Research in our lab focuses on characterizing physiological responses of marine organisms to environmental change. Major themes include Environmental Epigenetics, Reproductive Biology, and Genomics.

Environmental Epigenetics

Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?

Summary: Marine ecosystems worldwide are threatened by ocean acidification, a process caused by the unprecedented rate at which carbon dioxide is increasing in the atmosphere. Since ocean change is predicted to be rapid, extreme, and widespread, marine species may face an “adapt-or-die” scenario. However, modifications to the DNA sequence may be induced in response to a stress like ocean acidification and then inherited. Such “epigenetic” modifications may hold the key to population viability under global climate change, but they have been understudied. The aim of this research is to characterize the role of DNA methylation, a heritable epigenetic system, in the response of Eastern oysters (Crassostrea virginica) to ocean acidification. The intellectual merit lies in the integrative approach, which will characterize the role of DNA methylation in the intergenerational response of oysters to ocean acidification. These interdisciplinary data, spanning from molecular to organismal levels, will provide insight into mechanisms that underlie the capacity of marine invertebrates to respond to ocean acidification and lay the foundation for future transgenerational studies. Ocean acidification currently threatens marine species worldwide and has already caused significant losses in aquaculture, especially in Crassostrea species. This research has broader impacts for breeding, aquaculture, and the economy. Under the investigators’ “Epigenetics to Ocean” (E2O) training program, the investigators will build STEM talent in bioinformatics and biogeochemistry, expose girls in low-income school districts to careers in genomics, and advance the field through open science and reproducibility.

Elucidating the physiological and epigenetic response of tetraploid and triploid Pacific Oysters (Crassostrea gigas) to environmental stressors

Summary: Basic physiological studies will be conducted with diploid, triploid and tetraploid larvae produced from the same MBP lines to determine tolerances to three environmental factors which are being altered by climate change. These include temperature, salinity and low pH, individually and in combination. Differential response will be assessed by changes in oxygen consumption rates, shell morphology and survival rates. Cohorts of diploid, triploid and tetraploid juvenile oysters will be grown out in several locations in the two States and closely monitored for survival and performance (e.g. growth rate, condition index). Shotgun proteomics will be used to permit efficient comparison of protein expression patterns on the entire genome. Changes in global DNA methylation will also be examined to assess the role of the environment in influencing the epigenetic landscape, and how this translates to phenotype. A subset of oysters from the first experiments will be selected for spawning larvae that can then be similarly assessed to determine how parental environmental conditions affect larval performance.

Developing genomic resources to support restoration and protection of the Olympia Oyster in Puget Sound

Summary: There is a significant gap in our fundamental understanding of this species’ resilience in the face of environmental change, ecological interactions, and population structure. This information is critical to local restoration efforts and to predicting how molluscs will adapt to long-term environmental change. There is recent evidence that oysters have the capacity to respond to environmental change at a rate beyond what would be predicted by genetic variation alone. The overall objective of this research is to produce genomic resources and capacity to understand the response of Olympia oysters to environmental change. Specifically, a draft genome assembly for the Olympia oyster will be produced and used to understand how responses of the Olympia oyster to environmental changes are inherited (i.e., genetic or epigenetic) using restriction site associated DNA sequencing (RAD-Seq) and bisulfite sequencing (BS-Seq). A web-based platform will be developed based on these resources that will be used for discovery and further collaboration.

Assessing the Capacity for Evolutionary Adaptation to Ocean Acidification in Geoduck

Summary: We will investigate the roles of standing genetic (DNA sequence) and epigenetic (DNA methylation) variation in the response to ocean acidification and elevated temperature in geoduck at the vulnerable larval stage. The specific research objectives are to (1) characterize changes in allele frequencies under ocean acidification and temperature stress at single nucleotide polymorphisms (SNPs) throughout the genome, and (2) determine the change in frequency of methylation states (epialleles) under ocean acidification and temperature stress throughout the epigenome. To meet our objectives, we will employ a within-generation selection experiment on larvae subjected to ambient and high pCO2 and ambient and high temperature in a factorial cross. This experimental design allows us to uncover changes in standing genetic and epigenetic variation in response to ocean acidification and elevated temperature, and will provide essential information on how marine invertebrate populations can respond to, and persist in, an acidifying ocean.

Evaluating the role of DNA methylation in phenotypic plasticity and response to environmental change in tropical reef corals

Summary: Phenotypic plasticity is critical to the survival of many organisms in a rapidly changing environment, especially threatened species like tropical reef corals. This project will assess whether DNA methylation plays a role in coral phenotypic plasticity. Caribbean corals of the genus Porites will be used as primary research models. The project will first assess whether differential methylation patterns are associated with alternative phenotypes, as well as determine whether methylation and phenotype change and co-vary in reponse to experimental manipulations. Further work will evaluate relationships between methylation and transcription, test for a causative role of DNA methylation in coral thermal tolerance plasticity, and assess heritability of DNA methylation by comparison of methylation patterns in adult corals and their larval offspring.

Reproductive Biology and Ecology

Using satellite pop-up tags to track movements of sablefish during spawning and changes in vertical position in the water column

Summary: The Sablefish (Anoplopoma fimbria) is a deep-water groundfish species widely distributed throughout the northern Pacific Ocean. While some broadscale movements of sablefish have been addressed with tagging studies, two fundamental questions related to sablefish movements are 1) Where do sablefish go during spawning and; 2) Are sablefish adults exclusively benthic inhabitants? To address these questions we will use “pop-up” satellite tag (PSAT) technology. Pop-up satellite tags are composed of a data-logger and battery, and a float with attached antenna. The tag is tethered to the fish and the data logger is programmed to continually collect depth, temperature, and location for a specified duration (weeks to months). At the end of the programmed time, a detachment mechanism is automatically activated that releases the data logger/float and antenna from the tether. The float carries the data logger to the surface where the antenna transmits the data to an orbiting satellite of the ARGOS System that then transmits data back to the researcher. Time series analysis will be employed to determine periodicity in depth profiles and relationships with other environmental parameters such as temperature. Data from this study will allow us to discern daily/weekly and monthly patterns in vertical positioning in the water column and will provide information on possible spawning locations.

Eelgrass as refuge: exploring diurnal distribution of bivalve larvae across habitats

Summary: To evaluate the distribution of Pacific oyster (Crassostrea gigas) and geoduck (Panopea generosa) larvae across eelgrass (Zostera marina) and unstructured habitats, and to quantify temporal and spatial variation in larval supply across sites in Puget Sound and the Washington coast through the collection of field data in targeted experiments. Results will assist scientists in developing stewardship recommendations to adaptively manage leased activities and wildstock geoduck harvest on State Owned Aquatic Lands.

Proteomic response of shellfish to environmental stress

Summary: Shellfish in Puget Sound face a changing environment, as climate change drives increased water temperature and ocean acidification results in decreased pH/Ωaragonite. Careful laboratory work has shown that shellfish demonstrate a sub-lethal response to these stressors, even when they exhibit no change in rates of survival or growth. This part of the project will measure when and where outplanted C. gigas and P. generosa show a sub-lethal response in protein expression and morphology across sites that span Washington waters. The results will shed light on the relative stress burden of C. gigas and P. generosa populations on SOAL, guiding future work on restoration priorities.

Effects of temperature change and Hematodinium sp. infection (Bitter Crab Disease) on Tanner crab (Chionoecetes bairdi)

Summary: Changing climate conditions, due to increasing releases of CO2 into the atmosphere, are causing warming of the world’s oceans. Changes in seawater temperatures are predicted to cause a shift in the distribution and a change in the abundance of most plants and animals. For most species, the magnitude of the impact, the potential for adaptation to future temperatures, and the mechanisms for adaptation are unknown. Features of parasite/disease ecology are also predicted to change as oceans warm, including susceptibility of hosts to disease, host ability to combat disease once infected, and alterations in pathogen virulence. Alaskan Tanner crab stocks, supporting fisheries worth $21 million in 2014, are expected to be significantly impacted directly and indirectly by warming temperatures. The Alaska Department of Fish and Game considers bitter crab disease, caused by a parasitic dinoflagellate, Hematodinium, to be the ‘principle threat’ to Alaskan Tanner crab stocks. Infection rates in the Bering Sea and southeast Alaska range from 2-5% and 0-100%, respectively. In heavily infected hosts, the meat is soft and chalky with a bitter taste, rendering the crabs unmarketable. The disease is believed fatal, although the time from infection to death remains uncertain. Recent worldwide spread of Hematodinium infections appears to have closely followed warming trends in the Atlantic and Pacific Oceans. We postulate that increased temperature in the North Pacific will physiologically stress Tanner crabs and also lead to increased prevalence of Hematodinium infections, either of which may lead to increased mortality in Tanner crabs. We propose to hold healthy and Hematodinium-infected Tanner crabs under different temperature regimes testing for a genetic response to infection and temperature. Our research will provide insight into the underlying mechanistic linkages between potential effects of climate change and important processes such as recruitment, growth and natural mortality on Alaskan Tanner crab stocks.

Aquaculture Resource Development

Engaging Students and Public in Marine Conservation through Sustainable Shellfish Aquaculture

Summary: The UW Shellfish Farm is a project conceived by several graduate students, faculty and staff at the School of Aquatic & Fishery Sciences (SAFS), in collaboration with the School of Marine & Environmental Affairs (SMEA) and the College of the Environment. We seek to establish a student-run shellfish farm at the Big Beef Creek Research Station, a SAFS field site on Hood Canal. The overarching goals of the project are:
1) Provide students and with a hands-on opportunity to experience sustainable seafood production.
2) Conduct outreach and education on estuarine health and climate change impacts on the marine environment.
3) Conduct monitoring to quantify environmental impacts of shellfish aquaculture on estuarine health.
4) Serve as a field site for ongoing shellfish research at UW.
5) Become self-sustaining by selling cultivated shellfish (e.g. clams, oysters) through wholesalers, UW dining establishments, a subscription service, and other outlets.
more info

A novel proteomic-based approach to identify and mitigate factors responsible for shellfish mortality events

Summary: The overall goal of this project is use a ‘bottom- up’ approach to investigate the process of Pacific oyster larval development. This includes identifying the most susceptible and environmentally sensitive stage of the setting process, characterizing the cause of mass mortalities, and providing guidance and advice for testing and altering culture practices that can obviate seed mortality. The effort includes a discovery-based proteomics approach to reveal critical differences in protein expression profiles between groups of Pacific oysters at three early life stages that are destined to die or survive. The identified suite of proteins will then be used in a targeted proteomics approach to develop a reproducible, quantifiable assay. The novel assay will be used to test specific hypotheses based on the response of Pacific oysters to their environment in hatchery and wild settings. An integrated collaboration between researchers, K-12 teachers, and students will build knowledge and increase connections among educators, the shellfish industry, and the scientific community. The specific research objectives of this project are to, 1a) Identify protein biomarkers indicative of Pacific oyster larvae mortality events, 1b) Characterize fundamental physiological changes in Pacific oyster larvae development, 2a) Develop targeted assay to query specific suites of proteins, and 2b) Perform the targeted assay on hatchery produced and wild Pacific oysters.

Characterization of SNPs in genes related to growth from transcriptomes of the flounder Paralichthys adspersus

Summary: Project: The main goal of this project is to: identify SNPs related to development and growth in larvae and juveniles of the flounder P. adspersus by the comparison of complete transcriptomes. The aims include 1) Characterize transcriptomes during early stages (larvae) of development, 2) Evaluate the transcriptome from different tissues of juveniles (of 6 months post hatching) under captivity with normal and low growth, and evaluate the expression patterns of genes associated with the growth of larvae compared to juveniles, and growth patterns, 3) Identify SNPs markers in genes associated with growth and its relationship to gene expression level, and 4) Validation and characterization of SNPs related to growth in different flounder families keep under controlled conditions.