Esta pesquisa teve como objetivo quantificar a emissão de metano (CH4) proveniente da vinhaça presente em diferentes sistemas de armazenamento e transporte e, adicionalmente, avaliar, por técnicas independentes de cultivo, a microbiota funcional relacionada à produção deste gás. Para atingir esta meta foram realizados três estudos complementares. O primeiro abordou a caracterização dos sistemas de armazenamento e transporte de vinhaça encontrados no Brasil baseado em um questionário aplicado às usinas produtoras de etanol. O segundo visou quantificar as emissões de CH4 em condições de campo provenientes da vinhaça nos canais e tanques e também em laboratório em um estudo de incubação. O terceiro estudo avaliou a microbiota funcional associada à emissão de CH4 através de técnicas independentes de cultivo, como PCR em tempo real (qPCR) e pirosequenciamento. As análises microbiológicas indicaram que as emissões de CH4 são produzidas, preferencialmente, através da decomposição anaeróbia do material orgânico dissolvido da vinhaça depositados no fundo dos sistemas. Estas emissões não são desprezíveis e devem ser consideradas nos cálculos de pegada de carbono do etanol. Nos canais sem revestimento a emissão média em dois anos safras consecutivos apresentou valor de 0,75 kg CO2 eq m-3 de vinhaça, aproximadamente 5 vezes superior às emissões na parte revestida. Nos tanques a emissão foi aproximadamente setenta vezes inferior quando comparada ao canal revestido. O experimento de incubação auxiliou no entendimento de que a vinhaça sozinha não produz quantidades significativas de CH4. Entende-se que os nichos microbianos metanogênicos provavelmente são formados no sedimento, enquanto que a vinhaça mantém as condições de anaerobiose do sedimento necessárias à metanogênese e fornece nutrientes para acelerar a reação. O gênero Methanobrevibacter se mostrou dominante na comunidade microbiana metanogênica, conforme demonstrado pelo pirosequenciamento do gene 16S rRNA. Houve correlação positiva entre a abundância do gene 16S rRNA de Arquéia e dos genes funcionais mcrA e mba com a emissão de CH4. As informações sobre produção e emissão de CH4 e das características da vinhaça constituem informações importantes para tomada de decisão sobre a mitigação e/ou aproveitamento do CH4 gerado para fins econômicos e ambientais. / This research aimed to quantify methane (CH4) emissions from the vinasse in different storage and transportation systems and, additionally, to evaluate the functional microbiota associated with the production of this gas by molecular biology approaches. Three complimentary studies were performed to reach this goal. The first one was related to the characterization of main vinasse storage and transportation systems adopted in Brazil based on a survey administered to the mills, in south-central region of Brazil, producing sugarcane etanol. The second aimed to quantify the CH4 emissions from vinasse in both, field - channels and thanks - and laboratory conditions. The third study evaluated the functional microbiota associated with the CH4 emission by molecular biology approaches like real time PCR ans pyrosequencing. Microbial analysis indicated that CH4 emissions are produced preferably by anaerobic decomposition of the organic material dissolved in the vinasse and deposited on the bottom of the systems. These emissions are not negligible and should be considered in ethanol\'s carbon footprint calculations. At the uncoated part of the channel, the average emission from two crop years was 0.75 kg CO2 eq m-3 of vinasse, about 5 times greater than the emissions at the coated part. Methane emissions from the tank were about seventy times lower than from the uncoated channel. The laboratory experiment supported the understanding that the vinasse alone produces no significant emission of CH4. The microbial methanogenic niches were probably formed in the sediment, while the vinasse keeps sediment anaerobic conditions necessary for methanogenesis and provides nutrients to speed up the reaction. The Methanobrevibacter genus showed dominant in methanogenic microbial community, as demonstrated by pyrosequencing of the 16S rRNA gene. There was a positive correlation between the abundance of 16S rRNA gene Archaea and the functional mcrA and mba genes with the emission of CH4. Information on production and emission of CH4 and vinasse characteristics are important for decision making on mitigation and/or use of gas generated for economic and environmental purposes.

Lipídeos contidos em resíduos de laticínios além de representarem uma perda industrial importante, interferem negativamente nos sistemas de tratamento de efluentes inibindo a atividade microbiana do consórcio (Mendes, 2005). O objetivo do presente trabalho foi estudar a degradação anaeróbia de gorduras do leite hidrolisadas com duas enzimas: lipase comercial de Candida rugosa (éster-inespecífica), e preparado enzimático de Geotrichum candidum (lipase éster-específica). Determinaram-se condições ótimas de hidrólise de gorduras do leite no tocante a tempo e temperatura de processo. Após esta etapa, determinou-se a produção metanogênica advinda da estabilização de esterco bovino combinado com gorduras de laticínios hidrolisadas e in natura. As condições ótimas de ação de lipase comercial de C. rugosa em gorduras do leite foram obtidas com temperatura de 40ºC e pH de 6,5. As condições ótimas de ação de preparado enzimático de G. candidum foram obtidas com temperatura de 40ºC e pH de 7,5. Os tempos de processo hidrolítico para a produção máxima de ácidos graxos foram de 8 horas e 16 horas quando se utilizaram preparado enzimático de G. candidum e solução de lipase comercial de C. rugosa respectivamente. As velocidades de processo, bem como os valores de biodegradabilidade anaeróbia, produção metanogênica específica e coeficiente de conversão (Yp/s) indicaram ser muito mais eficiente a utilização lipase de C. rugosa na hidrólise das gorduras do leite, quando o objetivo do processo é a produção de biogás. Além disso, o preparado enzimático de G. candidum ocasionou inibição da atividade metanogênica acetoclástica. Quando se realizou um estudo variando-se a concentração de gordura no tratamento enzimático, obteve-se a maior produção de ácido oléico quando se utilizaram 42 gramas de gordura por grama de enzima. Por outro lado, o melhor fator de conversão entre produto e substrato foi verificado quando a relação entre a massa de gordura e a massa de enzima foi igual a 6g/g. / Lipids in dairy waste as well as representing an important industrial loss, interfere negatively in wastewater treatment systems by inhibiting microbial activity of the consortium. The aim of this work was to study the anaerobic degradation of hydrolyzed milk fats using two enzymes: lipase from Candida rugosa, which is an ester unspecific enzyme; and other specific lipase obtained from Geotrichum candidum. Optimal conditions for hydrolysis of milk fat regarding pH, time and temperature were determined. After that, the methanogenic production from the stabilization of cattle manure combined with fats (hydrolyzed and in nature) was evaluated. The optimum conditions for the action of commercial C. rugosa lipase were obtained at 40ºC and pH 6.5. The optimum conditions for the action of G. candidum preparation were obtained at 40ºC and pH 7.5. Maximum product concentrations were obtained within 8 hours and 16 hours when preparation of G. candidum and C. rugosa lipase were used, respectively. The initial methanogenic production rate, the values of anaerobic biodegradation, the specific methanogenic production and the methane yield as well, showed that the use of C. rugosa lipase in the hydrolysis of fats is more efficient when the goal of the process is the production of biogas. The use of the enzymatic preparation of G. candidum did not cause any benefits, and in addition, caused bigger inhibition of acetoclastic methanogenic activity. When the initial concentration of substrate was varied for the enzymatic treatment, it was possible to verify higher oleic acid accumulated production when 42 grams of fat where used per gram of enzyme. On the other hand, the higher conversion factor between product and substrate was obtained when the relation between the mass of fat and the mass of enzyme was 6g/g.

abstract: Nitrous oxide (N2O) is an important greenhouse gas and an oxidant respired by a diverse range of anaerobic microbes, but its sources and sinks are poorly understood. The overarching goal of my dissertation is to explore abiotic N2O formation and microbial N2O consumption across reducing environments of the early and modern Earth. By combining experiments as well as diffusion and atmospheric modeling, I present evidence that N2O production can be catalyzed on iron mineral surfaces that may have been present in shallow waters of the Archean ocean. Using photochemical models, I showed that tropospheric N2O concentrations close to modern ones (ppb range) were possible before O2 accumulated. In peatlands of the Amazon basin (modern Earth), unexpected abiotic activity became apparent under anoxic conditions. However, care has to be taken to adequately disentangle abiotic from biotic reactions. I identified significant sterilant-induced changes in Fe2+ and dissolved organic matter pools (determined by fluorescence spectroscopy). Among all chemical and physical sterilants tested, γ - irradiation showed the least effect on reactant pools. Targeting geochemically diverse peatlands across Central and South America, I present evidence that coupled abiotic and biotic cycling of N2O could be a widespread phenomenon. Using isotopic tracers in the field, I showed that abiotic N2O fluxes rival biotic ones under in-situ conditions. Moreover, once N2O is produced, it is rapidly consumed by N2O-reducing microbes. Using amplicon sequencing and metagenomics, I demonstrated that this surprising N2O sink potential is associated with diverse bacteria, including the recently discovered clade II that is present in high proportions at Amazonian sites based on nosZ quantities. Finally, to evaluate the impact of nitrogen oxides on methane production in peatlands, I characterized soil nitrite (NO2–) and N2O abundances along soil profiles. I complemented field analyses with molecular work by deploying amplicon-based 16S rRNA and mcrA sequencing. The diversity and activity of soil methanogens was affected by the presence of NO2– and N2O, suggesting that methane emissions could be influenced by N2O cycling dynamics. Overall, my work proposes a key role for N2O in Earth systems across time and a central position in tropical microbial ecosystems. / Dissertation/Thesis / Doctoral Dissertation Microbiology 2020

Das Wachstum von M. acetivorans mit Kohlenmonoxid (CO) als Energiesubstrat unterscheidet sich deutlich von dem anderer methanogener Archaeen. M. acetivorans kann während des Wachstums auf CO zwischen Methanogenese und Azetogenese wechseln. Ein wichtiges Enzym, welches den Kohlenstoff-Fluss im Energiestoffwechsel von M. acetivorans reguliert, ist die N5-Methyl-H4SPT:HS-CoM-Methyltransferase Mtr. Durch die Deletion dieses Enzyms konnte ein Stamm, MKOmtr3, erhalten werden, welcher prinzipiell azetogen auf CO wächst, aber geringe Mengen an zusätzlichen Methylgruppen benötigt. Es zeigte sich, dass das bei der Methylgruppen-Reduktion gebildete Heterodisulfid aus HS-CoB und HS-CoM höchstwahrscheinlich für (eine) essentielle anabole Reaktion(en) benötigt wird. In Zellsuspensionen mit MKOmtr3 wurde festgestellt, dass M. acetivorans aus CO kein Methan bildet, d.h. die Mtr-Reaktion nicht umgangen werden kann. Demgegenüber wurde bei Supplementation mit einem Methylgruppen-Donor CO2 gebildet. Mit Hilfe von [13C]-Markierung konnte gezeigt werden, dass das CO2 nicht aus dem Methylgruppen-Donor, sondern aus intrazellulären Speicherstoffen gebildet wird und die Methylgruppen als Elektronenakzeptor fungieren. Somit konnte in dieser Arbeit die von anderer Seite aufgestellte Hypothese, dass es einen cytoplasmatischen Mtr-Bypass gibt, widerlegt werden. Durch Selektion konnten mehrere Suppressoren von MKOmtr3 erhalten werden, welche in der Lage waren mit CO ohne zusätzliche Methylgruppen zu wachsen. Dabei wurde festgestellt, dass diese Stämme nur noch Spuren von Methan bildeten und somit ausschließlich azetogen wuchsen. Dem Suppressor MKOmtrSF fehlte HdrD, das aktive Zentrum der membranständigen Heterodisulfid-Reduktase (HdrED). Das Fehlen der bisher als essentiell bezeichneten HdrED konnte durch Quantifizierung der Enzymaktivität und gezielter Deletion der codierenden Gene bestätigt werden. Trotz der azetogenen Lebensweise von MKOmtrSF und MKOmtrhdr blieb Mcr essentiell, da es weder gelang das Enzym zu inhibieren, ohne die Lebensfähigkeit des Stammes zu verlieren, noch die codierenden Gene zu deletieren. Um einen maximalen Fluss der geringen Mengen an Heterodisulfid, welche von Mcr noch produziert wird, zum Anabolismus zu gewährleisten, wird anscheinend der Haupt-“Verbraucher“, HdrED, ausgeschaltet. In dieser Arbeit wurde somit erstmals gezeigt, dass die Methanogenese nicht zwangsläufig essentiell in methanogenen Archaeen ist, sondern durch eine Variante des reduktiven Azetyl-CoA-Weges ersetzt werden kann.:Abkürzungsverzeichnis 4 1. Einleitung 7 1.1 Methan 7 1.2 Methanogene und Methanogenese 7 1.2.1 Hydrogenotrophe Methanogenese 9 1.2.2 Methylotrophe Methanogenese 12 1.2.3 Azetiklastische Methanogenese 14 1.2.4 Carboxidotrophe Methanogenese 16 1.3 M. acetivorans als Modellorganismus 20 1.4 Ziele dieser Arbeit 23 2. Material und Methoden 25 2.1 Chemikalien 25 2.2 Anaerobes Arbeiten 25 2.3 Verwendete Mikroorganismen 26 2.4 Mikrobiologische Methoden 27 2.4.1 Kultivierung von E. coli 27 2.4.2 Kultivierung von M. acetivorans 28 2.4.3 Bestimmung der Zellausbeute 31 2.4.4 Herstellung von Zellsuspensionen von M. acetivorans 32 2.4.5 Herstellung elektroporationskompetenter E. coli-Zellen 33 2.4.6 Transformation von E. coli 33 2.4.7 Polyethylenglykol-vermittelte Transformation von M. acetivorans 34 2.4.8 Liposomen-vermittelte Transformation von M. acetivorans 35 2.5 Molekularbiologische Methoden 36 2.5.1 Plasmide 36 2.5.2 Oligonukleotide 38 2.5.3 Isolierung von Plasmiden 43 2.5.4 Isolierung von genomischer DNA 43 2.5.5 Restriktionsverdau 44 2.5.6 Ligation mehrerer DNA-Fragmente 44 2.5.7 Cointegration von pAMG40 in pDN201-Derivate 45 2.5.8 Polymerase-Ketten-Reaktion (PCR) 45 2.5.9 Agarose-Gelelektrophorese 46 2.5.10 Sequenzierung von DNA 47 2.6 Analyse von Proteinen 47 2.6.1 Auftrennung von Proteinen mittels SDS-Polyacrylamid-Gelelektrophorese 47 2.6.2 Bestimmung der Proteinkonzentration 48 2.6.3 Proteomanalyse 49 2.6.4 Bestimmung der Fumarat-Reduktase-Aktivität 51 2.6.5 Bestimmung der Heterodisulfid-Reduktase-Aktivität 52 2.7 Quantifizierung von Metaboliten 53 2.7.1 Quantifizierung gasförmiger Metabolite 53 2.7.2 Quantifizierung gelöster Metabolite 55 3. Ergebnisse 57 3.1 Wachstum von M. acetivorans M42 57 3.2 Deletion der Molybdän-abhängigen Formylmethanofuran-Dehydrogenasen 61 3.2.1 Deletion von Fmd1 61 3.2.2 Phänotypische Analyse von MKOfmd1 62 3.2.3 Deletion von Fmd2 64 3.3 Deletion der Formyltransferase Ftr 64 3.4 Deletion der Methyltransferase Mtr 67 3.4.1 Wachstum von MKOmtr3 mit Azetat + MeOH 67 3.4.2 Wachstum von MKOmtr3 mit CO + MeOH 70 3.5 Analyse von möglichen Mtr-Bypässen 74 3.5.1 Metabolitenbildung in Zellsuspensionen aus CO, MeOH und Trimethylamin 74 3.5.2 Deletion von Mtr in DmtsDFH 77 3.5.3 Markierung mit [13C]-MeOH 79 3.6 Überwindung der Methylgruppen-Abhängigkeit von MKOmtr3 82 3.6.1 Ersatz von MeOH bei Wachstum auf CO 82 3.6.2 Genom-Analyse von ausgewählten Suppressoren 85 3.6.3 Proteom-Analyse von ausgewählten Suppressoren 91 3.6.4 Physiologie von MKOmtrSF 96 3.6.5 Komplementation von MKOmtrSF mit MA2238 100 3.6.6 Fumarat-Reduktase-Aktivität in M. acetivorans? 101 3.6.7 Abhängigkeit der Azetogenese vom Elektronentransport über die Zellmembran 101 3.7 Deletion der Heterodisulfid-Reduktase HdrED1 in MKOmtrSF 103 3.7.1 Anpassung der PEG-Transformationsmethode für MKOmtrSF 103 3.7.2 Konstruktion des Stammes MKOmtrhdr und dessen Wachstum 104 3.7.3 Heterodisulfid-Reduktase-Aktivität in M. acetivorans 105 3.8 Untersuchung der Essentialität von Mcr in MKOmtrSF 107 3.8.1 Inhibierung mit Bromethansulfonat und 3-Nitrooxy-Propanol 107 3.8.2 Deletion der Methyl-S-CoM Reduktase Mcr 109 4. Diskussion 113 4.1 Die Formiatbildung von M. acetivorans beim Wachstum auf CO 113 4.2 Methanogenese oder Azetogenese – die Rolle von Mtr als „Schalter“ 116 4.3 In M. acetivorans gibt es keinen cytoplasmatischen Mtr-Bypass 117 4.4 Die Abhängigkeit von MKOmtr3 von Methylgruppen und wie diese umgangen werden konnte 118 4.4.1 Der Verlust von MA2238 118 4.4.2 Der Verlust von MA2285 in MKOmtrSF 119 4.5 Katabole Methyl-Reduktion von MKOmtr3 120 4.6 Eine anabole Rolle von CoB-S-S-CoM in M. acetivorans? 120 4.7 Woher kommt CH3-S-CoM in MKOmtrSF? 122 4.8 Benötigt M. acetivorans für die Azetogenese Elektronentransport über die Membran? 123 4.9 Nichtmethanogenes Wachstum von M. acetivorans 127 4.10 Warum findet sich bisher kein ausschließlich mit Azetogenese wachsendes Archaeon? 128 4.11 Anwendungsmöglichkeiten für ein azetogenes Archaeon 132 Kurzfassung 137 Literaturverzeichnis 138 Anhang 154 Lebenslauf & Publikationen 163 Danksagung 164 Erklärung 165

The Newmarket Till is a regional aquitard in southern Ontario that overlies the Illinoian to Middle Wisconsinan Lower Sediments and is overlain by the Oak Ridges Moraine (ORM). Geological investigations have mapped the distribution of the till and it is understood that erosional channels, subsequently infilled with fluvial material, breach the till and may create enhanced hydraulic connection between overlying and underlying aquifers. However, little is known about the protective capability of the Newmarket Till where it is intact. This study used natural tracers to assess the extent of transport in the aquitard-aquifer system. Stable isotopes of water (δ18O and δ2H) showed a depletion trend versus depth. In the Newmarket Till most of the samples had isotope ratios similar to meteoric water data from the nearest location (Egbert, ON). The depleted values of δ18O in the Thorncliffe Formation suggest a remnant signature of early-Holocene precipitation (-16‰ at the depth of 60 m). Elevated levels of NO3- and Cl- were detected near the surface and because of the low permeability aquitard (Newmarket Till), they could not migrate to depth. Total extractable ammonium concentrations are ranging from 4.09 ppm from near the surface to 60 ppm in the lowest part of the Newmarket and then gradually increase to 514 ppm in the bottom of the Thorncliffe Formation. The combination of high NH4+ values and organic carbon content in the Thorncliffe Formation suggests a natural source from mineralization of organic N. The fractionation which happened between δ15Nsediment and δ15N-NH4 may have three explanations: (1) lighter isotopes diffuse faster than heavier ones, so the higher rate of diffusion can cause fractionation; (2) heavier isotopes partition to exchange sites, causing fractionation along the transport pathway; (3) dissociation of NH4+ to NH3 under anaerobic condition. Positive values for δ13C in groundwater in the Thorncliffe Formation are likely due to i) a contribution of carbonate mineral dissolution, and ii) methanogenesis - the Archea favor the lighter isotope of C (12C). Methanogenesis, therefore, enriches the δ13C-DIC was enriched; however, the δ13C in dissolved organic carbon (DOC) is depleted. These geochemical characteristics demonstrate a long residence time for the porewater in the system and indicate that the Newmarket till inhibits recharge of recent precipitation, thereby providing protection to the underlying aquifers from surface-derived contaminants.

Im Rahmen des BioPara Netzwerkes: „Gesamterfassung von biochemischen und metagenomischen Parametern in Biogasanlagen und deren Korrelation zur Produkteffizienz“ erfolgte die in dieser Arbeit durchgeführte Isolierung und Charakterisierung von prozessrelevanten methanogenen Archaeen aus frischen Schlammproben einer kommerziellen Biogasanlage. Insgesamt wurden sechs verschiedene Arten der Gattungen Methanobacterium, Methanoculleus sowie Methanosarcina isoliert und als Reinkultur kultiviert. Darunter wurden mit Methanobacterium aggregans und Methanosarcina flavescens bis dahin unbekannte Spezies identifiziert und umfassend charakterisiert. Außerdem erfolgte mit Methanoculleus bourgensis und M. flavescens die Anreicherung der beiden abundantesten methanoarchaealen Mikroorganismen des beprobten Biogasreaktors. Weiterführend wurde ein anaerobes Testsystem etabliert, um die Methanproduktivität der analysierten Biogasanlagen im Labormaßstab abzubilden. Mit diesem Testsystem wurden die hydrogenotrophen und methylotrophen Wege der Methanogenese als potentiell raten-limitierende Schritte des Biogasprozesses in NawaRo-Anlagen analysiert. Die hydrogenotrophe Methanogenese verlief in allen beprobten Biogasreaktoren nicht an der maximalen Kapazitätsgrenze und stellte daher keinen raten-limitierenden Schritt dar. Weiterführend wurde die methylotrophe Methanogenese bei hohen Methanosarcina-Abundanzen als nicht-ratenlimitierender Prozess identifiziert und durch die Zugabe von Isolat E03.2 zu inaktivierten Schlammproben der untersuchten Biogasanlagen, ergaben sich Hinweise auf die Anwesenheit von Methoxygruppen. Aufgrund der fundamentalen Bedeutung des Wasserstoff-Stoffwechsels in NawaRo-Biogasanlagen, wurden u.a. Wasserstoff-abhängige Gesamt- sowie methanoarchaeale Enzymreaktionen aus frischen Schlammproben quantifiziert und als mögliche Parameter zur Prozessüberwachung analysiert. Dabei konnte eine positive Korrelation der Gesamt-Hydrogenaseaktivität mit der Methanproduktivität in den untersuchten Biogasanlagen gezeigt werden. Die Gesamt-Hydrogenaseaktivität ist somit einen aussagekräftiger Parameter zur Prozesskontrolle.

No description available.

Compound specific isotope analysis of lake sediments is a powerful tool in deciphering evidence of changing climatic and paleoenvironmental conditions through time. Isotopic analysis of Lake El’gygytgyn pilot sediment cores, PG1351 and LZ1029, have contributed increased insight into paleoenvironmental interpretations regarding conditions of permanent ice cover and water column anoxia at the lake over the past 250 kyr. Bulk sediment δ15N was measured as a proxy for denitrification and a possible indicator for water column anoxia intensity. However, it appears that insufficient quantities of water column nitrate to fuel denitrification make its correlation with anoxia intensity ineffective. In pilot core LZ1029, compound-specific δ13C of alkanes, fatty acids, and alcohols were analyzed to determine the changing sources of organic matter as well as the source of a strong negative isotopic shift in the bulk sediment δ13C (-26‰ to -33‰) over the past 50 kyr. Results indicate that the majority of alkanes, fatty acids, and alcohols are long chain compounds consistent with a terrestrial plant origin, with increased aquatic contribution during the local last glacial maximum (LLGM). Among the compound classes examined, only the mid chain fatty acids display a strong LLGM depletion (δ13C = -43‰). Short chain fatty acids exhibit an LLGM depletion (δ13C = -35‰) similar to bulk sediment δ13C, while the δ13C trend of long chain alkanes, fatty acids, and alcohols differ from the bulk sediment δ13C trend, suggesting an autochthonous source of bulk isotope depletion. Evidence of methane cycling exists only in the presence and isotopic value of diplopterol (LLGM δ13C = -93.4‰), a biomarker for aerobic oxidation of methane. Two compounds indicative of archaeal lipids were present at considerable concentrations during the LLGM (394 and 668 µg/g TOC), but without the extreme negative δ13C associated with methanogenesis and methanotrophy. These results suggest insufficient generation of methane in the lake to have derived from such a large anaerobic archaeal methanogen community suggesting that archaea are not acting entirely as methanogens. Furthermore, it appears unlikely that a significant anoxic layer existed in the water column of Lake El’gygytgyn during the past ~50kyr. The results of this work will be applied to ongoing investigations on the newest cores from Lake El’gygytgyn, which represent the past 3.5 Myr.

No description available.

Methyl-coenzyme M reductase (MCR) is the key enzyme involved in the production of methane by methanogenic archaea and its consumption by anaerobic methanotrophs (ANME). MCR is a multimeric complex composed of six different subunits arranged in a 2α, 2β, 2γ configuration that requires two molecules of its nickel-containing tetrapyrrole prosthetic group, coenzyme F430. Additionally, the α subunits of MCR house a variety of different post-translational modifications across both methanogens and ANME. In methanogens, MCR is encoded in a conserved mcrBDCGA gene cluster, which encodes accessory proteins McrD and McrC. These are believed to be involved in the assembly and activation of MCR, respectively. However, one or both accessory proteins are often omitted from the operon in other MCR-containing archaea as is the case in ANME. MCR knowledge is mostly limited to methanogens due to difficulties associated with large-scale cultivation of ANME and other MCR-containing archaea. Due to the complexity of MCR, studies on this enzyme are also largely limited to native enzymes. Developing methods for the detailed biochemical characterization ANME MCRs would be highly desirable since these enzymes are proposed to be optimized for methane oxidation and thus have immense potential for bioenergy and greenhouse gas mitigation applications. In addition to containing the necessary machinery for the production of an assembled and active MCR, model methanogens are easier to culture and have established genetic manipulation techniques, making them ideal candidates for the development of heterologous expression systems. Thus, here we sought to generate such a system for the study of various ANME MCRs in the methanogen, Methanococcus maripaludis. We report the successful expression and purification of an ANME-2d MCR, marking a significant step toward the development of a heterologous MCR expression system. Additionally, our attempts to purify various recombinant MCRs revealed the importance of including accessory proteins, particularly McrD, within expression constructs. Therefore, we also sought to functionally characterize McrD, which we show is likely an MCR chaperone that plays a key role in MCR maturation. Taken together, our work has provided key insights into MCR assembly as well as provided a foundation for the eventual development of MCR based biocatalytic systems to be used for methane mitigation strategies and bioenergy platforms. / Doctor of Philosophy / Life is divided into three domains known as Bacteria, Eukarya, and Archaea. Methanogens are anerobic microbes belonging to the domain Archaea, which can be found across a wide variety of oxygen deprived environments. These organisms can turn different carbon-containing compounds into energy and methane gas in a process known as methanogenesis. This results in roughly 90 billion tons of biologically produced methane, making methanogenesis a key point of interest for potential greenhouse gas mitigation. The methane-generating step of methanogenesis is performed by methyl-coenzyme M reductase (MCR), a large enzyme composed of two α subunits, two β subunits, and two γ subunits. Additionally, this enzyme harbors a nickel-containing cofactor which is responsible for catalyzing the difficult methane formation reaction. In addition to the MCR-encoding genes, MCR gene clusters contain two extra genes that encode accessory proteins, named McrC and McrD, which are believed to play an important role in the activation and the assembly of the enzyme, respectively. Relatives of methanogens known as Anerobic Methanotrophs (ANME) are a different type of archaea which consume methane by reversing methanogenesis in a process known as anerobic methane oxidation. Because of their ability to consume methane, there is a large interest in studying MCR from these organisms to potentially use it for methane mitigation strategies and for bioenergy applications to convert methane to more usable liquid fuels. However, due to the high difficulty of growing ANME in a lab setting, studying any biochemical processes from ANME is a difficult task. Luckily, genetic manipulation techniques are available for many methanogens, making them ideal candidates to study MCR from ANME organisms. In this work, we sought to develop a system to express and purify MCR from different methanogens and ANME in a methanogenic host, Methanococcus maripaludis. We also sought to understand the role and importance of accessory protein McrD, especially with respect to developing a proper expression system for MCRs. We were able to successfully express a ANME MCR in M. maripaludis and found that McrD is an important aspect to consider when expressing MCRs in a methanogen, although it is not essential for this protein to exist within the MCR gene cluster. This work sets the stage for the future biotechnological use of MCR for methane mitigation and bioenergy applications.