Drone-assisted collection of environmental DNA from tree branches for biodiversity monitoring

Science Robotics, Journal Year: 2023, Volume and Issue: 8(74)

Published: Jan. 18, 2023

The protection and restoration of the biosphere is crucial for human resilience well-being, but scarcity data on status distribution biodiversity puts these efforts at risk. DNA released into environment by organisms, i.e., environmental (eDNA), can be used to monitor in a scalable manner if equipped with appropriate tool. However, collection eDNA terrestrial environments remains challenge because many potential surfaces sources that need surveyed their limited accessibility. Here, we propose survey sampling outer branches tree canopies an aerial robot. drone combines force-sensing cage haptic-based control strategy establish maintain contact upper surface branches. Surface then collected using adhesive integrated drone. We show autonomously land variety stiffnesses between 1 103 newton/meter without prior knowledge structural stiffness robustness linear angular misalignments. Validation natural demonstrates our method successful detecting animal species, including arthropods vertebrates. Combining robotics from unreachable aboveground substrates offer solution broad-scale monitoring biodiversity.

Language: Английский

---

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

---

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

---

Extracting abundance information from DNA‐based data

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(1), P. 174 - 189

Published: Aug. 20, 2022

The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food-web reconstruction, the inference species interactions, modelling population dynamics distributions, biomonitoring environmental state change, false positives negatives. However, multiple sources bias noise in sampling processing combine inject error into sets. To understand how extract abundance information, it is useful distinguish two concepts. (i) Within-sample across-species quantification describes relative abundances one sample. (ii) Across-sample within-species each individual varies sample sample, such as over a time series, an gradient or different experimental treatments. First, we review literature on methods recover (by removing what call "species pipeline biases") "pipeline noise"). We argue that many ecological questions can be answered with just quantification, therefore demonstrate use "DNA spike-in" correct for information. also introduce model-based estimator used sets without physical spike-in approximate noise.

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

---

Monitoring terrestrial rewilding with environmental DNA metabarcoding: a systematic review of current trends and recommendations

Frontiers in Conservation Science, Journal Year: 2025, Volume and Issue: 5

Published: Jan. 2, 2025

Introduction Rewilding, the facilitation of self-sustaining and resilient ecosystems by restoring natural processes, is an increasingly popular conservation approach potential solution to biodiversity climate crises. Outcomes rewilding can be unpredictable, monitoring essential determine whether are recovering. Metabarcoding, particularly environmental DNA (eDNA), revolutionizing could play important role in understanding impacts but has mostly been applied within aquatic systems. Methods This systematic review focuses on applications eDNA metabarcoding terrestrial monitoring, with additional insights from bulk ingested DNA. We examine publication trends, choice sampling substrate focal taxa, investigate how well performs compared other methods (e.g. camera trapping). Results Terrestrial represented a small proportion total papers, forests most studied system, soil water substrates, vertebrates targeted taxa. Most studies focused measuring species richness, few included analyzes functional diversity. Greater richness was found when using multiple took this approach. Metabarcoding did not consistently outperform terms number vertebrate taxa detected, likely influenced marker, habitat. Discussion Our findings indicate that metabarcoding, eDNA, key rewilding, further ground- truthing needed establish appropriate experimental pipelines for target system interest. Systematic Review Registration https://osf.io/38w9q/?view_only=47fdab224a7a43d298eccbe578f1fcf0 , identifier 38w9q.

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

---

A review of applications of environmental DNA for reptile conservation and management

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(6)

Published: June 1, 2022

Abstract Reptile populations are in decline globally, with total reptile abundance halving the past half century, and approximately a fifth of species currently threatened extinction. Research on distributions, population trends, trophic interactions can greatly improve accuracy conservation listings planning for recovery, but data deficiency is an impediment many species. Environmental DNA (eDNA) detect measure community diversity at diverse spatio‐temporal scales, especially useful detection elusive, cryptic, or rare species, making it potentially very valuable herpetology. We aim to summarize utility eDNA as tool informing management discuss benefits limitations this approach. A literature review was conducted collect all studies that used focus ecology, conservation, management. Results search summarized into key discussion points, also draws from other taxa highlight methodological challenges identify future research directions. has had limited application reptiles, relative vertebrate groups, little use regions high richness. techniques have been more successfully applied aquatic reptiles than terrestrial most (64%) focused habitats. Two four reptilian orders dominate existing (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our provides direction emerging ecology when be paired traditional monitoring approaches. Technologies associated rapidly advancing, become sensitive accessible, we expect will increasingly addressing knowledge gaps reptiles.

Language: Английский

---

Combining surface and soil environmental DNA with artificial cover objects to improve terrestrial reptile survey detection

Conservation Biology, Journal Year: 2022, Volume and Issue: 36(6)

Published: Aug. 24, 2022

Reptiles are increasingly of conservation concern due to their susceptibility habitat loss, emerging disease, and harvest in the wildlife trade. However, reptile populations often difficult monitor given frequency crypsis life history. This difficulty has left uncertain status many species efficacy actions unknown. Environmental DNA (eDNA) surveys consistently elevate detection rate they designed monitor, while use is promising for terrestrial conservation, successes developing such have been sparse. We tested degree which inclusion surface soil eDNA sampling into conventional artificial-cover methods elevates probability a small, cryptic lizard, Scincella lateralis. The cover object surfaces with paint rollers elevated per sample probabilities this 4-16 times compared visual alone. readily detected S. lateralis under objects up 2 weeks after last detection, at some where no were visually observed prior months. With sufficient intensity, testing produced comparable as roller methods. Our results suggest that combining can considerably increase power monitoring programs, allowing more accurate estimates population size, temporal spatial changes use, tracking success restoration efforts. Further research deposition decay rates objects, well tailored protocols different habitats, needed bring technique widespread use.El interés por la conservación de los reptiles es cada vez mayor debido su susceptibilidad ante pérdida del hábitat, enfermedades emergentes y captura para el mercado fauna. Sin embargo, las poblaciones son difíciles monitorear lo frecuente que cripsis en sus historias vida. Esta dificultad deja incierto estado muchas especies desconocida eficacia acciones conservación. Los censos ADN ambiental (DNAa) elevan sistemáticamente tasa detección monitorean, aunque uso prometedor terrestres, han sido escasos éxitos desarrollo dichos censos. Analizamos grado al inclusión muestreo DNAa superficial suelo métodos convencionales cobertura artificial eleva probabilidad una pequeña lagartija terrestre críptica: El superficies con objetos rodillos pintura elevó probabilidades muestra esta especie veces más visuales. Detectamos fácilmente bajo cubierta hasta dos semanas después última algunos donde se había observado meses previos Con suficiente intensidad muestreo, análisis produjo comparables como rodillo superficial. Nuestros resultados sugieren combinación puede incrementar considerablemente poder programas monitoreo reptiles, permite estimaciones precisas tamaño poblacional, cambios espaciales temporales hábitat éxito rastreo esfuerzos restauración. Además, necesita investigación sobre tasas depósito descomposición cubierta, así protocolos hechos diferentes hábitats, técnica entre difundido.

Language: Английский

---

Sampling environmental DNA from trees and soil to detect cryptic arboreal mammals

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

Published: Jan. 5, 2023

Abstract Environmental DNA (eDNA) approaches to monitoring biodiversity in terrestrial environments have largely focused on sampling water bodies, potentially limiting the geographic and taxonomic scope of eDNA investigations. We assessed performance two strictly detect arboreal mammals, a guild with many threatened poorly studied taxa worldwide, within central New Jersey (USA) woodlands. evaluated species detected metabarcoding using collection methods (tree bark vs. soil sampling), compared detection (qPCR metabarcoding) single species. Our survey, which included 94 events at 21 trees, 16 representing over 60% diversity expected area. More was found for 8 versus non-arboreal (mean: 2466 289 reads/sample). Soil samples revealed generally similar composition, but lower diversity, mammal Detection rates big brown bat were 3.4 × higher qPCR metabarcoding, illustrating enhanced sensitivity single-species approaches. results suggest that from around trees could serve as useful new tool cryptic communities globally.

Language: Английский

---