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

---

Towards a toolkit for global insect biodiversity monitoring

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1904)

Published: May 5, 2024

Insects are the most diverse group of animals on Earth, yet our knowledge their diversity, ecology and population trends remains abysmally poor. Four major technological approaches coming to fruition for use in insect monitoring ecological research—molecular methods, computer vision, autonomous acoustic radar-based remote sensing—each which has seen advances over past years. Together, they have potential revolutionize ecology, make all-taxa, fine-grained feasible across globe. So far, within among technologies largely taken place isolation, parallel efforts projects led redundancy a methodological sprawl; yet, given commonalities goals approaches, increased collaboration integration could provide unprecedented improvements taxonomic spatio-temporal resolution coverage. This theme issue showcases recent developments state-of-the-art applications these technologies, outlines way forward regarding data processing, cost-effectiveness, meaningful trend analysis, open requirements. papers set stage future automated monitoring. article is part ‘Towards toolkit global biodiversity monitoring’.

Language: Английский

---

eDITH: An R‐package to spatially project eDNA‐based biodiversity across river networks with minimal prior information

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(5), P. 806 - 815

Published: March 27, 2024

Abstract Ecological and ecosystem monitoring is rapidly shifting towards using environmental DNA (eDNA) data, particularly in aquatic systems. This approach enables a combined coverage of biodiversity across all major organismal groups the assessment ecological indices. Yet, most current approaches are not exploiting full potential eDNA largely interpreting results localized perspective. In riverine networks, by explicitly modelling hydrological transport associated decay, hydrology‐based models enable upscaling eDNA‐based diversity information, providing spatially integrated inference. To capitalize on these unprecedented data translate it into space‐filling projections, streamlined implementation needed. Here, we introduce eDITH R‐package, implementing model to project networks with minimal prior information. couples species distribution relating local taxon's shedding rate streamwater covariates, mass balance expressing concentration at river's cross‐section as weighted sum upstream contributions, an observational accounting for uncertainties measurements. By leveraging replicated measurements hydro‐morphological disentangling various sources, produces maps spatial any chosen resolution. applicable both metabarcoding taxon whose can be retrieved streamwater. The package provides user‐friendly functions single‐run execution fitting Bayesian methods (via BayesianTools package) non‐linear optimization. An interface DHARMa allows validation via posterior predictive checks. Necessary preliminary steps such watershed delineation characterization implemented rivnet package. We illustrate 's workflow functionalities two case studies from published fish data. eDITH, specifically intended ecologists conservation biologists. It used without previous knowledge but also customization experienced users. Ultimately, river globally, transforming how state change systems tracked high resolution highly versatile manner.

Language: Английский

---

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

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1904)

Published: May 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’.

Language: Английский

---

Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Environmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling analytical efforts are needed to improve estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade-offs design effective eDNA monitoring studies. We conducted a water survey of vertebrates Mediterranean watershed identify key factors influencing species richness composition estimates. examined the impacts using high- versus low-capacity filtration capsules, varying levels biological technical replication, pooling PCR replicates before indexing. The primary sources variation identified were capsule capacity site replication across watershed. While within sites also improved effects comparatively smaller. Pooling indexing performed more poorly than analysing them independently. Methodological stronger on terrestrial aquatic species. Based these results, we recommend priority should be given high-capacity multiple sites. Site-level deserves lower priority, especially when filtering large volumes. crucial for detecting rare but balanced with eventually site-level replication. Avoiding important enhance sensitivity Overall, stress importance balancing choices constraints goals, emphasise need assessing different systems.

Language: Английский

---

Modelling environmental DNA transport in rivers reveals highly resolved spatio-temporal biodiversity patterns

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: May 31, 2023

Abstract The ever-increasing threats to riverine ecosystems call for novel approaches highly resolved biodiversity assessments across taxonomic groups and spatio-temporal scales. Recent advances in the joint use of environmental DNA (eDNA) data eDNA transport models rivers (e.g., eDITH) allow uncovering full structure biodiversity, hence elucidating ecosystem processes supporting conservation measures. We applied eDITH a metabarcoding dataset covering three (fish, invertebrates, bacteria) seasons catchment sampled at 73 sites. upscaled eDNA-based predictions approximately 1900 reaches, assessed α - β -diversity patterns over whole network. Genus richness predicted by was generally higher than values from direct analysis. Both varied depending on season group. Predicted fish increased downstream all seasons, while invertebrate bacteria either decreased or were unrelated network position. Spatial mostly downstream, especially bacteria. model yielded more refined assessment freshwater as compared raw data, both terms spatial coverage, diversity effect covariates, thus providing complete picture biodiversity.

Language: Английский

---

Evaluating eDNA and eRNA metabarcoding for aquatic biodiversity assessment: From bacteria to vertebrates

Environmental Science and Ecotechnology, Journal Year: 2024, Volume and Issue: 21, P. 100441 - 100441

Published: June 12, 2024

The monitoring and management of aquatic ecosystems depend on precise estimates biodiversity. Metabarcoding analyses environmental nucleic acids (eNAs), including DNA (eDNA) RNA (eRNA), have garnered attention for their cost-effective non-invasive biomonitoring capabilities. However, the accuracy biodiversity obtained through eNAs can vary among different organismal groups. Here we evaluate performance eDNA eRNA metabarcoding across nine groups, ranging from bacteria to terrestrial vertebrates, in three cross-sections Yangtze River, China. We observe robust complementarity between data. relative detectability was notably influenced by major taxonomic groups sizes, with providing more signals larger organisms. Both exhibited similar cross-sectional longitudinal patterns. organisms declined metabarcoding, possibly due differential release decay or sizes. While underscoring potential large river biomonitoring, emphasize need interpretation versus This highlights importance careful method selection studies.

Language: Английский

---

Coupling remote sensing and eDNA to monitor environmental impact: A pilot to quantify the environmental benefits of sustainable agriculture in the Brazilian Amazon

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(2), P. e0289437 - e0289437

Published: Feb. 14, 2024

Monitoring is essential to ensure that environmental goals are being achieved, including those of sustainable agriculture. Growing interest in monitoring provides an opportunity improve practices. Approaches directly monitor land cover change and biodiversity annually by coupling the wall-to-wall coverage from remote sensing site-specific community composition DNA (eDNA) can provide timely, relevant results for parties interested success agricultural To measured impacts due projects not exogenous factors, sites where have been implemented should be benchmarked against counterfactuals (no project) control (natural habitat) sites. Results then used calculate diverse sets indicators customized different projects. Here, we report on our experience developing applying one such approach assess impact shaded cocoa Instituto de Manejo e Certificação Florestal Agrícola (IMAFLORA) near São Félix do Xingu, Pará, Brazil. We Continuous Degradation Detection (CODED) LandTrendr algorithms create a sensing-based assessment forest disturbance regeneration, estimate carbon sequestration, changes habitats. coupled these methods with eDNA analyses using arthropod-targeted primers collecting soil samples intervention counterfactual pasture field secondary forest. custom set pilot application framework called TerraBio. Our suggest that, IMAFLORA’s projects, over 400 acres were restored area arthropods closer second-growth forests than pastures. In reviewing approach, found multiple aspects worked well, conclude presenting lessons learned.

Language: Английский

---

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

Ecography, Journal Year: 2024, Volume and Issue: 2024(8)

Published: May 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.

Language: Английский

---

Enhancing environmental DNA metabarcoding from marine ecosystems: Impact of filter type, storage method, and storage time on the assessment of fish alpha and beta diversity

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(3)

Published: May 1, 2024

Abstract The collection of environmental DNA (eDNA) and subsequent metabarcoding are useful tools for assessing marine fish biodiversity noninvasively. It is particular importance to evaluate in regions that hard access thus less well studied. Sampling preservation methods tailored the specific circumstances required. Aquatic eDNA often captured on filters made different materials pore sizes, subsequently stored under divergent conditions varying periods time. Previous studies multispecies detection systems have primarily focused capture extraction effects. Our study, contrast, examined effects filter type, storage method, time yield, alpha (i.e., ZOTU richness) beta diversity composition) recovered from a ecosystem Shark Bay, Western Australia. We compared two types (cellulose‐nitrate with sizes 0.45 μm; glass‐fiber 0.1 μm), (preservation Longmire's solution drying, respectively), various times (30–68 days) assays using fish‐specific primers. results showed decreased yield affected estimates. Cellulose‐nitrate proved be best combination smallest decrease no effect consistent community compositions. Storing led estimates increasing Furthermore, largest change each metabarcode was found regardless method. highlight considering interactions between method when analyzing results, especially storing samples an extended period or comparison durations.

Language: Английский

---