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

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(13), P. 3497 - 3512

Published: April 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.

Language: Английский

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Environmental DNA time series analysis of a temperate stream reveals distinct seasonal community and functional shifts

River Research and Applications, Journal Year: 2024, Volume and Issue: 40(5), P. 850 - 862

Published: March 9, 2024

Abstract Environmental DNA (eDNA) extracted from water is routinely used in river biodiversity research, and via metabarcoding eDNA can provide comprehensive taxa lists with little effort cost. However, eDNA‐based species detection streams rivers may be influenced by sampling season other key factors such as temperature discharge. Research linking these also informing on the potential of to detect shifts ecological signatures, phenology functional feeding groups across seasons, missing. To address this gap, we collected samples every 2 weeks for 15 months at a long‐term research (LTER) site three different positions river's cross section, specifically surface, riverbed, riverbank. For 102 samples, analyzed macroinvertebrate molecular operational taxonomic unit (OTU) richness temporal community turnover seasons based cytochrome c oxidase subunit I (COI) data. Using Generalized Additive Models, found significant influence richness. Community followed cyclic pattern, reflecting continuous change throughout year (“seasonal clock”). Although had no inferred richness, higher discharge reduced number Annelida Ephemeroptera detectable eDNA. Most showed highest spring, particular merolimnic univoltine life cycles. Further, detected an increase proportion shredders winter parasites summer. Our results show usefulness highly resolved time series data monitoring rivers.

Language: Английский

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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

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Integrating citizen science and environmental DNA metabarcoding to study biodiversity of groundwater amphipods in Switzerland

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

Published: Oct. 23, 2023

Groundwater is the physically largest freshwater ecosystem, yet one of least explored habitats on earth, both because accessing difficulties and scarcity organisms inhabiting it. Here, we demonstrate how a two-fold approach provides complementary information occurrence diversity groundwater amphipods. Firstly, used citizen science in collaboration with municipal water providers who sampled their spring catchment boxes over multiple weeks, followed by DNA barcoding. Secondly, collected four 10 L samples at each site, sampling event, for environmental (eDNA) metabarcoding. We found that was very effective describing distribution abundance Although single time-point eDNA did not detect as many amphipods, it allowed assessment entire community, including microorganisms. By combining methods, different amphipod species co-occurring distinct sequences from eDNA-metabarcoding dataset, representing mainly micro-eukaryotic species. also correlation between amphipods overall biodiversity detected site. thus suggest these approaches can be to get better understanding subterranean biodiversity.

Language: Английский

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Comparing morphological and DNA-based bioassessment methodologies for macroinvertebrates in Neotropical streams: a case study from Ecuador

Metabarcoding and Metagenomics, Journal Year: 2025, Volume and Issue: 9

Published: Feb. 25, 2025

As unimpacted freshwater environments decline worldwide, developing effective and accurate biomonitoring approaches is critical for detecting ecosystem deterioration facilitating conservation efforts. Freshwater macroinvertebrate communities comprise several phyla thus a broad taxonomic expertise required to identify these precisely. Molecular characterizing invertebrate have the potential be more accurate, time-effective, less costly than traditional morphological methods. However, evaluations comparing two methods macroinvertebrates are lacking in Neotropics, where rapid deployment increased accuracy due escalating of environments. In this study, we compared performance DNA bulk tissue metabarcoding using an eDNA primer pair (fwhF2 & EPTDr2n) methodologies identifying communities. Our aim was evaluate suitability assessing biological quality Ecuadorian streams along altitudinal gradient. We found low overlap between at family genus ranks, though many molecular OTUs were unclassified levels. Morphological identification resulted higher Andean-Amazonian Biotic Index (AAMBI) scores each site, with only three sites classified into same category both methodologies. One reason that family-level information used AAMBI. Existing barcode reference libraries contained incomplete coverage taxa specimens determined approach, indicating need improve representation generate complete determinations. study suggests requires development Neotropics should, moment, complementary approaches.

Language: Английский

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Environmental Matrices Need Consideration: Insights From Water and Biofilm Environmental DNA for Multi‐Taxonomic Biomonitoring

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Environmental DNA (eDNA) is revolutionizing biodiversity monitoring, offering a unique approach to assess multi‐taxonomic diversity with various applications related evaluation, protection, and restoration of aquatic ecosystems. However, there still lack sufficient studies the complementarity environmental matrices their contribution enhancing detection. This study evaluates impact eDNA sampling in different measure taxonomic groups. We set up year‐long water biofilm large lake littoral zone (Lake Geneva), focusing on microalgae, benthic macroinvertebrates, fish. first assessed primer specificity, which was high for microalgae (23S) fish (12S) but lower macroinvertebrates (COI). then evaluated signals biofilms. For communities from were highly different: almost exclusively detected planktonic taxa while predominantly taxa. biofilms also different, could detect mostly Chironomidae. Finally, fish, both enabled us similar even if few rare species only water. In framework assessment ecosystem quality or actions success, we recommend diversifying collect capture complete picture macroinvertebrate communities. it possible sample biofilms, keeping mind that has become standard practice sampling.

Language: Английский

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Assessing metabarcoding-based identifications for monitoring beetle communities in temperate forests

Basic and Applied Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

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River benthic macroinvertebrates and environmental DNA metabarcoding: a scoping review of eDNA sampling, extraction, amplification and sequencing methods

Biodiversity and Conservation, Journal Year: 2023, Volume and Issue: 32(13), P. 4221 - 4238

Published: Sept. 12, 2023

Abstract There is a growing body of literature on the use molecular methods for ecological assessment rivers based benthic macroinvertebrates. Previous research has established benefits environmental DNA (eDNA) to assess macroinvertebrate communities as being more efficient, less subjective, and non-invasive compared traditional methods. The aim this review synthesize existing knowledge eDNA sampling, extraction, amplification sequencing regarding river metabarcoding studies. Literature searches were performed using two online databases, following screening process, 46 papers published between 2012 2022 met eligibility criteria be included in review. Since macrobial ecology fast-evolving field, results showed that methodologies used vary considerably among A variety filters are capturing from water or preservative ethanol different sources (i.e., sediment, biofilm) also explored. This identified 12 extraction 15 primer pairs than once Therefore, there need standardization some key steps process increase comparability robustness further implementation into large-scale monitoring programs.

Language: Английский

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A combination of machine‐learning and eDNA reveals the genetic signature of environmental change at the landscape levels

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(17), P. 4791 - 4800

Published: July 12, 2023

Abstract The current advances of environmental DNA (eDNA) bring profound changes to ecological monitoring and provide unique insights on the biological diversity ecosystems. very nature eDNA data is challenging yet also revolutionizing how information analysed. In particular, new metrics approaches should take full advantage extent detail molecular produced by genetic methods. this perspective, machine learning algorithms are particularly promising as they can capture complex relationships between multiple pressures communities. We investigated potential a generation biomonitoring tools that implement machine‐learning techniques fully exploit datasets. trained model discriminate reference impacted communities freshwater macroinvertebrates assessed its performances using large dataset collected at 64 standard federal sites across Switzerland. show significantly better than naive performs similarly traditional data. Our proof‐of‐concept shows such combination has complement or even replace monitoring, could be scaled along temporal spatial dimensions.

Language: Английский

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