Environmental RNA as a non-invasive tool for assessing toxic effects in fish: a proof-of-concept study using Japanese medaka exposed to pyrene

Abstract

Although environmental RNA (eRNA) is emerging as a non-invasive tool to assess the health status of aquatic macro-organisms, the potential of eRNA remains largely untested. In this study, we investigated the ability of eRNA to detect changes in gene expression in Japanese medaka fish (Oryzias latipes) in response to sub-lethal pyrene exposure, as a model toxic chemical. We performed standardized acute toxicity tests and collected eRNA from tank water and RNA from fish tissue after 96 h of exposure. Our results showed that over 1000 genes were detected in eRNA and the sequenced read counts of these genes correlated with those in fish tissue (r = 0.50). Moreover, eRNA detected 86 differentially expressed genes in response to pyrene, some of which were shared by fish RNA, including suppression of collagen fiber genes. These results suggest that eRNA has the potential to detect changes in gene expression in fish in response to environmental stressors without the need for sacrificing or causing pain to fish. However, we also found that the majority of sequenced reads of eRNA (> 99%) were not mapped to the reference medaka genome and they originated from bacteria and fungi, resulting in low sequencing-depth. In addition, eRNA, in particular nuclear genes, was highly degraded with a median transcript integrity number (TIN) of < 20. These limitations highlight the need for future studies to improve the analytical methods of eRNA application.