Stream microbiomes are composed of diverse collection of microbes that play an important role in keeping the surrounding riparian zones and life within the streams healthy and thriving. The Chehalis River provides habitats in favor of fish spawning and juvenile development, but fish return populations upstream haves decreased in recent years. The aim of this study was to identify and characterize microbes within the Chehalis River tributaries, in correlation to fish populations, that are causing part of an invisible fish barrier. An invisible fish barrier is an undefined barrier that is blocking or preventing the return of fish. When water conditions are altered by human impacts or water quality is poor, it can result in microbial communities to shift. These communities can become harmful and potentially pathogenic to the surrounding hosts and environment. Microbial identification specifically within the stream in relation to fish populations could help to find ways to improve overall water quality for fish health. This analysis may provide a holistic indicator for necessary renovation and restoration of fish passages. Sites that lack species diversity in their riparian zones, and were closer to urbanization, show diversity in potentially harmful microbes like Camplyobacter, Sanguibacter and Shewanella, in correlation to low fish population. Continued monitoring will help correlate trends that are influencing riparian zones, water quality conditions and fish populations during the process of stream restoration.

Pollution from human influences is a growing problem in the Chehalis River and tributaries causing deleterious effects on stream health. Pollution runoff happens when rainfall or snow melt pick up and carry human-made or natural pollutants and are then deposited into streams, lakes, and rivers. With a better understanding of microbial populations within streams you can correlate the role that the surrounding environment is playing on overall stream health. Stream water has been facing a decline in quality from the leading cause of pollution from agriculture and manufacturer run-offs. Previous studies have linked increasing industrialization to ecological losses. Pollution entering a stream can influence and alter the abundance and diversity of aquatic life, especially at a microbial level. Although there have been many studies relating to run-off pollution affecting streams, there are no in-depth studies done on the taxonomy and functionality of microbes in urban water ecosystems, so it is important for this to be further investigated. For this project, overall stream health was measure by assessing seven locations along Alder and Fry creek. Environmental factors, percentage of man-made covering, and potential pollution runoffs were all considered and analyzed. A stream microbiome analysis was done along all sites sampled using 16s sequencing. The microbes present are a strong indicator of the health of the ecosystem. From this information, future studies can draw how to improve stream restoration efforts based off the abundance and diversity of organisms within streams facing variation in levels of human impacts.

In the Pacific Northwest the Endangered Species Act (ESA) protects wild salmonids from commercial fishing. The current commercial fishing gear, including gill nets but not limited to, disrupts the recovery of these species because fishermen can not selectively harvest the hatchery fisheries without wild salmonids as bycatch, which have high mortality rates. Once ESA quotas are met this can effectively shut down commercial fisheries. The exploration of alternative fishing tools that can select for certain species will lower bycatch mortality rates of ESA species, and in turn allow commercial fisheries to operate longer. On August 26th through September 29th of 2017 Wild Fish Conservancy conducted follow up research, to a 2016 pilot study of Pound nets, in the Lower Columbia River Sub-Basin. Post release survival rates were evaluated in a modified stock selective pound-net. Using Mark Recapture methodology, with a Passive Integrated Transponder (PIT) tags, and genetic clippings for later analysis. Survival rates of control specimen to treatment specimen were captured as they traveled past dams upstream. Data analyzed were total catch, catch per unit effort and covariates of recapture probabilities. The preliminary results show that fishing with stock selective nets can effectively target hatchery fisheries while successfully releasing ESA listed species, reducing mortality rates. In 33 days WFC and a local fisherman captured and released 7,129 salmonids with a post release survival for steelhead and trout ( Oncorhynchus Mykiss) of 94.0%, and 96.6% for Chinook salmon (Oncorhynchus Tshawytscha) listed as ESA species. Hatchery fisheries of these species along with coho salmon (Oncorhynchus kisutch) were effectively selected with viable commercial quantities. Future subset data of genetic clips and a Jolly-Seber analysis will give more precise information of these post-release survival estimates.

Herbivorous fishes feed on stems, leaves, flowers, seeds, fruits, and nuts of diverse aquatic plants, as well as algae. In the Neotropics, many of these fishes have intricately tied ecologies with their prey plant’s life history and facilitate seed dispersal; including the herbivorous cousins of piranhas, pacus. Most pacus experience fluctuation in their diet that reflects the changes in seasonality and plant part availability. A few species of pacus, however, exhibit a specialized feeding strategy known as phytophagy; solely consuming the plant material of Podostemaceae (riverweed). This trend of dietary specialization may be paralleled by a similar shift, away from general herbivory, and towards a specialized phytophage morphology. To investigate the link between diet and morphology within the greater scope of herbivory, we examined four coexisting species including: the seemingly specialized phytophage, Ossubtus xinguense; the generalized phytophages, Tometes kranponhah and Tometes ancylorhynchus; and a facultative phytophage, Myloplus rhomboidalis. We compared the gross morphology of these species with several other serrasalmids using micro-computed tomography scanning to measure functional jaw characteristics, as well as using geometric morphometrics to compare body shapes. Jaw biomechanics indicate that O. xinguense produces the weakest jaw leverage potentially as a result of its sub-terminal mouth. However, we also concluded that the phytophagous species as a group, do not overtly differ from the more generalized herbivorous pacus in terms of jaw mechanics (but remain distinct from the piscivorous piranhas). Body shape analyses also show little divergence among phytophage and herbivore body shapes, suggesting that many herbivores share a similar bauplan adapted for fast flowing waters. With the exception of O. xinguense, phytophagous pacus appear to be equipped with a general herbivory feeding morphology sufficient for a specialized diet. This suggests that phytophagy is not a particularly challenging feeding strategy, but performance may be augmented by additional morphological specialization.

Sea otters (Enhydra lutris), members of the mustelid family, are distributed in the near-shore marine environment along the west coast of North America from southern California to Alaska. Sea otters are unique among marine mammals, in that they bring all captured prey to the surface to handle and consume. This behavior allows scientists to directly observe their foraging and estimate energy intake rates based on time spent at the surface processing and consuming prey (handling time), prey type and size, and dive time. The foraging behavior of sea otters is observed using standardized methods throughout the sea otter’s North American range. One assumption made when calculating sea otter energy intake rates is that the same prey type of a given size is equivalent across regions. However, an anomaly in the handling time of kelp crabs (Pugettia spp.) has been discovered, where Washington sea otters (Enydra lutris kenyoni) handle kelp crabs 1.5-2 times faster than sea otters in California (Enhydra lutris nereies). One hypothesis to explain this difference is that Washington kelp crabs have a lower edible biomass than kelp crabs in California, allowing for faster handling times by sea otters. To explore this hypothesis, I collected kelp crabs at two sites on the Washington coast. I measured and compared kelp crab maximum width and edible biomass to test whether kelp crabs in Washington are an equivalent sea otter prey item to kelp crabs in California. Kelp crabs comprise 20% of the overall diet of Washington sea otters, so accurately measuring the edible biomass of kelp crabs enhances the precision of estimating sea otter energy intake rates. Estimating the energy intake rate of sea otters provides additional information on their population health.

Dungeness crabs (Cancer [Metacarcinus] magister) hold commercial and cultural value in Washington State, yet little is known about the effects of climate change on their population--even less is known about their competitor, the graceful crab (C. [M.] gracilis). To investigate the effects of temperature and size on feeding rate, we conducted consumption experiments in aquaria at multiple temperatures and across a variety of sizes (70-100mm carapace width) of Dungeness and graceful crabs. We investigated their weight-specific feeding rates, egestion, and excretion via a basic mass balance bioenergetic equation in which consumption must equal respiration, egestion, excretion, and growth. We measured the egestion and excretion components of consumption by collecting unconsumed food material and fecal material, respectively. This multi-species comparison evaluates size and temperature-dependent feeding patterns that have implications for future spatial distributions and energy requirements of Dungeness and graceful crabs across Puget Sound. Future management of the fishery and ecological impacts under changing conditions are discussed.

Prevention of aquatic invasive species transmission by recreational fishing and boating is a fundamental management challenge. These activities can entrain non-native plants and animals via tangled lines, bait buckets, or hull encrustation, leading to introductions into new waterbodies. With hundreds of millions of people participating in fishing trips each year, understanding angler movement behavior can provide critical insight into the most effective locations and scales at which to apply preventative measures. Angler behavior is often inferred from infrequently and sparsely conducted surveys that provide limited spatial and temporal insight into this challenge. Here we capitalize on a big data opportunity provided by ReelSonar’s recently launched iBobber, a sonar-enabled bobber with over 3,000,000 records of fishing location, water depth, and environmental variables collected over three years. By quantifying geographic patterns of fishing activities and assessing how these patterns change seasonally, we explore angler behavior in terms of fishing frequency and distance traveled between sites, and characterize the attributes of fished ecosystems. Our study offers novel insight into spatiotemporal patterns of angler behavior and carries important implications for predicting and preventing future transmission of aquatic invasive species via recreational fishing.

Skeletal reduction is a common feature among deep-sea fishes that have diversified from shallow-water relatives, such as snailfishes. These skeletal reductions may be an adaptation to environmental conditions of high pressures, low temperatures, declining luminosity and limited food availability. Snailfishes (family Liparidae) are found across a large bathymetric range (0 –>8,000 m), with intertidal ancestors giving rise to a large clade of deep-sea species. We used microcomputed tomography (micro-CT) to estimate average bone mineral density and examine jaw, pectoral girdle, and neurocranium morphology. Our results suggest at least three mechanisms of skeletal reduction: (1) reduction of bone size, (2) reduction of bone density, and (3) loss of skeletal elements. First, using phylogenetic generalized least squares (PGLS) analysis, we found that the change in cranial dimensions with depth was not uniform. While the size of the maxilla, dentary, and pectoral girdle decreased with greater depth, length of the upper premaxilla and the neurocranium did not vary with collection depth. Second, average density of the lower jaw decreased with increasing depth. Lastly, the ventral suction disc has been lost multiple times within the deep sea lineage. While all three methods are seen in snailfishes, other groups may use some or all of these mechanisms to different extents. Some mechanisms of skeletal reduction may be more advantageous than others. The extent to which a structure is retained in deep-dwelling fishes may indicate its functional importance. Variable skeletal reduction in the family Liparidae provides insights into the physiological adaptations that allow fishes to survive in deep-water environments. We conclude that some skeletal elements are maintained at the expense of others as fishes balance the functional demands of life in the deep sea.

Imidacloprid (IMI), a neonicotinoid, is being sought as an alternative to the carbamate pesticide, carbaryl to control burrowing shrimp (ghost shrimp, Neotropea californiensis) in Willapa Bay and Grays Harbor, Washington. The shrimp destabilize sediments resulting in poor survival and low yields of the commercially harvested Pacific oyster (Crassostrea gigas). Previous laboratory tests indicate juvenile and adult ghost shrimp are overtly affected (immobilized) when exposed to IMI in artificial seawater (SW) at concentrations expected during control operations, but not killed and subsequently recover. Our objective was to determine if emamectin benzoate (EB) is an alternative to IMI. EB, the active ingredient (a.i.) in Slice®, is currently registered for use in marine waters for the control of sea lice on farmed salmon. We targeted juvenile shrimp because they are likely more sensitive than adults and reside within the upper 10-15 cm of the sediment facilitating control. In an initial test to determine the effective range, we exposed juvenile ghost shrimp (mean carapace length = 2.3 mm) to static concentrations of EB (as the insecticide Proclaim®) ranging from 0.01 to 100 ppb a.i. within artificial SW for 96 h. All shrimp within the 100 ppb treatment died within 48 h and 27% exposed to 10 ppb succumbed by 96 h. In a subsequent 96-h test (static 48-h renewal), we exposed juveniles (mean carapace length = 2.1 mm) to concentrations of EB ranging from 10 to 100 ppb to determine the median lethal concentration (LC50). All shrimp exposed to 100 ppb died within 24 h. The 96-h LC50 was 18.8 ppb compared to >12,000 ppb for IMI. EB may provide more effective control than IMI because it targets the primary neurophysiology of the shrimp. Further tests are required to determine effective concentrations within sediment, assess potential non-target effects, and evaluate environmental fate.

Parasite burden can vary over time due to a variety of factors, including environmental change, competition, and niche differentiation. Clavinema mariae is a parasitic “blood worm” nematode that affects several species of commercially important fishes in Puget Sound, living below their skin and feeding on their blood. C. mariae burden increased dramatically in English sole, Parophrys vetulus, from 1930 to 2016, but it is unclear whether this same pattern affected other host species, including the southern rock sole, Lepidopsetta bilineata. I used rock sole specimens from the Burke Museum’s Ichthyology Collection to determine whether the burden of C. mariae changed over time in this host species. I examined preserved specimens that were collected from various locations in Puget Sound in the period of 1930 to 2016, taking note of the abundance of C. mariae in each individual. Creating a timeline of the parasite’s abundance helps us to narrow in on the various factors, such as fishing pressure, climate change, and nutrient pollution, that may influence C. mariae abundance. Parasite burden can negatively impact commercial fisheries and the overall health of the environment, making this study important for both economic and conservation purposes.

Flatfishes of Puget Sound commonly host Clavinema mariae nematode “blood worms”, which reside in the subcutaneous tissue of the host, rendering them unmarketable. Recently, we observed C. mariae in blackbelly eelpout, Lycodes pacificus, which has never before been reported to carry this parasite. Because blackbelly eelpouts have no economic importance, there may have been little incentive for reporting this infection in the past; whether our recent observations of eelpout infection represent a new development or a long-standing host–parasite relationship is therefore unclear. To estimate C. mariae burden in eelpouts from Puget Sound, I am counting subcutaneous parasites in preserved specimens collected between 1911 and 2014, from the University of Washington Ichthyology Collection. If C. mariae appear only in eelpout collected recently, this may indicate a host switch from flatfishes to eelpouts. In the future, DNA sequence analysis will be conducted to determine if C. mariae from flatfishes and eelpouts are indeed the same species. Our work will reveal whether the recent appearance of C. mariae in eelpout is due to host-switching, parasite spillover, or improved observation and reporting.

The exceptional biodiversity in the Coral Triangle is partially attributed to the elevated rates of evolution that occur in the shallow reefs of the Indo-Pacific Ocean. Its current geographical location and complex oceanographic history have facilitated rapid speciation in many lineages of coral reef fishes. The processes causing these unique evolutionary patterns can be closely studied in Eviota (Gobiidae), a widespread lineage of rapidly diverging marine fishes. Their restricted dispersal capabilities, short generation time, and specific habitat preferences have facilitated repeated exploitation of novel niches and thus catalyzed their high species diversity. Here, we examine morphological and genetic diversity in relation to biogeography in the Blackbelly Dwarfgoby, the Eviota atriventris species complex. This study analyses E. atriventris from nine localities across its range spanning the Indo-Australian Archipelago to determine whether recent speciation has occurred at fine scales across the Coral Triangle. Our combined morphological and molecular phylogenetic analysis examines differences in meristic, coloration, morphometrics, and gene sequence data from seven mitochondrial and nuclear genes. Results show strong divergence in mitochondrial DNA sequences in Milne Bay, Papua New Guinea and Solomon Islands (eastern) populations, as compared with a western haplotype from Indonesia. This suggests that lineages within E. atriventris are geographically and genetically isolated. However, evidence from nuclear gene sequences show few differences between groups, and morphological data to support the separation of these populations are inconclusive. These similarities imply that eastern and western haplotypes may be in the early stages of speciation. Due to phylogenetic evidence and lack of geographic overlap, these lineages may be considered separate species under some species concepts. This study illustrates challenges in separating and defining species concepts for closely related species with conserved morphology.

Marine mammals are federally-protected species of interest, however their parasites are vastly unexamined. A lack of data regarding this host-parasite relationship hinders the understanding of ecosystem interactions, which poses consequences for successful conservation and management of marine mammals. To better understand the impacts of parasites on their marine mammal hosts, my research assessed the intestinal parasite burden of harbor seals (Phoca vitulina richardsi) in south Puget Sound. Harbor seal scats were collected under permit from the Commencement Bay floating dock haul-out site each month during and after the pupping timeframe. Non-invasive fecal floatation methods were used on scats to quantify the abundance and diversity of parasites from July 2017 to February 2018. An increase in prevalence of parasites within the population is expected following the weaning of seal pups as they begin feeding on invertebrates and fish implicated in parasite lifecycles. This research establishes baseline data on the intestinal parasite assemblage of Pacific harbor seals within Puget Sound, and the data will later be used in conjunction with molecular diet analysis to deduce the source of parasitic infection. My research can be used to assist with conservation efforts of harbor seals and can be broadly applied to other marine mammals within and outside of Puget Sound, serving as an example for future studies that consider the relationship between marine mammal hosts and their parasites.

Puget Sound is renowned for its biological productivity, but seasonal upwelling feeds this system with waters rich in dissolved CO₂ and consequentially accelerates the acidification of these ecosystems. In this region, aquaculture of bivalves has important economic and cultural roles that are threatened by ongoing changes in climate and water chemistry. For mussels and oysters, shell strength and integrity are the first defense in combating biotic and abiotic stressors but exposure to low pH can drastically weaken calcium carbonate shells. This study examined the effects of variable pH on the shell strength of the Mediterranean mussel, Mytilus galloprovincialis, and the Olympia oyster, Ostrea lurida. M. galloprovincialis and O. lurida were attached to ORCA buoys at three sites in Puget Sound, at either 5m or 20m depth on the buoy tether for three months. This spatial diversity exposed the bivalves to naturally occurring variations in pH which were continuously measured in situ by the ORCA buoys. The resulting shell strength was measured using an Instron Universal Testing Machine by puncturing a small hole in each shell. These results were evaluated using a two-way ANOVA between sites and depths. We expected that both species will have much weaker shells at deeper depths where pH is generally lower. This study can provide physiological thresholds of economically and ecologically important species under current and future oceanographic conditions.

Energetic tradeoffs are responsible for the shift of energy allocation between various physiological processes within an organism which define life history traits. By understanding energetic tradeoffs, we can make predictions about growth and maturation during different life history stages. In aquacultured species, such life history traits determine meat production and time to harvest, and are thus important for profitability of operations. The purple-hinged rock scallop is being developed for commercial production in Puget Sound. Two common products for scallop meat are adductor muscle and the whole animal served on the half shell. Understanding the relationship between maturity of the gonad and size of the adductor muscle would inform market choice between these options for the emerging industry. Previous research on scallop energy allocation suggests that scallops may allocate energy away from the adductor and into the gonad during maturation. To evaluate this energetic tradeoff in rock scallops, 1200 scallops were out-planted in Puget Sound, 400 at each of 3 sites: Neah Bay, Dabob Bay, and South Puget Sound. Shell height, shell width, and shell depth were measured at three time points: initial outplanting (10/28/16), a sampling midpoint (03/06/17), and final sampling (06/08/17 – 06/11/17). Final sampling also included whole weight, meat weight, adductor diameter, and samples of gonad tissue for histology. The gonad tissue samples were mounted on slides, and analyzed to determine sexual maturation levels. Using maturation ratios, I will investigate whether there is correlation between adductor size and maturation, and whether any detected correlation is consistent across outplanting sites. Such a correlation would provide evidence of an energetic tradeoff during maturation as an individual shifts energy stored in the adductor muscle into the gonad. This data will build on previous research and inform the emerging rock scallop aquaculture industry on market selection.

Symbiotic relationships are vital to the survival of a vast array of organisms. A well-documented set of symbiotic relationships in the marine environment are between bivalve mollusks and the variety of epibionts that encrust their shells. Marine sponges are some of the most frequently observed epibionts of bivalves, and can confer both positive and negative effects on their hosts. The Puget Sound sponge species Myxilla incrustans lives almost exclusively on the valves of the scallops Chlamys rubida and Chlamys hastata. Studies have found that this symbiosis is mutualistic, with both the scallop and the sponge acting as predator deterrent for the other, among other interactions. Additional research has shown that presence of sponge does not significantly affect the swimming distance of scallops, however little has been done to look at the effect of different predators on scallop swims, as different scallop species may invest different amounts into protecting their sponge symbionts. This study aimed to evaluate the responses of two species of scallops to two species of predatory sea star to determine if they react differently and if one species of scallop is a better host to the sponge. Scallops were placed in tanks with either the sponge predator Pteraster tesselatus or the scallop predator Pycnopodia helianthoides and the scallop-sea star interactions were recorded. Time and distance of swims were measured for each scallop swim and were categorized by what initiated the swim. Distance and duration of swims were used to evaluate the response of the scallops to different predators to determine if there was a difference between the two species.

Microhabitat association is a key factor contributing to the diversification of coral reef fishes. For species with specific microhabitat associations, a change in host organism (a coral, sponge, or other organism) on a reef could enable sympatric speciation, where a new species evolves in the same geographic area as the ancestral species. The tusked goby, Risor ruber, is a poorly studied obligate sponge-dwelling coral-reef fish. Preliminary genetic data on R. ruber indicate that there are eight genetically distinguishable lineages based on mitochondrial DNA sequence data and that these linages often live on specific host sponges, pointing to a possibility of ecologically-driven speciation. This study aims to uncover potential connections between morphology, microhabitat, and genetics, by determining if the morphological variation of the recurved canines and other morphological features, such as body length versus depth, correspond with the genetic lineages identified and their host sponge preferences. Measurements will be taken from CT scans and preserved specimens. Fin counts, vertebral counts, and teeth will be examined on cleared and stained specimens. Results of this study may lead to new species descriptions within the genus Risor.