Environmental science

Stream solutes are strongly linked to hydrology, and as such, we sought to better understand how hydrology, particularly flooding, influences nitrogen (N) and phosphorus (P) levels. We used a long-term dataset of monthly water quality samples for many Ontario, Canada, catchments to assess the effects of landscape variables, such as land use and physiography, on the export of nutrients during floods, and to characterize overall concentration-discharge patterns. In general, we found that landscape variables could partially explain the export variation in flood waters, but that the importance of specific variables depended on flood characteristics. We also found that overall concentration-discharge relationships for N and P C were positive, but non-linear, with greater concentrations on the rising limb of the hydrograph depending on the nutrient. With these results, we have identified general patterns between nutrients and hydrology, which will be helpful for managing the ecological effects of flooding.

Author Keywords: C-Q relationships, Discharge, Export, Flooding, Nutrients, Thresholds

In 2008, the first North American water soldier (Stratiotes aloides) population was discovered in the Trent River, Ontario. Water soldier is an invasive aquatic plant with sharp, serrated leaves that has the potential to spread rapidly through dispersed vegetative fragments. Although it is too late to prevent water soldier establishment in the Trent River, its local distribution remains limited. In this study, environmental DNA (eDNA) was explored as a potential tool for early detection of water soldier. Species-specific markers were designed from chloroplast DNA regions matK and rbcL, and a qPCR assay with rbcL primers yielded the most sensitive detection of water soldier eDNA. Positive detections were obtained from six of 40 sampling locations, of which five were collected in Seymour Lake, an area with large patches of water soldier. As water soldier plants were known to be present at these sites, high eDNA concentrations were expected. The sixth positive detection from Trent Lock 5 (50 km downstream of Lake Seymour) was unexpected as it was obtained at a site with no water soldier sightings. This is one of the first studies to demonstrate the effectiveness of eDNA detection from aquatic plants.

Author Keywords: aquatic plant, eDNA, environmental DNA, invasive species, Stratiotes aloides, water soldier

Environmental DNA (eDNA) metabarcoding targets sequences with interspecific

variation that can be amplified using universal primers allowing simultaneous detection

of multiple species from environmental samples. I developed novel primers for three

barcodes commonly used to identify plant species, and compared amplification success

for aquatic plant DNA against pre-existing primers. Control eDNA samples of 45 plant

species showed that species-level identification was highest for novel matK and preexisting

ITS2 primers (42% each); remaining primers each identified between 24% and

33% of species. Novel matK, rbcL, and pre-existing ITS2 primers combined identified

88% of aquatic species. The novel matK primers identified the largest number of species

from eDNA collected from the Black River, Ontario; 21 aquatic plant species were

identified using all primers. This study showed that eDNA metabarcoding allows for

simultaneous detection of aquatic plants including invasive species and species-at-risk,

thereby providing a biodiversity assessment tool with a variety of applications.

Author Keywords: aquatic plants, biodiversity, bioinformatics, environmental DNA (eDNA), high-throughput sequencing, metabarcoding

Soluble uranium (U) has been observed continuously in the porewaters of Bentley Lake,

a lake with semi-permanent anoxic sediments, despite the fact that reduced U(IV) is known to be

insoluble. To be able to predict the fate and mobility of U that has been deposited in lake

sediments, it is very important to understand the factors that determine soluble uranium in anoxic

environments. Understanding soluble U species is crucial for predicting its behavior in natural

systems as well as for the development of U remediation schemes.

To explore the factors affecting soluble U in natural environments, anoxic lake sediments

and porewaters were tested using two analytic methods, ICP-MS and ESI-HR-MS. Reduced

uranium (U(IV)) can be precipitated as U(IV)-NdF3. Using this method revealed that most of the

uranium in porewater is not able to be co-precipitated with NdF3. In addition, UO2+ was found

using ESI-HR-MS, showing uranyl ions exist in reduced porewater. However, the UO2+ might be

attached to some organic groups rather than present as free ions.

Seasonal variation and air exposure experiments on the mobility of U between sediments

and porewater were observed to test for changes of the redox state of U as a function of sample

collection and storage. The results of this study will contribute to better remediation strategies for

U tailings and will help U mining operations in the future.

The Kentucky coffee tree (Gymnocladus dioicus) is an endangered tree species native to the American Midwest and Southwestern Ontario. Significant habitat loss and fragmentation due to agricultural, industrial and urban development has caused gradual decline across its native range. The aims of this study were to investigate: (1) patterns of genetic diversity and, (2) genetic differentiation (3) relative levels of sexual vs. clonal reproduction, and (4) potential for reduced genetic diversity at range edge for wild G. dioicus populations. An analysis of variation at nine microsatellite loci from populations in the core of the species distribution in the U.S.A. and 4 regions of Southwestern Ontario indicated that G. dioicus has remarkably high genetic similarity across its range (average pairwise FST= 0.05). Germination trials revealed that the seed coats require highly invasive treatments (e.g. 17.93 mol/L H2SO4) to facilitate imbibition, with negligible germination observed in treatments meant to emulate prevailing conditions in natural populations. Low levels of sexual reproduction, high genetic similarity, and habitat degradation are issues that exist across the entire native range of G. dioicus.

Threats such as climate change and increased anthropogenic activity such as shipping, are expected to negatively affect the Arctic. Lack of data on Arctic systems restricts our current understanding of these sensitive systems and limits our ability to predict future impacts. Lakes and ponds are a major feature of the Arctic landscape and are recognized as 'sentinels of change', as they integrate processes at a landscape scale. A total of 1300 aquatic sites were assessed for common chemical and physical characteristics. Geology type was found to be the greatest driver of water chemistry for Arctic lakes and ponds. Acid-sensitivity was assessed using the Steady State Water Chemistry model and a subset of 1138 sites from across the Canadian Arctic. A large portion of sites (40.0%, n = 455) were classified as highly sensitive to acidic deposition, which resulted in a median value of 35.8 meq·m―2·yr―1 for the Canadian Arctic. Under modelled sulphur deposition scenarios for the year 2010, exceedances associated with shipping is 12.5% (n = 142) and 12.0% (n = 136) for without shipping, suggesting that impacts of shipping are relatively small.

Author Keywords: Acidic deposition, Arctic lakes, Critical loads, Shipping emissions, Steady-State Water Chemistry Model, Water chemistry

Understanding the maintenance and spread of invasive diseases is critical in evaluating threats to biodiversity and how to best minimize their impact, which can by done by monitoring disease occurrences across time and space. I sought to apply existing and upcoming molecular tools to assess fluctuations in both presence and strain variation of frog virus 3 (FV3), a species of Ranavirus, across Canadian waterbodies. I explored the temporal patterns and spatial distribution of ranavirus presence across multiple months and seasons using environmental DNA techniques. Results indicate that ranavirus was present in approximately 72.5% of waterbodies sampled on a fine geographical scale (<10km between sites, 7,150 km2), with higher detection rates in later summer months than earlier. I then explored the sequence variability at the major capsid protein gene (MCP) and putative virulence gene (vIF-2α) of FV3 samples from Ontario, Alberta, and the Northwest Territories, with the premise of understanding pathogen movement across the landscape. However, a lack of genetic diversity was found across regions, likely due to a lack of informative variation at the chosen genetic markers or lack of mutation. Instead, I found a novel FV3-like ranavirus and evidence for a recombinant between FV3 and a ranavirus of another lineage. This thesis provides a deeper understanding into the spatio-temporal distribution of FV3, with an idea of how widespread and threatening ranaviruses are to amphibian diversity.

Keywords: ranavirus, frog virus 3, amphibians, environmental DNA, phylogenetics, wildlife disease, disease surveillance, major capsid protein, vIF-2α

Author Keywords: amphibians, environmental DNA, frog virus 3, phylogenetics, ranavirus, wildlife disease

Atmospheric pollutant deposition poses a risk to ecosystem health; therefore, monitoring the spatial and temporal trends of deposition is integral to environmental sustainability. Although moss biomonitoring is a common method to monitor various pollutants in Europe, offering a cost-effective approach compared to traditional methods of monitoring, it is rarely used in Canada. The focus of this study was a spatial assessment of trace element deposition across a region with a known large-point source of emissions using the moss biomonitoring method. Moss tissues presented strong correlations with modelled deposition in the region, suggesting mosses are a valuable biomonitoring tool of trace element deposition, especially in regions dominated by large-point emission sources. Additionally, a moss species endemic to Canada was compared to commonly used moss species with results indicating this species (Isothecium stoloniferum) can be used reliably as a biomonitor. Moss biomonitoring is recommended as a compliment to fill in spatial gaps in current monitoring networks across the country.

Author Keywords: biomonitoring, bryophytes, Hylocomium splendens, moss, Pleurozium schreberi, trace elements

Early developmental stages of cold-adapted ectotherms such as brook trout

(Salvelinus fontinalis) are at risk of mortality with increasing water temperatures because

of their sensitivity to changes in their environment. I studied the mass and routine

metabolic rate (RMR) of wild-origin brook trout eggs, alevin and young fry reared at

normal (5°C) and elevated (9°C) temperatures for the duration of the study or at

mismatched temperatures. This setup determined if preconditioning acclimation for one

temperature benefits or hinders the organism later in life. Three levels of biological

organization (ancestry, population, family) were studied using Akaike's Information

Criterion (AIC) to identify models that best accounted for variation in the data. Family,

mass and temperature were most important in predicting body mass and mass-adjusted

RMR, although population and ancestral-level differences were also detected at some life

stages. Strong variation in body mass and mass-adjusted RMR among families may

indicate adaptive potential within brook trout populations to respond to increases in water

temperature with climate change.

Author Keywords: Acclimation, AIC, Brook trout (Salvelinus fontinalis), Environmental matching, Routine metabolic rate, Temperature

The spatial and temporal variation in atmospheric nitrogen dioxide (NO2), ammonia (NH3), and 17 elements (V, Cr, Fe, Ni, Cu, Zn, As, Cd, Pb, Mg, Al, Ca, Co, Se, Sb, Mn, and Na) were measured at 40 road side locations along a ~250 km traffic density gradient of 40,000–400,000 vehicles on the King's Highway 401, in Ontario, Canada. Elemental concentrations were measured over a year, using moss bags as passive samplers, for four quarterly three-month exposure periods (October 2015 – October 2016). Gaseous NO2 and NH3 concentrations were measured using Willem's badge passive diffusive samplers for twelve one-week exposure periods (one per month: October 2015–October 2016). Dry deposition of nitrogen was estimated using the inferential method. There were significant linear relationships between NO2 and NH3 and average annual daily traffic (AADT) volumes across the study area; higher concentrations corresponded to higher volume traffic sites. Average NO2 concentrations at sites ranged from 23.5 to 73 μg/m3, with an annual average of 43.7 μg/m3. Ammonia ranged from 2.56 to 13.55 μg/m3, with an annual average of 6.44 μg/m3. There were significant quarterly variations in NO2, with concentrations peaking during the winter months. In contrast, NH3 showed no significant quarterly variation, but a slight peak occurred during the summer. Gaseous NO2 and NH3 were highly positively correlated (r = 0.63), suggesting a common emission source from traffic. Concentrations in exposed moss were determined by subtracting the total concentration of each metal in the exposed sample from the background concentration present in the moss. Relative accumulation factors (RAF) and contamination factors were also calculated to determine the anthropogenic influence on tissue concentrations in exposed moss. All metals showed elevated levels versus background concentrations, with all metals except Ni and Co showing considerable enrichment. The highest levels of contamination were from V, Cr, Fe, Zn, Cd, Sb, Pb and Na. Principal component analysis indicated 5 clear clusters of related elements, with PC1 accounting for 36.2% and PC2 accounting for 25.6% of the variance. Average annual daily traffic was significantly related to Cr, Fe, Cu, Sb, Mn, Al, and Na. Road side monitoring shows consistently higher concentrations than active monitoring sites located further from the edge of the road, indicating a need for increased road side monitoring in Ontario, Canada.