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Methanogen genomics

Hirohito Tsurumaru, Naofumi Ito, Koji Mori, Satoshi Wakai, Taku Uchiyama, Takao Iino, Akira Hosoyama, Hanako Ataku, Keiko Nishijima, Miyako Mise, Ai Shimizu, Takeshi Harada, Hiroshi Horikawa, Natsuko Ichikawa, Tomohiro Sekigawa, Koji Jinno, Satoshi Tanikawa, Jun Yamazaki, Kazumi Sasaki, Syuji Yamazaki, Nobuyuki Fujita, Shigeaki Harayama
Certain methanogens deteriorate steel surfaces through a process called microbiologically influenced corrosion (MIC). However, the mechanisms of MIC, whereby methanogens oxidize zerovalent iron (Fe0 ), are largely unknown. In this study, Fe0 -corroding Methanococcus maripaludis strain OS7 and its derivative (strain OS7mut1) defective in Fe0 -corroding activity were isolated. Genomic analysis of these strains demonstrated that the strain OS7mut1 contained a 12-kb chromosomal deletion. The deleted region, termed "MIC island", encoded the genes for the large and small subunits of a [NiFe] hydrogenase, the TatA/TatC genes necessary for the secretion of the [NiFe] hydrogenase, and a gene for the hydrogenase maturation protease...
October 11, 2018: Scientific Reports
Pratishtha Vedalankar, Baishnab C Tripathy
The nonhomologous enzymes, the light-independent protochlorophyllide reductase (DPOR) and the light-dependent protochlorophyllide oxidoreductase (LPOR), catalyze the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) in the penultimate step of biosynthesis of chlorophyll (Chl) required for photosynthetic light absorption and energy conversion. The two enzymes differ with respect to the requirement of light for catalysis and oxygen sensitivity. DPOR and LPOR initially evolved in the ancestral prokaryotic genome perhaps at different times...
October 6, 2018: Protoplasma
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
Cong Liu, Lihui Mao, Xiongmin Zheng, Jiangan Yuan, Beijuan Hu, Yaohui Cai, Hongwei Xie, Xiaojue Peng, Xia Ding
The growth of all methanogens is limited to a specific temperature range. However, Methanothermobacter thermautotrophicus can be found in a variety of natural and artificial environments, the temperatures of which sometimes even exceed the temperature growth ranges of thermophiles. As a result, the extent to which methane production and survival are affected by temperature remains unclear. To investigate the mechanisms of methanogenesis that Archaea have evolved to cope with drastic temperature shifts, the responses of Methanothermobacter thermautotrophicus to temperature were investigated under a high temperature growth (71°C) and cold shock (4°C) using Isobaric tags for relative and absolute quantitation (iTRAQ)...
September 10, 2018: MicrobiologyOpen
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
Anja Poehlein, Dominik Schneider, Melissa Soh, Rolf Daniel, Henning Seedorf
Methanobrevibacter and Methanosphaera species represent some of the most prevalent methanogenic archaea in the gastrointestinal tract of animals and humans and play an important role in this environment. The aim of this study was to identify genomic features that are shared or specific for members of each genus with a special emphasis of the analysis on the assimilation of nitrogen and acetate and the utilization of methanol and ethanol for methanogenesis. Here, draft genome sequences of Methanobrevibacter thaueri strain DSM 11995T , Methanobrevibacter woesei strain DSM 11979T , and Methanosphaera cuniculi strain 4103T are reported and compared to those of 16 other Methanobrevibacter and Methanosphaera genomes, including genomes of the 13 currently available types of strains of the two genera...
2018: Archaea: An International Microbiological Journal
Hadi Nazem-Bokaee, Costas D Maranas
The abundance of methane in shale gas and of other gases such as carbon monoxide, hydrogen, and carbon dioxide as chemical process byproducts has motivated the use of gas fermentation for bioproduction. Recent advances in metabolic engineering and synthetic biology allow for engineering of microbes metabolizing a variety of chemicals including gaseous feeds into a number of biorenewables and transportation liquid fuels. New computational tools enable the systematic exploration of all feasible conversion alternatives...
2018: Frontiers in Microbiology
F Beulig, H Røy, S E McGlynn, B B Jørgensen
Methane in the seabed is mostly oxidized to CO2 with sulfate as the oxidant before it reaches the overlying water column. This microbial oxidation takes place within the sulfate-methane transition (SMT), a sediment horizon where the downward diffusive flux of sulfate encounters an upward flux of methane. Across multiple sites in the Baltic Sea, we identified a systematic discrepancy between the opposing fluxes, such that more sulfate was consumed than expected from the 1:1 stoichiometry of methane oxidation with sulfate...
September 7, 2018: ISME Journal
Catalina A Hidalgo, Masaru K Nobu, Takashi Narihiro, Hideyuki Tamaki, Wen-Tso Liu, Yoichi Kamagata, Alfons J M Stams, Hiroyuki Imachi, Diana Z Sousa
Under methanogenic conditions, short-chain fatty acids are common byproducts from degradation of organic compounds and conversion of these acids is an important component of the global carbon cycle. Due to the thermodynamic difficulty of propionate degradation, this process requires syntrophic interaction between a bacterium and partner methanogen; however, the metabolic strategies and behavior involved are not fully understood. In this study, the first genome analysis of obligately syntrophic propionate degraders (Pelotomaculum schinkii HH and P...
August 20, 2018: Environmental Microbiology
Saroj Poudel, Eric C Dunham, Melody R Lindsay, Maximiliano J Amenabar, Elizabeth M Fones, Daniel R Colman, Eric S Boyd
Twelve evolutionarily unrelated oxidoreductases form enzyme complexes that catalyze the simultaneous coupling of exergonic and endergonic oxidation-reduction reactions to circumvent thermodynamic barriers and minimize free energy loss in a process known as flavin-based electron bifurcation. Common to these 12 bifurcating (Bf) enzymes are protein-bound flavin, the proposed site of bifurcation, and the electron carrier ferredoxin. Despite the documented role of Bf enzymes in balancing the redox state of intracellular electron carriers and in improving the efficiency of cellular metabolism, a comprehensive description of the diversity and evolutionary history of Bf enzymes is lacking...
2018: Frontiers in Microbiology
Nina Lackner, Anna Hintersonnleitner, Andreas Otto Wagner, Paul Illmer
Although Methanosarcinales are versatile concerning their methanogenic substrates, the ability of Methanosarcina thermophila to use carbon dioxide (CO2 ) for catabolic and anabolic metabolism was not proven until now. Here, we show that M. thermophila used CO2 to perform hydrogenotrophic methanogenesis in the presence as well as in the absence of methanol. During incubation with hydrogen, the methanogen utilized the substrates methanol and CO2 consecutively, resulting in a biphasic methane production. Growth exclusively from CO2 occurred slowly but reproducibly with concomitant production of biomass, verified by DNA quantification...
2018: Archaea: An International Microbiological Journal
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 with the genomes of free-living Methanobacterium, the endosymbiont did not show significant reduction in genome size or GC content...
July 2018: Environmental Microbiology
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