No abstract

Given the rapid rise of environmental DNA (eDNA) surveys in ecology and environmental science, it is important to be able to compare the results of these surveys to traditional methods of measuring biodiversity. Here we compare samples from a traditional method (a manual tow-net) to companion eDNA samples sequenced at three different genetic loci. We find only partial taxonomic overlap among the resulting datasets, with each reflecting a portion of the larger suite of taxa present in the sampled nearshore marine environment. In the larger context of eDNA sequencing surveys, our results suggest that primer amplification bias drives much of the taxonomic bias in eDNA detection, and that the baseline probability of detecting any given taxon with a broad-spectrum primer set is likely to be low. Whether catching fish with different nets or using different PCR primer sets, multiple data types can provide complementary views of a common ecosystem. However, it remains difficult to cross-validate eDNA sequencing techniques in the field, either for presence/absence or for abundance, particularly for primer sets that target very wide taxonomic ranges. Finally, our results highlight the breadth of diversity in a single habitat, and although eDNA does capture a richer sample of the community than traditional methods of sampling, a large number of eDNA primer sets focusing on different subsets of the biota would be necessary to survey any ecological community in a reasonably comprehensive way.

The recent decline in Lake Michigan productivity is often attributed to filter feeding by invasive quagga mussels, but some studies also implicate reductions in lakewide nutrient concentrations. We use a 3‐D coupled hydrodynamic‐biogeochemical model to evaluate the effect of changing nutrient concentrations and quagga mussel filtering on phytoplankton production and phytoplankton and zooplankton biomass. Sensitivity experiments are used to assess the net effect of each change separately and in unison. Quagga mussels are found to have the greatest impact during periods of isothermal mixing, while nutrients have the greatest impact during thermal stratification. Quagga mussels also act to enhance spatial heterogeneity, particularly between nearshore‐offshore regions. This effect produces a reversal in the gradient of nearshore‐offshore productivity: from relatively greater nearshore productivity in the prequagga lake to relatively lesser nearshore productivity after quaggas. The combined impact of both processes drives substantial reductions in phytoplankton and zooplankton biomass, as well as significant modifications to the seasonality of surface water pCO2, particularly in nearshore regions where mussel grazing continues year‐round. These results support growing concern that considerable losses of phytoplankton and zooplankton will yield concurrent losses at higher trophic levels. Comparisons to observed productivity suggest that both quagga mussel filtration and lower lakewide total phosphorus are necessary to accurately simulate recent changes in primary productivity in Lake Michigan.