Next-Gen gene sequencing to understand effects of ocean acidification on Alaskan crab and fish

Chris Long - NOAA/NMFS Alaska Fisheries Science Center

Using next-generation sequencing techniques to assess adaptive capacity and illuminate mechanisms underlying the effects of high pCO2 on Alaskan crab and fish species

Why we care
Many economically important crab and fish species are negatively affected by exposure to ocean acidification predicted to occur throughout their ranges in the coming decades. Ocean acidification results in decreased growth, altered development, weaker exoskeletons, increased energy outputs, altered immune systems, altered behavior, and increased mortality in some of these species. Other stressors such as increased temperature can have interactive negative effects when combined with ocean acidification. Traditional laboratory experiments cannot duplicate the gradual changes that will affect species populations over multiple life-history stages and generations, so using next-generation genetic approaches provide insight into effects beyond specific life stages.

What we are doing 
This study will use next-generation sequencing techniques to identify specific alterations in the molecular, metabolic, and physiological pathways of individuals exposed to ocean acidification. This is a way to identify pathways that impart tolerance to ocean acidification and warming. This project determines the effect of ocean acidification and thermal stress on gene expression in Pacific cod larvae and juvenile Tanner crab and identifies genetic markers indicating ocean acidification resilience. 

Benefits of our work
Investigators will identify the cellular pathways that impart tolerance to ocean acidification. By comparing individuals that demonstrate low sensitivity to ocean acidification and with the general population, we enhance the ability to predict how adaptation will alter the species’ response to future ocean conditions. This research will inform the fishing industry and coastal, fisheries-dependent Alaskan communities about potential effects of ocean change on commercially important species. Outcomes can be used to drive future responses and adaptations in these industries regarding affected fisheries.

Thursday, May 26, 2022

Tracking Ocean Alkalinity using New Carbon Measurement Technologies (TAACT)

Joe Salisbury

This project will expand the quantity and quality of ocean acidification (OA) monitoring across Northeastern U.S. coastal waters. The new OA data and incorporation of the world’s first commercial total alkalinity (TA) sensor into our regional observing system (NERACOOS) are designed to supply needed baseline information in support of a healthy and sustainable shellfish industry, and to aid in assessments and projections for wild fisheries. In working with partners to develop this proposal, clear concerns were brought forward regarding the potential impacts of increasing ocean acidity that extend from nearshore hatcheries and aquaculture to broader Gulf of Maine finfish and shellfish industries and their management. Stakeholder input and needs shaped the project scope such that both nearshore and offshore users will be served by TA sensor deployments on partner platforms, including time series data collection at an oyster aquaculture site, on the NOAA Ship of Opportunity AX-2 line, and on federal and State of Maine regional fish trawl surveys. In all, five different deployment platforms will be used to enhance ocean acidification monitoring within the Northeast Coastal Acidification Network (NE-CAN) with significant improvement in temporal and spatial coverage.

 Adding the all-new TA measurement capability to the regional observation network will provide more accurate, certain, and reliable OA monitoring, and an important project objective is to demonstrate and relay this information to regional partners. Data products to be developed from the multi-year measurements include nearshore and offshore baseline OA seasonal time series as well as threshold indices tied to acidification impacts on larval production at the Mook Sea Farm oyster hatchery. An outreach and technical supervision component will include the transfer of carbonate system observing technologies to our partners and to the broader fishing industry, resource management, and science communities. NERACOOS will provide data management and communication (DMAC) services and work towards implementing these technological advances into the IOOS network.

Wednesday, January 25, 2017
Categories: Projects

Interactions between ocean acidification and eutrophication in estuaries: Modeling opportunities and limitations for shellfish restoration

Jeremy Testa, University of Maryland Center for Environmental Science (UMCES) Chesapeake Biological Laboratory

The objective of this project is to make significant strides in bridging the gap between scientific knowledge and current management needs by integrating existing biogeochemical model frameworks, field measurements, and experimental work toward the goals of (1) delineating atmospheric and eutrophication drivers of Chesapeake Bay acidification and improve our understanding of estuarine carbonate chemistry, (2) developing a spatially explicit framework to identify shellfish restoration areas most and least prone to acidification impacts, and (3) better understanding feedbacks associated with future environmental conditions and shellfish restoration goals estuary-wide and within a model tributary. This effort includes (1) a field campaign to make the first comprehensive study of the spatial and temporal variability in the carbonate system in Chesapeake Bay, (2) experiments to quantify both carbonate and nutrient exchange between intact oyster reefs and the surrounding water while measuring response of these fluxes to reef structure and acidification, and (3) an advancement in numerical modeling tools to simultaneously simulate the dynamics of eutrophication, hypoxia, carbonate chemistry, and oyster reef growth and interaction with the water-column under present and future conditions.

Wednesday, January 25, 2017
Categories: Projects

Flexing mussels: Does Mytilus edulis have the capacity to overcome effects of Ocean Acidification?

Dianna K Padilla, Stony Brook University

We are likely to see "winners", those species or individuals that are most resilient in the face of climate change, and "losers" those species or individuals that are least capable of robust performance under stressful conditions.  At present, we cannot predict winners and losers, and do not know whether responses to environmental stress are primarily driven by phenotypic plasticity, broad performance under different environmental conditions, or if there are genetic or epigenetic factors that can result in cross-generational directional changes in populations, resulting in more resilience under stressful conditions of OA.   This project has two objectives: 

1)  To test for cross-generational adaptation to the impacts of increasing ocean acidification on blue mussels, either through phenotypic acclimation or through heritable changes. 

2)  To determine if there are tradeoffs in growth and development across life stages in response to stress induced by ocean acidification in blue mussels.\

The results of our experiments can then be used to develop management practices for wild populations and more robust aquaculture practices for blue mussels. From an aquaculture perspective, if animals from certain source populations are more resilient to OA stress, those locations could be targeted for collection of wild seed that will produce resilient mussels in aquaculture leases.  Furthermore, the environmental characteristics of these advantageous site(s) could then be characterized to predict other sites that may also produce resilient mussels.  Overall, the data obtained from this proposed work could be used to enhance mussel culture, an economically important activity of growing importance in our region.

Wednesday, January 25, 2017
Categories: Projects

Sensitivity of larval and juvenile sand lance Ammodytes dubius on Stellwagen Bank to predicted ocean warming, acidification, and deoxygenation

Hannes Baumann, University of Connecticut

This proposal will quantify the sensitivity of a key forage fish in the Northwest Atlantic to the individual and combined effects of the major factors comprising the ocean climate change syndrome: warming, acidification, and deoxygenation. We will rear embryos of Northern sand lance Ammodytes dubius, obtained by strip-spawning wild adults from the Stellwagen Bank National Marine Sanctuary (SBNMS) through larval and early juvenile stages in a purpose- built factorial system at different factorial combinations of temperature, CO2 and oxygen.

Our first objective is to quantify individual and combined effects of temperature × CO2 (year 1) and temperature × CO2 × DO (year 2) on A. dubius growth and survival. We hypothesize that warming in combination with high CO2 (low pH)  will have additive or synergistically negative effects, whereas the addition of low DO as a third stressor will have stark, synergistically negative effects on all traits. Our second objective is to characterize the swimming behavior of A. dubius larvae that have been reared under combinations of elevated temperature × CO2. We hypothesize that combined stressors will have synergistically negative effects on the development of larval sensory systems, which express themselves and can thus be quantified as changes in larval swimming behavior. Our third objective is to take advantage of the rare winter sampling activities for this project to quantify CO2, pH, and DO variability in benthic waters on Stellwagen Bank through bottle collections and short-term sensor deployments. We hypothesize that bottom water pH and DO levels during the sand lance spawning season might be routinely lower than levels in surface waters.

Wednesday, January 25, 2017
Categories: Projects

Probing molecular determinants of bivalve resilience to ocean acidification

Bassem Allam, Stony Brook University

The overall aim of this proposal is to identify molecular mechanisms and markers that segregate "Winners" from "Losers" in three regionally-important bivalve species. The proposed research will identify molecular markers and mechanisms associated with resilience to acidification in some of the most important bivalve species along the east coasts: the eastern oyster (Crassostrea virginica), the hard clam (Mercenaria mercenaria), and the blue mussel Mytilus edulis. Furthermore, identified genetic markers will be validated with the aim of providing the aquaculture industry with tools needed to produce superior crops.

We have three specific objectives:   

(1) To identify molecular processes involved in bivalve resilience to ocean acidification and to characterize genetic markers associated with resilience 

 (2) To  validate  the  ability  of  identified  markers  to  predict resilience towards acidification  

(3)   To determine the physiological cost of resilience   

This research has major implications for basic and applied science. It will determine molecular and physiological mechanisms and pathways involved in bivalve natural resilience to acidification and identify molecular features associated with resilience. This information is greatly needed for the management of wild fisheries and for the development of resilient varieties of aquacultured stocks. Resilient broodstocks will provide the industry with superior germline to face current and projected episodes of acidification in local waters.

Wednesday, January 25, 2017
Categories: Projects

Genetic and phenotypic response of larval American lobster to ocean warming and acidification across New England’s steep thermal gradient

Dr. Richard Wahle & Dr. David Fields, University of Maine & Bigelow Laboratory for Ocean Sciences

Co-PI's Wahle (UMaine) and Fields (Bigelow Laboratory) join Co-investigator Greenwood (UPEI) in this US-Canadian collaboration. The proposed study is designed to fill knowledge gaps in our understanding of the response of lobster larvae to ocean warming and acidification across lobster subpopulations occupying New England’s steep north-south thermal gradient. The research involves a comprehensive assessment of the physiological and behavioral response of lobster larvae to climate model-projected end-century ocean temperature and acidification conditions. We will address the following two primary objectives over the 2-year duration of the proposed study:

(1)  To determine whether projected end-century warming and acidification impact lobster larval survival, development, respiration rate, behavior and gene expression; and

(2)  To determine whether larvae from southern subpopulations are more resistant than larvae from northern populations to elevated temperature and pCO2.

Wednesday, January 25, 2017
Categories: Projects

Synthesis and understanding of ocean acidification biological effects data by use of attribute-specific, individual-based models

Chris Chambers, NOAA Northeast Fisheries Science Center

This project uses data from experimental studies on the biological effects of ocean acidification (OA), largely funded by NOAA's Ocean Acidification Program (OAP), to construct realistic population‐process models of marine finfish populations.  The models are of an individual‐ based model (IBM) category that use detailed biological responses of individuals to OA.  This tool synthesizes OA data in two different ways.  First, it accumulates and connects data through mechanistic relationships between the environment and fish life‐history.  Second, it allows exploration of the population‐level consequences of CO2 effects (the source of OA) which explicitly include population effects carried over from the highly sensitive early life‐stages (ELS).   This information is fundamental to understanding the community and ecosystem effects of OA on living marine resources.  

Project efforts are directed at two different, complimentary levels.   At the more detailed, specific level, winter flounder – an economically important, well‐studied fish of Mid‐Atlantic to New England waters – will be used as a model subject.  Prior studies on winter flounder, augmented by OAP‐funded experimental work at NOAA/NEFSC, will provide estimates of CO2 effects on key life‐history and ecological parameters (e.g., fertilization, larval growth, development, and survival).  An IBM previously developed by the PIs will be updated and expanded to include OA effects on these parameters.  The winter flounder OA‐IBM will be exercised by evaluating the responses of the ELSs of this species under multiple scenarios:  high average levels of CO2 representing future oceans in shelf habitats; high and variable CO2 depicting future inshore, estuarine habitats; and covariances of CO2 with other environmental stressors (e.g., warmer waters, hypoxia).  At a general level and applicable to other species, the project will develop a web‐based tool that allows users to add details from other marine finfish of the NE USA and OA‐affected processes as relevant OA data on those species become available. 

Wednesday, November 16, 2016
Categories: Projects

Testing critical population level hypothesis regarding OA effects on early life history stages of marine fish for the N.E. U.S.

Chris Chambers, NOAA Northeast Fisheries Science Center

The primary goal of our OA projects (NEFSC Howard Laboratory) is to understand the impacts of increased CO2 and acidity of ocean and estuarine waters on important finfish species of our region. Our tactical objectives during FY12-14 were to develop, test, and then implement an experimental system that allows for the estimation of impacts of high CO2 and associated increased acidity of marine waters on the ELS of economically and ecologically important finfish species important to the NE USA. In FY15-17 we are building upon investments in research capacity and knowledge, and our experiments are addressing higher order questions that fold very well into one of the goals of the Interagency Working Group on OA – undertaking research to examine species-specific and multi-species physiological responses including behavioral and evolutionary adaptive capacities. We have four higher level objectives for our FY15-17 studies. 

First, we are testing our hypothesis that the resilience of the individuals in a population is inversely related to the variability of the CO2 in the habitat the population occupies (see also, Murray et al. 2014). This evaluation is being done by conducting comparative experiments among winter flounder from separate and distinct source populations whose resident habitats differ in characteristic levels and stability in CO2. Second, we are evaluating the role of parental exposure in the resilience / susceptibility of offspring to elevated CO2 (Sunday et al. 2014, Malvezzi et al. 2015). For these transgenerational studies, we are using three different forage species (original intent was to use Atlantic cod broodstock housed at the University of Maine but logistics and staffing decisions there precluded our use of those fish). Third, we are expanding our synthesis and meta-analysis of biological effects of CO2 on finfish. Lastly, we continue our education and outreach efforts on OA themes by mentoring students, conducting surveys, and providing tours of our OA experimental facilities.

Wednesday, November 16, 2016
Categories: Projects