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Journal Article

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

MPS-Authors

Kitzinger,  Katharina
Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Ahmerkamp,  Soeren
Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Kitzinger20.pdf
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Citation

Mooshammer, M., Kitzinger, K., Schintlmeister, A., Ahmerkamp, S., Nielsen, J. L., Nielsen, P. H., et al. (2020). Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities. The ISME Journal. doi:10.1038/s41396-020-00761-5.


Cite as: http://hdl.handle.net/21.11116/0000-0007-6287-2
Abstract
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.