This research investigates a novel approach to methanol production from methane. The high use of fossil fuels in New Zealand and around the world causes global warming. Using clearer, renewable fuels the problem could potentially be reduced. Biomass energy is energy stored in organic matter such as plants and animals and is one of the options for a cleaner, renewable energy source. A common biofuel is methane that is produced by anaerobic digestion. Although methane is a good fuel, the energy is more accessible if it is converted to methanol. While technology exists to produce methanol from methane, these processes are thermo-chemical and require large scale production to be economic. Nitrosomonas europaea, a nitrifying bacterium, has been shown to oxidize methane to methanol (Hyman and Wood 1983). This research investigates the possibility of converting methane into methanol using immobilized N. europaea for use in smaller applications. A trickle bed bioreactor was developed, containing a pure culture of N. europaea immobilized in a biofilm on ceramic raschig rings. The reactor had a biomass concentration of 7.82 ± 0.43 g VSS/l. This was between 4 – 15 times higher than other systems aimed at biologically producing methanol. However, the immobilization dramatically affected the methanol production ability of the cells. Methanol was shown to be produced by the immobilized cells with a maximum production activity of 0.12 ± 0.08 mmol/gVSS.hr. This activity was much lower than the typical reported value of 1.0 mmol/g dry weight.hr (Hyman and Wood 1983). The maximum methanol concentration achieved in this system was 0.129 ± 0.102 mM, significantly lower than previous reported values, ranging between 0.6 mM and 2 mM (Chapman, Gostomski, and Thiele 2004). The results also showed that the addition of methane had an effect on the energy gaining metabolism (ammonia oxidation) of the bacteria, reducing the ammonia oxidation capacity by up to 70%. It was concluded, because of the low methanol production activity and the low methanol concentrations produced, that this system was not suitable for a methanol biosynthesis process.

Thesis (Ph. D.)--Oregon State University, 2008. / Printout. Includes bibliographical references (leaves 90-97). Also available on the World Wide Web.

Techn. Univ., Diss.--Hamburg-Harburg, 2004.

abstract: A novel small metal-binding protein (SmbP), with only 93 residues and no similarity to other known proteins, has been isolated from the periplasm of Nitrosomonas europaea. It is characterized by its high percentage (17%) of histidines, a motif of ten repeats of seven residues, a four α-helix bundle structure, and a high binding affinity to about six equivalents of Cu2+. The goal of this study is to investigate the Cu2+ binding sites in SmbP and to understand how Cu2+ stabilizes the protein. Preliminary folding experiments indicated that Cu2+ greatly stabilizes SmbP. In this study, protein folding data from circular dichroism (CD) spectroscopy was used to elucidate the role of Cu2+ in stabilizing SmbP structure against unfolding induced by decreased pH, increased temperature, and chemical denaturants. The significant stabilization effects of Cu2+ were demonstrated by the observation that Cu2+-SmbP remained fully folded under extreme environmental conditions, such as acidic pH, 96 °C, and 8 M urea. Also, it was shown that Cu2+ is able to induce the refolding of unfolded SmbP in acidic solutions. These findings imply that the coordination of Cu2+ to histidine residues is responsible for the stabilization effects. The crystal structure of SmbP without Cu2+ has been determined. However, attempts to crystallize Cu2+-SmbP have not been successful. In this study, multidimensional NMR experiments were conducted in order to gain additional information regarding the Cu2+-SmbP structure, in particular its metal binding sites. Unambiguous resonance assignments were successfully made. Cα secondary chemical shifts confirmed that SmbP has a four α-helical structure. A Cu2+-protein titration experiment monitored by NMR indicated a top-to-bottom, sequential metal binding pattern for SmbP. In addition, several bioinformatics tools were used to complement the experimental approach and identity of the ligands in Cu2+-binding sites in SmbP is proposed. / Dissertation/Thesis / Ph.D. Chemistry 2010

Les procédés actuellement utilisés à bord de la Station Spatiale Internationale permettent un traitement physico-chimique des déchets avec un recyclage partiel des éléments en minimisant le réapprovisionnement en eau et oxygène. Voyager plus loin et sur de plus longues durées n’est possible que si un système de support de vie, permettant d’assurer une autonomie plus importante, est mis en place. Le projet MELiSSA est un système de support de vie biorégénératif ayant pour objectifs de recycler les déchets produits par l’homme, de régénérer l’oxygène et l’eau et d’assurer une production de nourriture. L’utilisation de microorganismes pour assurer ces différentes fonctions, n’est réalisable qu’en ayant la meilleure connaissance possible et surtout la maîtrise des processus et des souches impliqués. L’objectif de cette thèse est de développer un modèle prédictif pour le compartiment nitrificateur de la boucle MELiSSA. Dans un premier temps, les souches Nitrosomonas europaea ATCC® 19718 et Nitrobacter winogradskyi ATCC® 25391 ont été étudiées et ont permis de définir un modèle cinétique de ces deux bactéries en culture immergée. Dans un second temps, ce modèle a été combiné à un modèle N-bacs en série pour composer un modèle de nitrification dans une colonne à lit fixe à biomasse fixée : le modèle NitriSim. Ce modèle a été testé sur une expérience de long-terme menée dans une colonne à lit fixe dont le support est composé de billes Biostyr®. Le dernier chapitre de ce manuscrit décrit l’utilisation d’une souche dégradant l’urée, Cupriavidus pinatubonensis, dans le réacteur à lit fixe. Les différents résultats ont permis de définir un modèle de nitrification dans un réacteur à lit fixe et de présenter des perspectives possibles pour le traitement de l’urine au niveau du compartiment nitrifiant de MELiSSA. / Physico-chemical processes are used on the International Space Station for partial recycling of wastes in order to minimize the resupplies of oxygen and water. Further and longer explorations can only be possible if a life support system is applied to enhance autonomy to the station. MELiSSA is a biological life support system project aiming for waste recycling, water and air regeneration and production of simple food. The only way to assure these functions is the use of microorganisms which is requiring a high knowledge and a perfect control of processes implicated. The thesis objectives consist in developing a predictive model for the MELiSSA nitrifying compartment. First, a kinetic study of Nitrosomonas europaea ATCC® 19718 and Nitrobacter winogradskyi ATCC® 25391 in submerged bioreactors allowed defining a kinetic model of nitrification. Secondly, this model was combined to an N-tanks in series one to compose a nitrification model in fixed-bed biorectors : NitriSim. It was applied on a long-term experiment in a fixed-bed bioreactors where the bed was composed of Biostyr® beads. The last part of this work was about the use of a urea-degradating bacteria, Cupriavidus pinatubonensis, in the fixed-bed bioreactor. All of these results leaded to the development of a nitrification in fixed-bed reactors model and opened up interesting prospects for the urine degradation in the nitrifying compartment of MELiSSA.

This research investigates the physiological and transcriptional responses of Nitrosomonas europaea when exposed to chlorinated aromatic compounds and heavy metals under varying environmental conditions. It was found that transcriptional responses of identified sentinel genes correlate well with nitrification inhibition. Sorption of metals to biomass was also investigated and found not to correlate well with N. europaea inhibition. Whole genome microarray experiments were performed to define the transcriptional response of N. europaea when exposed to chlorobenzene. 13 out of 2460 N. europaea genes were significantly up-regulated after a 1-hour exposure to 4 μM chlorobenzene. HPLC analysis revealed that chlorobenzene was being oxidized primarily into 4-chlorophenol, and further physiological studies revealed that the presence of 4-chlorophenol could account for the inhibitory responses observed. RT-qPCR analysis of several differentially regulated genes verified that similar transcriptional responses were occurring for both chlorobenzene and 4-chlorophenol. 50% inhibitory concentrations of chlorobenzene and 4-chlorophenol resulted in moderate up-regulation of studied genes, however, increasing the concentration of 4-chlorophenol to achieve nitrification inhibition of 93% or more dramatically increased the fold regulation of several of the identified up- and down- regulated genes of interest. Increasing the 4-chlorophenol exposure time to 3 hours at the higher inhibition levels led to a general decrease in amplitude of transcriptional response for all genes tested. Cultures of N. europaea were exposed to various amounts of cadmium in aqueous solution containing EDTA, a strong metal-chelating organic, to control free ionic cadmium²⁺ (Cd²⁺) concentrations. Inhibition of ammonia oxidation as well as transcriptional up-regulation of merA, an identified sentinel gene for exposure to cadmium was found to correlate well with the concentration of Cd²⁺. The concentration of Cd²⁺ required to significantly affect N. europaea cells was found to be in the nanomolar range, which is several orders of magnitude lower than values reported in the literature for cadmium inhibition to mixed-culture activated sludge systems. The sorption of cadmium to the cells was found to be proportional to both the concentration of total cadmium and the concentration of Cd²⁺. At the concentration of metals required to cause approximately 50% nitrification inhibition, specific oxygen uptake results indicate the inhibition is specific to AMO with HAO and downstream energy-generation processes intact. To investigate more closely the inhibitory interactions between heavy metals and AMO, N. europaea inhibition by cadmium, zinc and silver was studied under substrate-limiting conditions. Unlike incubation in oxic environments, 1 hour incubations of N. europaea with cadmium and silver under anoxic conditions did not cause inhibition of nitrification activity after re-suspension in oxic media. In contrast, zinc, which is normally considered an analogue of cadmium in terms of toxic effect and transport mechanisms, was non-inhibitory to N. europaea when exposed in media lacking ammonia. Transcriptional response of merA closely followed the inhibition patterns, with samples which were inhibited after the removal of the metal having significant up-regulation of the gene, and those samples which were uninhibited showing no significant change in merA transcript levels compared to controls. Although sorbed metal concentrations were not found to be predictive of either extent of inhibition or transcriptional response, significantly more cadmium, zinc and silver were sorbed to biomass when incubated in aerobic media compared to anoxic media. Sorption in oxic media was found to be independent of AMO activity and similar results were obtained using Deinococcus radiodurans, a non-nitrifying gram-positive extremophile. The results indicate that greater heavy metal sorption to biomass in oxic environments may be due to general membrane chemistry effects. / Graduation date: 2011 / Access restricted to the OSU Community at author's request from March 31, 2011 - March 31, 2012

Although wastewater treatment plants are a line of defense in minimizing indiscriminate output of microconstituents to natural waters, we do not possess a fundamental understanding of the mechanisms involved in microconstituent removal during wastewater treatment. With this in mind, experiments were designed to investigate the factors that can influence the fate of four microconstituents, carbamazepine (CBZ), 17alpha-ethinylestradiol (EE2), iopromide (IOP), and trimethoprim (TMP), during biological suspended culture treatment. Specifically, the role that various ecological members of biological treatment systems play in biotransforming these compounds was evaluated. Sorption assays were performed with inactivated biomass samples (ammonia oxidizing bacteria (AOB), laboratory enriched heterotrophic cultures free of active nitrifiers with low (Ox⁻) or high (Ox⁺) oxygenase activity, and a nitrifying activated sludge (NAS) from a full-scale wastewater treatment plant) to determine whether partitioning dictates removal of individual microconstituents. No microconstituents sorbed to the AOB culture. Neither CBZ nor IOP sorbed to Ox⁻, Ox⁺ and NAS cultures; however, EE2 and TMP sorbed to the Ox⁻, Ox⁺ and NAS biomass. Sorption was positively influenced by the presence of exopolymeric substances (EPS) associated with the cultures. The protein content of EPS affected EE2 and TMP sorption more appreciably than the polysaccharide content of EPS. Further experiments were performed to investigate microconstituent biodegradation by AOBs, Ox⁻ and Ox⁺ cultures. The influence of growth state and oxygenase activity on biotransformation by each culture was also evaluated. Results indicate that EE2 was the only microconstituent that was amenable to biotransformation by batch cultured AOB and heterotrophic cultures. EE2 was biotransformed but not mineralized by AOB chemostat and batch cultures. TMP was not transformed by AOB batch or chemostat cultures; however both EE2 and TMP were transformed by Ox⁻ and Ox⁺ chemostat cultures. Radiolabeled studies showed that EE2 was mineralized by this culture. Kinetically, AOBs dominated EE2 transformation to monohydroxylated metabolites; however, both Ox⁻ and Ox⁺ cultures further degraded and mineralized EE2 and metabolites generated by AOBs. These results indicate that biotransformation of EE2 by NAS may be limited by heterotrophic activity whereas TMP fate may be a function of heterotrophic activity only. Oxygenase activity did not limit EE2 or TMP biotransformation in chemostat cultures. Subsequent experiments that were performed to identify the factors that influence heterotrophic degradation of EE2 and TMP indicated that the presence of readily biodegradable substrates slows EE2 and TMP biotransformation. The impact of slowly biodegradable substrates like EPS on EE2 and TMP degradation was unclear. These results suggest that EE2 and TMP are most amenable to biodegradation in bioreactors where endogenous conditions dominate. / Ph. D.

Tetrahydrofolate (THF) is an essential cofactor for one-carbon transfer reactions in various biochemical pathways including DNA and amino acid biosynthesis. This cofactor is made up of three distinct moieties: a pteridine ring, p-aminobenzoate (pABA), and glutamate residues. Most bacteria and plants can synthesize folate de novo, unlike animals that obtain folate from their diet. An established pathway for THF biosynthesis exists in most bacteria, but there is evidence of some organisms such as Chlamydia trachomatis and Nitrosomonas europaea which do not contain the canonical THF biosynthesis genes, despite still being able to synthesize THF de novo. Previous studies have shown that these organisms do not contain the pabABC genes, normally required to synthesize the pABA portion of THF, and can circumvent their presence with just a single gene: ct610 and ne1434 from C. trachomatis and N. europaea, respectively. Interestingly, these novel enzymes for pABA synthesis do not use the canonical substrates, chorismate or other shikimate pathway intermediates. The gene product of ct610 was named Chlamydia Protein Associating with Death Domains (CADD) due to its established role in host mediated apoptosis, while the crystal structure showed an architecture similar to know diiron oxygenases. However, we provide evidence of a moonlighting function in pABA synthesis. Isotopic labeling experiments to understand what substrate might be used by CADD found that isotopically labeled tyrosine was incorporated into the final pABA product. Compellingly, CADD was able to produce pABA in the presence of molecular oxygen and a reducing agent alone without the addition of any exogenous substrate, implicating this unusual enzyme as a self-sacrificing pABA synthase from C. trachomatis. Here, we provide strong evidence for Tyr27 being a sacrificial residue that is cleaved from the protein backbone to serve as the pABA scaffold. Furthermore, we also provide evidence that K152 is an internal amino donor for this pABA synthase reaction performed by CADD. In the case of NE1434, we have conducted initial experiments such as site-directed mutagenesis and our findings suggest that these self-sacrificing residues are conserved between two distantly related organisms. Finally, the pABA synthase activity is reliant on an oxygenated dimetal cofactor and despite the crystal structure of CADD depicting a diiron active site, we have demonstrated that CADD's pABA synthase activity is dependent on a heterodinuclear Mn/Fe cofactor. Conversely, NE1434 demonstrates no preference for manganese and likely employs a more traditional Fe/Fe cofactor for catalysis. Our results implicate the CADD and NE1434 as self-sacrificing pABA synthases that have diverging metal requirements for catalysis. / Master of Science in Life Sciences / Folate is a molecule used by all organisms that is necessary for survival. Many kinds of bacteria are able to make this molecule with proteins called enzymes, which help by quickening the rate of a reaction. Enzymes are catalysts that usually work by binding a molecule, called a substrate, and will act on this substrate to generate a product; the enzyme remains unchanged in this process, which allows it to facilitate many more of these reactions. Chlamydia trachomatis, which is a leading cause of sexually transmitted infections (STIs) in the United States, and Nitrosomonas europaea, an environmental bacterium, are able to use enzymes to make their own folate, but not in the way that many other bacteria do. These organisms contain enzymes that use a part of their own structure as a substrate, making them "sacrificial lambs". Our study provides evidence of how these organisms carry out an abnormal chemical reaction to make folate which can help scientists target this pathway for the development of antibiotics.

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