The use of extracellular DNA as a proxy for specific microbial activity

Area of Science:

• Microbiology
• Molecular Biology
• Environmental Science

Background:

• Extracellular DNA (exDNA) is increasingly recognized for its importance in medicine and environmental microbiology.
• Ratios of intracellular DNA (iDNA) to exDNA can indicate the activity of microbial systems.
• Current activity measurements, like RNA-based methods, can be time-consuming.

Purpose of the Study:

• To develop and evaluate a method for discriminating between internal, bound, and free exDNA.
• To assess the utility of exDNA fractions and ratios as alternatives to RNA-based activity measurements.
• To introduce a qPCR protocol for targeting anaerobic fungi.

Main Methods:

• Discrimination of internal DNA (iDNA), bound exDNA, and free exDNA (fDNA).
• Comparison of DNA-based ratios (exDNA:iDNA) with dehydrogenase and RNA-based activity measurements.
• Development of a 28S rRNA gene-specific primer set and qPCR protocol for anaerobic fungi (Neocallimastigomycota).

Main Results:

• The amount of actively released free exDNA (fDNA) strongly correlates with established microbial activity measurements.
• The proposed exDNA-based method provides a fast, convenient, and reliable alternative to RNA-based activity assessments.
• The qPCR protocol effectively targets anaerobic fungi.

Conclusions:

• Free extracellular DNA (fDNA) can serve as a robust proxy for microbial activity.
• This DNA-based approach offers a valuable tool for assessing microbial activity in various consortia.
• The findings support the use of fDNA as a rapid indicator in environmental and medical microbiology.