Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches.

Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey. Species-specific detection using a Taqman qPCR assay showed concordance between the methods, but a weak eDNA signal. Informed by the results of field sampling, an experiment was designed to assess how turbidity and filtration methods influence detection of a rare target. Water from non-turbid (5 NTU) and turbid (50 NTU) estuarine sites was spiked with small volumes (0.5 and 1 mL) of water from a delta smelt tank to generate low eDNA concentrations. Samples were filtered using four filter types: cartridge filters (pore size 0.45 µm) and 47 mm filters (glass fiber, pore size 1.6 µm and polycarbonate, pore sizes 5 and 10 µm). Prefiltration was also tested as an addition to the filtration protocol for turbid water samples. eDNA copy numbers were analyzed using a censored data method for qPCR data. The assay limits and lack of PCR inhibition indicated an optimized assay. Glass fiber filters yielded the highest detection rates and eDNA copies in non-turbid and turbid water. Prefiltration improved detection in turbid water only when used with cartridge and polycarbonate filters. Statistical analysis identified turbidity as a significant effect on detection probability and eDNA copies detected; filter type and an interaction between filter type and prefilter were significant effects on eDNA copies detected, suggesting that particulate-filter interactions can affect detection sensitivity. Pilot experiments and transparent criteria for positive detection could improve eDNA surveys of rare species in turbid environments.

Evaluating top-down, bottom-up, and environmental drivers of pelagic food web dynamics along an estuarine gradient.

Identification of the key biotic and abiotic drivers within food webs is important for understanding species abundance changes in ecosystems, particularly across ecotones where there may be strong variation in interaction strengths. Using structural equation models (SEMs) and four decades of integrated data from the San Francisco Estuary, we investigated the relative effects of top-down, bottom-up, and environmental drivers on multiple trophic levels of the pelagic food web along an estuarine salinity gradient and at both annual and monthly temporal resolutions. We found that interactions varied across the estuarine gradient and that the detectability of different interactions depended on timescale. For example, for zooplankton and estuarine fishes, bottom-up effects appeared to be stronger in the freshwater upstream regions, while top-down effects were stronger in the brackish downstream regions. Some relationships (e.g., bottom-up effects of phytoplankton on zooplankton) were seen primarily at annual timescales, whereas others (e.g., temperature effects) were only observed at monthly timescales. We also found that the net effect of environmental drivers was similar to or greater than bottom-up and top-down effects for all food web components. These findings can help identify which trophic levels or environmental factors could be targeted by management actions to have the greatest impact on estuarine forage fishes and the spatial and temporal scale at which responses might be observed. More broadly, this study highlights how environmental gradients can structure community interactions and how long-term data sets can be leveraged to generate insights across multiple scales.