Multi-Method Approaches to Assess Fish Assemblages and Community Structure in Temperate Mesophotic Reef EcosystemsUnderexplored Reefs

Alejandro Perez Matus^1,2,3, Evie Wieters^1,2,3, Miriam Fernandez^1,2,3, Sergio Navarrete^1,2,3, Pablo Saenz-Agudelo^4,3, Mauro Zucconi³

¹Pontificia Universidad Católica, Chile - ²Estación Costera de Investigaciones Marinas (ECIM), Chile - ³Millennium Nucleus for the Ecology and Conservation of Temperate Mesophotic reef ecosystem, Chile - ⁴Universidad Austral de Chile, Chile

Temperate mesophotic reef ecosystems harbor rich biodiversity and provide essential ecosystem services, yet they are increasingly threatened by anthropogenic pressures such as overfishing, habitat degradation, and climate change. To effectively manage and conserve these ecosystems, robust methodologies are required to assess fish biodiversity and community dynamics. In this study, we compared multiple sampling methodologies—including environmental DNA (eDNA) metabarcoding, Baited Remote Underwater Video Systems (BRUVs), Diver-Operated Video Systems (DUVS), and rebreather diving visual censuses—to evaluate their effectiveness in capturing the diversity and structure of fish communities in temperate reef environments. Fieldwork was conducted in key temperate reef locations along the Chilean coast, where each method was applied to assess fish richness, abundance, and community composition across varying depths (up to 60m) and habitat types. Results indicate that each methodology has distinct advantages and limitations: eDNA was highly effective in detecting cryptic and rare species, BRUVs provided unique insights into the behavior of mobile carnivorous species, and DUVS and visual censuses excelled in capturing species richness and community complexity at shallow to mid-range depths. The integration of these methods revealed complementary datasets that collectively enhanced our understanding of fish biodiversity and habitat associations. Additionally, we observed significant spatial variability in community composition, emphasizing the need for localized management strategies. This study highlights the critical importance of adopting multi-method approaches to improve the accuracy and reliability of biodiversity assessments in temperate reef ecosystems. Our findings underscore the potential for these methodologies to inform conservation policies and marine spatial planning, particularly in regions facing mounting environmental pressures. By leveraging the strengths of diverse sampling techniques, researchers and practitioners can achieve more comprehensive and actionable insights into the dynamics of the unknown mesophotic temperate reef ecosystems.