Agricultural expansion has transformed and fragmented natural forest habitats at an alarming rate, and dramatic increases in agricultural intensification have since taken place in order to keep pace with human population growth and food demands. This simultaneously poses a considerable threat to biodiversity in agricultural landscapes, as production land is now one of the largest terrestrial biomes on the planet. Therefore, its contribution to biodiversity conservation is critical. Links between the intensification of agricultural systems and ‘in situ’ declines of biodiversity on farmland have been well documented. However, despite growing recognition that system inputs such as fertiliser and livestock can move or ‘spillover’ into adjacent natural habitats, there has been no direct quantification of the extent of impacts in recipient ecosystems. These abiotic and biotic pathways can cause dramatic impacts on the diversity, composition, and functioning of remaining natural ecosystems, and on their ability to provide a variety of essential ecosystem services. Due to concerns regarding future food security, balancing trade-offs between agriculture and conservation has subsequently become a hot topic in ecological research. However, without any direct quantification of the off-site ecological impacts of agricultural intensification in mosaic landscapes, it is inherently difficult to fully evaluate strategies aimed at balancing production and conservation. Using New Zealand farming systems as a case study, this thesis aims to address gaps in our current understanding of how increasing agricultural intensification impacts biodiversity in native forest remnants embedded within production landscapes. The first main chapter explores whether the magnitude of ecological impact in forest remnants (for a suite of 26 response measures) and severity of edge effects, scale with the degree of land-use intensity in surrounding agricultural pastures. This chapter also examines whether ecological responses differ in remnants ‘spared’ for conservation purposes (i.e. where livestock are excluded by fencing). The second chapter uses a model food-chain approach native to New Zealand, to test whether nutrient spillover from agricultural pastures influences plant-herbivore and herbivore-parasitoid interactions in forest remnants. This chapter also includes a large-scale common garden fertilisation experiment using the same tri-trophic system, which was established to examine bottom-up multi-trophic responses to the independent and combined effects of Nitrogen (N), Phosphorus (P) and cow dung and urine. The third main chapter uses a novel stable isotope approach for quantifying community-wide incorporation of resources into trophic structure. I test for the first time whether increasing intensity of farming systems drives greater nutrient spillover spatially into adjacent forest remnant soils and examine scaling effects of 15N (as a marker for anthropogenic N) through multiple trophic levels. Beyond finding that agricultural land-use intensity generally has negative off-site effects on biodiversity, the key findings of this thesis were (i) spillover of nitrogen and phosphorus from agricultural systems into adjacent remnant soils is exacerbated by increases in land-use intensity, with (ii) percolating bottom-up effects on plant and insect community dynamics. (iii) The magnitude of ecological impacts in forest remnants scales linearly with increasing land-use intensity, as does (iv) direct anthropogenic N enrichment across multiple trophic levels, which has the potential to severely jeopardise the stability of ecologically important remnant habitats. (v) Although there were stark structural differences in remnants with and without livestock exclusion, impacts of land-use intensity on ecological response metrics were actually comparable across all sites. (vi) Livestock exclusion should be a priority first step towards conserving native forest remnants, however it should be recognised that fencing does not prevent abiotic channels of nutrient spillover (fertiliser drift, overland flow, leaching) in land characteristic of land spared for nature. (vii) Consequently, increasing land-use intensity compromises the effectiveness of the land-sparing trajectory for conserving native biodiversity, which is currently undertaken in New Zealand production systems. Given the overall strength of these findings and the novel, ecosystem-wide and landscape-scale approaches taken to address fundamental questions, the work in this thesis greatly enhances our knowledge of the relationships between agricultural productivity and ecological impacts in spatially-coupled ecosystems. This is highly important, not only in New Zealand but worldwide, as it is anticipated that unstoppable human population growth and food security pressures will cause ecological impacts both on the farm and in adjacent natural ecosystems to become even more severe. Therefore, determining the relationship between land-use intensification and biodiversity loss represents the cornerstone of sustainable agricultural development in the future.

In land-based integrated aquaculture of marine finfish and macroalgae, rearing space is a large expense. Increasing algal stocking density can increase efficiency, but this may require greater irradiance because of self-shading. To determine the irradiance needed, experiments were conducted in one-litre flasks with enriched seawater under natural and artificial illumination. Under natural illumination, a Daily Photon Dose of 17 mol m-2 d-1 at 10 and 14 ºC, Palmaria palmata cultured at 10 g L-1 grew 100 % faster and absorbed 20 % more nutrients than Chondrus crispus. However, Atlantic halibut farm effluent can reach up to 19 ºC in summer, too high for P. palmata. Under artificial illumination, C. crispus performed better than under natural illumination. Light saturation curves indicated nutrient uptake by C. crispus at 10 g L-1 and 10 ºC was highest at 23 mol m-2 d-1 irradiance, equivalent to 400 µmol m-2 s-1 for 16 hours

The advent of next generation sequencing technologies has had a major impact on inference methods for population genetics. For example, community ecology studies can now assess species interactions using population history parameters estimated from genomic scale data. Figs and their pollinating fig wasps are obligate mutualists thought to have coevolved for some 75 million years. This relationship, along with additional interactions with many species of non-pollinating fig wasps (NPFW), makes this system an excellent model for studying multi-trophic community interactions. A common way of investigating the population histories of a community's component species is to use genetic markers to estimate demographic parameters such as divergence times and effective population sizes. The extent to which histories are congruent gives insights into the way in which the community has assembled. Because of coalescent variance, using thousands of loci from the genomes of a small number of individuals gives more statistical power and more realistic estimates of population parameters than previous methods using just a handful of loci from many individuals. In this thesis, I use genomic data from eleven fig wasp species, which are associated with three fig species located along the east coast of Australia, to characterise community assembly in this system. The first results chapter describes the laboratory and bioinformatic protocols required to generate genomic data from individual wasps, and assesses the level of genetic variation present across populations using simple summaries. The second results chapter presents a detailed demographic analysis of the pollinating fig wasp, Pleistodontes nigriventris. The inferences were made using a likelihood modelling framework and the pairwise sequentially Markovian coalescent (PSMC) method. The final results chapter characterises community assembly by assessing congruence between the population histories inferred for eight fig wasp species. The population histories were inferred using a new composite likelihood modelling framework. I conclude by discussing the implications of the results presented along with potential future directions for the research carried out in this thesis.

Ett stagnerat globalt fiske har lett till en snabb utökning av vattenbruket för att tillgodose den globala marknaden. Traditionellt vattenbruk har i västvärlden kännetecknats av monospecifika odlingar, ofta med mycket grav påverkan på sin omnejd. Ett återupptäckt alternativ till denna i längden ohållbara tappning av vattenbruk har därför växt fram. Integrerad multi-trofiskt vattenbruk (IMTA) är en teknik som, genom att odla organismer från flera trofiska nivåer tillsammans, kan minska utsläppen och öka produktiviteten hos en odling. En växande global befolkningen kommer dock leda till ökande konflikter mellan kustnära vattenbruk och intressenter såsom industrier, myndigheter och privatpersoner. Då vattenbruket fortsätter att växa skulle en lösning på dessa konflikter vara att rikta dess expansion mot det öppna havet. Frågan är då om IMTA vore effektivt utomskärs och hur det i så fall skulle kunna optimeras ur både produktions- och kostnadsperspektiv. Denna undersökning tyder på att en pelagial expansion skulle ge en positiv påverkan av de olika ekologiska, ekonomiska och infrastrukturella aspekter rörande utomskärs-IMTA. Dock kräver en sådan förflyttning omfattande förarbete i utvärdering av lämpliga lokaler. En analys av olika arter och dess egenskaper, monetära värde, tillika möjligheter att optimera systemet visar på att utomskärs IMTA är möjligt, men begränsas av ingenjörsmässiga faktorer. / The stagnated global fishing has led to a fast expansion of aquaculture to meet the increasing global demand for seafood. Traditionally aquaculture in the western world has been defined as large monospecific cultures, often with grave implications on its surrounding environment. An alternative to the conventional and unsustainable method has thus been rediscovered and developed. Integrated Multi-Trophic Aquaculture (IMTA) is a technique that, by cultivating organisms of different trophic levels together, can decrease effluents and increase the productivity of a farm. Furthermore, the growing global population will lead to increasing conflicts between coastal aquaculture and other stakeholders such as industries, governments, and private citizens. Since aquaculture continues to grow, a possible solution to such conflicts could be an offshore expansion of aquaculture. However, whether an IMTA system still would be effective in an offshore setting is unclear. This is also the case regarding the possibility to optimize an offshore IMTA system concerning productivity and investment costs.  The present article shows that a pelagic expansion of IMTA would positively affect the ecological, economical and infrastructural aspects regarding offshore IMTA compared to inshore IMTA. However, such a transposition would require comprehensive preparatory evaluations of suitable sites. An analysis of several species and their attributes, monetary value, and capability of optimizing the system indicates that offshore IMTA is possible but is limited by structural-engineering factors.

Bark beetles regulate forest succession by removing weakened or stressed trees and exposing understory species to light from canopy gaps. Subterranean termites are predominate decomposers of coarse woody debris in southern pine forests; however, little is known about their role in forest health and succession. Both groups of insects rely heavily on fungal symbioses to fill their respective ecological niches in southern pine forests. During recent inspections of southern pine timber, we observed that trees in the early stages of bark beetle attack often had subterranean termites in blue-stained portions of the trunk. The frequency of subterranean termite presence in blue-stained areas of trees increased proportionally to the stage of bark beetle attack. However, practically no research has undertaken the challenge of describing how woody resources created by bark beetles are identified and utilized by subterranean termites before any signs of stress are visible. Therefore, this study examined possible facilitative interactions between subterranean termites, bark beetles and their blue-stain fungal associates, and other invertebrates, and investigated the effect of blue-stain fungi on surface properties of wood. Both native (Reticulitermes spp.) and Formosan subterranean termites exhibited a higher feeding preference for blue-stained sapwood than for unstained sapwood in laboratory assays. Native subterranean termites also consumed blue-stained sapwood at a higher rate than decayed wood. This study was the first to demonstrate that wood containing a non-decay fungus could elicit a feeding response from subterranean termites greater than that observed for decayed wood. Additionally, the surface properties of bark beetle-attacked southern pine were initially reduced by blue-stain fungal infection; however, the process of kiln-drying reversed this effect, resulting in a surface that was more conducive to wood product manufacturing.

Achieving optimization of IMTA sites and modeling the efficiency of such a system requires knowledge of the spatiotemporal distribution and variability of TPM surrounding the finfish farms. The objective of this study was to quantify the impact of finfish farms on the surrounding particle field. Platforms equipped with transmissometers, fluorometers and CTD’s were towed around the sites while undulating through the water column in a high-resolution 3D spatial survey approach. In addition, combination turbidity and chlorophyll a sensors were moored at a variety of locations and depths. Surveys were conducted concurrently with the deployment of current meters. Farms surveyed were found to have little impact on the surrounding suspended particle field (mean effect < 1 mg L-1). Results provided evidence of minimal enhancement from fish farm wastes, primarily in surficial waters (0.5- 2 m depth) immediately adjacent to the cages, and evidence of predominantly tidal driven (M2) TPM dynamics.

To assess the spatial distribution of nutrient wastes around an open-water integrated fish/mollusk/kelp farm in-situ kelp bioassays were employed. Growth rates were measured over a four-month growing season and used as a proxy for relative nutrient concentrations. Seasonality and depth effects on growth rate were also assessed. Growth around the pens was 0.20 cm • day-1 higher than at the control, and reached a maximum of 1.4 cm • day-1. Optimal growth was achieved at 8 m. Growth at 8 m was significantly higher by 1.5 cm • day-1 compared to surface waters at 2 m. Early spring had the highest growth rates with a peak of 1.4 cm • day-1 recorded on June 21. This study re-iterates the fundamental benefits of IMTA and shows the potential of in-situ assay as an alternative to error-prone and costly water sampling to asses nutrient status in water. / Graduate

The goal of this thesis was to detail spatial and temporal organic particulate dynamics at an integrated multi-trophic aquaculture (IMTA) site on the west coast of Vancouver Island, Canada. To accomplish this goal, in-situ optical measurements of particulate scattering (bp), particulate backscattering (bbp) and the particulate backscattering ratio (bbp:bp) were collected in conjunction with discrete sampling for particulate organic carbon (POC) and chlorophyll a (chl a) concentrations. These measurements were performed over three seasons (autumn, winter and summer) at reference sites and at sites within and directly adjacent to the fish component of the IMTA system. Chapter 2 of this thesis focused on the examination of bio-optical relationships over various timescales (seasonally, daily and within-day) to describe temporal and vertical particulate variability and to assess the effectiveness of bio-optical methods for environmental monitoring. Autumn showed low bio-optical magnitudes with distinct lower cage increases possibly attributable to aquaculture derived wastes. In spring, sampling was performed over diatom bloom conditions, dominating the bio-optical measurements. During summer, an Emiliania Huxleyi bloom likely occurred, strongly enhancing bbp and bbp:bp magnitudes in the thermally stratified upper water column. Throughout these conditions, bp was predominantly influenced by chl a suggesting sensitivity to phytoplankton concentrations. While bbp was conditioned by chl a during the diatom bloom, it was also highly sensitive to the presence of inorganic and likely detrital materials. Finally, bbp:bp was sensitive to particulate compositions, showing low values (< 0.010) in diatom dominated waters and high values when refractive coccoliths were likely present. Notably, in autumn, bbp:bp was conditioned by detrital particles and along with bbp, showed post-feeding lower cage increases suggesting that these parameters could be useful candidates for particulate waste tracking during low ambient particle conditions. In chapter 3, the temporal, vertical and horizontal dispersion of the aquaculture derived particulate wastes are detailed. Autumn was the only period to show waste signals, likely due to their quick dilution into the particulate rich fields in spring/summer. During this period, post-feeding particulate waste increases were focused at the bottom of the cage with possible vertical sinking towards the seafloor. Minimal horizontal dispersion towards the scallop portion of the system was observed; however, more comprehensive sampling over differing hydrographic regimes is necessary to characterize waste dispersion. Based on our temporally limited autumn results, the most appropriate placement of uptake species for waste assimilation would be directly below the studied cage. Our results highlight the need for high spatial and temporal resolution methods for particulate monitoring within IMTA settings as discrete sampling may miss “patchy” waste dispersal streams. The bio-optical measurements performed during this study could fill this need as they can provide high resolution information on particulate concentrations and compositions not achievable solely through the use of discrete water sampling. With further research, optical instrumentation could be incorporated into IMTA systems allowing for the near real time and continuous collection of data on particulate dynamics. This knowledge could greatly aid in the design and implementation of systems optimized for waste removal by uptake species. / Graduate / 0792 / 0768 / 0752 / jdelbel@uvic.ca

Among efforts to develop sustainable approaches towards the intensive rearing of finfish within open marine waters, is the development of integrated aquaculture techniques. Integrated Multi-Trophic Aquaculture (IMTA), has been promoted as a way to reduce unwanted environmental impacts associated with the intensive production of marine finfish within net-pens. The principle aim of this concept, is the bioremediation of nutrient discharges from fish aquaculture. This is to be achieved by integrating fish cultivation with the growing of species from lower trophic levels, which use the nutrient discharges as a food source. Many studies have been performed that investigate the ability of various species of macroalgae to remove dissolved nutrient discharges, and the ability bivalves to remove solid-bound nutrients, presented as either fish faeces, or an enhanced production of phytoplankton that may be promoted by nutrients emitted by fish-farms. IMTA has also been suggested as a means to improve overall productivity per unit of feed applied to fish, through the conversion of nutrient emissions into additional biomass, such as the tissues of macroalgae or bivalves. Within the research community which focuses upon the environmental impacts of aquaculture, there is a growing awareness that sustainable solutions to aquaculture production cannot be realised through a focus restricted to the growing-phase, and to a limited set of environmental impacts which may this activity may produce. This is because changes to a specific production phase often promote changes at phases located elsewhere along a products value chain. Life-Cycle Assessment (LCA), is a method employed for modelling the environmental impacts that may potentially be generated across the value chain of a product. It is particularly useful for identifying instances of environmental impact shifting; a term used to describe situations where efforts to reduce the contribution of a specific production phase towards one or more environmental impacts, has the effect of either displacing this contribution to another phase, or increases the contribution of production towards different environmental impacts. Despite its apparent suitability, LCA has not previously been fully applied to the environmental impact modelling of open-water IMTA systems. The work presented in the following thesis advances this research front, by using LCA to explore the potential for environmental problem shifting occurring as a consequence of replacing intensive monoculture production, with IMTA. Comprehensive datasets have been acquired from the Chilean aquaculture industry, describing the production of aquafeed and Salmo salar, as well as for the production of the Phaeophytic macroalga, Macrocystis pyrifera, and the molluscan bivalve, Mytilus chilensis. Using LCA methodology, the production of salmon feed, and the production of S.salar, M.pyrifera and M.chilensis, have been assessed for their capacity to contribute towards a variety of global-scale, environmental impacts. IMTA consisting of either S.salar and M.pyrifera, S.salar and M.chilensis, or all three of these species, and combined at ratios required for a bioremediation efficiency of 100 %, 50%, or 20 % of either nitrogen or phosphorous emission from fish, is compared to the monoculture production of S.salar. The comparison is based upon a standardised functional unit, with each species produced through IMTA, being modelled as part of the reference flow required to fulfil the functional unit. Monoculture is compared to IMTA upon the basis of nutritional function, by using a functional unit of mass-adjusted protein content, and mass-adjusted economic value. The use of economic value is based upon the ‘best-case’ assumption, that it serves as a proxy for the total nutritional function that each product offers to human society. The LCAs presented in this study have produced a number of results. Salmon ingredients derived from agricultural crops and animals account for the majority (between 71 % to 98 %) of contributions towards the impacts of compound salmon feed. In general, agricultural crops ingredients contribute more to these impacts than do agricultural animal ingredients, and account for between 31 % and 87 % of the contributions from all ingredients and inputs. In contrast, the combined supply of fish meal and fish oil from capture fisheries is responsible for between 0.13 % and 11 % of all impacts. Vegetable oil accounts for the vast majority of contributions from ingredients derived from agricultural crops. Vegetable oil is modelled as a 50 : 50 blend of sunflower oil and rapeseed, oil, but sunflower oil accounts not only for most of the contributions from vegetable oil, it is responsible for over 50 % of the contributions that all agricultural crop based ingredients contributes towards some impact categories. Replacing sunflower oil with rapeseed oil reduces the contributions of salmon feed by between 6 % and 24 % across 10 out of the 11 impact categories. When compared upon the basis of equal weight, the contributions of fish oil are between 18 % and 99 % lower than those from rapeseed oil. The production of feed is responsible for the majority of contributions (between 32 % and 86 % ) to all impacts of salmon grow-out production. The production of salmon-smolts accounts for between 3 % and 18 %. The majority (64 %) of contributions towards the eutrophication potential of salmon production are from nutrient emissions, which are the result of fish metabolism, whilst nutrients released through the production of feed, the majority of these being from the agricultural production of crop and animals, account for 32 %. Feed production is also a major contributor to the impacts of land-based smolt production, but these contributions (between 12 % and 37 % across all impact categories) are of a lower magnitude than those from the supply of feed to the grow-out phase. Inputs of salt, and inputs of both electricity produced in a diesel power generator and obtained from the national electricity network, are also notable contributors (between 5 % and 67 %, 4 % and 29 %, and 2 % 47 %, respectively) towards the impacts of smolt-production. The main contributors towards the potential impacts of kelp grow-out production (excluding eutrophication potential) are the supply of infrastructure (between 14 % and 89 %), operation of a diesel-powered motorboat for maintenance purposes (between 1 % and 89 %), and the supply ‘of seeded cartridges’ (between 9 and 49 %). The major contributors from the production of ‘seeded cartriges’ in a land-based facility are the supply of electricity from the national electricity network, the supply of fresh water, and the treatment of waste water. The impact potentials of producing seed in this facility might be reduced if the scale of operation is increased. Removal of nitrogen and phosphorous upon the harvesting of kelp is calculated based upon kelp tissue contents of these nutrients. The harvesting of 200 tonnes ha / yr-1, results in a eutrophic potential with a negative value (-376.51 kg of phosphate equivalents). The removal of such a quantity of nutrients might be beneficial if the local marine environment is at risk of hypernutrification, but when no such problem is present, the potential for undesirable consequences of nutrient sequestration should be considered. The major contributor towards the impacts of mussels is the provision of infrastructure (between 25 % and 99.5 %, excluding eutrophication potential). Infrastructure is also responsible for the majority of contributions from mussel seed production. The provision of cotton mesh bags, which are used to aid attatchment of seed to drop-ropes in the grow-out phase, account for between 37% and 99 % of the contributions from the infrastructure from the grow-out phase. This result suggest that either the impacts of mussel production can be reduced by using an alternative material with lower environmental impact potentials, or the inventory data describing the producing of cottonmesh bags requires some improvement. The outcomes of the LCAs of the different IMTA scenarios, are interesting. The results show that choice of species, and the ratios of their combination as required for the different efficiencies of bioremediation, can have a significant effect upon the comparison between IMTA and monoculture. / The study demonstrates a potential for environmental problem shifting as being a consequence of IMTA, especially when the functional unit is mass-adjusted economic value. As bioremediation efficiency increases, contributions towards eutrophication decrease. However, this reduction is achieved at the cost of increasing the contributions of IMTA towards those impact categories, such as ‘ozone layer depletion,’ for which it has a greater contribution than does monoculture. In general, it cannot be concluded from these results that open-water IMTA represents a more sustainable alternative to the monoculture production of Atlantic salmon. The sustainability of IMTA is shown to be dependent upon a variety of trade-offs, between individual environmental impacts, and between these impacts and the nutritional function that the system is capable of providing.

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