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

DwC ファイルとしてのデータ	ダウンロード 160,114 レコード English で (17 MB) - 更新頻度: as needed
EML ファイルとしてのメタデータ	ダウンロード English で (43 KB)
RTF ファイルとしてのメタデータ	ダウンロード English で (0 bytes)

データレコード

このオカレンス（観察データと標本) リソース内のデータは、1 つまたは複数のデータテーブルとして生物多様性データを共有するための標準化された形式であるダーウィンコアアーカイブ (DwC-A) として公開されています。コアデータテーブルには、160,114 レコードが含まれています。

拡張データテーブルは2 件存在しています。拡張レコードは、コアのレコードについての追加情報を提供するものです。各拡張データテーブル内のレコード数を以下に示します。

160114

320228

160114

この IPT はデータをアーカイブし、データリポジトリとして機能します。データとリソースのメタデータは、ダウンロードセクションからダウンロードできます。バージョンテーブルから公開可能な他のバージョンを閲覧でき、リソースに加えられた変更を知ることができます。

バージョン

次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。

引用方法

研究者はこの研究内容を以下のように引用する必要があります。:

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. https://ipt-obis.gbif.us/resource?r=shea_boehm_2024&v=1.5

権利

研究者は権利に関する下記ステートメントを尊重する必要があります。:

パブリッシャーとライセンス保持者権利者は United States Geological Survey。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF登録

このリソースをはGBIF と登録されており GBIF UUID: 9358fbd7-cfd0-4eab-99fa-0934396a0529が割り当てられています。 GBIF-US によって承認されたデータパブリッシャーとして GBIF に登録されているUnited States Geological Survey が、このリソースをパブリッシュしました。

キーワード

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

連絡先

Meghan M. Shea

メタデータ提供者 ●
最初のデータ採集者 ●
データ処理者 ●
連絡先

PhD Candidate

Stanford University

Stanford

CA

US

mshea@stanford.edu

https://orcid.org/0000-0002-7419-6654

Alexandria B. Boehm

最初のデータ採集者 ●
研究代表者

Professor, Department of Civil and Environmental Engineering

Stanford University

Stanford

CA

US

aboehm@stanford.edu

https://orcid.org/0000-0002-8162-5090

地理的範囲

Pillar Point, Half Moon Bay, California, USA

座標（緯度経度）	南西 [37.495, -122.499], 北東 [37.495, -122.499]

生物分類学的範囲

N/A

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

時間的範囲

開始日	2022-01-28

収集方法

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.

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:

Environmental DNA Field Sampling and Gravity Filtration: https://dx.doi.org/10.17504/protocols.io.bp2l69y7klqe/v2
DNA Extraction from Sterivex Filters: https://dx.doi.org/10.17504/protocols.io.ewov1qyyygr2/v1
COI PCR Amplification: https://dx.doi.org/10.17504/protocols.io.dm6gp3wpdvzp/v1
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
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
Data Analysis: see https://github.com/meghanmshea/intertidal-eDNA (archived version: https://10.5281/zenodo.8213050)

書誌情報の引用

Shea, M. M., & Boehm, A. B. (2024). Environmental DNA metabarcoding differentiates between micro-habitats within the rocky intertidal. Environmental DNA. https://doi.org/10.1002/edn3.521

追加のメタデータ

目的	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.
代替識別子	9358fbd7-cfd0-4eab-99fa-0934396a0529
	https://obis.org/dataset/54bc0e9c-e857-4216-a6ce-46cd6ae58cd7
	https://ipt-obis.gbif.us/resource?r=shea_boehm_2024