DNAqua‐Net conference unites participants from around the world with the quest to standardize and implement DNA‐based aquatic biomonitoring

Bohmann, Kristine; Chua, Physilia; Holman, Luke E.; Lynggaard, Christina

doi:10.1002/edn3.207

Cited by 7 publications

(4 citation statements)

References 15 publications

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“…Standardized protocols to process eDNA are under development (e.g. Bohmann et al, 2021), but to implement these efficiently it is necessary to compare biases in taxa detection associated with different protocols. Here, we have explored the detection biases in community composition introduced by freezing water samples prior to filtration (for storage purposes), and the use of sediment samples as an alternative to sampling turbid waters.…”

Section: Discussionmentioning

confidence: 99%

Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

Turba¹,

Thai²,

Jacobs³

2023

Peer Community Journal

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Section: Discussionmentioning

confidence: 99%

Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

Turba¹,

Thai²,

Jacobs³

2023

Peer Community Journal

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“…DNA‐based methods, especially metabarcoding of water eDNA, has shown great promise for biodiversity monitoring (Cordier et al, 2018; Deiner et al, 2021; Fediajevaite et al, 2021; Pawlowski et al, 2018; Porter & Hajibabaei, 2018; Ruppert et al, 2019; Zieritz et al, 2022). Therefore, large consortia are forming to explore the use of eDNA for assessing the biodiversity of freshwater habitats in many countries (e.g., DNAqua‐Net: Bohmann et al, 2021; Leese et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, large consortia are forming to explore the use of eDNA for assessing the biodiversity of freshwater habitats in many countries (e.g., DNAqua-Net: Bohmann et al, 2021;Leese et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Toward eDNA‐based bioassessment of freshwater reservoirs with small volumes of water: Robust molecular protocols

et al. 2022

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Bioassessment of freshwater quality with eDNA is a powerful alternative to traditional methods involving collecting, sorting, and identifying metazoan taxa with morphology (e.g., macroinvertebrates). Particularly attractive for routine monitoring would be an eDNA method that uses a remote-controlled boat for collecting small volumes of water without filtration in order to simplify sampling. Such a method would not likely capture eDNA signals for all metazoan species, but may nevertheless allow for cost-effective, and frequent monitoring of water quality, which is important for tropical waterbodies that require year-round surveillance. We here optimize a molecular protocol for capturing metazoan signatures based on eDNA obtained from 15 ml of water. To test the robustness of the method, we used samples from two tropical reservoirs with known differences in water quality to optimize molecular procedures so that they yield repeatable results. Each reservoir was sampled at three sites ("biological replicates") and each water sample was subsampled twice before extracting the eDNA using ethanol precipitation for both subsamples ("technical replicates"). We then tested how much DNA (0.1 ng to 15 ng) and how many PCR cycles (25 or 35) minimized the variance of the metazoan eDNA signal between biological and technical replicates. For this purpose, we amplified a 313 bp COI minibarcode using a universal metazoan primer pair. We found that regardless of template amounts or PCR cycle numbers, the eDNA signatures for both reservoirs were distinct because only 17 of 59 mOTUs (mainly planktonic crustaceans and rotifers) were shared. We also found that template amounts between 0.5 and 15 ng yielded overall similar results, but the use of 35 PCR cycles significantly depressed the number of detected species (p-value < 0.05). Fortunately, the differences between the detected metazoan community of the reservoirs were so strong that all biological and technical replicates could be assigned unambiguously to their source reservoir although the variance between technical replicates remained high for all PCR experiments (Bray-Curtis dissimilarity: 5%-20%; Jaccard distance: 10%-40%).

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“…, Tautz et al, 2003 ), and identification with DNA-barcodes ( Hebert et al, 2003 ) been used as efficient alternatives to traditional methods. The technological developments of high throughput DNA sequencing have offered new tools to study biodiversity based on environmental DNA (eDNA) ( Taberlet et al, 2012a , 2012b ; Ji et al, 2013 ; Gibson et al, 2015 ; Lacoursière-Roussel et al, 2018 ; Wangensteen & Turon, 2017 ; Schadewell & Adams, 2021 ; Bohmann et al, 2021 ; Mugnai et al, 2021 ). Whilst some applications in marine environments have been relatively open-end inventories of metazoan diversity ( e.g.…”

Section: Introductionmentioning

confidence: 99%

Benthic invertebrates in Svalbard fjords—when metabarcoding does not outperform traditional biodiversity assessment

Willassen

Westgaard

Kongsrud

et al. 2022

PeerJ

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To protect and restore ecosystems and biodiversity is one of the 10 challenges identified by the United Nations’s Decade of the Ocean Science. In this study we used eDNA from sediments collected in two fjords of the Svalbard archipelago and compared the taxonomic composition with traditional methods through metabarcoding, targeting mitochondrial CO1, to survey benthos. Clustering of 21.6 mill sequence reads with a d value of 13 in swarm, returned about 25 K OTU reads. An identification search with the BOLD database returned 12,000 taxonomy annotated sequences spanning a similarity range of 50% to 100%. Using an acceptance filter of minimum 90% similarity to the CO1 reference sequence, we found that 74% of the ca 100 taxon identified sequence reads were Polychaeta and 22% Nematoda. Relatively few other benthic invertebrate species were detected. Many of the identified sequence reads were extra-organismal DNA from terrestrial, planktonic, and photic zone sources. For the species rich Polychaeta, we found that, on average, only 20.6% of the species identified from morphology were also detected with DNA. This discrepancy was not due to missing reference sequences in the search database, because 90–100% (mean 96.7%) of the visually identified species at each station were represented with barcodes in Boldsystems. The volume of DNA samples is small compared with the volume searched in visual sorting, and the replicate DNA-samples in sum covered only about 2% of the surface area of a grab. This may considerably reduce the detection rate of species that are not uniformly distributed in the sediments. Along with PCR amplification bias and primer mismatch, this may be an important reason for the limited congruence of species identified with the two approaches. However, metabarcoding also identified 69 additional species that are usually overlooked in visual sample sorting, demonstrating how metabarcoding can complement traditional methodology by detecting additional, less conspicuous groups of organisms.

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DNAqua‐Net conference unites participants from around the world with the quest to standardize and implement DNA‐based aquatic biomonitoring

Cited by 7 publications

References 15 publications

Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

Toward eDNA‐based bioassessment of freshwater reservoirs with small volumes of water: Robust molecular protocols

Benthic invertebrates in Svalbard fjords—when metabarcoding does not outperform traditional biodiversity assessment

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