The structure and function of the microbial food web of Lake Ontario was assessed at 15 stations distributed across 4 transects during the spring and summer of 2003. This was the first major binational study of Lake Ontario since the Lake Ontario Trophic Transfer initiative of 1990. The microbial loop (bacteria, autotrophic picoplankton, heterotrophic nanoflagellates (HNF) and ciliates) and phytoplankton, were enumerated microscopically in addition to measurements of chlorophyll a, size fractionated primary productivity (14C) and bacterial growth (3H). HNF dominated the total biomass in spring (≈300 mg m−3) and summer (≈1250 mg m−3). The size of the organic carbon pool increased from ≈90 mg C m−3 in spring to ≈270 mg C m−3 with HNF contributing 36% of the total organic carbon in the spring and 52% in the summer; however the net balance of the organic carbon pool shifted from autotrophic in the spring to heterotrophic in the summer. The available evidence suggests that HNF are a poor quality food resource for zooplankton and it is likely that the carbon sequestered by HNF is not available to higher trophic levels resulting in dietary stress for planktivores. The implications of high HNF for both organic carbon cycling and maintaining healthy fisheries needs further research. Independent observations show that oligotrophic conditions prevail as evidenced by low phosphorus, low chlorophyll a, low plankton and high water clarity. Such conditions have been generally regarded as the gold standard for managing healthy lakes. Lake Ontario is oligotrophic and healthy from a water quality perspective, but from a food web dynamics point of view, Lake Ontario appears to be unhealthy due to the dominance of HNF, low zooplankton and poor quality of food available to higher trophic levels. We hypothesize that the lake's poor health is attributable to inefficient energy transfer from lower to higher trophic levels. The traditional understanding of trophic state based mainly on water quality criteria needs to be broadened by the inclusion of food web and fisheries based metrics.

Hamilton Harbour is a chronically eutrophic embayment located at the western end of Lake Ontario that has experienced many decades of agricultural, industrial, and urban contamination. It has been identified as an Area of Concern under the terms of the Great Lakes Water Quality Agreement between Canada and the United States. This study examines the ecology of the phytoplankton communities at one centrally located station during the ice-free period (May–October) of three non-consecutive years: 2002, 2004 and 2006. This was the first comprehensive study to be conducted since the 1970s. It was found that the phytoplankton communities are diverse and fluctuate throughout the year, along with changing nutrient, physical and environmental conditions. No consistent patterns of seasonal succession were observed throughout the study. Phytoflagellates including Cryptophyceae and Dinophyceae had a tendency to outnumber and out-compete other phytoplankton since they are mobile and able to seek out optimal habitats within the water column. For a highly eutrophic water body, algal biomass (annual mean ≈ 2.0 g m−3) was lower than expected and more consistent with mesotrophic conditions–an observation first made by researchers in the 1970s and attributed to the highly variable physical environment. While our study supports these earlier results, we also conclude that zooplankton grazing likely has a significant role in limiting the size of the algal standing crop. Several algal bloom events were captured during our study. In addition to the somewhat predictable blooms of Diatomeae in the spring and Cyanophyta in the summer, we also observed blooms of Cryptophyceae and Dinophyceae. In one case we observed a bloom with no dominant taxon–it contained a diverse mixture of Cryptophyceae, Euglenophyta and Dinophyceae–challenging the commonly held notion that algal blooms are essentially monocultures. Our results show that such a variable and stressed ecosystem requires frequent sampling to capture the rapid changes that occur.

Lake Erie has a long history of natural and cultural perturbations ranging from glacial origins, arrival of Europeans, exploration-early colonization, degradation, exotic invasion, and phosphorus reduction to its recent recovery. Is Lake Erie a resilient ecosystem responding to phosphorus abatement and exotic invasion? It is believed that Erie was an oligotrophic system when glaciers receded followed by a long period of mesotrophic conditions. It has been classified from mesotrophic to eutrophic ecosystem during the past three decades. In the 1970s the Great Lakes Water Quality Agreement was signed between Canada and the United States and steps were taken to reduce the phosphorus loading to the Great Lakes including Lake Erie. Total phosphorus and chlorophyll a levels in the eutrophic west have dropped from 41 µg L −1 and 13.8 µg L −1 in the 1970s to <20 µg L −1 and 5.6 µg L −1 in the 1990s. Similarly a significant decrease in phytoplankton biomass was recorded from 1970 to 1992 in the western basin. During the same period Diatomeae decreased markedly from 55% to 10% whereas Chlorophyta increased from 8% to 55%. Similar trends were evident in the other biota. Primary production rates in the 1990s were dominated by small sized organisms (picoplankton and nanoplankton) similar to Lake Superior—a pristine oligotrophic ecosystem. Based on several criteria such as reduction of biomass and primary production, high species diversity, decrease of eutrophic and increase of mesotrophic-oligotrophic species and prevalence of picoplankton-nanoplankton, Lake Erie appears to be a rapidly changing and resilient ecosystem altering from eutrophic to meso-oligotrophic conditions. These observations are also supported by the response of other biota such as zooplankton and benthos. For example during 1993 the non-zebra mussel benthic biomass in the western basin had returned to a similar composition observed earlier in 1952 including the recovery of the mayfly. On the other hand eastern basin benthos has not shown the same extent of recovery as the west. Fish community trends are very complex, but the return of the walleye and whitefish in the western and eastern basins respectively are encouraging signs of recovery. The changes observed at various trophic levels are indicative of a meso-oligotrophic environment.

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The deepwater amphipod Diporeia hoyi has disappeared from Lake Erie and much of Lake Ontario at depths <80 m. This amphipod had supplied 20 percent of the fisheries energy budget in the Great Lakes. The exotic mussel Dreissena bugensis now forms most of the benthic biomass above 60 m depth, but Diporeia is absent over large areas where Dreissena are rare. The filamentous bacterium Thioploca ingrica is now common at many sites between 30 and 40 m where Diporeia has disappeared. Fisheries and Oceans, Canada, investigated the causes of the decline by examining the sediment chemistry, bacterial production and conducted sediment bioassays using Diporeia, Hyalella and Microtox R . Microtox R showed no evidence of toxicity in sediments now devoid of Diporeia. Amphipod survival and growth was greatest in sediment that rapidly lost its Diporeia population in 1993. Presence of Thioploca had no effect on Diporeia survival. Hyalella was more sensitive than Diporeia to test sediments and to filtered water from mussel cultures. Sediment from sites with dense Dreissena populations had lower Diporeia survival. A diet of mussel pseudofaeces caused significantly lower survival in both Hyalella and Diporeia. The exact mechanism causing lower survival is currently unknown and may be related to a nutritional problem or associated waste metabolites.