UC Davis

To monitor the health of Chinook Salmon populations in California’s Central Valley, it’s necessary to measure and evaluate all stages of their life cycle. The outmigration journey of the pre-smolt juvenile Chinook is one of the least understood life stages, yet it’s also one of the most dangerous for the species. Rising water temperatures, drought, invasive predatory species and degradation of the marshland habitats in the San Francisco Bay-Delta (SFBD) created an unsustainable environment where most juvenile Chinook never make it to the Pacific Ocean. Although multiple marsh restoration projects are being developed to lessen the anthropogenic impact, the Chinook Salmon populations are still declining. An increased focus in monitoring the habitat use of pre-smolt Chinook salmon in the shallow-water marsh habitat of the upper SFBD can provide an invaluable insight into the best management strategies to ensure the survival of the species. Due to complications in monitoring the marsh habitats with conventional methods, I evaluated the use of environmental DNA (eDNA) as an alternative indicator of Chinook salmon presence. For the best use of this novel technology in the marsh conditions, we validated and optimized the performance of a Chinook salmon eDNA assay for use in an estuarine environment. Then we compared the effectiveness of eDNA detection to trawling, measuring the sensitivity of each method as well as identifying the biases, optimal working conditions, advantages, and disadvantages of these survey methods for mapping habitat use of the pre-smolt Chinook salmon.eDNA is a stable molecule that can persist in the environment for long periods. Since all living creatures release eDNA into the environment, almost any environmental sample contains eDNA. The eDNA can reflect current or historical distributions of the species living in the environment sampled, with environmental conditions such as eDNA transport, eDNA degradation, sedimentation and PCR inhibitors regulating the shape and duration of the eDNA plumes produced by our target species. Conducting a single species eDNA assay in an aquatic environment consists of four main steps: water filtration, DNA extraction, PCR inhibitor removal and qPCR amplification. In the filtration step a fixed amount of water, normally 1 L per sample, is filtered through a material which will capture the eDNA while the flowthrough is discarded. The filter pore size is the factor that determines the state of the eDNA that will be measured. Larger pores prioritize larger particles such as scales and eggs while smaller pores favor individual cells, subcellular structures and free eDNA. Then the extraction step isolates the eDNA from the filter, and the yield of this step largely influences the sensitivity of the assay. The PCR Inhibitor removal step works to remove any possible contaminants that might impact the amplification of eDNA; therefore, this step is essential to provide reliability of the assay across different environments. Last, the qPCR step amplifies the eDNA to a detectable amount of fluorescence. Marsh habitat is a challenging environment for eDNA surveys because it is associated with an elevated turbidity, which may clog filters and elevate presence of qPCR inhibitors. The first objective of my dissertation was to optimize a Chinook salmon qPCR assay to detect Chinook eDNA in the marshy and estuarine conditions of the SFBD. As the goal for the study was to implement the assay on a large scale, I not only focused on the sensitivity of the assay, but also accounted for the time and costs associated with sampling. I tested a total of 27 combinations of filters, extraction, and inhibitor removal methods. For the conditions of the SFBD we opted for a protocol using glass fiber filters, magnetic bead DNA extraction, and an extra step for PCR inhibitor removal, to best achieve our goals of a large scale eDNA monitoring system for juvenile Chinook salmon in the Upper SFBD. The second chapter of my dissertation determined how best to interpret the meaning of an eDNA positive or negative detection. To do so, I needed to evaluate the dispersion of the eDNA once it is released to better characterize the distribution of the juvenile Chinook salmon. In the literature, eDNA particles have initially been described as fine particulate organic matter (FPOM) particles and simulated as such with hydrological models. For all hydrological models for eDNA, three factors are essential: eDNA production, eDNA degradation and eDNA transport. In general, eDNA production is considered proportional to the mass of the target species, although more recent papers suggest that eDNA production is more correlated with surface area in the case of fishes. Stress, death, and environmental conditions may also affect the release of eDNA. Meanwhile eDNA degradation is mostly dependent on the environment with the bacterial activity dictating most of the eDNA destruction. eDNA can also become undetectable due to precipitation and binding to molecules that inhibit the amplification step of the assay. eDNA transport mostly is dictated by advection in the case of marine and lotic water bodies while in lentic systems turbulent diffusion is the main factor for eDNA dispersion. I built a simplified one-dimensional riverine eDNA transport model to estimate the detection radius of an individual eDNA source and evaluate the effects of the degradation rate, eDNA diffusion coefficient and river advection onto the distance that the eDNA particles can travel before degrading or settling in the bottom of the river. I identified that the main driver of eDNA dispersion is in most cases the advection of the system, which can greatly influence the transport of eDNA. Due to this effect the model can be used to estimate the effective part of the river that was measured for presence or absence of Chinook salmon with the eDNA assay. The modeling also suggests that transect sampling can be a valuable alternative to discrete, or point, sampling in order to increase the repeatability of detection and increase the sensitivity of the assay, with medium sized transects (250-500 m) providing most of the benefits of transect sampling. The model also uses a Bayesian Monte Carlo Markov chain to estimate degradation rates, production rates and diffusion coefficients for further cage studies. Between the years 2018 and 2021, I collaborated with the California Department of Water Resources on a study that performed pairwise sampling of eDNA and trawling to compare the detection rate of both methods to estimate their biases. Water conditions were also measured to describe the sampled environments. I observed that the eDNA survey had a higher detection rate than the trawling survey, with a 45% detection rate compared to 13% detection rate for trawling. eDNA detection was present in a broad set of environments while trawling detections were confined mostly to a narrow set of salinity and dissolved oxygen conditions. Trawling detections were correlated with shoals in the main corridor of Suisun Marsh while detection was minimal in the upper marshlands. eDNA positivity was similar throughout the sampled years while trawl detection occurred mostly in the wet year of 2019. Trawling seems more efficient when river discharge is high, possibly caused by a higher movement or by a higher number of juvenile Chinook throughout the system. My results suggest that trawling surveys may be hampered by dense vegetation and muddy substrates found in the upper marshlands, while eDNA is a promising alternative survey method for these conditions. With the increasing frequency of drought and reduced flows in the SFBD, we expect that eDNA surveys will be a valuable strategy to monitor the Chinook salmon population as well as measure the efficiency of conservation efforts in the region. Although the eDNA detection rate can be a better indicator of Chinook salmon habitat use, trawling and other fish capture survey methods can generate additional information about the health of populations with measures such as size, weight, diet, age, and origin. Therefore, eDNA and trawling provide a complementary view of the juvenile Chinook salmon population. We recommend that managers conduct eDNA surveys to estimate the habitat use and occupancy rates and use targeted trawling surveys to confirm Chinook presence and provide information that cannot be obtained from eDNA alone.