Spatial Complexity and Rare‐Taxon Turnover Structures Benthic Coral Reef eDNA Communities

2026/07/01 by Patrick K. Nichols, Peter B. Marko · 1 voice
Environmental Science · Biochemistry, Genetics and Molecular Biology · #Environmental DNA in Biodiversity Studies #Genomics and Phylogenetic Studies #Protist diversity and phylogeny

paper · doi:10.1111/mec.70479

openalex publication_date 2026/07/01 · openalex created_date 2026/07/28 · openalex updated_date 2026/07/31

Abstract

Environmental DNA (eDNA) metabarcoding has transformed spatial biodiversity assessments, although its capacity to distinguish persistent from dynamic elements of ecological communities through time remains largely unknown. We asked to what degree eDNA signals on coral reefs are temporally consistent representations of community composition or are dominated by short-lived fluctuations, and how this distinction influences interpretation of biodiversity data through time. We assessed these questions in Hawaiian coral reef communities over 2 years, replicated with two universal eDNA markers (nuclear 18S and mitochondrial COI). Our analyses revealed that community composition differed strongly among sites, while within-site assemblages were relatively stable through time. Despite high per-sample richness, a smaller core of reef taxa, including sponges, annelids, and red algae, were consistently detected across sites and sampling dates, indicating that eDNA reliably captures dominant community members despite natural variability in DNA production, degradation, and transport. This core assemblage anchored site distinctiveness, while temporal variation was driven by the appearance and disappearance of a comparatively large number of rare or transient taxa. This temporal variation was detectable but smaller in magnitude and associated with environmental factors such as wind, waves, tides, and lunar cycles, highlighting their role in modulating patterns of taxon detectability. Overall, eDNA signals primarily reflect underlying spatial heterogeneity rather than transient fluctuations, demonstrating that routine eDNA surveys can robustly track community dynamics across space and time. By identifying the ecological and environmental correlates of eDNA signal variation, our study demonstrates that spatially structured community differences dominate eDNA profiles on coral reefs and allow persistent biodiversity patterns to be distinguished from short-term temporal variability. Although eDNA integrates biological and physical processes distinct from direct observation, the resulting patterns are highly similar to those generated by visual reef surveys, in which strong site-level differentiation is maintained by a small set of persistent taxa, while a large pool of rare species contributes to transient variability. The convergence between molecular and observational approaches links eDNA-derived biodiversity patterns to underlying community assembly processes and enhances ecological interpretation of molecular data in tropical reef ecosystems.

Citations

• The Commonness, And Rarity, of Species
• Reproduction and recruitment of corals: comparisons among the Caribbean, the Tropical Pacific, and the Red Sea
• Temporal and spatial scaling of planktonic responses to nutrient inputs into a subtropical embayment
• Conceptual Synthesis in Community Ecology
• Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity
• A numerical study of circulation in a coastal reef‐lagoon system
• The role of cryptobenthic reef fishes in coral reef trophodynamics
• Long-term datasets in biodiversity research and monitoring: assessing change in ecological communities through time
• Novel ecosystems: implications for conservation and restoration
• Vegetation of the Siskiyou Mountains, Oregon and California
• Motile cryptofauna of a coral reef: abundance, distribution and trophic potential
• Ecological interactions of marine sponges
• Mechanisms of Maintenance of Species Diversity
• Quantifying the impact of watershed urbanization on a coral reef: Maunalua Bay, Hawaii
• The Problem of Pattern and Scale in Ecology: The Robert H. MacArthur Award Lecture
• EnvironmentalDNAmetabarcoding of lake fish communities reflects long‐term data from established survey methods
• Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
• Reef sponges facilitate the transfer of coral-derived organic matter to their associated fauna via the sponge loop
• Environmental DNA Time Series in Ecology
• Coral species composition drives key ecosystem function on coral reefs
• Autumn coral bleaching in Hawai‘i
• Interdisciplinary analysis of larval dispersal for a coral reef fish: opening the black box
• A tiny fraction of all species forms most of nature: Rarity as a sticky state
• Macroalgae traits and seasonality as drivers of polychaete assemblages on macroalgae of tropical sandstone reefs
• Scalable semantic 3D mapping of coral reefs with deep learning
• A systematic review evaluating the performance of eDNA methods relative to conventional methods for biodiversity monitoring
• Scalable Semantic 3D Mapping of Coral Reefs with Deep Learning
• The ecology of environmental DNA and implications for conservation genetics
• Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies
• Spawning dynamics in the Hawaiian reef-building coral Montipora capitata
• Hydrodynamics of a bathymetrically complex fringing coral reef embayment: Wave climate, in situ observations, and wave prediction
• Monitoring of biological diversity in space and time
• Biodiversity change is uncoupled from species richness trends: Consequences for conservation and monitoring

Discussions

• 2 yrs of eDNA on Hawaiian reefs shows a persistent core (sponges, annelids, algae) anchors site identity. Rare taxa drive temporal noise (wind/waves/tides). eDNA = stable communities, not just transie [bsky, 0 points, 0 comments]