Reconstruction of a Nearly Complete Pseudomonas Draft Genome Sequence from a Coalbed Methane-Produced Water Metagenome.
Ontology highlight
ABSTRACT:
SUBMITTER: Ross DE
PROVIDER: S-EPMC5054310 | biostudies-literature | 2016 Oct
REPOSITORIES: biostudies-literature
Publications
Reconstruction of a Nearly Complete Pseudomonas Draft Genome Sequence from a Coalbed Methane-Produced Water Metagenome.
Ross Daniel E DE Gulliver Djuna D
Genome announcements 20161006 5
The draft genome sequence of Pseudomonas stutzeri strain K35 was separated from a metagenome derived from a produced water microbial community of a coalbed methane well. The genome encodes a complete nitrogen fixation pathway and the upper and lower naphthalene degradation pathways. ...[more]
Similar Datasets
Project description:Microorganisms play a crucial role in mediating global biogeochemical cycles in the marine environment. By reconstructing the genomes of environmental organisms through metagenomics, researchers are able to study the metabolic potential of Bacteria and Archaea that are resistant to isolation in the laboratory. Utilizing the large metagenomic dataset generated from 234 samples collected during the Tara Oceans circumnavigation expedition, we were able to assemble 102 billion paired-end reads into 562 million contigs, which in turn were co-assembled and consolidated in to 7.2 million contigs ?2?kb in length. Approximately 1 million of these contigs were binned to reconstruct draft genomes. In total, 2,631 draft genomes with an estimated completion of ?50% were generated (1,491 draft genomes >70% complete; 603 genomes >90% complete). A majority of the draft genomes were manually assigned phylogeny based on sets of concatenated phylogenetic marker genes and/or 16S rRNA gene sequences. The draft genomes are now publically available for the research community at-large.
| S-EPMC5769542 | biostudies-literature
Project description:Hydraulic fracturing can improve the permeability of coalbed methane (CBM) reservoirs effectively, which is of great significance to the commercial production of CBM. However, the efficiency of hydraulic fracturing is affected by multiple factors. The mechanism of fracture initiation, morphology and propagation in CBM reservoirs is not clear and need to be further explored. Hydraulic fracturing experiment is an accurate tool to explore these mechanisms. The quantity of experimental coal rock is large and processing method is complex, so specimen made of similar materials was applied to replace coal rock. The true triaxial hydraulic fracturing experimental apparatus, 3D scanning device for coal rock section were applied to carry out hydraulic fracturing experiment. The results show that the initiation pressure is inversely proportional to the horizontal stress difference (??) and positively related to fracturing fluid injection rate. When vertical stress (?v) is constant, the initiation pressure and fracture width decrease with the increasing of ??. Natural fractures can be connected by main fracture when propagates perpendicular to the direction of minimum horizontal stress (?h), then secondary fractures and fracture network form in CBM reservoirs. When two stresses of crustal stress are close and far different from the third one, the fracture morphology and propagation become complex. Influenced by perforations and filtration of fracturing fluid in specimen, fracturing fluid flows to downward easily after comparing horizontal well fracturing with vertical well fracturing. Fracture width increases with the decreasing of elastic modulus, the intensity of fracture is positively related with the elastic modulus of coal rock. The research results can provide theoretical basis and technical support for the efficient development of CBM.
| S-EPMC5886525 | biostudies-literature
Project description:We evaluated water quality characteristics in the northern Raton Basin of Colorado and documented the response of the Poison Canyon aquifer system several years after upward migration of methane gas occurred from the deeper Vermejo Formation coalbed production zone. Results show persistent secondary water quality impacts related to the biodegradation of methane. We identify four distinct characteristics of groundwater-methane attenuation in the Poison Canyon aquifer: (i) consumption of methane and sulfate and production of sulfide and bicarbonate, (ii) methane loss coupled to production of higher molecular weight (C2+) gaseous hydrocarbons, (iii) patterns of 13C enrichment and depletion in methane and dissolved inorganic carbon, and (iv) a systematic shift in sulfur and oxygen isotope ratios of sulfate, indicative of microbial sulfate reduction. We also show that the biogeochemical response of the aquifer system has not mobilized naturally occurring trace metals, including arsenic, chromium, cobalt, nickel, and lead, likely due to the microbial production of hydrogen sulfide which favors stabilization of metals in aquifer solids.
| S-EPMC7392614 | biostudies-literature
Project description:Phosphoesterases are involved in the degradation of organophosphorus compounds. Although phosphomonoesterases and phosphotriesterases have been studied in detail, studies on phosphodiesterases are rather limited. In our search to find novel phosphodiesterases using metagenomic approach, we cloned a gene encoding a putative phosphodiesterase (PdeM) from the metagenome of the formation water collected from an Indian coal bed. Bioinformatic analysis showed that PdeM sequence possessed the characteristic signature motifs of the class III phosphodiesterases and phylogenetic study of PdeM enabled us to identify three distinct subclasses (A, B, and C) within class III phosphodiesterases, PdeM clustering in new subclass IIIB. Bioinformatic, biochemical and biophysical characterization of PdeM further revealed some of the characteristic features of the phosphodiesterases belonging to newly described subclass IIIB. PdeM is a monomer of 29.3 kDa, which exhibits optimum activity at 25°C and pH 8.5, but low affinity for bis(pNPP) as well as pNPPP. The recombinant PdeM possessed phosphodiesterase, phosphonate-ester hydrolase and nuclease activity. It lacked phosphomonoesterase, phosphotriesterase, and RNAse activities. Overexpression of PdeM in E.coli neither affected catabolite respression nor did the recombinant protein hydrolyzed cAMP in vitro, indicating its inability to hydrolyze cAMP. Although Mn2+ was required for the activity of PdeM, but addition of metals (Mn2+ or Fe3+) did not induce oligomerization. Further increase in concentration of Mn2+ upto 3 mM, increased ?-helical content as well as the phosphodiesterase activity. Structural comparison of PdeM with its homologs showed that it lacked critical residues required for dimerization, cAMP hydrolysis, and for the high affinity binding of bis(pNPP). PdeM, thus, is a novel representative of new subclass of class III phosphodiesterases.
| S-EPMC4320098 | biostudies-literature
Project description:The influence of the depressurization rate on coalbed methane desorption and percolation was studied using physical experiment and numerical simulation. First, low-field nuclear magnetic resonance technology provided a new approach to conduct desorption experiments with different depressurization schemes and obtain the compressibility (C f) of coal samples. Then, the productivity calculation of different depressurization schemes was carried out via numerical simulation. The results showed that the first-slow-then-fast (FSTF) depressurization scheme had the highest desorption efficiency (94%), followed by one-stop desorption (85%), first-fast-then-slow desorption (79%), and uniform depressurization desorption (61%). T 2 cutoff values and the corresponding compressibility were obtained by the saturation-centrifugation method and spectral morphology method, and a high-precision permeability expression for dynamic evaluation of numerical simulation was established by the historical production data fitting approach. Through numerical simulation, high production efficiency can be achieved using depressurization rates of medium (15 kPa/d) and FSTF schemes (8 & 50 kPa/d), and depressurization funnel expansion in the single-phase water flow stage plays a decisive role in stable and high-yield production in the later stage. Thus, the FSTF pressure reduction strategy could be advocated to promote gas production. Slow depressurization should be applied in ineffective desorption and the slow desorption stage for saturated coal seam or single-phase flow stage for undersaturated coal seam, given the higher single-phase water permeability. During the rapid and sensitive desorption stage, rapid depressurization is recommended because of large desorption capacity and low water phase permeability. This paper provides a possibility for the optimization of coalbed methane field production management.
| S-EPMC7482415 | biostudies-literature
Project description:Pseudomonas aeruginosa is one of the most common model bacterial species, and genomes of hundreds of strains of this species have been sequenced to date. However, currently there is only one available genome of an oceanic isolate. Here, we report two complete and six draft genome sequences of P. aeruginosa isolates from the open ocean.
| S-EPMC5668555 | biostudies-literature
Project description:The permeability of the coal body is the key parameter restricting the efficient extraction of coalbed methane, and scholars have analysed it from two angles of the change of stress state and porosity of the coal body. However, there is still a lack of study on the mechanism of gas migration and movement in soft coalbed methane reservoir under the coupling between the true triaxial stress field (maximum principal stress ? 1 > intermediate principal stress ? 2 > minimum principal stress ? 3) and the gas pressure field. In this paper, the coal gas adsorption and seepage experiments are conducted through the self-developed true triaxial 'gas-solid' coupled coal mass seepage system with gas as the adsorption and seepage medium and coal briquette taking the place of soft coalbed methane reservoirs. Furthermore, the coal gas adsorption deformation model and the permeability evolution model taking gas adsorption into account are developed. Through analysis of both experimental and theoretic results, the main conclusions are drawn as follows: (i) With the increase in gas pressure, the adsorption deformation variation of coal mass is divided into a slow growth zone, a stable growth zone and a rapid growth zone. (ii) The gas adsorption deformation model developed can predict the variation trend of coal mass adsorption volumetric strains for different types of soft coalbeds, and the fitting variance of experimental and theoretical volumetric strains is above 98%. (iii) With the increase in maximum principal stress difference, the coal permeability variation curve shows two obvious turning points, which can be divided into a slow reduction zone, a rapid reduction zone and a steady reduction zone. (iv) The permeability model of coal mass considering the gas adsorption effect can reflect the variation characteristics of permeability in the rapid reduction zone, and the overall fitting variance of experimental and theoretical permeabilities is above 91%. The above results could provide a reliable experimental and theoretical basis for improving coalbed methane extraction rates.
| S-EPMC6837214 | biostudies-literature
Project description:Despite the significance of biogenic methane generation in coal beds, there has never been a systematic long-term evaluation of the ecological response to biostimulation for enhanced methanogenesis in situ. Biostimulation tests in a gas-free coal seam were analysed over 1.5 years encompassing methane production, cell abundance, planktonic and surface associated community composition and chemical parameters of the coal formation water. Evidence is presented that sulfate reducing bacteria are energy limited whilst methanogenic archaea are nutrient limited. Methane production was highest in a nutrient amended well after an oxic preincubation phase to enhance coal biofragmentation (calcium peroxide amendment). Compound-specific isotope analyses indicated the predominance of acetoclastic methanogenesis. Acetoclastic methanogenic archaea of the Methanosaeta and Methanosarcina genera increased with methane concentration. Acetate was the main precursor for methanogenesis, however more acetate was consumed than methane produced in an acetate amended well. DNA stable isotope probing showed incorporation of 13C-labelled acetate into methanogenic archaea, Geobacter species and sulfate reducing bacteria. Community characterisation of coal surfaces confirmed that methanogenic archaea make up a substantial proportion of coal associated biofilm communities. Ultimately, methane production from a gas-free subbituminous coal seam was stimulated despite high concentrations of sulfate and sulfate-reducing bacteria in the coal formation water. These findings provide a new conceptual framework for understanding the coal reservoir biosphere.
| S-EPMC6461797 | biostudies-literature
Project description:Here, we report 11 metagenome-assembled genomes (MAGs) reconstructed from freshwater and saltwater aquaria, including representatives of Polynucleobacter, Anaerolinea, Roseobacter, Flavobacteriia, Octadecabacter, Mycobacterium, and Candidate Phyla Radiation (CPR) members. These MAGs can serve as a resource for aquatic research and elucidating the role of CPR taxa in the built environment.
| S-EPMC8340870 | biostudies-literature
Project description:Pseudomonas cannabina pv. alisalensis and Pseudomonas syringae pv. maculicola cause bacterial leaf blight and bacterial leaf spot of crucifers (Brassicaceae). Both pathogens are threats to the cultivation of cruciferous crops. Here, we sequenced two strains of each pathogen, which will contribute to the development of countermeasures for the above diseases.
| S-EPMC8086205 | biostudies-literature