Restoration of the Nisqually River Delta and increased rearing opportunities for salmonids

Estuarine wetlands in the Salish Sea provide important rearing habitat for migrating juvenile Pacific salmon, contributing to their overall productivity and ocean survival. Substantial loss of historical estuarine habitat in the Salish Sea due to diking, draining and development has contributed to the decline of Pacific salmon populations (Oncorhynchus spp.). The return of tidal inundation through a series of dike removals to 364 hectares of the Nisqually River Delta (Olympia, Washington, USA) represents one of the most significant advances to date towards the recovery of the threatened Nisqually Fall Chinook stock. Our objective was to assess the collective Nisqually Delta restorations in terms of increased rearing opportunity for juvenile salmon. Metrics consisted of physical conditions that allow juvenile salmon to access the estuarine restorations such as delta connectivity, full tidal inundation and channel development. Unlike most studies, we put these physical metrics in terms of juvenile Chinook by constraining our inundation model to outmigration season (Mar – Aug) and those tidal depths supporting juvenile Chinook (\u3e 0.4 m). We used these criteria, verified by presence of juvenile salmonids in three restored and two reference tidal channels, to measure the change in opportunity potential from pre-restoration to post-restoration condition for juvenile Chinook to access and rear in the Nisqually estuary. We found landscape connectivity to be strongly tied to tidal height and increased throughout the estuary with dike removal. Tidal channel development was most rapid in the first and second year post-restoration; with channel outlets widening and deepening to accommodate restored tidal prisms. Chum salmon, natural origin Chinook and hatchery origin Chinook salmon accessed all three restored marshes within two years post-restoration, although responses varied among years, marshes and salmon species. These results suggest that the Nisqually Delta restorations are providing increased rearing opportunity for juvenile salmon

Stable isotope analysis reveals different trophic niche spaces for wild and hatchery origin juvenile Chinook salmon in the Nisqually Delta

Hatchery programs have been used as a conservation tool to bolster declining Chinook salmon (Oncorhynchus tshawytscha) populations throughout much of the Salish Sea. In many watersheds, hatchery fish are released concurrently with the natural-origin population, thus raising the potential for density dependent effects via depleted prey resources, territorial behavior, and movement into sub-optimal habitats. Competition during the critical period for early marine growth and survival might have detrimental effects for wild Chinook salmon populations, highlighting the potential importance of a productive delta habitat mosaic. We used an integrated diet approach with stomach content and stable isotope analyses to evaluate differential patterns of habitat use and prey consumption in a fall run population of juvenile Chinook salmon from the Nisqually River Delta in Puget Sound. We examined size class and origin-level differences throughout the out-migration gradient, from freshwater riverine to nearshore habitat. Natural- and hatchery-origin smolts exhibited distinct habitat use patterns, whereby hatchery-origin individuals were captured less frequently in forested and transitional habitats, and more frequently in the nearshore. Consequently, hatchery-origin juveniles were less likely to consume terrestrial insect drift that was almost twice as energy rich as nearshore crustacean prey. Stable isotope signatures from muscle and liver tissues corroborated this finding, showing that while natural-origin Chinook salmon derived 24–31% of their diets from terrestrially sourced prey, terrestrial insects only made up 2–8% of hatchery-origin diets. This may have explained why natural-origin fish were in better condition and had stomach contents that were 15% more energy-rich on average than hatchery-origin fish. We did not observe strong evidence for trophic overlap in natural- and hatchery-origin juvenile Chinook salmon, but our results suggest that hatchery fish are less likely to take advantage of the terrestrial-aquatic interface, and could suffer behaviorally-mediated consequences to early marine growth and survival

Density-dependent and landscape effects upon estuary rearing in Chinook salmon: insights from long-term monitoring in four Puget Sound estuaries

Juvenile Chinook salmon are well known for utilizing estuarine habitats within the tidal delta for rearing during outmigration. Several studies have linked population responses to availability of estuary habitat, and support the hypothesis that estuarine habitats are vital rearing areas for juvenile Chinook salmon. However, these coarse-scale studies provide little insight on how specific estuarine habitats contribute to rearing potential for salmon. We integrate long-term monitoring data from four estuaries of Puget Sound (Nooksack, Skagit, Snohomish, and Nisqually) to examine whether 1) Chinook populations in these rivers are limited by restricted estuary habitat, 2) hatchery releases can influence density dependent relationships in estuaries, 3) highly connected sites support higher densities of salmon, and 4) different habitat types support higher rearing densities of Chinook salmon. Across sampling locations within estuary systems, average annual rearing densities varied over four orders of magnitude. We found strong support for density dependence, habitat type, landscape connectivity, and hatchery release numbers influencing rearing densities, although all factors were not necessarily as important within each system, and effects of habitat type were particularly variable. Further work using bioenergetics models suggest that habitat-dependent variation in temperature can strongly influence growth in different systems, and that multiple habitats are likely important to provide suitable habitat for extended estuary rearing. These analyses are useful for determining the relative contribution of connectivity, cohort population size, and local habitat conditions for growth potential of Chinook salmon using estuarine habitats at early life stages, and shed light on likely impacts of climate change upon rearing conditions

Variation in juvenile Chinook salmon diet composition and foraging success between two estuaries with contrasting land-use histories

The transition of juveniles from fresh water to estuarine and marine environments is a critical period in the life cycle of Pacific salmon, during which survival can be strongly size-selective. Because the amount and quality of food consumed are major determinants of juvenile salmon growth, successful acquisition of energy rich prey during estuarine residence is critical for survival. Humans have likely impacted the feeding relationships of juvenile salmon in estuaries by destroying estuarine wetlands and by altering the abundance of salmon in estuaries. While the estuarine foraging habits of juvenile salmon have been extensively examined, few studies have conducted quantitative comparisons between estuaries that have experienced different levels of human modification. However, comparisons between whole estuaries with different degrees of wetland loss and degradation may be a useful scale of analysis for the diet composition and consumption rates of mobile consumers such as juvenile salmon. To improve our understanding of the effects of wetland loss and conspecific density on juvenile Chinook salmon consumption rate and diet composition in estuaries, we assembled Chinook salmon density and diet data from two Salish Sea estuaries with dramatically different levels of wetland loss and modification. We compared juvenile Chinook salmon diet composition, diet energy density, and instantaneous ration (a proxy for consumption rate) between the two estuaries. We also evaluated the effect of conspecific density on instantaneous ration. We found significant differences in diet composition between juvenile Chinook salmon in the two estuaries, but little difference in instantaneous ration or diet energy density. However, in the highly modified estuary, conspecific density had a significant, negative effect on instantaneous ration, while in the more natural estuary there was little effect on instantaneous ration. These findings suggest that wetland loss may interact with salmon density to constrain the consumption rates of juvenile salmon in estuaries, with resulting consequences for growth and survival

Progressing from multidisciplinary to interdisciplinary restoration science: monitoring and applied studies on the Nisqually River Delta

Restoration science is often described as an ultimate test of ecological theory; assessing the value of restoration actions is challenged by difficulties in measuring complex interactions between restored physical processes and the response of biological resources. Yet, demonstrating the value of restoration is a key to sustaining future public investment, especially in light of uncertainty of future climate change effects. At the Nisqually River Delta, a restoration partnership between the U. S. Fish and Wildlife Service Nisqually National Wildlife Refuge (Refuge), the Nisqually Indian Tribe (Tribe), and Ducks Unlimited culminated in re-established tidal flow to 360 ha of historic floodplain and delta representing the largest estuarine restoration in the Pacific Northwest. Restoration of this large delta was expected to result in a substantial improvement in ecological functions and services in southern Puget Sound. The goal of our scientific team, led by the U. S. Geological Survey (USGS) for the project partners, was to assess the biophysical response to restoration. Science objectives were built into a monitoring framework to include hydrodynamics, geomorphology, sedimentation and nearshore processes with vegetation, invertebrate food resources, waterbird, and fisheries. Our science partners included the U. S. Geological Survey, Refuge, Tribe, non-governmental organizations, and universities representing several disciplines. Funding the science was challenging, since as with most wetland restoration projects, adequate funds are rarely included in costs. Instead, the managers and scientists worked together to raise funds through special funds and competitive grants including addressing climate change. With this funding model, a major challenge for the team was communicating and sustaining a vision to make separate multidisciplinary efforts into unified interdisciplinary science. Here, we use lessons learned from early results of the Nisqually River Delta restoration to discuss restoration science in planning processes, funding costs and approaches, monitoring versus applied studies, and advancing interdisciplinary findings from multidisciplinary efforts

Remote Sensing for Wetland Mapping and Historical Change Detection at the Nisqually River Delta

Coastal wetlands are important ecosystems for carbon storage and coastal resilience to climate change and sea-level rise. As such, changes in wetland habitat types can also impact ecosystem functions. Our goal was to quantify historical vegetation change within the Nisqually River watershed relevant to carbon storage, wildlife habitat, and wetland sustainability, and identify watershed-scale anthropogenic and hydrodynamic drivers of these changes. To achieve this, we produced time-series classifications of habitat, photosynthetic pathway functional types and species in the Nisqually River Delta for the years 1957, 1980, and 2015. Using an object-oriented approach, we performed a hierarchical classification on historical and current imagery to identify change within the watershed and wetland ecosystems. We found a 188.4 ha (79%) increase in emergent marsh wetland within the Nisqually River Delta between 1957 and 2015 as a result of restoration efforts that occurred in several phases through 2009. Despite these wetland gains, a total of 83.1 ha (35%) of marsh was lost between 1957 and 2015, particularly in areas near the Nisqually River mouth due to erosion and shifting river channels, resulting in a net wetland gain of 105.4 ha (44%). We found the trajectory of wetland recovery coincided with previous studies, demonstrating the role of remote sensing for historical wetland change detection as well as future coastal wetland monitoring

Elucidating patterns of channel erosion, sediment deposition, and vegetative regrowth on the restored Nisqually River Delta

Tidally-influenced salt marshes are an ideal habitat for a variety of species including overwintering waterfowl and outmigrating juvenile salmon. Post-restoration salt marsh formation is dependent upon several factors such as frequency and duration of tidal inundation, sediment input from upstream sources, and local prevalence of halophilic plant species. Here we present five years of monitoring data to examine biophysical and vegetative changes on the restored Nisqually River Delta in Puget Sound, Washington, USA. We used these data to evaluate tidal channel morphology, marsh elevation, and vegetative community structure through time. Overall, major channel area increased 42% and major channel length increased 131% from pre- to post-restoration conditions across the Delta, with channel bed erosion occurring at rates of 6.5 cm/year on average. Furthermore, our analyses suggested that mudflat elevations in the restoration area were increasing at a rate of 0-3 cm/year, with Sloughs closer to the mouth of the Nisqually River experiencing more rapid sediment accretion rates as a result of higher initial elevations. These factors interacted to determine vegetative community composition on the Delta. Low marsh, saline-tolerant species were prevalent at newly colonizing restored sites, while high marsh halophilic and brackish species were dominant at two unaltered reference sites. Vegetation colonization occurred faster at sites with higher initial elevations, although species diversity still increased slightly (about 10%) through time at low elevation sites closer to open water. This integrative approach can be used as a tool for scientists and managers to evaluate the immediate effects of dike or levee removal. By incorporating multiple years of monitoring data into a spatially explicit model, we can provide simple projections of geomorphological changes following restoration

Assessing the restoring landscape within the Nisqually River Delta for invertebrate prey production

At the Nisqually River Delta, almost 900 acres have been reconnected to Puget Sound waters, representing the largest estuary restoration project in the Pacific Northwest. The restoring landscape mosaic represents one of the most significant advances towards the recovery of Puget Sound. The ultimate goal of the restoration is to increase the capacity of the estuary to support a diversity of wildlife, waterbirds, and native fish such as the Nisqually Fall Chinook (Oncorhynchus tshawytscha), a threatened population and a vital cultural resource. Here we compare invertebrate prey production and foodwebs throughout the Nisqually River Delta habitat types: Forested, Transition, Tidal marsh, Mudflat, and Eelgrass. We sampled terrestrial, aquatic, benthic and epifaunal (eelgrass only) invertebrates through the chinook outmigration season (Mar-Jul) in 2014 and 2015. These habitat types had distinct invertebrate assemblages and temporal patterns. For example, we detected two pulses of polychaete abundances in the Tidal Marsh in March and June, compared to the epifaunal invertebrates in Eelgrass beds that increased over time and peaked in July. We also used a stable isotope approach to identify and compare the carbon sources that support fish foodwebs within the landscape mosaic. Primary producers (above ground vegetation, macroalgae, particulate organic matter) showed distinct isotopic signatures (d13C and d15N) by habitat type. Tidal Marsh showed the broadest d13C values, while Forested and Freshwater habitats had somewhat overlapping values. Understanding the variation in the abundance and timing of invertebrate assemblages between habitat types can help us determine the restoration capacity for foodweb support and identify areas of high foraging value

River Delta Eelgrass Supports Extended Estuary Residence and Foraging by Outmigrating Chinook Salmon

Eelgrass can enhance marine survival of juvenile salmon by providing food and refuge but data to quantify these functions are scarce. Eelgrass on river deltas may be particularly important as the first eelgrass encountered during outmigration. We used a lampara net to capture juvenile Chinook salmon from a range of eelgrass and non-eelgrass habitats during April-September, monthly 2008-2010 and 2015 in the Skagit River delta and biweekly 2010-2015 in the Nisqually River delta and reach. At Nisqually a subsample of Chinook was retained for otolith, coded-wire tag and diet analysis, and in 2014 and 2015 we sampled potential prey items (infauna, epifauna, and neuston) from the same eelgrass sites and on the same schedule as fish. High catch rates and unique diets indicated the importance of eelgrass growing on the outer edge of deltas (delta front eelgrass) to Chinook salmon in summer. At Nisqually in July-August in delta front eelgrass catch rates were at least twice as high as in other delta flat and nearshore habitats and diets were distinctive in having relatively high percentages of shrimp zoea, mysid shrimp, and crab megalopa. During the peak of outmigration in May-June Nisqually Chinook were abundant in non-eelgrass as well as eelgrass and diets were more homogenous among habitats. At Skagit Chinook also frequented delta front eelgrass in July-August and were more widespread earlier on. Changes in habitat-specific prey abundance or size of prey needed may account for Chinook shifting from a wide distribution in May-June to concentrating in delta front eelgrass later on. Eelgrass epifauna suggested a correspondence between diets and invertebrates produced in eelgrass but infauna and neuston results are needed to fully characterize prey availability. Knowing where, when, and how eelgrass benefits salmon is relevant to both salmon and eelgrass restoration. Our data begin to answer these questions