eDNA Project: Sampling Soil for Antibiotic Resistance
Join a nationwide monitoring program
that tests for antibiotic resistance genes in environmental soil
samples. Students will collect soil samples based on their own
hypotheses about antibiotic resistance hotspots, extract total
environmental DNA from soil, and use the molecular methods of PCR and
gel electrophoresis to test their samples for evidence of tetracycline
resistance. They will then contribute their data to a national database
of antibiotic resistance surveillance.
This lab has been developed in
conjunction with the PARE (Prevalence of Antibiotic Resistance in the
Environment) project. The PARE project engages students to test and
report the prevalence of tetracycline-resistant bacteria from soil at
diverse geographic sites, engaging students in one of the great
environmental and health challenges of our time. Learn more about the
PARE project: https://sites.tufts.edu/ctse/pare
- Techniques: Micropipetting, eDNA extraction, PCR, gel electrophoresis
- Topics: Environmental monitoring, molecular biology, biotechnology
- Time required: This is a project-based activity that requires at least three to four class periods for completion
- Level: Advanced high school, college
This is an advanced lab activity with
unknown outcomes and is ideal for independent research projects.
Students performing this lab should have experience following complex
molecular protocols. For a case study approach to the same curriculum,
try the Antibiotic Resistance Lab.
This lab kit provides enough reagents for 5 lab groups:
- ZymoBIOMICS DNA Miniprep Kit
- EZ PCR Master Mix, Load-Ready™
- 16S Primer Mix
- tetB Primer Mix
- tetM Primer Mix
- Positive Control Plasmid
- Fast DNA Ladder 1
- Nuclease Free Water
Supplied by user:
Standard reagents and consumables must be supplied by the user. The Learning Lab Companion Kit
(catalog no. KT-1510-01) contains all the consumables (except water and
95% ethanol) needed for 5 or more lab groups. These reagents and
consumables can also be sourced independently.
Reagents and consumables supplied by user:
- Agarose (electrophoresis grade)
- DNA stain (e.g., SeeGreen™ or GelGreen®)
- Gel electrophoresis buffer (e.g., 1X TBE)
- Distilled or deionized H2O (to dilute buffer concentrate – not included in Lab Companion Kit)
- Microtubes
- PCR tubes
Reagents not included in Lab Companion Kit:
Required equipment:
- Micropipettes and tips
- Tissue homogeneizer or vortex mixer with microtube holder attachment
- Microcentrifuge
- Thermal cycler
- Gel electrophoresis and visualization system
Storage notes:
- Reagents may ship at room temperature, but require freezer storage upon arrival
- Frozen reagents are stable for 12 months when stored in freezer
- ZymoBIOMICS DNA Miniprep Kit is stable for 6 months when stored at room temperature
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