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Methanogen genomics

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
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
Sandeep Kumar, Bryan P Treloar, Koon Hoong Teh, Catherine M McKenzie, Gemma Henderson, Graeme T Attwood, Sinéad M Waters, Mark L Patchett, Peter H Janssen
Sharpea and Kandleria are associated with rumen samples from low-methane-emitting sheep. Four strains of each genus were studied in culture, and the genomes of nine strains were analysed, to understand the physiology of these bacteria. All eight cultures grew equally well with d-glucose, d-fructose, d-galactose, cellobiose, and sucrose supplementation. d-Lactate was the major end product, with small amounts of the mixed acid fermentation products formate, acetate and ethanol. Genes encoding the enzymes necessary for this fermentation pattern were found in the genomes of four strains of Sharpea and five of Kandleria...
July 25, 2018: Anaerobe
Joanne B Emerson, Simon Roux, Jennifer R Brum, Benjamin Bolduc, Ben J Woodcroft, Ho Bin Jang, Caitlin M Singleton, Lindsey M Solden, Adrian E Naas, Joel A Boyd, Suzanne B Hodgkins, Rachel M Wilson, Gareth Trubl, Changsheng Li, Steve Frolking, Phillip B Pope, Kelly C Wrighton, Patrick M Crill, Jeffrey P Chanton, Scott R Saleska, Gene W Tyson, Virginia I Rich, Matthew B Sullivan
Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1-7 . The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8-10 , remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden...
August 2018: Nature Microbiology
Anders E Lind, William H Lewis, Anja Spang, Lionel Guy, T Martin Embley, Thijs J G Ettema
Endosymbiosis is a widespread phenomenon in the microbial world and can be based on diverse interactions between endosymbiont and host cell. The vast majority of the known endosymbiotic interactions involve bacteria that have invaded eukaryotic host cells. However, methanogenic archaea have been found to thrive in anaerobic, hydrogenosome-containing protists and it was suggested that this symbiosis is based on the transfer of hydrogen. Here, we used culture-independent genomics approaches to sequence the genomes of two distantly related methanogenic endosymbionts that have been acquired in two independent events by closely related anaerobic ciliate hosts Nyctotherus ovalis and Metopus contortus, respectively...
July 10, 2018: ISME Journal
Ayyappa Kumar Sista Kameshwar, Wensheng Qin
Ruminating animals, especially cattle lack the carbohydrate active enzyme encoding genes which are required for the degradation of the glycosidic linkages of plant cell wall carbohydrates (such as cellulose, hemicellulose, lignin and pectin). Thus, ruminating animals are completely dependent on the microorganisms (anaerobic bacteria and fungi, methanogenic archaea and protozoa) residing in their rumen (hindgut). In this study, we have retrieved and analyzed the complete genome wide annotations of the Neocallimastigomycota division fungi such as Anaeromyces robustus, Neocallismatix californiae, Orpinomyces sp, Piromyces finnis, Piromyces sp E2...
2018: Journal of Genomics
Tatiana A Vishnivetskaya, Joy Buongiorno, Jordan Bird, Kirill Krivushin, Elena V Spirina, Victoria Oshurkova, Victoria A Shcherbakova, Gary Wilson, Karen G Lloyd, Elizaveta M Rivkina
Polar permafrost is at the forefront of climate change, yet only a few studies have enriched the native methane-producing microbes that might provide positive feedbacks to climate change. Samples Ant1 and Ant2, collected in Antarctic Miers Valley from permafrost sediments, with and without biogenic methane, respectively, were evaluated for methanogenic activity and presence of methanogens. After a one-year incubation of both samples under anaerobic conditions, methane production was observed only at room temperature in microcosm Ant1 with CO2/H2 (20/80) as carbon and energy sources and was monitored during the subsequent 10 years...
August 1, 2018: FEMS Microbiology Ecology
R A Beinart, J Rotterová, I Čepička, R J Gast, V P Edgcomb
The methanogenic endosymbionts of anaerobic protists represent the only known intracellular archaea, yet, almost nothing is known about genome structure and content in these lineages. Here, an almost complete genome of an intracellular Methanobacterium species was assembled from a metagenome derived from its host ciliate, a Heterometopus species. Phylogenomic analysis showed that the endosymbiont was closely related to free-living Methanobacterium isolates, and when compared to the genomes of free-living Methanobacterium, the endosymbiont did not show significant reduction in genome size or GC content...
May 24, 2018: Environmental Microbiology
Zhichao Zhou, Jie Pan, Fengping Wang, Ji-Dong Gu, Meng Li
Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundant archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to the marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-CoA centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, (v) and/or potentially other organic matter...
May 21, 2018: FEMS Microbiology Reviews
Feng Ju, Yubo Wang, Tong Zhang
Background: Methanogenic biodegradation of aromatic compounds depends on syntrophic metabolism. However, metabolic enzymes and pathways of uncultured microorganisms and their ecological interactions with methanogenic consortia are unknown because of their resistance to isolation and limited genomic information. Results: Genome-resolved metagenomics approaches were used to reconstruct and dissect 23 prokaryotic genomes from 37 and 20 °C methanogenic phenol-degrading reactors...
2018: Biotechnology for Biofuels
Anna Detman, Damian Mielecki, Łukasz Pleśniak, Michał Bucha, Marek Janiga, Irena Matyasik, Aleksandra Chojnacka, Mariusz-Orion Jędrysek, Mieczysław K Błaszczyk, Anna Sikora
Background: Anaerobic digestion, whose final products are methane and carbon dioxide, ensures energy flow and circulation of matter in ecosystems. This naturally occurring process is used for the production of renewable energy from biomass. Lactate, a common product of acidic fermentation, is a key intermediate in anaerobic digestion of biomass in the environment and biogas plants. Effective utilization of lactate has been observed in many experimental approaches used to study anaerobic digestion...
2018: Biotechnology for Biofuels
Julia Hassa, Irena Maus, Sandra Off, Alfred Pühler, Paul Scherer, Michael Klocke, Andreas Schlüter
The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters...
June 2018: Applied Microbiology and Biotechnology
Yangyang Jia, Siu-Kin Ng, Hongyuan Lu, Mingwei Cai, Patrick K H Lee
Background: Although anaerobic digestion for biogas production is used worldwide in treatment processes to recover energy from carbon-rich waste such as cellulosic biomass, the activities and interactions among the microbial populations that perform anaerobic digestion deserve further investigations, especially at the population genome level. To understand the cellulosic biomass-degrading potentials in two full-scale digesters, this study examined five methanogenic enrichment cultures derived from the digesters that anaerobically digested cellulose or xylan for more than 2 years under 35 or 55 °C conditions...
2018: Biotechnology for Biofuels
Stefano Campanaro, Laura Treu, Panagiotis G Kougias, Gang Luo, Irini Angelidaki
The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome...
September 1, 2018: Water Research
Shahid Manzoor, Anna Schnürer, Erik Bongcam-Rudloff, Bettina Müller
Syntrophic acetate oxidation operates close to the thermodynamic equilibrium and very little is known about the participating organisms and their metabolism. Clostridium ultunense is one of the most abundant syntrophic acetate-oxidising bacteria (SAOB) that are found in engineered biogas processes operating with high ammonia concentrations. It has been proven to oxidise acetate in cooperation with hydrogenotrophic methanogens. There is evidence that the Wood-Ljungdahl (WL) pathway plays an important role in acetate oxidation...
April 23, 2018: Genes
Monique Aouad, Najwa Taib, Anne Oudart, Michel Lecocq, Manolo Gouy, Céline Brochier-Armanet
Phylogenetic analyses of conserved core genes have disentangled most of the ancient relationships in Archaea. However, some groups remain debated, like the DPANN, a deep-branching super-phylum composed of nanosized archaea with reduced genomes. Among these, the Nanohaloarchaea require high-salt concentrations for growth. Their discovery in 2012 was significant because they represent, together with Halobacteria (a Class belonging to Euryarchaeota), the only two described lineages of extreme halophilic archaea...
October 2018: Molecular Phylogenetics and Evolution
Ying Li, Lianhua Li, Yongming Sun, Zhenhong Yuan
To investigate whether bioaugmentation could improve the digestion performance of high C/N ratio feedstock without co-digestion with nitrogen-rich substrate, different forms of enriched methanogenic culture were introduced to the continuous feed digesters. The performance efficiency of bioaugmentation on digestion improvement was compared. The effect of bioaugmentation on microbial community composition was revealed as well. Results demonstrated that routine bioaugmentation with liquid culture (containing the microbes and the medium remains) showed the best performance, with the organic loading rate (OLR), methane percentage, volumetric methane production (VMP) and volatile solid methane production (VSMP) higher at 1...
August 2018: Bioresource Technology
Florence Mus, Alexander B Alleman, Natasha Pence, Lance C Seefeldt, John W Peters
Most biological nitrogen fixation (BNF) results from the activity of the molybdenum nitrogenase (Mo-nitrogenase, Nif), an oxygen-sensitive metalloenzyme complex found in all known diazotrophs. Two alternative forms of nitrogenase, the vanadium nitrogenase (V-nitrogenase, Vnf) and the iron-only nitrogenase (Fe-only nitrogenase, Anf) have also been identified in the genome of some organisms that encode for Nif. It has been suggested that alternative nitrogenases were responsible for N2-fixation on early Earth because oceans were depleted of bioavailable Mo...
April 25, 2018: Metallomics: Integrated Biometal Science
Bastian Vögeli, Sylvain Engilberge, Eric Girard, François Riobé, Olivier Maury, Tobias J Erb, Seigo Shima, Tristan Wagner
Many reactions within a cell are thermodynamically unfavorable. To efficiently run some of those endergonic reactions, nature evolved intermediate-channeling enzyme complexes, in which the products of the first endergonic reactions are immediately consumed by the second exergonic reactions. Based on this concept, we studied how archaea overcome the unfavorable first reaction of isoprenoid biosynthesis-the condensation of two molecules of acetyl-CoA to acetoacetyl-CoA catalyzed by acetoacetyl-CoA thiolases (thiolases)...
March 27, 2018: Proceedings of the National Academy of Sciences of the United States of America
Sheng-Chung Chen, Hsing-Hua Huang, Mei-Chin Lai, Chieh-Yin Weng, Hsiu-Hui Chiu, Sen-Lin Tang, Denis Yu Rogozin, Andrey G Degermendzhy
A psychrotolerant, methylotrophic methanogen, strain YSF-03T , was isolated from the saline meromictic Lake Shira in Siberia. Cells of strain YSF-03T were non-motile, irregular cocci and 0.8-1.2 µm in diameter. The methanogenic substrates utilized by strain YSF-03T were methanol and trimethylamine. The temperature range of growth for strain YSF-03T was from 0 to 37 °C. The optimum growth conditions were 30-37 °C, pH 7.0-7.4 and 0.17 M NaCl. The G+C content of the genome of strain YSF-03T was 41...
April 2018: International Journal of Systematic and Evolutionary Microbiology
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