Youngiibacter fragilis gen. nov., sp. nov., isolated from natural gas production-water and reclassification of Acetivibrio multivorans as Youngiibacter multivorans comb. nov.

A taxonomic study employing a polyphasic approach was performed on a novel anaerobic bacterium isolated from natural gas production-water. The bacterium stained Gram-negative and consisted of non-motile, non-spore-forming, rod-shaped cells. Products of glucose or starch fermentation were ethanol, CO2, formate, acetate and H2. The predominant fatty acids were C16 : 0 ALDE and summed feature 3 comprising C16 : 1ω7c and/or C16 : 1ω6c. The DNA G+C content was 45.5 mol%. 16S rRNA gene sequence analysis demonstrated that the nearest phylogenetic neighbours of the novel strain were Acetivibrio multivorans DSM 6139(T) (98.5 %) and Proteiniclasticum ruminis JCM 14817(T) (95.4 %). The DNA-DNA hybridization value between the novel organism and Acetivibrio multivorans PeC1 DSM 6139(T) was determined to be only 30.2 %, demonstrating the separateness of the two species. Based on phylogenetic, phenotypic and chemotaxonomic evidence that clearly distinguished strain 232.1(T) from Proteiniclasticum ruminis and other close relatives, it is proposed that the novel isolate be classified as representing a novel species of a new genus within the family Clostridiaceae, Youngiibacter fragilis gen. nov., sp. nov. The type strain of the type species is 232.1(T) ( = ATCC BAA-2257(T) = DSM 24749(T)). In addition, Acetivibrio multivorans is proposed to be reclassified as Youngiibacter multivorans comb. nov.

Temporal dynamics and controlling factors of CO2 and CH4 variability in the urban atmosphere of Wroclaw, Poland.

Temporal and spatial distribution of both biogenic and anthropogenic components of atmospheric carbon dioxide (CO2) and methane (CH4) is crucial for understanding the environmental impacts of climate change over urban areas. This research focuses on applying stable isotope source-partitioning studies to determine the interactions between biogenic and anthropogenic CO2 and CH4 emissions in an average-sized city environment. Study signifies the weight of instantaneous variability and diurnal averaging as compared with seasonal records of variations of the atmospheric CO2 and CH4 at a variety of typical urban sites in the city of Wroclaw, conducted during a one-year period from June 2017 to August 2018. The findings reveal distinct temporal variations in atmospheric CO2 and CH4 mole fractions and their isotopic composition. The average atmospheric CO2 and CH4 mole fractions during the study period were 416.4 ± 20.5 ppm, and 1.95 ± 0.09 ppm, respectively. The study highlights the high variability of driving forces, including current energy use patterns, natural carbon reservoirs, planetary boundary layer dynamics, and atmospheric transport. Additionally, the relationship between the evolution of the convective boundary layer depth and the CO2 budget was analyzed using the CLASS model with input parameters based on field observations, resulting in insights such as an increase in the range of 25-65 ppm of CO2 during stable nocturnal boundary layers. The observed changes in stable isotopic signatures of air samples allowed for the identification of two main source categories in the city area: fuel combustion and biogenic processes. The δ13C-CO2 values of collected samples suggest that biogenic emissions dominate (up to 60 % of CO2 excess mole fraction) during the growing season, but are reduced by plant photosynthesis during summer afternoons. In contrast, local fossil-fuel CO2 contribution (up to 90 % of excess CO2 mole fraction) from domestic heating, vehicle emissions, and heat and power plants predominantly influence the urban GHG budget during winter. The δ13C-CH4 values indicate anthropogenic sources related to fossil fuel combustion during winter, with values ranging from -44.2 ‰ to -51.4 ‰, while slightly more depleted values, between -47.1 ‰ and -54.2 ‰, reflect a larger input of biological processes in the methane urban budget during summer. Overall, instantaneous and hourly variability of the above-mentioned readings of gas mole fraction and isotopic composition, have shown higher variability than seasonal amplitudes. Hence, respecting this granularity is the key to alignment and understanding significance of such localized atmospheric pollution studies. Additionally, the changing overprint of the system's framework, such as variability of wind and atmospheric layering patterns, weather events, provides context of sampling and data analysis at different frequencies.

Quantitative fluorescence in situ hybridization analysis of microbial consortia from a biogenic gas field in Alaska's Cook Inlet basin.

Filter-collected production water samples from a methane-rich gas field in the Cook Inlet basin of Alaska were investigated using whole-cell rRNA-targeted fluorescence in situ hybridization (FISH) and 16S rRNA tag pyrosequencing. Both techniques were consistent in determining the microbial community composition, including the archaeal or bacterial dominance of samples. The archaeal community is dominated by the obligate methylotrophic methanogen genus Methanolobus as well as the nutritional generalist methanogen genus Methanosarcina, which is capable of utilizing acetate, CO(2), and methyl-bearing compounds. The most-abundant bacterial groups are Firmicutes, notably of the Acetobacterium genus, and Cytophaga-Flexibacter-Bacteroides species (CFBs) affiliated with the order Bacteroidales. We observed spatial variation among samples in both the percentage of members of Archaea compared to that of members of Bacteria and the dominant members of the bacterial community, differences which could not be explained with the available geochemical data. Based upon the microbial community composition and the isotopic signature of methane associated with the Cook Inlet basin site, we propose a simplified reaction network beginning with the breakdown of coal macromolecules, followed by fermentation and methylotrophic and acetoclastic methane production.

Methane-producing microbial community in a coal bed of the Illinois basin.

A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H(2) and CO(2), which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both the in situ microbial community and highly purified, methanogenic enrichments indicated that Methanocorpusculum is the dominant genus. Additionally, we characterized this methanogenic microorganism using scanning electron microscopy and distribution of intact polar cell membrane lipids. Phylogenetic studies of coal water samples helped us develop a model of methanogenic biodegradation of macromolecular coal and coal-derived oil by a complex microbial community. Based on enrichments, phylogenetic analyses, and calculated free energies at in situ subsurface conditions for relevant metabolisms (H(2)-utilizing methanogenesis, acetoclastic methanogenesis, and homoacetogenesis), H(2)-utilizing methanogenesis appears to be the dominant terminal process of biodegradation of coal organic matter at this location.

Isotopic composition of sulphates from meteoric precipitation as an indicator of pollutant origin in Wroclaw (SW Poland).

This paper describes the results of isotopic analyses of (i) hydrogen and oxygen in water (delta DH2O and delta18OH2O ) and (ii) sulphur and oxygen in sulphates (delta34Ssulphate and delta18Osulphate) from atmospheric precipitation collected within a one-year period between 25 May 2004 and 25 May 2005 in Wroclaw (SW Poland). The resulting equation of Local Meteoric Water Line for Wroclaw is delta D=6.373xdelta18O-0.047, (r2=0.97, n=32). The delta34Ssulphate varies from 1.1 to 4.2 per thousand (with an average of 2.5 per thousand), delta18Osulphate varies from 9.0 to 16.7 per thousand (with an average of 13.8 per thousand) and delta18OH2O varies from-0.8 to-16.3 per thousand (with an average of-8.2 per thousand). The above results indicate two main sources of sulphates in Wroclaw precipitation: (i) low-temperature secondary sulphates forming in situ in Wroclaw from the atmospheric SO2 as well as precipitation water (heterogeneous and homogeneous pathways oxidation) and (ii) high-temperature primary sulphates forming in rapid high-temperature hydratation of SO3- in an immediate proximity of industrial chimneys. We hypothesise that the secondary low-temperature type of sulphates is probably formed from the local sulphur and oxygen reservoirs, whereas the primary high-temperature type is allochthonous and it is probably transported from industrial areas located outside of Wroclaw.

Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin.

The bioconversion of coal to methane in the San Juan Basin, New Mexico, was investigated. Production waters were analyzed via enrichment studies, metabolite-profiling, and culture-independent methods. Analysis of 16S rRNA gene sequences indicated the presence of methanogens potentially capable of acetoclastic, hydrogenotrophic, and methylotrophic metabolisms, predominantly belonging to the Methanosarcinales and Methanomicrobiales. Incubations of produced water and coal readily produced methane, but there was no correlation between the thermal maturity and methanogenesis. Coal methanogenesis was greater when samples with a greater richness of Firmicutes were utilized. A greater archaeal diversity was observed in the presence of several aromatic and short-chain fatty acid metabolites. Incubations amended with lactate, hydrogen, formate, and short-chain alcohols produced methane above un-amended controls. Methanogenesis from acetate was not observed. Metabolite profiling showed the widespread occurrence of putative aromatic ring intermediates including benzoate, toluic acids, phthalic acids, and cresols. The detection of saturated and unsaturated alkylsuccinic acids indicated n-alkane and cyclic alkane/alkene metabolism. Microarray analysis complemented observations based on hybridization to functional genes related to the anaerobic metabolism of aromatic and aliphatic substrates. These data suggest that coal methanogenesis is unlikely to be limited by methanogen biomass, but rather the activation and degradation of coal constituents.

Versatile inlet system for on-line compound-specific deltaD and delta13C gas chromatography-oxidation/reduction-isotope ratio mass spectrometry analysis of gaseous mixtures.

Compound-specific deltaD and delta13C analyses of gas mixtures are useful indicators of geochemical and environmental factors. However, the relative concentrations of individual components in gas mixtures (e.g., H2, CO2, methane, ethane, propane, i-butane, n-butane) may vary over several orders of magnitude. The determination of hydrogen and carbon compound-specific stable isotope ratios requires that the hydrogen and carbon dioxide produced from each separated component has a concentration adjusted to match the dynamic range of the stable isotope mass spectrometer. We present a custom-built gas sampling and injection system (GASIS) linked with a Delta Plus XP mass spectrometer that provides flexibility, ease of operation, and economical use of small gas samples with wide ranges of analyte concentrations. The overall on-line GC-ox/red-IRMS (Gas Chromatography - oxidation/reduction - Isotope Ratio Mass Spectrometry) system consists of (i) a customized GASIS inlet system and (ii) two alternative reactors, namely an oxidative Cu-Ni-Pt reactor at 950 degrees C for production of CO2 and a reductive graphitized Al2O3 reactor at 1420 degrees C for production of H2. In addition, the system is equipped with (iii) a liquid nitrogen spray-cooling unit for cryo-GC-focusing at -20 degrees C, and (iv) a Nafion dryer for removal of water vapor from product CO2. The three injection loops of the GASIS inlet allow flexibility in the volume of injected analyte gas (e.g., from 0.06 to 500 microL) in order to measure reproducible deltaD and delta13C values for gases at concentrations ranging from 100% down to 10 ppm. We calibrate our GC-ox/red-IRMS system with two isotopically distinct methane references gases that are combusted off-line and characterized using dual-inlet IRMS.