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Methanogen genomics

Yuanfei Li, Yuqi Li, Wei Jin, Thomas J Sharpton, Roderick I Mackie, Isaac Cann, Yanfen Cheng, Weiyun Zhu
In this study, the effects of a syntrophic methanogen on the growth of Pecoramyces sp. F1 was investigated by characterizing fermentation profiles, as well as functional genomic, transcriptomic, and proteomic analysis. The estimated genome size, GC content, and protein coding regions of strain F1 are 106.83 Mb, 16.07%, and 23.54%, respectively. Comparison of the fungal monoculture with the methanogen co-culture demonstrated that during the fermentation of glucose, the co-culture initially expressed and then down-regulated a large number of genes encoding both enzymes involved in intermediate metabolism and plant cell wall degradation...
2019: Frontiers in Microbiology
Sanae Sakai, Yoshihiro Takaki, Masayuki Miyazaki, Miyuki Ogawara, Katsunori Yanagawa, Junichi Miyazaki, Ken Takai
A novel hydrogenotrophic methanogen, strain HHBT , was isolated from a deep-sea hydrothermal vent chimney sample collected from Beebe Vent Field at the Mid-Cayman Spreading Center, Caribbean Sea. The cells were non-motile regular to irregular cocci possessing several flagella. The novel isolate grew at 60-80 °C, pH 5.0-7.4 and with 1-4 % of NaCl (w/v). The isolate utilized H2/CO2 as the only substrates for growth and methane production. The results of phylogenetic analyses of both 16S rRNA and mcrA gene sequences and comparative genome analysis indicated that HHBT represented a member of the order Methanococcales, and was closely related to the members of the genera Methanothermococcus and Methanotorris...
March 7, 2019: International Journal of Systematic and Evolutionary Microbiology
Susanne Wörner, Michael Pester
Active sulfate-reducing microorganisms (SRM) in freshwater sediments are under-examined, despite the well-documented cryptic sulfur cycle occurring in these low-sulfate habitats. In Lake Constance sediment, sulfate reduction rates of up to 1,800 nmol cm-3 day-1 were previously measured. To characterize its SRM community, we used a tripartite amplicon sequencing approach based on 16S rRNA genes, 16S rRNA, and dsrB transcripts (encoding the beta subunit of dissimilatory sulfite reductase). We followed the respective amplicon dynamics in four anoxic microcosm setups supplemented either with (i) chitin and sulfate, (ii) sulfate only, (iii) chitin only, or (iv) no amendment...
2019: Frontiers in Microbiology
E Sogodogo, M Drancourt, Ghiles Grine
Methanogens are strictly anaerobic archaea metabolising by-products of bacterial fermentation into methane by using three known metabolic pathways, i.e. the reduction of carbon dioxide, the fermentation of acetate or the dismutation of methanol or methylamines. Methanogens described in human microbiota include only Euryarchaeota, i.e. Methanobrevibacter smithii, Methanobrevibacter oralis, Methanobrevibacter arbophilus, Methanobrevibacter massiliensis, Methanomassiliicoccus luminyensis, Methanosphaera stadtmanae and Ca...
February 22, 2019: European Journal of Clinical Microbiology & Infectious Diseases
Nozomi Nakahara, Masaru K Nobu, Yoshihiro Takaki, Masayuki Miyazaki, Eiji Tasumi, Sanae Sakai, Miyuki Ogawara, Naoko Yoshida, Hideyuki Tamaki, Yuko Yamanaka, Arata Katayama, Takashi Yamaguchi, Ken Takai, Hiroyuki Imachi
A novel slow-growing, facultatively anaerobic, filamentous bacterium, strain MO-CFX2T , was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediment collected off the Shimokita Peninsula of Japan. Cells were multicellular filamentous, non-motile and Gram-stain-negative. The filaments were generally more than 20 µm (up to approximately 200 µm) long and 0.5-0.6 µm wide. Cells possessed pili-like structures on the cell surface and a multilayer structure in the cytoplasm...
February 18, 2019: International Journal of Systematic and Evolutionary Microbiology
Ai Minobe, Kenji Fukui, Hitomi Yonezu, Koki Ohshita, Saki Mizobuchi, Takashi Morisawa, Yuichi Hakumai, Takato Yano, Makoto Ashiuchi, Taisuke Wakamatsu
In eukaryotes and most bacteria, the MutS1/MutL-dependent mismatch repair system (MMR) corrects DNA mismatches that arise as replication errors. MutS1 recognizes mismatched DNA and stimulates the nicking endonuclease activity of MutL to incise mismatch-containing DNA. In archaea, there has been no experimental evidence to support the existence of the MutS1/MutL-dependent MMR. Instead, it was revealed that a large part of archaea possess mismatch-specific endonuclease EndoMS, indicating that the EndoMS-dependent MMR is widely adopted in archaea...
January 25, 2019: DNA Repair
Soham D Pore, Anupama Engineer, Sumit Singh Dagar, Prashant K Dhakephalkar
Biomethanation of rice straw was performed at 55 °C without thermochemical pretreatment using cattle dung supplemented with Methanothermobacter thermautotrophicus strains. Methane yield of 323 ml g-1 VS obtained under optimized conditions such as particle size (1 mm), carbon to nitrogen ratio (15:1), substrate to inoculum ratio (1:1), organic loading rate (7.5% w/v) and hydraulic retention time (20 days), was one of the highest ever reported from rice straw. Metagenome analysis revealed several putative novel taxa among resident microbes...
January 23, 2019: Bioresource Technology
Liang Wang, Qinghua Liu, Xiang Wu, Yue Huang, Michael J Wise, Zhanzhong Liu, Wei Wang, Junfeng Hu, Chunying Wang
Energy storage compounds play crucial roles in prokaryotic physiology. Five chemical compounds have been identified in prokaryotes as energy reserves: polyphosphate (polyP), polyhydroxyalkanoates (PHAs), glycogen, wax ester (WE) and triacylglycerol (TAG). Currently, no systematic study of archaeal energy storage metabolism exists. In this study, we collected 427 archaeal reference sequences from UniProt database. A thorough pathway screening of energy reserves led to an overview of distribution patterns of energy metabolism in archaea...
January 31, 2019: Scientific Reports
Xinyu Zhu, Stefano Campanaro, Laura Treu, Panagiotis G Kougias, Irini Angelidaki
In typical anaerobic digestion (AD) systems, the microbial functional assertion is hampered by synchronised versatile metabolism required for heterogeneous substrates degradation. Thus, the intricate methanogenic process from organic compounds remains an enigma after decades of empirical operation. In this study, simplified AD microbial communities were obtained with substrate specifications and continuous reactor operation. Genome-centric metagenomic approach was followed to holistically investigate the metabolic pathways of the AD and the microbial synergistic networks...
December 27, 2018: Water Research
Hang Yu, Dwi Susanti, Shawn E McGlynn, Connor T Skennerton, Karuna Chourey, Ramsunder Iyer, Silvan Scheller, Patricia L Tavormina, Robert L Hettich, Biswarup Mukhopadhyay, Victoria J Orphan
Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases...
2018: Frontiers in Microbiology
Yung Mi Lee, Kyuin Hwang, Jae Il Lee, Mincheol Kim, Chung Yeon Hwang, Hyun-Ju Noh, Hakkyum Choi, Hong Kum Lee, Jongsik Chun, Soon Gyu Hong, Seung Chul Shin
Candidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylum have remained elusive. Here, we examined the microbial communities of marine sediments of the Ross Sea, Antarctica, and found candidate phylum Atribacteria JS1 lineage was the most abundant candidate phylum accounting for 9...
2018: Frontiers in Microbiology
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
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