Enterocytozoon schreckii n. sp. Infects the Enterocytes of Adult Chinook Salmon ( Oncorhynchus tshawytscha ) and May Be a Sentinel of Immunosenescence

In this work, we describe a new microsporidian species that infects the enterocytes of Chinook salmon. This novel pathogen is closely related to Enterocytozoon bieneusi , an opportunistic pathogen commonly found in AIDS patients and other severely immunocompromised humans.

A non-functional copy of the salmonid sex determining gene (sdY) is responsible for the “apparent” XY females in Chinook salmon, Oncorhynchus tshawytscha

Many salmonids have a male heterogametic (XX/XY) sex determination system, and they are supposed to have a conserved master sex determining gene (sdY), that interacts at the protein level with Foxl2 leading to the blockage of the synergistic induction of Foxl2 and Nr5a1 of the cyp19a1a promoter. However, this hypothesis of a conserved master sex determining role of sdY in salmonids is challenged by a few exceptions, one of them being the presence of naturally occurring “apparent” XY Chinook salmon, Oncorhynchus tshawytscha, females. Here we show that some XY Chinook salmon females have a sdY gene (sdY-N183), with one missense mutation leading to a substitution of a conserved isoleucine to an asparagine (I183N). In contrast, Chinook salmon males have both a non-mutated sdY-I183 gene and the missense mutation sdY-N183 gene. The 3D model of SdY-I183N predicts that the I183N hydrophobic to hydrophilic amino acid change leads to a modification of the SdY β-sandwich structure. Using in vitro cell transfection assays we found that SdY-I183N, like the wildtype SdY, is preferentially localized in the cytoplasm. However, compared to wildtype SdY, SdY-I183N is more prone to degradation, its nuclear translocation by Foxl2 is reduced and SdY-I183N is unable to significantly repress the synergistic Foxl2/Nr5a1 induction of the cyp19a1a promoter. Altogether our results suggest that the sdY-N183 gene of XY Chinook females is non-functional and that SdY-I183N is no longer able to promote testicular differentiation by impairing the synthesis of estrogens in the early differentiating gonads of wild Chinook salmon XY females.

Effects of In-Channel Structure on Chinook Salmon Spawning Habitat and Embryo Production

Adult salmonids are frequently observed building redds adjacent to in-channel structure, including boulders and large woody debris. These areas are thought to be preferentially selected for a variety of reasons, including energy and/or predation refugia for spawners, and increased hyporheic exchange for incubating embryos. This research sought to quantify in-channel structure effects on local hydraulics and hyporheic flow and provide a mechanistic link between these changes and the survival, development, and growth of Chinook salmon Oncorhynchus tshawytscha embryos. Data were collected in an eight-kilometer reach, on the regulated lower Mokelumne River, in the California Central Valley. Nine paired sites, consisting of an area containing in-channel structure paired with an adjacent area lacking in-channel structure, were evaluated. Results indicated that in-channel structure disrupts surface water velocity patterns, creating pressure differences that significantly increase vertical hydraulic gradients within the subsurface. Overall, in-channel structure did not significantly increase survival, development, and growth of Chinook salmon embryos. However, at several low gradient downstream sites containing in-channel structure, embryo survival, development, and growth were significantly higher relative to paired sites lacking such features. Preliminary data indicate that adding or maintaining in-channel structure, including woody material, in suboptimal spawning reaches improves the incubation environment for salmonid embryos in regulated reaches of a lowland stream. More research examining temporal variation and a full range of incubation depths is needed to further assess these findings.

Spatially overlapping salmon species have varied population response to early life history mortality from increased peak flows

In the Pacific Northwest, USA, climate change is expected to result in a shift in average hydrologic conditions and increase variability. The relative vulnerabilities to peak flow changes among salmonid species within the same basin have not been widely evaluated. We assessed the impacts of predicted increases in peak flows on four salmonid populations in the Chehalis River basin. Coupling observations of peak flows, emissions projections, and multi-stage Beverton–Holt matrix-type life cycle models, we ran 100-year simulations of spawner abundance under baseline, mid-century, and late-century climate change scenarios. Coho (Oncorhynchus kisutch) and spring Chinook salmon (Oncorhynchus tshawytscha) shared the highest projected increase in interannual variability (SD = ±15%). Spring Chinook salmon had the greatest reduction in median spawner abundance (–13% to –15%), followed by coho and fall Chinook salmon (–7% to –9%), then steelhead (Oncorhynchus mykiss) (–4%). Our results show that interspecies and life history variability within a single basin is important to consider. Species with diverse age structures are partially buffered from population variability, which may increase population resilience to climate change.

Reconnecting the Elwha River: Spatial Patterns of Fish Response to Dam Removal

The removal of two large dams on the Elwha River was completed in 2014 with a goal of restoring anadromous salmonid populations. Using observations from ongoing field studies, we compiled a timeline of migratory fish passage upstream of each dam. We also used spatially continuous snorkeling surveys in consecutive years before (2007, 2008) and after (2018, 2019) dam removal during summer baseflow to assess changes in fish distribution and density over 65 km of the mainstem Elwha River. Before dam removal, anadromous fishes were limited to the 7.9 km section of river downstream of Elwha Dam, potamodromous species could not migrate throughout the river system, and resident trout were the most abundant species. After dam removal, there was rapid passage into areas upstream of Elwha Dam, with 8 anadromous species (Chinook, Coho, Sockeye, Pink, Chum, Winter Steelhead, Summer Steelhead, Pacific Lamprey, and Bull Trout) observed within 2.5 years. All of these runs except Chum Salmon were also observed in upper Elwha upstream of Glines Canyon Dam within 5 years. The spatial extent of fish passage by adult Chinook Salmon and Summer Steelhead increased by 50 km and 60 km, respectively, after dam removal. Adult Chinook Salmon densities in some previously inaccessible reaches in the middle section of the river exceeded the highest densities observed in the lower section of the river prior to dam removal. The large number (>100) of adult Summer Steelhead in the upper river after dam removal was notable because it was among the rarest anadromous species in the Elwha River prior to dam removal. The spatial extent of trout and Bull Trout remained unchanged after dam removal, but their total abundance increased and their highest densities shifted from the lower 25 km of the river to the upper 40 km. Our results show that reconnecting the Elwha River through dam removal provided fish access to portions of the watershed that had been blocked for nearly a century.

Investigating barotrauma in juvenile salmon passing through a very low head turbine using response surface methodology

Although hydropower is a clean source of energy, in some cases, it can jeopardize the life of some species of riverine fish. Very Low Head (VLH) water turbine is an innovative design that aims at reducing the adverse effects of such hydroelectric facilities. In this research, two methodologies are integrated to investigate barotrauma in juvenile salmons passing through this particular turbine. First, to quantify barotrauma, we implement a method known as BioPA (Biological Performance Assessment) by combining the results of some laboratory experiments on juvenile Chinook salmon moving through a simulated turbine passage with the Computational Fluid Dynamics (CFD) simulation of the flow field in this environment. In the second part, we added surrogate-based modeling as a tool, which enabled us to study the effects of two geometrical parameters on the environmental performance of the VLH turbine with low computational costs. The results indicate a significant dependency between the installation angle of the VLH turbine and the severity of the barotrauma of this particular fish. In addition, further investigations suggest that the region near the middle of blades is the safest for fish in the case of decompression.

Evaluating Tag-Reliant Harvest Estimators in Chinook Salmon Mixed-Stock Fisheries Using Simulations

Management of mixed-stock Chinook salmon fisheries requires balancing fishery access and conservation of vulnerable stocks. Although accurate, timely estimates of stock-specific harvest are crucial in achieving competing objectives, limited numbers of stock assignments (e.g., tag recoveries) can diminish the utility of estimates. We used a flexible simulation approach, applied to both a theoretical and real-world fishery case study, to compare the performance of competing monitoring alternatives and estimators for harvest. We sought to improve accuracy for point estimates of harvest and harvest trajectories over time. Bayesian models provided similarly accurate point estimates to existing models at high levels of data aggregation, generally improved estimates of harvest trajectories at intermediate aggregation, and reliable estimates of uncertainty. Incorporation of time-lagged prior information inconsistently improved estimates of harvest trajectories. Among monitoring alternatives yielding equal increases (33%) in CWT recoveries, increasing tagging rates resulted in the greatest decrease in estimate uncertainty for target stocks (37.5 to 45.3%). Variable performances of mixed-stock harvest estimators suggest their use should considered on a stock- and fishery-specific basis, potentially using a simulation-based approach.