Periodic monitoring of contaminant levels in fish from the Yukon Territory indicated that organochlorine (OC) contaminants had rapidly declined since the early 1990s. This study examined OC concentrations, including chlordane (sigma-CHL), sigma-DDT, hexachlorocyclohexane (sigma-HCH), toxaphene (sigma-CHB), sigma-PCB and chlorinated benzenes (sigma-CBz) in sentinel fish (species of consistent annual observation and collection) from two Yukon lakes (Kusawa, Quiet), and from the aquatic food web of a focus lake (Lake Laberge) across several temporal points between 1993 and 2003. OC analysis and phytoplankton counts from dated sediment cores as well as climate data were also collected. Population, morphological (length, weight, age), biochemical (lipid content, delta-13C, delta-15N) and OC contaminant data for fish and invertebrates (zooplankton, snails, clams) were reviewed to elucidate the primary causes for these OC declines. Although some spatial differences in contaminant levels exist between the Yukon lakes, OC concentrations were declining for lake trout in all three lakes, with declines also noted for burbot from Lake Laberge. Several other fish species as well as zooplankton from Lake Laberge exhibited decreases in contaminant levels except northern pike, which registered consistently higher levels from 1993 to 2001. There was no evidence to support the hypotheses of changes in fish trophic levels or food sources with the exception of burbot, which marginally decreased, and northern pike, which climbed a half trophic level. Through OC flux analysis in dated sediments, the hypothesis that declines in abiotic deposition affected the contaminant levels in the food web was also negated. The closure of the Lake Laberge commercial fishery resulted in faster fish growth and larger fish populations, which are contributing to biomass dilution of OC concentrations, higher OC biomagnification factors for some species and likely changes in predator-prey interactions as resource competition increases. The large ratio of OC decreases in the lower vs. higher trophic levels of Lake Laberge have increased food web magnification factors (FWMF) for all six OC groups. It is also suspected that above-average temperatures and below-average precipitation in the lower Yukon region over the 1990s may have contributed towards an increase in lake primary production resulting in biomass dilution of contaminants in zooplankton for all three study lakes. Concurrently, shifts in the Lake Laberge zooplankton community, from climate fluctuations or increased fish predation, have gone from an abundance of Cyclops scutifer in 1993 to dominance by Diaptomus pribilofensis in 2001, although sample sites were limited. Characteristics specific to each species (e.g. body size, composition and metabolism) likely play a role in the significant OC declines measured in zooplankton. Fluctuations in population dynamics, species characteristics and OC contaminant concentrations in the Lake Laberge ecosystem may continue for several years to come. Sentinel species such as lake trout, burbot, whitefish, cisco and plankton should continue to be monitored in all three Yukon lakes for future temporal correlations with contaminants or climate change.

Humans impact rivers in many ways that modify ecological processes yielding ecosystem services. In order to mitigate anthropogenic impacts, scientists are challenged to understand interactions among physicochemical factors affecting large river food webs. An understanding of socioeconomic factors also is critical for ecosystem management. In this dissertation, I explore spatiotemporal patterns in floodplain river food webs and political barriers to management of environmental flows, an important factor influencing river ecology. In Chapter II, I reviewed the scientific literature to test conceptual models of river food webs and predictions of environmental factors that might produce variation in basal production sources supporting consumer biomass. My review indicates that algae are the predominant production source for large rivers worldwide, but consumers assimilate C3 plants in rivers 1) with high sediment loads and low transparency during high flow pulses, 2) with high dissolved organic matter concentrations, and 3) following periods of high discharge or leaf litter fall that increase the amount of terrestrial material in the particulate organic matter pool. In Chapter III, I descrobe field research conducted to examine relationships among hydrology, nutrient concentrations, turbidity, and algal primary production and biomass in the littoral zone of five rivers in Texas, Peru, and Venezuela differing in physicochemical conditions. I used stable isotope signatures to estimate contributions of algal-versus terrestrial-based production sources to consumers during different hydrologic periods. My research indicates that during flow pulses in floodplain rivers, a decrease in algal biomass and productivity, combined with increased inputs of terrestrial organic matter, can result in increased terrestrial support of metazoan consumers in the aquatic food web. In 2007, Texas Senate Bill 3 directed that environmental flow recommendations be developed for river basins. Despite emphasis on use of the "best available science" to develop environmental flow regimes and "stakeholder involvement" to address needs of all water users, for the first two basins to complete the SB3 process, final environmental flow rules did not mimic a natural flow regime. In Chapter IV, I reviewed this process, concluding that incentives for river authorities to increase compromise with diverse stakeholders should result in more sustainable management of freshwater.

Ecological communities along gradients of environmental stress are thought to be structured by trade-offs between resisting biotic interactions in physically benign habitats and successfully exploiting physically stressful habitats. However, these trade-offs are likely to be affected by the predictability of abiotic stressors, and variation in the strength of biotic interactions. I investigated community assembly and food web interactions in ponds across an unpredictable gradient of water inundation (pond permanence) in Canterbury, New Zealand. Pond community composition and species richness were strongly influenced by pond permanence. However, species in temporary ponds were a nested subset of generalists that were also found in permanent ponds, rather than a unique assemblage of temporary pond specialists. Subsequent experiments indicated predator impact decreased with pond permanence, partially due to the foraging suppression of predatory invertebrates in permanent ponds by fish. Weak predation in permanent ponds combined with unpredictable drying regimes likely selected for generalist traits, and resulted in community assembly being driven by a gradient of drying stress rather than trade-offs between biotic interactions and drying. Furthermore, predator impact increased over time in temporary ponds. In predictable snow-melt ponds in the Colorado Rocky Mountains, seasonal windows of weak predation were exploited by vulnerable species, leading to increased diversity within habitats. However in unpredictable systems like Canterbury, temporal increases in predation risk that depend on drying history are likely to increase variability in the spatial arrangement of suitable habitats for particular species. This should further favour the evolution of generalist traits and reduce the importance of trade-offs between predation and drying in the assembly of communities. Considering the predictability of disturbance regimes and the spatial and temporal variation in biotic interactions will greatly enhance understanding and management of communities in heterogeneous landscapes.

This work exploits the general equilibrium modeling framework to simulate complex systems, an economy and an ecosystem. In an economic application, this work leverages a novel data revision scheme to integrate technological detail on electricity generation and pollution abatement into national accounts data in a traditional economic computed general equilibrium (CGE) model. This integration provides a rich characterization of generation and abatement for multiple fuel sources and pollutants across 72 different generation-abatement technology configurations. Results reveal that the benefits of reductions in oxides of nitrogen and sulfur from a carbon policy in the US electric sector are on the order of $10 bn., which rival the policy's welfare costs and make 12-13% carbon abatement economically justifiable without considering any climate benefits. For ecosystem applications, this work demonstrates how the structure of economic CGE modeling can be adapted to construct a Biological General Equilibrium (BGE) model grounded in the theoretical biology literature. The BGE model contributes a novel synthesis of micro-behavioral, bioenergetic features with macroscopic ecosystem outcomes and empirical food web data. Species respond to prevailing ecosystem scarcity conditions that impinge on their energy budgets driving population outcomes within and across model periods. This adaptive capacity is a critical advance over the commonly-taken phenomenological or first-order parametric approaches. The distinctive design of the BGE model enables numerical examination of how changes in scarcity drives biomass production and consumption in a complex food web. Moreover, the BGE model design can exploit empirical datasets used by extant ecosystem models to offer this level of insight for a wide cast of ecosystems. Monte carlo simulations demonstrate that the BGE framework can produce stable results for the ecosystem robust to a variety of shocks and parameterizations. The BGE model's validity is supported in tests against real-world phenomena within the Aleutian ecosystem - both an invasive species and a harvesting-induced trophic cascade - by mimicking key features of these phenomena. The BGE model's micro-founded dynamics, the stability and robustness of its results, and its validity against real-world phenomena offer a unique and valuable contribution to ecosystem modeling and a way forward for the integrated assessment of human-ecosystem interactions.

Les microorganismes jouent un rôle prépondérant dans le fonctionnement des écosystèmes aquatiques, où ils sont à la base de la minéralisation et du recyclage de la matière organique. Les« vrais » champignons, ou Eumycètes, font partie de ces microorganismes hétérotrophes qui permettent le renouvellement de la matière organique dans les écosystèmes. Pourtant, la diversité et l’importance quantitative et fonctionnelle des champignons restent très largement méconnues dans les milieux pélagiques. Récemment, l’utilisation de méthodes moléculaires pour étudier la diversité des picoeucaryotes (de taille < 5 μm) lacustres a mis en évidence l’importance des champignons microscopiques avec, notamment, la présence de chytridiomycètes (chytrides). Cette découverte, en conjonction avec le rôle important connu des Eumycètes dans d’autres écosystèmes naturels, nous a amené à poser l’hypothèse d’une diversité et d’un rôle fonctionnel importants des champignons dans les écosystèmes pélagiques. Ce travail vise à préciser la diversité globale, la structure génétique et l’importance quantitative des différentes divisions du règne des Eumycota dans les écosystèmes pélagiques lacustres, et à proposer des outils méthodologiques pour l’étude écologique de ces peuplements. La diversité phylogénétique et l’importance des champignons de taille comprise entre 0,6 et 150 μm ont été analysées dans trois milieux pélagiques différents. Une étude de clonage-séquençage de l’ADNr 18S et de l’ITS a été réalisée au printemps 2007 dans les lacs Pavin (oligomésotrophe), Aydat (eutrophe) et Vassivière (mésotrophe, humique). L’affiliation phylogénétique des séquences a permis, non seulement de confirmer la présence d’une importante diversité de chytridiomycètes parasites du phytoplancton, mais aussi de mettre en évidence la présence non négligeable d’ascomycètes et de basidiomycètes, potentiellement saprophytes. L’étude de la dynamique saisonnière de la structure des peuplements (par TRFLP) et de l’importance quantitative de différentes divisions (par PCR quantitative) de la communauté fongique ont permis de déceler des différences en fonction des saisons et de l’écosystème. Ces différences ont été reliées à la dynamique des peuplements phytoplanctoniques, avec une influence des apports allochtones, principalement dans le lac eutrophe d’Aydat. De plus, les séquences moléculaires générées au cours de ces dernières années ont permis l’élaboration d’amorces ciblant des clades de champignons microscopiques d’intérêt, pour une étude écologique de la dynamique des peuplements, par des approches PCR à temps réel et FISH (fluorescent in situ hybridization). Enfin, nous considérons que l’acquisition de données complémentaires permettra d’intégrer les champignons saprophytes et parasites dans les flux de matière et d’énergie qui transitent par les écosystèmes pélagiques et les cycles biogéochimiques associés. / Microorganisms play major roles in aquatic ecosystems, primarily as the main actors for organic matter mineralization and recycling. “True” fungi (i.e. Eumycota) are among heterotrophic microorganisms that are highly efficient in recycling organic materials in natural ecosystems. However, the overall diversity of fungi and their quantitative and functional importance remain largely unknown in typical pelagic ecosystems. Environmental 18S rDNA surveys have recently highlighted the importance of microscopic fungi in the diversity of picoeukaryotes (size < 5 μm) in lake ecosystems, including particularly the members of chytridiomycetes (i.e. chytrids) as the dominant phyla. These studies and the known major roles of fungi in natural ecosystems such as soils have leaded us to venture the hypothesis that fungal diversity and functional roles are important structuring factors in pelagic ecosystems. The main aims of the thesis were to examine the overall diversity, genetic structure and quantitative importance of various phyla belonging to the Kingdom Fungi in freshwater pelagic ecosystems. Methodological tools were also developed for ecological investigations of fungal populations of interest. Phylogenetic diversity and quantitative importance of fungi (size classe: 0.6 and 150 μm) were analysed in three contrasting pelagic lakes. Environmental 18S and ITS rDNA surveys were performed during spring 2007 in the oligomesotrophic Lake Pavin, the eutrophic Lake Aydat, and the mesotrophic and humic Lake Vassivière, all located in the French Massif Central. Phylogenetic affiliation of sequences confirmed the presence and the substantial diversity of chytridiomycetes, known as parasites of primarily phytoplankton. We also have unveiled a sizeable number of sequences belonging to the fungal lineages of ascomycetes and basidiomycetes, mainly known as saprophytes. The seasonal dynamics of fungal community structure (essayed by TRFLP),and the quantitative importance of various taxonomic divisions (estimates by real time quantitative PCR or qPCR), revealed significant differences with seasons and with ecosystems. These differences were linked to phytoplankton composition and population successions, with at times the influence of allochthonous inputs, primarily for the eutrophic Lake Aydat. Finally, molecular sequences obtained during the few past years allowed the development of primers for targeting microscopic fungal lineages of interest, and the ecological study of their in situ dynamics using qPCR and FISH (fluorescent in situ hybridization) approaches. Overall, we consider that the acquisition of complementary data is necessary to allow the inclusion of fungi and their main functions (i.e. saprophytisms and parasitism) in the energy and matter fluxes in pelagics ecosystems, and the related biogeochemical cycling.

abstract: The explicit role of soil organisms in shaping soil health, rates of pedogenesis, and resistance to erosion has only just recently begun to be explored in the last century. However, much of the research regarding soil biota and soil processes is centered on maintaining soil fertility (e.g., plant nutrient availability) and soil structure in mesic- and agro- ecosystems. Despite the empirical and theoretical strides made in soil ecology over the last few decades, questions regarding ecosystem function and soil processes remain, especially for arid areas. Arid areas have unique ecosystem biogeochemistry, decomposition processes, and soil microbial responses to moisture inputs that deviate from predictions derived using data generated in more mesic systems. For example, current paradigm predicts that soil microbes will respond positively to increasing moisture inputs in a water-limited environment, yet data collected in arid regions are not congruent with this hypothesis. The influence of abiotic factors on litter decomposition rates (e.g., photodegradation), litter quality and availability, soil moisture pulse size, and resulting feedbacks on detrital food web structure must be explicitly considered for advancing our understanding of arid land ecology. However, empirical data coupling arid belowground food webs and ecosystem processes are lacking. My dissertation explores the resource controls (soil organic matter and soil moisture) on food web network structure, size, and presence/absence of expected belowground trophic groups across a variety of sites in Arizona. / Dissertation/Thesis / Ph.D. Biology 2014

Nanoflagellates were found to be abundant in a coastal area of the northern Bothnian Sea. The maximum concentration of nanoflagellates, approximately 8000 cells ml-1, was observed in July, coinciding with a decrease in the abundance of cyanobacteria. Pigmented and non-pigmented nanoflagellates were approximately equally distributed throughout the year. Most of the identified genera are known as being phagotrophic, independent if autotrophic or not. A non-cyst-forming pigmented flagellate, Ochromonas sp., was isolated and nutritionally characterized. This chrysophycean flagellate was shown to be a mainly heterotrophic organism: Photosynthesis was too poor to support multiplication of the cells, whereas when feeding on bacteria, high growth rates were obtained. The biological function of the photosynthetic apparatus is suggested to be a survival mechanism during poor bacterial conditions. The flagellate grazed bacteria selectively, preferring cyanobacteria and large cells of heterotrophic bacteria, presumably depending on size-selective grazing. Despite higher growth rates of the bacteria in the sea during summer (July) than spring (May), heterotrophic bacteria in the sea was observed to be smaller in the summer. Nanoflagellates showed a maximum in July, and by selective grazing of large bacteria they might have caused the decrease in the average size of the bacteria and the decrease in the abundance of cyanobacteria. During the consumption of bacteria the flagellate was shown to remineralize nutrients at high rates and excrete dissolved free amino acids. Assuming the existence of a protozoan predator-prey chain of several trophic levels, it seems likely that a significant part of the nutrients fixed by primary producers is remineralized in the euphotic zone. Furthermore, data from this work indicate that flagellate activity may be a significant source of dissolved free amino acids, utilizable for the heterotrophic bacteria. / digitalisering@umu

Two differently structured food webs can be distinguished in the pelagic habitat of aquatic systems; the classical one (autotrophic) with phytoplankton as a base and the microbial food web (heterotrophic) with bacteria as a base. Energy (produced at the basal trophic level) reaches higher trophic levels, i.e. zooplankton, directly in the classical food web in contrast to the microbial food web where it passes through additional trophic levels before reaching zooplankton. Energy is lost between each trophic level and therefore less energy should reach higher trophic levels in the microbial food web than in the classical food web. However, factors such as edibility of prey, temperature and properties of the predator, might also influence the food web structures and functions. In this thesis I studied which factors are important for an efficient carbon transfer and how a potential climate change might alter the food web efficiency in pelagic and pelagic-benthic food webs in the Baltic Sea. Furthermore, one of the most dominant zooplankton in the northern Baltic Sea, Limnocalanus macrurus, was studied in order to establish the seasonal pattern of lipid reserves in relation to food consumption. My studies showed that the carbon transfer efficiency during summer was not directly connected to the basal production, but factors such as the ratio between heterotrophs and autotrophs, the relationship between cladocerans and calanoid copepods and the size and community structure of both phytoplankton and zooplankton were important for the carbon transfer efficiency. In a climate change perspective, the temperature as well as the relative importance of the microbial food web is likely to increase. A temperature increase may have a positive effect on the pelagic food web efficiency, whereas increasing heterotrophy will have a negative effect on the pelagic and pelagic-benthic food web efficiency, reduce the fatty acid content of zooplankton and reduce the individual weight of both zooplankton and the benthic amphipod Monoporeia affinis. During the seasonal study on the calanoid copepod L. macrurus, I found that this species is mainly a carnivore, feeding on mesozooplankton during most of the year but switches to feeding on phytoplankton when these are abundant. Furthermore, when food is scarce, it utilizes lipids that are built up during the course of the year. From these studies I can draw some major conclusions; there are many factors that influence how efficient carbon is transferred in the food web and different factors are probably of various importance in different areas. In order to determine the carbon transfer efficiency, the various strategies exerted by different organism groups have to be considered, as for example that some zooplankton utilize lipid reserves instead of feeding all year around. Also, in a climate change perspective, the pelagic-benthic food web efficiency will decrease, as will the quality of zooplankton and M. affinis, possibly having implications for higher trophic levels such as fish.

The majority of lakes on Earth are shallow, unproductive and located at high latitudes. These lakes are experiencing big changes due to climate change, where two environmental drivers operate simultaneously, browning and warming. How they affect lake ecosystems is not well understood. Here, I addressed this issue by using a theoretical and an experimental approach. In particular, I generated model predictions and compared them with the results of a realistic large-scale experiment, where browning and warming were manipulated in a factorial design. In addition, model outcomes were compared with data from 12 unproductive lakes sampled along a gradient of browning. Another novelty of my thesis is that it integrates benthic and pelagic food web components in the model and experimental approaches. I found that browning affected the resources availability for benthic and pelagic producers in the model and in the experiment. With browning, benthic primary producers became increasingly light limited and declined, while pelagic producers became less nutrient limited and increased. Pelagic nutrient limitation was alleviated by two non-exclusive mechanisms. Browning directly enriched the water with nutrients, and browning indirectly increased the nutrient flowing from the sediment to the pelagic habitat via suppression of benthic producers. To tease apart these two mechanisms I applied structural equation modeling (SEM). The indirect evidence by SEM suggests that both mechanisms contributed equally to the pelagic nutrient concentration in the experiment. Interestingly, a model food web with only primary producers shows similar qualitative behavior as a food web with grazers and carnivores included. This happens because carnivorous fish exert strong top-down control in the more productive habitat, which relaxes grazing pressure on primary producers and increases resource limitation in the adjacent habitat. Biomass of benthic and pelagic consumers followed the same pattern as their resources. The lake data were largely congruent with model expectations and supported the findings of the experiment. Furthermore, the model also predicted a negative relationship between total phosphorus and both primary and fish production, which was observed across the 12 lakes. Warming effects were more complex. The model predicts that warming effects should depend on browning and are expected to be strongest in the more productive of the two (benthic and pelagic) habitats. For example, at low levels of browning the biomasses of benthic algae and fish are expected to decline with warming, which was observed in the experiment. In contrast, observed warming effects at high levels of browning deviated from model expectations. The mechanisms by which browning and warming interactively affect lake food webs are still poorly understood. This thesis offers a conceptual foundation for their further study through the integration of within- and between-habitat interactions.

Global records of temperature show a warming trend both in the atmosphere and in the oceans. Current climate change scenarios indicate that global temperature will continue to increase in the future. The effects will however be very different in different geographic regions. In northern Europe precipitation is projected to increase along with temperature. Increased precipitation will lead to higher river discharge to the Baltic Sea, which will be accompanied by higher inflow of allochthonous organic matter (ADOM) from the terrestrial system. Both changes in temperature and ADOM may affect community composition, altering the ratio between heterotrophic and autotrophic organisms. Climate changes may thus have severe and complex effects in the Baltic Sea, which has low species diversity and is highly vulnerable to environmental change. The aim of my thesis was to acquire a conceptual understanding of aquatic food web responses to increased temperature and inputs of ADOM. These factors were chosen to reflect plausible climate change scenarios. I performed microcosm and mesocosm experiments as well as a theoretical modeling study. My studies had a holistic approach as they covered entire food webs, from bacteria and phytoplankton to planktivorous fish. The results indicate a strong positive effect of increased temperature and ADOM input on the bacterial community and the microbial food web. However, at the prevailing naturally low nutrient concentrations in the Baltic Sea, the effect of increased temperature may be hampered by nutrient deficiency. In general my results show that inputs of ADOM will cause an increase of the bacterial production. This in turn can negatively affect the production at higher trophic levels, due to establishment of an intermediate trophic level, consisting of protozoa. However, the described effects can be counteracted by a number of factors, as for example the relatively high temperature optimum of fish, which will lead to a more efficient exploitation of the system. Furthermore, the length of the food web was observed to be a strong regulating factor for food web responses and ecosystem functioning. Hence, the effect of environmental changes may differ quite drastically depending on the number of trophic levels and community composition of the system. The results of my thesis are of importance as they predict possible ecological consequences of climate change, and as they also demonstrate that variables cannot be examined separately. / <p>This thesis was supported by grants from the Swedish Research Council FORMAS to AA and SL (217-2006-674), the Centre for Environmental Research in Umeå (CMF) to UB, AA and SL, and by the Swedish strategic research program ECOCHANGE to Umeå University.</p>