Ankita Dua

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.

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.

Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite

A yellow-pigmented, Gram-negative, aerobic, non-motile, non-spore-forming, rod-shaped-bacterium, LE124(T), was isolated from a hexachlorocyclohexane (HCH) dumpsite located in Lucknow, India. The type strain LE124(T) grew well with hexachlorocyclohexane as a sole carbon source, degrading it within 24 h of incubation. Phylogenetic analysis of strain LE124(T) showed highest 16S rRNA gene sequence similarity to Novosphingobium barchaimii LL02(T) (98.5%), Novosphingobium panipatense SM16(T) (98.1%), Novosphingobium soli CC-TPE-1(T) (97.9%), Novosphingobium naphthalenivorans TUT562(T) (97.6%), Novosphingobium mathurense SM117(T) (97.5%) and Novosphingobium resinovorum NCIMB 8767(T) (97.5%) and lower sequence similarity (<97%) to all other members of the genus Novosphingobium. The DNA-DNA relatedness between strain LE124(T) and N. barchaimii LL02(T) and other related type strains was found to vary from 15% to 45% confirming that it represents a novel species. The genomic DNA G+C content of strain LE124(T) was 60.7 mol%. The predominant fatty acids were summed feature 8 (C18:1ω7c, 49.1%), summed feature 3 (C16:1ω7c/C16:1ω6c, 19.9%), C16:0 (6.7%), C17:1ω6c (4.9%) and a few hydroxyl fatty acids, C14:0 2-OH (9.4%) and C16:0 2-OH (2.1%). Polar lipids consisted mainly of phosphatidyldimethylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, sphingoglycolipid and some unidentified lipids. The major respiratory quinone was ubiquinone Q-10. Spermidine was the major polyamine observed. Phylogenetic analysis, DNA-DNA hybridization, chemotaxonomic and phenotypic analysis support the conclusion that strain LE124(T) represents a novel species within the genus Novosphingobium for which we propose the name Novosphingbium lindaniclasticum sp. nov. The type strain is LE124(T) (=CCM 7976(T)=DSM 25409(T)).

Devosia lucknowensis sp. nov., a bacterium isolated from hexachlorocyclohexane (HCH) contaminated pond soil.

Strain L15T, a Gram-negative, motile, orange colored bacterium was isolated from pond soil in the surrounding area of a hexachlorocyclohexane (HCH) dump site at Ummari village in Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain L15T belongs to the family Hyphomicrobiaceae in the order Rhizobiales. Strain L15T showed highest 16S rRNA gene sequence similarity to Devosia chinhatensis IPL18T (98.0%). Chemotaxonomic data revealed that the major fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), C18:1ω7c 11-methyl, C16:0 and C18:0. The major polar lipids of strain L15T were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content of strain L15T was 59.8%. Polyamine profile showed the presence of sym-homospermidine with traces of putrescine. Ubiquinone Q-10 was the major respiratory quinone present. Based on these data, strain L15T (=CCM 7977T =DSM 25398T) was classified as a type strain of a novel species, for which the name Devosia lucknowensis sp. nov. is proposed.

Sphingopyxis indica sp. nov., isolated from a high dose point hexachlorocyclohexane (HCH)-contaminated dumpsite

A Gram-stain-negative, aerobic, non-motile, non-spore-forming, rod-shaped and light-yellow-pigmented bacterium, designated DS15(T), was isolated from a soil sample collected from a hexachlorocyclohexane dumpsite in Lucknow, Uttar Pradesh, India. Strain DS15(T) showed highest 16S rRNA gene sequence similarity to Sphingopyxis panaciterrulae DCY34(T) (98.7%) and Sphingopyxis soli BL03(T) (98.0%). The 16S rRNA gene sequence similarity between strain DS15(T) and species of genus Sphingopyxis with validly published names ranged from 92.5% to 98.7%. The DNA G+C content of strain DS15(T) was 67.5 mol%. The chemotaxonomic markers in strain DS15(T) were consistent with its classification in the genus Sphingopyxis, i.e. Q-10 as the major ubiquinone and summed feature 8 (C18:1ω7c/C18:1ω9c), C17:1ω6c, summed feature 3 (C16:1ω7c/C16:1ω6c), C14:0 2-OH, C15:0 2-OH, C16:0 and C17:1ω8c as the predominant fatty acids. The major polar lipids of strain DS15(T) were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidylglycerol (PG) and sphingoglycolipids (SGL) and spermidine was detected as the major polyamine. Phylogenetic analysis, DNA-DNA hybridization, and chemotaxonomic and phenotypic analysis support the conclusion that strain DS15(T) represents a novel species within the genus Sphingopyxis, for which the name Sphingopyxis indica is proposed. The type strain is DS15(T) (=MTCC 9455(T)=CCM 7542(T)=MCC 2023(T)).

Genome Sequence of Acinetobacter sp. Strain HA, Isolated from the Gut of the Polyphagous Insect Pest Helicoverpa armigera

In this study, Acinetobacter sp. strain HA was isolated from the midgut of a fifth-instar larva of Helicoverpa armigera. Here, we report the draft genome sequence (3,125,085 bp) of this strain that consists of 102 contigs, 2,911 predicted coding sequences, and a G+C content of 41%.

Draft Genome Sequence of Sphingobium ummariense Strain RL-3, a Hexachlorocyclohexane-Degrading Bacterium

ABSTRACT Here, we report the draft genome sequence of the hexachlorocyclohexane (HCH)-degrading bacterium Sphingobium ummariense strain RL-3, which was isolated from the HCH dumpsite located in Lucknow, India (27°00′N and 81°09′E). The annotated draft genome sequence (4.75 Mb) of strain RL-3 consisted of 139 contigs, 4,645 coding sequences, and 65% G+C content.

Draft Genome Sequence of Agrobacterium sp. Strain UHFBA-218, Isolated from Rhizosphere Soil of Crown Gall-Infected Cherry Rootstock Colt

ABSTRACT We report here the draft genome sequence of the alphaproteobacterium Agrobacterium sp. strain UHFBA-218, which was isolated from rhizosphere soil of crown gall-infected cherry rootstock Colt. The draft genome of strain UHFBA-218 consists of 112 contigs (5,425,303 bp) and 5,063 coding sequences with a G+C content of 59.8%.

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.

A new life in a bacterium through synthetic genome: a successful venture by craig venter

The fi rst synthetic genome, a stripped down version of a natural organism, is only the beginning. I now want to go further. My company Synthetic Genomics Inc., is already trying to develop cassettes-modules of genes-to turn an organism into a biofactory that could make clean hydrogen fuel from sunlight and water or soak up more carbon dioxide. From there I want to take us far from shore into unknown waters, to a new phase of evolution, to the day when one DNA-based species can sit down at a computer to design another. I plan to show that we understand the software of life by creating true artifi cial life. And in this way I want to discover whether a life decoded is truly a life understood [1]. – A Life Decoded By J. Craig Venter