Using Ponds and Aquatic Organisms to Understand Host–Microbe–Environment Interactions Across Geographic and Temporal Scales

For decades, standing freshwater environments have served as powerful model systems for ecologists to study the hierarchical nature of biological organization. As our understanding of host-microbe interactions grows, these systems offer a tractable framework for examining how landscape and regional factors shape local microbial communities, the microbial members that associate with hosts, and resulting consequences for holobiont performance and fitness. Here, we highlight temperate freshwater ponds and resident larval amphibians (tadpoles) as model systems for studying these multidirectional interactions. We present empirical data on aquatic microbial communities and gut microbiomes of wood frog tadpoles (Lithobates sylvaticus) sampled across multiple sites in Western Pennsylvania. Aquatic microbial communities were more diverse than amphibian-associated communities. Local environmental conditions significantly contributed to tadpole gut community membership. We observe significant variation across ponds and months, with community turnover driven by geographic distance and environmental variables (e.g., dissolved oxygen, pH), and time. We also identify microbial taxa enriched in the tadpole gut beyond neutral model expectations, suggesting deterministic processes that select for or retain these taxa. Moving forward, expanded sampling over greater geographic and temporal scales will reveal the nature of these interactions and how they vary across geographic sites, seasons, and host species. Controlled studies in experimental mesocosms in the field or lab-based microcosms will uncover the mechanistic basis of these interactions. Together, these approaches will illuminate the directionality and relative importance of the ecological and evolutionary processes governing host-microbe-environment interactions.