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mCRA gene

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
Hiroki Matsui, Tomoyo Ishimoto-Tsuchiya, Sakiko Maekawa, Tomomi Ban-Tokuda
Marker gene analysis was performed to assess the effect of energy level on the diversity and population density of methanogens in pig fecal material. Crossbred pigs were fed high or low energy level diets, a high-energy (HE) diet that satisfied daily gain at 1.2 kg, and a low-energy (LE) diet with amount of 0.6 times of the HE diet. Growth performance and short-chain fatty acid in feces were examined. Diversity of methanogen was analyzed by the α-subunit of methyl coenzyme-M reductase gene (mcrA) clone library from fecal DNA...
July 15, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
Chun-Yu Lai, Qiu-Yi Dong, Bruce E Rittmann, He-Ping Zhao
Employing a special anaerobic membrane biofilm batch reactor (MBBR), we demonstrated antimonate (Sb(V)) reduction using methane (CH4 ) as the sole electron donor. Scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and Raman and photoluminescence (PL) spectra identified that Sb2 O3 microcrystals were the main reduced products. The Sb(V) reduction rate increased continually over the 111-day experiment, which supports the enrichment of the microorganisms responsible for Sb(V) reduction to Sb(III)...
July 24, 2018: Environmental Science & Technology
Xiang-Yu Hu, Qiu-Jie Xiang, Zhi-Jian Mu
In this study, the effects of gypsum (FGD) on CH4 emission and functional microbial community in paddy soil were identified under five treatments, including FGDG0 (0 t·hm-2 ), FGDG1 (2 t·hm-2 ), FGDG2 (4 t·hm-2 ), FGDG3 (8 t·hm-2 ), and FGDG4 (16 t·hm-2 ). The methane flux was determined using static chamber and chromatography. Bacterial community structure and its effect on soil bacterial community structure, and the abundance of methanogenic and methanotrophs were measured via high-throughput sequencing and quantitative PCR...
August 8, 2018: Huan Jing Ke Xue= Huanjing Kexue
Ke Zhang, Hongbing Luo, Zhanyuan Zhu, Wei Chen, Jia Chen, You Mo
To investigate the effects of emergent plants on CH4 efflux and elucidate the key factors responsible for these effects, annual monitoring of CH4 emissions and methanogen community dynamics in a full-scale constructed wetland (CW) was conducted. Five emergent plants (Typha orientalis, Cyperus alternifolius, Arundo domax, Iris pseudacorus, and Thalia dealbata) commonly used in CWs were selected for investigation. The greatest CH4 flux (annual mean 19.4 mg m-2  h-1 ) was observed from I. pseudacorus, while the lowest CH4 flux (7...
July 9, 2018: Environmental Science and Pollution Research International
Aurèle Vuillemin, Fabian Horn, André Friese, Matthias Winkel, Mashal Alawi, Dirk Wagner, Cynthia Henny, William D Orsi, Sean A Crowe, Jens Kallmeyer
Ferruginous (Fe-rich, SO4 -poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment...
July 2, 2018: Environmental Microbiology
Xue Ping Chen, Jing Sun, Yi Wang, Heng Yang Zhang, Chi Quan He, Xiao Yan Liu, Nai Shun Bu, Xi-En Long
Methane production by methanogens in wetland is recognized as a significant contributor to global warming. Spartina alterniflora (S. alterniflora), which is an invasion plant in China's wetland, was reported to have enormous effects on methane production. But studies on shifts in the methanogen community in response to S. alterniflora invasion at temporal and spatial scales in the initial invasion years are rare. Sediments derived from the invasive species S. alterniflora and the native species Phragmites australis (P...
July 2018: Journal of Microbiology / the Microbiological Society of Korea
Souad Belkacemi, Anthony Mazel, Delphine Tardivo, Patrick Tavitian, Grégory Stephan, Giancarlo Bianca, Elodie Terrer, Michel Drancourt, Gérard Aboudharam
Methanogens have already been described in periodontitis but not in peri-implantitis. Thirty peri-implantitis samples and 28 control samples were collected in 28 consenting peri-implantitis patients. PCR-sequencing of the 16S rRNA gene was used as a broad-spectrum screening method and results were further confirmed by real-time quantitative PCR targeting the mcrA genes. Results showed a methanogen community dominated by Methanobrevibacter oralis in 31/58 (51%) samples including 16/28 (57%) control samples and 15/30 (50%) peri-implantitis samples...
June 21, 2018: Scientific Reports
Gui Feng Gao, Peng Fei Li, Zhi Jun Shen, Ying Ying Qin, Xi Min Zhang, Kabir Ghoto, Xue Yi Zhu, Hai Lei Zheng
Mangroves are critical in global carbon budget while vulnerable to exotic plant invasion. Spartina alterniflora, one of typical salt marsh plant grows forcefully along the coast of China, has invaded the native mangrove habitats in Zhangjiang Estuary. However, the effects of S. alterniflora invasion on soil carbon gases (CH4 and CO2 ) emission from mangroves are not fully understood. Accordingly, we conducted a field experiment to investigate the soil CH4 and CO2 emission during growing seasons in 2016 and 2017 at four adjacent wetlands, namely bare mudflat (Mud), Kandelia obovata (KO), Avicennia marina (AM) and S...
June 18, 2018: Scientific Reports
Prasant Kumar Jena, Lili Sheng, Nidhi Nagar, Chao Wu, Daniela Barile, David A Mills, Yui-Jui Yvonne Wan
Probiotic Bifidobacterium longum subspecies infantis ( Bifidobacterium infantis ) consumes human milk oligosaccharides (MO) and protects intestinal permeability thereby having anti-inflammatory effects (Underwood et al., 2015; Bode, 2006; Asakuma et al., 2011) [1-3]. Via the gut-liver axis, gut barrier disruption and dysbiosis lead to hepatic inflammation (Sheng et al., 2017; Jena et al., 2017) [4,5,6]. Our published data revealed that butyrate, as well as synbiotics of B. infantis in combination with MO, had protective effects against cancer-prone non-alcoholic steatohepatitis (NASH) mouse models, i...
August 2018: Data in Brief
Ting Xie, Qi Yang, Mari K H Winkler, Dongbo Wang, Yu Zhong, Hongxue An, Fei Chen, Fubin Yao, Xiaolin Wang, Jiawei Wu, Xiaoming Li
Perchlorate bioreduction coupled to methane oxidation was successfully achieved without the addition of nitrate or nitrite in a membrane biofilm reactor (MBfR) inoculated with a mixture of freshwater sediments and anaerobic digester sludge as well as return activated sludge. The reactor was operated at different methane pressures (60, 40 and 20 Kpa) and influent perchlorate concentrations (1, 5 and 10 mg/L) to evaluate the biochemical process of perchlorate bioreduction coupled to methane oxidation. Perchlorate was completely reduced with a higher removal flux of 92...
September 5, 2018: Journal of Hazardous Materials
Tai-Ho Hu, Liang-Ming Whang, Chi-Yu Huang
This study evaluated the methanogens responsible for methanogenic degradation of tetramethylammonium hydroxide (TMAH) in a continuous flow bioreactor. The enriched methanogens attained an estimated maximum specific TMAH degradation rate and half-saturation constant of 39.5 mg TMAH/gVSS/h and 820 mg/L, following the Monod-type kinetic expression for methanogenic TMAH degradation. Presence of sulfide more than 20 mg/L significantly extended lag period and slowed down specific TMAH degradation rates. The results of terminal restriction fragment length polymorphism (T-RFLP), cloning/sequencing, and quantitative real-time PCR analyses targeting on the methyl coenzyme M reductase alpha subunit (mcrA) genes retrieved from the bioreactor and batch experiments indicated that Methanomethylovorans species were the dominant methanogens responsible for methanogenic degradation of TMAH...
September 5, 2018: Journal of Hazardous Materials
Cristina P Fernández-Baca, Allison M Truhlar, Amir-Eldin H Omar, Brian G Rahm, M Todd Walter, Ruth E Richardson
Onsite septic systems use soil microbial communities to treat wastewater, in the process creating potent greenhouse gases (GHGs): methane (CH4 ) and nitrous oxide (N2 O). Subsurface soil dispersal systems of septic tank overflow, known as leach fields, are an important part of wastewater treatment and have the potential to contribute significantly to GHG cycling. This study aimed to characterize soil microbial communities associated with leach field systems and quantify the abundance and distribution of microbial populations involved in CH4 and N2 O cycling...
November 1, 2018: Science of the Total Environment
Oscar Franchi, Patricia Bovio, Eduardo Ortega-Martínez, Francisca Rosenkranz, Rolando Chamy
The aim of the present work was to investigate the dynamics of microbial community at DNA and RNA level and the role of bamA and mcrA gene during anaerobic digestion of phenol and p-cresol. Anaerobic digestion was conducted in batch reactors and microbial community dynamics was analysed. Results showed that active microbial community was quite dissimilar in comparison to the total microbial community. Syntrophorhabdus and Bacillus were the dominant active bacterial genera whereas Methanosaeta together with Methanobacterium showed the highest potential activity in the Archaea domain indicating a relevant role of these microorganisms in the anaerobic process...
September 2018: Bioresource Technology
Sergi Compte-Port, Carles M Borrego, Hélène Moussard, Mathilde Jeanbille, Claudia Ximena Restrepo-Ortiz, Alberto de Diego, Azibar Rodriguez-Iruretagoiena, Ainara Gredilla, Silvia Fdez-Ortiz de Vallejuelo, Pierre E Galand, Dimitri Kalenitchenko, Jean-Luc Rols, Oleg S Pokrovsky, Aridane G Gonzalez, Lluis Camarero, Selene Muñiz, Enrique Navarro-Navarro, Jean-Christophe Auguet
Using the 16S rRNA and mcrA genes, we investigated the composition, abundance and activity of sediment archaeal communities within 18 high-mountain lakes under contrasted metal levels from different origins (bedrock erosion, past-mining activities and atmospheric depositions). Bathyarchaeota, Euryarchaeota and Woesearchaeota were the major phyla found at the meta-community scale, representing 48%, 18.3% and 15.2% of the archaeal community respectively. Metals were equally important as physicochemical variables in explaining the assemblage of archaeal communities and their abundance...
April 24, 2018: Environmental Microbiology
Anna Banach, Sławomir Ciesielski, Tomasz Bacza, Marek Pieczykolan, Aleksandra Ziembińska-Buczyńska
More information on the connection between anaerobic digestion (AD) parameters and composition of the microbial community involved in the AD process is required to gain a better understanding of how a bioreactor functions. The aim of this study was to analyse the composition of microbial communities and the dynamics of methanogens' biodiversity changes during the shift from mesophilic (38°C) to thermophilic (55°C) conditions during biogas production. The total microbial composition was examined via the metagenomic approach based on 16S rRNA gene sequencing, whereas the methanogen communities were analysed using PCR-DGGE (Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis) of mcrA...
May 3, 2018: Environmental Technology
Shailendra Yadav, Arvind Kumar, Manish Gupta, S S Maitra
16S ribosomal RNA gene sequences are characteristically used as gold-standard genetic marker for the determination of bacterial and/or archaeal biodiversity, and community profiling of environmental samples. The 16S rRNA amplicon analysis till-date is taken as a standard method for investigation and identification of uncultivable bacteria in microbial diversity studies. The accuracy of these analyses strongly depends upon the choice of primers. It is presumed that these primers do not participate in non-specific amplifications...
August 2018: Current Microbiology
Babett Wintsche, Nico Jehmlich, Denny Popp, Hauke Harms, Sabine Kleinsteuber
Anaerobic digestion (AD) is a complex multi-stage process relying on the activity of highly diverse microbial communities including hydrolytic, acidogenic and syntrophic acetogenic bacteria as well as methanogenic archaea. The lower diversity of methanogenic archaea compared to the bacterial groups involved in AD and the corresponding lack of functional redundancy cause a stronger susceptibility of methanogenesis to unfavorable process conditions such as trace element (TE) deprivation, thus controlling the stability of the overall process...
2018: Frontiers in Microbiology
Joel A Boyd, Ben J Woodcroft, Gene W Tyson
Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial communities. Gene-centric approaches can be used to gain a comprehensive view of diversity by examining each read independently, but traditional pairwise comparison approaches typically over-classify taxonomy and scale poorly with increasing metagenome and database sizes. Here we introduce GraftM, a tool that uses gene specific packages to rapidly identify gene families in metagenomic data using hidden Markov models (HMMs) or DIAMOND databases, and classifies these sequences using placement into pre-constructed gene trees...
June 1, 2018: Nucleic Acids Research
Sieglinde Debruyne, Alexis Ruiz-González, Einar Artiles-Ortega, Bart Ampe, Wim Van Den Broeck, Ellen De Keyser, Leen Vandaele, Karen Goossens, Veerle Fievez
The aim of this study was to investigate the methane (CH4) reducing potential of a combination of prenatal and/or postnatal treatment with coconut oil medium chain fatty acids (CO MCFA) in goat kids. The hypothesis is that influencing rumen function during early life has more chances for success than in the adult life, related to the resilience of the mature rumen microbiota. Forty-eight pregnant does were split into two experimental groups: treated does (D+) received 40 g/d of CO MCFA in a test compound feed, while control does (D-) received a control compound feed, during the last 3 wk of gestation...
May 4, 2018: Journal of Animal Science
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