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This thesis shows how to use Operations Research tools, e.g. Markov chains, optimization, game theory, and matchings, to understand problems that appear in biological contexts. We focus on two biological systems – the activation of the immune system in response to pathogens, and the metabolism of communities of different species of microbes. In Chapter 1, we study a Markov chain model of the activation of individual T-cells, and use the model to analyze how cells make trade-offs between various metrics such as speed and accuracy. In Chapter 2, we provide a detailed model of microbial community metabolism and show how incorporating aspects of game theory and dynamic stability can improve predictions of the behavior of microbial communities. Chapter 3 takes a matching approach to modeling microbial community metabolism by modeling the relationship between species and their environment using the stable marriage problem.

The rumen microbiome constitutes a unique genetic resource of plant fiber degrading microbial enzymes that could be used for agricultural and industrial purposes. Anaeromyces mucronatus is a poorly characterized anaerobic lignocellulolytic fungus in the rumen. This thesis aimed at better understanding A. mucronatus YE505 and the particle associated rumen microbiota based on transcriptomic and metatranscriptomic approaches. High quality RNA was isolated from the fiber-associated rumen sample based on an improved RNA extraction method. A transcriptomic study was performed to investigate the expression of the fiber degrading system of A. mucronatus YE505, and the functional diversity of the fiber-associated eukaryotes from the rumen of muskoxen (Ovibos moschatus) was explored by a metatranscriptomic study. Much carbohydrate degradation related protein modules were detected. This study established effective approaches to characterizing the functional contents of rumen eukaryotic microbiome as well as rumen fungi, and identified several candidate genes that merit further investigation. / xiv leaves : ill. (some col.) ; 29 cm

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<p>Microbial decomposition of organic matter in aquatic environments plays an important role in natural fluxes of methane and carbon dioxide because the gases are end-products in microbial energy metabolism of organic matter. Microbial metabolism depends on the use of electron donors and electron acceptors in redox reactions that generate energy for growth and maintenance. Energy yields can be used to envisage specific patterns of microbial redox reactions and these predictions depend on the hypothesis that, in a specified environment, the metabolic reaction that yields most energy will dominate over any competing reactions. The energy yield hypothesis indicates a sequential order in electron acceptor use by microbes and also make it tempting to conclude that degradation rate of organic matter is different depending on available electron acceptors. The main purpose of this thesis was to study how the presences of different electron acceptors in freshwater sediments influence organic matter decomposition. Mineralization rates of organic matter under six different conditions regarding the electron acceptor availability were investigated in a river sediment sample from Stångån, Sweden, by measuring carbon dioxide and methane production using gas chromatography. This was done during a fixed time period, in vials containing a mixture of water, sediment, buffer solution and a dominating electron acceptor. Six different metabolic processes; aerobic respiration, denitrification, manganese reduction, iron reduction, sulphate reduction and methanogenesis were included. The overall result indicates similar mineralization rates in both oxic and anoxic treatments. The result also indicates that methane formation was present in the iron reduction and methanogenesis treatments and not evident in the oxic treatments. Sulphate reduction, denitrification and manganese reduction seems to inhibit methanogenesis, but the result also indicates that no significant total mineralization was apparent when NO3- and Mn(IV) were the dominating electron acceptors. The similarities between oxic and anoxic mineralization rates indicates that organic matter degradation rates are not dependent on available electron acceptors and that degradation rates of organic matter are independent of the thermodynamically based energy yield.</p>

Ethanol from lignocellulosic biomass is a promising alternative to rapidly depleting oil reserves. However, natural recalcitrance of lignocelluloses to biological and chemical treatments presents major engineering challenges in designing an ethanol conversion process. Current methods for pretreatment and hydrolysis of lignocelluloses generate a mixture of pentose (C5) and hexose (C6) sugars, and several microbial growth inhibitors such as acetic acid and phenolic compounds. Hence, an efficient ethanol production process requires a fermenting microorganism not only capable of converting mixed sugars to ethanol with high yield and productivity, but also having high tolerance to inhibitors. Although recombinant bacteria and yeast strains have been developed, ethanol yield and productivity from C5 sugars in the presence of inhibitors remain low and need to be further improved for a commercial ethanol production. The overarching objective of this work is to transform Zymomonas mobilis into an efficient whole-cell biocatalyst for ethanol production from lignocelluloses. Z. mobilis, a natural ethanologen, is ideal for this application but xylose (a C5 sugar) is not its 'natural' substrate. Back in 1995, researches at National Renewable Energy Laboratory (NREL) had managed to overcome this obstacle by metabolically engineering Z. mobilis to utilize xylose. However, even after more than a decade of research, xylose fermentation by Z. mobilis is still inefficient compared to that of glucose. For example, volumetric productivity of ethanol from xylose fermentation is 3- to 4- fold lower than that from glucose fermentation. Further reduction or complete inhibition of xylose fermentation occurs under adverse conditions. Also, high concentrations of xylose do not get metabolized completely. Thus, improvement in xylose fermentation by Z. mobilis is required. In this work, xylose fermentation in a metabolically engineered Z. mobilis was markedly improved by applying the technique of adaptive mutation. The adapted strain was able to grow on 10% (w/v) xylose and rapidly ferment xylose to ethanol within 2 days and retained high ethanol yield. Similarly, in mixed glucose-xylose fermentation, the strain produced a total of 9% (w/v) ethanol from two doses of 5% glucose and 5% xylose (or a total of 10% glucose and 10% xylose). Investigation was done to identify the molecular basis for efficient biocatalysis. An altered xylitol metabolism with reduced xylitol formation, increased xylitol tolerance and higher xylose isomerase activity were found to contribute towards improvement in xylose fermentation. Lower xylitol production in adapted strain was due to a single mutation in ZMO0976 gene, which drastically lowered the reductase activity of ZMO0976 protein. ZMO0976 was characterized as a novel aldo-keto reductase capable of reducing xylose, xylulose, benzaldehyde, furfural, 5-hydroxymethyl furfural, and acetaldehyde, but not glucose or fructose. It exhibited nearly 150-times higher affinity with benzaldehyde than xylose. Knockout of ZMO0976 was found to facilitate the establishment of xylose fermentation in Z. mobilis ZM4. Equipped with molecular level understanding of the biocatalytic process and insight into Z. mobilis central carbon metabolism, further genetic engineering of Z. mobilis was undertaken to improve the fermentation of sugars and lignocellulosic hydrolysates. These efforts culminated in construction of a strain capable of fermenting glucose-xylose mixture in presence of high concentration of acetic acid and another strain with a partially operational EMP pathway.

Environmental regulation of nitrogen cycling processes, denitrification and nitrification, was studied in sediment of Hamilton Harbour, with particular emphasis on the role of CH$ sb4$ metabolism (production and consumption). Through extensive sediment sampling and numerical analysis, it was found that particulate carbon was the best predictor of potential for anaerobic production of CH$ sb4$ and CO$ sb2$. The only predictor of denitrification capacity was anaerobic CO$ sb2$ production, indicating that beside NO$ sb3 sp-$ and O$ sb2$, a biotic factor involved in carbon metabolism may be important in the control of this activity. / Suppression of aerobic N$ sb2$O production in sediment slurries by C$ rm sb2H sb2$ and correlation with NO$ sb3$-production indicated that it was dependent on chemolithotrophic nitrification. Although CH$ sb4$ (1 to 24 $ mu$M) stimulated production of NO$ sb3 sp-$ and N$ sb2$O, we found that CH$ sb4$ at 84 $ mu$M or greater suppressed nitrification. Following extensive studies of pore water chemistry, potential microbial activities, and counts of nitrifiers and methanotrophs, we found that CH$ sb4$ oxidation (i) is more likely to suppress nitrification by competition for O$ sb2$ and NH$ sb4 sp+$ between methanotrophs and nitrifiers, and (ii) may be more important than nitrification as a sink of hypolimnetic O$ sb2$ in Hamilton Harbour. / Amongst a number of inhibitors, allylsulfide was found to be a differential inhibitor with much less effect on CH$ sb4$ oxidation in sediment slurries or in axenic cultures of Methylosinus trichosporium OB3b than on nitrification in sediment slurries.