From storms to warming seas: a long-term metabarcoding survey reveals seasonal dynamics and genetic resilience of non-indigenous species in port communities

Ports are key gateways for the introduction and spread of non-indigenous species (NIS), yet the ecological and genetic temporal dynamics of these introductions remain poorly understood. Long term temporal monitoring is essential to unravel invasion processes, anticipate biodiversity shifts, and inform effective management and biosecurity strategies. In this study, we conducted a five-year (2019-2024) monthly metabarcoding survey in a northwestern Mediterranean port using artificial collectors. By sequencing a fragment of the Cytochrome Oxidase I gene, we identified 2,190 metazoan Molecular Operational Taxonomic Units (MOTUs), including 75 NIS, while another 338 MOTUs were identified as native species. In addition, we examined both interspecific temporal patterns and intraspecific trends of genetic diversity over time. A strong seasonal component was detected in community composition and structure, both for the whole dataset and for the NIS and native species datasets. Although NIS accounted for only 3.4% of total species richness, they represented ca. 26% of total read abundance, underscoring their strong influence on community structure. Interestingly, NIS had a significantly more homogeneous species composition through time than native species. In 2020, the passage of the Gloria storm reshaped community dynamics, triggering a temporary rise in species richness and MOTU counts, likely due to an influx of native taxa, and a marked decline in NIS abundance. Genetic analyses revealed that NIS exhibited higher haplotypic diversity and lower genetic differentiation than native taxa, suggesting sustained gene flow, potentially facilitated by maritime transport. MOTUs with longer temporal persistence, particularly among NIS, also showed greater intraspecific diversity, supporting the “insurance hypothesis” and highlighting the role of genetic variability in resilience and invasion success. Overall, our findings showed that NIS, despite their low species richness, maintain high abundances, connectivity, and genetic diversity over time. These attributes likely enhance the NIS ability to persist in dynamic and disturbed port environments, and provide key information for understanding the invasion process. This study highlights the need to integrate genetic diversity metrics into marine biomonitoring assessments and management.