Cyanobacterial and algal blooms can negatively affect water quality particularly when producing toxins that affect human health and wildlife. While reports of blooms are on the rise globally, their underlying causes remain unclear. The goal of this thesis was to determine temporal changes in cyanobacterial abundance and composition through sediment cores in relation to (1) altered land-use leading to cultural eutrophication and (2) warmer air temperatures that have been recorded in the past few decades. This involved evaluating the use of DNA extracted from lake sediments to quantify cyanobacterial abundance and composition. Lake sediments preserved under appropriate storage conditions showed the potential to yield high quality DNA for downstream molecular applications. Cyanobacteria, quantified using the 16S rRNA gene, were found to have increased over the last three decades in comparison to historical averages (since the 1850s) both inside and outside a protected area in western Quebec, Canada, in concert with recent regional warming. Copy numbers of 16S rRNA genes specific to cyanobacteria largely correlated to temporal trends in cyanobacterial pigments. Larger percent increases were seen in cyanobacterial genes in recent times compared to changes in the eubacterial glutamine synthetase (glnA) gene. The mcyD gene was quantified as a proxy for microcystin production through sediment cores from two lakes of western Canada. Copy numbers of both mcyD and Microcystis 16S rRNA correlated with chemical analyses of microcystin through time in cores. Cyanobacteria in the more eutrophic of these lakes shifted toward less diverse assemblages and more toxigenic taxa in recent years. Lastly, temporal and spatial changes in cyanobacterial diversity were analyzed through pyrosequencing of cyanobacterial 16S rRNA along a latitudinal transect representative of northern Canada. Significant shifts towards less diverse assemblages were found, composed of potentially toxigenic strains, suggestive of climate warming in northern latitudes. These results support recent reports of increased abundance and geographic expansion of cyanobacteria and point to increases in cyanotoxins in some cases. Using DNA archived in sediments to determine the historical state of cyanobacterial abundance and diversity could help inform lake management policies.

Climate change and eutrophication, accelerated by anthropogenic activities, have impacted aquatic ecosystems worldwide. These impacts have stimulated the expansion of cyanobacterial blooms which pose severe threats to ecosystem functioning, environmental health, and the economy. However, the long-term effects of environmental change on bloom-forming cyanobacteria are not well understood as traditional paleolimnological approaches are of limited use in the reconstruction of cyanobacterial dynamics through time. Here, sediment DNA (sedDNA) was used to investigate long-term cyanobacterial trends using sediments from two experimental (fertilized L227 and acidified L223) and two reference (L224 and L442) lakes in the Experimental Lakes Area, Canada. First, to determine whether taxonomic bias might arise from the cyanobacterial sediment record, I performed a 1-year incubation experiment comparing the degradation rates of selected cyanobacterial genes under contrasting environmental conditions. Based on first-order linear decay models, Synechococcus sp. (Synechococcales) decayed the slowest under cold, anoxic conditions, followed by Trichormus (Nostocales), then Microcystis (Chroococcales), suggesting differential preservation of DNA. I then compared the quantitative performance of droplet digital polymerase chain reaction (ddPCR) and high-throughput sequencing (HTS) for the analysis of sedDNA and found that the ddPCR results were more consistent with the known history of the lakes. Furthermore, ddPCR showed that cyanobacterial abundance increased over the past century in all study lakes, but the greatest increase was observed in experimentally fertilized L227. HTS revealed shifts in the cyanobacterial community towards Nostocales dominance and a decrease in alpha diversity in response to phosphorus-only additions. An increase in abundance of the mcyE gene (indicative of microcystin producing taxa) was uniquely observed in L227 when nitrogen additions ceased. Heating degree days were important in explaining variation in the cyanobacterial community composition in all lakes, but nutrients had a greater influence on the L227 community. When sediment data were compared to historical surface water phytoplankton records, moderate to strong correlations between the two archives were found, validating the use of sedDNA. This research demonstrated that sedDNA can elucidate cyanobacterial trends at the community, population, and species level over multidecadal timescales in response to environmental change.