Environmental versus extra‐organismal DNA

Pawłowski, Jan; Apothéloz-Perret-Gentil, Laure; Altermatt, Florian

doi:10.1111/mec.16144

Cited by 6 publications

(6 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Multiple reviews synthesised eDNA developments (e.g. Cristescu & Hebert, 2018; Deiner et al., 2017; Takahashi et al., 2023) to provide general recommendations for ecologists (Creer et al., 2016; Dickie et al., 2018; Goldberg et al., 2016; Pawlowski, Apothéloz‐Perret‐Gentil, et al., 2021; Pawlowski, Bonin, et al., 2021) or specific best practices for aquatic (e.g. Bruce et al., 2021; Pawlowski, Apothéloz‐Perret‐Gentil, & Altermatt, 2020; Pawlowski, Apothéloz‐Perret‐Gentil, Mächler, et al., 2020; Taberlet et al., 2018) or terrestrial (e.g.…”

Section: Current State and Future Needsmentioning

confidence: 99%

Environmental DNA: The next chapter

Blackman,

Couton,

Keck

et al. 2024

Molecular Ecology

Self Cite

View full text Add to dashboard Cite

Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well‐studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land‐mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer‐reviewed literature with a survey of eDNA users including academics, end‐users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever‐increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.

show abstract

Section: Current State and Future Needsmentioning

confidence: 99%

Environmental DNA: The next chapter

Blackman,

Couton,

Keck

et al. 2024

Molecular Ecology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Environmental DNA (eDNA) has been recently adopted as a base method to be used to detect DNA molecules that are shed, excreted, or otherwise derived from living or dead organisms, and left behind in the environment [3,4]. Based on recent discussions in the literature, the definition of eDNA includes the whole DNA present in an environmental sample, also incorporating that derived from entire microorganisms as well as microscopic stages of macroorganisms (e.g., larvae) [5,6].…”

Section: Introductionmentioning

confidence: 99%

Harmonizing perspectives: an integrative approach to monitoring metazoan diversity in a Mediterranean coastal area through morphology and organismal eDNA

Capua,

Luise,

Zampicinini

et al. 2024

Preprint

View full text Add to dashboard Cite

The use of metabarcoding has greatly improved the assessment of marine metazoans. However, it is still uncertain whether metabarcoding analyses (eDNA) accurately captures the diversity in the field. This study aims to use an integrated approach merging α-taxonomy and organismal eDNA analysis of two genetic markers (COI and 18S), to observe for the first time the metazoan community inhabiting in a submarine Canyon and compare it with already well-known at a Long-Term Ecological Research. Our research has emphasized the importance of harmonizing perspectives involved in assessing the planktonic metazoan community. This includes developing a consistent sampling strategy, obtaining high-quality DNA, ad hoc bioinformatic pipelines, interpreting results accurately, and finally microscopy-based identification to confirm molecular inference. All of these steps are crucial for monitoring metazoan diversity and distribution patterns. We have observed over 200 metazoan taxa and identified 174 species using COI, 107 using V9, and 84 using morphology-based methods. Our coverage is comprehensive and includes both holo- and mero-zooplanktonic organisms, with a wide taxonomic range that even includes fish. This study has revealed a extraordinary biodiversity of these Mediterranean Sea sites, highlighting both known and previously unidentified species (new entries and non-indigenous) and providing a holistic view of the pelagic realm.

show abstract

“…Based on both simulations and empirical data, we propose a set of criteria for the development of unbiased biodiversity detection when planning an eDNA sampling campaign for conservation and management. We focus on eDNA in the wider sense, that is, including both intra‐ and extracellular DNA, yet acknowledge the ongoing discussion about how the targeted DNA potentially reflects a wide range of organisms and possible states (see Pawlowski et al, 2021; Pawlowski, Apothéloz‐Perret‐Gentil, & Altermatt, 2020; Rodriguez‐Ezpeleta et al, 2021). Our general conclusions hold true irrespective of the different states of DNA, yet the specific recommendations for sampling may vary.…”

Section: Introductionmentioning

confidence: 99%

Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs

Altermatt

Carraro

Antonetti³

et al. 2023

Environmental DNA

Self Cite

View full text Add to dashboard Cite

Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems and informing policy and decision-making, especially in an era of massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at the forefront of technological advances in biodiversity monitoring, and the last few years have seen major progress and solutions to technical challenges from the laboratory to bioinformatics. Water eDNA has been shown to allow the fast and

show abstract

Environmental versus extra‐organismal DNA

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 6 publications

References 12 publications

Environmental DNA: The next chapter

Environmental DNA: The next chapter

Harmonizing perspectives: an integrative approach to monitoring metazoan diversity in a Mediterranean coastal area through morphology and organismal eDNA

Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs

Contact Info

Product

Resources

About