Detecting the Invisible: Early Monitoring of Cyanobacterial Harmful Algal Blooms with Quantitative PCR

Abstract

The emergence and persistence of cyanobacterial harmful algal blooms (CHABs), comprising multiple toxicity-producing cyanobacteria genera, pose great threats to aquatic environments, to many native species, and to human health. However, recent CHAB monitoring systems using traditional methods lack the ability to detect cyanobacterial blooms at their earliest stages and thus to predict actual cyanobacterial risks. The sequencing of cyanobacterial genomes led to the description of gene clusters responsible for cyanotoxin production, which paved the way for the use of these genes as targets for PCR and quantitative PCR (qPCR). qPCR shows a great potential for detecting, monitoring, and even predicting future CHABs. In my study, I evaluated the use of qPCR in CHAB monitoring and early warning. I reviewed the studies that reported the detection of microcystin genes in natural populations from 2002 to 2019. These suggested that qPCR serves as a rapid and convenient method for monitoring the abundance of toxigenic and non-toxigenic populations of harmful algal species. I found that the variation in the proportion of cells bearing Microcystis mcy genes to Microcystis 16S gene (toxigenic Microcystis to total Microcystis) was usually stable across water bodies in the range of 20%. I discuss the possible issues associated with contradictory findings in the literature, present methodological limitations, and consider the use of qPCR as an indicator of CHAB risk. In addition to this literature review, I conducted field research on Dog Lake and three experimental ponds in the environs of Kingston, Ontario, Canada. At both sites, I did long-term monitoring and found seasonal variation in Microcystis abundance. I found large differences in the mcyE/16S proportions between Dog Lake and the experimental ponds, which averaged approximately 30% and 1%, respectively. Among the three experimental ponds, I found that proportion was related to the abundance of Viviparus georgianus (the banded mystery snail). My experimental study verified the effectiveness of qPCR for long-term monitoring of the abundance of toxigenic and non-toxigenic Microcystis. My results also supported the hypothesis that the proportion of toxigenic Microcystis to total Microcystis is stable in particular water bodies at least across one year. Moreover, I quantified the Microcystis overwintering distribution pattern under the ice cover in winter. I found that the abundance of Microcystis decreased with increasing depth and that the proportion of toxigenic Microcystis to total Microcystis did not change between winter and incoming summer. In shallow water, the benthic Microcystis abundance in winter was consistently similar to pelagic Microcystis abundance in spring, where I assumed that benthic overwintering Microcystis played significant roles in subsequent CHABs. I concluded that the quantification of Microcystis genes and the proportion of toxigenic Microcystis to total Microcystis could serve as new indicators to estimate the potential toxicity of future CHABs.