Uncovering the Secrets of Coral Reef Biodiversity: Using Environmental DNA (eDNA) to Assess Diurnal and Nocturnal Shifts in the Florida Keys

Caribbean coral reefs, particularly those in the Florida Keys, are experiencing significant degradation driven by anthropogenic stressors. The most prominent of these is the phase-shift from coral-dominated to macroalgae-dominated ecosystems. These ecosystems are shaped by complex ecological interactions among reef organisms, with community composition varying between day and night. Many reef species exhibit different behaviors or become cryptic at night, leading to biases in traditional visual surveys and incomplete biodiversity assessments.
Environmental DNA (eDNA) has emerged as a transformative tool for biodiversity monitoring. This non-invasive molecular technique captures genetic material (e.g., skin cells, mucus) shed by organisms into their environment, enabling the detection of species presence and the identification of cryptic or elusive species that traditional survey methods might miss. While eDNA has been successfully applied in terrestrial and freshwater ecosystems, its use in marine environments, particularly coral reefs, remains an evolving field.
This study represents a novel application of eDNA to explore temporal variations in biodiversity on coral reefs, focusing on differences between diurnal and nocturnal periods in the Florida Keys. The primary objectives of this research are: (1) to investigate potential differences in eDNA profiles between day and night sampling, and (2) to complement traditional visual surveys with genetic data, potentially uncovering hidden species that might otherwise be overlooked. Water samples were collected from 13 reefs across the northern Florida Keys, using a Smith-Root eDNA backpack sampler, during both daylight and nighttime. Samples were filtered through self-preserving filters and analyzed by Jonah Ventures for DNA extraction and sequencing. Three genetic markers (16S, 18S, and COI) were used to characterize biodiversity across samples.
This study is innovative in its approach to understanding the full extent of biodiversity on coral reefs by integrating both temporal and genetic dimensions. The comparison of eDNA profiles between day and night sampling periods not only highlights the limitations of current eDNA practices but also underscores the necessity of accounting for temporal biodiversity shifts in monitoring efforts. By facilitating biodiversity assessments during nocturnal periods—when many species are most active—our approach aims to enhance the accuracy and completeness of biodiversity data. Furthermore, by generating genetic data from a broad spectrum of species, including those that are nocturnal or cryptic, this study will contribute to expanding eDNA reference libraries. A more comprehensive reference library enables more accurate species identification, which is essential for improving the reliability and scope of future eDNA studies across diverse marine ecosystems. This is critical for more effective conservation and management of vulnerable coral reef ecosystems.
Incorporating eDNA into coral reef monitoring offers a holistic, less invasive, view of species diversity and ecosystem health, providing insights that can inform restoration efforts and conservation strategies. By addressing the often-overlooked nocturnal component of reef biodiversity, this work contributes to a more nuanced understanding of ecosystem dynamics. Ultimately, this research will help refine eDNA methodology in marine environments and guide more targeted conservation and management practices for the coral reefs of the Florida Keys, and similar ecosystems globally.