Research in our lab focuses on characterizing physiological responses of marine organisms to environmental change. Using integrative approaches we strive to examine impacts and adaptive potential from the nucleotide to organismal level. A core component of this includes investigating the functional relationship of genetics, epigenetics, and protein expression. Three major themes of are current projects include Environmental Epigenetics, Reproductive Biology and Ecology, and Aquaculture Resource Development.

Environmental Epigenetics

Collaborative Research: URoL : Epigenetics 2: Predicting phenotypic and eco-evolutionary consequences of environmental-energetic-epigenetic linkages

Summary: Living organisms may acclimate to environmental changes through epigenetic modifications to DNA, which alter the way genetic instructions are interpreted without altering the DNA code itself. While these modifications to organismal phenotype or function can be reversible, some of them may be inherited by offspring, potentially producing multiple, heritable outcomes from a single genome and affecting ecological and evolutionary outcomes. This project uses symbiotic, metabolically complex reef building corals as a model system to test the connections between physiological, epigenetic, and metabolic states, and predict how population and community dynamics are influenced by epigenetically-modulated phenotypes. This work will advance biological knowledge by delineating fundamental links (Rules of Life) between ubiquitous organismal energetic processes, epigenetics, and eco-evolutionary outcomes. The Broader Impacts activities parallel the project’s integrative approach, linking insights from Environment x Energetics x Epigenetics x Ecology for Education into an E5 platform. The E5 platform will provide i) early career STEM training, ii) local and global community education, and iii) educational resources for open science, quantitative approaches, and research reproducibility. Further, this E5 platform will train and inform the next generation of diverse scientists and public by combining local and global initiatives focusing on groups underrepresented in STEM.

This project examines how nutrient metabolism in the mitochondria generates cofactors and energy that will instruct the epigenetic machinery in the cell nucleus to modulate genome function to appropriately respond to environmental conditions. Environmentally-responsive metabolic function and energetic-epigenetic linkages act as drivers of complex emergent phenotypes. To elucidate relationships that are the basis for Rules of Life with respect to epigenetics, this project will use integrative experimental and modeling approaches focused on reef building corals to: 1) link nutritionally-provisioned metabolites with epigenetic and organismal state through seasonal sampling across environmental gradients; 2) expand current Dynamic Energy Budget (DEB) models for symbiotic organisms to further integrate critical facets of nutritional symbiosis and calcification; 3) experimentally modulate metabolic and therefore epigenetic states through repeated exposure to increased temperature and nutrients, to test intra- and trans-generational epigenetic inheritance; 4) use DEB theory to identify shifts in energetics associated with epigenetic modulation, and link these sub-organismal processes to higher levels of organization; and 5) integrate findings into a generalizable, predictive eco-evolutionary model that links nutritional interactions, metabolic states, and subsequent epigenetic effects to the timescales regulating organismal processes and eco-evolutionary outcomes. This effort will provide characterization of environmental epigenetic phenomena in ecosystem-engineering marine invertebrates. This characterization includes determining the mechanisms and the degree of epigenetic ‘memory’ both within and across generations. By including information on environmental legacies, propagated by epigenetics, this project will advance both organismal and population-based models and improve capacity to predict responses to acute and chronic environmental signals.

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.

Improving 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.

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.

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

Development of environmental conditioning practices to decrease impacts of climate change on shellfish aquaculture

Summary: The project will be completed using commercial hatchery rearing of geoduck clams. We will test and implement shellfish performance enhancement methods through the use of environmental stressor preconditioning, or “hardening”. The objectives of this work are to A) Identify key stages in the geoduck life cycle when environmental conditioning can be applied for optimal benefits to productivity, including: – Broodstock conditioning and reproductive performance, – Larval growth and survivorship, and – Juvenile resistance to stress through repeated exposures, B) Use genomics and epigenomics to identify underlying mechanisms involved in enhanced performance. This will provide mechanistic information that enables the application of optimal preconditioning approaches in other shellfish species.
This project directly addresses the research topics of genomics, quantitative genetics, and phenomics in the less studied, yet viable, geoduck clam. The proposed work is based on our group’s prior finding that some exposure to low pH conditions can improve larval and juvenile performance traits. The research proposed will integrate and further test these findings in a commercial shellfish hatchery setting and determine the genetic and epigenetic markers associated with improved performance. In addition, we will explore how the “memory” of prior exposure increases later performance such that epigenetic markers could be leveraged in broodstock management and hatchery practices. A number of phenotypes will be assessed, as well as the underlying genomic factors, including fecundity, survival, and growth.

CaligusLIFE: Scientific research of excellence towards understanding sea lice biology and its application in control strategies for the salmon industry

Summary: This project will address specifically the generation of new knowledge in the areas of the Biological Cycle of Caligus and Genomics. The aim is to identify those environmental and genetic factors that significantly impact the life cycle of Caligus. This information will be used to generate mathematical models that calculate fecundity and production of Caligus and describe the spatio-temporal patterns of dispersion that explain the observed patterns of infestation in the field. The genomic part will include wide genome sequencing (WGS), assembly and functional annotation of Caligus and epigenomics.

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