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Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica)

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Abstract

Ocean acidification (OA) is a major stressor threatening marine calcifiers, including the eastern oyster (Crassostrea virginica). In this paper, we provide insight into the molecular mechanisms associated with resilience to OA, with the dual intentions of probing both acclimation and adaptation potential in this species. C. virginica were spawned, and larvae were reared in control or acidified conditions immediately after fertilization. RNA samples were collected from larvae and juveniles, and DNA samples were collected from juveniles after undergoing OA-induced mortality and used to contrast gene expression (RNAseq) and SNP (ddRADseq) profiles from animals reared under both conditions. Results showed convergence of evidence from both approaches, particularly in genes involved in biomineralization that displayed significant changes in variant frequencies and gene expression levels among juveniles that survived acidification as compared to controls. Downregulated genes were related to immune processes, supporting previous studies demonstrating a reduction in immunity from exposure to OA. Acclimation to OA via regulation of gene expression might confer short-term resilience to immediate threats; however, the costs may not be sustainable, underscoring the importance of selection of resilient genotypes. Here, we identified SNPs associated with survival under OA conditions, suggesting that this commercially and ecologically important species might have the genetic variation needed for adaptation to future acidification. The identification of genetic features associated with OA resilience is a highly-needed step for the development of marker-assisted selection of oyster stocks for aquaculture and restoration activities.

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Data Accessibility

Sequence reads are deposited in the SRA NCBI database and can be found under the BioProject ID PRJNA765289.

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Acknowledgements

The authors would like to thank Marty Byrnes and Rebecca Resner of the Great Atlantic Shellfish Hatchery for providing access to their hatchery and logistical support. We would also like to thank the Marine Animal Disease Laboratory intern Margot Eckstein for help with bivalve maintenance. In addition, we would also like to thank Dr. Christopher Gobler and Andrew Lundstrom for processing DIC samples.

Funding

This research was funded by the New York Sea Grant (Projects R/XG-24 and R/XG-33 to Bassem Allam and Emmanuelle Pales Espinosa). Additional support was provided by the National Science Foundation (IOS 1656753) and the Atlantic States Marine Fisheries Commission (Contract 19–0802).

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Authors and Affiliations

  1. School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA

    Caroline Schwaner, Sarah Farhat, Michelle Barbosa, Denis Grouzdev, Emmanuelle Pales Espinosa & Bassem Allam

  2. Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France

    Sarah Farhat

  3. Station Biologique de Roscoff, CNRS/Sorbonne Université, Place Georges Teissier 29680, Roscoff, France

    Isabelle Boutet & Arnaud Tanguy

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  1. Caroline Schwaner
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Contributions

Caroline Schwaner contributed to formal analysis, investigation, methodology, and writing the original draft. Sarah Farhat contributed to formal analysis and manuscript revisions. Isabelle Boutet and Arnaud Tanguy assisted with investigation and methodology. Michelle Barbosa helped with investigation. Denis Grouzdev assisted with formal analysis. Emmanuelle Pales Espinosa helped with methodology, manuscript revisions, and funding. Bassem Allam provided funding, assisted with investigation, conceptualization, project administration, and reviewing and editing.

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Correspondence to Bassem Allam.

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Schwaner, C., Farhat, S., Boutet, I. et al. Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica). Mar Biotechnol 25, 997–1019 (2023). https://doi.org/10.1007/s10126-023-10255-y

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