The development of biofilms at solid-liquid interfaces has been investigated extensively, whereas the yield of planktonic cells from biofilms has received comparatively little attention. The detachment of single cells from biofilms has been attributed mainly to the erosive action of flowing liquid or the dispersal of cells from within biofilm microcolonies. The result has been an underestimation of the active role that biofilms can play in microbial proliferation through the production and release of planktonic cells to the environment. In this study, the cultivation of Pseudomonas sp. strain CT07 biofilms in conventional flowcells, glass tubes and a novel CO2 evolution measurement system was utilized to show that biofilm-derived planktonic cell yield was initiated within 6 hours of initial surface colonization and increased in conjunction with biofilm development. The magnitude of the yield was influenced by the metabolic activity of the biofilm, which was in turn dependent on environmental conditions, such as carbon availability. The physiologically active region of the biofilm was responsible for the yield of significant numbers of planktonic cells (~107 CFU.cm-2.h-1), whereas a less active biofilm zone was optimized for survival during unfavourable conditions and shown to be responsible for the subsequent re-establishment of biofilm structure, activity and cell yield. Despite the yield of numerically considerable numbers of planktonic cells (~1010 CFU), a carbon balance revealed that the carbon investment required to maintain this yield was insignificant (~1%) compared to the amount of carbon channelled into CO2 production (~54%). Together, these results indicate that biofilm-derived planktonic cell yield represents an efficient proliferation mechanism and support the view that the biofilm lifestyle affords microbes a dual survival-proliferation strategy, where the dominant strategy depends on the prevailing environmental conditions. An alternative model of biofilm development is presented to account for planktonic cell yield during all stages of biofilm development.

Ecological problems often require multivariate analyses. Ever since Bray and Curtis (1957) drew an analogy between Euclidean distance and community dissimilarity, most multivariate ecological inference has been based on geometric ideas. For example, ecologists routinely use distance-based ordination methods (e.g. multidimensional scaling) to enhance the interpretability of multivariate data. More recently, distance-based diversity indices that account for functional differences between species are now routinely used. But in most other areas of science, inference is based on Fisher's (1922) likelihood concept; statisticians view likelihood as an advance over purely geometric approaches. Nevertheless, likelihood-based reasoning is rare in multivariate statistical ecology. Using ordination and functional diversity as case studies, my thesis addresses the questions: Why is likelihood rare in multivariate statistical ecology? Can likelihood be of practical use in multivariate analyses of real ecological data? Should the likelihood concept replace multidimensional geometry as the foundation for multivariate statistical ecology? I trace the history of quantitative plant ecology to argue that the geometric focus of contemporary multivariate statistical ecology is a legacy of an early 20th century debate on the nature of plant communities. Using the Rao-Blackwell and Lehmann-Scheffé theorems, which both depend on the likelihood concept, I show how to reduce bias and sampling variability in estimators of functional diversity. I also show how to use likelihood-based information criteria to select among ordination methods. Using computationally intensive Markov-chain Monte Carlo methods, I demonstrate how to expand the range of likelihood-based ordination procedures that are computationally feasible. Finally, using philosophical ideas from formal measurement theory, I argue that a likelihood-based multivariate statistical ecology outperforms the geometry-based alternative by providing a stronger connection between analysis and the real world. Likelihood should be used more often in multivariate ecology.

The thesis examines the dynamics of intraguild predation models incorporating adaptive behaviour. The top predator varies its relative consumption of the intermediate consumer and the basal resource. The consumer alters its activity level in response to the threat of predation. Incorporating these adaptive behaviours facilitated three species coexistence, but restricted omnivory by promoting the formation of three species food chains. Model modifications which promoted omnivory also tended to reduce three species coexistence. It is predicted that omnivory should be most common when the intermediate and the basal species are similarly profitable to the predator. The model also predicts two types of omnivory. Strong omnivory occurs when the predator always consumes intermediate amounts of both prey items. Weak omnivory occurs when the predator preys almost exclusively on one prey at most times, but rapidly switches to include the other when the relative abundance of that second prey exceeds a certain level.

In situ bioremediation by Fe(III) reducers is a strategy for clean-up of ground water through reductive immobilization. The dynamics of the community involved is complex and needs to be understood better for improving the bioremediation. Here, we have created a dynamic genome-scale metabolic model of Geobacter sulfurreducens and Rhodoferax ferrireducens, the two primary iron-reducers in subsurface environments, in order to understand the community competition prior to and during uranium- bioremediation. The simulation results suggest that the community competition is modulated by two factors: the ability of G. sulfurreducens to fix nitrogen under ammonium limitation, and a rate vs. yield trade-off between these two organisms. This model will be an important tool for the analyses of more complex microbial communities and the design of effective uranium-bioremediation strategies.

In situ bioremediation by Fe(III) reducers is a strategy for clean-up of ground water through reductive immobilization. The dynamics of the community involved is complex and needs to be understood better for improving the bioremediation. Here, we have created a dynamic genome-scale metabolic model of Geobacter sulfurreducens and Rhodoferax ferrireducens, the two primary iron-reducers in subsurface environments, in order to understand the community competition prior to and during uranium- bioremediation. The simulation results suggest that the community competition is modulated by two factors: the ability of G. sulfurreducens to fix nitrogen under ammonium limitation, and a rate vs. yield trade-off between these two organisms. This model will be an important tool for the analyses of more complex microbial communities and the design of effective uranium-bioremediation strategies.

Climate change is shifting the seasonal timing of many biological events, and the possibility of non-parallel shifts in different taxa has raised concerns about phenological decoupling of interacting species. My thesis investigates interactions between climate, phenology, and pollination, using the plants and pollinators of Rocky Mountain meadows as a study system. Interannual variation in timing of snowmelt since the 1970s has been associated with changes in the assemblages of concurrently flowering species in these meadows, suggesting that plant species differ in their phenological responses to climate. Differences between plants and pollinators in responsiveness to changing climate could, in principle, cause early-flowering plants to flower too early in warm years, before pollinators are active. In fact, I found only transient evidence for pollinator deficits in one early-flowering species (Mertensia fusiformis), even in an early-snowmelt year. However, the assemblage of pollinators visiting M. fusiformis does change predictably over the season, with likely consequences for selection on floral morphology in years when pollen is limiting. Hence, early- and late-flowering populations may evolve in response to phenology of the pollinator community. Differences between plant and pollinator phenologies appear to be due to generally lower temperature thresholds for development in plants, combined with microclimate differences between the soil and the above-ground nests of some pollinators. Phenological decoupling between plants and pollinators seems possible but unlikely to be catastrophic, since many taxa possess adaptations to temporally variable environments. Nevertheless, for many species, adaptation to novel climates will entail evolutionary change, and species interactions can influence evolutionary trajectories. For species affected by increasing late-summer drought, earlier flowering may be advantageous. However, in laboratory experiments, bumble bees avoid rare, unfamiliar flower types, causing simulated plant populations to fail to adapt to changing conditions. Overall, my work emphasizes the importance of the interplay between species interactions and environmental change.

The thesis examines the dynamics of intraguild predation models incorporating adaptive behaviour. The top predator varies its relative consumption of the intermediate consumer and the basal resource. The consumer alters its activity level in response to the threat of predation. Incorporating these adaptive behaviours facilitated three species coexistence, but restricted omnivory by promoting the formation of three species food chains. Model modifications which promoted omnivory also tended to reduce three species coexistence. It is predicted that omnivory should be most common when the intermediate and the basal species are similarly profitable to the predator. The model also predicts two types of omnivory. Strong omnivory occurs when the predator always consumes intermediate amounts of both prey items. Weak omnivory occurs when the predator preys almost exclusively on one prey at most times, but rapidly switches to include the other when the relative abundance of that second prey exceeds a certain level.

Climate change is shifting the seasonal timing of many biological events, and the possibility of non-parallel shifts in different taxa has raised concerns about phenological decoupling of interacting species. My thesis investigates interactions between climate, phenology, and pollination, using the plants and pollinators of Rocky Mountain meadows as a study system. Interannual variation in timing of snowmelt since the 1970s has been associated with changes in the assemblages of concurrently flowering species in these meadows, suggesting that plant species differ in their phenological responses to climate. Differences between plants and pollinators in responsiveness to changing climate could, in principle, cause early-flowering plants to flower too early in warm years, before pollinators are active. In fact, I found only transient evidence for pollinator deficits in one early-flowering species (Mertensia fusiformis), even in an early-snowmelt year. However, the assemblage of pollinators visiting M. fusiformis does change predictably over the season, with likely consequences for selection on floral morphology in years when pollen is limiting. Hence, early- and late-flowering populations may evolve in response to phenology of the pollinator community. Differences between plant and pollinator phenologies appear to be due to generally lower temperature thresholds for development in plants, combined with microclimate differences between the soil and the above-ground nests of some pollinators. Phenological decoupling between plants and pollinators seems possible but unlikely to be catastrophic, since many taxa possess adaptations to temporally variable environments. Nevertheless, for many species, adaptation to novel climates will entail evolutionary change, and species interactions can influence evolutionary trajectories. For species affected by increasing late-summer drought, earlier flowering may be advantageous. However, in laboratory experiments, bumble bees avoid rare, unfamiliar flower types, causing simulated plant populations to fail to adapt to changing conditions. Overall, my work emphasizes the importance of the interplay between species interactions and environmental change.

Questions surrounding the causes and consequences of diversity lie at the centre of community ecology. Understanding the mechanisms by which species diversity is maintained motivates much experimental and theoretical work, but this work often focuses on fluctuation-independent mechanisms. Variability in habitat suitability is ubiquitous through space and time however, and provides another important path through which species diversity can be maintained. As a result, considering environmental variability has value for conservation and management. Finally, differences through space and time in the mechanisms that promote and maintain diversity produce spatially varying patterns of diversity. Spatial variation in different forms of diversity (species (SR), phylogenetic (PD), and functional diversity (FD)) creates difficult decisions about prioritization and reserve locations. This thesis uses experimental, observational, and theoretical methods to explore the causes and consequences of diversity. I show that variation in space and time has important implications for species coexistence and diversity maintenance. In microbial nectar communities, temperature variation through space and time alters the importance of priority effects on community assembly. Using models of warming temperatures in annual plant communities I show that considering temporal partitioning of flowering (a strategy to minimize competition) introduces constraints on phenological shifts: this has implications for phenological monitoring programs. Finally, I show that variability in the timing of fire events in Mediterranean shrublands contributes to coexistence between life forms, suggesting that it should be considered for fire management. In the final two chapters, I focus on conservation prioritization. Comparisons of species richness and evolutionary diversity through space in the Cape Floristic Region of South Africa show that existing reserves protect Proteaceae richness, but fail to capture evolutionary distinct species. More generally, in the final chapter I suggest that SR and PD should be congruent through space when species are of similar ages, regions are depauperate, or ranges are discontinuous.

Populations in fragmented habitat patches may show ecological differentiation, which has implications for metapopulation viability. In this study we used a common garden with two watering treatments to contrast mean differences in ecophysiological traits and the relationships between traits and performance among seven populations of three alvar species. These species differ in their alvar specialization in Ontario, from almost endemic (Solidago ptarmicoides) to highly confined (Dasiphora fruticosa) to a widespread generalist (Hypericum perforatum). Populations of all species exhibited mean differences in at least one trait: photosynthesis (Amax), growth rate and specific leaf area. More surprisingly, the relationship between functional traits and performance was significantly different among populations in all species, suggesting different strategies for maximizing growth in different environments. The ecological differentiation observed affected all species regardless of distribution and is likely genetically based. This differentiation may destabilize metapopulation dynamics and reduce rates of spread if colonization is negatively impacted.