Meta‐analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards

Fediajevaite, Julija; Priestley, Victoria; Arnold, Richard; Savolainen, Vincent

doi:10.1002/ece3.7382

Cited by 119 publications

(109 citation statements)

References 130 publications

(141 reference statements)

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“…Emerging DNA-based approaches have the potential to contribute towards evaluating river restoration success in several ways. DNA metabarcoding has repeatedly been shown to detect a greater number of species than traditional monitoring approaches such as kick-sampling and electrofishing [126]. Field, laboratory, and bioinformatic protocols to optimise the process are becoming better established for a range of taxa, from diatoms to fish and mammals.…”

Section: Dna-based Approachesmentioning

confidence: 99%

“…Certain genes and transcripts have known ecological functions (e.g., cellulose degradation) and have been shown to respond with high specificity to particular stressors [127]. For example, the bacterial organophosphate hydrolase gene (opd) indicates pesticide degradation, whilst the ammonia monoxygenase gene (amoA) is activated during periods of intense organic matter breakdown [126]. New applications of these approaches from microbial ecology could be used to identify the main stressors on potential restoration sites and to monitor the status of those stressors at restored sites.…”

Section: Dna-based Approachesmentioning

confidence: 99%

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Best Practices for Monitoring and Assessing the Ecological Response to River Restoration

England

Angelopoulos²,

Cooksley

et al. 2021

Water

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Nature-based solutions are widely advocated for freshwater ecosystem conservation and restoration. As increasing amounts of river restoration are undertaken, the need to understand the ecological response to different measures and where measures are best applied becomes more pressing. It is essential that appraisal methods follow a sound scientific approach. Here, experienced restoration appraisal experts review current best practice and academic knowledge to make recommendations and provide guidance that will enable practitioners to gather and analyse meaningful data, using scientific rigor to appraise restoration success. What should be monitored depends on the river type and the type and scale of intervention. By understanding how habitats are likely to change we can anticipate what species, life stages, and communities are likely to be affected. Monitoring should therefore be integrated and include both environmental/habitat and biota assessments. A robust scientific approach to monitoring and appraisal is resource intensive. We recommend that appraisal efforts be directed to where they will provide the greatest evidence, including ‘flagship’ restoration schemes for detailed long-term monitoring. Such an approach will provide the evidence needed to understand which restoration measures work where and ensure that they can be applied with confidence elsewhere.

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Section: Dna-based Approachesmentioning

confidence: 99%

Section: Dna-based Approachesmentioning

confidence: 99%

Best Practices for Monitoring and Assessing the Ecological Response to River Restoration

England

Angelopoulos²,

Cooksley

et al. 2021

Water

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“…The incorporation of species detection through bulk DNA obtained from environmental samples (environmental DNA, eDNA) is revolutionizing the way researchers monitor the marine biome (Bowers et al, 2021; Ficetola et al, 2008). By inferring species presence and absence indirectly through molecular approaches, eDNA surveys do not rely on visual observations, thereby simplifying species detection within inaccessible environments (Fediajevaite et al, 2021). In addition, the complexity of the DNA signal contained within environmental samples facilitates the detection of a broad range of taxonomic groups, and a larger number of individual species, than can be achieved using traditional monitoring (Jeunen et al, 2020; Kelly et al, 2017; Kim et al, 2019; Thomsen et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Jeunen

Cane

Ferreira

et al. 2021

Preprint

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Aquatic environmental DNA (eDNA) surveys are transforming how we monitor marine ecosystems. The time-consuming pre-processing step of active filtration, however, remains a bottleneck. Hence, new approaches omitting active filtration are in great demand. One exciting prospect is to use the filtering power of invertebrates to collect eDNA. While proof-of-concept has been achieved, comparative studies between aquatic and filter feeder eDNA signals are lacking. Here, we investigated the differences among four eDNA sources (water; bivalves; sponges; and ethanol in which filter-feeding organisms were stored) along a vertical transect in Doubtful Sound, New Zealand using three metabarcoding primers (fish (16S); MiFish-E/U). While concurrent SCUBA diver observations validated eDNA results, laboratory trials corroborated in-field bivalve eDNA detection results. Combined, eDNA sources detected 59 vertebrates, while divers observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was detected in ethanol, although only a reduced number of species were detected. Bivalves failed to reliably detect eDNA in both field and mesocosm experiments. While additional research into filter feeder eDNA accumulation efficiency is essential, our results provide strong evidence for the potential of incorporating sponges into eDNA surveys.

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“…Studies have demonstrated that the amplification of DNA barcode regions from eDNA (i.e. eDNA metabarcoding) can be used to detect marine NNS [32][33][34][35] and that it is a sensitive and accurate method for biomonitoring [36,37]. However, eDNA surveys are rarely used in conjunction with existing methods to detect NNS range shifts, and eDNA metabarcoding can validate, endorse, or highlight flaws, in current biodiversity management strategies.…”

Section: Introductionmentioning

confidence: 99%

Managing human mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

Holman

Parker-Nance

Bruyn

et al. 2021

Preprint

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The use of molecular methods to manage natural resources is increasingly common. However, DNA-based methods are seldom used to understand the spatial and temporal dynamics of species' range shifts. This is important when managing range-shifting species such as non-native species (NNS), which can have negative impacts on biotic communities. Here we investigated the range-shifting NNS Ciona robusta, Clavelina lepadiformis, Microcosmus squamiger and Styela plicata using a combined methodological approach. We first conducted non-molecular biodiversity surveys for these NSS along the South African coastline, and compared the results with historical surveys. We detected no consistent change in range size across species, with some displaying range stability and others showing range shifts. We then sequenced a section of cytochrome c oxidase subunit I (COI) from tissue samples and found genetic differences along the coastline but no change over recent times. Finally, we found that environmental DNA metabarcoding data showed broad congruence with both the non-molecular biodiversity and the COI datasets, but failed to capture complete incidence of all NSS. Overall, we demonstrated how a combined methodological approach can effectively detect spatial and temporal variation in genetic composition and range size, which is key for managing biodiversity changes of both threatened and NSS.

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Meta‐analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards

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 119 publications

References 130 publications

Best Practices for Monitoring and Assessing the Ecological Response to River Restoration

Best Practices for Monitoring and Assessing the Ecological Response to River Restoration

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Managing human mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

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