A Novel Taxonomic Database for eukaryotic Mitochondrial Cytochrome Oxidase subunit I Gene (eKOI): Enhancing taxonomic resolution at community-level in metabarcoding analyses DOI Creative Commons
Rubén González‐Miguéns, Alex Gàlvez-Morante,

Margarita Skamnelou

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 9, 2024

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

Language: Английский

Coastal eutrophication transforms shallow micro-benthic reef communities DOI Creative Commons
Elsa B. Girard,

Andi Muh. Agung Pratama,

Laura Del Rio-Hortega

et al.

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 961, P. 178252 - 178252

Published: Jan. 1, 2025

Coral reefs are impacted worldwide by coastal eutrophication, which is often translated a decrease in coral cover and an increase potentially harmful invertebrates algal blooms. Additionally to corals other macro-benthos, micro-benthic communities affected tremendously, however few studies reported the specific effect of eutrophication on those communities. This study addresses how turbidity associated eutrophication. To answer this question, we compared three groups that have been previously suggested as bioindicators reef environmental conditions: foraminifera, diatoms bacteria, from 12 islands (and 600 samples) Spermonde Archipelago (Indonesia) along near- offshore gradient. Insights DNA metabarcoding satellite images highlighted differences between slope (deep) flat (shallow) communities, distinction has omitted most previous studies. The were 1.5- 2-fold more parameters slope, argue related Based work, expected prokaryotes would be group water quality. However, found large benthic foraminifera diatom highly turbidity, whereas prokaryotic primarily shaped substrate type. Additionally, total 112 exact sequence variants (ESVs) identified indicators different levels, 87 ESVs with high-moderate turbid waters. Our revealed fundamental knowledge provides key information habitat variables (substrate type area) We local regional participates shaping may therefore play important role early warning signals for degradation reefs.

Language: Английский

Citations

0
Changes in the Microbial Community Associated with the Large Benthic Foraminifera Cycloclypeus Carpenteri, Along a Depth Gradient DOI Open Access

Elien Versteegen,

Jan‐Niklas Macher, Sonia J. Rowley

et al.

The Journal of Foraminiferal Research, Journal Year: 2024, Volume and Issue: 54(1), P. 65 - 74

Published: Jan. 1, 2024

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

Language: Английский

Citations

2
Quantitative assessment of reef foraminifera community from metabarcoding data DOI Creative Commons
Elsa B. Girard, Emilie A. Didaskalou,

Andi Muh. Agung Pratama

et al.

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(7)

Published: July 23, 2024

Abstract Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it challenging produce fast and accurate depiction of due methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative genes that may not correctly represent communities from environmental DNA assessed morphological methods. However, has the potential deliver descriptions provided interpreted validated species‐specific calibrations reference databases. Here, we developed quantitative approach retrieve data assemblages large benthic foraminifera (LBF), photosymbiotic calcifying protists, Indonesian coral reefs are under increasing anthropogenic pressure. To depict diversity, calculated taxon‐specific correction factors reduce biological biases by comparing surface area, biovolume calcite volume, number mitochondrial gene copies seven common LBF species. validate approach, compared calibrated datasets mock samples bulk reef sediment; both sample types were metabarcoded. The calibration significantly improved estimations genus abundance, difference ±5% on average, allowing for comparison past future molecular ones. Our results also highlight application our support monitoring operations capturing fine‐scale processes, such as seasonal pollution‐driven dynamics, require high‐throughput sampling treatment.

Language: Английский

Citations

1
COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies DOI
Elsa B. Girard, Jan‐Niklas Macher, Jamaluddin Jompa

et al.

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(11)

Published: Nov. 1, 2022

Abstract Monitoring community composition of Foraminifera (single‐celled marine protists) provides valuable insights into environmental conditions in ecosystems. Despite the efficiency DNA (eDNA) and bulk‐sample (bulk‐DNA) metabarcoding to assess presence multiple taxa, this has not been straightforward for partially due high genetic variability widely used ribosomal markers. Here, we test correctness retrieving foraminiferal communities by mock communities, bulk‐DNA from coral reef sediment samples, eDNA their associated ethanol preservative using recently sequenced cytochrome c oxidase subunit 1 (COI) marker. To detection success, compared our results with large benthic previously reported same sampling sites. Results demonstrate that all species were detected two but one remaining four. Technical replicates highly similar number reads each assigned ASV both samples. Bulk‐DNA showed a significantly higher richness than also additional what was already at specific Our study confirms COI marker adequately retrieves diversity With its decreased commonly nuclear 18 S rRNA, renders powerful tool under condition reference database is adequate target taxa.

Language: Английский

Citations

6
Changes in the Microbial Community Associated with the Large Benthic Foraminifera Cycloclypeus Carpenteri, Along a Depth Gradient DOI

Elien Versteegen,

Jan‐Niklas Macher, Sonia J. Rowley

et al.

The Journal of Foraminiferal Research, Journal Year: 2024, Volume and Issue: 54(1), P. 65 - 74

Published: Jan. 1, 2024

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

Language: Английский

Citations

0
A Novel Taxonomic Database for eukaryotic Mitochondrial Cytochrome Oxidase subunit I Gene (eKOI): Enhancing taxonomic resolution at community-level in metabarcoding analyses DOI Creative Commons
Rubén González‐Miguéns, Alex Gàlvez-Morante,

Margarita Skamnelou

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 9, 2024

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

Language: Английский

Citations

0