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

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亦存在 2 筆延伸集的資料表。延伸集中的紀錄補充核心集中紀錄的額外資訊。每個延伸集資料表中資料筆數顯示如下。

160114

320228

160114

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如何引用

研究者應依照以下指示引用此資源。:

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

權利

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此資料的發布者及權利單位為 United States Geological Survey。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF 註冊

此資源已向GBIF註冊，並指定以下之GBIF UUID: 9358fbd7-cfd0-4eab-99fa-0934396a0529。 United States Geological Survey 發佈此資源，並經由GBIF-US同意向GBIF註冊成為資料發佈者。

關鍵字

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

聯絡資訊

Meghan M. Shea

元數據提供者 ●
出處 ●
處理者 ●
連絡人

PhD Candidate

Stanford University

Stanford

CA

US

mshea@stanford.edu

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

Alexandria B. Boehm

出處 ●
研究主持人

Professor, Department of Civil and Environmental Engineering

Stanford University

Stanford

CA

US

aboehm@stanford.edu

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

地理涵蓋範圍

Pillar Point, Half Moon Bay, California, USA

界定座標範圍	緯度南界經度西界 [37.495, -122.499], 緯度北界經度東界 [37.495, -122.499]

分類群涵蓋範圍

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

時間涵蓋範圍

起始日期	2022-01-28

取樣方法

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).

研究範圍	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.

研究範圍

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.

方法步驟描述:

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)

引用文獻

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

額外的詮釋資料

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