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Methanogen characterization

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https://www.readbyqxmd.com/read/30529479/physicochemical-and-microbiological-monitoring-of-anaerobic-digestion-at-laboratory-and-low-cost-tubular-digester
#1
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
https://www.readbyqxmd.com/read/30524401/influence-of-co-2-degassing-on-the-microbial-community-in-a-dry-mofette-field-in-hartou%C3%A5-ov-czech-republic-western-eger-rift
#2
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
https://www.readbyqxmd.com/read/30523430/characterization-of-the-lytic-archaeal-virus-drs3-infecting-methanobacterium-formicicum
#3
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
https://www.readbyqxmd.com/read/30509471/production-and-properties-of-enzymes-that-activate-and-produce-carbon-monoxide
#4
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
https://www.readbyqxmd.com/read/30498478/members-of-marinobacter-and-arcobacter-influence-system-biogeochemistry-during-early-production-of-hydraulically-fractured-natural-gas-wells-in-the-appalachian-basin
#5
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
https://www.readbyqxmd.com/read/30496201/rumen-microbiome-in-dairy-calves-fed-copper-and-grape-pomace-dietary-supplementations-composition-and-predicted-functional-profile
#6
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
https://www.readbyqxmd.com/read/30408686/performance-of-anaerobic-treatment-of-blackwater-collected-from-different-toilet-flushing-systems-can-we-achieve-both-energy-recovery-and-water-conservation
#7
Mengjiao Gao, Lei Zhang, Anna P Florentino, Yang Liu
Source-diverted blackwater (toilet wastewater) contains most of the organic energy in domestic wastewater and can be treated anaerobically to maximize energy recovery. Blackwater collected from toilets of different water saving options (e.g., conventional, dual and vacuum toilets) represents different characteristics, but their digestibility has not been discussed. In the present study, blackwater collected from different toilet flushing systems were characterized and compared in terms of chemical composition, digestibility and microbial population development during biochemical methane potential (BMP) tests...
October 25, 2018: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/30348104/petroleum-hydrocarbon-rich-oil-refinery-sludge-of-north-east-india-harbours-anaerobic-fermentative-sulfate-reducing-syntrophic-and-methanogenic-microbial-populations
#8
Ajoy Roy, Pinaki Sar, Jayeeta Sarkar, Avishek Dutta, Poulomi Sarkar, Abhishek Gupta, Balaram Mohapatra, Siddhartha Pal, Sufia K Kazy
BACKGROUND: Sustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on-site bioremediation...
October 22, 2018: BMC Microbiology
https://www.readbyqxmd.com/read/30340252/potential-methane-production-and-molecular-characterization-of-bacterial-and-archaeal-communities-in-a-horizontal-subsurface-flow-constructed-wetland-under-cold-and-warm-seasons
#9
Daniela López, Mario Sepúlveda-Mardones, Nathaly Ruiz-Tagle, Katherine Sossa, Enrica Uggetti, Gladys Vidal
Organic matter removal in a horizontal subsurface flow constructed wetland (HSSF) treating wastewater is associated with the presence of bacteria and archaea. These organisms perform anaerobic microbial processes such as methanogenesis, which can lead to methane emissions. The aim of this study was to evaluate methane production and characterize the bacterial and archaeal communities found in HSSFs treating secondary urban wastewater during cold and warm seasons. The pilot system used in this study corresponds to four HSSFs, two planted with Phragmites australis (HSSF-Phr) and two planted with Schoenoplectus californicus (HSSF-Sch), the monitoring was carried out for 1335 days...
January 15, 2019: Science of the Total Environment
https://www.readbyqxmd.com/read/30335986/unraveling-microbial-communities-associated-with-methylmercury-production-in-paddy-soils
#10
Yu-Rong Liu, Alexander Johs, Li Bi, Xia Lu, Hang-Wei Hu, Dan Sun, Ji-Zheng He, Baohua Gu
Rice consumption is now recognized as an important pathway of human exposure to the neurotoxin methylmercury (MeHg), particularly in countries where rice is a staple food. Although the discovery of a two-gene cluster hgcAB has linked Hg methylation to several phylogenetically diverse groups of anaerobic microorganisms converting inorganic mercury (Hg) to MeHg, the prevalence and diversity of Hg methylators in microbial communities of rice paddy soils remain unclear. We characterized the abundance and distribution of hgcAB genes using third-generation PacBio long-read sequencing and Illumina short-read metagenomic sequencing, in combination with quantitative PCR analyses in several mine-impacted paddy soils from southwest China...
November 6, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/30291120/response-of-the-anaerobic-methanotroph-candidatus-methanoperedens-nitroreducens-to-oxygen-stress
#11
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
https://www.readbyqxmd.com/read/30242005/methanogens-and-iron-reducing-bacteria-the-overlooked-members-of-mercury-methylating-microbial-communities-in-boreal-lakes
#12
Andrea G Bravo, Sari Peura, Moritz Buck, Omneya Ahmed, Alejandro Mateos-Rivera, Sonia Herrero Ortega, Jeffra K Schaefer, Sylvain Bouchet, Julie Tolu, Erik Björn, Stefan Bertilsson
Methylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, the diversity of these mercury methylating microbial communities remains largely unexplored. Previous studies have implicated sulphate-reducing bacteria as the main mercury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury methylating microbial communities of boreal lake sediments using high-throughput sequencing of 16S rRNA and hgcA genes...
September 21, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/30231929/metatranscriptomics-reveals-a-differential-temperature-effect-on-the-structural-and-functional-organization-of-the-anaerobic-food-web-in-rice-field-soil
#13
Jingjing Peng, Carl-Eric Wegner, Qicheng Bei, Pengfei Liu, Werner Liesack
BACKGROUND: The expected increase in global surface temperature due to climate change may have a tremendous effect on the structure and function of the anaerobic food web in flooded rice field soil. Here, we used the metatranscriptomic analysis of total RNA to gain a system-level understanding of this temperature effect on the methanogenic food web. RESULTS: Mesophilic (30 °C) and thermophilic (45 °C) food web communities had a modular structure. Family-specific rRNA dynamics indicated that each network module represents a particular function within the food webs...
September 19, 2018: Microbiome
https://www.readbyqxmd.com/read/30231921/a-metagenomics-roadmap-to-the-uncultured-genome-diversity-in-hypersaline-soda-lake-sediments
#14
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
https://www.readbyqxmd.com/read/30220912/machine-learning-analysis-of-microbial-flow-cytometry-data-from-nanoparticles-antibiotics-and-carbon-sources-perturbed-anaerobic-microbiomes
#15
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
https://www.readbyqxmd.com/read/30176486/functional-biodiversity-and-plasticity-of-methanogenic-biomass-from-a-full-scale-mesophilic-anaerobic-digester-treating-nitrogen-rich-agricultural-wastes
#16
J Ruiz-Sánchez, M Guivernau, B Fernández, J Vila, M Viñas, V Riau, F X Prenafeta-Boldú
The effect of ammonia on methanogenic biomass from a full-scale agricultural digester treating nitrogen-rich materials was characterized in batch activity assays subjected to increasing concentrations of total ammonia N. Acetotrophic and methanogenic profiles displayed prolonged lag phases and reduced specific activity rates at 6.0 gN-TAN L-1 , though identical methane yields were ultimately reached. These results agreed with the expression levels of selected genes from bacteria and methanogenic archaea (qPCR of 16S rRNA and mrcA cDNA transcripts)...
February 1, 2019: Science of the Total Environment
https://www.readbyqxmd.com/read/30142616/effect-of-different-particle-size-biochar-on-methane-emissions-during-pig-manure-wheat-straw-aerobic-composting-insights-into-pore-characterization-and-microbial-mechanisms
#17
Xueqin He, Hongjie Yin, Xiaoxi Sun, Lujia Han, Guangqun Huang
This study explored the effects of different particle sizes of rice straw biochar (RSB) on the methane emissions of pig manure/wheat straw aerobic composting experiments to provide a theoretical suggestion for biochar application. The experiments were conducted with a control group, powder (<1 mm) group, and granular (4 mm-1 cm) group. Methane emissions increased by 56.84% in the powder group but decreased by 22.15% in the granular group during the aerobic composting. Methane was generated by methanogens and methanotrophs in the specific anaerobic micro-environment characterized by X-ray micro-computed tomography (micro-CT)...
November 2018: Bioresource Technology
https://www.readbyqxmd.com/read/30136425/co-occurrence-network-analysis-reveals-thermodynamics-driven-microbial-interactions-in-methanogenic-bioreactors
#18
Takashi Narihiro, Masaru K Nobu, Ben T W Bocher, Ran Mei, Wen-Tso Liu
Methanogenic bioreactors have been applied to treat purified terephthalic acid (PTA) wastewater containing complex aromatic compounds, such as terephthalic acid, para-toluic acid and benzoic acid. This study characterized the interaction of microbial populations in 42 samples obtained from 10 PTA-degrading methanogenic bioreactors. Approximately, 54 dominant populations (11 methanogens, 8 syntrophs and 35 functionally unknown clades) that represented 73.9% of total 16S rRNA gene iTag sequence reads were identified...
August 22, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30121030/characteristics-of-microbial-community-indicate-anthropogenic-impact-on-the-sediments-along-the-yangtze-estuary-and-its-coastal-area-china
#19
Xing-Pan Guo, Yi Yang, Zuo-Shun Niu, Da-Pei Lu, Chun-Hong Zhu, Jing-Nan Feng, Jia-Yuan Wu, Yu-Ru Chen, Fei-Yun Tou, Min Liu, Lijun Hou
In the contaminated coastal sediments, variations of microbial community can reflect the impact of anthropogenic activities. The identification, evaluation and monitoring of the potential bio-indicator species and biomarker communities are vital for the ecological studies in sedimentary environments. Based on the high-throughput sequencing, the microbial communities were characterized in the sediments along the Yangtze Estuary and its coastal area. The results showed that the structure and composition of microbial communities varied greatly among different sampling sites at the phyla level, especially for Euryarchaeota...
January 15, 2019: Science of the Total Environment
https://www.readbyqxmd.com/read/30120599/bacterial-and-archaeal-profiling-of-hypersaline-microbial-mats-and-endoevaporites-under-natural-conditions-and-methanogenic-microcosm-experiments
#20
José Q García-Maldonado, Alejandra Escobar-Zepeda, Luciana Raggi, Brad M Bebout, Alejandro Sanchez-Flores, Alejandro López-Cortés
Bacterial and archaeal community structure of five microbial communities, developing at different salinities in Baja California Sur, Mexico, were characterized by 16S rRNA sequencing. The response of the microbial community to artificial changes in salinity-sulfate concentrations and to addition of trimethylamine was also evaluated in microcosm experiments. Ordination analyses of the microbial community structure showed that microbial composition was distinctive for each hypersaline site. Members of bacteria were dominated by Bacteroidetes and Proteobacteria phyla, while Halobacteria of the Euryarchaeota phylum was the most represented class of archaea for all the environmental samples...
November 2018: Extremophiles: Life Under Extreme Conditions
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