Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring

Molecular Ecology, Journal Year: 2020, Volume and Issue: 29(22), P. 4258 - 4264

Published: Sept. 23, 2020

The last decade brought a spectacular development of so-called environmental (e)DNA studies. In general, "environmental DNA" is defined as DNA isolated from samples, in contrast to genomic that extracted directly specimens. However, the variety different sources eDNA and range taxonomic groups are targeted by studies large, which has led some discussion about breadth concept. particular, there recent trend restrict use term "eDNA" macro-organisms, not physically present samples. this paper, we argue such distinction may be ideal, because signal can come organisms across whole tree life. Consequently, advocate should used its generic sense, originally defined, encompassing all including microbial, meiofaunal macrobial taxa. We first suggest specifying origin sample, water eDNA, sediment or soil eDNA. A second specification would then define group through polymerase chain reaction amplification, fish invertebrate bacterial This terminology does also require assumptions specific state sampled (intracellular extracellular). hope will help better scope studies, especially for managers, who them reference routine biomonitoring bioassessment.

Language: Английский

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Multiple stressors determine river ecological status at the European scale: Towards an integrated understanding of river status deterioration

Global Change Biology, Journal Year: 2020, Volume and Issue: 27(9), P. 1962 - 1975

Published: Dec. 29, 2020

Abstract The biota of European rivers are affected by a wide range stressors impairing water quality and hydro‐morphology. Only about 40% Europe's reach ‘good ecological status’, target set the Water Framework Directive (WFD) indicated biota. It is yet unknown how different in concert impact status relationship between differs river types. We linked intensity seven to recently measured data for more than 50,000 sub‐catchment units (covering almost 80% surface area), which were distributed among 12 broad Stressor either derived from remote sensing (extent urban agricultural land use riparian zone) or modelled (alteration mean annual flow base flow, total phosphorous load, nitrogen load mixture toxic pressure, composite metric substances), while on taken national statutory reporting second WFD River Basin Management Plans years 2010–2015. used Boosted Regression Trees link stressor intensities. explained average 61% deviance individual types, with all contributing considerably this explanation. On average, 39.4% was altered hydro‐morphology (morphology: 23.2%; hydrology: 16.2%), 34.4% nutrient enrichment 26.2% substances. More half interaction, substances interacting most frequently strongly. Our results underline that types determined co‐occurring multiple stressors, lending support conclusion fundamental management strategies at catchment scale required ambitious objective good waters.

Language: Английский

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Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(6), P. 1820 - 1835

Published: Jan. 25, 2022

Abstract DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated consistency this technique with traditional morpho‐taxonomic approaches. These individual to assess diversity community structure organisms both in marine freshwater systems globally over last decade. However, a systematic analysis comparability effectiveness DNA‐based across all these has hitherto been lacking. Here, we performed first meta‐analysis available comparing methods measure biological key groups, including plankton, microphytobentos, macroinvertebrates, fish. Across 215 data sets, found that provides richness estimates are consistent those obtained using methods, at local regional scale. also generates species inventories highly congruent Contrastingly, microphytobenthos macroinvertebrates by showed pronounced differences missing some taxa but same time detecting otherwise overseen diversity. The method generally sufficiently advanced study composition fish communities replace more invasive methods. For smaller organisms, like plankton microphytobenthos, may continue give complementary rather than identical compared Systematic comparable collection will increase understanding different aspects complementarity, adequate interpretation results.

Language: Английский

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Environmental DNA: The next chapter

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(11)

Published: April 16, 2024

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

Language: Английский

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Reviving Europe's rivers: Seven challenges in the implementation of the Nature Restoration Law to restore free‐flowing rivers

Wiley Interdisciplinary Reviews Water, Journal Year: 2024, Volume and Issue: 11(3)

Published: Jan. 30, 2024

Abstract The EU Nature Restoration Law represents an important opportunity for freshwater habitat restoration and, consequently, biodiversity protection. However, a number of challenges must be anticipated in its implementation, which may compromise success. Some aspects, particularly those relating to ecosystems, require more clarification. We use riverine ecosystems illustrate existing ambiguities the proposed legislation and potential consequences leaving these aspects open interpretation during implementation process. also discuss solutions problems could help ensure that law's objectives are met. argue river network structure connectivity dimensions, result into meta‐ecosystems, explicitly considered. For purpose, we ask clear definitions critical terms “free‐flowing rivers,” “barriers,” “reference areas.” In addition, recommend developing methods integrated assessment across networks. As key property this used prioritize actions increase length free‐flowing rivers. Adequate planning at larger spatial scales will benefit from meta‐ecosystem perspective accurate representation aquatic‐terrestrial linkages, significantly improve efficacy efforts. Furthermore, stakeholder citizen engagement offer opportunities local, national, European scales, should fostered inclusive decision‐making. conservation outlined here rivers, but they have implications other ecosystems. These considerations useful policymakers, conservationists, stakeholders involved related policy initiatives. This article is categorized under: Water Life > Stresses Pressures on Ecosystems Conservation, Management, Awareness Human Governance

Language: Английский

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Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: July 17, 2020

Abstract The alarming declines of freshwater biodiversity call for efficient biomonitoring at fine spatiotemporal scales, such that conservation measures be grounded upon accurate data. Here, we show combining environmental DNA (eDNA) extracted from stream water samples with models based on hydrological first principles allows upscaling estimates aquatic insects very high spatial resolution. Our model decouples the diverse upstream contributions to eDNA data, enabling reconstruction taxa distribution patterns. Across a 740-km 2 basin, obtain space-filling prediction grain size resolution 1-km long sections. model’s accuracy in matching direct observations insects’ local occurrence ranges between 57–100%. results demonstrate how can used high-resolution assessments rivers minimal prior knowledge system. approach identification hotspots could otherwise overlooked, implementation focused strategies.

Language: Английский

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Human activities' fingerprint on multitrophic biodiversity and ecosystem functions across a major river catchment in China

Global Change Biology, Journal Year: 2020, Volume and Issue: 26(12), P. 6867 - 6879

Published: Sept. 16, 2020

Abstract Human‐induced global change dramatically alters individual aspects of river biodiversity, such as taxonomic, phylogenetic or functional diversity, and is predicted to lead losses associated ecosystem functions. Understanding these dependencies are critical human well‐being. Until now, however, most studies have only looked either at organismal groups single functions, little known on the effect activities multitrophic biodiversity multifunctionality in riverine ecosystem. Here we profiled from bacteria invertebrates based environmental DNA (hereafter, ‘eDNA’) samples across a major catchment China, analysed their with multiple especially linked C/N/P‐cycling. Firstly, found spatial cross‐taxon congruence pattern communities' structure network Shaying river, which was related strong filtering due land use. Secondly, use explained decline multifaceted but increased redundancy Thirdly, function relationships an integrative level showed concave‐up (non‐saturating) shape. Finally, structural equation modeling suggested that affects functions through biodiversity‐mediated pathways, including loss altered community interdependence groups. Our study highlights value complete inclusive assessment for integrated land‐use management ecosystems.

Language: Английский

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Sampling and modelling rare species: Conceptual guidelines for the neglected majority

Global Change Biology, Journal Year: 2022, Volume and Issue: 28(12), P. 3754 - 3777

Published: Jan. 31, 2022

Biodiversity conservation faces a methodological conundrum: measurement often relies on species, most of which are rare at various scales, especially prone to extinction under global change, but also the challenging sample and model. Predicting distribution change species using conventional models is because hardly captured by survey systems. When enough data available, predictions usually spatially biased towards locations where likely occur, violating assumptions many modelling frameworks. Workflows predict eventually map distributions imply important trade-offs between quantity, quality, representativeness model complexity that need be considered prior analysis. Our opinion study designs carefully integrate different steps, from sampling modelling, in accordance with types rarity available order improve our capacity for sound assessment prediction distribution. In this article, we summarize comment how categories lead occurrence depending choices made during process, namely spatial samples (where sample) protocol each selected location (how sample). We then clarify suitable model). Among others, forms, highlight insights systematic species-targeted coupled hierarchical allow correcting overdispersion sources bias. article provides scientists practitioners much-needed guide through ever-increasing diversity developments type data.

Language: Английский

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Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics uncovered across a river catchment using environmental DNA

Communications Biology, Journal Year: 2022, Volume and Issue: 5(1)

Published: March 23, 2022

Abstract Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study multi-trophic food webs at a large spatial temporal resolution has been prohibited by the lack appropriate access such data from natural systems. Here, we assessed characteristics across 700 km 2 riverine network over seasons using environmental DNA. We found contrasting patterns between major taxonomic groups. Local richness showed statistically significant, season-dependent increases decreases towards downstream location within catchment fish bacteria, respectively. Meanwhile, invertebrate remained spatially unchanged but varied seasons. The local webs, as link density nestedness, also space time. these did not necessarily mirror those observed functional feeding characteristics. Our results suggest that dynamics are directly scalable each other even same scales. In order conserve species diversity well trophic integrity communities, must thus be jointly studied.

Language: Английский

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

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(4), P. 671 - 682

Published: May 16, 2023

Abstract Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems informing policy decision‐making, especially in an era massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at forefront technological advances monitoring, last few years have seen major progress solutions to technical challenges from laboratory bioinformatics. Water eDNA has been shown allow fast efficient recovery signals, but rapid pace development meant that some important principles regarding sampling design, which well established traditional inventories, neglected. Using a spatially explicit river flow model, we illustrate how must be adjusted size watercourse increase quality signal recovered. We additionally investigate effect parameters (volume, number sites, sequencing depth) detection probability empirical data set. Based principles, propose aquatic replication volume scaled match organisms' ecosystems' properties provide reliable estimates. present generalizable conceptual equation describing features as function ecosystem monitored, abundance target organisms, procedure. The aim this formalization enhance standardization critical steps design inventory studies using eDNA. More robust standards will generate more eDNA, necessary method's long‐term plausibility comparability.

Language: Английский

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