Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(4), P. 742 - 755

Published: Dec. 8, 2022

Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, sciences and monitoring. Thereby, the taxonomic identification species their sequences relies strongly on reference databases that link genetic to names. These vary completeness availability, depending group studied region targeted. The incompleteness an important argument explain nondetection by supposedly present. However, there exist further generally overlooked problems with can lead false inaccurate inferences assignment. Here, we synthesize all possible inherent databases. In particular, identify a complete, mutually nonexclusive list seven classes challenges when it comes selecting, developing database for are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) (v) low resolution, (vi) missing taxa (vii) intraspecific variants. For each problem identified, provide description consequences assignment process. We illustrate respective examples taken literature obtained quantitative analyses public databases, GenBank BOLD. Finally, discuss solutions identified how navigate them. Only raising users' awareness limitations data will adequate interpretations these be achieved.

Language: Английский

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Measuring the state of aquatic environments using eDNA—upscaling spatial resolution of biotic indices

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1904)

Published: May 5, 2024

Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they strongly affected by anthropogenic activities. As of these taxa highly sensitive to environmental change, offer particularly good early warning system for human-induced thus leading their intense monitoring. In ecosystems there is plethora biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported freshwater alone. Ultimately, macroinvertebrates used calculate ecological indices describing the state systems. Many not only hard compare, but especially difficult scale in time space. Novel DNA-based approaches measure change environments now unprecedented opportunities, also possible integration towards commonly applicable indices. Here, we first give perspective on organisms, focus insects, how move beyond traditional point-based Second, demonstrate proof-of-concept spatially upscaling based DNA, demonstrating novel molecular hydrological models allows an accurate evaluation at catchment scale. This article part theme issue ‘Towards toolkit global biodiversity monitoring’.

Language: Английский

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Assessing the relevance of DNA metabarcoding compared to morphological identification for lake phytoplankton monitoring

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 914, P. 169774 - 169774

Published: Jan. 11, 2024

Language: Английский

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Groundwater environmental DNA metabarcoding reveals hidden diversity and reflects land‐use and geology

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(13), P. 3497 - 3512

Published: April 17, 2023

Abstract Despite being the most important source of liquid freshwater on planet, groundwater is severely threatened by climate change, agriculture, or industrial mining. It thus extensively monitored for pollutants and declines in quantity. The organisms living groundwater, however, are rarely target surveillance programmes little known about fauna inhabiting underground habitats. difficulties accessing lack expertise, apparent scarcity these challenge sampling prohibit adequate knowledge fauna. Environmental DNA (eDNA) metabarcoding provides an approach to overcome limitations but largely unexplored. Here, we sampled water 20 communal spring catchment boxes used drinking provisioning Switzerland, with a high level replication at both filtration amplification steps. We sequenced portion COI mitochondrial gene, which resulted 4917 ASVs, yet only 3% reads could be assigned species, genus, family more than 90% identity. Careful evaluation unassigned corroborated that sequences were true belonging mostly diverse eukaryotic groups, not present reference databases. Principal component analyses showed strong correlation community composition surface land‐use (agriculture vs. forest) geology (fissured rock unconsolidated sediment). While incomplete databases limit assignment taxa eDNA metabarcoding, taxonomy‐free approaches can reveal large hidden diversity couple it major drivers, revealing their imprint chemical biological properties groundwater.

Language: Английский

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Biomonitoring for Watershed Protection from a Multiscale Land-Use Perspective

Diversity, Journal Year: 2023, Volume and Issue: 15(5), P. 636 - 636

Published: May 8, 2023

The types and intensification of land use in the watershed affect living organisms aquatic ecosystems differently; this impact will also vary according to temporal spatial scales. Understanding these interactions is crucial design biomonitoring programs detect effect different pollutants freshwater improve management conservation strategies. Therefore, paper qualitatively reviews studies evaluate on multiple scales watersheds. organized into four sections. first section presents systems (streams, rivers, lakes, reservoirs). In second section, we describe characteristics main types. third explain how biomonitoring. Finally, fourth focus planning future prediction discuss models eDNA Our review assist decision-making regarding watersheds guide bioindicators for various diverse worldwide.

Language: Английский

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Opportunities and inherent limits of using environmental DNA for population genetics

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(5), P. 1048 - 1064

Published: Aug. 9, 2023

Abstract Molecular techniques using DNA retrieved from community or environmental samples, in particular (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template population genetics, several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types “community‐based” such possibility to target multiple species same time, generated great enthusiasm expectations genetics. However, not every aspect genetics can be addressed eDNA‐based data some inherent limitations may challenge its conclusions. Here, we firstly review state current knowledge samples Then, focusing on eDNA, summarize but detail four main use population‐level inferences, namely, (1) difficulty retrieve species‐specific dataset, (2) potential lack correlation between observed true allelic frequencies, (3) loss information multi‐locus genotyping linkage loci, (4) uncertainty about individuals contributing sampled pool (e.g., number, life‐stage, sex). Some might overcome development new technologies models that account specificities eDNA. Others, however, inherent, their effect inferences must thoroughly evaluated. The gaining insights into genetic diversity structure is appealing scientists, conservation managers, other practitioners. Yet, avoid false incorrect it imperative known considered alongside advantages.

Language: Английский

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General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

Environmental DNA, Journal Year: 2022, Volume and Issue: 5(2), P. 326 - 342

Published: Dec. 18, 2022

Abstract Metabarcoding of environmental DNA (eDNA) is a powerful tool for describing biodiversity, such as finding keystone species or detecting invasive in samples. Continuous improvements the method and advances sequencing platforms over last decade have meant this approach now widely used biodiversity sciences biomonitoring. For its general use, hinges on correct identification taxa. However, past studies shown how crucially depends important decisions during sampling, sample processing, subsequent handling data. With no clear consensus to best practice, particularly latter has led varied bioinformatic approaches recommendations data preparation taxonomic identification. In study, using large freshwater fish eDNA sequence dataset, we compared frequently zero‐radius Operational Taxonomic Unit (zOTU) our raw reads assigned it taxonomically (i) combination with publicly available reference sequences (open databases) (ii) an OSU (Operational Sequence Units) database approach, curated generated from specimen barcoding (closed database). We show both gave comparable results common species. commonalities between decreased read abundance were thus less reliable not rare The success zOTU depended suitability, rather than size, database. Contrastingly, often enabled species‐level identifications, yet resolution recent phylogenetic age need include target group coverage, outgroups full annotation databases avoid misleading annotations that can occur when short amplicon sizes commonly metabarcoding studies. Finally, make suggestions improve construction use future.

Language: Английский

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Comparing morphological and DNA-based bioassessment methodologies for macroinvertebrates in Neotropical streams: a case study from Ecuador

Metabarcoding and Metagenomics, Journal Year: 2025, Volume and Issue: 9

Published: Feb. 25, 2025

As unimpacted freshwater environments decline worldwide, developing effective and accurate biomonitoring approaches is critical for detecting ecosystem deterioration facilitating conservation efforts. Freshwater macroinvertebrate communities comprise several phyla thus a broad taxonomic expertise required to identify these precisely. Molecular characterizing invertebrate have the potential be more accurate, time-effective, less costly than traditional morphological methods. However, evaluations comparing two methods macroinvertebrates are lacking in Neotropics, where rapid deployment increased accuracy due escalating of environments. In this study, we compared performance DNA bulk tissue metabarcoding using an eDNA primer pair (fwhF2 & EPTDr2n) methodologies identifying communities. Our aim was evaluate suitability assessing biological quality Ecuadorian streams along altitudinal gradient. We found low overlap between at family genus ranks, though many molecular OTUs were unclassified levels. Morphological identification resulted higher Andean-Amazonian Biotic Index (AAMBI) scores each site, with only three sites classified into same category both methodologies. One reason that family-level information used AAMBI. Existing barcode reference libraries contained incomplete coverage taxa specimens determined approach, indicating need improve representation generate complete determinations. study suggests requires development Neotropics should, moment, complementary approaches.

Language: Английский

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An integrative taxonomic approach reveals unexplored diversity in Croatian planarians

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 16, 2025

Abstract Background Freshwater ecosystems are among the most endangered habitats on Earth, with approximately one-fourth of aquatic species at risk extinction. Effective conservation efforts require comprehensive monitoring and accurate identification, including often overlooked groups. DNA barcoding promises rapid accessible identification but requires availability “universal” primer pairs robust, taxonomically curated reference libraries. Planarian flatworms one such group for which these resources currently lacking, even though they common constituents freshwater worldwide. As a result, true extent planarian diversity remains underappreciated in many areas. Results Motivated by highly skewed representation current GenBank records gene mitochondrial cytochrome c oxidase subunit I (COI), we optimised existing primers tested them planarians collected species-rich but, so far, poorly surveyed region Croatia. Using an integrative approach combining new primers, traditional taxonomy karyology, generated COI barcode sequences European dugesiids, dendrocoelids planariids, which, case latter two groups, represent substantial increase number entries those families. Our resulted several significant findings, description pigmented Dendrocoelum species, pigmentatum sp. nov, discovery differentiated haplotypic clades Schmidtea lugubris , rediscovery Polycladodes alba Croatia after century. Conclusions Overall, our work extends utility species-level to previously inaccessible Additionally, it integrates as underexplored into endeavour systematically describe fauna Europe. The expansion known Croatian from eight sixteen new, large continental Europe, demonstrate effectiveness approach. highlights planarians, Europe supports practical preserve biodiversity.

Language: Английский

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Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 21, 2025

Abstract Biodiversity loss is a global challenge of the 21st century. Environmental DNA (eDNA)-based metabarcoding offers cost- and time-efficient alternative to conventional biodiversity surveys, enabling detection rare, cryptic, elusive species from environmental samples. However, limited access genomic technologies restricts application eDNA in highly biodiverse remote regions low- middle-income countries. Here, we directly compared latest portable nanopore sequencing methods with established Illumina for vertebrate Zambian water We also evaluated cost-effective versus filtration approaches, contrasted comprehensive, computationally intensive taxonomic database search streamlined, manually curated search. Our results show that due recent improvements chemistry optimized basecalling, can recover many detected by sequencing, demonstrating feasibility situ assessment using platforms. We, however, found accurate remains superior quantity detections, eDNA- camera trap-based detections had minimal overlap, suggesting complementary rather than substituting these monitoring technologies. Finally, our findings underscore role completeness assignments, emphasizing need high-quality ecosystem-specific reference databases research.

Language: Английский

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