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Related Experiment Video

Updated: Apr 28, 2026

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
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Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

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Microbial groundwater sampling protocol for fecal-rich environments.

Thomas Harter1, Naoko Watanabe, Xunde Li

  • 1Faculty of Engineering, Division of Energy and Environmental Systems, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo-shi, Hokkaido, 060-8628 Japan.

Ground Water
|June 7, 2014
PubMed
Summary
This summary is machine-generated.

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Extended purging effectively prevents groundwater contamination from sampling equipment and wellbore issues in confined animal feeding operations (CAFOs). However, ambient air can still introduce fecal indicator bacteria into samples.

Area of Science:

  • Environmental Science
  • Microbiology
  • Water Quality Management

Background:

  • Confined animal farming operations (CAFOs) pose risks of groundwater contamination by enteric pathogens.
  • Sampling wells in these environments presents challenges due to microbial ubiquity and economic constraints.

Purpose of the Study:

  • To evaluate a groundwater sampling protocol using extended purging as an alternative to equipment sterilization.
  • To assess the effectiveness of this protocol in controlling cross-contamination from equipment, wellbore, and ambient air.

Main Methods:

  • The study utilized a portable submersible pump and Teflon tubing for groundwater sampling.
  • Enterococcus, a fecal indicator bacterium (FIB), was used in laboratory and field tests.
  • A multi-year field campaign involved sampling 17 wells across 2 CAFOs.

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Main Results:

  • Extended purging successfully mitigated cross-contamination from sampling equipment and wellbore sources.
  • Enterococcus was frequently found to contaminate samples when exposed to ambient air during collection.
  • The proposed strategy addresses wellbore and air contamination challenges not covered by equipment sterilization.

Conclusions:

  • Extended purging is a cost-effective method for reducing groundwater sampling contamination in CAFOs.
  • Ambient air poses a significant contamination risk that requires specific quality assurance/quality control (QA/QC) measures.
  • The evaluated protocol offers a practical solution for monitoring groundwater quality in challenging agricultural settings.