Macrozoobenthos monitoring in Portuguese transitional waters in the scope of the water framework directive using morphology and DNA metabarcoding

Estuarine Coastal and Shelf Science, Journal Year: 2022, Volume and Issue: 281, P. 108207 - 108207

Published: Dec. 29, 2022

Language: Английский

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Contrasting seasonal patterns in diet and dung‐associated invertebrates of feral cattle and horses in a rewilding area

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(8), P. 2071 - 2091

Published: Feb. 6, 2023

Abstract Trophic rewilding is increasingly applied in restoration efforts, with the aim of reintroducing ecological functions provided by large‐bodied mammals and thereby promote self‐regulating, biodiverse ecosystems. However, empirical evidence for effects megafauna introductions on abundance richness other organisms such as plants invertebrates, mechanisms involved still need strengthening. In this study, we use environmental DNA (eDNA) metabarcoding dung from co‐existing feral cattle horses to assess seasonal variation plant diet dung‐associated arthropods nematodes. We found consistently high horses, low variability, while generally lower dietary diversity increased substantially during summer. Intriguingly, season‐specific diets differed, a greater proportion trees horses' winter, where relied more shrubs. Graminoids were predominantly but underrepresented compared previous studies, possibly due prevalence forbs study area. Dung‐associated arthropod was higher cattle, largely flies Several species primarily one two herbivores, our data confirmed known patterns activity. Nematode constantly nematode communities markedly different between species. Our results demonstrate complementary through differences invertebrate communities, enhancing understanding large herbivore vegetation associated biodiversity. These are directly applicable decision‐making projects, suggesting biodiversity‐benefits inclusion functionally herbivores.

Language: Английский

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Mock samples resolve biases in diversity estimates and quantitative interpretation of zooplankton metabarcoding data

Marine Biodiversity, Journal Year: 2023, Volume and Issue: 53(5)

Published: Aug. 29, 2023

Abstract Metabarcoding is a rapidly developing tool in marine zooplankton ecology, although most surveys continue to rely on visual identification for monitoring purposes. We attempted resolve some of the biases associated with metabarcoding by sequencing 313-b.p. fragment COI gene 34 “mock” samples from North Sea which were pre-sorted species level, biomass and abundance estimates obtained each taxonomic group. The preserved either 97% ethanol or dehydrated 24 h drying oven at 65 °C (the routine way preserving dry weight measurements). yielded total 59 unique holoplanktonic 16 meroplanktonic species/taxa. identified 86 124 species/taxa, included all but 3 visually as well numerous hard-to-identify crustaceans, hydrozoan jellyfish, larvae benthic animals. On sample-to-sample basis, typically 90–95% registered recovered, number false positives was also high. demonstrate robust correlations relative sequence abundances groups develop conversion factors different taxa account biases. then combine adjusted data single bulk measurement entire sample produce quantitative parameter akin biomass. When examined multivariate statistics, this parameter, we call BWSR (biomass-weighed reads) showed very similar trends comparable patterns abundance, highlighting potential not only biodiversity estimation mapping presence/absence assessment communities.

Language: Английский

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Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon

Metabarcoding and Metagenomics, Journal Year: 2021, Volume and Issue: 5

Published: Dec. 16, 2021

The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy sequence quality. considerable growth in barcode data requires stringent curation, especially taxonomically difficult groups such as marine invertebrates. A major effort curating the Barcode Life Data Systems (BOLD) was undertaken during 8 th International Conference (Trondheim, Norway, 2019). Major taxonomic (crustaceans, echinoderms, molluscs, polychaetes) were reviewed to identify those which had disagreement between Linnaean names Index Numbers (BINs). annotated four tags: a) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous unresolved existing data), c) COMPLEX (species occurring multiple BINs), d) SHARE (barcodes shared species). total 83,712 corresponding 7,576 species 39% tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, 1% SHARE). High percentages (>50%) tags recorded gastropods, whereas dominated crustaceans polychaetes. high proportion reflects either flaws workflow (e.g., misidentification, cross-contamination) difficulties synonyms, undescribed Although curation is essential for applications, manual attempts examine large datasets are unsustainable automated solutions extremely desirable.

Language: Английский

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Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(2), P. 511 - 518

Published: Oct. 14, 2022

DNA barcoding and metabarcoding are revolutionizing the study survey of biodiversity. In order to assign taxonomic labels sequence data retrieved, these methods strongly dependent on comprehensive accurate reference databases. Producing reliable databases linking biological sequences can be-and often has been-done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when amount increases thousands taxa be matched, validation operations more complex error prone if done in a manual way. Thus, there is clear need for providing scientists with user-friendly, powerful manipulate manage tractable, sound efficient ways. Here, we introduce R package refdb an environment semi-automatic assisted construction libraries. The database manager offering set functions import, organize, clean, filter, audit export data. It broadly applicable generally obtained biodiversity biomonitoring studies. We present main features outline how speed up generation, management handling, thus contribute standardization repeatability

Language: Английский

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Maximizing the reliability and the number of species assignments in metabarcoding studies using a curated regional library and a public repository

Metabarcoding and Metagenomics, Journal Year: 2023, Volume and Issue: 7

Published: Feb. 23, 2023

Biodiversity assessments relying on DNA have increased rapidly over the last decade. However, reliability of taxonomic assignments in metabarcoding studies is variable and affected by reference databases assignment methods used. Species level are usually considered as reliable using regional libraries but unreliable public repositories. In this study, we aimed to test assumption for metazoan species detected Gulf St. Lawrence Northwest Atlantic. We first created a library (GSL-rl) data mining COI barcode sequences from BOLD, included ranking system assignments. then estimated 1) accuracy precision repository NCBI-nt 2) compared detection dataset either or popular methods. With library, BLAST-LCA (least common ancestor) method was most precise assignments, higher with BLAST-TopHit (>80% all taxa, between 70% 90% amongst groups). dataset, greater GSL-rl NCBI-nt. also observed that total number could be maximized both different optimized The use two-step approach i.e., repository, improve studies.

Language: Английский

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The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(2)

Published: Feb. 1, 2023

The main aim of this study was to curate a COI barcode library Chironomidae from the Tibetan Plateau (TP) as an essential supplement public database. Another is evaluate current status database in aspects taxonomic coverage, geographic representation, quality, and efficiency for molecular identification, Plateau, China. In study, 512 individuals TP were identified based on morphological taxonomy analysis. metadata records downloaded BOLD, quality barcodes ranked using BAGS program. reliability identification evaluated with newly curated BLAST method. comprised 159 species 54 genera, which 58.4% likely new science. There great gaps coverage representation database, only 29.18% at level. concern, 20% being determined concordant between BINs species. accuracy poor, about 50% matched could be correctly level identity threshold 97%. Based these data, some recommendations are included here improving barcoding studies Chironomidae. richness much higher than ever recorded. Barcodes more groups regions urgently needed fill gap Users should take caution when databases adopted reference libraries assignment.

Language: Английский

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Using the long-term genetic monitoring network ARMS-MBON to detect marine non-indigenous species along the European coasts

Biological Invasions, Journal Year: 2025, Volume and Issue: 27(2)

Published: Feb. 1, 2025

Abstract The increasing prevalence of non-indigenous species (NIS) in marine ecosystems poses significant challenges for biodiversity conservation and ecosystem management. Advances molecular techniques enable early detection long-term monitoring such taxa, especially when coupled with spatio-temporally wide sampling by networks as the European ARMS Marine Biodiversity Observation Network (ARMS-MBON). This initiative performs standardised campaigns using autonomous reef structures (ARMS) along coasts adjacent regions, providing open-access DNA metabarcoding data sets. We tested potential genetic observatory to detect monitor NIS analysing all publicly available ARMS-MBON cytochrome c oxidase subunit I (COI) 18S rRNA amplicon sequencing February 2024 a customised bioinformatic pipeline. Screening against World Register Introduced Species (WRiMS) applying manual curation, we identified 63 taxa considered at one or more locations. included widespread new introductions, Eucheilota menoni Adriatic Sea. found no significantly higher number samples from locations particularly impacted maritime traffic compared other areas. Our results suggest that network approach is powerful detecting NIS, curation still an essential step obtaining reliable results. recommend key improvements including spatially intense across diverse environments well enhancement reference checklists databases ensure accurate identification both known unknown Europe.

Language: Английский

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An annotated reference library for supporting DNA metabarcoding analysis of aquatic macroinvertebrates in French freshwater environments

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

Published: April 7, 2025

Freshwater ecosystems are increasingly threatened by human activities, leading to biodiversity loss and ecosystem degradation. Effective monitoring, particularly through the use of aquatic macroinvertebrates as bioindicators, is crucial for assessing ecological health. While traditional morphological methods face limitations, DNA metabarcoding offers higher accuracy efficiency in species identification using environmental DNA. However, success contingent on quality reference libraries, which often incomplete or biased. This study aimed construct share a comprehensive COI-based barcode library freshwater France, specifically targeting short gene regions amplified with fwhF2/fwhR2N primers, suitable degraded A list occurring French was established from official national checklists Alpine lake surveys. The resulting analysed taxonomic completeness, coverage cryptic diversity. checklist consisted 2,841 across 10 phyla, 56% had at least one COI-5P sequence available Barcode Life Data System (BOLD). analysis diversity, based Index Numbers (BINs) highlighted potential high rate although it might have been overestimated due wide geographic origin sequences. Alignment challenges primers were identified certain taxa, amongst Coleoptera, Diptera Malacostraca. genetic diversity approached number haplotypes per that most limited only three having more than 100 haplotypes. Finally, this showed total 57 shared 116 distinct species. work emphasises need expanded sequencing efforts improve pitfalls associated these further assessment

Language: Английский

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Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates

Metabarcoding and Metagenomics, Journal Year: 2021, Volume and Issue: 5

Published: Dec. 29, 2021

DNA metabarcoding has great potential to improve marine biomonitoring programs by providing a rapid and accurate assessment of species composition in zoobenthic communities. However, some methodological improvements are still required, especially regarding failed detections, primers efficiency incompleteness databases. Here we assessed the two different marker loci (COI 18S) three primer pairs detection through macrozoobenthic communities colonizing types artificial substrates (slate, PVC granite), sampled between 3 15 months deployment. To accurately compare success markers, also compared representativeness detected public databases revised reliability taxonomic assignments. Globally, recorded extensive complementarity each marker, with 69% exclusively either 18S or COI. Individually, recovered, at most, 52% all on samples, showing abilities amplify specific groups. Most have reliable reference sequences their respective (82% for COI 72% 18S), meaning that when was one not other, it most likely due faulty amplification, lack matching database. Overall, results showed impact applied ability indicated that, currently, if only single pair is employed zoobenthos metabarcoding, fair portion diversity may be overlooked.

Language: Английский

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