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The soil microbial communities and factors therein play important role in maintaining nutrient turnover in forest ecosystem. A biolog ecoplate based approach was applied to a dry deciduous tropical forest to investigate metabolic profile of soil microbial communities in relation to topography and seasonality. Significant (p < 0.05) effect of seasonality on metabolic profile was observed. The average well color development (AWCD), rate of change (r) and metabolic diversity indices (functional diversity indices) were recorded maximum in rainy season followed by winter and summer indicating maximum microbial activity in rainy season. Principal component analysis revealed seasonality to be the major determinant of soil metabolic profile, a key aspect of ecosystem functioning.

The whole genome sequencing of a novel isoprene degrading strain of

Forest soil contributes to global methane (CH4) cycle as the natural sink for atmospheric CH4 by methane-oxidizing bacteria (MOB). In this study, high-throughput sequencing of pmoA gene amplicons based approach was used to investigate temporal variations in molecular diversity of MOB in soil of tropical dry forest. Quantitative PCR (qPCR) analysis revealed pmoA and 16S rRNA gene copy numbers (copies g−1 dws) ranging from 2.23 × 106 to 14.62 × 106 and from 0.92 × 109 to 14.99 × 109, respectively, in the year 2016. In 2017, the respective values varied from 1.96 × 106 to 13.62 × 106 and from 2.55 × 109 to 20.15 × 109, respectively. The sequence analysis revealed the existence of both type I and type II methanotrophs in soils. The average observed OTUs were about 800/sample, and Shannon diversity index ranged between 4.24 and 6.22 being highest in winter season. The rice paddy clusters (RPCs), Methylocystis, Methlylocystis-Methylosinus and JR2 and JR3, dominated the methanotrophic community with relative abundance of 32.7–50.2, 15.4–34.2, 0.45–15.8, 0.0–17.8 and 1.6–19.2%, respectively. Relatively, higher CH4 oxidation potential (MOP) (ng CH4 g−1 h−1 dws) was observed in winter (14.12) compared with rainy (2.10) and summer (3.72) coinciding with high methanotrophic diversity and abundance. Overall, the study suggests that tropical dry deciduous forest soils favour considerable range of methanotrophic diversity and abundance that positively correlates with MOP of soils across season.

Nutrient procurement specifically from nutrient-limiting environment is essential for pathogenic bacteria to survive and/or persist within the host. Long-term survival or persistent infection is one of the main reasons for the overuse of antibiotics, and contributes to the development and spread of antibiotic resistance. Mycobacterium tuberculosis is known for long-term survival within the host, and develops multidrug resistance. Before and during infection, the pathogen encounters various harsh environmental conditions. To cope up with such nutrient-limiting conditions, it is crucial to uptake essential nutrients such as ions, sugars, amino acids, peptides, and metals, necessary for numerous vital biological activities. Among the various types of transporters, ATP-binding cassette (ABC) importers are essentially unique to bacteria, accessible as drug targets without penetrating the cytoplasmic membrane, and offer an ATP-dependent gateway into the cell by mimicking substrates of the importer and designing inhibitors against substrate-binding proteins, ABC importers endeavour for the development of successful drug candidates and antibiotics. Alternatively, the production of antibodies against substrate-binding proteins could lead to vaccine development. In this review, we will emphasize the role of M. tuberculosis ABC importers for survival and virulence within the host. Furthermore, we will elucidate their unique characteristics to discover emerging therapies to combat tuberculosis.

Imidacloprid (C

The bacterial degradation of isoprene is important for maintaining its atmospheric concentration in unpolluted environment. It may be possible to use natural isoprene degrading bacteria in engineered systems to eliminate or limit isoprene emissions from various sources. Biodegradation of isoprene by Arthrobacter sp. strain BHU FT2 was investigated. The genome was found to contain 4151545 bp long chromosome having 3747 coding genes, and coded potential isoprene degrading enzymes. The molecular docking of monooxygenases with isoprene displayed a higher binding energy (−4.59 kcal/mol) for WP_015938387.1 monooxygenase. Analysis of the identified monooxygenases with the known isoprene monooxygenases revealed 67% sequence identity of WP_015938387.1 (Locus tag JHV56_10705) monooxygenase of the considered strain with the OPX16961.1 monooxygenase of Gordonia sp. i37 isoprene degrading starin. These results provided a strong evidence for the high isoprene degrading potential of the Arthrobacter sp. BHU FT2 which could be efficiently exploited for isoprene degradation in large scale bio-filtration units.

The role and activity of bacterial endophytes remains largely unexplored and detail insight into Indian rice agro ecosystem is still little explored. In this study, we examined the diversity of endophytic bacteria in aerobic rice (variety ARB6) under aerobic and flooded field conditions. Based on 16S rRNA gene RFLP cloning sequencing, 900 clones with 144 representatives (72 aerobic and 72 flooded) revealed majority of clones affiliated to Gammaproteobacteria (64.58%), Betaproteobacteria (9.72%), Alphaproteobacteria (17.36), Firmicutes (6.26%) and Bacteroidetes (2.08). The study suggests that the aerobic rice variety harbours plant growth promoting (PGP) genera (viz. Pantoea, Enterobacter, Paenibacillus, etc). Investigations on aerobic rice under aerobic and flooded conditions revealed high richness and diversity of endophytic bacteria under aerobic condition inferring that the endophytic bacteria are beneficial for rice growth and productivity, and hence, would be helpful in designing better strategies for rice cultivation under drought or water scarce conditions.

Cellulose, the most abundant polysaccharide in nature, is a rich source of renewable energy and sustains soil nutrients. Among the microorganisms known to degrade cellulose, bacteria are less studied compared to fungi. In the present work, we have investigated the culturable bacteria actively involved in cellulose degradation in forest and crop field soils. Based on clear zone formation and enzyme activity assay, we identified 7 bacterial strains positive for cellulose degradation. Of these, two most efficient strains (Bacillus cereus strains BHU1 and BHU2) were selected for whole genome sequencing, annotation, and information regarding GC content, number of genes, total subsystems, starch, and cellulose degradation pathways. Average nucleotide identity (ANI) showed more than 90% similarity between both the strains (BHU1 and BHU2) and with B. cereus ATCC 14579. Both the strains have genes and enzyme families like endoglucanase and β-glucosidase as evident from whole genome sequence. Cellulase containing gene families (GH5, GH8, GH1), and many other carbohydrate-degrading enzymes, were present in both the bacterial strains. Taken together, the results suggest that the strains were efficient in cellulose degradation, and can be used for energy generation and production of value-added product.

The microbial community mediated biogeochemical cycles play important role in global C-cycle and display a sensitive response to environmental changes. Limited information is available on microbial composition and functional diversity controlling biogeochemical cycles in the riverine environment. The Ganga River water and sediment samples were studied for environmental gene tags with reference to carbohydrate metabolism, photoheterotrophy and chemolithotrophy using high throughput shotgun metagenomic sequencing and functional annotation. The diversity of environmental gene tags specific microbial community was annotated against reference sequence database using Kaiju taxonomic classifier. The metagenomic analyses revealed that the river harbored a broad range of carbohydrate and energy metabolism genes. The in-depth investigation of metagenomic data revealed that the enzymes associated with reverse TCA cycle, Calvin-Benson cycle enzyme RuBisCO, starch and sucrose metabolism genes were highly abundant. The enzymes associated with sulfur metabolism such as EC:2.7.7.4 (sulfate to ammonium per sulfate), EC:1.8.1.2, EC:1.8.7.1 (sulfite to H2S) were prevalent in both the class of samples. The principal component analysis of the functional profiles revealed that the water and sediment samples were clustered distinctly suggesting that both the sites had variable abundance of functional genes and associated microbiota. The taxonomic classification showed abundance of Proteobacteria, Actinobacteria and Bacteroidetes phyla. Also, the metagenomic study showed the presence of purple sulfur bacteria viz. Thiodictyon, Nitrosococcus and purple non-sulfur bacteria viz. Bradyrhozobium and Rhodobacter. The study demonstrates that the Ganga River microbiome has prevalence of functional genes involved in carbohydrate anabolism and catabolism, and CO2 fixation with great prospects in cellulose and sulfide degrading enzyme production and characterization.

Isoprene, the highly reactive volatile organic compound, is used as monomer for the synthesis of several useful polymers. Its extensive production and usage leads to contamination of air. Once released, it alters the atmospheric chemistry by reacting with hydroxyl radicals (OH) and nitrogen oxides (NOx) to generate tropospheric ozone. Its prolonged exposure causes deleterious effects in human and plants. Therefore, its removal from the contaminated environment through biodegradation, provides a promising remedial solution. In the present study, isoprene utilizing bacteria namely, Pseudomonas sp., Arthrobacter sp., Bacillus sp. Sphingobacterium sp., Sphingobium sp., and Pantoea sp. were isolated and characterized from leaf surface of Madhuca latifolia and Tectona grandis, and also from soils under these plants. Their isoprene degrading capability and kinetics were assessed in batch mode. The isoprene degradation study indicated Pseudomonas sp. to be the most efficient isoprene degrader.

The large scale usage of antibiotics and trace elements leads to their progressive release in the environment, and ultimately the spread of antibiotic resistance genes (ARGs) and metal ion resistance genes (MRGs) in bacteria. A high-throughput metagenomic sequencing of the microbial community in water and sediments in the river Ganges harboring resistance genes was performed. The results revealed that the river harbors a broad spectrum of resistance genes with high abundance in sediments. The highly dominant ARGs type was beta-lactam, multidrug/efflux and elfamycin. The ARGs such as (tuf, parY, ileS, mfd) were highly abundant in water and sediments. The MRGs subtype acn was the most abundant metal resistance gene in water and sediments. Majority of ARGs types showed significant (p ≤ 0.05) positive correlation with the MRGs types in the river environment suggesting their distribution and transfer to be possibly linked. Taxonomic classification revealed that Proteobacteria and Actinobacteria were the two most abundant phyla in water and sediments. Arcobacter, Terrimicrobium, Acidibacter and Pseudomonas were the most abundant genera. This study suggests that antibiotics and metals are the driving force for the emergence of resistance genes, and their subsequent propagation and accumulation in the environmental bacteria. The present metagenomic investigation highlights significance of such study, and attracts attention for the mitigation of pollutants associated with the propagation of ARGs and MRGs in the river environment.

Recent advances in microbial ecology have incited research on rhizosphere microflora under the effect of improved crop variety. Effects have often been assessed with the use of culture-dependent and culture-independent methods, but these usually delude the conclusions of evaluation due to improper hypothesis and redundant use of DNA fingerprinting methods. In view of our incomplete knowledge of the microbial communities and processes in plant-soil systems, recent technological and conceptual improvements do offer a way forward. We propose a framework that encompasses both, a sensible selection of process and general parameters for assessing the impact of improved crop variety on rhizosphere microorganisms.

The enzyme β-glucosidase mediates the rate limiting step of conversion of cellobiose to glucose and thus plays a vital role in the process of cellulose degradation. The present study deals with analysis of the effective novel strain of Paenibacillus lautus BHU3 for identifying high-efficiency thermostable, glucose tolerant β-glucosidases. Seven counterparts with elevated Tm values ranging from 64.6 to 75.8 °C with high thermo-stability, were revealed through this analysis. The blind molecular docking of the model enzymes structures with cellobiose and pNPG gave high negative interaction energies ranging from −11.33 to −13.29 and −6.43 to −9.054 (kcal mol−1), respectively. The enzyme WP_096774744.1 effectively formed 5 hydrogen bonds with the highest interaction energy (−13.29 kcal mol−1) with cellobiose at its catalytic site. Molecular dynamics simulation analysis performed for the WP_096774744.1-pNPG complex predicted Glu5, Arg7, Lue68, Gly69 and Phe325 as the major contributing residues for accomplishing hydrolysis of β-1-4-linkage. Further, the molecular docking of WP_096774744.1 enzyme with glucose revealed a distinct glucose-binding site distant from the substrate-binding site, thus confirming the deficient competitive inhibition by glucose. Hence, WP_096774744.1 β-glucosidase appears to be an efficient enzyme with enhanced activity to biodegrade the cellulosic materials and highly relevant for waste management and various industrial applications.

The early detection of Listeria monocytogenes (L. monocytogenes) and understanding the disease burden is of paramount interest. The failure to detect pathogenic bacteria in the food industry may have terrible consequences, and poses deleterious effects on human health. Therefore, integration of methods to detect and trace the route of pathogens along the entire food supply network might facilitate elucidation of the main contamination sources. Recent research interest has been oriented towards the development of rapid and affordable pathogen detection tools/techniques. An innovative and new approach like biosensors has been quite promising in revealing the foodborne pathogens. In spite of the existing knowledge, advanced research is still needed to substantiate the expeditious nature and sensitivity of biosensors for rapid and in situ analysis of foodborne pathogens. This review summarizes recent developments in optical, piezoelectric, cell-based, and electrochemical biosensors for Listeria sp. detection in clinical diagnostics, food analysis, and environmental monitoring, and also lists their drawbacks and advantages.

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 150ppm isoprene. The degradation products were also analyzed using FTIR.

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 .

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.

Use of abundantly available virgin and waste biomasses as feed-stock for producing gaseous (bio-gas) and liquid fuels (bio-methanol, bio-ethanol and bio-butanol) is being considered as the sustainable and viable alternative to fossil fuels (coal, natural gas and petro-fuels like gasoline and diesel). Out of these bio-methanol is being considered as an attractive liquid fuel as well as feed-stock for the synthesis of enumerable valuable organic compounds currently being produced from coal, natural gas, and petroleum feed stocks. This review presents an overview of various thermo-chemical and biochemical routes that are being explored for the sustainable production of bio-methanol from waste biomass. The advantages and limitations of both the routes are discussed to provide a brief account of their basic principles and also indicate the issues to be addressed through further technological up-gradations for satiating the future energy demand. It focuses specially on the biochemical conversion route which utilizes microbes as biocatalysts for methanol production under normal temperature and pressure conditions. Available information on various process parameters affecting microbial production of bio-methanol have been critically reviewed. To make the process cost effective certain improvements like utilization of raw biogas instead of natural gas for methanol production and development of methane-utilizing microbes through genetic engineering as the subject for future research are discussed. The gap existing in the current knowledge that needs to be bridged to facilitate development of technology for large scale production of bio-methanol at an economical rate to meet the future demands are also pointed out.

In natural ecosystems such as forests topographical gradients, species composition variability and seasonality, are the potential drivers of methane (CH 4 ) metabolism, and thus, of the population size and activities of methane oxidizing bacteria (MOB). To test the hypothesis that topography, tree species and seasonal variability influence MOB population and soil methane oxidation potential (MOP), we conducted two consecutive years of study selecting three sites in a dry deciduous tropical forest in Chandauli district of eastern Uttar Pradesh, India. The qPCR results showed a large variation in MOB population size (copies g −1 dws), ranging from 1.0 × 10 6 to 2.1 × 10 7 and 9.0 × 10 5 to 2.2 × 10 7 during 2016 and 2017 respectively. The distribution of MOB population revealed the trend: hilltop > middle > hillbase with its maxima in the winter and minima in the rainy season. Laboratory incubation study revealed a similar trend in soil MOP (ng CH 4 g −1 h −1 dws), it varied from 10.6 to 20.6 and 10.5 to 20.7 during 2016 and 2017 respectively. The outer canopy soils showed lower MOB population and MOP compared to under canopy soils of tree species Butea monosperma, Madhuca indica and Tectona grandis during both years of study. The topography, season and tree species significantly influenced the MOB population size and MOP. Soil MOP showed a highly significant correlation (r = 0.89; p < 0.01) with MOB population, and a negative correlation was found with soil moisture (r = 0.76; p < 0.01). The results indicate that the dry deciduous tropical forest soils are potential sinks of atmospheric CH 4 wherein, the MOB population characteristically responds to topographical changes, tree species and seasonal shifts driving collectively the overall MOP of forest soils.

The aim of this work was to study cellulose degradation and whole genome sequence of Paenibacillus lautus BHU3 isolate. The 16S rRNA gene sequence analysis revealed genetic relatedness (99%) of Iso 7 with Paenibacillus lautus, Iso 8 with Paenibacillus lactis, and Iso 9 with Bacillus amyloliquefaciens. Clear zone formation followed by CMCase and FPase assays exhibited cellulolytic potential in the order: P. lautus > P. lactis > B. amyloliquefaciens. The most potent isolate, Paenibacillus lautus strain BHU3 was subjected to whole genome analysis with reference to the genomic basis of cellulose degradation. Results showed that P. lautus strain BHU3 contains 6234 protein coding genes of which, 316 were associated with the carbohydrate metabolism. Further, genomic CAZymes analysis indicated that the P. lautus strain BHU3 comprising a range of glycoside hydrolase (GH) family genes (143), may play the vital role(s) in enhancing the cellulolytic attributes, and could be the useful tool for lignocellulosic biomass degradation and waste management.

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.

Isoprene, the ubiquitous, highly emitted non-methane volatile hydrocarbon, affects atmospheric chemistry and human health, and this makes its removal from the contaminated environment imperative. Physicochemical degradation of isoprene is inefficient and generates secondary pollutants. Therefore, biodegradation can be considered as the safer approach for its efficient abatement. This review summarizes efforts in this regard that led to tracking the diverse groups of isoprene degrading bacteria such as Methanotrophs, Xanthobacter, Nocardia, Alcaligenes, Rhodococcus, Actinobacteria, Alphaproteobacteria, Bacteriodetes, Pseudomonas, and Alcanivorax. Biodegradation of isoprene by such bacteria in batch and continuous modes has been elaborated. The products, pathways and the key enzymes associated with isoprene biodegradation have also been presented.

Bacterial isolates from contaminated soil of a waste rubber dumping site were isolated and characterized using biochemical and molecular approaches. Isoprene degradation kinetics in batch mode (isoprene concentration: 100-1000 ppm) revealed the degradation efficiency of isolates as: Pseudomonas sp. (83%)>Alcaligenes sp. (70%)>Klebsiella sp. (68.5%). The most efficient isolate Pseudomonas sp. was finally inoculated in a specifically designed bioreactor system comprising a bioscrubber and a biofilter packed with polyurethane foam connected in series. The bioscrubber and biofilter units when operated in a series showed more than 90% removal efficiency up to the inlet loading rate (IL) of 371.1g/m(3)/h. Maximum elimination capacity (EC) of biofilter was found to be an order of magnitude greater than that for bioscrubber. Oxidative cleavage of the double bond of isoprene has been revealed through IR spectra of the leachate.

In this article, we describe the development of a simple and cost-effective genosensor probe based on a glassy carbon electrode modified with platinum nanomaterials dispersed in a chitosan matrix. Further, this probe was explored for the label-free detection of Listeria monocytogenes obtained from milk samples. DNA-based interfacial interaction between target DNA and platinum nanomaterials (PtNPs) immobilized with 24 mer ssDNA was investigated using impedance spectroscopy. As-prepared nanomaterials (for electrode fabrication) were characterized by UV-vis, FT-IR, TEM and cyclic voltammetry before fabricating the impedimetric sensor platform. The interfacial interaction between PtNPs and DNA results in the increase of charge transfer resistance (RCT) on hybridization with consecutive increasing concentrations of target DNA. This user-friendly and simple platform was used for the detection of target DNA and shows excellent response and specificity (even for 1-bp mismatch of target DNA). Also, this sensing platform was utilized for the detection of Listeria monocytogenes in real samples (milk beverage) and had a wide range of detection from 1 × 10−12 M to 1 × 10−4 M. In general, our simple and user-friendly sensor probe shows potential for detection of Listeria monocytogenes in food samples with high specificity.

A microcosm-based study was conducted to evaluate the effects of varying concentrations of biogas digested slurry-based biochar on CH4 flux, associated methanogenic archaeal community, soil chemical and microbial properties, and plant biomass in paddy soil. Our results showed that biochar application significantly increased the CH4 flux compared to untreated soil, and it increased with the increase in biochar concentration. The NH4+-N concentration also increased significantly in biochar treated soils due to more reducible conditions in the soil which prevented NH4+-N conversion to NO3–-N. The application of biochar significantly increased soluble organic carbon, microbial biomass carbon and soluble total nitrogen content of the soils without affecting microbial biomass nitrogen contents. Paddy plant biomass such as shoot weight, panicle numbers and weight of panicles were also higher in biochar treated soils. Denaturing gradient gel electrophoresis revealed all methanogenic groups with the dominance of Methanosaetaceae and Methanocellales groups, whereas no differences were found in methanogenic archaeal diversity among biochar treated and non-treated soils. Thus, the increase in CH4 flux with the application of varying biochar concentration is possibly due to the variation in the soil variables and plant biomass without affecting methanogenic archaeal diversity.

Methane leads to global warming owing to its warming potential higher than carbon dioxide (CO2). Rice fields represent the major source of methane (CH4) emission as the recent estimates range from 34 to 112 Tg CH4 per year. Biogenic methane is produced by anaerobic methanogenic archaea. Advances in high-throughput sequencing technologies and isolation methodologies enabled investigators to decipher methanogens to be unexpectedly diverse in phylogeny and ecology. Exploring the link between biogeochemical methane cycling and methanogen community dynamics can, therefore, provide a more effective mechanistic understanding of CH4 emission from rice fields. In this review, we summarize the current knowledge on the diversity and activity of methanogens, factors controlling their ecology, possible interactions between rice plants and methanogens, and their potential involvement in the source relationship of greenhouse gas emissions from rice fields.

The main objective of this study was to evaluate the performance of wood charcoal as biofilter media under transient and high loading condition. Biofiltration of xylene was investigated for 150 days in a laboratory scale unit packed with wood charcoal and inoculated with mixed microbial culture at the xylene loading rates ranged from 12 to 553 g m−3 h−1. The kinetic analysis of the xylene revealed absence of substrate inhibition and possibility of achieving higher elimination under optimum condition. The pH, temperature, pressure drop and CO2 production rate were regularly monitored during the experiments. Throughout experimental period, the removal efficiency (RE) was found to be in the range of 65–98.7% and the maximum elimination capacity (EC) was 405.7 g m−3 h−1. Molecular characterization results show Bacillus sp. as dominating microbial group in the biofilm.

Aerobic biodegradation of chlorpyrifos (CP) by Aspergillus sp. was investigated in batch and continuous packed bed bioreactors. The optimal process parameters for achieving the maximum removal efficiency (RE), determined using a batch bioreactor packed with polyurethane foam pieces, were inoculum level: 2.5 mg (wet weight) mL(-1), pH 7.0, temperature 28 °C, DO 5.8 mg L(-1), and CP concentration 300 mg L(-1). The continuous packed bed bioreactor was operated at flow rates ranging from 10 to 40 mL h(-1) while keeping other parameters at their optimal level. Steady-state CP removal efficiencies greater than 85 % were obtained up to the inlet loading of 180 mg L(-1) d(-1). The continuous bioreactor behaved as a plug flow unit and was able to stabilize quickly after perturbation in the inlet loading.

The discrimination between Listeria monocytogenes and Listeria species has been detected. The 16S rRNA and hlyA were PCR amplified with set of oligonucleotide primers with flank 1,500 and 456 bp fragments, respectively. Based on the differences in 16S rRNA and hlyA genes, a total 80 isolates from different environmental, food and clinical samples confirmed it to be L. monocytogenes. The 16S rRNA sequence similarity suggested that the isolates were similar to the previously reported ones from different habitats by others. The phylogenetic interrelationships of the genus Listeria were investigated by sequencing of 16S rRNA and hlyA gene. The 16S rRNA sequence indicated that genus Listeria is comprised of following closely related but distinct lines of descent, one is the L. monocytogenes species group (including L. innocua, L. ivanovii, L. seeligeri and L. welshimeri) and other, the species L. grayi, L. rocourtiae and L. fleischmannii. The phylogenetic tree based on hlyA gene sequence clearly differentiates between the L. monocytogenes, L. ivanovii and L. seeligeri. In the present study, we identified 80 isolates of L. monocytogenes originating from different clinical, food and environmental samples based on 16S rRNA and hlyA gene sequence similarity.

A microcosm-based study was conducted to evaluate the effects of application of biogas digested liquid or chemical fertilizer on CH4 flux, associated methanogenic archaeal community, soil chemical and microbial properties, and aboveground plant biomass in paddy soil. Our results showed that digested liquid application significantly decreased the seasonal and cumulative CH4 flux compared to chemical fertilizer treatment. The application of digested liquid treatment significantly decreased NH4+-N and soluble total nitrogen content without affecting NO3−-N and microbial biomass nitrogen. The soluble organic carbon and microbial biomass carbon contents were nearly similar for digested liquid and chemical fertilizer treatments. Paddy plant biomass (shoot weight, panicle numbers and weight of panicles) were found to be lower in the digested liquid treated containers but it did not affect the cumulative CH4 flux g−1 yield. Denaturing Gradient Gel Electrophoresis gave similar banding patterns indicating no differences in the methanogenic archaeal diversity among the control, digested liquid and chemical fertilizer treated containers. Thus, the observed decrease in CH4 flux with the application of digested liquid is possibly due to the variation in the soil variables and aboveground plant biomass without affecting the methanogenic archaeal diversity.

Aims: The objective of this study was to investigate the influence of Cry1Ac gene expressing brinjal (VRBT-8) on the rhizospheric fungal community structure. Methods and Results: qPCR indicated variations in the fungal ITS rRNA copy numbers of non-Bt (1� 43–4� 43) 9 10 9 g � 1 dws and Bt (1� 43–3� 32) 9 10 9 g � 1 dws plots. Phylogenetic analysis of ITS rRNA clones indicated fungal-related group majority of being Ascomycota compared to that of Basidiomycota and Zygomycota in non-Bt- and Bt-planted soils. Sordariomycetes was the dominant class detected in all the stages. Conclusions: Despite the variations in the population size and the distribution pattern observed across the non-Bt and Bt brinjal, plant-growth-dependent variability was more prominent compared with genetic modification. Therefore, this study concludes that genetic modification of brinjal crop has minor effect on the fungal community. Significance and Impact of the Study: Brinjal, the important solanaceous crop, is also prone to attack by many insect pests, especially by Leucinoides orbonalis, resulting in significant losses in the crop yield. However, the reports on the effect of transgenic crops and the associated microbial community are inconsistent. The present communication takes into account for the first time the possible interactions between Bt brinjal and the associated fungal community; the latter playing a significant role in maintaining soil fertility. As this study is limited to the structural diversity of fungal community, additional information regarding the functional diversity of the group seems imperative before recommending the commercialization of GM crops.

Soil characteristics regulate various belowground microbial processes including methanogenesis and, consequently, affect the structure and function of methanogenic archaeal communities due to change in soil type which in turn influences the CH4 production potential of soils. Thus, five different soil orders (Alfisol, Entisol, Inceptisol, Podzol and Vertisol) were studied to assess their CH4 production potential and also the methanogenic archaeal community structure in dryland irrigated Indian paddy soils. Soil incubation experiments revealed CH4 production to range from 178.4 to 431.2 μg CH4 g-1 dws in all soil orders as: Vertisol

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.

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.

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 K(s) and V(max) were different for different isolates. The K(s) ranged from 66.66 to 169.5mg/L and V(max) 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.

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, E C m a x ; substrate constant, K s and E C m a x / K s for Michaelis-Menten model were evaluated. The lower K s for the WC packed bioreactor indicated that E C m a x achieved, was faster compared to others, while higher E C m a x and E C m a x / K s 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.