Biodiversity Information Science and Standards :
Conference Abstract
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Corresponding author: Luke Thompson (luke.thompson@noaa.gov)
Received: 11 Aug 2023 | Published: 15 Aug 2023
© 2023 Katherine Silliman, Sean Anderson, Rachael Storo, Luke Thompson
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Silliman K, Anderson S, Storo R, Thompson L (2023) A Case Study in Sharing Marine eDNA Metabarcoding Data to OBIS. Biodiversity Information Science and Standards 7: e111048. https://doi.org/10.3897/biss.7.111048
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Metabarcoding of DNA collected from an environmental sample (eDNA) is increasingly employed in marine biodiversity surveys, with the ability to target taxa from microbes to plankton to large vertebrates depending on the molecular markers used. These techniques are often the only viable method to detect certain taxonomic groups, and therefore provide observations that are currently under-represented on existing biodiversity data platforms, such as the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF). Some of the reasons for this disconnect include the unique data structures inherent to eDNA datasets, the complexities of combining marine observation data and environmental data (
Here we present a detailed case study on the preparation of marine metabarcoding survey data for publication to OBIS. This data comes from the 2021 Gulf of Mexico Ecosystems and Carbon Cycle (GOMECC) cruise led by the National Oceanic and Atmospheric Administration (NOAA), employing 17 coastal-offshore transects across the Gulf of Mexico and the Atlantic Ocean. Metabarcoding libraries targeted bacteria and archaea with the 16S rRNA marker and eukaryotes with the 18S rRNA marker. Amplicon sequence variants (ASVs) were inferred for each marker, then taxonomy was assigned to these ASVs using the open-sourced reference databases PR2 5.0.1 and SILVA 138.1. OBIS requires that taxonomic assignments are converted to the World Register of Marine Species (WoRMS) nomenclature, which can be particularly challenging for marine bacteria and archaea as these taxa are underrepresented on WoRMS. Three tables—the per-sample ASV observation counts, assigned taxonomy of the ASV sequences, and sample collection data—were then converted to the DNA derived extension for Darwin Core (
Some of the key challenges to navigate when preparing metabarcoding data for OBIS include:
We describe our workflow for tackling these challenges, with the aim of fostering discussion on best practices for publishing marine eDNA data to biodiversity data platforms. This work is part of a larger effort across NOAA ’Omics to develop a comprehensive bioinformatics platform and data management framework for marine eDNA and microbiome data.
DNA barcodes, marine biodiversity monitoring, ASV sequences, Darwin Core
Katherine Silliman
TDWG 2023
The authors would like to thank Stephen Formel and Abigail Benson for their guidance o working with OBIS.
This work was supported by award NA21OAR4320190 to the Northern Gulf Institute, by NOAA Ocean Exploration via the Northern Gulf Institute, and by the NOAA Ocean Acidification Program (project number 21392), each from NOAA’s Office of Oceanic and Atmospheric Research, U.S. Department of Commerce.
NOAA Atlantic Oceanographic and Meteorological Laboratory and the Northern Gulf Institute