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Methanogen characterization

Simon Guerrero-Cruz, Geert Cremers, Theo A van Alen, Huub J M Op den Camp, Mike S M Jetten, Olivia Rasigraf, Annika Vaksmaa
' Candidatus Methanoperedens nitroreducens' is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In natural and man-made ecosystems, this archaeon is often found at oxic-anoxic interfaces where nitrate, the product of aerobic nitrification, co-occurs with methane produced by methanogens. As such, populations of ' Ca M. nitroreducens' could be prone to regular oxygen exposure. Here, we investigated the effect of 5% (v/v) oxygen exposure on a ' Ca M. nitroreducens' culture enriched from an Italian paddy field, in batch activity assays...
October 5, 2018: Applied and Environmental Microbiology
Andrea G Bravo, Sari Peura, Moritz Buck, Omneya Ahmed, Alejandro Mateos-Rivera, Sonia Herrero Ortega, Jeffra K Schaefer, Sylvain Bouchet, Julie Tolu, Erik Björn, Stefan Bertilsson
Methylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, the diversity of these mercury methylating microbial communities remains largely unexplored. Previous studies have implicated sulphate-reducing bacteria as the main mercury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury methylating microbial communities of boreal lake sediments using high-throughput sequencing of 16S rRNA and hgcA genes...
September 21, 2018: Applied and Environmental Microbiology
Jingjing Peng, Carl-Eric Wegner, Qicheng Bei, Pengfei Liu, Werner Liesack
BACKGROUND: The expected increase in global surface temperature due to climate change may have a tremendous effect on the structure and function of the anaerobic food web in flooded rice field soil. Here, we used the metatranscriptomic analysis of total RNA to gain a system-level understanding of this temperature effect on the methanogenic food web. RESULTS: Mesophilic (30 °C) and thermophilic (45 °C) food web communities had a modular structure. Family-specific rRNA dynamics indicated that each network module represents a particular function within the food webs...
September 19, 2018: Microbiome
Charlotte D Vavourakis, Adrian-Stefan Andrei, Maliheh Mehrshad, Rohit Ghai, Dimitry Y Sorokin, Gerard Muyzer
BACKGROUND: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages...
September 19, 2018: Microbiome
Abhishek S Dhoble, Pratik Lahiri, Kaustubh D Bhalerao
Background: Flow cytometry, with its high throughput nature, combined with the ability to measure an increasing number of cell parameters at once can surpass the throughput of prevalent genomic and metagenomic approaches in the study of microbiomes. Novel computational approaches to analyze flow cytometry data will result in greater insights and actionability as compared to traditional tools used in the analysis of microbiomes. This paper is a demonstration of the fruitfulness of machine learning in analyzing microbial flow cytometry data generated in anaerobic microbiome perturbation experiments...
2018: Journal of Biological Engineering
J Ruiz-Sánchez, M Guivernau, B Fernández, J Vila, M Viñas, V Riau, F X Prenafeta-Boldú
The effect of ammonia on methanogenic biomass from a full-scale agricultural digester treating nitrogen-rich materials was characterized in batch activity assays subjected to increasing concentrations of total ammonia N. Acetotrophic and methanogenic profiles displayed prolonged lag phases and reduced specific activity rates at 6.0 gN-TAN L-1 , though identical methane yields were ultimately reached. These results agreed with the expression levels of selected genes from bacteria and methanogenic archaea (qPCR of 16S rRNA and mrcA cDNA transcripts)...
February 1, 2019: Science of the Total Environment
Xueqin He, Hongjie Yin, Xiaoxi Sun, Lujia Han, Guangqun Huang
This study explored the effects of different particle sizes of rice straw biochar (RSB) on the methane emissions of pig manure/wheat straw aerobic composting experiments to provide a theoretical suggestion for biochar application. The experiments were conducted with a control group, powder (<1 mm) group, and granular (4 mm-1 cm) group. Methane emissions increased by 56.84% in the powder group but decreased by 22.15% in the granular group during the aerobic composting. Methane was generated by methanogens and methanotrophs in the specific anaerobic micro-environment characterized by X-ray micro-computed tomography (micro-CT)...
August 16, 2018: Bioresource Technology
Takashi Narihiro, Masaru K Nobu, Ben T W Bocher, Ran Mei, Wen-Tso Liu
Methanogenic bioreactors have been applied to treat purified terephthalic acid (PTA) wastewater containing complex aromatic compounds, such as terephthalic acid, para-toluic acid and benzoic acid. This study characterized the interaction of microbial populations in 42 samples obtained from 10 PTA-degrading methanogenic bioreactors. Approximately, 54 dominant populations (11 methanogens, 8 syntrophs and 35 functionally unknown clades) that represented 73.9% of total 16S rRNA gene iTag sequence reads were identified...
August 22, 2018: Environmental Microbiology Reports
Xing-Pan Guo, Yi Yang, Zuo-Shun Niu, Da-Pei Lu, Chun-Hong Zhu, Jing-Nan Feng, Jia-Yuan Wu, Yu-Ru Chen, Fei-Yun Tou, Min Liu, Lijun Hou
In the contaminated coastal sediments, variations of microbial community can reflect the impact of anthropogenic activities. The identification, evaluation and monitoring of the potential bio-indicator species and biomarker communities are vital for the ecological studies in sedimentary environments. Based on the high-throughput sequencing, the microbial communities were characterized in the sediments along the Yangtze Estuary and its coastal area. The results showed that the structure and composition of microbial communities varied greatly among different sampling sites at the phyla level, especially for Euryarchaeota...
August 14, 2018: Science of the Total Environment
José Q García-Maldonado, Alejandra Escobar-Zepeda, Luciana Raggi, Brad M Bebout, Alejandro Sanchez-Flores, Alejandro López-Cortés
Bacterial and archaeal community structure of five microbial communities, developing at different salinities in Baja California Sur, Mexico, were characterized by 16S rRNA sequencing. The response of the microbial community to artificial changes in salinity-sulfate concentrations and to addition of trimethylamine was also evaluated in microcosm experiments. Ordination analyses of the microbial community structure showed that microbial composition was distinctive for each hypersaline site. Members of bacteria were dominated by Bacteroidetes and Proteobacteria phyla, while Halobacteria of the Euryarchaeota phylum was the most represented class of archaea for all the environmental samples...
November 2018: Extremophiles: Life Under Extreme Conditions
Tansol Park, Zhongtang Yu
Ruminal ciliates both preys on and form symbiotic relationships with other members of the ruminal microbiota for their survival. However, it remains elusive if they have selectivity over their preys or symbionts. In the present study, we investigated the above selectivity by identifying and comparing the free-living prokaryotes (FLP) and the ciliate-associated prokaryotes (CAP) using Illumina MiSeq sequencing of 16S rRNA gene amplicons. We used single ciliates cells of both monocultures of Entodinium caudatum and Epidinium caudatum and eight different ciliate genera isolated from fresh rumen fluid of dairy cows...
2018: Frontiers in Microbiology
Zhe Kong, Lu Li, Yu-You Li
A lab-scale UASB was operated successfully to anaerobically treat wastewater containing approximately 2000 mg L-1 N, N-dimethylformamide (DMF) by artificially mixing anaerobic granular sludge with DMF-degrading activated sludge. DMF was effectively degraded by the UASB under a low OLR of 1.63-4.22 g COD L-1  d-1 , with over 96% DMF removal efficiency and a high methane production rate. However, the DMF-degrading ability gradually weakened along with increases in the OLR. The analysis of the microbial community structure by high-throughput sequencing revealed a decline in the abundance of the facultatively anaerobic DMF-hydrolyzing bacteria originating from activated sludge with increasing OLR, further deteriorating the methanogenic degradation of DMF...
August 7, 2018: Bioresource Technology
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
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
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
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
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...
October 15, 2018: Journal of Bacteriology
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
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
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
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