All raw data for Fig 2C.

Metabolic cross-feeding networks are central to shaping microbial community dynamics in environments ranging from the rhizosphere, gut, and marine carbon cycling. Yet cross-feeding has predominantly been viewed by examining exchanged small metabolites. In contrast, the role of extracellular polymeric substance (EPS)—a complex mixture of proteins, polysaccharides, DNA, and humic-like compounds—in cross-feeding remains poorly understood, mainly due to technical challenges in measuring their secretion relative to small metabolites. Using chitin-degrading microbes as a model system, we used a bicarbonate-buffered bioreactor coupled with elemental analysis, which allowed us to quantify both EPS and small metabolite secretion. This revealed that ~25% of carbon exuded by a chitin degrader is in the form of EPS. EPS was produced at similar levels across marine chitin-degrading isolates and seawater communities, underscoring its importance relative to small metabolites. Notably, different sources of EPS were found to select for distinct and diverse microbial communities. Combining in vitro enzyme assays and untargeted metabolomics, we show that EPS undergoes sequential degradation—from large oligomers to smaller, broadly accessible monomers. This sequential breakdown creates a temporal succession of metabolic niches, potentially fueling a shift from specialist species degrading complex substrates to a more diverse community of generalists using simpler monomers. By identifying EPS as a major and dynamic contributor to cross-feeding networks, our findings reveal a hidden layer of complexity in how microbial communities assemble and function across ecosystems.

代谢互养网络（metabolic cross-feeding networks）在塑造根际、肠道与海洋碳循环等各类环境中的微生物群落动态方面发挥核心作用。然而过往针对互养过程的研究大多仅关注微生物间相互交换的小型代谢物（small metabolites）。与之形成鲜明对比的是，细胞外聚合物（extracellular polymeric substance, EPS）——一种由蛋白质、多糖、DNA与类腐殖质化合物组成的复杂混合物——在互养过程中所扮演的角色仍鲜为人知，这主要是因为相较于小型代谢物，定量检测其分泌量存在技术瓶颈。
本研究以几丁质降解微生物为模式系统，采用碳酸氢盐缓冲生物反应器耦合元素分析的方法，实现了对EPS与小型代谢物分泌量的同步定量。该方法揭示：几丁质降解菌分泌的碳源中约25%以EPS的形式存在。海洋几丁质降解分离菌株与海水微生物群落所产生的EPS水平相近，这凸显了EPS相较于小型代谢物的重要性。值得注意的是，不同来源的EPS可筛选出截然不同且多样性丰富的微生物群落。
结合体外酶活实验与非靶向代谢组学（untargeted metabolomics）分析，本研究证实EPS会经历逐步降解过程：从大型寡聚体拆解为可被广泛利用的小型单体。这种逐步降解过程会形成随时间更迭的代谢生态位，进而可能推动微生物群落从降解复杂底物的特化物种，向利用简单单体的泛化物种组成的更多样化群落转变。本研究明确EPS是互养网络的核心动态贡献因子，研究结果揭示了各类生态系统中微生物群落组装与功能发挥背后一层尚未被发掘的复杂机制。