Savu Sea-Indonesia eDNA Dataset

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 2,063 records.

1 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

Researchers should cite this work as follows:

Anggoro A (2023). Savu Sea-Indonesia eDNA Dataset. Version 1.97. BIONESIA. Occurrence dataset. https://cloud.gbif.org/asia/resource?r=edna_id_2022&v=1.97

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is BIONESIA. This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: bbb81807-fc4c-4e4e-bc1c-2caee84a4a06.  BIONESIA publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Participant Node Managers Committee.

Keywords

Occurrence; Observation

Contacts

Geographic Coverage

The Savu Sea is a small sea within Indonesia named for the island of Savu (Sawu) on its southern boundary. It is bounded by Savu and Rai Jua to the south, the islands of Rote and Timor (split between East Timor and Indonesia) to the east, Flores and the Alor archipelago to the north/northwest, and the island of Sumba to the west/northwest. Between these islands, it flows into the Indian Ocean to the south and west, the Flores Sea to the north, and the Banda Sea to the northeast.

Taxonomic Coverage

DNA sequences from water samples will be identified to species whenever possible. When sequences were unable to be assigned to a taxonomic name, a dedicated OTU (Operational Taxonomic Name)/occurenceID will be given to the sequences

Project Data

The proposal aims to enrich existing 2000 coral reef fish database species found in Eastern Indonesia, by particularly focusing on elasmobranch, one of the species that are heavily targeted in global fisheries industries. Major activities will include comprehensively list the group using the most updated eDNA metabarcoding technique and train conservationists to use molecular data for conservation purposes. An important target for the project is to develop a practical field guidebook to collect and analyze eDNA data for research and conservation purposes. The combined activities will contribute massively for education, research and marine conservation activities in the region.

The personnel involved in the project:

Sampling Methods

The sampling collection event summarized the collection event across 4 locations in Savu Sea waters. We collected surface seawater samples at 5 sites from each location. eDNA samples from seawater sample were collected across 4 designated locations across the Sawu Sea, with 5 sites in each location. 2 liters of seawater samples were collected with sterile Nalgene bottle from the sea surface in every site. Water sample than filtered through a 0.22-133 micron Sterivex™ filter. eDNA samples and blanks will be extracted using the DNeasy Blood & Tissue Kit (QIAGEN, Hilden, 143 Germany). Extracted DNA was then sent to a sequencing facility for the NGS metabarcoding method using the Illumina platform.

Method step description:

1. 1. For each of the sampling sites, one water samples were collected an homogenized 2. DNA was extracted from each of the samples with a modified protocol based on PowerMax soil kit (MoBio, now Qiagen) 3. For each DNA extract 1 µl, the COI region was amplified in triplicates with the primers mlCOIintF and jgCOIR, using Amplitaq Gold. 4. All PCR products were built into Illumina sequencing libraries with the TruSeq PCR free kit. 5. Sequencing of the 10 samples was done with the Illumina MiSeq platform using the V2 kit 250 bp paired end sequencing. 6. Paired reads were demultiplexed and analyzed with Metaworks https://github.com/terrimporter/MetaWorks using cutadapt, vsearch and dada2, and vsearch. 7. Sequences were annotated by comparison with the Ribosomal Database classifier v2.13 (RDP classifier)

Additional Metadata