The Planet Earth is a microbial world, and the health of its inhabitants rests on the proverbial backs of microscopic organisms within oceans, rivers, soils and air. The oceans, in particular, are fundamental to the life-sustaining capabilities of Planet Earth, enabling all organisms from microbes to humans to persist and thrive. Within the oceans, microbes have an essential role, making the oxygen we breathe, removing greenhouse gas carbon dioxide from the atmosphere, anchoring the marine food web, fueling life within coral reefs, and promoting the health of fisheries and marine mammals. Detailed studies of microbial metabolism, therefore, provide fundamental knowledge about the life-sustaining processes on Earth. Recent work in this field has focused on the first order question of “who is there?” but second-order questions such as “what are they doing” and “how” are equally critical to assessing the role of microbial reactions in the global carbon cycle. Metabolomics, or the study of biochemical molecules, is one lens through which the chemical capacity of microbes can be viewed. In this presentation, I offer two case studies in which we use metabolomics to understand the chemical interplay of microbes. First, I will present work showing the role of microbes in particle remineralization in the open ocean, with implications for global carbon cycling. Second, I will present work showing the role of human and earth microbiomes in the chemistry of human sewage. These case studies are linked by the over-arching theme of microbial metabolism and its sentinel roles in understanding critical processes on our planet and will highlight the continuing role of analytical chemistry in elucidating fundamental earth system functions.