<scp>COI</scp> metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies

Girard, Elsa B.; Macher, Jan‐Niklas; Jompa, Jamaluddìn; Renema, Willem

doi:10.1002/ece3.9549

Cited by 4 publications

(1 citation statement)

References 47 publications

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“…Variation within C. carpenteri specimens in 18S, possibly due to the presence of multiple nuclei per specimen, has been reported for foraminifera and can be as high as 5% (Weber & Pawlowski, 2014;Girard et al, 2022). The molecular data of the two most abundant and core foraminiferal OTUs did not distinguish between Heterostegina and the only Cycloclypeus sequence deposited in the NCBI GenBank reference database.…”

Section: Discussionmentioning

confidence: 85%

Changes in the Microbial Community Associated with the Large Benthic Foraminifera Cycloclypeus Carpenteri, Along a Depth Gradient

Versteegen,

Macher,

Rowley

et al. 2024

Journal of Foraminiferal Research

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Cycloclypeus carpenteri is one of the deepest living large benthic foraminifera. It has an obligatory relationship with diatom photosymbionts, and, in addition, houses a diverse prokaryotic community. Variations in the eukaryotic and prokaryotic endobiotic community composition might be key in allowing Cycloclypeus to occur in low light environments. We assessed the variability of the prokaryotic and eukaryotic communities associated with Cycloclypeus along a depth gradient from 50 to 130 m at two locations in the Federated States of Micronesia (Northwest Pacific) by metabarcoding of the 18S V9 rRNA region for eukaryotes and the 16S V3-V4 rRNA region for prokaryotes. We observed a single foraminiferal operational taxonomic unit (OTU), as well as a single dominant diatom OTU that was abundant in all sequenced specimens. Both the prokaryotic and the eukaryotic endobiotic communities (excluding the dominant diatom) changed with water depth and associated irradiance levels. We observed a distinct change in the prokaryotic community composition around 90–100 m water depth at Pohnpei, equivalent to ∼1% surface radiation. This change in microbial communities in the Cycloclypeus holobiont suggests a potential role of the associated microbial communities in accommodating differences in (micro)habitat, although we cannot exclude that the prokaryote community is to a large extent driven by their community composition in the ambient environment.

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Section: Discussionmentioning

confidence: 85%

Changes in the Microbial Community Associated with the Large Benthic Foraminifera Cycloclypeus Carpenteri, Along a Depth Gradient

Versteegen,

Macher,

Rowley

et al. 2024

Journal of Foraminiferal Research

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A Novel Taxonomic Database for eukaryotic Mitochondrial Cytochrome Oxidase subunit I Gene (eKOI): Enhancing taxonomic resolution at community-level in metabarcoding analyses

González-Miguéns,

Gàlvez-Morante,

Skamnelou

et al. 2024

Preprint

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Metabarcoding has emerged as a robust method for understanding biodiversity patterns by retrieving environmental DNA (eDNA) directly from ecosystems. Its low cost and accessibility have extended its use across biological topics, from symbiosis to biogeography, and ecology. A successful metabarcoding application depends on accurate and comprehensive reference databases for proper taxonomic assignment. The 18S rRNA gene is the primary genetic marker used for general/broad eukaryotic metabarcoding due to its combination of conserved and hypervariable regions, and the availability of extensive taxonomically-informed reference databases like PR2 and SILVA. Despite its advantages, 18S rRNA has certain limitations at lower taxonomic levels, depending on the lineage. Alternative fast-evolving molecular markers, such as the mitochondrial cytochrome oxidase subunit I (COI) gene, have been adopted as widely used "barcoding genes" for eukaryotes due to their resolution to the species level. However, the COI gene lacks a curated taxonomically-informed database covering all eukaryotes, including protists, comparable to those available for 18S rRNA. To address this gap, we introduce eKOI, a curated COI gene database aimed at enhancing the taxonomic annotation and primer design for COI-based metabarcoding at the community level. This database integrates COI gene data from GenBank and mitochondrial genomes that are publicly available, followed by rigorous manual curation to eliminate redundancies and contaminants and to correct taxonomic annotations. We validate using the eKOI database for taxonomic annotation of protists by re-annotating several COI-based metabarcoding studies, revealing previously unidentified biodiversity. Phylogenetic analyses confirmed the accuracy of the taxonomic annotations, highlighting the potential of eKOI to uncover new biodiversity in various eukaryotic lineages.

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Quantitative assessment of reef foraminifera community from metabarcoding data

Girard,

Didaskalou,

Pratama

et al. 2024

Molecular Ecology Resources

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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.

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COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 4 publications

References 47 publications

Changes in the Microbial Community Associated with the Large Benthic Foraminifera Cycloclypeus Carpenteri, Along a Depth Gradient

Changes in the Microbial Community Associated with the Large Benthic Foraminifera Cycloclypeus Carpenteri, Along a Depth Gradient

A Novel Taxonomic Database for eukaryotic Mitochondrial Cytochrome Oxidase subunit I Gene (eKOI): Enhancing taxonomic resolution at community-level in metabarcoding analyses

Quantitative assessment of reef foraminifera community from metabarcoding data

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