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Laboratory and In-Field Metagenomics for Environmental Monitoring.

Harry T Child1, Daniel G Barber1, Supattra Maneein2,3

  • 1Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, Devon, UK.

Methods in Molecular Biology (Clifton, N.J.)
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Summary

We present a field-deployable protocol for environmental DNA (eDNA) metagenomics using Oxford Nanopore sequencing. This method enables comprehensive habitat analysis through direct DNA sequencing from environmental samples.

Keywords:
Biodiversity monitoringMicrobiomeMolecular ecologyOxford NanoporeeDNA

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Area of Science:

  • Environmental science
  • Genomics
  • Bioinformatics

Background:

  • Environmental DNA (eDNA) analysis is a powerful tool for biodiversity assessment.
  • Metagenomic sequencing provides a comprehensive view of microbial communities in various habitats.
  • Existing protocols can be complex and lab-dependent.

Purpose of the Study:

  • To develop and validate an end-to-end metagenomic protocol for environmental samples.
  • To adapt the protocol for both field and laboratory settings.
  • To utilize the Oxford Nanopore Technologies MinION platform for eDNA analysis.

Main Methods:

  • The protocol covers three key stages: DNA purification, library preparation and sequencing, and bioinformatic analysis.
  • Direct DNA sequencing from environmental samples is employed.
  • The Oxford Nanopore MinION platform is used for real-time sequencing.

Main Results:

  • An integrated protocol for metagenomic analysis of eDNA was successfully demonstrated.
  • The protocol is adaptable for field-based environmental monitoring.
  • The MinION platform provides a viable option for rapid eDNA analysis.

Conclusions:

  • This study provides a robust and accessible protocol for eDNA metagenomics.
  • The developed method facilitates on-site environmental assessments.
  • This approach enhances the potential for broad application of eDNA in ecological research.