I compared changes in offshore Lake Ontario major species-group biomass, production and diets before (1987-1991) and after (2001-2005) invasion-induced ecological change. I synthesized the observations into carbon-based mass-balanced food webs linking two pathways of energy flow; the grazing chain (phytoplankton-zooplankton-fish) and the microbial loop (autotrophic bacteria-heterotrophic protozoans) and determined how the structure and function of the food web changed between time-periods. I use the food web descriptions to simulate the reestablishment of native deepwater bloater. I developed empirical models describing spatial variation in temperature and applied them to investigate predator temperature distributions, bioenergetic consequences of alewife diet and distribution shifts, and zooplankton productivity. Primary production declined as did the biomass and production of all species-groups except Chinook salmon. Total zooplankton production declined by approximately half with cyclopoid copepod production declining proportionately more. Zooplankton species richness and diversity were unaffected. Alewife adapted to low zooplankton production by consuming more Mysis, increasing their trophic level. The increased prey-size and exploitation of spatial heterogeneity in resource patches and temperature may have allowed alewife to maintain their growth efficiency. The trophic level also increased for smelt, adult sculpin, adult alewife and Chinook salmon. Phytoplankton grazing rates declined and predation pressure increased on Mysis, adult smelt and alewife, and decreased on protozoans. Resource to consumer trophic transfer efficiencies changed; increasing for protozoans, Mysis, Chinook salmon and other salmonines and decreasing for zooplankton, prey-fish and benthos. The changes suggest both bottom-up and top-down influences on food web structure. The direct trophic influences of invasive species on the offshore Lake Ontario food web were minor. Carbon flows to Mysis indicated an important, and changing ecological role for this species and we hypothesize that Mysis may have contributed to Diporeia declines. Simulations suggest that only a small reestablished bloater population, limited by Diporeia production, could be sustained.

I compared changes in offshore Lake Ontario major species-group biomass, production and diets before (1987-1991) and after (2001-2005) invasion-induced ecological change. I synthesized the observations into carbon-based mass-balanced food webs linking two pathways of energy flow; the grazing chain (phytoplankton-zooplankton-fish) and the microbial loop (autotrophic bacteria-heterotrophic protozoans) and determined how the structure and function of the food web changed between time-periods. I use the food web descriptions to simulate the reestablishment of native deepwater bloater. I developed empirical models describing spatial variation in temperature and applied them to investigate predator temperature distributions, bioenergetic consequences of alewife diet and distribution shifts, and zooplankton productivity. Primary production declined as did the biomass and production of all species-groups except Chinook salmon. Total zooplankton production declined by approximately half with cyclopoid copepod production declining proportionately more. Zooplankton species richness and diversity were unaffected. Alewife adapted to low zooplankton production by consuming more Mysis, increasing their trophic level. The increased prey-size and exploitation of spatial heterogeneity in resource patches and temperature may have allowed alewife to maintain their growth efficiency. The trophic level also increased for smelt, adult sculpin, adult alewife and Chinook salmon. Phytoplankton grazing rates declined and predation pressure increased on Mysis, adult smelt and alewife, and decreased on protozoans. Resource to consumer trophic transfer efficiencies changed; increasing for protozoans, Mysis, Chinook salmon and other salmonines and decreasing for zooplankton, prey-fish and benthos. The changes suggest both bottom-up and top-down influences on food web structure. The direct trophic influences of invasive species on the offshore Lake Ontario food web were minor. Carbon flows to Mysis indicated an important, and changing ecological role for this species and we hypothesize that Mysis may have contributed to Diporeia declines. Simulations suggest that only a small reestablished bloater population, limited by Diporeia production, could be sustained.

Geosmin is an odorous secondary metabolite produced by some cyanobacteria during growth and released from the cells. Little is known about the biosynthesis of geosmin and the gene(s) required for its production have not been characterized. During late August and early September geosmin episodes due to planktonic cyanobacteria frequently occur in the northwest basin of Lake Ontario waters resulting in taste and odour episodes in drinking water that serves more than 5 million people. At high concentrations geosmin evades traditional drinking water treatment and reaches the tap. These episodes often elicit consumer concern and are wrongly construed to reflect impaired drinking water safety. Water quality managers in the region have generally been unable to prevent or control taste and odour episodes via a proactive approach due to the lack of knowledge of cyanobacterial communities in offshore waters as well as the inability to predict when geosmin will reach intake pipes due to downwelling, the process by which the surface waters mix with the hypolimnion. This study evaluated denaturing gradient gel electrophoresis (DGGE) as a molecular tool for proactive monitoring of potential taste and odour-causing cyanobacteria in environmental samples. The 16S rRNA gene was assessed for its ability to distinguish among geosmin-producing and non-producing strains. This study also examined the evolutionary relationships among geosmin-producing cyanobacteria using the full-length 16S rRNA gene and compared phylogenies with current taxonomy. <br /><br /> A DGGE standard using the V3 hypervariable region of the 16S rRNA gene was developed using geosmin-producing and non-producing isolates of cyanobacteria. Included in the standard was the suspected primary contributor to Lake Ontario taste and odour, <em>Anabaena lemmermannii</em> Richter. This standard was then applied to various environmental collections from Lake Ontario (August 2005) to examine the cyanobacterial community composition. DGGE profiles were consistent with the presence of <em>An. lemmermannii</em> at locations with increased geosmin concentrations (determined using gas chromatography-mass spectrometry), supporting hypothesis that <em>An. lemmermannii</em> is the primary contributor to northwestern Lake Ontario taste and odour. In addition, the application of DGGE in the identification of potential geosmin-producing species of cyanobacteria was deemed to be a potentially useful approach to monitoring cyanobacterial communities in source waters. The 16S rRNA-V3 region alone did not distinguish among geosmin-producing and non-producing strains, however with additional data (actual geosmin concentration) it was showed relationships. <br /><br /> In the phylogenetic analyses, geosmin-producing cyanobacteria did not group monophyletically and it was not possible to state that a single evolutionary event has led to the acquisition of the geosmin-producing trait. Phylogenies also showed that the taxonomy of the Cyanobacteria is largely unresolved. All five Sections (bacteriological classification)/four orders (Komárek & Anagnostidis classification) were paraphyletic, however the heterocystous cyanobacteria (Sections IV and V/Nostocales and Stigonematales) grouped separately from the non-heterocystous cyanobacteria (Sections I, III/Chroococcales and Oscillatoriales). Although both systems of classification compared in this study were similar, nomenclature and groupings were occasionally different among the groups. This demonstrates the incongruity between bacteriologists and phycologists and emphasizes the need for a consensus system of classification for the Cyanobacteria.

Geosmin is an odorous secondary metabolite produced by some cyanobacteria during growth and released from the cells. Little is known about the biosynthesis of geosmin and the gene(s) required for its production have not been characterized. During late August and early September geosmin episodes due to planktonic cyanobacteria frequently occur in the northwest basin of Lake Ontario waters resulting in taste and odour episodes in drinking water that serves more than 5 million people. At high concentrations geosmin evades traditional drinking water treatment and reaches the tap. These episodes often elicit consumer concern and are wrongly construed to reflect impaired drinking water safety. Water quality managers in the region have generally been unable to prevent or control taste and odour episodes via a proactive approach due to the lack of knowledge of cyanobacterial communities in offshore waters as well as the inability to predict when geosmin will reach intake pipes due to downwelling, the process by which the surface waters mix with the hypolimnion. This study evaluated denaturing gradient gel electrophoresis (DGGE) as a molecular tool for proactive monitoring of potential taste and odour-causing cyanobacteria in environmental samples. The 16S rRNA gene was assessed for its ability to distinguish among geosmin-producing and non-producing strains. This study also examined the evolutionary relationships among geosmin-producing cyanobacteria using the full-length 16S rRNA gene and compared phylogenies with current taxonomy. <br /><br /> A DGGE standard using the V3 hypervariable region of the 16S rRNA gene was developed using geosmin-producing and non-producing isolates of cyanobacteria. Included in the standard was the suspected primary contributor to Lake Ontario taste and odour, <em>Anabaena lemmermannii</em> Richter. This standard was then applied to various environmental collections from Lake Ontario (August 2005) to examine the cyanobacterial community composition. DGGE profiles were consistent with the presence of <em>An. lemmermannii</em> at locations with increased geosmin concentrations (determined using gas chromatography-mass spectrometry), supporting hypothesis that <em>An. lemmermannii</em> is the primary contributor to northwestern Lake Ontario taste and odour. In addition, the application of DGGE in the identification of potential geosmin-producing species of cyanobacteria was deemed to be a potentially useful approach to monitoring cyanobacterial communities in source waters. The 16S rRNA-V3 region alone did not distinguish among geosmin-producing and non-producing strains, however with additional data (actual geosmin concentration) it was showed relationships. <br /><br /> In the phylogenetic analyses, geosmin-producing cyanobacteria did not group monophyletically and it was not possible to state that a single evolutionary event has led to the acquisition of the geosmin-producing trait. Phylogenies also showed that the taxonomy of the Cyanobacteria is largely unresolved. All five Sections (bacteriological classification)/four orders (Komárek & Anagnostidis classification) were paraphyletic, however the heterocystous cyanobacteria (Sections IV and V/Nostocales and Stigonematales) grouped separately from the non-heterocystous cyanobacteria (Sections I, III/Chroococcales and Oscillatoriales). Although both systems of classification compared in this study were similar, nomenclature and groupings were occasionally different among the groups. This demonstrates the incongruity between bacteriologists and phycologists and emphasizes the need for a consensus system of classification for the Cyanobacteria.

Concern over recent declines in many wetland-dependent bird species has led to a need to monitor marsh bird populations in response to anthropogenic activities. I conducted point counts and vegetation surveys at 26 coastal wetlands in the Laurentian Great Lakes Region of Canada from 2006-2008 to determine 1) effective methods to monitor marsh birds, and 2) the impacts of land use surrounding coastal wetlands on marsh bird communities. The first part of this dissertation showed that call-broadcasts are effective tools for monitoring marsh birds and that point counts for marsh birds should be conducted from both the shoreline and from the interior of large marshes. Because of the species-area relationship for wetland birds in southern Ontario, sampling effort should increase proportionally with wetland area to attempt the detection of all species present. In the second part of this thesis, I showed that marsh obligate-nesters preferred wetlands in rural areas as opposed to urban areas, while generalist marsh-nesting species showed no apparent difference in use. The Index of Marsh Bird Community Integrity (IMBCI), a biological index used to indicate wetland health, was significantly higher in rural than in urban marshes. Marsh isolation was also an important factor in predicting the marsh bird community, with more isolated wetlands containing fewer obligate species and associated with a lower IMBCI value. Wetlands of Georgian Bay were found to have quite different bird and plant communities than wetlands of Lake Ontario. Even though wetlands of Lake Ontario were considerably more degraded than those in Georgian Bay (according to land use alteration and degree of water quality impairment), these two regions produced similar IMBCI scores, and this draws into question the applicability of some indicators on a basin-wide scale. The results of this thesis indicate how survey protocols in existing wetland bird monitoring programs should be modified and support current literature that urbanization negatively affects the marsh bird community. </p> / Thesis / Doctor of Philosophy (PhD)

<p> Isostatic rebound and climatic changes throughout the Holocene have resulted in several periods of lowered water-levels in the Great Lakes watershed. The Early Holocene lowstand phase corresponds with the Paleoindian period in the Great Lakes Region (11,000-9000 YBP), and subsequent water-level rise has inundated Paleoindian archaeological sites. This research sought to reconstruct the water-level history of Rice Lake (located north of Lake Ontario) in order to identify areas of high potential for submerged prehistoric sites. </p> <p> Over 750 line km of detailed geophysical data (single-beam bathymetry) and 16 sediment cores were collected over a 30 km2 area of Rice Lake. Sediment cores were visually logged and analyzed for particle size, microfossils and microdebitage. Water-level reconstructions accounting for sediment infill and isostatic rebound of the lake record a post Lake Iroquois (after 12 ka BP) Early Holocene lowstand (~10-12 m below present level (bpl)) (EH-1). At 10 ka BP, gradually rising water-levels and establishment of wetlands as indicated by thecamoebian assemblages coincide with a newly discovered Paleoindian occupation of the Mcintyre basin, where quartz microdebitage was found. Waterlevel continued to rise to almost 2 m bpi until 6.5 ka BP, when warmer and drier temperatures caused a sudden drop in water-levels as recorded by a pollen hiatus. After 4 ka BP, water-levels quickly recovered and stabilized as shown by rapid recovery of pre-hiatus thecamoebian biofacies and the establishment of wild rice stands. </p> <p> The small number of known, well-preserved Great Lakes Paleoindian sites has limited analysis of Early Holocene population densities, migration patterns, cultural diffusion, or the chronology of settlement. The method of modelling water-level fluctuations and associated archaeological potential developed in this thesis represents a substantial advance in our understanding of Early Holocene archaeology in the Great Lakes. These methods will have broader application to exploration of submerged terrestrial landscapes elsewhere in the Great Lakes and will allow for future regional synthesis of archaeological site distribution and characteristics. </p> / Thesis / Doctor of Philosophy (PhD)

<p>Frenchman's Bay is a shallow coastal lagoon (0.84 km2) located near the eastern limits of the Toronto urban area. Wholesale land clearance in the 1850's and subsequent industrialization and urbanization of the watershed have had severely impacted wetland habitats and degraded sediment and water quality. Prior to implementation of remediation work, a detailed sedimentologic and magnetic property study was conducted to determine the impacts of post-colonial land use changes in Frenchman's Bay. 11 vibrocores (2-4.5m length) were extracted from the lagoon and 3 5 magnetic susceptibility profiles were collected using a probe driven 1-2 m in the lagoon floor. The core lithofacies were logged in detail and magnetic susceptibility (K, x.) and remanence parameters (NRM, SIRM, Bcr) were measured at 2 cm intervals. Magnetic property and lithofacies data were integrated with geochemical analyses (TOC, C03) and 210Pb dating of core in order to reconstruct the lagoon lithostratigraphy and the thickness of the post-colonial 'anthropogenic layer'. </p> <p>The stratigraphic succession in the lagoon consists of a thick upper sequence of marly gyttja and peat-rich silty marls overlying Holocene laminated marls. The postcolonial layer (Unit 1) is recognized as an uppermost high magnetic susceptibility (x = ~200-300 xl0-8 m3/Kg) gyttja layer that extends to 1-1.5 m depth. The base of the unit has a 210Pb age of 1850 (±55.6), corresponding with the main phase of land clearance and onset of industrialization of the harbour. Titanomagnetite, maghemite and magnetite spherules are the primary magnetic minerals, indicating soil erosion and coal burning as the predominant sources of magnetic particles. The underlying Unit 2 consists of peaty marls with abundant plant fragments recording a more extensive marsh. Unit 3 consists of more carbonate-rich laminated sands (magnetic susceptibility x = 6000 x10-8 m3/Kg) deposited in a low energy oligotrophic lagoon. The basal layer (Unit 4) consists of high magnetic susceptibility massive pebbly muds, which record a pre-lagoon phase of higher water levels in post-glacial Lake Iroquois (ca. 13,500 Ka). </p> <p> Isopach mapping of the magnetostratigraphic units clearly identifies that the anthropogenic layer (Unit I; post-1850) is thickest within a central basin which has acted as trap for sediment carried into the lagoon by several streams. The total volume of impacted anthropogenic sediment is estimated at 4 x105 m3. Isopach maps also identify two thin(< 2 m) wedges of sand (9.6 x104 m3) near the north and southern shores of the bay that records periodic overwash and growth of the beach barrier. </p> <p>The major environmental changes in the lagoon since it inception (ca. 2. 7 Ka include: 1. The formation of a shallow coastal embayment following water level rise from a mid-Holocene low-stand in Lake Ontario (Unit 4); 2. Development of a spit and beach barrier by eastward longshore transport (Unit 3); 3. Closure of the lagoon and development of a stabilized marsh habitat with low sedimentation levels (Unit 2); 4. Destruction of marsh habitats and eutrophication of the lagoon coinciding with land clearance (post-1850's) and an increased in the influx of sediments eroded from the catchment area. </p> / Thesis / Master of Science (MS)

<p>Hamilton Harbour is one of the most polluted sites on the Great Lakes, affected by airborne and sedimentary contamination as a result of both heavy vehicle traffic and thousands of kilograms of industrial steel emissions. Polycyclic Aromatic Hydrocarbons (PAHs) are ubiquitous mutagenic byproducts of incomplete organic combustion; they are present at very high concentrations in the air and sediment of Hamilton Harbour. We quantified DNA mutation rates in three different nesting colonies of Double-crested Cormorants (<em>Phalacrocorax auritus</em>) using five microsatellite markers. These colonies were located at various distances from sources of PAHs and other contamination. We compared pollution-exposed and reference colonies, hypothesizing that cormorants living closest to pollution will have higher rates of germline microsatellite mutations than those living farther away from pollution sources. Using a pedigree approach, we identified mutations when chicks showed microsatellite alleles not found in either parent, and other explanations such as extra-pair parentage had been ruled out. Microsatellite mutation rates were 4.4 times higher at the Hamilton Harbour site closest to the industrial sources of PAH contamination than the other Hamilton Harbour site, and both were higher than the reference colony. Metabolites of the PAH benzo[a]pyrene in cormorant tissues from both Hamilton Harbour sites were identified by LC-MS/MS, demonstrating that cormorants in Hamilton Harbour are exposed to, and metabolizing, PAHs. Diet was not substantially different between the two Hamilton Harbour colonies when measured with regurgitated samples and fatty acid analysis. This suggests airborne pollution in Hamilton Harbour induced germline mutations in cormorants.</p> / Master of Science (MSc)

No description available.

The western embayment of Lake Ontario, Hamilton Harbour, is one of the most polluted sites in the Laurentian Great Lakes and in recent years has seen a reoccurrence of cyanobacterial blooms. This study uses a multidisciplinary approach to examine the presences of toxic Cyanobacteria in the harbour in order to gain insight into these recurrent blooms. Microscopic analyses of phytoplankton samples collected during the 2009 summer-fall sampling season from two locations within the harbour showed the spatial and seasonal diversity of the contemporary cyanobacterial community. Microcystis colonies relative abundances in relation to total algal numbers were estimated. The lowest and highest relative abundances of Microcystis in the phytoplankton population were 0.6% and 9.7%, respectively, and showed seasonal variability between stations. Fourteen cyanobacterial genera comprising six families and three orders were identified and for which the most abundant filamentous genera during the summer-fall sampling season were Planktothrix, Aphanizomenon and Limnothrix. Potential microcystin producers Microcystis, Planktothrix, Aphanizomenon and Dolichospermum were also present and during the sampling period Microcystis was recorded at both stations on all dates, however, its relative abundance was below 10 % throughout the study period. The composition and abundance of filamentous cyanobacteria were observed to be positively statistically correlated to water quality environmental parameters dissolved nitrates (NO3/NO2), dissolved inorganic carbon (DIC), and conductivity. Redundancy analysis (RDA) found that 53.35% total variance of Aphanizomenon was correlated to low water column NO3/NO2 and conductivity, and higher water column DIC. 58.13% of the relative abundance of Planktothrix was correlated to high concentrations of dissolved nitrates, while 51.69% of total variance of Limnothrix was correlated to higher DIC and lower water column dissolved nitrate concentrations. Information about past cyanobacterial communities was obtained from the sediment core analysis, using paleolimnological and modern molecular methods. The age of the 100.5 cm long sediment core retrieved from the deepest part of Hamilton Harbour was established to be 140 years (1869-2009), using the Constant Rate of Supply (CRS) 210Pb age model. This age was not sufficient to provide information of harbour’s environmental conditions, presence of the blooms, and triggers for their occurrence before European settlement in the area. Results of the HPLC analysis of fossil pigments indicated that the dominant members of the algal community have not changed over the 140 years and that cyanobacteria were regular members of the phytoplankton community. The composition of the major chlorophyll pigments indicated high presence of Chlorophyta and Bacillariophyta in the harbour at all times. The main algal groups identified on the basis of marker pigments presence, besides the Chlorophyta and Bacillariophyta, were the Dinophyta and the Cryptophyta. The presence of a scytonemin derivative, compound B, indicated that cyanobacterial blooms were occurring in past, before the first officially recorded blooms in the 1960s. Cyanobacterial pigments presence indicated that Cyanobacteria have been a regular but not dominant feature of Hamilton Harbour phytoplankton in the past. To our knowledge, this study is the first one examining fossil pigments from Hamilton Harbour. Results of the PCR-DGGE molecular analysis of 16S rRNA-V3 gene fragments from sedimentary DNA revealed the presence of thirteen cyanobacterial genotypes. The temporal change in the cyanobacterial community composition was indicated by the increasing number of species over time, from the oldest to the most recent sediment layers. The deepest sediment strata showed the lowest number (two bands) and intensity of bands. The most recent sediment layer had the greatest numbers (11) and intensity of bands. This increased diversity indicated changing environmental conditions in the harbour, primarily nutrient pollution and worsening water quality. Results of the PCR-DGGE molecular analysis of mcyE-AMT gene fragments showed that Microcystis aeruginosa and Planktothrix rubescens were two microcystin producers present in Hamilton Harbour over the last 80 years. The persistent presence and resilience of these two genera indicated a more serious and longer-term issue of toxic blooms than previously recognized. Historical records show that noticeable anthropogenic impact on Lake Ontario environment has been measurable since the 1780s, the first dramatic impact on the Lake Ontario watershed was evident from the mid1880s, the earliest evidence of eutrophication in the lake occurred between 1820 and 1850, while human induced environmental changes in Hamilton Harbour date back ca. 350 years. In the 1960s, cyanobacterial blooms were first officially recognized in the harbour and the lower Great Lakes. The present research is the first report of the mcyE module and AMT domain of microcystin genes being amplified from sediment of North American lakes, and showed that toxic Cyanobacterial have been regular members of Hamilton Harbour phytoplankton community for almost a century. This research considerably deepened the knowledge of the past toxic cyanobacterial blooms in Hamilton Harbour and their possible causes. It also showed that in the absence of historical records, both the PCR-DGGE method and the mcyE-AMT gene may be used for reconstruction of the past toxic blooms not only in the Laurentian Great Lakes, but also in other aquatic regions of the world impacted by toxic cyanobacterial blooms. Also, it demonstrated the utility of the combined molecular and paleolimnological analyses, which might become a useful tool in the determination of the bloom causes factors and in the mitigation of the future production of toxic blooms.