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Relevant bibliographies by topics / Methanobacteriaceae

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Academic literature on the topic 'Methanobacteriaceae'

Author: Grafiati

Published: 4 June 2021

Last updated: 27 January 2023

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Journal articles on the topic "Methanobacteriaceae"

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Tagawa, T., K. Syutsubo, Y. Sekiguchil, A. Ohashi, and H. Harada. "Quantification of methanogen cell density in anaerobic granular sludge consortia by fluorescence in-situ hybridization." Water Science and Technology 42, no. 3-4 (August 1, 2000): 77–82. http://dx.doi.org/10.2166/wst.2000.0361.

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Whole cell fluorescence in-situ hybridization (FISH) with 16S rRNA targeted oligonucleotides was applied to reveal the microbial ecological structure of UASB-grown granular sludge. The FISH analysis indicated that the members of the domain Archaea accounted for 28 to 53% of the total cells in various granular sludge sources, while Methanosaeta and Methanobacteriaceae cells accounted for 13 to 38%, and 4 to 27%, respectively. Methanosaeta cell density and Methanobacteriaceae cell density were strongly correlated, respectively, with acetate-utilizing methane production activity and with hydrogen-utilizing methane production activity.

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Kotsyurbenko, O. R., M. W. Friedrich, M. V. Simankova, A. N. Nozhevnikova, P. N. Golyshin, K. N. Timmis, and R. Conrad. "Shift from Acetoclastic to H2-Dependent Methanogenesis in a West Siberian Peat Bog at Low pH Values and Isolation of an Acidophilic Methanobacterium Strain." Applied and Environmental Microbiology 73, no. 7 (February 2, 2007): 2344–48. http://dx.doi.org/10.1128/aem.02413-06.

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ABSTRACT Methane production and archaeal community composition were studied in samples from an acidic peat bog incubated at different temperatures and pH values. H2-dependent methanogenesis increased strongly at the lowest pH, 3.8, and Methanobacteriaceae became important except for Methanomicrobiaceae and Methanosarcinaceae. An acidophilic and psychrotolerant Methanobacterium sp. was isolated using H2-plus-CO2-supplemented medium at pH 4.5.

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Depkat-Jakob, Peter S., Sindy Hunger, Kristin Schulz, George G. Brown, Siu M. Tsai, and Harold L. Drake. "Emission of Methane by Eudrilus eugeniae and Other Earthworms from Brazil." Applied and Environmental Microbiology 78, no. 8 (February 17, 2012): 3014–19. http://dx.doi.org/10.1128/aem.07949-11.

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ABSTRACTEarthworms emit denitrification-derived nitrous oxide and fermentation-derived molecular hydrogen. The present study demonstrated that the earthwormEudrilus eugeniae, obtained in Brazil, emitted methane. Other worms displayed a lesser or no capacity to emit methane. Gene and transcript analyses ofmcrA(encoding the alpha subunit of methyl-CoM reductase) in gut contents ofE. eugeniaesuggested thatMethanosarcinaceae,Methanobacteriaceae, andMethanomicrobiaceaemight be associated with this emission.

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Xing, Peng, Huabing Li, Qing Liu, and Jiuwen Zheng. "Composition of the archaeal community involved in methane production during the decomposition of Microcystis blooms in the laboratory." Canadian Journal of Microbiology 58, no. 10 (October 2012): 1153–58. http://dx.doi.org/10.1139/w2012-097.

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We investigated the microbial processes involved in methane (CH4) production from Microcystis bloom scums at different temperatures. A Microcystis slurry was collected from Lake Taihu and incubated in airtight bottles at 15, 25, and 35 °C. The production of CH4 was monitored, and the emission rate was calculated. The dynamics of the methanogenic community were analyzed by terminal restriction fragment length polymorphism analysis of archaeal 16S rRNA genes. Phylogenetic information for the methanogens was obtained by cloning and sequencing selected samples. Significant CH4 emission from the Microcystis scums was delayed by approximately 12 days by the natural oxygen depletion process, and CH4 production was enhanced at higher temperatures. Phylogenetic analysis indicated that the archaeal community was composed of Methanomicrobiales, Methanobacteriaceae, and a novel cluster of Archaea. An apparent succession of the methanogenic community was demonstrated, with a predominance of Methanobacteriaceae at higher temperatures. Higher temperatures enhanced the methanogenic transformation of the Microcystis biomass and the phylogenetic dominance of hydrogenotrophic methanogens, suggesting that H2 and CO2 might be the primary substrates for CH4 production during Microcystis decomposition without the participation of lake sediment. This work provides insight into the microbial components involved in Microcystis biomass fermentation in controlled systems.

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Steinberg, Lisa M., and John M. Regan. "mcrA-Targeted Real-Time Quantitative PCR Method To Examine Methanogen Communities." Applied and Environmental Microbiology 75, no. 13 (May 15, 2009): 4435–42. http://dx.doi.org/10.1128/aem.02858-08.

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ABSTRACT Methanogens are of great importance in carbon cycling and alternative energy production, but quantitation with culture-based methods is time-consuming and biased against methanogen groups that are difficult to cultivate in a laboratory. For these reasons, methanogens are typically studied through culture-independent molecular techniques. We developed a SYBR green I quantitative PCR (qPCR) assay to quantify total numbers of methyl coenzyme M reductase α-subunit (mcrA) genes. TaqMan probes were also designed to target nine different phylogenetic groups of methanogens in qPCR assays. Total mcrA and mcrA levels of different methanogen phylogenetic groups were determined from six samples: four samples from anaerobic digesters used to treat either primarily cow or pig manure and two aliquots from an acidic peat sample stored at 4°C or 20°C. Only members of the Methanosaetaceae, Methanosarcina, Methanobacteriaceae, and Methanocorpusculaceae and Fen cluster were detected in the environmental samples. The three samples obtained from cow manure digesters were dominated by members of the genus Methanosarcina, whereas the sample from the pig manure digester contained detectable levels of only members of the Methanobacteriaceae. The acidic peat samples were dominated by both Methanosarcina spp. and members of the Fen cluster. In two of the manure digester samples only one methanogen group was detected, but in both of the acidic peat samples and two of the manure digester samples, multiple methanogen groups were detected. The TaqMan qPCR assays were successfully able to determine the environmental abundance of different phylogenetic groups of methanogens, including several groups with few or no cultivated members.

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Hunger, Sindy, Oliver Schmidt, Maik Hilgarth, Marcus A. Horn, Steffen Kolb, Ralf Conrad, and Harold L. Drake. "Competing Formate- and Carbon Dioxide-Utilizing Prokaryotes in an Anoxic Methane-Emitting Fen Soil." Applied and Environmental Microbiology 77, no. 11 (April 8, 2011): 3773–85. http://dx.doi.org/10.1128/aem.00282-11.

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ABSTRACTMethanogenesis in wetlands is dependent on intermediary substrates derived from the degradation of biopolymers. Formate is one such substrate and is stimulatory to methanogenesis and acetogenesis in anoxic microcosms of soil from the fen Schlöppnerbrunnen. Formate dissimilation also yields CO2as a potential secondary substrate. The objective of this study was to resolve potential differences between anaerobic formate- and CO2-utilizing prokaryotes of this fen by stable isotope probing. Anoxic soil microcosms were pulsed daily with low concentrations of [13C]formate or13CO2(i.e., [13C]bicarbonate). Taxa were evaluated by assessment of 16S rRNA genes,mcrA(encoding the alpha-subunit of methyl-coenzyme M reductase), andfhs(encoding formyltetrahydrofolate synthetase). Methanogens, acetogens, and formate-hydrogen lyase-containing taxa appeared to compete for formate. Genes affiliated withMethanocellaceae,Methanobacteriaceae,Acetobacteraceae, andRhodospirillaceaewere13C enriched (i.e., labeled) in [13C]formate treatments, whereas genes affiliated withMethanosarcinaceae,Conexibacteraceae, andSolirubrobacteraceaewere labeled in13CO2treatments. [13C]acetate was enriched in [13C]formate treatments, but labeling of known acetogenic taxa was not detected. However, several phylotypes were affiliated with acetogen-containing taxa (e.g.,Sporomusa).Methanosaetaceae-affiliated methanogens appeared to participate in the consumption of acetate. Twelve and 58 family-level archaeal and bacterial 16S rRNA phylotypes, respectively, were detected, approximately half of which had no isolated representatives.Crenarchaeotaconstituted half of the detected archaeal 16S rRNA phylotypes. The results highlight the unresolved microbial diversity of the fen Schlöppnerbrunnen, suggest that differing taxa competed for the same substrate, and indicate thatMethanocellaceae,Methanobacteriaceae,Methanosarcinaceae, andMethanosaetaceaewere linked to the production of methane, but they do not clearly resolve the taxa responsible for the apparent conversion of formate to acetate.

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Nakamura, Kohei, Takeshi Terada, Yuji Sekiguchi, Naoya Shinzato, Xian-Ying Meng, Miho Enoki, and Yoichi Kamagata. "Application of Pseudomurein Endoisopeptidase to Fluorescence In Situ Hybridization of Methanogens within the Family Methanobacteriaceae." Applied and Environmental Microbiology 72, no. 11 (September 1, 2006): 6907–13. http://dx.doi.org/10.1128/aem.01499-06.

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ABSTRACT In situ detection of methanogens within the family Methanobacteriaceae is sometimes known to be unsuccessful due to the difficulty in permeability of oligonucleotide probes. Pseudomurein endoisopeptidase (Pei), a lytic enzyme that specifically acts on their cell walls, was applied prior to 16S rRNA-targeting fluorescence in situ hybridization (FISH). For this purpose, pure cultured methanogens within this family, Methanobacterium bryantii, Methanobrevibacter ruminantium, Methanosphaera stadtmanae, and Methanothermobacter thermautotrophicus together with a Methanothermobacter thermautotrophicus-containing syntrophic acetate-oxidizing coculture, endosymbiotic Methanobrevibacter methanogens within an anaerobic ciliate, and an upflow anaerobic sludge blanket (UASB) granule were examined. Even without the Pei treatment, Methanobacterium bryantii and Methanothermobacter thermautotrophicus cells are relatively well hybridized with oligonucleotide probes. However, almost none of the cells of Methanobrevibacter ruminantium, Methanosphaera stadtmanae, cocultured Methanothermobacter thermautotrophicus, and the endosymbiotic methanogens and the cells within UASB granule were hybridized. Pei treatment was able to increase the probe hybridization ratio in every specimen, particularly in the specimen that had shown little hybridization. Interestingly, the hybridizing signal intensity of Methanothermobacter thermautotrophicus cells in coculture with an acetate-oxidizing H2-producing syntroph was significantly improved by Pei pretreatment, whereas the probe was well hybridized with the cells of pure culture of the same strain. We found that the difference is attributed to the differences in cell wall thicknesses between the two culture conditions. These results indicate that Pei treatment is effective for FISH analysis of methanogens that show impermeability to the probe.

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MORII, Hiroyuki, Masateru NISHIHARA, and Yosuke KOGA. "Composition of polar lipids of Methanobrevibacter arboriphilicus and structure determination of the signature phosphoglycolipid of Methanobacteriaceae." Agricultural and Biological Chemistry 52, no. 12 (1988): 3149–56. http://dx.doi.org/10.1271/bbb1961.52.3149.

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Ruaud, Albane, Niklas Pfister, Ruth E. Ley, and Nicholas D. Youngblut. "Interpreting tree ensemble machine learning models with endoR." PLOS Computational Biology 18, no. 12 (December 14, 2022): e1010714. http://dx.doi.org/10.1371/journal.pcbi.1010714.

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Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa may be associated. We developed endoR, a method to interpret tree ensemble models. First, endoR simplifies the fitted model into a decision ensemble. Then, it extracts information on the importance of individual features and their pairwise interactions, displaying them as an interpretable network. Both the endoR network and importance scores provide insights into how features, and interactions between them, contribute to the predictive performance of the fitted model. Adjustable regularization and bootstrapping help reduce the complexity and ensure that only essential parts of the model are retained. We assessed endoR on both simulated and real metagenomic data. We found endoR to have comparable accuracy to other common approaches while easing and enhancing model interpretation. Using endoR, we also confirmed published results on gut microbiome differences between cirrhotic and healthy individuals. Finally, we utilized endoR to explore associations between human gut methanogens and microbiome components. Indeed, these hydrogen consumers are expected to interact with fermenting bacteria in a complex syntrophic network. Specifically, we analyzed a global metagenome dataset of 2203 individuals and confirmed the previously reported association between Methanobacteriaceae and Christensenellales. Additionally, we observed that Methanobacteriaceae are associated with a network of hydrogen-producing bacteria. Our method accurately captures how tree ensembles use features and interactions between them to predict a response. As demonstrated by our applications, the resultant visualizations and summary outputs facilitate model interpretation and enable the generation of novel hypotheses about complex systems.

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Horn, Marcus A., Carola Matthies, Kirsten Küsel, Andreas Schramm, and Harold L. Drake. "Hydrogenotrophic Methanogenesis by Moderately Acid-Tolerant Methanogens of a Methane-Emitting Acidic Peat." Applied and Environmental Microbiology 69, no. 1 (January 2003): 74–83. http://dx.doi.org/10.1128/aem.69.1.74-83.2003.

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ABSTRACT The emission of methane (1.3 mmol of CH4 m−2 day−1), precursors of methanogenesis, and the methanogenic microorganisms of acidic bog peat (pH 4.4) from a moderately reduced forest site were investigated by in situ measurements, microcosm incubations, and cultivation methods, respectively. Bog peat produced CH4 (0.4 to 1.7 μmol g [dry wt] of soil−1 day−1) under anoxic conditions. At in situ pH, supplemental H2-CO2, ethanol, and 1-propanol all increased CH4 production rates while formate, acetate, propionate, and butyrate inhibited the production of CH4; methanol had no effect. H2-dependent acetogenesis occurred in H2-CO2-supplemented bog peat only after extended incubation periods. Nonsupplemented bog peat initially produced small amounts of H2 that were subsequently consumed. The accumulation of H2 was stimulated by ethanol and 1-propanol or by inhibiting methanogenesis with bromoethanesulfonate, and the consumption of ethanol was inhibited by large amounts of H2; these results collectively indicated that ethanol- or 1-propanol-utilizing bacteria were trophically associated with H2-utilizing methanogens. A total of 109 anaerobes and 107 hydrogenotrophic methanogens per g (dry weight) of bog peat were enumerated by cultivation techniques. A stable methanogenic enrichment was obtained with an acidic, H2-CO2-supplemented, fatty acid-enriched defined medium. CH4 production rates by the enrichment were similar at pH 4.5 and 6.5, and acetate inhibited methanogenesis at pH 4.5 but not at pH 6.5. A total of 27 different archaeal 16S rRNA gene sequences indicative of Methanobacteriaceae, Methanomicrobiales, and Methanosarcinaceae were retrieved from the highest CH4-positive serial dilutions of bog peat and methanogenic enrichments. A total of 10 bacterial 16S rRNA gene sequences were also retrieved from the same dilutions and enrichments and were indicative of bacteria that might be responsible for the production of H2 that could be used by hydrogenotrophic methanogens. These results indicated that in this acidic bog peat, (i) H2 is an important substrate for acid-tolerant methanogens, (ii) interspecies hydrogen transfer is involved in the degradation of organic carbon, (iii) the accumulation of protonated volatile fatty acids inhibits methanogenesis, and (iv) methanogenesis might be due to the activities of methanogens that are phylogenetic members of the Methanobacteriaceae, Methanomicrobiales, and Methanosarcinaceae.

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Dissertations / Theses on the topic "Methanobacteriaceae"

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Morozova, Daria. "Tolerance limits and survival potential of methanogenic archaea from Siberian permafrost under extreme living conditions = Toleranzgrenzen und Überlebensstrategien von methanogenen Archaeen aus sibirischen Permafrosthabitaten unter Extrembedingungen /." Bremerhaven : Alfred-Wegener-Institut für Polar- und Meeresforschung, 2007. http://www.loc.gov/catdir/toc/fy0804/2008384365.html.

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Li, Jun, and 李俊. "Molecular evolution and phylogeny of methanogenic archael genomes." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/208152.

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Methane (CH4) is the major chemical component of natural gas, as well as a particularly potent greenhouse gas. Methanogens are the archaeal organisms that produce methane and play a key role in biological methanogenesis. A total of six taxonomic orders of archaeal methanogens have been discovered and almost all previous phylogenetics studies have confirmed that these methanogens are genetically diversified and do not belong to a phylogenetically monophyletic group. To date, the relationships between methanogens and closely related non-methanogen species at the taxonomic order level remain unresolved and different studies have often produced contradictory results based on different gene markers. These studies suggest the complicated and distinct evolutionary histories between different genes in these genomes. In this thesis, 74 fully sequenced archaeal genomes, including 41 methanogens, were collected and used in a comprehensive comparative genomics and evolutionary analysis. First, numerous phylogenomic trees were reconstructed based on various datasets using several methods and the results show that Methanopyrales is close to Methanobacteriales (or Methanopyrales) in the statistically best species tree. In addition, Methnocellales and Methanosarcinales, and as well as Methanomicrobiales and Halobacteriales are sister clades in the best species tree, but the confidence level is low. Further incongruence tests among the phylogenetic forest, which is composed of 3,694 ortholog gene families, reveal that the archaeal core genes have much stronger consistent vertical evolutionary signals than other genes, but these core genes are not topologically fully congruent with each other. Secondly, a series of weighted network analyses were implemented to decompose the hierarchical structure and to reveal the co-evolved gene modules, global and local features in the archaeal methanogen phylogenetic forest. The results show that this co-evolution network contains 7 statistical robust modules, and the module with the highest average node strength includes the majority of the core genes located in the central position of the network. Further in-depth evolutionary analysis reveals that the modularized evolution in the archaeal phylogenetic forest is closely related to the time of origin, HGT rate and ubiquitous vertical inheritance in gene families. Lastly, to investigate the causes for and factors related to the pervasive topology incongruence in the phylogenetic forest, in-depth clanistics analysis and HGT detection were carried out. These results show that (1) about 63% of gene families experienced at least 1 HGT event in their whole history; (2) core genes are not immune to HGT but they do have much lower HGT rates than other genes; (3) methanogens have distinct trends of HGTs from non-methanogen species; and (4) highly frequent inter-order HGTs, even for core genes, in methanogen genomes lead to their scrambled phylogenetic relationships. Further clanistics analysis screened out 119 candidate genes related to methanogenic pathways adaptation and most of these gene families have experienced at least one HGT. In conclusion, a complex evolutionary scenario for methanogenic archaeal species was described in this thesis as a combination of complicated vertical and non-vertical evolutionary processes in a modularized phylogenetic forest.
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Meakin, Stephanie Asalyn Carleton University Dissertation Biology. "The molecular biology of methanogens: cell lysis, plasmid survey and the characterization of a novel plasmid." Ottawa, 1992.

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Mashaphu, Nthabiseng. "The microbial composition of a natural methanogenic consortium." Thesis, University of the Western Cape, 2005. http://etd.uwc.ac.za/index.php?module=etd&amp.

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Wetlands account for approximately 20% of annual global methane emissions. Many wetlands receive inputs of organic matter, nutrients, metals and various toxic compounds from adjacent agricultural and industrial areas. The present study aimed to investigate the microbial composition of a natural methanogenic consortium. A consortium-based molecular approach to study diversity of methanogenic microbial communities in a natural wetland at the primary inflow was used. Key microorganisms of a nethane producing consortium were identified. Extracted high molecular mss DNA ws analysed by PCR combined with denaturing gradient gel electrophoresis and subsequent sequencing of 16S rDNA. This study was also aimed to identify syntrophic microorganisms in the wetland system. The data obtained suggest a well established syntrophic relationship within the wetland.

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Morris, Christina Jane. "DNA sequences and comparison of argininosuccinate synthetase genes from two methanogenic archaebacteria /." The Ohio State University, 1987. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487332636476356.

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Menaia, Jose Antonio Gomes Ferreira. "Osmotics of halophilic methanogenic archaeobacteria /." Full text open access at:, 1992. http://content.ohsu.edu/u?/etd,239.

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Jablonski, Peter Edward. "Studies on two nickel-containing enzymes from Methanosarcina thermophila TM-1." Diss., This resource online, 1992. http://scholar.lib.vt.edu/theses/available/etd-07282008-134014/.

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Obata, Oluwatosin Olubunmi. "Molecular biology approach to the anaerobic digestion of macroalgae." Thesis, University of Aberdeen, 2015. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=230588.

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Kadam, Priya. "Physiology of halophilic, methylotrophic methanogens /." Full text open access at:, 1996. http://content.ohsu.edu/u?/etd,652.

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10

Bachoon, Dave S. "Potential rates of methanogenesis in peat and marl sawgrass wetlands in the Florida Everglades." FIU Digital Commons, 1990. http://digitalcommons.fiu.edu/etd/1362.

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Methanogenesis was studied in soils from two sawgrass wetlands of the Florida Everglades. Marl soils exhibited a significantly higher potential rate of methanogenesis than peat soils. In these wetlands, methanogenesis: (1) decreased rapidly with increasing soil depth, (2) increased at higher temperatures and lower Eh, (3) was stimulated by organic compounds (cellulose, glucose and acetate), and (4) remained unaffected by added ammonium. Lowering the Eh in the peat and marl soils with sulfide or sulfate stimulated methanogenesis. In January 1990, phosphate caused a significant increase in methanogenesis. The potential rates of methanogenesis decreased to undetectable levels when water levels dropped below the surface, and peaked one month after the start of the wet season. Methanogenesis appeared to be a relatively important process in carbon cycling in marl soils and these soils do not accumulate peat. Therefore, one possible explanation for peat accumulation in sawgrass wetlands may be their low rates of methanogenesis.

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Books on the topic "Methanobacteriaceae"

1

Morozova, Daria. Tolerance limits and survival potential of methanogenic archaea from Siberian permafrost under extreme living conditions =: Toleranzgrenzen und Überlebensstrategien von methanogenen Archaeen aus sibirischen Permafrosthabitaten unter Extrembedingungen. Bremerhaven: Alfred-Wegener-Institut für Polar- und Meeresforschung, 2007.

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2

Methods in methane metabolism,: Methanogenesis. Amsterdam: Academic, 2011.

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Thebrath, Bernward. Bildung, Oxidation und Emission von Methan sowie anaerobe Stoffumsätze in limnischen Standorten. Konstanz: Hartung-Gorre, 1991.

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Methods in methane metabolism: Methanotrophy. Amsterdam, [Netherlands]: Elsevier/Academic Press, 2011.

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G, Ferry J., ed. Methanogenesis: Ecology, physiology, biochemistry & genetics. New York: Chapman & Hall, 1993.

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Methanogenesis: Biochemistry, Ecological Functions, Natural and Engineered Environments. Nova Science Publishers, Incorporated, 2014.

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Robinson, Ralph Wendell. Life cycles in the methanogenic archaebacterium Methanosarcina mazei. 1985.

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Stuart, Sheryl L. The effect of environmental conditions on the reductive dechlorination of pentachlorophenol by a mixed, methanogenic culture. 1996.

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Ferry, James G. Methanogenesis: Ecology, Physiology, Biochemistry and Genetics. Springer London, Limited, 2012.

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Ferry, James G. Methanogenesis: Ecology, Physiology, Biochemistry and Genetics. Springer, 2012.

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Book chapters on the topic "Methanobacteriaceae"

1

Oren, Aharon. "The Family Methanobacteriaceae." In The Prokaryotes, 165–93. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-38954-2_411.

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