The phytoplankton community of Lake Ontario was assessed during April, July and September 2008 as part of the Cooperative Science and Monitoring Initiative (CSMI) framework. Results were also compared with historic surveys that began in 1970. A total of 320 unique species were identified during 2008, the vast majority being considered ‘rare’ or ‘less common’. The biomass was found to be, on average, 1.6 g m−3 in spring, 3.0 g m−3 in early summer and 2.4 g m−3 in late summer with rare and less common species accounting for 60–80% of the total. Analysis of the size structure of the phytoplankton community combined with size fractionated primary productivity experiments revealed that one picoplankton (<2 μm) species, Chroococcus dispersus var. minor, accounted for up to half of the observed primary productivity, despite contributing 1% or less to total biomass. Our results also showed that the lake was mesotrophic during the summer of 2008 (July and September) and that trophic state has fluctuated between hyper-eutrophic and ultra-oligotrophic since monitoring began in 1970. These findings demonstrate that the Lake Ontario ecosystem is continually changing and more frequent sampling is needed. A high level of taxonomic expertise is required for even the most basic assessments of the phytoplankton community structure and improved taxonomic training and implementation of standardized techniques are necessary.

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