Environmental DNA-RNA dynamics provide insights for effective monitoring of marine invasive species

The primary objective of this study was to investigate the in-situ persistence and decay rates of eDNA and eRNA shed from a model coastal marine non-indigenous species (NIS), Sabella spallanzanii (Gmelin, 1791), a large Mediterranean fanworm. This experiment was conducted using solute permeable dialysis bags as they allow water and dissolved constituents to flow through the sample, mimicking realistic environmental conditions, while preventing the passage of larger molecules or particles, including target eDNA and eRNA fragments. On June 11, 2021, the dialysis bags were filled with 500 mL of ambient marine water collected in the close vicinity of a visually observed S. spallanzanii population at the Viaduct marina, Waitemata Harbour (Auckland, New Zealand) and were deployed in the field for 24 hours and sampled periodically to study the dynamics of the eDNA and eRNA signal in situ. Additionally, to investigate the effects of sample transportation and storage conditions, a subset of bags was stored on ice for 24 hours, simulating conventional field storage conditions. To assess the composition of total eDNA, including the identification and analysis of S. spallanzanii-specific eDNA fragments, we performed adaptive sequencing and metagenomic analysis using long-read sequencing with Oxford Nanopore Technology MinION (Oxford Nanopore Technologies, UK). This understanding is crucial for refining survey interpretation and sampling design for effective environmental management. Note this experiment includes positive controls intentionally spiked with naked 100 ng/uL of S. spallanzanii DNA/RNA, and 9 bags were spiked with S. spallanzanii tissue (to mimic the heterogenetic complexity of eDNA and eRNA found in natural samples) suspended both on ice and in the harbor. Negative control bags were suspended in the harbour.