National Oceanic and
Atmospheric Administration
United States Department of Commerce



Using ‘omics to monitor fast-changing West Coast marine ecosystems

The California Current Large Marine Ecosystem is dramatically changing in response to climate change driven increases in warming, ocean acidification, and hypoxia. These combined impacts are exceeding tolerance thresholds for ecologically and economically important species with potentially severe consequences on marine communities and resources. Key to forecasting and predicting marine ecosystem responses to changing ocean conditions is our ability to link physiological stress to changes in population dynamics. However, such efforts have been hindered by the difficulty of scaling biodiversity monitoring, and the limited resolution of biological data to a handful of species and sites. We address this by directly linking stress responses, which occur on the gene, cellular and organismal level, to field observations of stress, distribution, and abundances. In essence establishing early-detection signals that can track in situ stress. We leverage the scientific advancements in characterizing underlying metabolic pathways through gene expression (transcriptomics) and cellular biological molecules (proteomics, metabolomics, etc.) to better understand acute stress responses in marine organisms. Furthermore, we leverage the rapid progress in environmental DNA (eDNA) approaches to provide higher resolution abundance estimates for both individual priority indicator species as well as phytoplankton and zooplankton communities.

PMEL Ocean Molecular Ecology group is driven by these questions: 1) What are the genetic, cellular, physiological, and organismal responses of priority indicator species under interactive  multi-stressor warming, ocean acidification, and hypoxia stressor effects? 2) Are population level changes in abundances and distribution indicative of physiological stress responses? 3) Does the cumulative stress response under multi-stressor exposure result in changes to phytoplankton and zooplankton communities? By combining a variety of biological endpoints, we aim to delineate the in situ thresholds of co-occurring warming, ocean acidification, and hypoxia stressors that result in individual organismal, population, and community level impacts. Such work has been completed by pairing the biological and environmental sampling of West Coast Ocean Acidification (WCOA) cruises, Washington Ocean Acidification Center (WOAC) cruises, and autonomous eDNA sampling in Olympic Coast National Marine Sanctuary (OCNMS). These sampling efforts provide widespread and seasonally resolved physiological and population responses of key species, including early life stages of Dungeness crabs, krill, and pteropods. 

Map of the 'Omics Groups West Coast sampling sites
West Coast sampling sites for Ocean Molecular Ecology

This work is accomplished by measuring species-specific stress responses with carbonate chemistry at key biological stations, partnering collaboratively with the PMEL Carbon group. We then link these stress responses to changes in abundances using a combination of traditional microscopy as well as targeted quantitative PCR (qPCR) and metabarcoding eDNA approaches. Together these results provide high resolution inventories of species-specific stress responses alongside changes in phytoplankton and zooplankton communiities across multi-stressor gradients. Additionally, we are conducting two marine mammal focused studies demonstrating the value of ‘omics approaches to characterize stress responses and population connectivity in important charismatic megafauna. First, we are combining gene expression and cellular biological molecules through multi-omics (transcriptomics, hormones, proteomics, etc.) characterization of whale species to measure species-level stress responses and provide baseline physiological characterizations prior to marine energy developments. Furthermore, we are working with the PMEL Acoustics program to we are linking population genomics and acoustics of blue whales to delineate populations and migration patterns of this endangered and charismatic species in response to a changing ocean.


Using ‘omics to monitor effects of rapidly changing oceans on Alaska and Arctic marine ecosystems

The Arctic is undergoing a complete restructuring under climate change with current observing systems struggling to track and predict these changes. Advancing conservation genomics techniques provide the necessary tools to perform such biodiversity assessments and characterize the underlying mechanisms and linkages that drive marine ecosystem responses. The PMEL Ocean Molecular Ecology group has focused on building an extensive spatial and temporal sampling within the region to characterize changes in harmful algal blooms, zooplankton, fish, and marine mammal assemblages. Following the same research goals outlined above, our efforts aim to strengthen NOAA ‘Omics capabilities to generate, interpret, and apply biomolecular assays needed to understand the impacts of climate driven warming, ocean acidification, hypoxia impacts on biological communities. Paired with traditional sampling efforts, environmental DNA (eDNA), autonomous samplers, genomics, and transcriptomics allows us to leverage extensive PMEL sampling efforts. We are working closely with PMEL Ecosystem and Fisheries-Oceanography Coordinated Investigations (EcoFOCI) and the Arctic Marine Biodiversity Observation Network (AMBON) to characterize how Arctic ecosystems are responding to a rapidly changing ocean.

Ultimately, our work serves to connect organismal and ecosystem response to the ongoing physical, chemical, and acoustics research, allowing PMEL to meet key NOAA mission priorities to improve prediction and management of our marine resources.