Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna

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

Published: July 31, 2024

Abstract Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack reference DNA sequences available taxonomic annotation. Our study explores benefits combining targeted barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches globally important ecosystems inhabited meiofauna, microscopic animals living in interstitial space between sand grains, which play key role coastal biodiversity ecosystem dynamics. However, research on faces challenges due limited expertise sparse sampling. We generated 775 new cytochrome c oxidase I barcodes from specimens collected along Netherlands' west coast combined them with NCBI GenBank database. analysed alpha beta 561 samples 24 North Sea beaches, region extensively studied both enriched database without additional barcodes. results show 2.5‐fold increase sequence annotation doubling species‐level Operational Taxonomic Units (OTUs) identification when annotating data enhanced Additionally, our analyses revealed bell‐shaped curve OTU richness across intertidal zone, aligning more closely analysis patterns, defined community dissimilarity patterns supralittoral sites. highlights importance expanding molecular databases assessments, ultimately improving understanding ecosystems.

Language: Английский

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Comparing eDNA metabarcoding and conventional pelagic netting to inform biodiversity monitoring in deep ocean environments

ICES Journal of Marine Science, Journal Year: 2023, Volume and Issue: 80(10), P. 2545 - 2562

Published: Nov. 9, 2023

Abstract The performance of environmental DNA (eDNA) metabarcoding has rarely been evaluated against conventional sampling methods in deep ocean mesopelagic environments. We assessed the biodiversity patterns generated with eDNA and two co-located methods, oblique midwater trawls vertical multinets, to compare regional sample-level diversity. then concordance ecological across water column habitats how markers level effort influenced inferred community. found characterized diversity well, detecting more taxa while identifying similar as samples. Within locations, detected than one replicate. While were within sample stations, fewer compared multinets. Our simulations show greater would improve methods. also observed that using taxonomic data from multiple most those Patterns Exact Sequence Variants stable suggesting they are powerful for change. is a valuable tool monitoring biological hotspots but some methodological adjustments recommended

Language: Английский

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BFR2: a curated ribosomal reference dataset for benthic foraminifera

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: Nov. 27, 2024

Abstract Benthic foraminifera are one of the major groups marine protists that also occur in freshwater and terrestrial habitats. They widely used to monitor current past environmental conditions. Over last three decades, thousands DNA sequences have been obtained from benthic foraminiferal isolates. The results this long-term effort compiled here form first curated ribosomal reference dataset (BFR2). present contains over 5000 a fragment 18S rDNA gene, which is recognized as barcode foraminifera. represent 279 species 204 genera belonging 91 families. Thirteen percent these not assigned any morphologically described group may new science. Furthermore, forty-five previously published. BFR 2 aims collect all barcodes provide much-needed for rapidly developing field molecular studies.

Language: Английский

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Unlocking foraminiferal genetic diversity on estuarine mudflats with eDNA metabarcoding

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 902, P. 165983 - 165983

Published: Aug. 4, 2023

Language: Английский

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Metacommunity theory and metabarcoding reveal the environmental, spatial, and biotic drivers of meiofaunal communities in sandy beaches

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

Published: July 22, 2024

Abstract Sandy beaches are important ecosystems providing coastal protection and recreation, but they face significant threats from human activities sea level rise. They inhabited by meiofauna, small benthic invertebrates that highly abundant diverse, commonly understudied biotic components of beach ecosystems. Here, we investigate the factors shaping meiofaunal metacommunities employing Generalised Dissimilarity Modelling (GDM) Joint Species Distribution (JSDM) to study community turnover assembly processes. We analysed over 550 meiofauna samples a >650 km stretch southern North Sea coastline using metabarcoding approach. Our findings reveal environmental factors, especially Distance Low Tide Sediment Grain Size, drivers turnover. This highlights influence gradient marine terrestrial habitats sediment conditions. Spatial which indicate dispersal limitations, also significantly impact composition, challenging view have broad geographic distributions. The JSDM results show species sorting conditions is dominant process in with increasing differences between sampling sites, associations, or similar preferences, major driver at sites Further, find spatial across region. By facilitating inference ecological niches for high number taxa, provides powerful framework understanding ecology these animals. highlight importance considering gradients limitations ecosystem research, future research should aim adding information on functional traits interactions under varying understand dynamics resilience.

Language: Английский

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Metabarcoding the eukaryotic community of a threatened, iconic Mediterranean habitat: Posidonia oceanica seagrass meadows

Frontiers in Marine Science, Journal Year: 2023, Volume and Issue: 10

Published: April 6, 2023

Against the accelerating pace of worldwide species extinction, reliable biodiversity assessments are critical, both as baselines and to track potential declines. DNA metabarcoding techniques allow for fast comprehensive assessment in terrestrial marine habitats. However, these methods need be adapted standardised each ecosystem order effective. Seagrass meadows among most diverse habitats irreplaceable terms services they provide, yet has never been implemented systems. In this study, we developed tested a protocol eukaryotic community iconic species, Posidonia oceanica L. (Delile). This seagrass is main habitat-forming Mediterranean coastal waters known its high diversity due structural complexity canopy rhizome structures. habitat experiencing range-wide retreat, there an urgent efficient biomonitoring detection early changes. Our proposed method involves direct sampling community, collecting processing leaves strata separately. To test utility distinguishing between different meadow conditions, sampled two distinct that differ their prevailing wind surge nearby rocky reef comparison. We then pipeline COI using generalist primers target eukaryote present. detected analysed (3,350 molecular operational taxonomic units, dominated by Metazoa Archaeplastida) clear differentiation samples from those reefs. The rhizomes harboured clearly assemblages, differences were also sampled. new tool deliver big data way, which crucial implementation protection management measures key habitat.

Language: Английский

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Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria)

mBio, Journal Year: 2023, Volume and Issue: 14(2)

Published: March 20, 2023

Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and transfer to the nuclear genome. The diversity of mitochondrial genomes published date has revealed processes are ongoing in many lineages. Most well-studied eukaryotic lineages represented genome databases, except for superphylum Retaria-the lineage comprising Foraminifera Radiolaria. Using single-cell approaches, we determined two complete nearly radiolarians. We report coding content additional 14 foram species. show foraminiferan radiolarian contain a fully overlapping but reduced complement compared other sequenced rhizarians. In contrast animals fungi, protists encode diverse set proteins on their genomes, including several ribosomal genes; however, some aerobic (euglenids, myzozoans, chlamydomonas-like algae) have lack all genes. Similar these outliers, retarian protein tRNA genes, truncated divergent small large rRNA only or 15 protein-coding

Language: Английский

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Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: a case study on beach meiofauna

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

Published: April 1, 2024

Abstract Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack reference DNA sequences available taxonomic annotation. Our study explores benefits combining targeted barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches globally important ecosystems inhabited meiofauna, microscopic animals living in interstitial space between sand grains, which play key role coastal biodiversity ecosystem dynamics. However, research on faces challenges due limited expertise sparse sampling. We generated 775 new cytochrome c oxidase I barcodes from specimens collected along Netherlands’ west coast combined them with NCBI GenBank database. analysed alpha beta 561 samples 24 North Sea beaches, region extensively studied both enriched database without additional barcodes. results show 2.5-fold increase sequence annotation doubling species-level Operational Taxonomic Units (OTUs) identification when annotating data enhanced Additionally, our analyses revealed bell-shaped curve OTU richness across intertidal zone, aligning more closely analysis patterns, defined community dissimilarity patterns supralittoral sites. highlights importance expanding molecular databases assessments, ultimately improving understanding ecosystems.

Language: Английский

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Quantitative assessment of reef foraminifera community from metabarcoding data

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

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Meiofauna as sentinels of beach ecosystems: A quantitative review of gaps and opportunities in beach meiofauna research.

Estuarine Coastal and Shelf Science, Journal Year: 2024, Volume and Issue: 313, P. 109092 - 109092

Published: Dec. 17, 2024

Language: Английский

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