A Metagenome-Based Methodology to Track Genomically Recoded Strains and Assess Their Effects on Indigenous Microbes

Area of Science:

• Environmental microbiology
• Synthetic biology
• Microbial ecology

Background:

• Assessing environmental release of contained microorganisms is challenging using traditional methods.
• Tracking escaped organisms and their impact on native microbial communities requires advanced techniques.

Purpose of the Study:

• To evaluate the environmental impact and biocontainment efficacy of a synthetic Escherichia coli strain (DEP).
• To simulate an accidental release of a genetically modified microorganism in a controlled freshwater environment.

Main Methods:

• Laboratory mesocosms were used with freshwater spiked with synthetic Escherichia coli strain DEP.
• Shotgun metagenome sequencing was employed to track strain DEP and assess microbial community changes.
• Culturing on specific media was used to detect gene transfer.

Main Results:

• Synthetic strain DEP rapidly declined in relative abundance over time.
• Indigenous freshwater microbial communities showed minimal impact and recovered quickly.
• No transfer of nonstandard amino acid-dependent genes to native populations was detected.

Conclusions:

• Synthetic strain DEP poses a low environmental threat due to poor competitiveness and lack of gene escape.
• The study presents a comprehensive method for assessing the biocontainment of genetically modified organisms.