Express yourself – Assessing taxonomic diversity and functional gene expression of subtropical shallow water coral reefs based on environmental RNA

• Applicant: Dr. Fabian Gösser
• Subject Area: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 533095333

Subtropical and tropical shallow-water coral reefs are strongly influenced by human activities and environmental changes, resulting in changes in reef biota known as "phase shifts". Okinawa, an island in southern Japan, is particularly affected by anthropogenic stressors. While some aspects of coral reef diversity in Okinawa are well studied, knowledge of many other reef taxa and their response to deteriorating environmental conditions is limited. To better understand reef ecosystems and their responses to environmental change, information on taxon-specific diversity indices is critical. Environmental DNA (eDNA) has proven to be a valuable tool for assessing biodiversity but may be limited in the precise temporal resolution of biodiversity and may not adequately reflect short-term community changes in highly dynamic ecosystems such as coral reefs. Environmental RNA (eRNA) may be a promising alternative or complement, as it is both suitable for determining taxonomic diversity and provides higher temporal resolution of the actual active community of organisms. In addition, preliminary work suggests that eRNA may also be suitable for analyzing functional gene expression of a whole habitat, which could provide insight into the health status of coral reefs.However, the applicability of eRNA at coral reefs has not been adequately explored. Therefore, this project will investigate the potential of eRNA as a universal tool for biodiversity studies on coral reefs. The goal is to compare the effectiveness of eDNA and eRNA methods in detecting the biodiversity and to determine which method is better suited to detect short- and long-term community changes. In addition, the potential of eRNA expression profiles to assess the health status of coral reef ecosystems will be investigated. To this end, water samples will be collected at different time points from coral reefs along a previously described anthropogenic stress gradient. These coral reefs have been previously analyzed using visual methods and eDNA to determine the dominant reef communities. Water samples will be analyzed using established workflows for eDNA metabarcoding and newly developed methods for eRNA, where eDNA and eRNA will be co-extracted. Extracted eRNA will be transcribed into cDNA, and both eDNA and cDNA will be analyzed with an 18S rRNA marker to compare taxonomic resolution. In addition, extracted eRNA will be subjected to RNA-sequencing to screen emRNA for differential gene expression and explore the potential of this method for assessing the health status of coral reefs.

• DFG Programme: WBP Fellowship
• International Connection: Japan
• Host: Professor James Davis Reimer, Ph.D.