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

• Published in: The ISME Journal Vol. 15; no. 1; pp. 348 - 353
• Main Authors: Mooshammer, Maria, Kitzinger, Katharina, Schintlmeister, Arno, Ahmerkamp, Soeren, Nielsen, Jeppe Lund, Nielsen, Per Halkjær, Wagner, Michael
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.01.2021; Oxford University Press
• Subjects: 14/19; 14/32; 631/1647; 631/326; 631/443/319; 704/158/855; 704/47; Activated sludge; Bicarbonates; Biodegradation; Biomedical and Life Sciences; Brief Communication; Carbon Isotopes - analysis; Continuous flow; Degradation products; Ecology; Evolutionary Biology; Food Chain; Food chains; Food webs; Isotope Labeling; Isotopes; Life Sciences; Metabolites; Microbial activity; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Microbiomes; Microbiota; Microorganisms; Stable isotopes; Substrates; Syntrophism
• ISSN: 1751-7362; 1751-7370; 1751-7370
• DOI: 10.1038/s41396-020-00761-5

Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and 13 C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.