Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities

Area of Science:

• Microbiology
• Environmental Science
• Biogeochemistry

Background:

• Stable isotope probing (SIP) identifies microorganisms and quantifies their role in biogeochemical processes.
• Cross-feeding, where labeled products are consumed by other microbes, introduces uncertainty in SIP studies.

Purpose of the Study:

• To introduce and validate a novel SIP approach, Flow-SIP, designed to significantly reduce cross-feeding in complex microbial communities.
• To differentiate primary substrate consumers from other community members in microbial food webs.

Main Methods:

• Developed a Flow-SIP technique exposing microbial cells on a membrane filter to a continuous flow of labeled substrate.
• Implemented a continuous flow system to constantly remove metabolites and degradation products, preventing secondary substrate consumption.
• Conducted a nanoSIMS-based proof-of-concept experiment using nitrifiers and 13C-bicarbonate tracer.

Main Results:

• The Flow-SIP method demonstrated a significant reduction in cross-feeding compared to conventional SIP.
• The approach successfully distinguished primary consumers (nitrifiers) from other microorganisms in activated sludge.
• NanoSIMS analysis confirmed the effectiveness of Flow-SIP in tracing substrate utilization.

Conclusions:

• Flow-SIP offers a robust solution to mitigate cross-feeding artifacts in stable isotope probing studies.
• This method enhances the accuracy of identifying and quantifying microbial contributions to environmental processes.
• Flow-SIP is a valuable tool for dissecting microbial food web dynamics and understanding complex ecosystem functions.