Research Paper

Rediscovering the lost: eDNA detection of freshwater decapods on Réunion Island

¹ OCEA Consult, 19 Chemin Anda, 97432, Ravine des Cabris, La Réunion, France
² Laboratoire de Biologie des Organismes et Écosystèmes Aquatiques (BOREA), Muséum National d’Histoire Naturelle, CNRS-8067, IRD-207, Sorbonne Université, UA, Equipe Biodiversité, Plasticité, Adaptation et Conservation, 75005, Paris, France
³ IRD (French National Research Institute for Sustainable Development), UMR ENTROPIE, 15 Avenue René Cassin, CS 92003, 97744, Saint-Denis Cedex 9, La Réunion, France

^* Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.

Received: 23 September 2025
Accepted: 22 December 2025

Abstract

Freshwater ecosystems on tropical oceanic islands host unique biodiversity. On Réunion Island, freshwater decapod crustaceans are key indicators of ecosystem health, yet their distribution and conservation status remain poorly documented. This study aimed to investigate the presence of the endemic prawn Macrobrachium hirtimanus, historically reported but unconfirmed for decades, while producing the first island-wide molecular inventory of freshwater decapods using environmental DNA (eDNA) metabarcoding. Water samples (4 L) were collected from 19 riverine sites, and eDNA was extracted and amplified using mitochondrial 16S rRNA primers validated for crustacean detection, followed by high-throughput sequencing. Bioinformatics analyses yielded 250,545 reads and 198 operational taxonomic units (OTUs), representing diverse amphidromous freshwater, coastal marine, and terrestrial decapods. Species richness was largely uniform across sites, though Rivière des Roches, Sainte-Marie, and Saint-Denis hosted higher diversity. Beta diversity showed strong spatial structuring among watersheds, driven primarily by species turnover. Widespread taxa included Atyoida serrata, Caridina typus, and Macrobrachium australe, while C. henriettae and Halocaridinides sp. were more localized. M. hirtimanus was not detected, consistent with its current absence, though continued targeted surveys are required before any formal reassessment. Overall, this study demonstrates the utility of eDNA metabarcoding for monitoring freshwater biodiversity and informing conservation planning on tropical islands.