Impact of CO2-Induced Aquatic Acidification on Environmental DNA and RNA Shedding and Persistence

Anticipated future increases in CO₂ levels are predicted to have a diverse array of lethal and non-lethal effects on the marine ecosystem. While there has been extensive research on the physiological impacts of ocean acidification on marine species, our understanding of how increasing levels of carbon dioxide affect the shedding and decay of environmental DNA and RNA (eDNA/eRNA) in marine habitats is limited. This may impede the effective adoption of environmental nucleic acid–based molecular tools for monitoring marine biodiversity and detecting rare or invasive species. In the present study, we conducted mesocosm experiments to determine the shedding and decay rate constants of eDNA and eRNA in M. gigas (Magallana [Crassostrea] gigas) using mitochondrially encoded tRNA leucine 1 (mt-tl1) marker at various partial pressures of CO₂ in seawater. To our knowledge, this is the first study manipulating seawater pH using CO₂. We developed a sensitive and specific quantitative PCR-based assay to detect M. gigas eDNA and eRNA. Higher CO₂ levels increased shedding rates, indicating greater organism stress and biological effects on oysters. Additionally, increased CO₂ accelerates DNA and RNA decay, suggesting that ocean acidification may impact the reliability of eDNA-based biodiversity monitoring. Furthermore, eRNA displayed lower steady-state concentrations and a shorter persistence time in comparison to eDNA, as is consistent with known biochemical properties of the molecules. These findings are presented in the context of previous work that adjusted pH through acid–base adjustment and temperature and highlight the importance of considering ocean acidification caused by differing CO₂ levels when using molecular tools for marine conservation and fisheries management.