The overall aim of this thesis was to elucidate the relative importance of the bacterial and fungal energy channels within the soil food web and to differentiate and appreciate the differences in niche of the soil fauna when affected by differing land management. Feeding niche of the soil fauna is ambiguous and has been previously determined by observation, inference or biochemical studies. One method that can determine feeding preferences in situ is the use of stable isotopes. Stable isotopes trace the passage of C and N through different trophic levels, both at natural abundance and by the addition of a pulse of enrichment. The work described within this thesis describes the development of methods of culturing and labelling organisms for use in stable isotope studies. Bacteria, protozoa and fungi were cultured with stable isotopes enriched to 99 atom% and their growth and survival monitored. Utilising stable isotope enriched organisms means that empirical testing of the feeding interactions can occur and that differences between the bacterial and fungal energy channels can be explored. Two field sites were chosen to assess how management changes affect the food web, both sites were historically grassland with the same soil type, but one was converted to a willow woodland twenty years ago. The results of these studies have shown, at natural abundance a grassland and woodland habitat with very different stable isotope signatures, reflecting plant and soil composition, as well as differences in trophic niche and C drivers. The introduction of enriched bacteria illustrated that bacterial feeding was more widespread than normally portrayed in food web diagrams. The introduction of enriched protozoa highlighted that protozoan feeding by soil fauna was more prevalent in the grassland habitat; reflecting differences in linkages between trophic levels within the two habitats. Methods were also developed to “grow” enriched fungal hyphae back into soil food webs in a comparable way to the investigation of the bacterial energy channel. Different species of saprotrophic fungi were found to fractionate to differing extents when grown on the same natural abundance media and the fungus Absidia cylindrospora's growth was impacted when grown on a dually enriched medium. We can now infer that the bacterial energy channel is not as divergent from the fungal energy channel as previously hypothesised. The majority of soil fauna were found to be omnivorous through empirical results, consuming bacteria and protozoa, even when they were considered to be fungal feeders by the literature. The different habitats within the study were found to have different C drivers, with roots and soil being the primary driver in the grassland whilst litter was in the woodland, consequently favouring different food webs. This work makes a first step in measuring the contribution of the different feeding channels and feeding interactions occurring within the different trophic levels in the two habitats and shows the effect that one change in management has had over the entire faunal assemblage.

This dissertation includes 3 chapters which focus on algal bloom of the tidal fresh James River. The first chapter describes nutrient and light limitation assays performed on algal cultures and draw conclusions about long-term patterns in nutrient limitation by comparing results with a previous study . This chapter also describes the influence of riverine discharge upon nutrient limitation in a point-source dominated estuary. This chapter was published in Estuaries and Coasts (Wood and Bukaveckas 2014). The second chapter presents the first comprehensive assessment of the occurrence of the cyanotoxin Microcystin in water and biota of the James River. Data presented in this chapter show that bivalve grazing declines in the presence of Microcystin in the water. The chapter also describes feeding habits in fish as a predictor for inter-specific differences in Microcystin accumulation in their tissues. The work presented in this chapter was published in Environmental Science & Technology (Wood et al. 2014). The third chapter describes the fate of algal carbon in the James River Estuary and the importance of autochthonous and allochthonous sources of organic matter in supporting production of higher trophic levels. Here I draw upon ecosystem metabolism data (NPP and R), abundance and grazing estimates for primary consumers and estimates of advective losses of chlorophyll and external inputs of nitrogen to place ‘top-down’ effects in the broader context of factors influencing chlorophyll and nitrogen fluxes in the James. . This chapter also describes results from mesocosm experiments used to assess the influences of grazers on chlorophyll, nutrients and Microcystis. This work will be submitted in the summer of 2014 to the journal Ecosystems.

This thesis examines the contribution of a non-indigenous red alga, Mazzaella japonica, to wrack subsidies in Baynes Sound, British Columbia, and the effects of its removal by a commercial beach-cast harvest. Field and laboratory work was conducted to determine: 1) How large wrack inputs are in terms of biomass and spatial extent within the harvest region, and what proportion of this is comprised of M. japonica; 2) how wrack characteristics influence associated macrofauna communities; 3) if there is any detectable effect of beach-cast harvesting on either the wrack characteristics or macrofauna communities; and 4) if M. japonica provides a food source for native invertebrate consumers within the subtidal and supralittoral zones. Field surveys conducted from November 2014 through March 2015 found that wrack biomass within the harvest region could reach as much as 853 kg (±173 SD) per meter of shoreline, and cover up to 35 m2 (± 3 SD) of beach surface within this area. The macrophyte composition of the wrack was dominated by M. japonica, which accounted for 90% of the identifiable macrophyte biomass on average. Wrack in the later stages of decomposition hosted the most speciose and diverse assemblages of macrofauna, though community composition also differed among collection sites and with depth of the wrack. Though we were limited in our ability to disentangle the effects of beach-cast harvesting due to a concentration of effort at one site, we failed to detect any large influence on wrack biomass or macrofauna communities. Harvesting does, however, appear to be associated with a greater area of wrack cover and decreased mean depth. Stable isotope mixing models estimated that M. japonica contributed no more than 22% and 17% on average to the diets of supralittoral and subtidal consumers respectively, despite its overwhelming dominance in both environments. These results suggest that the non-indigenous red alga may experience a reprieve from herbivory within the subtidal environment. A lack of consumption within the supralittoral zone could influence nutrient cycling on recipient beaches and increase propagule pressure in the surrounding regions. Results from these studies are intended to help inform the management of M. japonica and its commercial harvesting. Combined, they indicate that this non-indigenous seaweed does not provide a substantial subsidy in the form of food provision for resident invertebrates. Furthermore, the commercial removal of M. japonica is small compared to the total biomass available, and had no detectable effect on the wrack-associated macrofauna communities examined. / Graduate / 2017-08-19 / jjulin.holden@gmail.com

This thesis investigates network properties of natural food webs. In particular, it focuses on the e ect that external disturbances have on their substructures and robustness. The importance of a network-level methodology lies in its capacity to capture entangling species interactions and identify inter-connecting properties in heterogeneous food webs. The research rst analysed the responses of freshwater food webs under the stress of drought. A core/periphery structure was detected and its relative size was found to be unchanged after drought despite a signi cant biodiversity loss. Species extinction triggered extensive link rewiring and movement of species from the core to the periphery. These results showed that the robustness was maintained indicating that the redundancy in the core can e ectively mitigate species level perturbations. Secondly, the research further examined the e ects of Genetically Modi ed Herbicide Tolerant (GMHT) management on food web properties and robustness. Network analysis showed that such change in farming practice has no signi cant impact on the agro-ecosystems. However, crop switching, a common practice in agriculture, was found to pose much more significant changes on network properties and robustness when compared to GMHT crops. Thirdly, the research examined over 50 empirical food webs and demonstrated that the relative core size is a much more e ective indicator of food web robustness than the classical ecological measure connectance, as the latter was found to be insensitive to changes in the interaction patterns. Lastly, the research established the relationships between centrality measures and species ecological and/or functional role in food webs, and how they impact on network robustness.

Bacteria-protozoa interactions are one of the oldest between prokaryotic and eukaryotic organisms. As such, their study offers a unique opportunity to understand the different relationships that have evolved between them, including pathogenesis, and how their interaction can affect some important processes, such as wastewater treatment. In the first part of the work described here, the grazing defence mechanisms employed by Pseudomonas aeruginosa against the surface grazer, Acanthamoeba castellanii, were investigated. P. aeruginosa cells from early logarithmic growth and stationary phase were found to use different defence strategies. The type-III secretion system (T3SS) was found to be responsible for cytotoxicity of early logarithmic growth cells against A. castellanii. Of the three exotoxins produced by P. aeruginosa PA99, the phospholipase ExoU was found to make the greatest contribution to bacterial toxicity against the amoebae. Interestingly, a PA99null mutant that does not produce any known exotoxins but synthesises a secretion apparatus, was also found to be toxic to the amoeba, suggesting that the T3SS was being used to translocate other unknown toxins. Quorum sensing regulated virulence factor production was found to be involved in the grazing defence response of stationary phase P. aeruginosa cells. A. castellanii was found to be most susceptible to hydrogen cyanide and elastase produced during late logarithmic and stationary phase. In the second part, a stable isotope probing method was developed to investigate carbon flow through bacteria-protozoa food webs in activated sludge. The method was subsequently used to track carbon from bicarbonate and acetate through bacteria-orotozoa food webs under ammonia oxidising and nitrate reducing conditions. It was found that the Peritrich ciliate Campanella umbellaria, dominated the acquisition of carbon from bacteria with access to CO2 under ammonia oxidising conditions. Thus it appears that some of these bacteria must live in the plankton, as C. umbellaria is a filter feeder. No specific protozoan groups were found to dominate carbon acquisition from bacteria with access to acetate, under nitrate reducing conditions, probably due to label dilution. Overall the results presented here showed how bacteria-protozoa interactions have shaped infectious processes in higher eukaryotes, and the dynamics of carbon flow in activated sludge.

<p>Many of the earth’s ecosystems are experiencing large species losses due to human impacts such as habitat destruction and fragmentation, climate change, species invasions, pollution, and overfishing. Due to the complex interactions between species in food webs the extinction of one species could lead to a cascade of further extinctions and hence cause dramatic changes in species composition and ecosystem processes. The complexity of ecological systems makes it difficult to study them empirically. The systems often consist of large species numbers with lots of interactions between species. Investigating ecological communities within a theoretical approach, using mathematical models and computer simulations, is an alternative or a complement to experimental studies. This thesis is a collection of theoretical studies. We use model food webs in order to explore how biodiversity (species number) affects the response of communities to species loss (Paper I-III) and to environmental variability (Paper IV).</p><p>In paper I and II we investigate the risk of secondary extinctions following deletion of one species. It is shown that resistance against additional species extinctions increases with redundancy (number of species per functional group) (Paper I) in the absence of competition between basal species but decreases with redundancy in the presence of competition between basal species (Paper II). It is further shown that food webs with low redundancy run the risk of losing a greater proportion of species following a species deletion in a deterministic environment but when demographic stochasticity is included the benefits of redundancy are largely lost (Paper II). This finding implies that in the construction of nature reserves the advantages of redundancy for conservation of communities may be lost if the reserves are small in size. Additionally, food webs show higher risks of further extinctions after the loss of basal species and herbivores than after the loss of top predators (Paper I and II).</p><p>Secondary extinctions caused by a primary extinction and mediated through direct and indirect effects, are likely to occur with a time delay since the manifestation of indirect effects can take long time to appear. In paper III we show that the loss of a top predator leads to a significantly earlier onset of secondary extinctions in model communities than does the loss of a species from other trophic levels. If local secondary extinctions occur early they are less likely to be balanced by immigration of species from local communities nearby implying that secondary extinctions caused by the loss of top predators are less likely to be balanced by dispersal than secondary extinctions caused by the loss of other species. As top predators are vulnerable to human-induced disturbances on ecosystems in the first place, our results suggest that conservation of top predators should be a priority. Moreover, in most cases time to secondary extinction is shown to increase with species richness indicating the decay of ecological communities to be slower in species-rich than in species-poor communities.</p><p>Apart from the human-induced disturbances that often force species towards extinction the environment is also, to a smaller or larger extent, varying over time in a natural way. Such environmental stochasticity influences the dynamics of populations. In paper IV we compare the responses of food webs of different sizes to environmental stochasticity. Species-rich webs are found to be more sensitive to environmental stochasticity. Particularly, species-rich webs lose a greater proportion of species than species-poor webs and they also begin losing species faster than species-poor webs. However, once one species is lost time to final extinction is longer in species-rich webs than in species-poor webs. We also find that the results differ depending on whether species respond similarly to environmental fluctuations or whether they are totally uncorrelated in their response. For a given species richness, communities with uncorrelated species responses run a considerable higher risk of losing a fixed proportion of species compared with communities with correlated species responses.</p>

Freshwater ecosystems are some of the most threatened on the planet. Efforts to conserve, restore, or otherwise manage large rivers and the services they provide are hindered by limited understanding of the functional dynamics of these systems. This shortcoming is especially evident with regard to trophic structure and energy flow. In this study I use natural abundances of carbon and nitrogen isotopes to examine patterns of energy flow and food-chain length of large-river food webs characterized by different landscape-scale hydrologic features. Ten locations along an approximately 500 km stretch of the Upper Paraná River Basin, Brazil, provided the setting for this work. Carbon derived from C3 plants and phytoplankton were the dominant energy sources across all webs, but relative contributions differed among landscape types (low-gradient river, high-gradient river, river stretches downstream of reservoirs, and reservoirs). Increases in food chain length corresponded with higher relative importance of phytoplankton derived carbon, likely due to size-structured effects of the phytoplankton-zooplankton-secondary consumer trophic link. River impoundment corresponded with decreased ecological and economic efficiency of fisheries production, an important ecosystem service provided by many tropical rivers.

Many of the earth’s ecosystems are experiencing large species losses due to human impacts such as habitat destruction and fragmentation, climate change, species invasions, pollution, and overfishing. Due to the complex interactions between species in food webs the extinction of one species could lead to a cascade of further extinctions and hence cause dramatic changes in species composition and ecosystem processes. The complexity of ecological systems makes it difficult to study them empirically. The systems often consist of large species numbers with lots of interactions between species. Investigating ecological communities within a theoretical approach, using mathematical models and computer simulations, is an alternative or a complement to experimental studies. This thesis is a collection of theoretical studies. We use model food webs in order to explore how biodiversity (species number) affects the response of communities to species loss (Paper I-III) and to environmental variability (Paper IV). In paper I and II we investigate the risk of secondary extinctions following deletion of one species. It is shown that resistance against additional species extinctions increases with redundancy (number of species per functional group) (Paper I) in the absence of competition between basal species but decreases with redundancy in the presence of competition between basal species (Paper II). It is further shown that food webs with low redundancy run the risk of losing a greater proportion of species following a species deletion in a deterministic environment but when demographic stochasticity is included the benefits of redundancy are largely lost (Paper II). This finding implies that in the construction of nature reserves the advantages of redundancy for conservation of communities may be lost if the reserves are small in size. Additionally, food webs show higher risks of further extinctions after the loss of basal species and herbivores than after the loss of top predators (Paper I and II). Secondary extinctions caused by a primary extinction and mediated through direct and indirect effects, are likely to occur with a time delay since the manifestation of indirect effects can take long time to appear. In paper III we show that the loss of a top predator leads to a significantly earlier onset of secondary extinctions in model communities than does the loss of a species from other trophic levels. If local secondary extinctions occur early they are less likely to be balanced by immigration of species from local communities nearby implying that secondary extinctions caused by the loss of top predators are less likely to be balanced by dispersal than secondary extinctions caused by the loss of other species. As top predators are vulnerable to human-induced disturbances on ecosystems in the first place, our results suggest that conservation of top predators should be a priority. Moreover, in most cases time to secondary extinction is shown to increase with species richness indicating the decay of ecological communities to be slower in species-rich than in species-poor communities. Apart from the human-induced disturbances that often force species towards extinction the environment is also, to a smaller or larger extent, varying over time in a natural way. Such environmental stochasticity influences the dynamics of populations. In paper IV we compare the responses of food webs of different sizes to environmental stochasticity. Species-rich webs are found to be more sensitive to environmental stochasticity. Particularly, species-rich webs lose a greater proportion of species than species-poor webs and they also begin losing species faster than species-poor webs. However, once one species is lost time to final extinction is longer in species-rich webs than in species-poor webs. We also find that the results differ depending on whether species respond similarly to environmental fluctuations or whether they are totally uncorrelated in their response. For a given species richness, communities with uncorrelated species responses run a considerable higher risk of losing a fixed proportion of species compared with communities with correlated species responses.

Invasive insects are considered one of the most serious threats affecting forests today; however, surprisingly little research has addressed the impacts of invasive species establishment on native forest insect communities. Such information is lacking for even the most thoroughly studied invasive forest insect, the gypsy moth. Using gypsy moth as a case study, my thesis addresses the questions: What are the ecological impacts of an exotic forest insect upon its establishment in a new community of native species? Does the community shift after the invasive establishes, and if so, what are the drivers in this realignment? I used multivariate analysis to assess native caterpillar communities collected in forest stands with and without a history of gypsy moth outbreak. I found that gypsy moth outbreak history had no significant effects on native caterpillar communities; however, current gypsy moth abundance was related to shifts in the structure of late season caterpillar assemblages. These results suggest that gypsy moth may affect native caterpillar communities through short-term mechanisms but not through long-term ecological changes. I used quantitative food webs to investigate the effects of gypsy moth on native host-parasitoid webs from the same caterpillar communities, and found that food web structure was resilient to both gypsy moth outbreak history and current abundance. The gypsy moth shared few parasitoids with native species in my study sites, none of numerical significance, thus minimizing the opportunity for enemy-mediated indirect interactions. Finally, I conducted a greenhouse experiment and found that early spring feeding by forest tent caterpillar can indirectly influence gypsy moth susceptibility to its virus, demonstrating that the complex interactions that can occur between native and exotic species do not always benefit the invader. Overall, I argue that the establishment of the gypsy moth into North American forests will not cause major changes in native caterpillar communities.

Invasive insects are considered one of the most serious threats affecting forests today; however, surprisingly little research has addressed the impacts of invasive species establishment on native forest insect communities. Such information is lacking for even the most thoroughly studied invasive forest insect, the gypsy moth. Using gypsy moth as a case study, my thesis addresses the questions: What are the ecological impacts of an exotic forest insect upon its establishment in a new community of native species? Does the community shift after the invasive establishes, and if so, what are the drivers in this realignment? I used multivariate analysis to assess native caterpillar communities collected in forest stands with and without a history of gypsy moth outbreak. I found that gypsy moth outbreak history had no significant effects on native caterpillar communities; however, current gypsy moth abundance was related to shifts in the structure of late season caterpillar assemblages. These results suggest that gypsy moth may affect native caterpillar communities through short-term mechanisms but not through long-term ecological changes. I used quantitative food webs to investigate the effects of gypsy moth on native host-parasitoid webs from the same caterpillar communities, and found that food web structure was resilient to both gypsy moth outbreak history and current abundance. The gypsy moth shared few parasitoids with native species in my study sites, none of numerical significance, thus minimizing the opportunity for enemy-mediated indirect interactions. Finally, I conducted a greenhouse experiment and found that early spring feeding by forest tent caterpillar can indirectly influence gypsy moth susceptibility to its virus, demonstrating that the complex interactions that can occur between native and exotic species do not always benefit the invader. Overall, I argue that the establishment of the gypsy moth into North American forests will not cause major changes in native caterpillar communities.