Role of benthic overwintering cyanobacteria seed stock on estuarine bloom dynamics

• First study to investigate Microcystis seed stock diversity across a large estuary. • Static peripheral areas are hotspots for overwintering Microcystis . • Overwintering Microcystis is at least partially responsible for inoculating water. • There is high genetic diversity of the Microcystis population in the estuary. Cyanobacteria blooms (cHABs) comprised of the potentially toxic cyanobacterium Microcystis , are increasing in waterbodies worldwide. CHABs in estuaries often originate from upstream locations with longer hydraulic residence times (e.g., reservoirs, static channels). These locations also accumulate higher concentrations of benthic overwintering cells that serve as inoculum for subsequent year's blooms. We investigated overwintering Microcystis seed stock in the hydrologically complex upper San Francisco Estuary also known as the Sacramento-San Joaquin Delta (Delta). Quantitative polymerase chain reaction (qPCR) was used to quantify total Microcystis in the sediments that was available to inoculate summertime blooms. To study bloom origin and succession, DNA from discrete water and sediment samples was PCR amplified using cyanobacteria-specific 16S-23S ITS rDNA primers. Results confirmed the hypothesis that static peripheral areas have the highest seed stock and generally the highest Microcystis concentrations in surface water. We also confirmed high genetic diversity of the Microcystis population in the Delta with 36 unique genotypes detected in the sediment and water column. This study demonstrates that overwintering cells should be considered when investigating Microcystis dynamics across large estuarine systems.