| Summary: | Cyanobacteria in the genus <i>Microcystis</i> are dominant components of many harmful algal blooms worldwide. Their pelagic–benthic life cycle helps them survive periods of adverse conditions and contributes greatly to their ecological success. Many studies on <i>Microcystis</i> overwintering have focused on benthic colonies and suggest that sediment serves as the major inoculum for subsequent summer blooms. However, the contemporaneous overwintering pelagic population may be important as well but is understudied. In this study, we investigated near-surface and near-bottom pelagic population dynamics of both microcystin-producing <i>Microcystis</i> and total <i>Microcystis</i> over six weeks in winter at Dog Lake (South Frontenac, ON, Canada). We quantified relative <i>Microcystis</i> concentrations using real-time PCR. Our results showed that the spatiotemporal distribution of overwintering pelagic <i>Microcystis</i> was depth dependent. The abundance of near-bottom pelagic <i>Microcystis</i> declined with increased depth with no influence of depth on near-surface <i>Microcystis</i> abundance. In the shallow region of the lake (<10 m), most pelagic <i>Microcystis</i> was found near the lake bottom (>90%). However, the proportion of near-surface <i>Microcystis</i> rose sharply to over 60% as the depth increased to approximately 18 m. The depth-dependent distribution pattern was found to be similar in both microcystin-producing <i>Microcystis</i> and total <i>Microcystis.</i> Our results suggest the top of the water column may be a more significant contributor of <i>Microcystis</i> recruitment inoculum than previously thought and merits more attention in early CHAB characterization and remediation.
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