Effects of Ocean Acidification on Marine Mussels: A Transcriptomic Approach Using Next Generation Sequencing

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Michael Lesser UNH - Department of Biological Sciences Principal Investigator
Daniel Brazeau University of New England Collaborator
Proposed Research
We have conducted two laboratory acclimation experiments on the effects of ocean acidification on two species of marine mytilid mussels: Mytilus edulis from the Gulf of Maine and Brachidontes exustus from the Bahamas. Both species were acclimated at pCO2 concentrations of 380 (pH 8.15), 560 (pH 7.91) and 970 (pH 7.7) ppm that reflect current and predicted CO2 concentrations in the year 2100 under both stabilized (B1) and a “business as usual” (A1F1) emission scenarios for 10-14 days. Initially, replicate samples (N=3) from the M. edulis experimental treatments will be processed by extracting total RNA, creating cDNA libraries for each individual using RNAseq techniques and submitting these libraries for sequencing using Illumina technology (see below). A unique feature of this approach is that not only will we be able to quantify the changes in gene expression in mussels from the different treatment groups, we will simultaneously be able to quantify any change in the bacterial communities associated with these mussels. A bioinformatics pipeline has been developed by my students and will be used to examine the treatment effects of the different ocean acidification exposures and the molecular responses of mussels at the transcriptome level (mRNA transcripts that lead to functional proteins), which will entail quantifying the response of thousands of genes and cataloguing them into functional groups. In particular, those genes involved in calcification, oxidative stress, intermediate metabolism and DNA damage will be quantified for differences in expression between treatment groups. 
This project is consistent with the 2011-2013 New Hampshire Sea Grant Strategic plan under the “ Hazard Resilience in Coastal Communities” and “Healthy Coastal Ecosystems” components of that plan. It will provide the data required for a full Sea Grant proposal in both an applied context of mussel aquaculture and for funding from federal agencies such as the National Science Foundation (Ocean Acidification solicitation) as mussels are critical ecological components of the rocky intertidal. Additionally, these techniques can readily be applied to other ecologically and commercially important species bivalve species such as soft-shell clams (Mya arenaria), hard clams(Mercenaria mercenaria)and oysters (Crossastrea virginica) in the future. Comparative studies at the molecular levels using next generation sequencing holds the best opportunity to identify critical pathways affected by ocean acidification that have not been identified as of yet, and potentially reveal important genetic markers that could be used to identify the effects of ocean acidification on product quality (e.g., decrease in tissue biomass) leading to specific action (e.g., harvesting and/or remediation in land based facilities with normal pH seawater) by those involved in mussel aquaculture.
2014 Accomplishment
NH researchers assess, annotate genetic transcripts for clams and mussels to determine impacts from ocean acidification
Ocean acidification is a concern for many marine organisms, particularly bivalve mollusks such as clams and mussels because low pH affects their ability to build hard carbonate shells. In addition to decreased calcification, a number of other negative impacts have been observed including an increase in oxidative stress that can damage critical macromolecules such as DNA. In 2014, N.H. Sea Grant-funded researchers assembled and annotated genetic transcripts for soft-shelled clams and blue mussels. These transcriptomes will help scientists to quantify differences in gene expression to better understand the role that ocean acidification is having on the genetics and recruitment of these two species.