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

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.

Sampling

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).

Method steps

1. Environmental DNA Field Sampling and Gravity Filtration: https://dx.doi.org/10.17504/protocols.io.bp2l69y7klqe/v2
2. DNA Extraction from Sterivex Filters: https://dx.doi.org/10.17504/protocols.io.ewov1qyyygr2/v1
3. COI PCR Amplification: https://dx.doi.org/10.17504/protocols.io.dm6gp3wpdvzp/v1
4. Library Preparation & Sequencing: conducted by the Georgia Genomics and Bioinformatics Core (GGBC, UG Athens, GA, RRID:SCR_010994); see https://doi.org/10.1101/2023.08.03.551543 for more methodological details
5. Bioinformatics: using the Anacapa Toolkit; see https://10.5281/zenodo.8201140 for our modified version of the toolkit and https://doi.org/10.1101/2023.08.03.551543 for more methodological details
6. Data Analysis: see https://github.com/meghanmshea/intertidal-eDNA (archived version: https://10.5281/zenodo.8213050)

N/A

1. Arthropoda
   rank: phylum
2. Dinophyceae
   rank: class
3. Chromista
   rank: kingdom
4. Nemertea
   rank: phylum
5. Palaeonemertea
   rank: class
6. Haptophyta
   rank: phylum
7. Clitellata
   rank: class
8. Bolidophyceae
   rank: class
9. Pyramimonadophyceae
   rank: class
10. Polychaeta
    rank: class
11. Hexacorallia
    rank: class
12. Phaeophyceae
    rank: class
13. Fungi
    rank: kingdom
14. Aves
    rank: class
15. Mucoromycotina incertae sedis
    rank: class
16. Ascidiacea
    rank: class
17. Cryptophyta incertae sedis
    rank: class
18. Myzozoa
    rank: phylum
19. Pycnogonida
    rank: class
20. Homoscleromorpha
    rank: class
21. Zygomycota
    rank: phylum
22. Dothideomycetes
    rank: class
23. Oomycota
    rank: phylum
24. Gastropoda
    rank: class
25. Echinodermata
    rank: phylum
26. Mollusca
    rank: phylum
27. Demospongiae
    rank: class
28. Bangiophyceae
    rank: class
29. Eurotatoria
    rank: class
30. Pilidiophora
    rank: class
31. Animalia
    rank: kingdom
32. Discosea
    rank: class
33. Protozoa
    rank: kingdom
34. Ascomycota
    rank: phylum
35. Pelagophyceae
    rank: class
36. Compsopogonophyceae
    rank: class
37. Gymnolaemata
    rank: class
38. Platyhelminthes
    rank: phylum
39. Elasmobranchii
    rank: class
40. Chloropicophyceae
    rank: class
41. Copepoda
    rank: class
42. Echinoidea
    rank: class
43. Bacillariophyta
    rank: phylum
44. Bacillariophyceae
    rank: class
45. Scyphozoa
    rank: class
46. Ophiuroidea
    rank: class
47. Malacostraca
    rank: class
48. Bryozoa
    rank: phylum
49. Holothuroidea
    rank: class
50. Hydrozoa
    rank: class
51. Hexapoda
    rank: class
52. Mamiellophyceae
    rank: class
53. Rotifera
    rank: phylum
54. Raphidophyceae
    rank: class
55. Annelida
    rank: phylum
56. Florideophyceae
    rank: class
57. Hoplonemertea
    rank: class
58. Chordata
    rank: phylum
59. Rhodophyta
    rank: phylum
60. Amoebozoa
    rank: phylum
61. Bivalvia
    rank: class
62. Coccolithophyceae
    rank: class
63. Mammalia
    rank: class
64. Microbotryomycetes
    rank: class
65. Chlorophyta
    rank: phylum
66. Dictyochophyceae
    rank: class
67. Cryptophyta
    rank: phylum
68. Lecanoromycetes
    rank: class
69. Porifera
    rank: phylum
70. Plantae
    rank: kingdom
71. Thecostraca
    rank: class
72. Basidiomycota
    rank: phylum
73. Polyplacophora
    rank: class
74. Phoronida
    rank: phylum
75. Ochrophyta
    rank: phylum
76. NA
    rank: class
77. Cephalopoda
    rank: class
78. Branchiopoda
    rank: class
79. Hexactinellida
    rank: class
80. Asteroidea
    rank: class
81. Teleostei
    rank: class
82. Cnidaria
    rank: phylum

Pillar Point, Half Moon Bay, California, USA