Environmental DNA: The next chapter

Molecular Ecology, Год журнала: 2024, Номер 33(11)

Опубликована: Апрель 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.

Язык: Английский

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TICI: a taxon-independent community index for eDNA-based ecological health assessment

PeerJ, Год журнала: 2024, Номер 12, С. e16963 - e16963

Опубликована: Фев. 26, 2024

Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods difficult scale, limited in scope, suffer prohibitive costs, skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible scalable solution survey across the tree-of-life with relatively low cost minimal expertise for sample collection. However, there remains need condense complex, multidimensional community information into simple, interpretable metrics of ecological health environmental management purposes. We developed riverine taxon-independent index (TICI) objectively assigns indicator values amplicon sequence variants (ASVs), significantly improves statistical power utility eDNA-based bioassessments. The TICI model training step uses Chessman iterative learning algorithm assign scores large number ASVs commonly encountered wide geographic range. New sites then evaluated by averaging value present site. trained on eDNA dataset from 53 well-studied monitoring Zealand, each sampled high level biological replication ( n = 16). Eight short-amplicon assays were used generate broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, animals. Site-specific strongly correlated historical stream macroinvertebrate assessments (macroinvertebrate MCI; R 2 0.82), variation replicates was (CV 0.013). Taken together, this demonstrates potential analysis provide reliable, robust low-cost assessment accessible managers, decision makers, wider community.

Язык: Английский

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Groundwater is a hidden global keystone ecosystem

Global Change Biology, Год журнала: 2023, Номер 30(1)

Опубликована: Дек. 12, 2023

Abstract Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being largest unfrozen freshwater resource, in period depletion by extraction pollution, groundwater environments have been repeatedly overlooked conservation agendas. Disregarding importance as an ignores its critical role preserving surface biomes. To foster timely groundwater, we propose elevating concept keystone species into realm ecosystems, claiming that influences integrity many dependent ecosystems. Our analysis shows over half land areas (52.6%) has medium‐to‐high interaction with reaching up 74.9% when deserts high mountains are excluded. We postulate intrinsic transboundary features for shifting perspectives towards more holistic approaches aquatic ecology beyond. Furthermore, eight key themes develop science‐policy integrated agenda. Given ecosystems above below ground intersect at levels, considering component planetary health pivotal reduce loss buffer against climate change.

Язык: Английский

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Toward a national eDNA strategy for the United States

Environmental DNA, Год журнала: 2023, Номер 6(1)

Опубликована: Май 24, 2023

Abstract Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution scale. As use‐cases multiply scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity decide how where fit into their mandates. Within United States, many federal state are individually using in various applications developing relevant expertise. A national strategy for implementation would capitalize on recent developments, providing a common set next‐generation tools natural resource management health protection. Such avoid patchwork possibly inconsistent guidelines different agencies, smoothing way efficient uptake management. Because analysis is already widespread use both ocean freshwater settings, we focus here these environments. However, foresee broad adoption meet issues across nation because same immediate terrestrial aerial applications.

Язык: Английский

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Navigating the depths of seafood authentication: Technologies, regulations, and future prospects

Measurement Food, Год журнала: 2024, Номер 14, С. 100165 - 100165

Опубликована: Апрель 4, 2024

This review presents a comprehensive analysis of the current advancements and challenges in seafood traceability authentication, emphasizing its ecological significance context global marine ecosystems. The study extensively explores various methodologies employed traceability, including isotope chemical fingerprinting, DNA identification, smart sensors, digital technologies, blockchain. Each method's efficacy determining provenance authenticity is critically examined, highlighting their roles mitigating issues like mislabeling illegal fishing. also delves into complex regulatory frameworks standards shaping industry, underscoring importance international collaboration standardizing practices ensuring compliance. Additionally, paper addresses policy implementation, particularly disparities technological infrastructure harmonization diverse legal systems. role eco-labels certification programs promoting sustainable ethical discussed. By integrating wide spectrum technologies policies, this not only sheds light on state but identifies key areas requiring further research development. findings underscore critical need for more integrated advanced approaches to enhance sustainability resources ensure long-term viability industry.

Язык: Английский

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Measuring the state of aquatic environments using eDNA—upscaling spatial resolution of biotic indices

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2024, Номер 379(1904)

Опубликована: Май 5, 2024

Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they strongly affected by anthropogenic activities. As of these taxa highly sensitive to environmental change, offer particularly good early warning system for human-induced thus leading their intense monitoring. In ecosystems there is plethora biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported freshwater alone. Ultimately, macroinvertebrates used calculate ecological indices describing the state systems. Many not only hard compare, but especially difficult scale in time space. Novel DNA-based approaches measure change environments now unprecedented opportunities, also possible integration towards commonly applicable indices. Here, we first give perspective on organisms, focus insects, how move beyond traditional point-based Second, demonstrate proof-of-concept spatially upscaling based DNA, demonstrating novel molecular hydrological models allows an accurate evaluation at catchment scale. This article part theme issue ‘Towards toolkit global biodiversity monitoring’.

Язык: Английский

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Fish as a Sustainable Biomonitoring Tool in Aquatic Environments

Опубликована: Янв. 1, 2024

Biomonitoring involves the use of biological organisms to detect or measure presence various toxic substances rather on land in water. Fish resides aquatic environments and its position at top food chain has made it a useful tool for biomonitoring. They can easily accumulate pollutants that are bio-available environment, most especially their gills. The composition, abundance, distribution fish species give potential indication condition environments. Other such as crustaceans, zooplankton, macro micro invertebrates also be used because they ubiquitous. is principally dictated by effects land-based activities, which affect water quality composition. Humans other hand exposed bio-accumulated when plants consumed from polluted In lieu this, therefore essential sustainably biomonitor environments, either with tool. Productivity impaired primary production inhibited increased concentration organic wastes. responses pollution biomonitoring recorded form percentage mortality, enzymatic responses, histological electrolyte haematological genotoxicity DNA changes. environment biotic abiotic components tool, may regulated biomarker application approaches. Conversely, sustainable approaches indicator geared. This review, therefore, emphasizes population composition relation pollution, human health monitoring, plant behavioural environmental factors pollutants, employed indication.

Язык: Английский

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LIFE PREDATOR: Prevent, detect, combat the spread of Silurus glanis in south European lakes to protect biodiversity

NeoBiota, Год журнала: 2024, Номер 93, С. 225 - 244

Опубликована: Июнь 13, 2024

The management of Invasive Alien Species (IAS) is often hindered by ecological, social and economic factors, resulting in inadequate biodiversity protection inefficient use public money. A clear example such aquatic ecosystems the European catfish Silurus glanis L. southern Europe. Native to central Eurasia, S. an emblematic controversial freshwater fish, being subject extensive profitable trophy angling Europe commercial fishing eastern Concurrently, western where it was introduced XIX century, considered a problematic invader. lack comprehensive information on invasive populations has limited effective management, which critical successfully control spread minimize negative impacts native species. LIFE PREDATOR, started September 2022 with budget € 2.85 million consortium six partners from three countries, aims at developing multidisciplinary transnational approach established , prevent further spreading future introductions lakes reservoirs. project will develop test early warning system based eDNA citizen science identify most selective capture techniques reduce abundance catfish, particularly Natura 2000 lakes, actively involving anglers professional fishermen this. Massive raising awareness campaigns be conducted targeting but also general public, protocols best practices transferred authorities. For long-term sustainability project, South Management Group created. Additionally, northern Italy, invasion more advanced, local circular economy implemented, increase pressure encouraging consumption as food.

Язык: Английский

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Quantifying invasion dynamics: Quantitative polymerase chain reaction vs. droplet digital polymerase chain reaction in monitoring the alien invasive bloody‐red shrimp Hemimysis anomala and its interaction with perch in Lake Geneva

Limnology and Oceanography Methods, Год журнала: 2025, Номер unknown

Опубликована: Янв. 7, 2025

Abstract Invasive alien species constitute a major threat to aquatic systems due their potential impact on endemic biodiversity, ecosystem functioning, infrastructure, and possible sanitary issues. It is therefore crucial obtain information presence, abundance, distribution. The bloody‐red shrimp Hemimysis anomala , which originated from the Ponto‐Caspian area, has recently settled in Western European lakes, including Lake Geneva. Although divers have frequently reported presence development of this small crustacean over last decade, no monitoring yet been proposed. During period 2.5 yr, we tested optimized an environmental deoxyribonucleic acid approach by comparing two polymerase chain reaction techniques, quantitative digital droplet reaction, assess dynamics animal as well that predator, perch ( Perca fluviatilis ). We show discuss efficiency methods reveal for first time seasonal at selected site highlight, agreement with diving observations, animal's abundance high winter declines rapidly early spring, concomitantly temperature increase presence.

Язык: Английский

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Targeting Terrestrial Vertebrates With eDNA: Trends, Perspectives, and Considerations for Sampling

Environmental DNA, Год журнала: 2025, Номер 7(1)

Опубликована: Янв. 1, 2025

ABSTRACT Terrestrial vertebrates are experiencing worldwide population declines and species extinctions. To effectively conserve remaining populations species, rapid, cost‐effective, scalable methods needed to complement longstanding monitoring methods. Increasingly, environmental DNA (eDNA)‐based approaches being used for terrestrial vertebrate biomonitoring within a range of environments. However, as we move eDNA onto land, presented with new set challenges. This necessitates the development “best‐practice” sample collection guidelines systems purpose detecting vertebrates. address these needs, conducted systematic literature review 143 peer‐reviewed papers applying (excluding Lissamphibia) that were published between 2012 2023. We summarize use biomonitoring, focusing on study design field techniques. Over decade observe steady growth in annual number publications, 3 33 The majority reviewed studies targeted mammals temperate forest regions. While an equal focused metabarcoding approach assess community taxon composition and/or species‐specific detection methods, novel uses increasingly published. These include animal behavior genetics. record three types sampling strategies, eight different substrate types, seven preservation suggesting there is no “one size fits all” eDNA‐based methodology when With multitude aims, across environments, target organisms ecologies, standardization extremely challenging. table known factors influencing Furthermore, identify five key considerations be addressed targeting aim guiding decision making.

Язык: Английский

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