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Methanogen characterization

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https://www.readbyqxmd.com/read/30097098/radical-s-adenosyl-l-methionine-sam-enzyme-involved-in-the-maturation-of-the-nitrogenase-cluster
#1
Lee Rettberg, Kazuki Tanifuji, Andrew Jasniewski, Markus Walter Ribbe, Yilin Hu
Nitrogenase is the only known enzymatic system that converts atmospheric dinitrogen (N2 ) into bioavailable ammonia (NH3 ). The active-site cofactor responsible for this reactivity is a [(R-homocitrate)MoFe7 S9 C] cluster that is designated as the M-cluster. This important cofactor is assembled stepwise from a pair of [Fe4 S4 ] clusters that become fused into a [Fe8 S9 C] core before additional refinements take place to complete the biosynthesis. NifB, a member of the radical S-adenosyl-l-methionine (SAM) superfamily, facilitates the conversion of the [Fe4 S4 ] clusters (called the K-cluster) to the [Fe8 S9 C] core (called the L-cluster)...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/30086797/viral-and-metabolic-controls-on-high-rates-of-microbial-sulfur-and-carbon-cycling-in-wetland-ecosystems
#2
Paula Dalcin Martins, Robert E Danczak, Simon Roux, Jeroen Frank, Mikayla A Borton, Richard A Wolfe, Marie N Burris, Michael J Wilkins
BACKGROUND: Microorganisms drive high rates of methanogenesis and carbon mineralization in wetland ecosystems. These signals are especially pronounced in the Prairie Pothole Region of North America, the tenth largest wetland ecosystem in the world. Sulfate reduction rates up to 22 μmol cm-3  day-1 have been measured in these wetland sediments, as well as methane fluxes up to 160 mg m-2  h-1 -some of the highest emissions ever measured in North American wetlands. While pore waters from PPR wetlands are characterized by high concentrations of sulfur species and dissolved organic carbon, the constraints on microbial activity are poorly understood...
August 7, 2018: Microbiome
https://www.readbyqxmd.com/read/30062777/active-microbiome-structure-and-its-association-with-environmental-factors-and-viruses-at-different-aquatic-sites-of-a-high-altitude-wetland
#3
Yoanna Eissler, María-Jesús Gálvez, Cristina Dorador, Martha Hengst, Verónica Molina
Salar de Huasco is a high-altitude wetland characterized by a highly diverse microbial life adapted to extreme climatic and environmental conditions. Our study aims to determine active microbial community structure changes within different aquatic sites and its relationship with environmental factors and viruses as potential drivers of diversification in different aquatic areas of this ecosystem. In this study, bacteria and archaea composition (16S rRNA subunit pyrolibraries) and picoplankton and viral abundance were determined at ponds, springs and lagoon sites of the wetland during wet and dry seasons (February and July 2012, respectively)...
July 30, 2018: MicrobiologyOpen
https://www.readbyqxmd.com/read/30056662/isolation-and-characterization-of-a-new-methanoculleus-bourgensis-strain-kor-2-from-the-rumen-of-holstein-steers
#4
Urantulkhuur Battumur, Manhee Lee, Gui Sek Bae, Chang Hyun Kim
Objective: To isolate and identify new methanogens from the rumen of Holstein steers in Korea. Methods: Representative rumen contents were obtained from three ruminally cannulated Holstein steers (793 ± 8 kg). Pre-reduced media were used for the growth and isolation of methanogens. Optimum growth temperature, pH, and sodium chloride (NaCl) concentration as well as substrate utilization and antibiotic tolerance were investigated to determine the physiological characteristics of the isolated strain...
July 26, 2018: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/30012731/genetic-biochemical-and-molecular-characterization-of-methanosarcina-barkeri-mutants-lacking-three-distinct-classes-of-hydrogenase
#5
Thomas D Mand, Gargi Kulkarni, William W Metcalf
The methanogenic archaeon Methanosarcina barkeri encodes three distinct types of hydrogenase, whose functions vary depending on the growth substrate. These include the F420-dependent (Frh), methanophenazine-dependent (Vht), and ferredoxin-dependent (Ech) hydrogenases. To investigate their physiological roles, we characterized a series of mutants lacking each hydrogenase in various combinations. Mutants lacking Frh, Vht, or Ech in any combination failed to grow on H2 /CO2 , whereas only Vht and Ech were essential for growth on acetate...
July 16, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29997601/assessing-the-effect-of-pretreatments-on-the-structure-and-functionality-of-microbial-communities-for-the-bioconversion-of-microalgae-to-biogas
#6
Olivia Córdova, Rolando Chamy, Lorna Guerrero, Aminael Sánchez-Rodríguez
Microalgae biomethanization is driven by anaerobic sludge associated microorganisms and is generally limited by the incomplete hydrolysis of the microalgae cell wall, which results in a low availability of microalgal biomass for the methanogenic community. The application of enzymatic pretreatments, e.g., with hydrolytic enzymes, is among the strategies used to work around the incomplete hydrolysis of the microalgae cell wall. Despite the proven efficacy of these pretreatments in increasing biomethanization, the changes that a given pretreatment may cause to the anaerobic sludge associated microorganisms during biomethanization are still unknown...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29996505/stable-isotope-and-metagenomic-profiling-of-a-methanogenic-naphthalene-degrading-enrichment-culture
#7
Courtney R A Toth, Carolina Berdugo-Clavijo, Corynne M O'Farrell, Gareth M Jones, Andriy Sheremet, Peter F Dunfield, Lisa M Gieg
Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due to the difficulty of cultivating PAH degraders, requiring lengthy incubations to yield sufficient biomass for biochemical analysis. Here, we sought to characterize a new methanogenic naphthalene-degrading enrichment culture using DNA-based stable isotope probing (SIP) and metagenomic analyses...
July 10, 2018: Microorganisms
https://www.readbyqxmd.com/read/29988389/influence-of-the-potential-carbon-sources-for-field-denitrification-beds-on-their-microbial-diversity-and-the-fate-of-carbon-and-nitrate
#8
Victoria Grießmeier, Johannes Gescher
Nitrogen based eutrophication of ecosystems is a global problem that gains momentum through a growing global population. The water quality of nitrate or ammonium contaminated rivers and streams cannot always be amended in centralized waste water treatment plants. Field denitrification plants were suggested as a solution for a decentralized reduction of nitrate to dinitrogen. Here, stable and cheap organic carbon sources serve as carbon and electron source for a microbial community. Still, our knowledge on the impact of these organic carbon sources on the development and diversity of these cultures is sparse...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29981518/succession-of-toxicity-and-microbiota-in-hydraulic-fracturing-flowback-and-produced-water-in-the-denver-julesburg-basin
#9
Natalie M Hull, James S Rosenblum, Charles E Robertson, J Kirk Harris, Karl G Linden
Hydraulic fracturing flowback and produced water (FPW) samples were analyzed for toxicity and microbiome characterization over 220 days for a horizontally drilled well in the Denver-Julesberg (DJ) Basin in Colorado. Cytotoxicity, mutagenicity, and estrogenicity of FPW were measured via the BioLuminescence Inhibition Assay (BLIA), Ames II mutagenicity assay (AMES), and Yeast Estrogen Screen (YES). Raw FPW stimulated bacteria in BLIA, but were cytotoxic to yeast in YES. Filtered FPW stimulated cell growth in both BLIA and YES...
July 4, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29970829/characterization-and-dynamic-shift-of-microbial-communities-during-start-up-overloading-and-steady-state-in-an-anaerobic-membrane-bioreactor
#10
Nsanzumukiza Martin Vincent, Yuansong Wei, Junya Zhang, Dawei Yu, Juan Tong
A lab-scale anaerobic membrane bioreactor (AnMBR) with a side stream tubular membrane was developed to treat synthetic domestic sewage to evaluate its performance and the dynamic shift of bacterial and archaeal communities during the start-up, steady-state, overloading and recovery periods of operation at mesophilic temperatures. During the start-up period, the bacterial and archaeal communities changed drastically, and Proteobacteria and Bacteroidetes predominated. During the steady-state period, the AnMBR exhibited excellent COD removal above 91%, and COD of the effluent was below 50 mg/L...
July 3, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29970471/energy-conservation-via-hydrogen-cycling-in-the-methanogenic-archaeon-methanosarcina-barkeri
#11
Gargi Kulkarni, Thomas D Mand, William W Metcalf
Energy conservation via hydrogen cycling, which generates proton motive force by intracellular H2 production coupled to extracellular consumption, has been controversial since it was first proposed in 1981. It was hypothesized that the methanogenic archaeon Methanosarcina barkeri is capable of energy conservation via H2 cycling, based on genetic data that suggest that H2 is a preferred, but nonessential, intermediate in the electron transport chain of this organism. Here, we characterize a series of hydrogenase mutants to provide direct evidence of H2 cycling...
July 3, 2018: MBio
https://www.readbyqxmd.com/read/29893836/diversity-and-functionality-of-archaeal-bacterial-and-fungal-communities-in-deep-archaean-bedrock-groundwater
#12
Lotta Purkamo, Riikka Kietäväinen, Hanna Miettinen, Elina Sohlberg, Ilmo Kukkonen, Merja Itävaara, Malin Bomberg
The diversity and metabolic functions of deep subsurface ecosystems remain relatively unexplored. Microbial communities in previously studied deep subsurface sites of the Fennoscandian Shield are distinctive to each site. Thus, we hypothesized that the microbial communities of the deep Archaean bedrock fracture aquifer in Romuvaara, northern Finland, differ both in community composition and metabolic functionality from the other sites in the Fennoscandian Shield. We characterized the composition, functionality and substrate preferences of the microbial communities at different depths in a 600 m deep borehole...
August 1, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29739901/compositional-and-functional-differences-in-the-human-gut-microbiome-correlate-with-clinical-outcome-following-infection-with-wild-type-salmonella-enterica-serovar-typhi
#13
Yan Zhang, Arthur Brady, Cheron Jones, Yang Song, Thomas C Darton, Claire Jones, Christoph J Blohmke, Andrew J Pollard, Laurence S Magder, Alessio Fasano, Marcelo B Sztein, Claire M Fraser
Insights into disease susceptibility as well as the efficacy of vaccines against typhoid and other enteric pathogens may be informed by better understanding the relationship between the effector immune response and the gut microbiota. In the present study, we characterized the composition (16S rRNA gene profiling) and function (RNA sequencing [RNA-seq]) of the gut microbiota following immunization and subsequent exposure to wild-type Salmonella enterica serovar Typhi in a human challenge model to further investigate the central hypothesis that clinical outcomes may be linked to the gut microbiota...
May 8, 2018: MBio
https://www.readbyqxmd.com/read/29696012/energy-gradients-structure-microbial-communities-across-sediment-horizons-in-deep-marine-sediments-of-the-south-china-sea
#14
Michael F Graw, Grace D'Angelo, Matthew Borchers, Andrew R Thurber, Joel E Johnson, Chuanlun Zhang, Haodong Liu, Frederick S Colwell
The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29688331/aerobic-microbial-taxa-dominate-deep-subsurface-cores-from-the-alberta-oil-sands
#15
Christina M Ridley, Gerrit Voordouw
Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche...
June 1, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29681206/characterizing-phenol-removing-consortia-under-methanogenic-and-sulfate-reducing-conditions-potential-metabolic-pathways
#16
Leandro Augusto Gouvêa de Godoi, Lucas Tadeu Fuess, Tiago Palladino Delforno, Eugenio Foresti, Marcia Helena Rissato Zamariolli Damianovic
Phenol removal was investigated in anaerobic fixed-structured bed reactors, namely R1 and R2, treating synthetic wastewater simulating the soluble fraction of vinasse under strictly methanogenic (R1) and simultaneous methanogenic/sulfidogenic conditions (R2). Next-generation sequencing (Illumina MiSeq System) was used to further characterize the microbial communities in both systems. Phenol was completely and stably removed in R1 after a short operating period (≈55 days). Conversely, phenol removal in R2 required a longer period for biomass acclimation (≈125 days) to reach levels equivalent to R1...
April 26, 2018: Environmental Technology
https://www.readbyqxmd.com/read/29660875/metagenomic-analysis-of-antibiotic-resistance-genes-args-during-refuse-decomposition
#17
Xi Liu, Shu Yang, Yangqing Wang, He-Ping Zhao, Liyan Song
Landfill is important reservoirs of residual antibiotics and antibiotic resistance genes (ARGs), but the mechanism of landfill application influence on antibiotic resistance remains unclear. Although refuse decomposition plays a crucial role in landfill stabilization, its impact on the antibiotic resistance has not been well characterized. To better understand the impact, we studied the dynamics of ARGs and the bacterial community composition during refuse decomposition in a bench-scale bioreactor after long term operation (265d) based on metagenomics analysis...
September 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29648587/characterisation-of-the-ruminal-fermentation-and-microbiome-in-lambs-supplemented-with-hydrolysable-and-condensed-tannins
#18
Saheed A Salami, Bernardo Valenti, Marco Bella, Michael N O'Grady, Giuseppe Luciano, Joseph P Kerry, Eleanor Jones, Alessandro Priolo, Charles J Newbold
This study characterised the response of ruminal fermentation and the rumen microbiome in lambs fed commercial vegetal sources of hydrolysable tannins (HT) and condensed tannins (CT). Forty-four lambs (19.56 ± 2.06 kg) were randomly assigned to either a concentrate diet (CON, n = 8) or CON supplemented with 4% of two HT [chestnut (Castanea sativa, HT-c) and tara (Caesalpinia spinosa, HT-t)] and CT [mimosa (Acacia negra, CT-m) and gambier (Uncaria gambir, CT-g)] extracts (all, n = 9) for 75 days pre-slaughter...
May 1, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29644945/quantitative-evaluation-of-ruminal-methane-and-carbon-dioxide-formation-from-formate-through-c-13-stable-isotope-analysis-in-a-batch-culture-system
#19
Z X He, J Y Qiao, Q X Yan, Z L Tan, M Wang
Methane produced from formate is one of the important methanogensis pathways in the rumen. However, quantitative information of CH4 production from formate has been rarely reported. The aim of this study was to characterize the conversion rate (CR) of formic acid into CH4 and CO2 by rumen microorganisms. Ground lucerne hay was incubated with buffered ruminal fluid for 6, 12, 24 and 48 h. Before the incubation, 13C-labeled H13COOH was also supplied into the incubation bottle at a dose of 0, 1.5, 2.2 or 2.9 mg/g of DM substrate...
April 12, 2018: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29606531/differentiated-stimulating-effects-of-activated-carbon-on-methanogenic-degradation-of-acetate-propionate-and-butyrate
#20
Suyun Xu, Runqi Han, Yuchen Zhang, Chuanqiu He, Hongbo Liu
Granular activated carbon (GAC) could promote methane production from organic wastes, but a wide range of dosages has been reported. In present study, different GAC dosages of 0, 0.5, 5 and 25 g/L were supplemented into anaerobic digesters and the methanogenic degradation kinetics of acetate, propionate and butyrate were characterized, respectively. At high organic load of 5 g/L, the degradation rates of propionate and butyrate increased by 1.5-4.7 and 2.5-7.0 times at varied GAC dosages. The methane production rates (Rmax ) from propionate and butyrate were significantly elevated when increasing GAC dosage up to 5 g/L...
June 2018: Waste Management
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