Harmful algal blooms are occurring in large river ecosystems and at the mouth of large rivers with increasing frequency. In lentic systems, the chemical and physical conditions that promote harmful algal blooms are somewhat predictable but tracking prevalence and conditions that promote harmful algal blooms in lotic systems is much more difficult. We captured two of the most extreme discharge years within the last 20 years occurring in the Upper Mississippi River, allowing a natural experiment that evaluated how major shifts in discharge drive environmental variation and associated shifts in phytoplankton. Statistical models describing significant environmental covariates for phytoplankton assemblages and specific taxa were developed and used to identify management‐relevant numeric breakpoints at which environmental variables may promote the growth of specific phytoplankton and/or cyanobacteria. Our analyses supported that potentially toxin‐producing cyanobacteria dominate under high phosphorus concentration, low nitrogen concentration, low nitrogen‐to‐phosphorus ratio, low turbulence, low flushing, adequate light and warm temperatures. Cyanobacteria dominated in 2009 when low discharge and low flushing likely led to optimal growth environments for Dolichospermum, Aphanizomenon and Microcystis. Rarely will a single factor lead to the dominance, but multiple positive factors working in concert can lead to cyanobacteria proliferation in large rivers. Certain isolated backwaters with high phosphorus, low nitrogen, warm water temperatures and low potential for flushing could benefit from increased connection to channel inputs to reduce cyanobacterial dominance. Numerous examples of this type of habitat currently exist in the Upper Mississippi River and could benefit from reconnection to channel habitats.
Ecological shifts, between a clear macrophyte-dominated state and a turbid state dominated by phytoplankton and high inorganic suspended solids, have been well described in shallow lake ecosystems. While few documented examples exist in rivers, models predict regime shifts, especially in regulated rivers with high water retention time. Here I quantified ecological shifts in a large, semi-regulated floodplain river during a transition from a turbid-to a clear-water state using water quality, aquatic vegetation and fisheries data from a rigorous, standardized long-term data set. My findings indicate that significant changes occurred in total suspended solids concentration, aquatic macrophyte abundance, native and non-native fish biomass, fish functional feeding guild patterns, fish habitat guild assemblages and fish spawning guild assemblage patterns over a nearly 20-year period in Navigation Pool 8 of the Upper Mississippi River. Transitions in physical and biological indicators were examined to identify mechanisms underlying the ecological shifts. Environmental variables driving fish assemblage changes were identified (total suspended solids and aquatic vegetation) and management-relevant thresholds are presented. Awareness of management thresholds is critical for resource managers to implement measures to prevent the river from moving to a degraded state characterized by high non-native fish abundance and low predatory fish species abundance.
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