Title : A preliminary assessment of marine biodiversity and crustacean assemblages in Mauritian seagrass habitats using environmental DNA metabarcoding
Abstract:
Seagrass ecosystems are productive marine habitats that support diverse communities, including crustaceans, which are often under-sampled because of their small size, cryptic behaviour and habitat complexity. Environmental DNA (eDNA) metabarcoding provides a non-destructive approach for detecting biodiversity through DNA released into the environment. This study presents the first published eDNA-based assessment of crustacean biodiversity in Mauritius, using a streamlined single-marker approach to characterise crustacean and broader biodiversity in seawater collected from two seagrass habitats, La Prairie and Poste La Fayette. Seawater samples were collected in three replicates per site, followed by DNA extraction, amplification using universal Folmer COI primers, and PacBio HiFi sequencing. Sequence data were processed using Galaxy and R workflows involving primer trimming, BLAST-based taxonomic assignment, duplicate removal and taxonomic validation against the World Register of Marine Species. Rank-specific thresholds of ≥80%, ≥90% and ≥97% sequence identity were applied for family/higher, genus and species-level assignments, respectively. At the species level, 322 and 281 unique assignments were obtained from La Prairie and Poste La Fayette, respectively. Crustacean analyses recovered 283 and 114 unique assignments at ≥80% identity, respectively, with 30 and 19 crustacean species-level assignments at ≥97%. Seventeen crustacean species-level assignments were shared between sites, with 13 unique to Poste La Fayette and two to La Prairie, yielding a Jaccard similarity of 0.53; broader biodiversity showed a Jaccard similarity of 0.64. Several assignments lacked previously documented Mauritius records and warrant independent validation. An assignment to Birgus latro, historically recorded but considered locally extinct in Mauritius, further highlights the need for cautious interpretation of unexpected eDNA detections. Overall, this proof-of-concept study provides a preliminary molecular baseline and supports further optimisation through complementary primers, reference-library development and increased sampling effort.
Keywords: Environmental DNA; metabarcoding; seagrass ecosystems; Mauritius; crustaceans; biodiversity
