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Methanogen genomics

Sandro Wolf, Martin A Fischer, Anne Kupczok, Jochen Reetz, Tobias Kern, Ruth A Schmitz, Michael Rother
Viruses are ubiquitous in the biosphere and greatly affect the hosts they infect. It is generally accepted that members of every microbial taxon are susceptible to at least one virus, and a plethora of bacterial viruses are known. In contrast, knowledge of the archaeal virosphere is still limited. Here, a novel lytic archaeal virus is described, designated "Drs3", as well as its host, Methanobacterium formicicum strain Khl10. This hydrogenotrophic methanogenic archaeon and its virus were isolated from the anaerobic digester of an experimental biogas plant in Germany...
December 6, 2018: Archives of Virology
Dipti D Nayak, William W Metcalf
Methanogenic archaea generate methane as a by-product of anaerobic respiration using CO2 , C1 compounds (like methanol or methylated amines), or acetate as terminal electron acceptors. Methanogens are an untapped resource for biotechnological advances related to methane production as well as methane consumption. However, key biological features of these organisms remain poorly understood. One such feature is the enzyme methyl-coenzyme M reductase (referred to as MCR), which catalyzes the last step in the methanogenic pathway and results in methane formation...
2018: Methods in Enzymology
Morgan V Evans, Jenny Panescu, Andrea J Hanson, Susan A Welch, Julia M Sheets, Nicholas Nastasi, Rebecca A Daly, David R Cole, Thomas H Darrah, Michael J Wilkins, Kelly C Wrighton, Paula J Mouser
Hydraulic fracturing is the prevailing method for enhancing recovery of hydrocarbon resources from unconventional shale formations, yet little is understood regarding the microbial impact on biogeochemical cycling in natural-gas wells. Although the metabolisms of certain fermentative bacteria and methanogenic archaea that dominate in later produced fluids have been well studied, few details have been reported on microorganisms prevelant during the early flowback period, when oxygen and other surface-derived oxyanions and nutrients become depleted...
2018: Frontiers in Microbiology
Filippo Biscarini, Fiorentina Palazzo, Federica Castellani, Giulia Masetti, Lisa Grotta, Angelo Cichelli, Giuseppe Martino
The rumen microbiome is fundamental for the productivity and health of dairy cattle and diet is known to influence the rumen microbiota composition. In this study, grape-pomace, a natural source of polyphenols, and copper sulfate were provided as feed supplementation in 15 Holstein-Friesian calves, including 5 controls. After 75 days of supplementation, genomic DNA was extracted from the rumen liquor and prepared for 16S rRNA-gene sequencing to characterize the composition of the rumen microbiota. From this, the rumen metagenome was predicted to obtain the associated gene functions and metabolic pathways in a cost-effective manner...
2018: PloS One
R Prathiviraj, P Chellapandi
Methanothermobacter thermautotrophicus ΔH (MTH) is a potential methanogen known to reduce CO2 with H2 for producing methane biofuel in thermophilic digesters. The genome of this organism contains ~50.5% conserved hypothetical proteins (HPs; operome) whose function is still not determined precisely. Here, we employed a combined bioinformatics approach to annotate a precise function to HPs and categorize them as enzymes, binding proteins, and transport proteins. Results of our study show that 315 (35.6%) HPs have exhibited well-defined functions contributing imperative roles in diverse cellular metabolism...
November 13, 2018: International Journal of Biological Macromolecules
Garrett J Smith, Jordan C Angle, Lindsey M Solden, Mikayla A Borton, Timothy H Morin, Rebecca A Daly, Michael D Johnston, Kay C Stefanik, Richard Wolfe, Bohrer Gil, Kelly C Wrighton
Microbial carbon degradation and methanogenesis in wetland soils generate a large proportion of atmospheric methane, a highly potent greenhouse gas. Despite their potential to mitigate greenhouse gas emissions, knowledge about methane-consuming methanotrophs is often limited to lower-resolution single-gene surveys that fail to capture the taxonomic and metabolic diversity of these microorganisms in soils. Here our objective was to use genome-enabled approaches to investigate methanotroph membership, distribution, and in situ activity across spatial and seasonal gradients in a freshwater wetland near Lake Erie...
November 6, 2018: MBio
Alessandra Fontana, Panagiotis G Kougias, Laura Treu, Adam Kovalovszki, Giorgio Valle, Fabrizio Cappa, Lorenzo Morelli, Irini Angelidaki, Stefano Campanaro
BACKGROUND: The expansion of renewable energy produced by windmills and photovoltaic panels has generated a considerable electricity surplus, which can be utilized in water electrolysis systems for hydrogen production. The resulting hydrogen can then be funneled to anaerobic digesters for biogas upgrading (biomethanation) purposes (power-to-methane) or to produce high value-added compounds such as short-chain fatty acids (power-to-chemicals). Genome-centric metagenomics and metatranscriptomic analyses were performed to better understand the metabolic dynamics associated with H2 injection in two different configurations of anaerobic digesters treating acidic wastes, specifically cheese manufacturing byproducts...
October 27, 2018: Microbiome
Leticia Abecia, Gonzalo Martínez-Fernandez, Kate Waddams, Antonio Ignacio Martín-García, Eric Pinloche, Christopher J Creevey, Stuart Edward Denman, Charles James Newbold, David R Yáñez-Ruiz
This work aimed to gain insight into the transition from milk to solid feeding at weaning combining genomics and metabolomics on rumen contents from goat kids treated with a methanogenic inhibitor (bromochloromethane, BCM). Sixteen goats giving birth to two kids were used. Eight does were treated (D+) with BCM after giving birth and over 2 months. One kid per doe in both groups was treated with BCM (k+) for 3 months while the other was untreated (k-). Rumen samples were collected from kids at weaning (W) and 1 (W + 1) and 4 (W + 4) months after and from does at weaning and subjected to 16S pyrosequencing and metabolomics analyses combining GC/LC-MS...
2018: Frontiers in Microbiology
Ying Li, Gaixiu Yang, Lianhua Li, Yongming Sun
This study aims to investigate the performance of bioaugmentation with an acid-tolerant methanogenic culture to recover deteriorated anaerobic digestion caused by organic overloading. The function of bioaugmentation was evaluated in terms of substance metabolism, microbial community structure, and gene function. Our findings demonstrate that routine bioaugmentation effectively recovered the failing digester by degrading accumulated volatile fatty acids and increasing pH. In contrast, a non-bioaugmentation reactor (control) did not recover by itself, while abiotic augmentation restored the digestion performance temporarily but the digester failed again at an organic loading rate of 1...
September 2018: Waste Management
Ran Mei, Masaru K Nobu, Takashi Narihiro, Jimmy Yu, Arun Sathyagal, Eric Willman, Wen-Tso Liu
To determine whether the addition of conductive materials could enhance methane production by direct interspecies electron transfer (DIET), we operated three anaerobic reactors amended with non-conductive (ceramic) or conductive materials (anthracite and granular activated carbon (GAC)). Throughout eight months of operation, ethanol was consistently detected as the major fermentation product. The specific yield in the anthracite and GAC-added reactors increased by 31.5% and 43.3%, respectively, compared to the ceramic-added reactor...
October 11, 2018: Water Research
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 P Hidalgo-Ahumada, 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 behaviour 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
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