High‐throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally

Couton, Marjorie; Baud, Aurélien; Daguin‐Thiébaut, Claire; Corre, Erwan; Comtet, Thierry; Viard, Frédérique

doi:10.1002/ece3.7453

Cited by 13 publications

(15 citation statements)

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“…For instance, although abundant in quadrats from every location, the invasive colonial ascidian Didemnum vexillum, was not recovered in water-eDNA, whereas Simpson et al (2017) detected it in water samples from Australia using species-specific primers. Similarly, the invasive tunicate B. violaceus remained undetected because of identical sequences with congeneric species, although it can be distinguished from the introduced B. diegensis and native B. leachii using genus-specific primers (Couton et al 2021). Issues related to taxonomic resolution/accuracy were here (partly) addressed by combining several markers, as suggested by Zhang et al (2018), and by producing reference sequences for at least one marker for each NIS observed within quadrats.…”

Section: Improving the Quality Of Reference Data And Targeting Severa...mentioning

confidence: 99%

Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring

et al. 2022

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Marinas are high-priority targets for marine non-indigenous species (NIS), where they compose a large portion of the biofouling communities. The practicality of water samples collection makes environmental DNA (eDNA) metabarcoding an interesting tool for routine NIS surveys. Here the effectiveness of water-eDNA-metabarcoding to identify biofouling NIS, in ten marinas from western France, was examined. Morphological identification of specimens collected in quadrats brought out 18 sessile benthic NIS beneath floating pontoons. Water-eDNA-metabarcoding detected two thirds of them, failing to detect important NIS. However, sampling and bioinformatics filtering steps can be optimized to identify more species. In addition, this method allowed the detection of additional NIS from neighboring micro-habitats. Caution should however be taken when reporting putative novel NIS, because of errors in species assignment. This work highlights that water-eDNAmetabarcoding is effective for active (targeted) NIS surveys, and could be significantly improved for its further use in marine NIS passive surveys.

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Section: Improving the Quality Of Reference Data And Targeting Severa...mentioning

confidence: 99%

Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring

et al. 2022

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“…2019, 2020; Persaud et al . 2021) or population genetics (Couton et al . 2021) with EtOH-based metabarcoding as a potential replacement for homogenate metabarcoding.…”

Section: Discussionmentioning

confidence: 99%

“…CC-BY-NC-ND 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted February 7, 2023. ; https://doi.org/10.1101/2023.02.07.527242 doi: bioRxiv preprint previous studies highlighting the potential to monitor freshwater ecosystems (Zizka et al 2018;Martins et al 2019Martins et al , 2020Persaud et al 2021) or population genetics (Couton et al 2021) with EtOH-based metabarcoding as a potential replacement for homogenate metabarcoding.…”

Section: Community Analyses and Terrestrial Insect Monitoring From Co...mentioning

confidence: 99%

“…In total, 15 other studies have successfully used EtOH-based DNA metabarcoding techniques to characterize complex communities (Zizka et al 2018;Barbato et al 2019;Erdozain et al 2019;;Marquina et al 2019;Gauthier et al 2020 ;Martins et al 2019Martins et al , 2020Milián-Garcίa et al 2020;Young et al 2020;Zenker et al 2020;Couton et al 2021;Persaud et al 2021;Wang et al 2021b;Chimeno et al 2022b;Kirse et al 2022). Most of these studies found dissimilar communities between EtOH-based metabarcoding and their morphological sorting, bulk homogenate or environmental DNA (eDNA) metabarcoding counterparts and highlighted many technical steps to account for those differences.…”

Section: Introductionmentioning

confidence: 99%

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Non-destructive DNA metabarcoding of arthropods using collection medium from passive traps

Sire

Yáñez

Bézier

et al. 2023

Preprint

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Background: Broad-scale monitoring of arthropods is often carried out with passive traps (e.g. Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates is faster and has been found to be efficient and reliable, but is destructive and prevents a posteriori validation of species occurrences and/or relative abundances. Non-destructive DNA metabarcoding from the collection medium has been applied in a limited number of studies, but further tests of efficiency are required in a broader range of circumstances to assess the consistency of the method. Methods: We quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two types of passive traps and collection media: 1) water with monopropylene glycol (H2O-MPG) used in window-flight traps (WFT, 53 in total); 2) ethanol with monopropylene glycol (EtOH-MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir (Abies alba) stands across a range of climate-induced tree dieback levels and forest management strategies. Results: Of the 53 H2O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total. None of those MOTUs were shared species with the 389 morphological taxa (343 of which were Coleoptera) obtained from the same traps. Metabarcoding of 26 EtOH-MPG samples from MTs detected more arthropod MOTUs (233) and insect orders (11) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders). Arachnida and Collembola were more diverse in EtOH-MPG samples, but Hymenoptera, Coleoptera and Lepidoptera were less represented than in homogenate. Overall, MOTU richness per trap similar for EtOH-MPG (21.81 MOTUs) than for homogenate (32.4 MOTUs). Arthropod communities from EtOH-MPG and homogenate metabarcoding were relatively distinct, with 162 MOTUs (53%) unique to the collection medium and only 71 MOTUs (23%) present in both treatments. Finally, collection medium did not reveal any significant changes in arthropod richness along a disturbance gradient in silver fir forests. We conclude that DNA metabarcoding of collection medium can be used to complement homogenate metabarcoding in inventories to favour the detection of soft-bodied arthropods like spiders.

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“…DNA metabarcoding studies are typically based on a succession of experimental steps governed by important methodological choices (Zinger et al 2019). These include a) the definition of sampling design and selection of sampling sites (Dickie et al 2018), b) the approach used for the preservation of the starting material (Tatangelo et al 2014, Guerrieri et al 2021, c) the protocol used for DNA extraction (Taberlet et al 2012, Eichmiller et al 2016, Zinger et al 2016, Lear et al 2018, Capo et al 2021 the selection of appropriate primers to amplify a taxonomically-informative genomic region (Elbrecht et al 2016, Fahner et al 2016), e) the strategy adopted for DNA amplification and high-throughput sequencing of amplicons (Nichols et al 2018, Bohmann et al 2022, f) the pipeline selected for bioinformatics analyses (Boyer et al 2016, Calderon-Sanou et al 2020, Capo et al 2021, Couton et al 2021, Macher et al 2021, Machler et al 2021, and g) the statistical approach used to translate metabarcoding data into ecological information (Paliy andShankar 2016, Chen andFicetola 2020). Each of these methodological choices can heavily influence the reliability and interpretation of results (Alberdi et al 2018, and there is thus a critical need for the development, proper assessment and optimization of methods specially dedicated to DNA metabarcoding.…”

Section: Introductionmentioning

confidence: 99%

Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies

Bonin¹,

Guerrieri

Ficetola

2021

Preprint

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Clustering approaches are pivotal to handle the many sequence variants obtained in DNA metabarcoding datasets, therefore they have become a key step of metabarcoding analysis pipelines. Clustering often relies on a sequence similarity threshold to gather sequences in Molecular Operational Taxonomic Units (MOTUs) that ideally each represent a homogeneous taxonomic entity, e.g. a species or a genus. However, the choice of the clustering threshold is rarely justified, and its impact on MOTU over-splitting or over-merging even less tested. Here, we evaluated clustering threshold values for several metabarcoding markers under different criteria: limitation of MOTU over-merging, limitation of MOTU over-splitting, and trade-off between over-merging and over-splitting. We extracted sequences from a public database for eight markers, ranging from generalist markers targeting Bacteria or Eukaryota, to more specific markers targeting a class or a subclass (e.g. Insecta, Oligochaeta). Based on the distributions of pairwise sequence similarities within species and within genera and on the rates of over-splitting and over-merging across different clustering thresholds, we were able to propose threshold values minimizing the risk of over-splitting, that of over-merging, or offering a trade-off between the two risks. For generalist markers, high similarity thresholds (0.96-0.99) are generally appropriate, while more specific markers require lower values (0.85-0.96). These results do not support the use of a fixed clustering threshold (e.g. 0.97). Instead, we advocate a careful examination of the most appropriate threshold based on the research objectives, the potential costs of over-splitting and over-merging, and the features of the studied markers.

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High‐throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally

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 13 publications

References 58 publications

Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring

Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring

Non-destructive DNA metabarcoding of arthropods using collection medium from passive traps

Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies

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