Boreal Ecology - Doctoral Theses

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Microbial ecology of wastewater treatment and residuals
(2023-10-02) Chan-Yam, Kelly
Every day, municipal activities and industrial processes consume and contaminate a large volume of water, which must then be treated before being returned to aquatic ecosystems. Wastewater treatment plants (WWTPs) use physical, chemical, and microbiological processes to clean the water, which in turn produces sludge. Sludge, an organic waste product, historically has been landfilled, but can be diverted from landfills if it used as a resource for biogas methane production or as organic fertiliser on damaged ecosystems. Microbial communities are the ecosystem engineers driving changes in organic matter and chemistry throughout wastewater treatment, methane production, and soil development, and modern mass sequencing tools allow us to survey the microbial community composition associated with different environments and outcomes. In this thesis, I looked at the microbial communities and treatment endpoints of interest associated with anaerobic digestion, land application, and production of WWTP sludge. In my first research project, I examined methane production from anaerobic digestion of 11 pulp and paper mill WWTP sludges. Mean methane potential varied between sludges, and kraft mill primary sludges produced more methane than biosludge, whereas other mills showed inhibition in primary sludge. Methane production only occurred in sludges with high diversity prior to anaerobic incubation. In my second project, 8 treatments of organic-derived industrial residuals, including WWTP sludges and controls, were applied to plots in semi-barren smelter- impacted land around Sudbury, and trees were planted to evaluate value in ecosystem restoration for the Sudbury Regreening Program. Treatment effect on soil chemistry and the microbial community was largely associated with pH changes, and soil metal concentrations did not increase beyond regulatory limits, so treatments with liming capacity are likely suitable for use in the Sudbury Regreening Program. In my third project, I surveyed the microbial communities of 4 WWTPs around Sudbury in summer and winter to compare seasonal differences. WWTPs had differences in bacterial, archaeal, and eukaryotic communities in summer and winter. Archaeal community changes showed similar patterns across WWTPs, but bacterial communities had different patterns for WWTPs that demonstrated nitrification, and eukaryotic communities had different patterns across all WWTPs. Overall, I demonstrated similarities and differences in microbial communities degrading organic matter across multiple treatments in association with WWTP sludge.
Reintroduction and management of at-risk freshwater turtles in an urban wetland complex in a protected area
(2023-12-15) Wijewardena, Tharusha
A headstarting program for the Blanding’s turtle (Emydoidea blandingii) was initiated by the Toronto Zoo in 2012 to supplement a functionally extinct population in the Rouge National Urban Park (RNUP) in Toronto, Ontario, Canada. Data collected from multiple years of radio- tracking (2014–2021) and mark-recapture (2018–2021) surveys were used to evaluate the success of the headstarting program. Based on demographic data, survival of headstarted turtles remained high, except during a mass-mortality event when a substantial decline in survival was observed. Male:female sex ratio measured using incubation temperatures shifted from 1:1.5 in captivity to 1:1 in the wild, and size-class distribution of the population remained juvenile- biased. Release methods did not improve post-release outcomes in terms of survival, somatic growth rate, body condition, or movement patterns, and headstarted turtles sustained similar health to wild juvenile conspecifics in other Ontario populations. Headstarted turtles selected hibernacula similar to wild adult conspecifics, and there was weak evidence towards sociality, specifically in terms of familiarity (i.e., individuals from the same release cohort) in overwintering site selection. Demographic data from other resident freshwater turtles indicated that multiple sources of ongoing threats and catastrophes can affect population stability. Headstarting also affected community diversity by shifting species richness and evenness. Overall, Blanding’s turtle headstarting program showed progress, but continued monitoring will be required to determine if headstarting will achieve its desired conservation goals. Conservation actions targeting multiple life-stages of the Blanding’s turtles will be necessary to address root causes of population decline and to ensure that the population will reach a self-sustaining level.
Using stable water isotopes and isotope-enabled hydrologic modelling to quantify water in Central and Northeastern Ontario
(2023-10-26) Tafvizi, Arghavan
The understanding of hydrologic processes in Central and Northern Ontario's mesoscale watersheds, located within the Precambrian Shield region, remains limited, posing challenges for accurate hydrological modeling and assessment of climate change impacts on water resources. This study focuses on Central and Northeastern Ontario, typically characterized by granitic bedrock, small depressions, and shallow acidic soils, where annual precipitation exceeds evapotranspiration, resulting in abundant surface waters. Changes in hydrological processes in this region can have significant consequences for the local ecosystem of mesoscale watersheds. Therefore, investigating the effects of climate change on water quantity is crucial. This research utilizes stable water isotopes (SWIs) as cost-effective tools to improve our understanding of hydrologic processes and flowpaths in mesoscale Precambrian Shield watersheds. By analyzing long-term meteorological, hydrometric, and SWI data from the Sturgeon River, French River, and Muskoka River watersheds, valuable insights are gained regarding the impacts of climate change on hydrological processes in these regions. The study employs a new isotope-enabled distributed hydrologic model, isoWATFLOOD, which provides a good representation of fluxes, storages, and their changes due to climate change in mesoscale and large- scale watersheds. The research objectives include exploring the key controls and importance of surface water storage (lakes and wetlands) on hydrologic function in the Sturgeon River-Lake Nipissing-French River (SNF) and Muskoka watersheds, evaluating isoWATFLOOD hydrologic model's performance in simulating streamflow and isotope values in the Sturgeon River-Lake Nipissing (SN) watershed, evaluating the importance of wetland connectivity representation in isoWATFLOOD performance across the SN watershed, and assessing the impacts of climate change on streamflow and hydrologic partitioning in the SN watershed using the isoWATFLOOD hydrologic model. PCA and HCPC approaches are used to identify variation in controls on hydrologic function in SNF and Muskoka watersheds using combination of hydrometric, geology, landscape and isotopic metrics. The findings reveal greater evaporative enrichment impacts in Muskoka compared to the SNF catchments, with Muskoka exhibiting less variability in streamflow isotopes. The study identifies a positive correlation between wetland area and damping ratio (coefficient of variation of isotopes in streamflow to coefficient of variation of isotopes in precipitation), suggesting that wetland connection/disconnection and varying evaporation impacts contribute to isotopic value variability in catchments with higher wetland coverage. Muskoka and SNF catchments generally fall into separate clusters, primarily influenced by wetland and lake area percentages, mean slope, and the extent of glacialacustrine and glaciofluvial outwash deposits. The combination of catchment classification analyses and stable isotopes (δ 18O and δ 2H) proved effective in studying how different catchment characteristics influence variations in hydrometric response. An application of isoWATFLOOD was set up for Sturgeon River-Lake Nipissing (SN) watershed. Five separate models with varied connected wetland (CW) ratios between 10% to 50% are set up to evaluate the importance of CW ratio in model performance. The SN isoWATFLOOD model, calibrated using isotope and streamflow data, successfully simulates streamflow and isotope values (KGE > 0.6) across 11 catchments. Wetland connectivity percentage significantly influences streamflow and isotope simulations, particularly during the calibration period. The most accurate streamflow simulations occur with 40% wetland connectivity, improving baseflow representation. This study advances isotope-enabled hydrologic simulations using isoWATFLOOD and provides insights into wetland connectivity representation, a critical landscape aspect of Precambrian Shield watersheds. Stable isotopes prove valuable in addressing the challenge of equifinality. Using the SN isoWATFLOOD model and considering 16 global climate model (GCM)- emission (RCP) models, findings project a future characterized by warmer and wetter climatic conditions (2020-2082) compared to the baseline period (1990-2019). On average, the study predicts an annual discharge increase ranging from 4.8% to 11.5%, with elevated winter and fall streamflow across the watershed. These changes result from warmer fall and winter seasons, reduced freezing days, increased annual precipitation, and more frequent extreme precipitation events. Additionally, the simulations indicate an earlier spring freshet peakflow, accompanied by a reduced peak flow rate. Furthermore, climate change will impact hydrological partitioning, leading to alterations in the contributions of annual average daily baseflow to streamflow. Moreover, there will be a rise in average annual daily direct runoff due to intensified annual precipitation, more frequent extreme precipitation events, and rain-on-snow occurrences within the watershed. The results highlight the significance of integrating climate change impacts into water resources management planning, specifically concerning peak flow timing, seasonality, and changes in flow volume during different seasons.
Recovery of smelter-impacted peatlands (Sudbury, Ontario): botanical and microbial community perspectives
(2023-08-18) Seward, James Donald; Seward III, James Donald
Over one century of mineral smelting activities in the Sudbury Basin denuded the regional landscape of vegetation near Sudbury, Ontario, previously (early 1960s) the once the world’s largest point source of SO2 and particulate Ni and Cu emissions. In 1986, fourteen years after the start of major local pollution controls, Gignac and Beckett reported that poor fen peatlands neighboring a Sudbury smelter contained flat, black, and barren peat, depicting severe pollutant stresses. I investigated the plant and microbial communities, and interrelated geochemical controls, in these severely smelter-damaged poor fens. Over the past 35 years Sphagnum moss, a keystone peatland genus, has re-established in poor fens as close as 4 km to smelters, whereas in 1986, Sphagnum was not observed until 12 km. Chemical analysis of the peat showed that total Ni and Cu concentrations in peat samples were lower than in 1986, and decreased with increasing distance from the smelter. As peatlands are globally important carbon sinks, with microbial communities mediating peatland C-cycling, I determined how smelter activity has altered peat moss and soil microbiomes. I showed that microbial community structure was controlled by plant species and microtopography in endophytic Sphagnum communities but was primarily influenced by metal contamination and pH in peat. After healthy Sphagnum and peat plugs were placed into a contaminated peatland. Sphagnum fuscum (a hummock species) and Sphagnum fallax (a lawn species) showed signs of successful establishment (expansion and new growth) after two years, suggesting that more efforts should be made to restore Sudbury’s peatlands. The transplant peat microbiome shifted towards a community structure mirroring the microbiome of the host peatland illustrating the central role of this genus as an ecosystem engineer. I conclude my thesis discussion that because Sudbury peatlands show signs of slow natural recovery and considering the results from the Sphagnum transplant study, that pollutant legacies are abating to the point that large-scale active restoration efforts can now begin.
Demographic processes and behaviour of snapping turtles (Chelydra serpentina) in the context of past catastrophes and ongoing threats
(2023-04-14) Keevil, Matthew G.
Lifetime patterns of somatic growth, reproduction, and survival comprise life history, which links individual traits to the vital rates that determine the properties of populations, such as generation time, potential rate of increase, and responses to environmental perturbation. Individual lifehistory traits, such as survival, age at first reproduction, reproductive frequency, and the size and number of offspring covary along a limited number of dimensions forming the pace-of-life continuum because they are tightly linked by trade-offs and constraints. Furthermore, variation in life history also covaries with morphological, physiological, and behavioural traits. This dissertation focuses on interconnectedness of life-history traits with social behaviour, population dynamics, and conservation. The Algonquin long-term field study of Snapping Turtles (Chelydra serpentina) provides a unique opportunity to analyze these relationships in a longlived organism with a slow life history by building upon a productive foundation of previous research. Turtles‘ slow life history, low and variable juvenile recruitment, and reliance on high adult survivorship makes them vulnerable to anthropogenic threats resulting in turtles being disproportionately imperilled. In Chapter 1, I analyzed the patterns of abundance and survival during and after a population catastrophe and revealed individuals transitioning between sites in a connected population but no recovery over 23 years. Because of their cryptic behaviour, the mating system of Snapping Turtles was poorly known, so in Chapter 2 I quantify sexual size dimorphism and frequency of wounds to infer patterns of intraspecific aggression consistent with a mating system mediated by male combat. The third chapter focused on the somatic growth component of life-history by refining growth modelling by developing a model of seasonal variation in growth rates. In Chapter 4, I examine the demography of Snapping Turtles dispersing across roads by testing hypotheses based on the mating system revealed in Chapter 2 using a demographic model parameterized with survivorship estimated in Chapter 1 and the growth modeling approach developed in Chapter 3. I show that juveniles are overrepresented on roads and face higher mortality risk and that the lost reproductive value of juveniles killed on roads contributes substantially to the overall burden of road mortality in this long-lived species.
Microbiota and species conservation: drivers of gut microbial communities variation in the context of captive breeding programs
(2022-03-28) Van Leeuwen, Pauline Mathilde Lucile
In this PhD study, I investigated two broad classes of drivers of gut microbial communities’ variation in threatened species under conservation breeding programs. Firstly, heritable drivers are potentially not reversible, or if so, over multiple host generations and therefore operate at long-term scales. Second, immediate drivers could induce variation in microbial community composition in a reversible manner and at the individual level of the host. I hypothesized that host genotype and birth location are heritable drivers, and host diet, biology (such as hibernation) and environment (captivity and geography) are short-term immediate drivers.
Optimizing monitoring of harvested moose (Alces alces) in Ontario, Canada
(2022-01-06) Priadka, Pauline
Monitoring of widely distributed wildlife species across multiple discrete management units presents challenges for the optimal allocation of monitoring effort. By balancing value in new information gained through monitoring with costs, monitoring effort can be optimally allocated to maximize benefit to wildlife management. The main research objective of this thesis was to identify factors affecting the optimal allocation of monitoring effort for moose (Alces alces) across multiple Wildlife Management Units (WMUs) in Ontario, Canada that have variable moose population densities and dynamics. Moose are a harvested species across their range in North America and require monitoring to ensure sustainable harvest and that population management objectives are met. The main approaches used to monitor moose in the study area included aerial surveys and hunter harvest information, and I used both sources of data collected by the Ontario Ministry of Natural Resources and Forestry. In this thesis, I determined (1) the utility of harvest data as a proxy of moose population abundance under a selective harvest system; (2) the role of synergistic climate-habitat relationships in shaping spatio-temporal variation in moose population dynamics; and (3) the monitoring design that optimized the use of aerial surveys to estimate population abundance, while balancing the needs and monitoring costs of multiple discrete WMUs. My findings revealed that restricted harvest of adult moose reflected spatial variability in moose abundance better than less restricted calf harvest; but this effect was impacted by high levels of both hunter effort and landscape disturbance that can influence the detectability of moose to hunters. Further, my work revealed that moose population response to climate was variable at local (i.e. WMU) scales and was mediated or exacerbated by habitat conditions that can alter ecological links, including parasite transmission and predation. I incorporated my findings of drivers of moose population variability into population models to evaluate how prioritizing alternative management criteria, in addition to using model-based estimates to replace information-gaps, impacted WMU-specific population and trend estimates. Also incorporated in the decision framework were WMU-specific costs and annual budget constraints. I further evaluated how the utility (based on minimizing population estimate uncertainty) of using a model-based estimate rather than conducting a survey was impacted by population density, severity of environmental stressors, and years since the last survey. My results showed that interval-based monitoring and incorporating model-based estimates that accounted for previous survey uncertainty captured population trends for the highest number of units across a 10-year period. The utility of conducting a survey increased with time since the last survey and was greater for low population densities when the severity of environmental stressors (i.e. winter severity) was high, while being greater for high population densities when winter severity was low. My thesis findings can be applied to other widely distributed and harvested species that are managed and monitored using multi-unit frameworks spanning environmental gradients that contribute to variability in population uncertainty.
A systematic study of interaction effects between plants, microbes, and metals in a model constructed wetland system treating mining influenced waters
(2020-04-16) Gupta, Varun
Constructed wetlands (CW)s have been utilized for decades to treat acid mine drainage (AMD), either directly or as a final polishing step in a series of treatment processes. However, the role of wetland plants and how they influence the treatment potential is still poorly understood, especially when testing is done in an open field-based setting. The main goal of my thesis research was to investigate how plants influence the underlying geochemical conditions and microbial communities in wetland soils and how they in turn affect metals removal and storage potential when wetlands are used to treat waters impacted by mine drainage. In order to achieve this goal, I designed a novel constructed floating wetland (CFW) system that was capable of replicating processes that occur in a subsurface flow wetland and survive repeated freeze-thaw cycles (Chapter 2). The successful CFWs design contained a 20 cm deep, organic rich sediment profile, and was planted with Carex lacustris, Typha latifolia and Juncus canadensis. Five of my designed CFWs were deployed in two waterbodies impacted by mine drainage and located either near an active, or closed, Ni and Cu metal smelter in Sudbury Ontario.I found that both C. lacustris and T. latifolia promoted reductive processes in the CFW soil profile and had significantly higher porewater sulfide than the unplanted control for the entire duration of our experiment (Chapter 2). Additionally, the sediments of these two plants had a higher relative abundance of microbes involved in sulfur cycling and higher relative abundances of enzymes involved in the assimilatory and dissimilatory sulfate reduction pathways (Chapter 3). On the other hand, J. canadensis promoted oxidative processes and had 2-3 times higher porewater sulfate concentration compared to the open water. Additionally, sediments of J. canadensis did not show any selectiveness towards sulfur reducing microbes, or the enzymes involved in the sulfate reduction pathway. Lastly, compared to the unplanted control, both C. lacustris and T. latifolia planted sediments had higher metal concentrations of Co, Cu and Ni, while J. canadensis did not. All the plants influenced metal partitioning to a certain degree and there was a strong site-specific influence on CFWs ability to remove metals (Chapter 4). My research provides a comprehensive look at how plants can either up-or-down regulate treatment potential of constructed wetlands and thus improves our understanding of how such systems can be used to better manage mining impacted waters.
A road to conservation: understanding the dynamics of road-effects and road-effect mitigation
(2019-05-30) Boyle, Sean P.
Globally, roads are one of the most ubiquitous forms of human infrastructure, and have been identified as a serious conservation concern. Though roads impact wildlife in a variety of ways, their effects are often negative. Perhaps the most concerning threats are habitat fragmentation and mortality via wildlife-vehicle collisions. Attempts to manage the negative effects of roads have had mixed results, and major gaps in our understanding of how roads affect wildlife populations and the effectiveness of strategies to mitigate road-effects remain. Many factors contribute to these gaps, particularly the logistical constraints associated with road-effect monitoring and weak study designs that inhibit strong inferences crucial for effective management. To this end, I approached road-effect mitigation in a holistic way. First, I documented and analyzed the local-scale population and spatial ecologies of large mammals around a newly twinned highway. I found that highway twinning, a common strategy to accommodate increased traffic volume, had little effect on large mammals. Second, I focused on the optimization and evaluation of road-effect mitigation (i.e., exclusion fencing and roadcrossing structures). I developed a procedure for identifying ideal locations for mitigation features by comparing road monitoring data to landscape resistance models for both large mammals and herpetofauna. Using this approach, I designed a mitigation plan for reptiles and amphibians, which I evaluated using a robust 6-year Before-After-Control-Impact design that included road surveys, trapping, and two methods of monitoring tunnel usage: trail cameras and PIT tag scanners. I found that exclusion fencing was effective for turtles and amphibians but had no impact on the number of snakes detected on the road. Crossing tunnels were well used by reptiles and amphibians and I demonstrated that for turtles, tunnels effectively facilitated connectivity at the population-level. Finally, I investigated the value of outreach as a long-term conservation strategy in the context of road ecology. I demonstrated that outreach programs significantly increase the perceptions of youth concerning their own likelihood to participate in conservation. Further, using a mixed-methods approach, I identified the aspects of outreach that were most effective at eliciting this change, creating broadly applicable guidelines to optimize future outreach endeavors. By addressing knowledge gaps pertaining to each phase of road-effect mitigation, I have provided a structural framework from which the field of road ecology can continue to flourish. My findings have serious implications for wildlife management and conservation because they increase our understanding of road-effects and importantly, how to increase the success of road-effect mitigation.
Mercury cycling in a remote boreal drainage basin
(2018-12-14) Lescord, Gretchen Lynne
The consumption of freshwater fish and seafood is the main source of mercury (Hg), a widespread neurotoxic pollutant, in humans, a fact which has sparked decades of research on Hg cycling in aquatic systems. More specifically, the formation and bioaccumulation of methylmercury (MeHg) is of particular importance because it biomagnifies through aquatic food webs, resulting in relatively high levels in predatory fish despite typically low concentrations in the surrounding water. The main goal of this thesis was to assess how various watershed-level processes affect Hg bioaccumulation and biomagnification through freshwater food webs across the relatively pristine Attawapiskat Drainage Basin (ADB) in the remote Far North of Ontario. This watershed overlaps with the mineral-rich region known as the “Ring of Fire” which is expected to be heavily developed in the coming decades, likely altering the physico-chemical environments of surrounding lakes and rivers. In total, 58 lakes and river sites across the ADB were sampled for surface water quality, aquatic macroinvertebrates, and fish from 2014 to 2016. Water samples were analyzed for 39 chemical parameters including total Hg (THg; the sum of all Hg species) and MeHg concentrations ([MeHg]). Biotic samples were analyzed for [THg] and/or [MeHg], as well as carbon and nitrogen stable isotope ratios, which are indicative of an animal’s food web position. In Chapter 1 of this thesis, I provide an overview of our current knowledge on Hg cycling in aquatic systems of the boreal region. In Chapter 2, I present an extensive assessment of the chemical, physical, and ecological gradients across the ADB, and an analysis of the relationships between Hg and these environmental gradients. I determined that less productive systems with higher concentrations of dissolved organic matter (DOM) had higher aqueous and biotic [Hg]. In Chapter 3, I examined how changes in the quality of DOM across the ADB relate to [Hg] in water and biota. Findings from this study suggest that more labile DOM complexes enhance MeHg bioaccumulation into food webs, while systems with more humic and aromatic DOM had higher aqueous total [Hg]. The fourth chapter critically examined the speciation of Hg in fish from across the ADB and showed substantially lower percentages of MeHg (relative to total Hg) in muscle of smaller-sized fish, particularly those which feed on littoral-based food webs and had higher lipid content in their tissue. These novel findings challenge the general assumption, used in many biomagnification studies and consumption guidelines, that all fish muscle tissue has > 95% MeHg. Finally, in Chapter 5, I discuss the implications of my research for subsistence fishers, specifically those from remote communities, where freshwater fish are important for both culture and sustenance. Here I developed some preliminary approaches to better communicating the risks and benefits of consuming fish when presenting fish tissue contaminant results in remote northern communities, including those in and around the ADB. Understanding the major influences on MeHg cycling is vital to properly monitoring the effects of industrial development (e.g., the Ring of Fire development) and climate change, which can greatly alter the physico-chemical environment of surrounding lakes and rivers. The results from my thesis indicate significant physical and chemical differences between waters in the two ecozones (i.e., the Boreal Shield and Hudson Bay Lowlands) across the ADB, presumably due to changes in bedrock geology and riparian characteristics. No other study, to my knowledge, has explored the effects of landscape position and the associated changes in physico-chemical characteristics on Hg bioaccumulation, speciation, and biomagnification on such a large scale. My findings demonstrate that monitoring programs will need to effectively track changing nutrient concentrations, DOM characteristics, and Hg bioaccumulation patterns that vary across large spatial gradients.
The ecology of lakes and rivers in the southern boreal shield: water quality, community structure, and cumulative effects
(2018-06-07) Jones, Fredric Christopher
Cumulative effects are the collective ecological effects of multiple human activities. Cumulative effects assessment (CEA) is concerned with quantifying effects of natural environmental factors and human activities. CEA has not lived up to its promise as a precautionary instrument for sustainability, in part because our knowledge of stressors and their effects is elementary; monitoring systems (needed to characterize ecological condition and how it changes over time) are insufficient; and numerical methods for associating stressors and effects, and for forecasting development outcomes, are lacking. This thesis reviews the environmental appraisal literature to synthesize CEA’s theoretical underpinnings, articulate its impediments, and establish that ecological monitoring and modelling activities are critical to success. Three research chapters overcome several scientific barriers to effective CEA. Data from spatial and temporal surveys of lake and stream water chemistry and benthic community structure are used to evaluate candidate monitoring indicators, identify minimally impacted reference waterbodies, characterize baseline water quality and biological condition, and quantify cumulative effects of land use and natural environmental variation (spatial survey: 107 lakes and 112 streams sampled in 2012 or 2013; temporal survey: 19 lakes sampled between 1993 and 2016). The research was conducted in Canada’s Muskoka River Watershed, a 5660 km2 area of Precambrian Shield that drains to Lake Huron. This area’s combination of extensive remaining natural areas and pervasive human influence makes it ideal for studying cumulative effects. It is also characterized by many lakes and their connecting stream and river channels, which integrate effects of stressors in their catchments and constitute logical focal points for CEA. Moreover, the local planning authority (District Municipality of Muskoka) is striving to implement CEA and establish a cumulative effects monitoring program centered on water as its foremost resource; therefore, practical applications of the research have, been identified. Universal numerical methods, which are transferrable to other study areas, are used. Random forest models (an extension of the algorithm used to produce classification or regression trees) are shown to model the singular and collective effects of land-use and natural factors on water chemistry and benthic community structure, and to quantify the sensitivities, and identify the important drivers of various chemical and biological indicators of aquatic ecosystem condition. Partial dependencies from the random forests (i.e., the mean predicted values of a given indicator that occurred across the observed range of a selected predictor) are paired with TITAN (Threshold Indicator Taxa Analysis) to investigate biological and chemical “onset-of-effect” thresholds along gradients of human development. Declining calcium concentrations and amphipod abundances are demonstrated in lakes, and generalized linear models forecast an average 57% decrease in the abundances of these animals to occur by the time lakewater calcium concentrations reach expected minima. As its key findings, the thesis highlights sensitive indicators that should be included in a cumulative effects monitoring program, and are to be preferred when forecasting outcomes of changed land-use or environmental attributes. Empirical breakpoints, where effects of stressor exposures become detectable, are also identified. These thresholds can be used to distinguish reference and impacted conditions, so that normal indicator ranges and associated assessment criteria (important CEA precursors) can be objectively derived. In addition, the potential severity of cumulative effects is exemplified by marked declines in the abundances of lake dwelling amphipods, which could propagate through food webs to substantially alter soft-water Boreal ecosystems.
Methane production in peatlands
(2018-03-23) Carson, Michael Andrew
Methane emissions from peatlands have been researched for decades, although our understanding of methane production at microbial scales is still limited, and this may hamper our ability to predict methane emissions from site-to regional- to global scales. Here, a multi scale approach is used to expand on current knowledge related to the controls and the microbial community responsible for methane production within peatlands. For the first time, an analysis of methane production from a global, coordinated sampling effort was done using a standardized laboratory methodology. Site pH and plant communities were shown to be the best predictors of methane production at the global scale, while peat organic chemical characteristics and abiotic factors including temperature, moisture, and nutrient concentrations, were also shown to be important. Around 5% of samples showed disproportionately high methane emissions compared to CO2. The second research project narrowed focus to a regional scale: peatlands in the Sudbury, ON region were evaluated to assess the role historic and contemporary smelting activities, and subsequent metals and sulfur deposition, have had on the methanogen community composition and methane production. In comparison to most peatland studies, the methanogens present in impacted sites were largely unclassified at the order level and production of methane was dramatically decreased compared to the reference locations. The third research project in the thesis focused even more exclusively at the microbial scale: enrichments of peat were used in an attempt to isolate novel methanogens. While no pure culture isolates were obtained, novel methanogens at the genera and species level where obtained from five of the seven known methanogenic archaeal orders. The case is made that obtaining enrichment (mixed) cultures is an important, underused methodology for discovering and learning about novel methanogens, which have very tight, perhaps inseparable, syntrophic relationships with other anaerobic microbes. Combining culture techniques with modern sequencing technologies was explored as a way forward in obtaining novel species genomes and related growth conditions. Taken together, the overall controls on methane production at global and local scales are commonly peat pH, plant community composition, and peat quality, while the methanogen communities responsible for methane production remain largely unknown and underrepresented in culture collections highlighting the need for further enrichment and isolation work.
Epidemiology of the amphibian pathogen Batrachochytrium dendrobatidis, across multiple spatial scales
(2017-06-15) McMillan, Kirsten Marie
Emerging infectious diseases are increasingly recognized as key threats to wildlife. Batrachochytrium dendrobatidis (Bd), the causative agent of chytridiomycosis, has been implicated in mass mortalities, population declines, and local and global extinctions of many species of amphibians around the world. As such, it is currently the largest infectious disease threat to biodiversity. Understanding the distribution and spatial dynamics of Bd is crucial to predicting spread to new geographic areas, revealing the history of infection, and developing appropriate management strategies. One of the most striking features of Bd is the variability in outcome of infection that has been observed within a species, among populations. By identifying and comparing differences in variables that co-vary between populations exhibiting different infection characteristics, we can start to disentangle the mechanisms allowing for parasite persistence and proliferation. However, infection dynamics operate across nested levels of biological organization: within-host processes underlie among-host processes within a population. As such, this thesis works within the classical themes of spatial epidemiology to consider: 1) the distribution of Bd and the evidence for spatial heterogeneity in both the prevalence and intensity of infection, and 2) the role of individual- and population-level traits in defining infection outcome. The research presented, identifies that Bd functions endemically within Rana pipiens populations in Ontario. Outbreaks of chytridiomycosis are not observed, but infection dynamics show significant interannual fluctuations related to stable geographic factors and local climatic nuances experienced at particular host life history stages. However, Rana pipiens also display variation in resistance to the pathogen, mediated by thermoregulation, dispersal behaviour, and phenotypic properties. Comparisons between host populations show variation in skin-associated bacterial communities, which may mediate susceptibility to chytridiomycosis. These bacterial communities are found to vary across latitude and between sites experiencing different levels of anthropogenic disturbance. Additionally, individual level traits, such as amphibian body temperature and body size are reported to influence bacterial community. Hence, this research highlights the importance of considering context-dependent individual- and populationlevel environmental heterogeneity, when attempting to predict the infection risk of Bd.
Population dynamics of reintroduced elk (Cervus elaphus) in eastern North America
(2017-04-20) Popp, Jesse N.
Studies that focus on identifying factors that influence reintroduction success have often taken an individual population approach; however, investigating multiple populations can provide additional insight. The overall objective of this research was to emphasize the value of using within- and among-population approaches to identifying factors that influence the population dynamics of a reintroduced species. Elk (Cervus elaphus), a species that was extirpated from eastern North America during the late 1800s, has been reintroduced to portions of its former range over the past century through several initiatives. Today, there are several established populations across eastern regions of the USA and Canada, for which extensive monitoring data are available, creating an opportunity to investigate reintroduction success. I aimed to use these data to identify factors associated with changes in the survival and population growth rates of 10 reintroduced elk populations across eastern North America. More specifically, I: (1) performed a literature review detailing the history of elk reintroduction in eastern North America over the past century, (2) identified factors associated with the variation in population growth rates (reintroduction success) for 10 reintroduced elk populations using an among-population approach, (3) identified and assessed how climate affected the population growth rates of 7 reintroduced elk populations, and (4) investigated direct causes of mortality (predation and train collisions) associated with a single elk population experiencing low population growth. Although the number of successful elk restoration attempts has increased over the past century, there has been substantial variation in population growth rates among reintroductions. Major iv causes of elk mortality in restored populations differed between the pre- to post-acclimation phases of reintroduction. Population growth rates were negatively related to the percentage of coniferous forest within elk population range, suggesting that expansive areas of coniferous forests in eastern North America may represent sub-optimal elk habitat. The Burwash elk population in Ontario had low growth rate compared to most other populations reintroduced into eastern North America. Predation and train collisions were the most important source of mortality for this population. The number of annual elk-train collisions, as well as their locations, were monitored and recorded over 14 years. Collision locations were highly sitespecific and were positively correlated to the proximity of bends in the railway. By relating the number of annual elk-train collisions to various climate factors, I found that collision rates were positively related to snow depth. By analyzing field camera data, I found that elk used the railway mostly during the fall and spring, when elk commonly travel to and from wintering grounds. However, by examining VHF telemetry locations, I determined that elk were closer to the railway in winter than in any other season. Railways likely are perceived by elk as easy travel corridors, especially in the winter, and deep snow might prevent escape from oncoming trains. Black bear (Ursus americanus) and wolves (Canis lupus) were the major predators of elk in the Burwash population. White-tailed deer (Odocoileus virginianus), elk (Cervus elaphus), and moose (Alces alces), were the ungulate prey species available to both predators. To determine if predators prefer one ungulate species over another, and to identify which predator species is likely to have a greater impact on elk survival, I investigated predator diets. To compare rates of v ungulate use by predators in relation to prey availability, I calculated the relative abundance of each ungulate species. I found that wolves used juvenile and adult elk as their primary ungulate prey in greater proportions in comparison to their availability. Bears on the other hand, tended to use all ungulate species in proportion to their availability. Climate is well known to affect ungulate population dynamics; however, several factors (e.g.: density, predator presence), can govern the response. Relating the annual growth rates of 7 elk populations to various climate factors I found that responses were population specific. Increased annual snow fall was associated with declines in population growth rates for 2 of the 7 populations assessed and only 1 population responded negatively to increased summer temperatures. Climate likely interacts with other environmental variables to influence fluctuations in annual population growth rates which warrants further investigation. The results of this research will contribute to informed planning of future elk reintroductions and should support development through improved management. In addition, this research highlights the importance of using within- and among- populations approaches to investigating factors that influence elk reintroduction success.
Interactions between metal and drought stressors on plant water relationships and their effects at ecosystem level
(Laurentian University of Sudbury, 2015-05-28) Tanentzap, Fallon M.
Heavy metals influence plant traits that are relevant to its internal water status. Therefore, knowledge of metal effects on a plant’s ability to tolerate other stresses such as drought is important to ensure sustainability of restoration efforts in contaminated landscapes, often prone to drought. The aim of this thesis was to gain understanding how heavy metal contamination influences plant-water relationships and how this interacts with effects of a simultaneous drought. Levels ranging from organs to ecosystem processes were investigated. Chapter 1 briefly reviews published studies on interactions between metal and drought stress and highlights potential gaps in literature. Chapter 2 presents results of a 2-year outdoor lysimeter study on the effects of Cu-Ni toxicity on plant-water relationships using saplings of Acer rubrum, Betula papyrifera, and Quercus rubra. The study shows that under elevated metal levels the plants use less water but suffer drought symptoms even if there is water available. Chapter 3 investigates, using B. papyrifera, whether such metal effects on water use are a result of short-term exposure of roots on their water uptake capacity, or due to long-term structural damage e.g. on hydraulic architecture. Both effects were found, but were smaller than hypothesized. In Chapter 4 influence of metals on plant’s vulnerability to xylem embolisms in Acer rubrum saplings is found to be higher in the metal contaminated region of Sudbury, Ontario, compared to surrounding uncontaminated regions. Chapter 5 establishes guidelines and limitations for transporting leaves from field to laboratory when measuring leaf relative water content, a method that is important for studying plant water relations in the field. Finally, I conclude with a general overall summary of results and proposed suggestions for reclamation projects.
Biogeochemistry of wetlands in watersheds affected by aerial deposition of metals, and linkages to aquatic ecosystem recovery.
(Laurentian University of Sudbury, 2014-10-22) Szkokan-Emilson, Erik John
Wetlands are prevalent in the boreal shield, and are efficient at retaining metals and thus modifying the chemistry of downstream receiving waters. The Sudbury region of Ontario, Canada has suffered over a century of elevated metal and sulphur deposition from mining and smelting activity, and wetlands in the area have provided an important ecosystem service by adsorbing large concentrations of metals over decades of emissions. However, metals can be released from peat in some circumstances such as during dry periods that result in a drop in water table height. With emissions declines in the region, there is the potential that wetlands have remained contaminated and are now acting as a source of metals at annual scales. Stream metal concentrations and dissolved organic matter (DOM) exports were evaluated in six Sudbury wetland-draining streams to address the question: Are wetlands in mining-impacted watersheds releasing potentially toxic metals to receiving waters? Water table declines occured in response to summer droughts, and some metals (Al, Co, Cu, Fe, Mn, Ni, and Zn) were released during rewetting events. Other metals that have a high affinity for DOM (Cu, Al, Fe) were also released from some wetlands in the summer in response to mineralization and DOM release. Concentrations in streams exceeded provincial guidelines and fluxes of some metals (e.g. Ni, Co) exceeded atmospheric deposition inputs to lakes by as much as 12 times. Changes in DOM concentration and composition occurred concurrently with the mobilization of metals after drought, with large decreases in aromaticity (SAC340) coupled with decreased DOC concentration. Biotic ligand modelling indicated that these drought-related DOM changes had a large effect on Cu toxicity, and while predicted Ni toxicity increased because of drought-related increases in Ni concentrations, predicted Cu toxicity increased primarily because of drought-related DOM changes. It is likely that these metal stores will take a very long time to deplete, iv and this offers important insight into the recovery trajectory of aquatic communities in watersheds affected by smelting. The results can be used to advance restoration efforts in the Sudbury region and other similar smelter-impacted areas affected by aerial depositon of metals.
Life history trade-offs, immune function and the expression of sexual signals in two model groups of birds (Psittaciformes, Charadriiformes)
(Laurentian University of Sudbury, 2014-05-21) Edwards, Darryl Bryce
Ecological immunology is the study of the ecological and evolutionary factors that explain variation in the function of, and investment in, the immune system. Within this field, reproduction-based trade-offs are an important focus, where studies often address the immunological costs associated with the expression of secondary sexual traits used in mate choice. Specifically, the Immunocompetence Handicap Hypothesis (ICHH) links the expression of secondary sexual traits to immune function, stating that testosterone promotes the expression of these traits while suppressing the immune system. In doing so, testosterone may maintain the honest expression of such traits, but also ultimately cause sex differences in immunity because males tend to have high levels of testosterone. I explore aspects of these topics using two model systems: the Psittaciformes (Parrots: Chapter 2) and the Charadriiformes (shorebirds), in particular the sex-role reversed Red phalarope (Phalaropus fulicarius). In Chapter 2, I employed a phylogenetically informed approach to investigate the relationships among immune investment, plumage colouration and longevity in parrots. I found that immune investment was greater in more colourful species, as well as in those with a slower pace-of-life (i.e., longer incubation periods), but not specifically in those with longer lifespans. In Chapter 3, I investigated the role that reproductive behaviours play in determining sex differences in corticosterone levels. One explanation for sex differences in the stress response is that selection favours a reduced response in incubating birds to reduce nest abandonment. I generally found little support for sex differences in corticosterone being driven by behaviours related to incubation. Moreover, in phalaropes, sex differences in corticosterone were already present prior to incubation. In Chapter 4, I found that males have higher levels of testosterone than females, but that females were immunosuppressed compared to males. However, I found evidence that testosterone may regulate immune function in females, but not males. The observation of female-biased immunosuppression is consistent with Bateman’s Principle, and although there was some evidence of a testosterone-mediated handicap acting through immune function, these results attest to a fundamental lability in the relationship between testosterone and immunity. In Chapter 5, I demonstrated that plumage colouration in phalaropes is condition-dependent and so potentially conveys useful information to conspecifics. Yet, the relationship was negative in both sexes such that more colourful individuals had poorer immunocompetence, which was contrary to predictions. In Chapter 6, I demonstrated that phalaropes pair assortatively (positively) based on plumage colouration, but negatively based on aspects of size. I discuss the results of this dissertation in the light of life history theory, as well as in the context of mechanisms maintaining signal honesty.
Genetic variation and population genetic structure of muskrat, Ondatra Zibethicus, at different spatial scales
(Laurentian University of Sudbury, 2014-03-19) Laurence, Sophie
Understanding the factors and processes that influence intraspecific genetic variation are essential to better understand evolutionary processes. In this research, I examined patterns of gene flow and their effects on the distribution of genetic variation and spatial genetic structuring at different spatial scales. I used a combination of population genetics, spatial analysis, morphometrics and phylogeography in order to understand the patterns of genetic variation and their resulting phenotypic variations in a semi-aquatic species, the muskrat (Ondatra zibethicus).

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