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 ¹³C-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.

稳定同位素探测 (SIP) 是鉴定微生物催化环境中特定底物周转并量化它们对生物地球化学过程的相对贡献的关键工具。然而，基于 SIP 的研究受到交叉喂养带来的不确定性的影响，其中微生物释放同位素标记的产物，然后被其他微生物使用，而不是直接加入添加的示踪剂。在这里，我们介绍了一种 SIP 方法，该方法有可能大大减少复杂微生物群落中的交叉喂养。在这种方法中，微生物细胞在膜过滤器上暴露于含有同位素标记底物的连续介质流中。因此，代谢物和降解产物不断被去除，防止这些次生底物的消耗。¹³ C-碳酸氢盐作为活性示踪剂表明，Flow-SIP 显着减少了交叉喂养，从而可以将主要消费者与微生物食物网的其他成员区分开来。