Mountain pine beetle (Dendroctonus ponderosae Hopkins) has caused extensive tree mortality in whitebark pine (Pinus albicaulis Engelm) forests. Previous studies conducted in various conifer forests have shown that fine surface fuels are significantly altered during a bark beetle outbreak. Bark beetle activity in conifer stands has also been shown to alter foliar fuel moisture content and chemistry over the course of the bark beetle rotation.The objective of this study was to evaluate changes to fine surface fuels, foliar fuel moisture and chemistry and litter chemistry in and under whitebark pine trees infested by mountain pine beetle. Fuels were measured beneath green (healthy) trees compared to red (two years since initial MPB attack with 50% or greater needles remaining) and gray (greater than two years since attack with between 15% and 45% needles remaining) trees. Foliar moisture content was measured in four mountain pine beetle crown condition classes: green-uninfested, green-infested (current year’s attack), yellow (last year’s attack), and red. Total terpene content was analyzed in whitebark pine needle litter and volatile terpenes were collected and analyzed from green, green-infested, yellow, and red trees.Significant differences were found in litter depths under green, red, and graytrees. Duff depths were significantly less beneath green trees than red and gray trees. One hour and ten hour fuels were more influenced by diameter and crown size than beetle crown condition classes. Foliar fuel moisture content dramatically decreased from green-infested to the red beetle crown condition class. No differences were detected in shrub and forb biomass between green, red, and gray trees. Green-infested trees had significantly lower foliar fuel moisture than green trees and by late in the season showed fuel moisture levels similar to red trees which had the lowest fuel moisture content. Litter beneath red trees contained large amounts of terpenes, including compounds known to increase foliage flammability that remain in the litter throughout the fire season. Total terpene content emitted from red foliage is greater than green-infested or yellow foliage.

The use of ethanol produced from lignocellulosic biomass for transportation fuel offers solutions in reducing environmental emission and the use of non-renewable fuels. However, lignocellulosic ethanol production is still hampered by economic and technical obstacles. For instance, the inhibitory effect of toxic compounds produced during biomass pretreatment was reported to inhibit the fermenting microorganisms, hence there was a decrease in ethanol yield and productivity. Thus, there is a need to improve the bioconversion of lignocellulosic biomass to ethanol in order to promote its commercialization. The research reported here investigated the use of poultry litter biochar to improve the ethanol production from steam-exploded poplar and corn stover. The effect of poultry litter biochar was first studied on Saccharomyces cerevisiae ATCC 204508/S288C growth, and second on the enzyme hydrolysis and fermentation of two steam-exploded biomasses: (poplar and corn stover). The third part of the study investigated optimal process parameters (biochar loading, biomass loading, and enzyme loading) on the reducing sugars production, and ethanol yield from steam-exploded corn stover. In this study, it has been shown that poultry litter biochar improved the S. cerevisiae growth and ethanol productivity; therefore poultry litter biochar could potentially be used to improve the ethanol production from steam-exploded lignocellulosic biomass.

Cette thèse comprend cinq manuscrits d'articles. Deux de ces manuscrits sont publiés, l’un est actuellement en révision et deux sont en préparation pour soumission.Les animaux diffèrent de manière stable au cours du temps et dans différents contextes dans leur comportement, un phénomène souvent nommé personnalité animale. Les animaux diffèrent ainsi dans leur niveau d’expression de différents traits de personnalités. Cependant l’étude de la stabilité des traits de personnalité chez les jeunes animaux apporte des résultats controversés. Les deux principaux objectifs de cette thèse ont donc été d’évaluer comment l’environnement précoce des animaux façonnait leur personnalité et si l’expression de leur comportement était stable au cours du développement. Notre modèle d’étude était un petit rongeur d’origine sauvage, la souris glaneuse Mus spicilegus. Cette souris se trouve dans les zones agricoles d’Europe centrale et orientale. Il s'agit d'une espèce monogame et la femelle et le mâle participent aux soins parentaux. Les principaux résultats de cette thèse soulignent la stabilité des réponses comportementales des souris glaneuses dans des contextes sociaux et non-sociaux tôt lors de la période post-natale jusqu’à la maturité. De nombreux traits de personnalité étaient associés à travers différents contextes ; formant ainsi ce qu'il est convenu d'appeler un syndrome comportemental. Cette stabilité dans le comportement était avérée que l'analyse porte sur la totalité de l'échantillon ou qu'elle prenait en compte les différences intra-portées. L’environnement précoce et en particulier la présence du père apparaissent déterminants dans l’émergence et la modulation de la personnalité. Les individus élevés sans père montraient une plus grande réactivité dans deux tests différents par rapport à ceux élevés avec les deux parents. Différentes personnalités étaient associées à des mécanismes physiologiques. Confrontés à un stresseur chronique, les individus exprimant différentes personnalités montraient des différences physiologiques caractérisées par des profils immunologiques et hormonaux distincts. D'autre part les couples possédant des scores similaires d’anxiété, indépendamment du score des deux partenaires du couple, avaient une plus grande probabilité de reproduction durant la période d’observation, que les couples aux scores différents suggérant de potentiels avantages évolutifs. Cette thèse aborde en parallèle les aspects proximaux et ultimes du comportement chez un même modèle biologique ce qui est un but rarement atteint dans une étude éthologique. / This thesis includes five manuscripts. Two are already published, one is currently under review and two others are in preparation for submission.Animals frequently show consistent individual differences in behaviour across time and contexts, a phenomenon called animal personality. Animals have been thus described to differ in the expression level of different specific personality traits. However, consistencies in animal personality traits in young animals are especially controversial. One of the main aims of this thesis was therefore to investigate how the early environment experienced shapes the behavioural phenotype and whether the expression of behaviour remains stable over ontogeny. To this end, we used a small rodent of wild origin, the mound-building mouse Mus spicilegus, as an animal model. This monogamous mouse occurs in a variety of agricultural and steppe-like habitats in Central and South Eastern Europe, and is characterized by bi-parental care. The main results of this thesis highlight the consistency of personality traits in the mound building mouse from the early postnatal period until around maturity, both in social and non-social contexts. Various personality traits were associated across context, thus forming a behavioural syndrome. Such consistencies across time and context were present when looking at the individual level but also when focusing on the relative differences among siblings within a litter. The early developmental environment proved to be decisive in modulating the emergence personality of the individual, via the presence or absence of the father. Pups growing up in absence of the father showed indications of a higher responsiveness in two different tests compared to pups raised by mothers only. We showed how personality differences are related to physiological parameters. Different personality types coped physiologically different with a chronic stressor, apparent by their hormonal and immunological profiles. Pairs with similar anxiety scores, independently of the scores of both partners of the pair, had a higher probability of breeding, and brought forward the onset of breeding during the observation period, which carries along potential fitness benefits. This dissertation brings thus together some insights into the proximate and ultimate aspects underlying consistent individual differences in behaviour, which is seldom the case in a same model species.

Abstract not available

[Typescript] Includes bibliography.

Typescript. Copies of two papers co-authored by the author, in back cover pocket. Bibliography: leaves 128-143.

Forest plantations, widely grown for wood production, involve the selective promotion of single tree species, or replacement of natural species by exotic tree species. Slash pine (Pinus elliottii) has been chosen for reforestation of infertile sandy soils in southeast Queensland, Australia. These exotic pine plantations minimise soil and water losses, and are important scientific study sites. The soil environment of these plantations, though devoid of sufficient nutrients, oxygen and other factors, harbours innumerable bacteria that may play a crucial role in maintaining soil quality and ecosystem functions. These soil microorganisms also have the potential for use as sensitive biological indicators to reflect environmental changes. It is therefore essential to understand the interrelationships amongst bacterial communities and their environment by assessing their structural and functional diversity, and their responses to disturbances. The microbial community of an exotic pine plantation of subtropical Australia was analysed by both culture-dependent and culture-independent methods. In this study, a leaf litter-soil core sample (25 cm x 40 cm) was collected from a 22-year-old slash pine plantation in southeast Queensland, Australia in October, 2003. The core sample was divided into three fractions, namely, L layer leaf litter, F layer leaf litter, and forest soil 0-10 cm. In the culture-independent study, a modified DNA extraction and purification method was used to obtain highly purified high-molecular-weight DNA. This DNA was successfully used to amplify bacterial 16S rRNA genes with universal primers Fd1 and R6, to produce products of approximately 1500 bp. PCRamplified 16S rRNA genes were subsequently cloned and a total of 194 clones from leaf litter and soil were partially sequenced (about 510 bp). The 16S rRNA gene sequences were analysed and grouped into several phylogroups (the sequences with a similarity value ¡Ý 98 % were regarded as phylogenetically similar and grouped into one phylogroup). Sequencing representatives (¡Ö 1400 nucleotides) from each phylogenetic group confirmed that five bacterial phyla were represented in the forest soil clone library. Phylum Acidobacterium was the most abundant phylogenetic group in terms of the number of clones and accounted for 42 % of all examined soil clones. The Verrucomicrobiales and Proteobacteria were the second and third most abundant phylogenetic groups found in the soil clone libraries, accounting for 12 % and 11 % of the soil clones, respectively. About 8 % of all examined soil clones were Planctomycetes and 27 % of soil clones were phylogenetically unidentified. The large amount of unclassified clone sequences could imply that novel groups of bacteria were present in the forest soil. When the two fractions of leaf litter clone libraries were compared, Firmicutes was the only phylum represented in the L layer leaf litter clone library. Similarly, Firmicutes dominated the F layer leaf litter (79 % of the library), was followed by Proteobacteria (21 %). For the culture-dependent study, a total of 21 isolates which were considered to represent 334 colonies from the leaf litter and forest soil were identified by 16S rRNA gene sequence analysis, indicating that L layer leaf litter and F layer leaf litter were dominated by Firmicutes (48 %) and Proteobacteria (69 %) respectively, and 91 % of the isolates from the forest soil were Firmicutes. Using culture-independent methods, Actinobacteria appeared to be absent from the L and F layer leaf litter and forest soil samples. The results implied that either the nucleic acids of Actinobacteria were difficult to extract or Actinobacteria were over represented in the culture-dependent examinations. Phylum Acidobacteria appeared to be numerically dominant and active members in most soils. However, only one named species had been isolated from an acid mine drainage site and reported by Kishimoto and Tano (1987). Analysis by culture-dependent methods revealed a different bacterial diversity, compared to the bacterial diversity from the 16S rRNA gene clone sequences. The most significant result was the observation that, as revealed by both culture-dependent and culture-independent methods, the bacterial diversity presented in the leaf litter was greatly different from the community of the soil. During the culture-dependent bacterial diversity study, four novel strains were isolated from the forest soil and leaf litter samples and complete characterisations of these novel strains were carried out. Reports on the descriptions of Bacillus decisifrondis strain E5HC-32T from forest soil and Frondicola australicus strain E1HC-02T from L layer leaf litter have been published (appendix). The information provided by assessing the microbial communities in different fractions of leaf litter and forest soil improves our understanding of the phylogenetic relationship between soil and leaf litter. It is suggested, in this study, to perform both culture-dependent and culture-independent methods to characterise the bacterial structure and diversity in forest litter and soil samples, particularly in response to different forest management practices and global change. This study also provides the basis for further functional studies of the forest soil and leaf litter of exotic pine plantation in subtropical Australia.

Bibliography: leaves 134-148. The objectives of this study are to determine if and how inorganic matrices influence organic matter decomposition with particular emphasis on the biochemical changes which occur as decomposition progresses. The influence of inorganic matrices (sand, sand + kaolin and loamy sand) on the decomposition of straw and Eucalyptus litter during incubations was followed by various chemical and spectroscopic methods to aid in the understanding of the mechanism of physical protection of organic matter in soils.

Globally, the forestry sector is the second largest contributor of greenhouse gases, and sustainable forest management is a major target of international environmental policy. However, there is the assumption underlying many policy recommendations that an increase in above-ground carbon stocks correspond to long term increases in ecosystem carbon stocks, the majority of which is stored in soils. We analyzed soil carbon and nitrogen dynamics in forest soils that had undergone twenty years of organic inputs manipulations as part of the Detritus Input and Removal Treatment (DIRT) network. There was no statistically significant effect of the rate of litter or root inputs on the carbon or nitrogen in bulk soil, on respiration rates of soil in laboratory incubations, on the non-hydrolyzed fraction of soil organic matter, or on any organic matter associated with any density. However, there is evidence for positive priming due to increased litter inputs; doubling the rate of litter inputs decreased C and N contents of bulk soil and decreased respiration rates of soil. Furthermore, there is evidence that roots influence soil organic matter dynamics more strongly than above-ground inputs. Both of these results trends match data from other DIRT sites, and are supported by the literature. / Graduation date: 2012

Cigarette butts are rapidly accumulating on our planet; trillions of them are discarded every year. In this paper, I examine why cigarette litter is a problem. I first discuss the biodegradability of filters and its scientific basis, including ways to enhance degradation rates by chemically manipulating filters. I also talk about the persistence of cigarette chemicals and their potential toxic effects on children and animals. I consider other social, economic, and environmental consequences of cigarette filters and chemicals. Furthermore, I discuss various solutions smokers and non-smokers alike have created to address the problem of cigarette litter; these methods come from a wide range of artistic, science-based, and policy-based perspectives. Finally, my thesis examines this issue in the context of a college campus – Pomona College in Claremont, CA. I discuss a map showing the number of cigarette litter around buildings and sidewalks on campus and consider factors that influence the location and high counts of litter. Finally, I make recommendations for the college based on my findings.