Browsing by Author "Suresh K. Dubey"

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Bio-filtration of trichloroethylene using diazotrophic bacterial community
(Elsevier Ltd, 2010) Awadhesh K. Shukla; Pranjali Vishwakarma; R.S. Singh; S.N. Upadhyay; Suresh K. Dubey
Biodegradation of TCE was studied in a biofilter packed with wood charcoal and inoculated with diazotrophic bacterial community isolated from local soil. Steady state TCE removal efficiencies higher than 85% were observed up to inlet load of 2.866 g m-3 h-1. The maximum elimination capacity of 5.31 gm-3 h-1 was observed at an inlet load of more than 7.90 g m-3 h-1. The biofilter was sensitive to fluctuations in the process conditions but could easily recover its performance after 10 days shutdown. Almost constant and small pressure drop per unit length and very negligible compaction was observed during the whole experimental period. The molecular analyses such as RT-PCR and gene sequencing revealed the presence of functionally active Azospirillum species in the biofilm. © 2009 Elsevier Ltd. All rights reserved.
Biodegradation of trichloroethylene (TCE) by methanotrophic community
(2009) Awadhesh K. Shukla; Pranjali Vishwakarma; S.N. Upadhyay; Anil K Tripathi; H.C. Prasana; Suresh K. Dubey
Laboratory incubation experiments were carried out to assess the potential of methanotrophic culture for degrading TCE. Measurements of the growth rate and TCE degradation showed that the methanotrophs not only grew in presence of TCE but also degraded TCE. The rate of TCE degradation was found to be 0.19 ppm h-1. The reverse transcriptase-PCR test was conducted to quantify expression of pmoA and mmoX genes. RT-PCR revealed expression of pmoA gene only. This observation provides evidence that the pmoA gene was functionally active for pMMO enzyme during the study. The diversity of the methanotrophs involved in TCE degradation was assessed by PCR amplification, cloning, restriction fragment length polymorphism and phylogenetic analysis of pmoA genes. Results suggested the occurrence of nine different phylotypes belonging to Type II methanotrophs in the enriched cultures. Out of the nine, five clustered with, genera Methylocystis and rest got clustered in to a separate group. © 2008 Elsevier Ltd. All rights reserved.
Changes in methanogenic population size and CH4 production potential in response to crop phenology in tropical rice field
(2013) Suresh K. Dubey; Alpana Singh; R.S. Singh; S.N. Upadhyay
In order to understand the microbial ecology of CH4 production in rice field, population size of methanogens and pattern of CH4 production potential was determined during rice cultivation for two years (2009 and 2010). Population size varied between 4.88 × 105 and 13.98 × 105 copies g-1 dws during the entire study period and followed the trend: flowering > ripening > tillering > post-harvest > pre-plantation. Pattern of CH4 production potential was similar to the population size for different stages of the crop and followed the pseudo-first order kinetics, indicating a positive relationship between the population size of methanogens and CH4 production potential. An exponential relationship between the cumulative methane production potential and methanogenic population size was established. © 2012 Elsevier Ltd.
Characterization of Listeria monocytogenes isolated from Ganges water, human clinical and milk samples at Varanasi, India
(2013) Dharmendra K. Soni; Rakesh K. Singh; Durg V. Singh; Suresh K. Dubey
Listeria monocytogenes isolated from Ganges water, human clinical and milk samples were characterized by antibiotic susceptibility, serotype identification, detection of virulence genes and ERIC- and REP-PCR fingerprint analyses. All isolates were uniformly resistant to ampicillin, except two isolates, and showed variable resistance to gentamicin, cotrimoxazole, ofloxacin, rifampicin and tetracycline. Of the 20 isolates found positive for pathogens, seven (four human and three water isolates) belong to serogroups 4b, 4d and 4e; six (one human and five water isolates) belong to serogroups 1/2c and 3c; four milk isolates belong to serogroups 1/2b and 3b; and three milk isolates belong to serogroups 1/2a and 3a. Two water isolates, all human isolates, except one (Pb1) lacking inlJ gene, and three milk isolates possess inlA, inlC, plcA, prfA, actA, hlyA and iap genes. The remaining water and milk isolates showed variable presence of inlJ, plcA, prfA, and iap genes. ERIC- and REP-PCR based analyses collectively indicated that isolates of human clinical samples belong to identical or similar clone and isolates of water and milk samples belong to different clones. Overall study demonstrates the prevalence of pathogenic L. monocytogenes species in the environmental and clinical samples. Most of the isolates were resistant to commonly used antibiotics. © 2012 Elsevier B.V.
Community structure of methanogenic archaea and methane production associated with compost-treated tropical rice-field soil
(2012) Alpana Singh; Ram S. Singh; Siddh N. Upadhyay; Chaitanya G. Joshi; Ajay K. Tripathi; Suresh K. Dubey
The diversity and density of methanogenic archaea and methane production were investigated ex situ at different growth stages of rice plant cultivated in compost-treated tropical rice fields. The qPCR analysis revealed variation in methanogens population from 3.40 × 106 to 1.11 × 107 copies g-1 dws, in the year 2009 and 4.37 × 106 to 1.36 × 107 copies g-1 dws in the year 2010. Apart from methanogens, a large number of bacterial (9.60 × 109-1.44 × 1010 copies g-1 dws) and archaeal (7.13 × 107-3.02 × 108 copies g-1 dws) communities were also associated with methanogenesis. Methanogen population size varied in the order: flowering > ripening > tillering > postharvest > preplantation stage. The RFLP-based 16S rRNA gene-targeted phylogenetic analysis showed that clones were closely related to diverse group of methanogens comprising members of Methanomicrobiaceae, Methanosarcinaceae, Methanosaetaceae and RC I. Laboratory incubation studies revealed higher amount of cumulative CH4 at the flowering stage. The integration of methanogenic community structure and CH4 production potential of soil resulted in a better understanding of the dynamics of CH4 production in organically treated rice-field soil. The hypothesis that the stages of plant development influence the methanogenic community structure leading to temporal variation in the CH4 production has been successfully tested. © 2012 Federation of European Microbiological Societies.
Comparative whole genome analysis of Listeria monocytogenes 4b strains reveals least genome diversification irrespective of their niche specificity
(Elsevier Inc, 2017) Dharmendra K. Soni; Arpita Ghosh; Surendra K. Chikara; Krishna M. Singh; Chaitanya G. Joshi; Suresh K. Dubey
Listeria monocytogenes has emerged as the deadly pathogen inflicting high mortality in humans and animals. To investigate the strain-specific characteristics of L. monocytogenes, and their role(s) in virulence and ecological sustenance, we sequenced genome of three L. monocytogenes strains BHU1, 2 and 3 isolated from the Ganges river, agricultural soil and human placenta bit, respectively, and compared it with L. monocytogenes EGD-e serovar 1/2a and L. monocytogenes F2365 serovar 4b strain. The contigs of all the three strains had a similarity (> 90%) in regions that aligned with EGD-e and F2365. A total of 2872 core genes on the set of strains were identified in BHU1, 2 and 3 strains. In the mice virulence assay, BHU2 and 3 strains showed pathogenicity while BHU1 was non-pathogenic. These strains were also characterized with unique genes (8 genes in BHU1, 12 in BHU 2, and 17 in BHU 3 strain). Phylogenetic analysis based on multilocus sequence typing revealed BHU1, 2 and 3 strains to be more closely related to lineage I, serotype 4b, clonal complex 1, and sequence type 328. BHU1 strain seemed to harbor nucleotide mutation from A to G in the major virulence genes i.e. hemolysin D and listeriolysin O. Strain-specific mutations 8, 5 and 2 were identified in BHU1, 2 and 3, respectively, compared to F2365. Though all the three strains were genetically very close, the observed differences may play the crucial role(s) in their virulence attributes, and also, in the prevalence of L. monocytogenes. © 2017 Elsevier Inc.
Degradation kinetics and metabolites in continuous biodegradation of isoprene
(Elsevier Ltd, 2016) Navnita Srivastva; Ram S. Singh; Siddh N. Upadhyay; Suresh K. Dubey
The kinetic parameters of isoprene biodegradation were studied in a bioreactor, comprising of bioscrubber and polyurethane foam packed biofilter in series and inoculated with Pseudomonas sp., using a Michaelis-Menten type model. The maximum elimination capacity, ECmax; substrate constant, Ks and ECmax/Ks values for bioscrubber were found to be 666.7 g m-3 h-1, 9.86 g m-3 and 67.56 h-1, respectively while those for biofilter were 3333 g m-3 h-1, 13.96 g m-3 and 238.7 h-1, respectively. The biofilter section exhibited better degradation efficiency compared to the bioscrubber unit. Around 62-75% of the feed isoprene got converted to carbon dioxide, indicating the efficient capability of bacteria to mineralize isoprene. The FTIR and GC-MS analyses of degradation products indicated oxidative cleavage of unsaturated bond of isoprene. These results were used for proposing a plausible degradation pathway for isoprene. © 2016 Elsevier Ltd.
Degradation kinetics of chlorpyrifos and 3,5,6-trichloro-2-pyridinol (TCP) by fungal communities
(Elsevier Ltd, 2012) K. Maya; S.N. Upadhyay; R.S. Singh; Suresh K. Dubey
Fungal isolates obtained from soil were used for degrading chlorpyrifos (CP) and TCP. The percentage degradation ranged from 69.4 to 89.8 for CP and 62.2 to 92.6 for TCP after one week. The values of Ks and Vmax were different for different isolates. The Ks ranged from 66.66 to 169.5 mg/L and Vmax from 6.56 to 40.4 mg/L/d for CP and from 53.19 to 163.9 mg/L and 3.41 to 40.40 mg/L/d, respectively, for TCP. Fungal community showed high affinity for both CP and TCP. The genetic relatedness of isolate F1 to Aspergillus sp., F2 and F3 to Penicillium sp., F4 to Eurotium sp. and F5 to Emericella sp. were confirmed. The degradation potential was in the order: F1 > F2 = F3 > F4 > F5. © 2012 Elsevier Ltd
Diversity of methanotrophs in urea-fertilized tropical rice agroecosystem
(2010) Pranjali Vishwakarma; Suresh K. Dubey
Laboratory experiments were conducted to study the population size, diversity and methane oxidation potential of methanotrophs in tropical rice agroecosystem under the influence of N-fertilizer. Results indicate that the diversity of methane oxidizing bacteria (MOB) is altered in fertilizer treated soils compared to untreated control. Nevertheless, Type I MOB still dominated in the fertilized soils whereas the diversity of Type II methanotrophs decreases. Control soils have higher MOB population and CH4 oxidation capacity than fertilized soils. Rhizospheric soil is more populated than non-rhizospheric soil in both unfertilized and fertilized conditions. Variation in Km and Vmax of methane oxidation in soils appears to be due to variation in methanotrophic community. Experimental results indicate that methanotrophic community differs both quantitatively and qualitatively in unfertilized and fertilized soils. © 2010 Association of Microbiologists of India.
DNA microarray analysis targeting pmoA gene reveals diverse community of methanotrophs in the rhizosphere of tropical rice soils
(2010) Pranjali Vishwakarma; Suresh K. Dubey
The diversity of the methanotrophs community of two different rice fields of a typical tropical rice agroecosystem was assessed using microarray targeting pmoA gene-based approach. The presence of types I and II methanotrophs was observed with the dominance of Methylocystis in both the fields. The study revealed that the Barkachcha rice field harbours more diverse groups of methanotrophs than the Ghazipur rice field. It was also observed that in some members of types I and II methanotrophs, even the peat-associated group was present in the enriched culture of the soils. The Ghazipur soil and its enriched mixed methanotrophic culture showed higher methane oxidation potential than the Barkachcha soil. These results suggest that the methanotrophs community and its potential for methane oxidation vary with change in soil type within the same ecosystem.
Ecological and molecular analyses of the rhizospheric methanotroph community in tropical rice soil: Effect of crop phenology and land-use history
(2009) Pranjali Vishwakarma; M.G. Dumont; L. Bodrossy; N. Stralis-Pavese; J.C. Murrell; Suresh K. Dubey
To study the effect of crop phenology and cultivation practices on methanotrophic communities, two tropical rice fields located in the upper Gangetic plain of India with similar soil type and different cropping history were selected. A laboratory incubation experiment for the enumeration of methanotrophs and for the measurement of CH4 oxidation potential was conducted on a parallel basis. The methanotroph population size was found to be significantly higher in the Banaras Hindu University (BHU), Varanasi soil than the Indian Institute of Vegetable Research (IIVR), Varanasi soil. The population size increased with the age of the plant for both the sites. The CH4 oxidation potential was higher with the BHU soil compared to the IIVR soil. The CH4 oxidation rate increased significantly from tillering to flowering to grain-filling stages, and finally there was no significant difference between the grain-filling and the grain-maturation stages. A diagnostic microarray targeting the pmoA gene and a 16S rRNA denaturing gradient gel electrophoresis (DGGE)-based approach were applied to assess the diversity of the methanotrophic community for the two sites. A broad diversity of methanotrophs was detected at both sites, including type I and type II methanotrophs of the genera Methylobacter, Methylomonas, Methylosarcina, Methylosphaera, Methylomicrobium and Methylocystis. Type II methanotrophs were found in higher abundance as compared to type I methanotrophs at both the sites. DGGE analysis indicated that the methanotroph community in BHU soil was more or less stable, while little variation was found in IIVR soil during crop growth.
Efficacy of wood charcoal and its modified form as packing media for biofiltration of isoprene
(Academic Press, 2017) Navnita Srivastva; Ram S. Singh; Suresh K. Dubey
The efficacy of wood charcoal (WC) and nutrient-enriched wood charcoal (NWC) as biofilter packing media were assessed for isoprene biodegradation in a bioreactor comprising bioscrubber and a biofilter connected in series and inoculated with Pseudomonas sp. The bioreactors using WC and NWC exhibited >90% removal efficiency and around 369 g m−3 h−1 elimination capacity at around 404 g m−3 h−1 inlet loading rate. In both the bioreactors, the biofilter component showed better degradation capacity compared to the bioscrubber unit. The kinetic parameters, maximum elimination capacity, ECmax; substrate constant, Ks and ECmax/Ks for Michaelis-Menten model were evaluated. The lower Ks for the WC packed bioreactor indicated that ECmax achieved, was faster compared to others, while higher ECmax and ECmax/Ks for the NWC packed bioreactor suggests its superiority in isoprene abatement in the continuous mode. A comparison of the available published information on biofiltration of isoprene reflected polyurethane foam as the superior packing media. © 2017 Elsevier Ltd
Kinetic analysis reveals bacterial efficacy for biodegradation of chlorpyrifos and its hydrolyzing metabolite TCP
(2011) K. Maya; R.S. Singh; S.N. Upadhyay; Suresh K. Dubey
Efficacy of soil bacterial communities comprising seven different isolates for biodegradation of chlorpyrifos and TCP (3,5,6-trichloro-2-pyridinol), a degradation product of chlorpyrifos, has been investigated. The concentration of chlorpyrifos has ranged from 25 to 200 mg chlorpyrifos/L, and that of TCP from 25 to 100 mg TCP/L. The average values of Ks and Vmax are found to be different for isolates 1-4, 5-6 and 7 for both chlorpyrifos and TCP. The Ks has ranged from 97 to 142.3 mg/L and Vmax from 7.4 to 12.1 mg/L/d for chlorpyrifos and 103.09 to 148.8 mg/L and 14.9 to 21.2 mg/L/d, respectively, for TCP. Results indicate the high affinity of bacterial community for degradation of both chlorpyrifos and TCP. The 16S rRNA gene sequence analysis has confirmed the genetic relatedness of isolates 1-4 with Pseudomonas, isolates 5 and 6 with Agrobacterium, and isolate 7 with Bacillus. Their degradation potential for chlorpyrifos and TCP has been found to be in the order: Pseudomonas > Agrobacterium > Bacillus. It has been also observed that all seven isolates are more efficient in degrading TCP compared to chlorpyrifos. © 2011 Elsevier Ltd. All rights reserved.
Kinetic and molecular analyses reveal isoprene degradation potential of Methylobacterium sp.
(Elsevier Ltd, 2017) Navnita Srivastva; P. Vishwakarma; Y. Bhardwaj; A. Singh; K. Manjunath; Suresh K. Dubey
Efforts were made to isolate and characterize bacteria capable of growing on methane and organic compounds, and to achieve the simultaneous degradation of more than one pollutant. Among the methanotrophs, species of Methylobacterium was able to catabolize a variety of hydrocarbons, including the branched-chain alkenes. Therefore, laboratory incubations experiments were carried out in batch mode to assess the potential of Methylobacterium sp. PV1 for degrading isoprene, the low-molecular-weight alkene, the most abundant non-methane volatile hydrocarbon present in the environment. Methylobacterium sp. PV1, isolated from paddy field soil, was characterized by pmoA and 16S rRNA gene sequencing and FAME analysis, and used for isoprene degradation. The kinetics of biodegradation is studied using the Michaelis-Menten model. The optimum degradation (80%) with maximum average relative degradation rate was observed at 150 ppm isoprene. The degradation products were also analyzed using FTIR. © 2017 Elsevier Ltd
Kinetics of bio-filtration of trichloroethylene by methanotrophs in presence of methanol
(2010) Awadhesh K. Shukla; R.S. Singh; S.N. Upadhyay; Suresh K. Dubey
The biodegradation of TCE was studied in a laboratory scale biofilter packed with wood charcoal and inoculated with mixed culture of methanotrophs isolated from local soil. The removal efficiency was found to be higher than 90% up to an inlet load of 5.1g/m3h. The maximum elimination capacity was 6.7g/m3h at an inlet loading rate of 11.3g/m3h. The reaction constants ECmax, Ks and Ki calculated from the experimental results are also presented. The biodegradation process is found to be inhibited at higher TCE concentration. The carbon dioxide production rate has been found to be a linear function of elimination capacity. The DNA finger printing techniques has indicated the presence of functionally active methanotrophic community including Methylocystis sp. in the biofilter. © 2010 Elsevier Ltd.
Methanogenic archaea in paddy agricultural fields
(Springer Singapore, 2018) Navnita Srivastva; Alpana Singh; Suresh K. Dubey
The analysis of methane-producing methanogenic archaea community structure will be helpful in enhancing the understanding of microbial ecology of methanogens and methane production potential of soil that is essential for formulation of strategies to mitigate methane emission from rice fields. Hence, the present study aimed to explore the methanogenic archaea community structure and their methane production potential in three different rice soil types (Alfisol, Inceptisol, and Vertisol). Phylogenetic analysis revealed the presence of Methanocellales, Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae, and Methanosaetaceae group common to all the soils with varying relative abundance. Methane production potential for soils was in order Alfisol < Inceptisol < Vertisol, following the first-order kinetics. Overall analyses suggested that there is homogeneity in soils for methanogenic diversity, although methane production potential varied, possibly due to the presence of methanogens in different proportions and difference in the soil characteristics. © Springer Nature Singapore Pte Ltd. 2018.
Nitrous oxide flux from komatsuna (Brassica rapa) vegetated soil: A comparison between biogas digested liquid and chemical fertilizer
(2013) Ankit Singla; Suresh K. Dubey; Hirokuni Iwasa; Kazuyuki Inubushi
Biogas production generates digested slurry as a by-product. It can be used as fertilizer especially after its conversion into digested liquid. A microcosm-based study was conducted in order to compare the effects of single application of digested liquid or chemical fertilizer on N2O flux and crop yield of komatsuna vegetable. Analysis revealed that digested liquid-treated soils released almost equal cumulative N2O (0.43 g N m-2) compared to chemical fertilizer (0.39 g N m-2). The uncropped soils treated with the digested liquid and chemical fertilizer released more N2O compared to corresponding cropped soils. The N2O emission factor and soil mineral N contents were similar for the digested liquid and chemical fertilizer-treated soils. Plant biomass in the first crop after digested liquid application was significantly higher (5.59 g plant-1) than that after applied chemical fertilizer (4.78 g plant-1); but there was no significant difference for the second crop. Nitrogen agronomic efficiency was improved by the digested liquid compared to chemical fertilizer. This study indicates that cumulative N2O flux was similar after application of the digested liquid and chemical fertilizer, while the overall yield from both croppings was increased in the digested liquid-treated soil compared to chemical fertilizer-treated soil. © 2013 Springer-Verlag Berlin Heidelberg.
Substrate inhibition during bio-filtration of TCE using diazotrophic bacterial community
(2011) Awadhesh K. Shukla; R.S. Singh; S.N. Upadhyay; Suresh K. Dubey
The kinetics of biodegradation of TCE in the biofilter packed with wood charcoal and inoculated with diazotrophic bacterial community had been investigated. Use of Michaelis-Menten type model showed that substrate inhibition was present in the system. The kinetic model proposed by Edwards (1970) was used to calculate kinetic parameters-maximum elimination capacity (ECmax), substrate constant (Ks), and inhibition constant (KI). The model fitted well with the experimental data and the ECmax was found to be in the range of 10.8-6.1g/m3h. The Ks values depended upon substrate concentration and ranged from 0.024 to 0.043g/m3 indicating the high affinity of diazotrophs for TCE. The KI values were low and nearly constant (0.011-0.015g/m3) indicating a moderate substrate inhibition. © 2010 Elsevier Ltd.
Temporal variation in methanogenic community structure and methane production potential of tropical rice ecosystem
(2012) Alpana Singh; Suresh K. Dubey
Temporal variations in diversity of methanogenic community and CH 4 production potential were analyzed in an Indian tropical rice ecosystem. Laboratory incubations showed that methane production varied from 20.86 to 134.11 μg CH 4 g -1 d.w.s. during the two consecutive years, 2009 and 2010. CH 4 production potential was high at the flowering stage of the rice crop followed by ripening, tillering, post-harvest and pre-plantation stage. Phylogenetic analysis of 16S rRNA genes of methanogenic community indicated that flowering and ripening stages comprised of Methanomicrobiaceae, Methanosarcinaceae, Methanosaetaceae and RC I methanogenic groups, while only the members of Methanomicrobiaceae and RC I were present in the remaining stages. Further, the dominance of RC I was observed in all stages. This study demonstrates that flowering and ripening stages of rice crop offer relatively favorable ecological niche for methanogenic community. The overall analyses suggest that the temporal change in diversity of methanogens regulates CH 4 production potential in rice field soils. © 2012 Elsevier Ltd.
Towards DNA-based technological advancement in Listeria monocytogenes detection
(Indian Academy of Sciences, 2018) Dharmendra K. Soni; Suresh K. Dubey
[No abstract available]