Quantitative assessment of reef foraminifera community from metabarcoding data.

Autor: Girard EB; Naturalis Biodiversity Center, Leiden, The Netherlands.; IBED, University of Amsterdam, Amsterdam, The Netherlands., Didaskalou EA; CML, University of Leiden, Leiden, The Netherlands., Pratama AMA; Marine Science Department, Faculty of Marine Science and Fisheries, Hasanuddin University, Makassar, Indonesia., Rattner C; Naturalis Biodiversity Center, Leiden, The Netherlands., Morard R; MARUM, University of Bremen, Bremen, Germany., Renema W; Naturalis Biodiversity Center, Leiden, The Netherlands.; IBED, University of Amsterdam, Amsterdam, The Netherlands.
Jazyk: angličtina
Zdroj: Molecular ecology resources [Mol Ecol Resour] 2024 Jul 23, pp. e14000. Date of Electronic Publication: 2024 Jul 23.
DOI: 10.1111/1755-0998.14000
Abstrakt: Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it is challenging to produce fast and accurate depiction of ecosystems due to methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative abundances of genes that may not correctly represent living communities from environmental DNA assessed with morphological methods. However, it has the potential to deliver fast descriptions of living communities provided that it is interpreted with validated species-specific calibrations and reference databases. Here, we developed a quantitative approach to retrieve from metabarcoding data the assemblages of living large benthic foraminifera (LBF), photosymbiotic calcifying protists, from Indonesian coral reefs that are under increasing anthropogenic pressure. To depict the diversity, we calculated taxon-specific correction factors to reduce biological biases by comparing surface area, biovolume and calcite volume, and the number of mitochondrial gene copies in seven common LBF species. To validate the approach, we compared calibrated datasets of morphological communities from mock samples with bulk reef sediment; both sample types were metabarcoded. The calibration of the data significantly improved the estimations of genus relative abundance, with a difference of ±5% on average, allowing for comparison of past morphological datasets with future molecular ones. Our results also highlight the application of our quantitative approach to support reef monitoring operations by capturing fine-scale processes, such as seasonal and pollution-driven dynamics, that require high-throughput sampling treatment.
(© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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