Abstract
Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07% of the taxa detected by a broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean.
Highlights
Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts
We test the efficacy of a broad metazoan Environmental DNA (eDNA) metabarcoding survey in tropical marine environments and validate the approach with an established visual survey protocol [i.e., Reef Life Surveys (RLS)32] for fish
The objectives of our study were to 1) examine patterns of community composition for metazoans using eDNA and 2) validate the resolution of a broad c. oxidase subunit I (COI) metazoan primer by comparing the subset of fish taxa detected by eDNA to those identified in traditional visual fish surveys and previously assembled taxonomic lists of reported species
Summary
Rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Few marine studies, have explicitly tested whether broad range eDNA surveys potentially targeting all metazoans simultaneously in a single PCR assay could effectively detect fine-scale patterns of community composition in spatially heterogeneous coastal seascapes[22,28,29,30] None of these studies attempted validation with visual surveys on subsets of the sampled communities, and just one was conducted in the tropics[30]. The semi-enclosed Almirante Bay in the Bocas del Toro archipelago on the Caribbean coast of Panama is an ideal system for testing the ability of eDNA to capture fine-scale patterns of marine diversity It contains all the primary tropical coastal habitats including coral reefs, seagrass meadows, mangrove forests, sandy unvegetated bottoms, and human-made structures, each with distinct communities that are in close proximity, forming a heterogeneous seascape[38,39]. Almirante Bay has served as a natural laboratory for numerous ecological studies utilizing visual survey and experimental methods to look at the response of coral reefs and associated reef fauna to anthropogenic and environmental stressors[43,44,45,46,47]
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