COI data from: Environmental DNA metabarcoding differentiates between micro-habitats within the rocky intertidal (Shea & Boehm, 2024)

Latest version published by United States Geological Survey on Jun 3, 2024 United States Geological Survey
Publication date:
3 June 2024
CC-BY 4.0

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This is mitochondrial Cytochrome c Oxidase I gene (COI) metabarcoding data of surface seawater metazoan communities from three distinct locations in the rocky intertidal, Pillar Point, Half Moon Bay, California, USA that were sampled over one tidal exposure period on 28 January 2022. This work is associated with a publication in Environmental DNA (

[This dataset was processed using the GBIF eDNA converter tool.]

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 160,114 records.

2 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.

Occurrence (core)

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How to cite

Researchers should cite this work as follows:

Shea M M, Boehm A B (2024). COI data from: Environmental DNA metabarcoding differentiates between micro-habitats within the rocky intertidal (Shea & Boehm, 2024). Version 1.5. United States Geological Survey. Occurrence dataset.


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The publisher and rights holder of this work is United States Geological Survey. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 9358fbd7-cfd0-4eab-99fa-0934396a0529.  United States Geological Survey publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF-US.


ENVIRONMENTAL DNA (eDNA) [4c0b1743-dfeb-4147-b89f-99386a370d42]; METABARCODING [c39bf4db-70d3-4921-bd5e-e7c390a980bb]; MARINE BIOLOGY [7dd847a0-47bf-466b-9bc8-c4fbe3dd8d3f]; COASTAL [ 47be68db-d10d-43e7-b150-61cfd3f06126]; MARINE ENVIRONMENT MONITORING [ca154e02-a226-4cc7-8e4a-4474e7eb1eeb]; Occurrence; Observation


Meghan M. Shea
  • Metadata Provider
  • Originator
  • Processor
  • Point Of Contact
PhD Candidate
Stanford University
Alexandria B. Boehm
  • Originator
  • Principal Investigator
Professor, Department of Civil and Environmental Engineering
Stanford University

Geographic Coverage

Pillar Point, Half Moon Bay, California, USA

Bounding Coordinates South West [37.495, -122.499], North East [37.495, -122.499]

Taxonomic Coverage


Kingdom Chromista, Fungi, Animalia, Protozoa, Plantae
Phylum Arthropoda, Nemertea, Haptophyta, Myzozoa, Zygomycota, Oomycota, Echinodermata, Mollusca, Ascomycota, Platyhelminthes, Bacillariophyta, Bryozoa, Rotifera, Annelida, Chordata, Rhodophyta, Amoebozoa, Chlorophyta, Cryptophyta, Porifera, Basidiomycota, Phoronida, Ochrophyta, Cnidaria
Class Dinophyceae, Palaeonemertea, Clitellata, Bolidophyceae, Pyramimonadophyceae, Polychaeta, Hexacorallia, Phaeophyceae, Aves, Mucoromycotina incertae sedis, Ascidiacea, Cryptophyta incertae sedis, Pycnogonida, Homoscleromorpha, Dothideomycetes, Gastropoda, Demospongiae, Bangiophyceae, Eurotatoria, Pilidiophora, Discosea, Pelagophyceae, Compsopogonophyceae, Gymnolaemata, Elasmobranchii, Chloropicophyceae, Copepoda, Echinoidea, Bacillariophyceae, Scyphozoa, Ophiuroidea, Malacostraca, Holothuroidea, Hydrozoa, Hexapoda, Mamiellophyceae, Raphidophyceae, Florideophyceae, Hoplonemertea, Bivalvia, Coccolithophyceae, Mammalia, Microbotryomycetes, Dictyochophyceae, Lecanoromycetes, Thecostraca, Polyplacophora, NA, Cephalopoda, Branchiopoda, Hexactinellida, Asteroidea, Teleostei

Temporal Coverage

Start Date 2022-01-28

Sampling Methods

We collected 1 L surface samples from each site every 30 minutes for the duration of time the rocky intertidal was exposed on 28 January 2022, using single-use enteral feeding pouches (Covidien, Dublin, Ireland). The sampling volume used, 1 L, has been shown to be sufficient for detecting a representative range of marine organisms in nearshore locations and is commonly used in aquatic eDNA studies. Sampling commenced at 11:30 PST; at each site, samples were collected from a consistent position across time points. We attached a sterile 0.22 μm pore size Sterivex cartridge (MilliporeSigma, Burlington, MA, USA) to the tubing of each feeding pouch, allowing samples to be immediately gravity filtered in the field. While gravity filtering (1-2 hours per sample), samples were shaded with an awning to prevent any degradation by sunlight. One sample fell during gravity filtration, resulting in a missing sample from S1 at 16:00 PST. At three time points at the beginning and end of the sampling period as well as at low tide (at 14:00 PST), we collected triplicate 1 L samples from each location as biological replicates. At the beginning and end of the sampling period, we also filtered 1 L MilliQ water via the procedure described above to serve as negative field controls. Additionally, using an Orion Model 1230 meter (Orion Research Inc., Beverly, MA, USA), we recorded temperature and salinity in each location directly after samples were collected. Once finished filtering, Sterivex cartridges were dried by pushing air through them using a sterile 3 mL syringe, capped, placed in sterile Whirl-Pak bags (Whirl-Pak, Madison, WI, USA). Then, samples were stored in a cooler on ice until transported back to the laboratory at the end of the sampling period. Samples were transferred to a -20°C freezer for up to 18 days, at which time they were processed to extract nucleic acids from the captured materials. This sampling scheme resulted in 53 field samples, processed as technical replicates in the laboratory (resulting in the 159 events published here).

Study Extent 53 water samples were collected in the rocky intertidal at Pillar Point, Half Moon Bay, California, USA on 28 January 2022. Within Pillar Point, we sampled at three discrete locations: two individual tide pools with a range of physical connectivity (Tide Pool 1, S1: 37.495306°, -122.498744°; Tide Pool 2, S2: 37.494992°, -122.498955°) and an equidistant location (Nearshore, N: 37.495288°, -122.499198°) where there was well-mixed offshore water for the duration of the tidal cycle. All three locations are about 40 meters apart from one another, and are fully isolated at low ride but otherwise interconnected. Ecologically, S1 is more characteristic of the high intertidal, and S2 is more characteristic of the low intertidal. The locationID field identifies the three specific samples locations.

Method step description:

  1. Environmental DNA Field Sampling and Gravity Filtration:
  2. DNA Extraction from Sterivex Filters:
  3. COI PCR Amplification:
  4. Library Preparation & Sequencing: conducted by the Georgia Genomics and Bioinformatics Core (GGBC, UG Athens, GA, RRID:SCR_010994); see for more methodological details
  5. Bioinformatics: using the Anacapa Toolkit; see https://10.5281/zenodo.8201140 for our modified version of the toolkit and for more methodological details
  6. Data Analysis: see (archived version: https://10.5281/zenodo.8213050)

Bibliographic Citations

  1. Shea, M. M., & Boehm, A. B. (2024). Environmental DNA metabarcoding differentiates between micro-habitats within the rocky intertidal. Environmental DNA.

Additional Metadata

Purpose Abstract: While the utility of environmental DNA (eDNA) metabarcoding surveys for biodiversity monitoring continues to be demonstrated, the spatial and temporal variability of eDNA, and thus the limits of the differentiability of an eDNA signal, remains under-characterized. In this study, we collected eDNA samples from distinct micro-habitats (~40 m apart) in a rocky intertidal ecosystem over their exposure period in a tidal cycle. During this period, the micro-habitats transitioned from being interconnected, to physically isolated, to interconnected again. Using a well-established eukaryotic (cytochrome oxidase subunit I) metabarcoding assay, we detected 415 species across 28 phyla. Across a variety of univariate and multivariate analyses, using exclusively taxonomically-assigned data as well as all detected amplicon sequence variants (ASVs), we identified unique eDNA signals from the different micro-habitats sampled. This differentiability paralleled expected ecological gradients and increased as the sites became more physically disconnected. Our results demonstrate that eDNA biomonitoring can differentiate micro-habitats in the rocky intertidal only 40 m apart, that these differences reflect known ecology in the area, and that physical connectivity informs the degree of differentiation possible. These findings showcase the potential power of eDNA biomonitoring to increase the spatial and temporal resolution of marine biodiversity data, aiding research, conservation, and management efforts.
Alternative Identifiers 9358fbd7-cfd0-4eab-99fa-0934396a0529