Microbes and invertebrates are “the little things that run the world” (Wilson 1987, Moreau 2017), but the intricacies of how these organisms impact our environment remains underexplored. Here I investigate how microbes and invertebrates interact and how these interactions scale-up to impact communities and ecosystem-level processes. This work focuses on tropical brown food webs because they are dominated by a diversity of microbe-invertebrate relationships that span from obligate symbioses to fierce competition. Initially, I examine the symbiotic relationship between a dominant canopy ant, Azteca trigona, and their microbiota. Here I describe the diversity of microbial communities associated with these ants and demonstrate the role of invertebrate activity in microbial dispersal (Ch. 1). Furthermore, the microbial community within these canopy ants provides the basis for a facultative relationship between ants and their host plants, as the ant endosymbionts increase plant growth and facilitate nutrient exchange (Ch. 2). I then transition to explore how competition between microbes and invertebrates can shape the local community in the ephemeral environment of tropical leaf litter (Ch. 3). I demonstrate that antibiotic production by microbes—long considered a potent mechanism of competition between microbes—can also be effective against invertebrates. This cross-domain competition likely contributes to the diversity of detrital food webs (Ch. 4). Combined, the results of these studies demonstrate how invertebrate-microbe interactions drive ecosystem structure and function.