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Dissertations / Theses on the topic 'Methanobacteriaceae'

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Published: 4 June 2021

Last updated: 27 January 2023

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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. http://www.loc.gov/catdir/toc/fy0804/2008384365.html.

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2

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.
published_or_final_version
Biological Sciences
Doctoral
Doctor of Philosophy

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3

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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4

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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5

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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6

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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7

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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8

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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9

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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11

Terlesky, Katherine C. "Studies on the carbon monoxide dehydrogenase enzyme complex present in acetate-grown Methanosarcina thermophila strain TM-1." Diss., Virginia Polytechnic Institute and State University, 1989. http://hdl.handle.net/10919/54440.

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The carbon monoxide dehydrogenase complex was purified from acetate-grown Methanosarcina thermophila. This complex made up greater than 10% of the cellular protein and the native enzyme formed aggregates with a Mr of approximately 1,000,000. The enzyme contained five subunits of different molecular weight suggesting a multifunctional enzyme complex. Nickel, iron, cobalt, zinc, inorganic sulfide, and a corrinoid were present in the complex. The electron paramagnetic resonance spectrum of CO-reduced enzyme at 113K contained g values of 2.073, 2.049, and 2.028. Isotopic substitution with ⁶¹Ni, ⁵⁷Fe, or ¹³Co resulted in broadening of the spectrum consistent with a Ni-Fe-C spin-coupled complex. Acetyl-CoA caused a perturbation of the signal that was not caused by acetyl-phosphate or mercaptoethanol indicating acetyl-CoA is a physiological substrate. Cell extracts from acetate-grown M. thermophila contained CO-oxidizing:H₂-evolving activity 16-fold greater than extracts of methanol-grown cells. CO-oxidizing:H₂-evolving activity was reconstituted upon combination of: (i) CO dehydrogenase complex, (ii) a ferredoxin, and (iii) purified membranes with associated hydrogenase and b-type cytochrome. The ferredoxin was a direct electron acceptor for the CO dehydrogenase complex. The molecular weight of the isolated protein was 16,400, and the apparent minimum molecular weight was 4,900. The ferredoxin contained 2.8 ± 0.56 Fe atoms and 1.98 ± 0.12 acid-labile sulfide. UV-visible absorption maxima were 395 and 295 nm with a A₃₉₅/A₂₉₅ ratio range of 0.80 to 0.88. The N-terminal amino acid sequence revealed a 4-cysteine cluster, similar to other Fe:S centers that coordinate a Fe:S center. A CH₃-B₁₂:HS-CoM methyltransferase activity was characterized in extracts of acetate- and methanol-grown cells. The activity from extracts of acetate-grown M. thermophila was stable at 70°C for 30 minutes. The activity in cell extracts of acetate- and methanol-grown cells was fractionated with ammonium sulfate treatment and FPLC phenyl superose chromatography. Two peaks of methyltransferase activity were observed in each cell extract sample following phenyl superose fractionation.
Ph. D.

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12

Tugtas, Adile Evren. "Effect of Nitrate Reduction on the Methanogenic Fermentation: Process Interactions and Modeling." Diss., Available online, Georgia Institute of Technology, 2007, 2007. http://etd.gatech.edu/theses/available/etd-01122007-155216/.

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Thesis (Ph. D.)--Civil and Environmental Engineering, Georgia Institute of Technology, 2007.
Sotira Yiacoumi, Committee Member ; Patricia Sobecky, Committee Member ; Ching-Hua Huang, Committee Member ; Dr. Spyros Pavlostathis, Committee Chair ; Frank Loeffler, Committee Member.

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13

Wade, Elizabeth M. "The importance of biogenic methane and sedimentation to benthic chironomid larvae in four reservoirs." Greensboro, N.C. : University of North Carolina at Greensboro, 2007. http://libres.uncg.edu/edocs/etd/1512Wade/umi-uncg-1512.pdf.

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Thesis (M.S.)--University of North Carolina at Greensboro, 2007.
Title from PDF t.p. (viewed Mar. 11, 2008). Directed by : Anne E. Hershey; submitted to the Dept. of Biology. Includes bibliographical references (p. 29-34).

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14

Blight, Sherry Kathleen. "Amber codon translation as pyrrolysine in Methanosarcina spp." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1149012579.

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15

Christophersen, Claus. "Grain and artificial stimulation of the rumen change the abundance and diversity of methanogens and their association with ciliates." University of Western Australia. School of Animal Biology, 2008. http://theses.library.uwa.edu.au/adt-WU2008.0114.

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[Truncated abstract] In Australia, there is pressure to reduce the amount of methane produced by ruminant livestock because they are the single largest source of methane emitted from anthropogenic sources, accounting for 70.7% of agricultural methane emissions. In addition, methane production represents a loss of gross energy intake to the animal. The organisms that are responsible for methane production in the animal gut are a distinct group of Archaea called methanogens. Methanogens occupy three different niches within the rumen. Some live freely in the rumen digesta (planktonic), others are attached to the outer surface of the rumen ciliates (ectosymbiotic), and some reside within the ciliates (endosymbiotic). The types and number of methanogens, as well as rumen ciliates and their symbiotic interactions, influence the amount of methane produced from the rumen. These factors in turn are affected by many factors, including diet and ruminal retention time. In this thesis, I tested the general hypothesis that increasing the amount of grain in the diet and reducing the retention time would affect the abundance and diversity of methanogens in their different niches, including their association with ruminal ciliates. Twenty-four fistulated sheep were used in a complete factorial design with the sheep randomly divided into four groups. ... The change in DGGE banding patterns and Shannon indices when sheep were fed grain indicated that the types of methanogens changed when sheep were fed low and high grain diets, but their diversity did not. In contrast, the diversity of rumen ciliates decreased when sheep were fed a high grain diet. A total of 18 bands from the DGGE analysis of the ciliates were sequenced. All except one, which was 98% similar to Cycloposthium sp. not found previously in the rumen, matched the sequences for previously identified rumen ciliates. Some of the rumen ciliates identified were not present in sheep fed the high grain diet. On a high grain diet, methanogens associate endosymbiotically with rumen ciliates to get better access to hydrogen. It appears that the association between methanogens and rumen ciliates is dictated by the availability of hydrogen in the rumen and not the generic composition of the ciliate population. Furthermore, endosymbiotic methanogens appear to produce less methane than methanogens in other niches. The pot scrubbers did not change ruminal retention time but they did reduce the acetate/propionate measurements observed in sheep on the high grain treatment. The reason why pot scrubbers had this effect remains unknown, but it is interesting to consider that some physical interaction has occurred between the pot scrubbers, the grain and the sheep that has improved the fermentation parameters in sheep fed a high grain diet. The results from this study have advanced our understanding of the interaction between methanogens and ruminal ciliates, and methanogenesis in the rumen in response to dietary changes and mechanical challenges. Extending this work to look more specifically at the species of methanogens that are most closely linked to high methane production and how they interact with the ruminal ciliates will be critical for manipulating enteric greenhouse gas emissions.

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16

Khelaifia, Saber. "Détection et culture des archaea associées aux muqueuses intestinale et orale humaines." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM5029.

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Les archaea constituent l'un des quatre domaines connus du vivant. Contrairement à ce que leur nom laisse supposer, elles ont colonisé tous les écosystèmes et les microbiotes de certains hôtes dont l'Homme. Chez l'homme, certaines espèces d'archaea méthanogènes ont été associées aux muqueuses orale, intestinale et vaginale. Ces archaea méthanogènes sont des procaryotes anaérobies stricts et leurs conditions de culture restent fastidieuses et très mal connues. Quatre archaea methanogènes seulement ont été isolées à partir de prélèvements humains y compris dans le microbiote digestif Methanobrevibacter smithii détectée dans 95,7% des individus, Methanosphaera stadtmanae retrouvée chez environ un tiers des individus et plus récemment dans notre laboratoire Methanomassilicoccus luminyensis détectée en moyenne chez 4% des individus avec une prévalence liée à l'âge ; et dans le microbiote orale Methanobrevibacter oralis isolée à partir de la plaque dentaire
Archaea is one of four known domains of life. Unlike what their name suggests, they some species of methanogenic archaea have been associated with oral, vaginal and intestinal mucosa. These methanogenic archaea are obligate anaerobic prokaryotes and their culture conditions are fastidious and very poorly known. Only four methanogenic archaea have been isolated from human samples including the digestive microbiota; Methanobrevibacter smithii detected in 95.7% of individuals Methanosphaera stadtmanae found in approximately one third of individuals and more recently in our laboratory Methanomassilicoccus luminyensis detected on average in 4% of individuals with a prevalence of age-related, and in the oral microbiota Methanobrevibacter oralis isolated from dental plaque

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17

Stuart, Sheryl L. "The effect of environmental conditions on the reductive dechlorination of pentachlorophenol by a mixed, methanogenic culture." Thesis, 1996. http://hdl.handle.net/1957/34451.

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18

Naidoo, Kewreshini K. "Assessment of the diversity of bacteria and methanogenic Archaea in Zebra faeces." Thesis, 2013. http://hdl.handle.net/10413/10929.

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The need to develop a renewable, environmentally friendly source of energy has become a primary focus in modern science, with bio gas showing considerable potential. Interest in the methanogenic Archaea has therefore grown in recent years and extensive studies have been carried out to investigate the population diversity in various habitats. Presently, there are only a few studies that have evaluated the microbial communities inhabiting the gastrointestinal tract of wildlife native to southern Africa. This study aimed to investigate the microbial diversity, in particular the bacterial and methanogen communities involved in fermentative digestion in the gastrointestinal tract of zebra. Assessment of the microbial diversity in zebra faeces included both culture-based techniques and nucleic acid targeting analysis via 16S rRNA gene sequencing. Quantitative analysis using selected solid media revealed high counts for aerobic and anaerobic Bacteria (7.51x108 and 2.45x109/gram of faecal sample respectively). The majority of aerobic colonies that were detected exhibited Bacillus-like morphology. Nucleic acid based analysis of the diversity of both Bacteria and methanogenic Archaea in zebra faecal material was performed. Both manual and kit based extractions were used for DNA isolation in order to compare the efficiency of the two methods. Results show that a vigorous mechanical treatment was best for the release of DNA from the faecal matter. Amplification of target gene regions was carried out using established primer pairs (ARCH69F/ARCH915R and EUB338F/EUB907R) for methanogen and bacterial DNA respectively. Amplified 16S rRNA gene regions were cloned into a high copy number vector and random clones were selected for evaluation. Clones containing the target gene were further analysed by ARDRA and were assigned to a specific phylotype. Two bacterial (105 clones in total) and three methanogen (178 clones in total) clone libraries were constructed, of which 24 phylotypes were established for Bacteria and 25 for methanogenic Archaea. A representative of each phylotype was analysed by sequencing and further phylogenetic analysis was conducted. Six bacterial phylotypes, which represented 56% of all bacterial clones, exhibited 99% sequence similarity to Bacillus species. Six methanogen phylotypes, which exhibited 99% sequence similarity to the hydrogenotrophic species Methanobrevibacter gottschalkii strain PG, were established to be predominant in zebra faeces. These phylotypes represented 71% of all archaeal clones selected for analysis in this study.
Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

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19

Guo, Chengmai. "Rapid densification of the oil sands mature fine tailings (MFT) by microbial activity." Phd thesis, 2009. http://hdl.handle.net/10048/702.

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Thesis (Ph.D.)--University of Alberta, 2009.
Title from PDF file main screen (viewed on Feb. 19, 2010). A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Geotechnical Engineering, [Department of] Civil and Environmental Engineering, University of Alberta. Includes bibliographical references.

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