Application of molecular tools for microbial source tracking and public health risk assessment of a Microcystis bloom traversing 300km of the Klamath River

•Microcystis blooms in Klamath River in 2012 were dominated by a toxic strain.•A new QPCR assay targeting the Microcystis cpcB gene minimized primer/probe mismatches.•Toxic Microcystis cells were transported 300km down the Klamath River from their source.•Upstream toxic blooms should be considered in public health risk assessments. Microcystis is a globally distributed cyanobacterium that forms dense surface scums in eutrophic freshwater bodies and is also capable of producing potent liver toxins (microcystins). Although it is not commonly observed in riverine environments, high concentrations of Microcystis cells – and microcystins – have been observed on a recurring basis in recent years throughout the Klamath River system (Oregon/California). In this study, a variety of genetic approaches were used to assess the connectivity of Microcystis populations found throughout the Klamath River. In 2012, samples were collected bi-weekly from 16 sites spanning the entire system, including all five reservoirs and Upper Klamath Lake. A newly designed QPCR assay targeting a conserved region within the c-phycocyanin β-subunit gene (cpcB) was used along with a microcystin synthetase gene (mcyE) targeting QPCR assay to quantify the spatiotemporal patterns of total and toxigenic Microcystis. These data were compared with traditional metrics, such as microscopic cell counts and analytical toxin measurements, and the public health implications are discussed. Overall, Microcystis was a minor constituent of the phytoplankton community above Copco and Iron Gate Reservoirs, although it was highly prolific within these reservoirs and our data indicate that most of these populations originate internally. Spatiotemporal variations in the proportional abundances of a single nucleotide polymorphism (SNP), identified by 454 deep sequencing of the cpcBA genes, was used to fingerprint Iron Gate Reservoir as the source of downriver Microcystis assemblages. Throughout the study period, the Microcystis populations remained highly toxic, with total microcystin concentrations ranging from 165μg/L in Copco Reservoir to 3.6μg/L within the lower estuary (0.8km from the Pacific Ocean). These results demonstrate that large quantities of intact and toxic Microcystis cells can withstand passage through hydroelectric installations and transport over distances exceeding 300km. This finding emphasizes that public health risk assessments should consider the impact of cyanobacterial blooms even when