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Methanogen characterization

Alejandro Salgado-Flores, Alexander T Tveit, Andre-Denis Wright, Phil B Pope, Monica A Sundset
Rock ptarmigans (Lagopus muta) are gallinaceous birds inhabiting arctic and sub-arctic environments. Their diet varies by season, including plants or plant parts of high nutritional value, but also toxic plant secondary metabolites (PSMs). Little is known about the microbes driving organic matter decomposition in the cecum of ptarmigans, especially the last steps leading to methanogenesis. The cecum microbiome in wild rock ptarmigans from Arctic Norway was characterized to unveil their functional potential for PSM detoxification, methanogenesis and polysaccharides degradation...
2019: PloS One
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
Antti J Rissanen, Sari Peura, Promise A Mpamah, Sami Taipale, Marja Tiirola, Christina Biasi, Anita Mäki, Hannu Nykänen
Although sediments of small boreal humic lakes are important carbon stores and greenhouse gas sources, the composition and structuring mechanisms of their microbial communities have remained understudied. We analyzed the vertical profiles of microbial biomass indicators (PLFAs, DNA and RNA) and the bacterial and archaeal community composition (sequencing of 16S rRNA gene amplicons and qPCR of mcrA) in sediment cores collected from a typical small boreal lake. While microbial biomass decreased with sediment depth, viable microbes (RNA and PLFA) were present all through the profiles...
February 26, 2019: FEMS Microbiology Letters
R Snell-Castro, H O Méndez-Acosta, J Arreola-Vargas, V González-Álvarez, M Pintado-González, M T González-Morales, J J Godon
AIMS: The purpose of this study was to apply cDNA approach for the characterization of active prokaryotic community to understand microbial scenarios and performance of an AnSBR digester fed with acid hydrolysates of Agave tequilana var. azul bagasse (ATAB). METHODS AND RESULTS: The digester was implemented for methane production under organic loading rate (OLR) disturbances to correlate physicochemical variables with changes in abundance, diversity and population dynamics of active Bacteria and Archaea by Principal Components Analysis (PCA)...
February 25, 2019: Journal of Applied Microbiology
Thomas Reid, Ian G Droppo, Subba Rao Chaganti, Christopher G Weisener
The success and sustainability of aquatic ecosystems are driven by the complex, cooperative metabolism of microbes. Ecological engineering strategies often strive to harness this syntrophic synergy of microbial metabolism for the reclamation of contaminated environments worldwide. Currently, there is a significant knowledge gap in our understanding of how the natural microbial ecology overcomes thermodynamic limitations in recovering contaminated environments. Here, we used in-situ metatranscriptomics and associated metataxonomic analyses on sediments collected from naturalized freshwater man-made reservoirs within the Athabasca Oil Sands region of Alberta, Canada...
February 8, 2019: Science of the Total Environment
A Jiménez-González, R Ramírez-Vargas, A Gomez-Valadez, M Gutiérrez-Rojas, O Monroy-Hermosillo, S A Medina-Moreno
The aims of this work were to characterize the sorption and evaluate the inhibitory effect of octylphenol ethoxylate Triton X-100 (OPEOTx) on methanogenic and denitrifying sludges. According to Langmuir isotherm, maximums OPEOTx sorption values on methanogenic and denitrifying sludges were 60.70 mg (gVSS)-1 and 87.47 mg (gVSS)-1 respectively. The specific removal rate of chemical oxygen demand (rCOD ) and the accumulated volume biogas (VBG ) were used to evaluate the OPEOTx inhibitory effect on sludges...
February 6, 2019: Journal of Environmental Management
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
Guilherme H R Braz, Nuria Fernandez-Gonzalez, Juan M Lema, Marta Carballa
There is still a lack of information about microbial interactions of anaerobic digestion microbiome during process disturbance which limits our ability to predict the mechanisms that drive community dynamics on these events. This paper aims to determine how an organic overloading affects these interactions and to characterize in detail the microbiome structure and diversity in sewage sludge anaerobic reactors during an acidosis event. Two identical sewage sludge anaerobic reactors were subjected to an organic loading shock by adding glycerol waste...
January 23, 2019: Chemosphere
Sabine Koch, Fabian Kohrs, Patrick Lahmann, Thomas Bissinger, Stefan Wendschuh, Dirk Benndorf, Udo Reichl, Steffen Klamt
Constraint-based modeling (CBM) is increasingly used to analyze the metabolism of complex microbial communities involved in ecology, biomedicine, and various biotechnological processes. While CBM is an established framework for studying the metabolism of single species with linear stoichiometric models, CBM of communities with balanced growth is more complicated, not only due to the larger size of the multi-species metabolic network but also because of the bilinear nature of the resulting community models. Moreover, the solution space of these community models often contains biologically unrealistic solutions, which, even with model linearization and under application of certain objective functions, cannot easily be excluded...
February 1, 2019: PLoS Computational Biology
Victoria L Jeter, Theodoric A Mattes, Nathaniel R Beattie, Jorge C Escalante-Semerena
Cobamides (Cbas) are coenzymes used by cells from all domains of life, but made de novo only by some bacteria and archaea. The last steps of the cobamide biosynthetic pathway activate the corrin ring and the lower ligand base, condense the activated intermediates, and dephosphorylate the product prior to the release of the biologically active coenzyme. In bacteria, a phosphoribosyltransferase (PRTase) enyzme activates the base into its α-mononucleotide. The enzyme from Salmonella enterica ( SeCobT) has been extensively biochemically and structurally characterized...
January 14, 2019: Biochemistry
C M Welty, B A Wenner, B K Wagner, Y Roman-Garcia, J E Plank, R A Meller, A M Gehman, J L Firkins
Nitrates have been fed to ruminants, including dairy cows, as an electron sink to mitigate CH4 emissions. In the NO3 - reduction process, NO2 - can accumulate, which could directly inhibit methanogens and possibly other microbes in the rumen. Saccharomyces cerevisiae yeast was hypothesized to decrease NO2 - through direct reduction or indirectly by stimulating the bacterium Selenomonas ruminantium, which is among the ruminal bacteria most well characterized to reduce both NO3 - and NO2 - . Ruminal fluid was incubated in continuous cultures fed diets without or with NaNO3 (1...
January 10, 2019: Journal of Dairy Science
Fuguang Xue, Xuemei Nan, Yunlei Li, Xiaohua Pan, Yuming Guo, Linshu Jiang, Benhai Xiong
BACKGROUND: Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows' production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear...
January 3, 2019: BMC Veterinary Research
Adam Pyzik, Martyna Ciezkowska, Pawel S Krawczyk, Adam Sobczak, Lukasz Drewniak, Andrzej Dziembowski, Leszek Lipinski
BACKGROUND: Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways...
December 20, 2018: Microbial Cell Factories
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
M Quintero, M Alzate, F Patiño, A Arboleda, Y Pinzón, A Mantilla, H Escalante
The aim of this work was to use an inexpensive technique, such as the most probable number, MPN to quantitatively and qualitatively examine microbial groups in anaerobic digestion, AD of cattle manure, CM. Different diluents and mixing ratios were evaluated in 100 mL reactors using biomethane potential, BMP, as output variable. MPN tests were performed to samples from a 23 L tank and 6.5 m3 low-cost tubular digester, LCTD. To monitor LCTD stability, volatile solids, VS, specific methanogenic activity, SMA, pH, volatile fatty acids, VFA, and chemical oxygen demand, COD were measured...
November 29, 2018: Bioresource Technology
Qi Liu, Horst Kämpf, Robert Bussert, Patryk Krauze, Fabian Horn, Tobias Nickschick, Birgit Plessen, Dirk Wagner, Mashal Alawi
The Cheb Basin (CZ) is a shallow Neogene intracontinental basin filled with fluvial and lacustrine sediments that is located in the western part of the Eger Rift. The basin is situated in a seismically active area and is characterized by diffuse degassing of mantle-derived CO2 in mofette fields. The Hartoušov mofette field shows a daily CO2 flux of 23-97 tons of CO2 released over an area of 0.35 km2 and a soil gas concentration of up to 100% CO2 . The present study aims to explore the geo-bio interactions provoked by the influence of elevated CO2 concentrations on the geochemistry and microbial community of soils and sediments...
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
Rodney Burton, Mehmet Can, Daniel Esckilsen, Seth Wiley, Stephen W Ragsdale
The chapter focuses on the methods involved in producing and characterizing two key nickel-iron-sulfur enzymes in the Wood-Ljungdahl pathway (WLP) of anaerobic conversion of carbon dioxide fixation into acetyl-CoA: carbon monoxide dehydrogenase (CODH) and acetyl-CoA synthase (ACS). The WLP is used for biosynthesis of cell material and energy conservation by anaerobic bacteria and archaea, and it is central to several industrial biotechnology processes aimed at using syngas and waste gases for the production of fuels and chemicals...
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
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