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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The Application of eDNA for Monitoring Aquatic Non-Indigenous Species: Practical and Policy Considerations

Diversity, Год журнала: 2023, Номер 15(5), С. 631 - 631

Опубликована: Май 6, 2023

Aquatic non-indigenous species (NIS) threaten biodiversity, ecosystem functions, and the economy worldwide. Monitoring NIS is of immediate concern to identify newly arriving species, assess efficacy mitigation measures, report long-term indicators introduction, spread, impacts. The challenges associated with conventional methods specimen collection morphological identification have led development alternative methods, such as DNA-based which could offer rapid cost-effective detection NIS. Depending on whether a few (targeted monitoring) or many (passive are being monitored, environmental DNA (eDNA) can infer presence-absence relative abundances, enabling informed decisions actions be made based patterns detection. Compared more eDNA tools increase levels sensitivity for rare elusive even noticeable some taxa when using targeted monitoring. use not only minimizes onus taxonomic expertise reduces resource demands but also sensitive cost-efficient in detecting NIS, thus proving its value an early warning tool. As nucleic acid (DNA/RNA) advance rapidly detection, there must balance between method sensitivity, logistical requirements, costs, factored into future management decisions. While complementary reviews available, our aim emphasize importance incorporating surveys highlight available opportunities this field.

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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Groundwater environmental DNA metabarcoding reveals hidden diversity and reflects land‐use and geology

Molecular Ecology, Год журнала: 2023, Номер 32(13), С. 3497 - 3512

Опубликована: Апрель 17, 2023

Abstract Despite being the most important source of liquid freshwater on planet, groundwater is severely threatened by climate change, agriculture, or industrial mining. It thus extensively monitored for pollutants and declines in quantity. The organisms living groundwater, however, are rarely target surveillance programmes little known about fauna inhabiting underground habitats. difficulties accessing lack expertise, apparent scarcity these challenge sampling prohibit adequate knowledge fauna. Environmental DNA (eDNA) metabarcoding provides an approach to overcome limitations but largely unexplored. Here, we sampled water 20 communal spring catchment boxes used drinking provisioning Switzerland, with a high level replication at both filtration amplification steps. We sequenced portion COI mitochondrial gene, which resulted 4917 ASVs, yet only 3% reads could be assigned species, genus, family more than 90% identity. Careful evaluation unassigned corroborated that sequences were true belonging mostly diverse eukaryotic groups, not present reference databases. Principal component analyses showed strong correlation community composition surface land‐use (agriculture vs. forest) geology (fissured rock unconsolidated sediment). While incomplete databases limit assignment taxa eDNA metabarcoding, taxonomy‐free approaches can reveal large hidden diversity couple it major drivers, revealing their imprint chemical biological properties groundwater.

Язык: Английский

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eDNA Is a Useful Environmental Monitoring Tool for Assessing Stream Ecological Health

Environmental DNA, Год журнала: 2024, Номер 6(4)

Опубликована: Июль 1, 2024

ABSTRACT Environmental DNA (eDNA) is increasingly used in biodiversity assessments, but there remain uncertainties regarding its congruence with data based on traditional approaches involving habitat sampling and morphological‐based taxonomy. Using eDNA for biomonitoring has several advantages, including improved processing efficiencies precision of taxonomic identification. In contrast, time‐consuming expensive, often limiting the number sites monitored. Establishing that eDNA‐derived metrics are congruent their equivalents a national scale would support wider use biomonitoring. Our study compared ecosystem health assessments made by techniques to those using from 53 throughout Aotearoa New Zealand. Because was not done concurrently benthic at most sites, we average community composition each site previous occasions. We also allocated species identified level identification allow comparisons broader groups. assessed similarities between three datasets found high degree correlation convergence biotic indices calculated different methods. did, however, appear under‐represent some taxa, reflecting challenges matching barcodes an often‐incomplete sequence library. did always perform better terms showing effects land invertebrate composition, all produced similar patterns. Multivariate analyses (redundancy analysis variation partitioning) relationships environmental spatial variables structure described replicated responses showed same overall patterns as traditionally collected data. suggest can complement methods, will least well detecting scale.

Язык: Английский

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Habitat suitability models reveal the spatial signal of environmental DNA in riverine networks

Ecography, Год журнала: 2024, Номер 2024(8)

Опубликована: Май 30, 2024

The rapid loss of biodiversity in freshwater systems asks for a robust and spatially explicit understanding species' occurrences. As two complementing approaches, habitat suitability models provide information about potential occurrence, while environmental DNA (eDNA) based assessments indication actual occurrence. Individually, both approaches are used ecological studies to characterize biodiversity, yet they rarely combined. Here, we integrated high‐resolution with eDNA‐based aquatic invertebrates riverine networks understand their individual combined capacity inform on We eDNA sampling data from 172 river sites the detection taxa three insect orders (Ephemeroptera, Plecoptera, Trichoptera; hereafter EPT) suitable predictions at subcatchment level (2 km 2 ). Overall, find congruence detections. Yet, predicted habitats beyond number detections by sampling, congruent niche being larger than realized niche. For local mismatches, where detected species but was not suitable, calculated minimal distance upstream patches, indicating possible sources signals subsequently transported along water flow. estimated median 1.06 (range 0.2–42 km) transport suitability, this significantly smaller expected null model predictions. This is range previously reported values allows extrapolations distances across many systems. Together, combination scale integrative inferences ultimately needed management protection biodiversity.

Язык: Английский

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Consideration of Multitrophic Biodiversity and Ecosystem Functions Improves Indices on River Ecological Status

Environmental Science & Technology, Год журнала: 2021, Номер 55(24), С. 16434 - 16444

Опубликована: Дек. 9, 2021

Biological quality elements have been developed worldwide to assess whether a water body is in good status or not. However, current studies mainly focus on single taxonomic group small set of species, often limited by methods morphological identification, and lack further aspects biodiversity (e.g., across taxa multiple attributes) ecosystem functions. Here, we advance framework for assessing the river's ecological based complete data measured environmental DNA (eDNA) metabarcoding measurements functions addition physicochemical large riverine system China. We identified 40 indicators functions, covering five groups from bacteria invertebrates, associated with attributes Our show that human impact ecosystems could be accurately predicted these eDNA-based using cross-validation known stressor gradient. Moreover, indices not only distinguish characteristics sites but also improve assessment accuracy 20–30% status. Overall, incorporating functional elements, multidimensional perspectives states provide additional information protect maintain rivers.

Язык: Английский

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General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

Environmental DNA, Год журнала: 2022, Номер 5(2), С. 326 - 342

Опубликована: Дек. 18, 2022

Abstract Metabarcoding of environmental DNA (eDNA) is a powerful tool for describing biodiversity, such as finding keystone species or detecting invasive in samples. Continuous improvements the method and advances sequencing platforms over last decade have meant this approach now widely used biodiversity sciences biomonitoring. For its general use, hinges on correct identification taxa. However, past studies shown how crucially depends important decisions during sampling, sample processing, subsequent handling data. With no clear consensus to best practice, particularly latter has led varied bioinformatic approaches recommendations data preparation taxonomic identification. In study, using large freshwater fish eDNA sequence dataset, we compared frequently zero‐radius Operational Taxonomic Unit (zOTU) our raw reads assigned it taxonomically (i) combination with publicly available reference sequences (open databases) (ii) an OSU (Operational Sequence Units) database approach, curated generated from specimen barcoding (closed database). We show both gave comparable results common species. commonalities between decreased read abundance were thus less reliable not rare The success zOTU depended suitability, rather than size, database. Contrastingly, often enabled species‐level identifications, yet resolution recent phylogenetic age need include target group coverage, outgroups full annotation databases avoid misleading annotations that can occur when short amplicon sizes commonly metabarcoding studies. Finally, make suggestions improve construction use future.

Язык: Английский

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Unsupervised biological integrity assessment by eDNA biomonitoring of multi-trophic aquatic taxa

Environment International, Год журнала: 2023, Номер 175, С. 107950 - 107950

Опубликована: Апрель 28, 2023

The biological integrity of global freshwater ecosystems is threatened by ever-increasing environmental stressors due to increased human activities, such as land-use change, eutrophication, toxic pollutants, overfishing, and exploitation. Traditional ecological assessments lake or riverine often require supervision a pre-selected reference area, using the current state area expected state. However, selecting an appropriate has become increasingly difficult with expansion activities. Here, unsupervised assessment framework based on DNA metabarcoding without prior proposed. Taxon richness, species dominance, co-occurrence network density, phylogenetic distance were used assess aquatic communities in Taihu Lake basin. Multi-gene revealed comprehensive biodiversity at multiple trophic levels including algae, protists, zooplankton, fish. Fish sequences mainly derived from 12S, zooplankton mitochondrial cytochrome C oxidase subunit I, algae protists 18S. There significant differences community composition among lakes, rivers, reservoirs but no four fundamental indicators. algal integrities positively correlated protist fish integrities, respectively. Additionally, lakes was found be significantly lower than that rivers. proposed this study allows different ecosystems, same ecosystem seasons, adopt indicators methods, which more convenient for management decision-making.

Язык: Английский

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Opportunities and inherent limits of using environmental DNA for population genetics

Environmental DNA, Год журнала: 2023, Номер 5(5), С. 1048 - 1064

Опубликована: Авг. 9, 2023

Abstract Molecular techniques using DNA retrieved from community or environmental samples, in particular (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template population genetics, several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types “community‐based” such possibility to target multiple species same time, generated great enthusiasm expectations genetics. However, not every aspect genetics can be addressed eDNA‐based data some inherent limitations may challenge its conclusions. Here, we firstly review state current knowledge samples Then, focusing on eDNA, summarize but detail four main use population‐level inferences, namely, (1) difficulty retrieve species‐specific dataset, (2) potential lack correlation between observed true allelic frequencies, (3) loss information multi‐locus genotyping linkage loci, (4) uncertainty about individuals contributing sampled pool (e.g., number, life‐stage, sex). Some might overcome development new technologies models that account specificities eDNA. Others, however, inherent, their effect inferences must thoroughly evaluated. The gaining insights into genetic diversity structure is appealing scientists, conservation managers, other practitioners. Yet, avoid false incorrect it imperative known considered alongside advantages.

Язык: Английский

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