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

Early marine survival of steelhead smolts in Puget Sound

Smolt-to adult survival rates for Puget Sound steelhead populations have declined substantially over the last 25 years and remain at or near historic lows. From 2006-2009, nearly 1,400 steelhead smolts from 9 watersheds within Puget Sound were tracked from river mouth to the Pacific Ocean using acoustic telemetry to: (1) estimate early marine survival through Puget Sound, (2) identify common areas of abnormally high mortality along the migration route, and (3) to identify factors that may influence survival. Cormac-Jolly-Seber mark-recapture models were used to jointly estimate survival and detection rate at telemetry arrays. Estimated survival rates from river mouths to near the Pacific Ocean ranged from 1.5% (Skokomish River hatchery smolts in 2009) to 34.0% (Big Beef Creek wild smolts in 2006), and averaged 14.9% for all populations. Factors influencing survival included population, migration segment, migration year, and rearing type (i.e., hatchery or wild), while geographic region, body length, and tag type (i.e., 7mm or 9mm) showed lesser effects. Comparison of survival rates between migration segments implicated central Puget Sound and Admiralty Inlet as potential areas of heightened mortality. Early marine survival rates estimated here are very low considering that steelhead smolts spend only about two to three weeks in Puget Sound before entering the Pacific Ocean. Mortality in Puget Sound may be a major driver behind low observed smolt-to adult survival rates. This study addresses a major gap in steelhead marine life history knowledge and can help to inform future Puget Sound steelhead recovery planning efforts

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

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

An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images

We describe an approach to the high-resolution three-dimensional structural determination of macromolecules that utilizes ultrashort, intense x-ray pulses to record diffraction data in combination with direct phase retrieval by the oversampling technique. It is shown that a simulated molecular diffraction pattern at 2.5-Å resolution accumulated from multiple copies of single rubisco biomolecules, each generated by a femtosecond-level x-ray free electron laser pulse, can be successfully phased and transformed into an accurate electron density map comparable to that obtained by more conventional methods. The phase problem is solved by using an iterative algorithm with a random phase set as an initial input. The convergence speed of the algorithm is reasonably fast, typically around a few hundred iterations. This approach and phasing method do not require any ab initio information about the molecule, do not require an extended ordered lattice array, and can tolerate high noise and some missing intensity data at the center of the diffraction pattern. With the prospects of the x-ray free electron lasers, this approach could provide a major new opportunity for the high-resolution three-dimensional structure determination of single biomolecules

Biplots of Nisqually River Delta invertebrate and fish stable isotope signatures.

To minimize variance and source overlap, invertebrates (Table 2) have been consolidated into coarser source groupings as follows: “riverine insects” (T1), “marsh insects” (T2), “riverine/marsh shoreflies and shorebugs” (T3/4/5), “riverine dipterans” (T6), “marsh dipterans” (T7), “riverine/marsh isopods” (A1/2), “delta mysids and shrimp” (A5/6), “riverine benthics” (B1/4/5), “marsh crustaceans” (B2), “delta crustaceans” (B3), and “delta polychaetes” (B6). Mean δ13C, δ15N, and δ34S values are adjusted for trophic fractionation based on estimates from Davis et al. [68]. Error bars represent ± 1 SD.</p

Map of stable isotope sampling sites in the Nisqually River Delta, Puget Sound, Washington, USA.

Primary producers and invertebrate consumers were collected from the freshwater forested (FW), tidally influenced forested (FOR), transitional emergent marsh (EFT), estuarine emergent salt marsh (EEM), delta mudflat (DMF), and eelgrass (EEL) habitats of the Nisqually River Delta in 2015. We also sampled diatoms in the mudflats adjacent to historically-unaltered Animal Slough (EEM) and Red Salmon Slough (RSS) and in restored Madrone Slough (MAD) in 2011 (white stars). Circles in the right-hand panel represent locations where we captured juvenile Chinook salmon in 2011 and 2015 (all locations) and sculpin in 2011 (fyke nets only). Fish samples were collected across a broader spatial scale including the marine intertidal zone to account for the migratory behavior of juvenile salmon. Aerial imagery of the Nisqually River Delta (47°4′48″N, 122°42′20″W) was acquired by GeoTerra Inc. (Portland, Oregon, USA) in 2015.</p

The Nisqually River Delta food web.

The Nisqually River Delta food web was interpreted from a Bayesian mixing model of δ13C and δ15N. Alphanumeric labels correspond with the source groupings in Table 1 and consumer groupings in Table 2. Thin arrows indicate a 10–24% proportion contribution to diet, medium arrows indicate a 25–50% proportion contribution to diet, and thick arrows indicate a >50% contribution to diet. White arrows show the diets of fish consumers, while black arrows show the diets of invertebrate consumers. Gray numbers along the left-hand side of the figure designate consumer trophic levels based on δ15N values. Primary sources and consumers are visualized along a gradient of delta habitat types with salinity increasing from left to right.</p

Consumer trophic levels.

Nisqually River Delta consumer δ15N values and trophic levels (shaded rectangles numbered 2–5). Consumer groups and their associated taxa are listed in Table 2. Error bars represent ± 1 SD.</p