eDNA along Houdong riverine zonation in Taiwan

Description

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 6,297 records.

4 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.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Please be aware, this is an old version of the dataset.  Researchers should cite this work as follows:

Hoh D (2023): eDNA along Houdong riverine zonation in Taiwan. v1.2. Taiwan Biodiversity Information Facility (TaiBIF). Dataset/Samplingevent. https://ipt.taibif.tw/resource?r=houdongkeng_water_edna&v=1.2

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is Taiwan Biodiversity Information Facility (TaiBIF). 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: 2615342d-7349-4e75-ae34-cda6cb403e2e.  Taiwan Biodiversity Information Facility (TaiBIF) publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Taiwan Biodiversity Information Facility.

Keywords

SamplingEvent

Contacts

Daphne Hoh

• Metadata Provider ●
• Originator ●
• Point Of Contact

Postdoctoral Researcher

Taiwan Biodiversity Information Facility

TW

daphnehohzhiwei@gmail.com

http://orcid.org/0000-0002-7810-1034

Min-Chen Wang

• Point Of Contact

Postdoctoral Researcher

Institute of Cellular and Organismic Biology, Academia Sinica

TW

mcwinlab@gmail.com

http://orcid.org/0000-0003-2044-1148

Geographic Coverage

Houdong River (猴洞坑), Jiaoxi Township, Yilan County, Taiwan

Taxonomic Coverage

We detected eukaryotic organisms in the water samples using the cytochrome oxidase subunit 1 (COI) mitochondrial gene. A total of 2,736 operational taxonomic units (OTUs) were identified, but only 421 of these could be successfully assigned to a taxonomic group at (at least) the kingdom level.

Temporal Coverage

Project Data

No Description available

The personnel involved in the project:

Daphne Hoh

• Processor

http://orcid.org/0000-0002-7810-1034

Chieh-Ping Lin

• Author

http://orcid.org/0009-0006-4210-1063

Yung-Che Tseng

• Author

http://orcid.org/0000-0001-7489-0403

Cheng-Wei Chen

• Author

http://orcid.org/0000-0001-9709-6739

John Wang

• Author

Chung-Hsin Huang

• Author

Mao-Ning Tuanmu

• Author

http://orcid.org/0000-0002-8233-2935

Min-Chen Wang

• Principal Investigator

http://orcid.org/0000-0003-2044-1148

Mark Angelo Bucay

• Author

http://orcid.org/0000-0002-8769-9592

Sampling Methods

Surface water was collected from each site on the same day, and various water quality parameters were measured on site, including temperature, pH, dissolved oxygen (DO) content, turbidity, and salinity, with three replicate measurements taken for each parameter. Samples were processed at the Marine Research Station of the Institute of Cellular and Organismic Biology and the Biodiversity Research Centre at Academia Sinica in Taiwan. To prepare the samples for eDNA metabarcoding analysis, each water sample was filtered twice. The first filtration step involved using a 75 µm pore size sieve to remove larger materials, such as debris. Next, a 0.22 μm PES filter membrane with a vacuum pump was used to collect eDNA from the filtered water. Two PES filter membranes were used at each site and each membrane was used to filter 2 L of water. The filtered membranes were then placed in sterile petri dishes and stored at -80 °C until DNA extraction.

Method step description:

1. Wet lab process description: pending.
2. Dry lab process description: pending.
3. Lowest taxon level-annotation of each OTU was extracted to perform a secondary species mapping to GBIF Backbone using the rgbif package (Chamberlain et al., 2023; version 3.7.7) in R (R Core Team, 2022; version 4.2.2).
4. Open data and code: We converted the occurrence data into Darwin Core Archive standard and validated data in both event and occurrence data sheets using the Data Validator developed by GBIF (Global Biodiversity Information Facility, 2017). We then published the dataset containing one event core and four extensions: occurrence, DNA derived data, extended measurement or facts, and resource relationship using The Integrated Publishing Toolkit (IPT) of GBIF installed under the Taiwan Biodiversity Information Facility (TaiBIF). DNA sequence data was submitted to European Nucleotide Archive under project accession PRJEB60905. All source codes used in the project can be found in the project GitHub repository (tbc link).

Bibliographic Citations

1. European Nucleotide Archive EMBL-EBI Project. https://www.ebi.ac.uk/ena/browser/view/PRJEB60905
2. Chamberlain S, Barve V, Mcglinn D, Oldoni D, Desmet P, Geffert L, Ram K (2023). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.7.7. https://CRAN.R-project.org/package=rgbif
3. R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/

Additional Metadata