Climate change is affecting how energy and matter flow within ecosystems, altering global carbon and nutrient cycles. Microorganisms play a fundamental role in carbon and nutrient cycling and are thus an integral link between ecosystems and climate. Here, we highlight a major black box hindering our ability to anticipate ecosystem climate responses: viral infections within complex microbial food webs. We show how understanding and predicting ecosystem responses to warming could be challenging—if not impossible—without accounting for the direct and indirect effects of viral infections on different microbes (bacteria, fungi, protists) that together perform diverse ecosystem functions. Importantly, understanding how rising temperatures associated with climate change influence viruses and virus-host dynamics is crucial to this task, yet severely understudied. In this perspective, we 1) synthesize existing knowledge about virus-microbe-temperature interactions and 2) identify important gaps to guide future investigations regarding how climate change might alter microbial food web effects on ecosystem functioning. To provide real-world context, we consider how these processes may operate in peatlands—globally significant carbon sinks that are threatened by climate change. We stress that understanding how warming affects biogeochemical cycles in any ecosystem hinges on disentangling complex interactions and temperature responses within microbial food webs.

Mixotrophs are ubiquitous and integral to microbial food webs, but their impacts on the dynamics and functioning of broader ecosystems are largely unresolved. Here, we show that mixotrophy produces a unique, dynamic type of food web module that exhibits unusual ecological dynamics, with surprising consequences for carbon flux under warming. We find that mixotrophs generate alternative stable carbon states across temperatures---including an autotrophy-dominant carbon sink state, a heterotrophy-dominant carbon source state, and cycling between these two. Moreover, warming always shifts this mixotrophic system from a carbon sink state to a carbon source state, but increasing nutrients erases early warning signals of this transition and expands hysteresis. This suggests that mixotrophs can generate critical carbon tipping points under warming that will be more abrupt and less reversible when combined with increased nutrient levels, having widespread implications for ecosystem functioning in the face of rapid global change.

Understanding which foodwebs thrive or collapse is a major challenge that has been mostly studied in terms of topology and interaction strength. Yet the relative importance of these properties is hotly debated due to limited research on how they interact and which forces generate them. Here, we construct a foodweb model that incorporates mass-based constraints on density dependence, maximum consumption rate, and the likelihood and strength of interactions, which in turn control overall topologies and interaction strength distributions. Our model predicts both stability and connectivity that closely match real foodwebs ranging widely in size (29-163 species) and connectivity (113-1086 interactions). Despite their absence in most research, density dependence and maximum consumption rate are not only required to accurately predict stability but have stronger impacts than the more-frequently-studied interaction strength. Our results demonstrate that predicting foodweb stability requires simultaneously considering multiple foodweb properties—all of which naturally emerge from species masses.