Microorganisms are found in nearly every environment on Earth, and despite their small size they comprise most of the Earth’s biomass and support the majority of global physical and biogeochemical transformations. In particular, microbes that live at the interface between terrestrial and aquatic environments catalyze key steps in the global biogeochemical cycles that determine the release or sequestration of greenhouse gases, the production or depletion of nutrients, and the fate and transport of anthropogenic contaminants. Theoretical and computational models of these dynamic processes still lack robust quantification, however, due to the sheer complexity of microbial diversity and the physical and biogeochemical heterogeneity that define this environmental interface. As a result, it is rare to find microbially mediated reactions explicitly included in higher-level process models. Periodically flooded environments are among the most critical and least-understood terrestrial-aquatic interfaces. Rapid shifts between oxic and anoxic conditions in these zones have significant impacts on the flux of important greenhouse gases such as nitrous oxide, carbon dioxide, and methane, due in part to shifts in microbial activity brought about by changing redox conditions. Existing predictive models for greenhouse gas emissions in these environments have large error ranges due to substantial parameter and structural uncertainty. This highlights the need for microbial and geochemical studies in these areas, especially those that take into consideration the underlying microbial ecology, genomics, and metabolic dynamics. Meeting the challenge of a warming planet requires a multifaceted scientific approach. We have organized this session to bring together thought leaders in environmental biogeochemistry, microbial genomics and ecology, metabolic modeling, ecosystem modeling, and systems biology, whose research areas span large-scale field experiments, detailed laboratory measurements, and the creation of ecologically-informed biogeochemical models. In doing so, we hope to both showcase the exciting work being done across this burgeoning field and highlight existing knowledge gaps to foster future collaborations.