Indu Thakur | Jawaharlal Nehru University (original) (raw)

Papers by Indu Thakur

Research paper thumbnail of {"__content__"=>"Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium sp. ISTKB.", "i"=>{"__content__"=>"Pandoraea"}}

Biotechnology for biofuels, 2018

Lignin is a major component of plant biomass and is recalcitrant to degradation due to its comple... more Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization. Genomic analysis of sp. ISTKB revealed the presence of strong lig...

Research paper thumbnail of {"__content__"=>"Production, process optimization and molecular characterization of polyhydroxyalkanoate (PHA) by COsequestering B. cereus SS105.", "sub"=>{"__content__"=>"2"}}

Bioresource technology, 2018

Carbon dioxide sequestering bacterial strains were previously isolated from free air COenriched (... more Carbon dioxide sequestering bacterial strains were previously isolated from free air COenriched (FACE) soil. In the present study, these strains were screened for PHA accumulation and Bacillus cereus SS105 was found to be the most prominent PHA accumulating strain on sodium bicarbonate and molasses as carbon source. This strain was further characterized by Spectrofluorometric method and Confocal microscopy after staining with Nile red. PHA granules in inclusion bodies were visualized by Transmission Electron Microscopy. The PHA and its monomer composition were characterized by GC-MS followed by FTIR and NMR. The genetic basis of PHA production was confirmed by the amplification, cloning and analysis of PHA biosynthesis genes phaR, phaB and phaC from B. cereus with the degenerate primers. The PHA production was further optimized by Response Surface Methodology and the percent increase observed after optimization was 55.16% (w/v).

Research paper thumbnail of Metagenomic Analysis of Microbial Diversity in Landfill Lysimeter Soil of Ghazipur Landfill Site, New Delhi, India

Genome announcements, Jan 19, 2017

We report the soil microbial diversity and functional aspects related to degradation of recalcitr... more We report the soil microbial diversity and functional aspects related to degradation of recalcitrant compounds, determined using a metagenomic approach, in a landfill lysimeter prepared with soil from Ghazipur landfill site, New Delhi, India. Metagenomic analysis revealed the presence and functional diversity of complex microbial communities responsible for waste degradation.

Research paper thumbnail of Genome Sequence of Pandoraea sp. ISTKB, a Lignin-Degrading Betaproteobacterium, Isolated from Rhizospheric Soil

Genome Announcements, 2016

We report here the genome sequence of Pandoraea sp. ISTKB, a betaproteobacterium isolated from rh... more We report here the genome sequence of Pandoraea sp. ISTKB, a betaproteobacterium isolated from rhizospheric soil in the backwaters of Alappuzha, Kerala, India. The strain is alkalotolerant and grows on medium containing lignin as a sole carbon source. Genes and pathways related to lignin degradation were complemented by genomic analysis.

Research paper thumbnail of Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks

Genome Announcements, 2016

The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO 2 )-sequestering bacte... more The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO 2 )-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO 3 ) as the sole carbon source. Here, we report the genome sequence of 5.07 Mb Serratia sp. ISTD04.

Research paper thumbnail of NADPH oxidase mediated superoxide production by intermediary bacterial metabolites of dibenzofuran: A potential cause for trans-mitochondrial membrane potential (ΔΨm) collapse in human hepatoma cells

Toxicological sciences : an official journal of the Society of Toxicology, 2015

Dibenzofuran is a direct precursor of extremely toxic compounds such as dioxins. It is widely dis... more Dibenzofuran is a direct precursor of extremely toxic compounds such as dioxins. It is widely distributed persistent organic pollutant in environment that potentiate oxidative stress, apoptosis and necrosis through bioactivation in HepG2 cells. An alkalotolerent Pseudomonas strain ISTDF1 can metabolize dibenzofuran as a sole source of carbon and energy through diverse dioxygenation. However, there is a paucity of information about the potential toxic effects of the intermediary metabolites that are formed during treatment with dibenzofuran. We have assessed and discovered the potential mechanism of toxicity induced by metabolites of dibenzofuran that were formed at 18 h and 36 h. Cell viability, CYP1A2 induction, ROS activity, Superoxide production, mitochondrial NADPH oxidase activity and mitochondrial trans-membrane potential were studied using different assays such as MTT, confocal laser scanning microscopy and Flow cytometry. Analysis revealed formation of 2-(1-carbonyl methylid...

Research paper thumbnail of Investigating the degradation process of kraft lignin by β-proteobacterium, Pandoraea sp. ISTKB

Environmental Science and Pollution Research, 2015

The present study investigates the kraft lignin (KL) degrading potential of novel alkalotolerant ... more The present study investigates the kraft lignin (KL) degrading potential of novel alkalotolerant Pandoraea sp. ISTKB utilizing KL as sole carbon source. The results displayed 50.2 % reduction in chemical oxygen demand (COD) and 41.1 % decolorization after bacterial treatment. The maximum lignin peroxidase (LiP) and manganese peroxidase (MnP) activity detected was 2.73 and 4.33 U ml −1 , respectively, on day 3. The maximum extracellular and intracellular laccase activities observed were 1.32 U ml −1 on day 5 and 4.53 U ml −1 on day 4, respectively. The decolorization and degradation was maximum on day 2. Further, it registered an increase with the production of extracellular laccase. This unusual trend of decolorization and degradation was studied using various aromatic compounds and dyes. SEM and FTIR results indicated significant change in surface morphology and functional group composition during the course of degradation. Gas chromatography and mass spectroscopy (GC-MS) analysis confirmed KL degradation by emergence of new peaks and the identification of low molecular weight aromatic intermediates in treated sample. The degradation of KL progressed through the generation of phenolic intermediates. The identified intermediates implied the degradation of hydroxyphenyl, ferulic acid, guaiacyl, syringyl, phenylcoumarane, and pinoresinol components commonly found in lignin. The degradation, decolorization, and GC-MS analysis indicated potential application of the isolate Pandoraea sp. ISTKB in treatment of lignin-containing pollutants and KL valorization.

Research paper thumbnail of Novel lipase from basidiomycetes Schizophyllum commune ISTL04, produced by solid state fermentation of Leucaena leucocephala seeds

Journal of Molecular Catalysis B: Enzymatic, 2014

The present investigation reports a novel thermoalkalotolerant lipase producing Basidiomycetes, S... more The present investigation reports a novel thermoalkalotolerant lipase producing Basidiomycetes, Schizophyllum commune ISTL04 for the first time. Abundantly available Leucaena leucocephala seeds were exploited as a cheap fermentable source for the feasible production of extracellular lipase. The isolate ISTL04 grew vigorously on Leucaena seeds in comparison to Soybean meal and Wheat bran exhibiting a lipase activity of 146.5 U/g. The S. commune ISTL04 (SCI) lipase was purified to 35.76 folds with a specific activity of 238.13 U/mg and an estimated mass of 60 kDa. The temperature and pH optima for lipolytic activity were 60 • C and 11, respectively. The enzyme exhibited remarkable stability in the presence of non-polar and polar organic solvents (50%, v/v), retaining more than 90% and 40% activity, respectively. The lipase activity increased significantly in the presence of Mg 2+ (154%), Ca 2+ (109.7%), Mn 2+ (106%) and Tween 80 (240%). The distinctive and broader operational properties of the SCI lipase make it a promising biocatalyst for various industrial processes.

Research paper thumbnail of Cloning and expression of gamma carbonic anhydrase from Serratia sp. ISTD04 for sequestration of carbon dioxide and formation of calcite

Bioresource Technology, 2015

h i g h l i g h t s Microbial community of marble mine was enriched and characterized. Carbonic a... more h i g h l i g h t s Microbial community of marble mine was enriched and characterized. Carbonic anhydrase (CA) gene of Serratia sp. was cloned. CA enzyme was characterized. Gamma carbonic anhydrase was reported homologous to archae and methanogens. Use of carbonic anhydrase enzyme for the sequestration of atmospheric CO 2 .

Research paper thumbnail of Immobilized lipase from Schizophyllum commune ISTL04 for the production of fatty acids methyl esters from cyanobacterial oil

Bioresource Technology, 2015

Novel lipase from model mushroom Schizophyllum commune strain ISTL04 produced by solid state ferm... more Novel lipase from model mushroom Schizophyllum commune strain ISTL04 produced by solid state fermentation of Leucaena leucocephala seeds, was immobilized onto Celite for enzymatic FAMEs production from cyanobacterial endolith Leptolyngbya ISTCY101. The isolate showed vigorous growth and produced remarkable lipase activity of 146.5Ug(-1) dry solid substrate, without any external lipase inducer. Single-factor experiments were carried out to study the effects of various reaction parameters on the FAMEs yield. The best conditions for enzymatic transesterification as revealed by the results were: 1:3 oil to methanol molar ratio, added at 3h intervals, 12% water content, 1581.5Ug(-1) immobilized lipase, temperature 45°C, and time 24h. Under these conditions, the maximum FAMEs yield reached 94%. The immobilized lipase was able to produce >90% of the relative FAMEs yield after four repeated transesterification cycles. This immobilized lipase exhibited potential for application in biodiesel industry.

Research paper thumbnail of Characterization of microalga Scenedesmus sp. ISTGA1 for potential CO 2 sequestration and biodiesel production

Research paper thumbnail of Characterization of endolithic cyanobacterial strain, Leptolyngbya sp. ISTCY101, for prospective recycling of CO₂ and biodiesel production

Bioresource technology, 2014

The present investigation evaluates the potential of an endolithic cyanobacterium isolated from m... more The present investigation evaluates the potential of an endolithic cyanobacterium isolated from marble rock to utilize sodium bicarbonate (NaHCO₃) as carbon source for prospective recycling of CO₂ into biodiesel. Microalgae thriving on marble were cultured and subjected to increasing NaHCO₃ concentration. The most competent isolate was identified and characterized in terms of growth, lipid content and fatty acid profile. A semicontinuous mesh incubator was designed for biofilm development. Isolate ISTCY101 was identified as Leptolyngbya sp. by 16S rRNA sequencing. Leptolyngbya ISTCY101 efficiently used BG-11 (50 mM NaHCO₃) and artificial seawater medium (25 gL(-1) NaCl) with biomass productivity 78.9 and 75.74 mg L(-1)d(-1), respectively. Maximum areal biomass productivity of 2.01 gm(-2)d(-1) was recorded in the mesh incubator, with complete exclusion of centrifugation for harvesting. Lipid content varied from 16% to 21%, consisting predominantly of C16:0, C16:1, C18:0, C18:1 fatty ...

Research paper thumbnail of Characterization of bacteria isolated from palaeoproterozoic metasediments for sequestration of carbon dioxide and formation of calcium carbonate

Environmental Science and Pollution Research, 2014

Bacterial community of palaeoproterozoic metasediments was enriched in the chemostat in the prese... more Bacterial community of palaeoproterozoic metasediments was enriched in the chemostat in the presence of different concentrations of NaHCO 3. Six bacterial isolates were isolated from the chemostat on nutrient agar plates on the basis of distinct morphology. Denaturing gradient gel electrophoresis (DGGE) proved the presence of six operational taxonomic units (OTUs) at 50 and 100 mM NaHCO 3. The OTU was reduced to three and one at enrichment concentration of 150 and 200 mM NaHCO 3 respectively. These six isolates were tested for sequestration of carbon dioxide by 14 C metabolic labeling of NaH 14 CO 3. Among the six isolates, one of the bacterium showed better potency to fix radiolabeled NaH 14 CO 3. The isolate (ISTD04) was identified as Serratia sp. by 16S ribosomal RNA (16S rRNA) sequence analysis and was found to be same as the DGGE OTU sequence at 200-mM NaHCO 3 concentration. The bacterium was tested for product formation in form of calcite crystals in presence of 5 % CO 2. Scanning electron microscopy (SEM) of product formed by the bacterium revealed defined faceted rhombohedral structure which resembled calcite and vaterite phases of the crystal. Formation of calcium carbonate crystals was further confirmed by Fourier transform infrared (FTIR) spectroscopy as carbonate group showing strong vibration at 1,456 cm −1. Major calcite phase diffraction peaks were determined by X-ray diffraction (XRD) analysis, and energy-dispersive X-ray (EDX) analysis showed the presence of CaO (72 %) and carbon (18 %). Bacterium use bicarbonate as carbon source for their growth as well as by-product formation in form of calcite shows carbon circulation and storage.

Research paper thumbnail of Bioremediation and Detoxification of Xenobiotic Organic Compounds in Landfill Leachate by Pseudomonas sp. ISTDF1

Management of Water, Energy and Bio-resources in the Era of Climate Change: Emerging Issues and Challenges, 2014

Increase in municipal solid waste (MSW) production has been a consequence of rapid population gro... more Increase in municipal solid waste (MSW) production has been a consequence of rapid population growth and urbanization in the past decade. It is startling to know that presently Delhi itself generates 8000 tonnes/day of MSW and to make the situation worse, it is projected to rise to 17,000-25,000 tonnes/day by the year 2021 (Talyan et al., 2008). The most commonly employed method for MSW management is landfill disposal. Landfill requires a close environmental engineering surveillance in its design and operation, as it is likely to generate leachate which would potentially contaminate nearby ground water and surface water (Mor et al., 2006). In spite of being economically viable, generation of heavily polluted leachate constitutes a major drawback of landfills. In the absence of leachate and landfill gas collection systems, these landfills are a major source of groundwater contamination and air pollution, including the generation of greenhouse gases (Talyan et al., 2008; Gardner et al., 1993).

Research paper thumbnail of Differential toxicological endpoints of di(2-ethylhexyl) phthalate (DEHP) exposure in MCF-7 and MDA-MB-231 cell lines: possible estrogen receptor alpha (ERalpha) independent modulations

Indian J Exp Biol, 2014

Wide spread use of Di-(2-ethylhexyl) phthalate (DEHP) has made it a ubiquitous contaminant in tod... more Wide spread use of Di-(2-ethylhexyl) phthalate (DEHP) has made it a ubiquitous contaminant in today's environment, responsible for possible carcinogenic and endocrine disrupting effects. In the present investigation an integrative toxicoproteomic approach was made to study the estrogenic potential of DEHP. In vitro experiments carried out with DEHP (0.1-100 microM) induced proliferations (E-screen assay) in human estrogen receptors-alpha (ERalpha) positive MCF-7 and ERalpha negative MDA-MB-231 breast cancer cells irrespective of their ERa status. Further, DEHP suppressed tamoxifen (a potent anti-breast cancer drug) induced apoptosis in both cell types as shown by flowcytometric cell cycle analysis. Label-free quantitative proteomics analysis of the cell secretome of both the cell lines indicated a wide array of stress related, structural and receptor binding proteins that were affected due to DEHP exposure. The secretome of DEHP treated MCF-7 cells revealed the down regulation o...

Research paper thumbnail of ASSESSMENT OFCryptococcus albidusFOR BIOPULPING OF EUCALYPTUS

Preparative Biochemistry and Biotechnology, 2013

Cryptococcus albidus shows delignification activity in nature. It was used for the biopulping of ... more Cryptococcus albidus shows delignification activity in nature. It was used for the biopulping of eucalyptus wood (Eucalyptus grandis) to access its potential for industrial application in the pulp and paper industry. Enzyme analysis on days 15, 30, and 60 showed the presence of laccase and xylanase as key enzymes. The production of endo-glucanase (CMCase) and exo-glucanase (FPase) was very low. Scanning electron microscopy (SEM) showed the surface colonization of wood and loosening of wood fibers in C. albidus-treated samples. Fourier-transformation infrared spectroscopy (FT-IR) indicated the chemical modification of eucalyptus wood. Denaturing gradient gel electrophoresis (DGGE) analysis on days 15, 30, and 60 confirmed the presence of C. albidus throughout the experiments. Cryptococcu albidus was able to suppress the growth of a native population. Further, after 60 days both the control and treated eucalyptus wood chips were given kraft pulping treatment. The kappa number of pulp of control wood was 21 and for treated wood was 17. Kappa number is considered a measure of lignin content in wood; hence the treatment of eucalyptus by C. albidus (biopulping) was effective in reducing its lignin content and can be used for biopulping in the pulp and paper industry.

Research paper thumbnail of Assessment of in vitro cyto/genotoxicity of sequentially treated electroplating effluent on the human hepatocarcinoma HuH-7 cell line

Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 2014

The present study compares in vitro toxicity of electroplating effluent after the batch treatment... more The present study compares in vitro toxicity of electroplating effluent after the batch treatment process with that obtained after the sequential treatment process. Activated charcoal prepared from sugarcane bagasse through chemical carbonization, and tolerant indigenous bacteria, Bacillus sp. strain IST105, were used individually and sequentially for the treatment of electroplating effluent. The sequential treatment involving activated charcoal followed by bacterial treatment removed 99% of Cr(VI) compared with the batch processes, which removed 40% (charcoal) and 75% (bacteria), respectively. Post-treatment in vitro cyto/genotoxicity was evaluated by the MTT test and the comet assay in human HuH-7 hepatocarcinoma cells. The sequentially treated sample showed an increase in LC50 value with a 6-fold decrease in comet-assay DNA migration compared with that of untreated samples. A significant decrease in DNA migration and an increase in LC50 value of treated effluent proved the higher effectiveness of the sequential treatment process over the individual batch processes.

Research paper thumbnail of In vitro toxicity evaluation of organic extract of landfill soil and its detoxification by indigenous pyrene-degrading Bacillus sp. ISTPY1

International Biodeterioration & Biodegradation, 2014

ABSTRACT Organic contaminants present in okhla landfill soil belong to the group polyaromatic hyd... more ABSTRACT Organic contaminants present in okhla landfill soil belong to the group polyaromatic hydrocarbons, pharmaceutical compounds, steroidal compounds, personal care products and their derivatives. An indigenous pyrene-degrading Bacillus sp. ISTPY1 was used to treat the Okhla landfill soil. GC–MS analysis of the organic extract before and after biodegradation with Bacillus sp. ISTPY1 showed the elimination of various polyaromatic hydrocarbons and other persistent aromatic compounds. Toxicity study was done on human hepato-carcinoma cell line HepG2 before and after treatment. The bacterium treated sample initially showed reduction in toxicity till 48 h. This was increased after 120 h due to formation of quinones intermediate and further decreased after 360 h. The LC50 value (MTT assay) also showed the same pattern. The reduction in Olive Tail Moment was observed after 360 h treatment. Result of the study indicated biodegradation and detoxification of major contaminants of Okhla landfill by Bacillus sp. ISTPY1.

Research paper thumbnail of Biodegradation of cypermethrin by Bacillus sp. in soil microcosm and in-vitro toxicity evaluation on human cell line

International Biodeterioration & Biodegradation, 2013

Soil microcosms were set up with cypermethrin (100 mg/kg of dry soil) to assess the biodegradatio... more Soil microcosms were set up with cypermethrin (100 mg/kg of dry soil) to assess the biodegradation by Bacillus sp. strain ISTDS2. Soil samples from the microcosms were collected at regular intervals during the biodegradation of cypermethrin and metabolites were extracted with hexane/Acetone (1:1v/v). GCeMS analysis of the soil extract showed formation of degraded compounds like cyclopropane, carboxylic acid, hydroxyacetonitrile and benzene ethanamine. The toxic effects of degraded product were studied on a human hepatocarcinoma cell line HuH7 before and after bacterial treatment. Methyltetrazolium (MTT) assay for cytotoxicity and alkaline comet assay for genotoxicity were carried for toxicity evaluation. The bacterium reduced toxicity as shown by a 10 5-fold increase in LC 50 value, and a 3-fold reduction in Olive Tail Moment after 30 days of treatment. Biodegradation ability of the strain without toxic by-products reveals its potential for further study as a biological agent for the remediation of soil contaminated with cypermethrin.

Research paper thumbnail of Mammalian cell line-based bioassays for toxicological evaluation of landfill leachate treated by Pseudomonas sp. ISTDF1

Environmental Science and Pollution Research, 2014

Landfill leachate has become a serious environmental concern because of the presence of many haza... more Landfill leachate has become a serious environmental concern because of the presence of many hazardous compounds which even at trace levels are a threat to human health and environment. Therefore, it is important to assess the toxicity of leachate generated and discharge it conforming to the safety standards. The present work examined the efficiency of an earlier reported Pseudomonas sp. strain ISTDF1 for detoxification of leachate collected from Okhla landfill site (New Delhi, India). GC-MS analysis performed after treatment showed the removal of compounds like alpha-limonene diepoxide, brominated dioxin-2-one, Bisphenol A, nitromusk, phthalate derivative, and nitrobenzene originally found in untreated leachate. ICP-AES analysis for heavy metals also showed reduction in concentrations of Zn, Cd, Cr, Fe, Ni, and Pb bringing them within the limit of safety discharge. Methyl tetrazolium (MTT) assay for cytotoxicity, alkaline comet assay for genotoxicity, and 7-ethoxyresorufin-O-deethylase (EROD) assay for dioxin-like behavior were carried out in human hepato-carcinoma cell line HepG2 to evaluate the toxic potential of treated and untreated leachates. The bacterium reduced toxicity as shown by 2.5-fold reduction of MTT EC50 value, 7-fold reduction in Olive Tail Moment, and 2.8-fold reduction in EROD induction after 240 h of bacterial treatment.

Research paper thumbnail of {"__content__"=>"Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium sp. ISTKB.", "i"=>{"__content__"=>"Pandoraea"}}

Biotechnology for biofuels, 2018

Lignin is a major component of plant biomass and is recalcitrant to degradation due to its comple... more Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization. Genomic analysis of sp. ISTKB revealed the presence of strong lig...

Research paper thumbnail of {"__content__"=>"Production, process optimization and molecular characterization of polyhydroxyalkanoate (PHA) by COsequestering B. cereus SS105.", "sub"=>{"__content__"=>"2"}}

Bioresource technology, 2018

Carbon dioxide sequestering bacterial strains were previously isolated from free air COenriched (... more Carbon dioxide sequestering bacterial strains were previously isolated from free air COenriched (FACE) soil. In the present study, these strains were screened for PHA accumulation and Bacillus cereus SS105 was found to be the most prominent PHA accumulating strain on sodium bicarbonate and molasses as carbon source. This strain was further characterized by Spectrofluorometric method and Confocal microscopy after staining with Nile red. PHA granules in inclusion bodies were visualized by Transmission Electron Microscopy. The PHA and its monomer composition were characterized by GC-MS followed by FTIR and NMR. The genetic basis of PHA production was confirmed by the amplification, cloning and analysis of PHA biosynthesis genes phaR, phaB and phaC from B. cereus with the degenerate primers. The PHA production was further optimized by Response Surface Methodology and the percent increase observed after optimization was 55.16% (w/v).

Research paper thumbnail of Metagenomic Analysis of Microbial Diversity in Landfill Lysimeter Soil of Ghazipur Landfill Site, New Delhi, India

Genome announcements, Jan 19, 2017

We report the soil microbial diversity and functional aspects related to degradation of recalcitr... more We report the soil microbial diversity and functional aspects related to degradation of recalcitrant compounds, determined using a metagenomic approach, in a landfill lysimeter prepared with soil from Ghazipur landfill site, New Delhi, India. Metagenomic analysis revealed the presence and functional diversity of complex microbial communities responsible for waste degradation.

Research paper thumbnail of Genome Sequence of Pandoraea sp. ISTKB, a Lignin-Degrading Betaproteobacterium, Isolated from Rhizospheric Soil

Genome Announcements, 2016

We report here the genome sequence of Pandoraea sp. ISTKB, a betaproteobacterium isolated from rh... more We report here the genome sequence of Pandoraea sp. ISTKB, a betaproteobacterium isolated from rhizospheric soil in the backwaters of Alappuzha, Kerala, India. The strain is alkalotolerant and grows on medium containing lignin as a sole carbon source. Genes and pathways related to lignin degradation were complemented by genomic analysis.

Research paper thumbnail of Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks

Genome Announcements, 2016

The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO 2 )-sequestering bacte... more The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO 2 )-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO 3 ) as the sole carbon source. Here, we report the genome sequence of 5.07 Mb Serratia sp. ISTD04.

Research paper thumbnail of NADPH oxidase mediated superoxide production by intermediary bacterial metabolites of dibenzofuran: A potential cause for trans-mitochondrial membrane potential (ΔΨm) collapse in human hepatoma cells

Toxicological sciences : an official journal of the Society of Toxicology, 2015

Dibenzofuran is a direct precursor of extremely toxic compounds such as dioxins. It is widely dis... more Dibenzofuran is a direct precursor of extremely toxic compounds such as dioxins. It is widely distributed persistent organic pollutant in environment that potentiate oxidative stress, apoptosis and necrosis through bioactivation in HepG2 cells. An alkalotolerent Pseudomonas strain ISTDF1 can metabolize dibenzofuran as a sole source of carbon and energy through diverse dioxygenation. However, there is a paucity of information about the potential toxic effects of the intermediary metabolites that are formed during treatment with dibenzofuran. We have assessed and discovered the potential mechanism of toxicity induced by metabolites of dibenzofuran that were formed at 18 h and 36 h. Cell viability, CYP1A2 induction, ROS activity, Superoxide production, mitochondrial NADPH oxidase activity and mitochondrial trans-membrane potential were studied using different assays such as MTT, confocal laser scanning microscopy and Flow cytometry. Analysis revealed formation of 2-(1-carbonyl methylid...

Research paper thumbnail of Investigating the degradation process of kraft lignin by β-proteobacterium, Pandoraea sp. ISTKB

Environmental Science and Pollution Research, 2015

The present study investigates the kraft lignin (KL) degrading potential of novel alkalotolerant ... more The present study investigates the kraft lignin (KL) degrading potential of novel alkalotolerant Pandoraea sp. ISTKB utilizing KL as sole carbon source. The results displayed 50.2 % reduction in chemical oxygen demand (COD) and 41.1 % decolorization after bacterial treatment. The maximum lignin peroxidase (LiP) and manganese peroxidase (MnP) activity detected was 2.73 and 4.33 U ml −1 , respectively, on day 3. The maximum extracellular and intracellular laccase activities observed were 1.32 U ml −1 on day 5 and 4.53 U ml −1 on day 4, respectively. The decolorization and degradation was maximum on day 2. Further, it registered an increase with the production of extracellular laccase. This unusual trend of decolorization and degradation was studied using various aromatic compounds and dyes. SEM and FTIR results indicated significant change in surface morphology and functional group composition during the course of degradation. Gas chromatography and mass spectroscopy (GC-MS) analysis confirmed KL degradation by emergence of new peaks and the identification of low molecular weight aromatic intermediates in treated sample. The degradation of KL progressed through the generation of phenolic intermediates. The identified intermediates implied the degradation of hydroxyphenyl, ferulic acid, guaiacyl, syringyl, phenylcoumarane, and pinoresinol components commonly found in lignin. The degradation, decolorization, and GC-MS analysis indicated potential application of the isolate Pandoraea sp. ISTKB in treatment of lignin-containing pollutants and KL valorization.

Research paper thumbnail of Novel lipase from basidiomycetes Schizophyllum commune ISTL04, produced by solid state fermentation of Leucaena leucocephala seeds

Journal of Molecular Catalysis B: Enzymatic, 2014

The present investigation reports a novel thermoalkalotolerant lipase producing Basidiomycetes, S... more The present investigation reports a novel thermoalkalotolerant lipase producing Basidiomycetes, Schizophyllum commune ISTL04 for the first time. Abundantly available Leucaena leucocephala seeds were exploited as a cheap fermentable source for the feasible production of extracellular lipase. The isolate ISTL04 grew vigorously on Leucaena seeds in comparison to Soybean meal and Wheat bran exhibiting a lipase activity of 146.5 U/g. The S. commune ISTL04 (SCI) lipase was purified to 35.76 folds with a specific activity of 238.13 U/mg and an estimated mass of 60 kDa. The temperature and pH optima for lipolytic activity were 60 • C and 11, respectively. The enzyme exhibited remarkable stability in the presence of non-polar and polar organic solvents (50%, v/v), retaining more than 90% and 40% activity, respectively. The lipase activity increased significantly in the presence of Mg 2+ (154%), Ca 2+ (109.7%), Mn 2+ (106%) and Tween 80 (240%). The distinctive and broader operational properties of the SCI lipase make it a promising biocatalyst for various industrial processes.

Research paper thumbnail of Cloning and expression of gamma carbonic anhydrase from Serratia sp. ISTD04 for sequestration of carbon dioxide and formation of calcite

Bioresource Technology, 2015

h i g h l i g h t s Microbial community of marble mine was enriched and characterized. Carbonic a... more h i g h l i g h t s Microbial community of marble mine was enriched and characterized. Carbonic anhydrase (CA) gene of Serratia sp. was cloned. CA enzyme was characterized. Gamma carbonic anhydrase was reported homologous to archae and methanogens. Use of carbonic anhydrase enzyme for the sequestration of atmospheric CO 2 .

Research paper thumbnail of Immobilized lipase from Schizophyllum commune ISTL04 for the production of fatty acids methyl esters from cyanobacterial oil

Bioresource Technology, 2015

Novel lipase from model mushroom Schizophyllum commune strain ISTL04 produced by solid state ferm... more Novel lipase from model mushroom Schizophyllum commune strain ISTL04 produced by solid state fermentation of Leucaena leucocephala seeds, was immobilized onto Celite for enzymatic FAMEs production from cyanobacterial endolith Leptolyngbya ISTCY101. The isolate showed vigorous growth and produced remarkable lipase activity of 146.5Ug(-1) dry solid substrate, without any external lipase inducer. Single-factor experiments were carried out to study the effects of various reaction parameters on the FAMEs yield. The best conditions for enzymatic transesterification as revealed by the results were: 1:3 oil to methanol molar ratio, added at 3h intervals, 12% water content, 1581.5Ug(-1) immobilized lipase, temperature 45°C, and time 24h. Under these conditions, the maximum FAMEs yield reached 94%. The immobilized lipase was able to produce >90% of the relative FAMEs yield after four repeated transesterification cycles. This immobilized lipase exhibited potential for application in biodiesel industry.

Research paper thumbnail of Characterization of microalga Scenedesmus sp. ISTGA1 for potential CO 2 sequestration and biodiesel production

Research paper thumbnail of Characterization of endolithic cyanobacterial strain, Leptolyngbya sp. ISTCY101, for prospective recycling of CO₂ and biodiesel production

Bioresource technology, 2014

The present investigation evaluates the potential of an endolithic cyanobacterium isolated from m... more The present investigation evaluates the potential of an endolithic cyanobacterium isolated from marble rock to utilize sodium bicarbonate (NaHCO₃) as carbon source for prospective recycling of CO₂ into biodiesel. Microalgae thriving on marble were cultured and subjected to increasing NaHCO₃ concentration. The most competent isolate was identified and characterized in terms of growth, lipid content and fatty acid profile. A semicontinuous mesh incubator was designed for biofilm development. Isolate ISTCY101 was identified as Leptolyngbya sp. by 16S rRNA sequencing. Leptolyngbya ISTCY101 efficiently used BG-11 (50 mM NaHCO₃) and artificial seawater medium (25 gL(-1) NaCl) with biomass productivity 78.9 and 75.74 mg L(-1)d(-1), respectively. Maximum areal biomass productivity of 2.01 gm(-2)d(-1) was recorded in the mesh incubator, with complete exclusion of centrifugation for harvesting. Lipid content varied from 16% to 21%, consisting predominantly of C16:0, C16:1, C18:0, C18:1 fatty ...

Research paper thumbnail of Characterization of bacteria isolated from palaeoproterozoic metasediments for sequestration of carbon dioxide and formation of calcium carbonate

Environmental Science and Pollution Research, 2014

Bacterial community of palaeoproterozoic metasediments was enriched in the chemostat in the prese... more Bacterial community of palaeoproterozoic metasediments was enriched in the chemostat in the presence of different concentrations of NaHCO 3. Six bacterial isolates were isolated from the chemostat on nutrient agar plates on the basis of distinct morphology. Denaturing gradient gel electrophoresis (DGGE) proved the presence of six operational taxonomic units (OTUs) at 50 and 100 mM NaHCO 3. The OTU was reduced to three and one at enrichment concentration of 150 and 200 mM NaHCO 3 respectively. These six isolates were tested for sequestration of carbon dioxide by 14 C metabolic labeling of NaH 14 CO 3. Among the six isolates, one of the bacterium showed better potency to fix radiolabeled NaH 14 CO 3. The isolate (ISTD04) was identified as Serratia sp. by 16S ribosomal RNA (16S rRNA) sequence analysis and was found to be same as the DGGE OTU sequence at 200-mM NaHCO 3 concentration. The bacterium was tested for product formation in form of calcite crystals in presence of 5 % CO 2. Scanning electron microscopy (SEM) of product formed by the bacterium revealed defined faceted rhombohedral structure which resembled calcite and vaterite phases of the crystal. Formation of calcium carbonate crystals was further confirmed by Fourier transform infrared (FTIR) spectroscopy as carbonate group showing strong vibration at 1,456 cm −1. Major calcite phase diffraction peaks were determined by X-ray diffraction (XRD) analysis, and energy-dispersive X-ray (EDX) analysis showed the presence of CaO (72 %) and carbon (18 %). Bacterium use bicarbonate as carbon source for their growth as well as by-product formation in form of calcite shows carbon circulation and storage.

Research paper thumbnail of Bioremediation and Detoxification of Xenobiotic Organic Compounds in Landfill Leachate by Pseudomonas sp. ISTDF1

Management of Water, Energy and Bio-resources in the Era of Climate Change: Emerging Issues and Challenges, 2014

Increase in municipal solid waste (MSW) production has been a consequence of rapid population gro... more Increase in municipal solid waste (MSW) production has been a consequence of rapid population growth and urbanization in the past decade. It is startling to know that presently Delhi itself generates 8000 tonnes/day of MSW and to make the situation worse, it is projected to rise to 17,000-25,000 tonnes/day by the year 2021 (Talyan et al., 2008). The most commonly employed method for MSW management is landfill disposal. Landfill requires a close environmental engineering surveillance in its design and operation, as it is likely to generate leachate which would potentially contaminate nearby ground water and surface water (Mor et al., 2006). In spite of being economically viable, generation of heavily polluted leachate constitutes a major drawback of landfills. In the absence of leachate and landfill gas collection systems, these landfills are a major source of groundwater contamination and air pollution, including the generation of greenhouse gases (Talyan et al., 2008; Gardner et al., 1993).

Research paper thumbnail of Differential toxicological endpoints of di(2-ethylhexyl) phthalate (DEHP) exposure in MCF-7 and MDA-MB-231 cell lines: possible estrogen receptor alpha (ERalpha) independent modulations

Indian J Exp Biol, 2014

Wide spread use of Di-(2-ethylhexyl) phthalate (DEHP) has made it a ubiquitous contaminant in tod... more Wide spread use of Di-(2-ethylhexyl) phthalate (DEHP) has made it a ubiquitous contaminant in today's environment, responsible for possible carcinogenic and endocrine disrupting effects. In the present investigation an integrative toxicoproteomic approach was made to study the estrogenic potential of DEHP. In vitro experiments carried out with DEHP (0.1-100 microM) induced proliferations (E-screen assay) in human estrogen receptors-alpha (ERalpha) positive MCF-7 and ERalpha negative MDA-MB-231 breast cancer cells irrespective of their ERa status. Further, DEHP suppressed tamoxifen (a potent anti-breast cancer drug) induced apoptosis in both cell types as shown by flowcytometric cell cycle analysis. Label-free quantitative proteomics analysis of the cell secretome of both the cell lines indicated a wide array of stress related, structural and receptor binding proteins that were affected due to DEHP exposure. The secretome of DEHP treated MCF-7 cells revealed the down regulation o...

Research paper thumbnail of ASSESSMENT OFCryptococcus albidusFOR BIOPULPING OF EUCALYPTUS

Preparative Biochemistry and Biotechnology, 2013

Cryptococcus albidus shows delignification activity in nature. It was used for the biopulping of ... more Cryptococcus albidus shows delignification activity in nature. It was used for the biopulping of eucalyptus wood (Eucalyptus grandis) to access its potential for industrial application in the pulp and paper industry. Enzyme analysis on days 15, 30, and 60 showed the presence of laccase and xylanase as key enzymes. The production of endo-glucanase (CMCase) and exo-glucanase (FPase) was very low. Scanning electron microscopy (SEM) showed the surface colonization of wood and loosening of wood fibers in C. albidus-treated samples. Fourier-transformation infrared spectroscopy (FT-IR) indicated the chemical modification of eucalyptus wood. Denaturing gradient gel electrophoresis (DGGE) analysis on days 15, 30, and 60 confirmed the presence of C. albidus throughout the experiments. Cryptococcu albidus was able to suppress the growth of a native population. Further, after 60 days both the control and treated eucalyptus wood chips were given kraft pulping treatment. The kappa number of pulp of control wood was 21 and for treated wood was 17. Kappa number is considered a measure of lignin content in wood; hence the treatment of eucalyptus by C. albidus (biopulping) was effective in reducing its lignin content and can be used for biopulping in the pulp and paper industry.

Research paper thumbnail of Assessment of in vitro cyto/genotoxicity of sequentially treated electroplating effluent on the human hepatocarcinoma HuH-7 cell line

Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 2014

The present study compares in vitro toxicity of electroplating effluent after the batch treatment... more The present study compares in vitro toxicity of electroplating effluent after the batch treatment process with that obtained after the sequential treatment process. Activated charcoal prepared from sugarcane bagasse through chemical carbonization, and tolerant indigenous bacteria, Bacillus sp. strain IST105, were used individually and sequentially for the treatment of electroplating effluent. The sequential treatment involving activated charcoal followed by bacterial treatment removed 99% of Cr(VI) compared with the batch processes, which removed 40% (charcoal) and 75% (bacteria), respectively. Post-treatment in vitro cyto/genotoxicity was evaluated by the MTT test and the comet assay in human HuH-7 hepatocarcinoma cells. The sequentially treated sample showed an increase in LC50 value with a 6-fold decrease in comet-assay DNA migration compared with that of untreated samples. A significant decrease in DNA migration and an increase in LC50 value of treated effluent proved the higher effectiveness of the sequential treatment process over the individual batch processes.

Research paper thumbnail of In vitro toxicity evaluation of organic extract of landfill soil and its detoxification by indigenous pyrene-degrading Bacillus sp. ISTPY1

International Biodeterioration & Biodegradation, 2014

ABSTRACT Organic contaminants present in okhla landfill soil belong to the group polyaromatic hyd... more ABSTRACT Organic contaminants present in okhla landfill soil belong to the group polyaromatic hydrocarbons, pharmaceutical compounds, steroidal compounds, personal care products and their derivatives. An indigenous pyrene-degrading Bacillus sp. ISTPY1 was used to treat the Okhla landfill soil. GC–MS analysis of the organic extract before and after biodegradation with Bacillus sp. ISTPY1 showed the elimination of various polyaromatic hydrocarbons and other persistent aromatic compounds. Toxicity study was done on human hepato-carcinoma cell line HepG2 before and after treatment. The bacterium treated sample initially showed reduction in toxicity till 48 h. This was increased after 120 h due to formation of quinones intermediate and further decreased after 360 h. The LC50 value (MTT assay) also showed the same pattern. The reduction in Olive Tail Moment was observed after 360 h treatment. Result of the study indicated biodegradation and detoxification of major contaminants of Okhla landfill by Bacillus sp. ISTPY1.

Research paper thumbnail of Biodegradation of cypermethrin by Bacillus sp. in soil microcosm and in-vitro toxicity evaluation on human cell line

International Biodeterioration & Biodegradation, 2013

Soil microcosms were set up with cypermethrin (100 mg/kg of dry soil) to assess the biodegradatio... more Soil microcosms were set up with cypermethrin (100 mg/kg of dry soil) to assess the biodegradation by Bacillus sp. strain ISTDS2. Soil samples from the microcosms were collected at regular intervals during the biodegradation of cypermethrin and metabolites were extracted with hexane/Acetone (1:1v/v). GCeMS analysis of the soil extract showed formation of degraded compounds like cyclopropane, carboxylic acid, hydroxyacetonitrile and benzene ethanamine. The toxic effects of degraded product were studied on a human hepatocarcinoma cell line HuH7 before and after bacterial treatment. Methyltetrazolium (MTT) assay for cytotoxicity and alkaline comet assay for genotoxicity were carried for toxicity evaluation. The bacterium reduced toxicity as shown by a 10 5-fold increase in LC 50 value, and a 3-fold reduction in Olive Tail Moment after 30 days of treatment. Biodegradation ability of the strain without toxic by-products reveals its potential for further study as a biological agent for the remediation of soil contaminated with cypermethrin.

Research paper thumbnail of Mammalian cell line-based bioassays for toxicological evaluation of landfill leachate treated by Pseudomonas sp. ISTDF1

Environmental Science and Pollution Research, 2014

Landfill leachate has become a serious environmental concern because of the presence of many haza... more Landfill leachate has become a serious environmental concern because of the presence of many hazardous compounds which even at trace levels are a threat to human health and environment. Therefore, it is important to assess the toxicity of leachate generated and discharge it conforming to the safety standards. The present work examined the efficiency of an earlier reported Pseudomonas sp. strain ISTDF1 for detoxification of leachate collected from Okhla landfill site (New Delhi, India). GC-MS analysis performed after treatment showed the removal of compounds like alpha-limonene diepoxide, brominated dioxin-2-one, Bisphenol A, nitromusk, phthalate derivative, and nitrobenzene originally found in untreated leachate. ICP-AES analysis for heavy metals also showed reduction in concentrations of Zn, Cd, Cr, Fe, Ni, and Pb bringing them within the limit of safety discharge. Methyl tetrazolium (MTT) assay for cytotoxicity, alkaline comet assay for genotoxicity, and 7-ethoxyresorufin-O-deethylase (EROD) assay for dioxin-like behavior were carried out in human hepato-carcinoma cell line HepG2 to evaluate the toxic potential of treated and untreated leachates. The bacterium reduced toxicity as shown by 2.5-fold reduction of MTT EC50 value, 7-fold reduction in Olive Tail Moment, and 2.8-fold reduction in EROD induction after 240 h of bacterial treatment.