain LP100(T) were anteiso-C17 : 0 A, iso-C15 : 0 and iso-C18 : 1 H. The polar lipid profile of strain LP100(T) showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, three unknown aminolipids and two unknown polar lipids. The G+C content of strain LP100(T) was 58.2 mol%. The results of DNA-DNA hybridization, biochemical and physiological tests clearly distinguish the novel strain from closely related species of the genus Pontibacter. Therefore, strain LP100(T) represents a novel species of the genus Pontibacter for which the name Pontibacter indicus is proposed. The type strain is LP100(T) ( = CCM8435(T) = MCC2027(T)).

Genome Sequence of Sphingobium indicum B90A, a Hexachlorocyclohexane-Degrading Bacterium

Sphingobium indicum B90A, an efficient degrader of hexachlorocyclohexane (HCH) isomers, was isolated in 1990 from sugarcane rhizosphere soil in Cuttack, India. Here we report the draft genome sequence of this bacterium, which has now become a model system for understanding the genetics, biochemistry, and physiology of HCH degradation.

Flavobacterium ummariense sp. nov., isolated from hexachlorocyclohexane-contaminated soil, and emended description of Flavobacterium ceti Vela et al. 2007.

A Gram-negative, strictly aerobic, yellow bacterial strain, designated DS-12(T), was isolated from hexachlorocyclohexane-contaminated soil in Lucknow, Uttar Pradesh, India. Strain DS-12(T) showed the highest 16S rRNA gene sequence similarity with Flavobacterium ceti 454-2(T) (94.2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-12(T) belonged to the genus Flavobacterium. Strain DS-12(T) produced flexirubin-type pigments. Gliding motility was not observed. The major fatty acids of strain DS-12(T) were iso-C(15:0) (48.0%), summed feature 9 (comprising iso-C(17:1)ω9c and/or C(16:0) 10-methyl; 19.3%), iso-C(17:0) 3-OH (8.5%) and summed feature 3 (comprising one or more of C(16:1)ω7c, C(16:1)ω6c and iso-C(15:0) 2-OH; 7.2%). The only respiratory quinone was menaquinone-6 and the major polyamine was homospermidine. Strain DS-12(T) contained phosphatidyldimethylethanolamine, phosphatidylserine, phosphatidylethanolamine, one unknown phospholipid and one unknown aminolipid. The DNA G+C content was 37.4 mol%. Phylogenetic inference and phenotypic properties indicated that strain DS-12(T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium ummariense sp. nov. is proposed. The type strain is DS-12(T) (=CCM 7847(T) =MTCC 10766(T)). An emended description of Flavobacterium ceti is also given.

Changes in the bacterial community and lin genes diversity during biostimulation of indigenous bacterial community of hexachlorocyclohexane (HCH) dumpsite soil

In this study hexachlorocyclohexane (HCH) contaminated soil (with HCH level 84 g/kg of soil) from HCH dumpsite (Ummari village, Lucknow, India) was used to demonstrate biostimulation approach for HCH bioremediation. Different nutrients (molasses and ammonium phosphate) were used in different pits having contaminated soil to stimulate the indigenous microbial community. There was a substantial reduction in the total HCH content of the soil in 12 months long experiment. Maximum reduction was seen in the pit that received a combination of molasses and ammonium phosphate. A change in the microbial community concomitant with degradation of HCH was observed. Sphingomonads, which are known degraders of HCH, were found to dominate the experimental pits. Moreover changes in linA and linB gene (primary genes involved in HCH degradation) diversity and number were also seen as revealed by T-RFLP and RT-PCR respectively. The study suggests the prospects of biostimulation in decontaminating soils heavily contaminated with HCH.

Draft Genome Sequence of Hexachlorohexane (HCH)-Degrading Sphingobium lucknowense Strain F2T, Isolated from an HCH Dumpsite

ABSTRACT Sphingobium lucknowense F2T, isolated from the hexachlorocylcohexane (HCH) dumpsite located in Ummari village, Lucknow, India, rapidly degrades HCH isomers. Here we report the draft genome of strain F2 (4.4 Mbp), consisting of 4,910 protein coding genes with an average G+C content of 64.3%.

Bioremediation of Hexachlorocyclohexane (HCH) Pollution at HCH Dump Sites

Globally, the period from early the 1950s to late 1980s has shown an increased use of primarily three pesticides namely DDT.