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Related Experiment Video

Updated: May 16, 2026

Continuous Instream Monitoring of Nutrients and Sediment in Agricultural Watersheds
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Fine-Scale Ecological Biomonitoring in a Large, Complex Agriculturally Impacted Watershed via eDNA Metabarcoding.

Bráulio S M L Silva1, Andrew C Riley1, Emilia Craiovan2

  • 1Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.

Molecular Ecology
|May 15, 2026
PubMed
Summary

DNA metabarcoding offers superior biodiversity assessment in Ontario watersheds compared to traditional methods. This DNA-based approach reveals more accurate ecological patterns influenced by land use and environmental factors.

Keywords:
COIDNA metabarcodingSouth Nation River watershedagricultural impactbenthic macroinvertebratesbiomonitoringenvironmental DNAfreshwater streamshigh‐throughput sequencing

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Area of Science:

  • Ecology
  • Environmental Science
  • Molecular Biology

Background:

  • Traditional morphology-based bioassessment has limitations in taxonomic resolution and cost-effectiveness.
  • High-throughput sequencing (HTS) and DNA metabarcoding offer advancements in ecological biomonitoring.
  • Agricultural land use significantly impacts aquatic ecosystems, necessitating precise monitoring tools.

Purpose of the Study:

  • To compare DNA metabarcoding with traditional morphology data for assessing benthic biodiversity in an Ontario watershed.
  • To understand biodiversity patterns across taxonomic scales in relation to land use gradients.
  • To evaluate the influence of environmental factors and land use on aquatic communities.

Main Methods:

  • Sampling of 18 watercourses across a forested-to-agricultural gradient in Ontario during summer and fall 2023.
  • Application of DNA metabarcoding for biodiversity assessment of benthic taxa.
  • Comparison of DNA metabarcoding results with historical morphological data and analysis of environmental variables.

Main Results:

  • DNA metabarcoding revealed significantly higher species and order richness compared to morphology data.
  • Morphology data had numerous unresolved taxa, while DNA metabarcoding captured broader taxonomic breadth.
  • Non-metric multidimensional scaling (NMDS) showed clearer separation of communities by land use using DNA data.
  • Land use and urban context significantly correlated with biodiversity patterns, with strong environmental signals (conductivity, turbidity, pH) in agricultural areas.

Conclusions:

  • DNA metabarcoding provides a more precise and comprehensive assessment of aquatic biodiversity than traditional methods.
  • Enhanced taxonomic resolution from DNA analysis is crucial for detecting community changes driven by anthropogenic and environmental factors.
  • This study underscores the value of DNA-based approaches for effective ecological biomonitoring in agriculturally impacted watersheds.