Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.

壶菌门 (chytrids) 的游动孢子真菌经常在淡水和海洋环境中支配远洋真菌群落。它们的生活方式从专性寄生虫到腐生菌不等。然而，将稀缺的可用序列数据与特定的生态特征或其宿主范围联系起来目前是一个重大挑战。我们将 28 S rRNA 基因扩增子测序与靶向分离和测序方法相结合，以及交叉感染检测和壶菌感染流行率分析，以获得对温带湖泊中壶菌多样性、生态学和季节性动态的新见解。寄生浮游植物-壶菌和腐生花粉-壶菌相互作用构成了游动孢子真菌读数的大部分。我们明确地证明了在频繁的硅藻开花期间寄生性壶菌和花粉雨期间腐生性壶菌的反复优势。硅藻特异性寄生进化枝的不同时间动态表明基于生态位分化和竞争策略的共存机制。本研究产生的壶菌分子和生态学信息将有助于进一步探索它们在世界范围内的时空分布模式。为了充分利用环境测序的力量来研究壶菌生态学和进化，我们强调需要加强当前壶菌的分离工作，并将分类学和进化学数据整合到长期研究和实验中。硅藻特异性寄生进化枝的不同时间动态表明基于生态位分化和竞争策略的共存机制。本研究产生的壶菌分子和生态学信息将有助于进一步探索它们在世界范围内的时空分布模式。为了充分利用环境测序的力量来研究壶菌生态学和进化，我们强调需要加强当前壶菌的分离工作，并将分类学和进化学数据整合到长期研究和实验中。硅藻特异性寄生进化枝的不同时间动态表明基于生态位分化和竞争策略的共存机制。本研究产生的壶菌分子和生态学信息将有助于进一步探索它们在世界范围内的时空分布模式。为了充分利用环境测序的力量来研究壶菌生态学和进化，我们强调需要加强当前壶菌的分离工作，并将分类学和进化学数据整合到长期研究和实验中。