IdentiFISH: implementation of novel molecular tools for monitoring mangrove fish communities

Tropical mangroves provide several ecosystem services that make them essential for ocean and coastal communities, while still representing one of the most threatened ecosystems on the planet. It is therefore a priority to monitor their biodiversity for good conservation practices, particularly in strong data-lacking areas such as the Maldives. The most common characterization and monitoring tools applied to mangrove habitats are often time- and resource- intensive, while also requiring substantial economical input. Environmental DNA (eDNA) presents itself as a valid alternative for quick and easy assessments: a whole community presents itself in a drop of water. Refinement and improvement, as well as vast application in mangrove habitats, are still required. Taxonomic resolution is often limited to higher taxa, due to commercial primers targeting only small fragments of genetic material. In this study, we improved the resolution of the method by designing tropical fish-specific primer pairs that target longer fragments of mitochondrial DNA (approx. 2kb) and can be used to distinguish the fish source down to species level. Alongside improved primers, novel sequencing techniques such as Oxford Nanopore Technologies will be applied for the identification of fish species present in mangrove embayments, to provide a portable, fast and comparatively cheap new tool that will significantly decrease sample processing times, often impairing when battling with DNA quick degradation. The combination of new molecular technologies will represent a step forward in habitat assessment and provide baseline data that will be provided to local communities to implement successful conservation practices.