The ocean ecosystems are changing—interactively with global climate change—and some changes may affect us in timeframes as short as years to decades. Predicting the shape of things to come is an urgent goal. Marine microbes play central roles in the structuring ocean’s ecosystems—and in the response of the ocean to global change. They pervasively interact with all organic phases and organisms to regulate ecosystems and influence global climate. Marine conservation, fisheries management and mariculture require ecosystem-based management. Such models have limited utility if they do not integrating the in situ functions of the highly diverse communities of marine microbes. Microbes cause change at the microscale---yet their cumulative effect is dramatically reflected at the global ocean scale. Understanding the ocean’s biogeochemical dynamics at the micrometer-scale is an exciting new challenge that promises fundamentally new knowledge and insights on the functioning of the ocean ecosystems. It is also becoming clear that ocean health and human health are intertwined. The ocean acts as “vector” for some human pathogens (e.g. Vibrio cholerae) and the changing ocean may offer new habitats for the proliferation and emergence of human pathogens. Further, global warming and sea-level rise may increase human exposure to such pathogens. There is urgent need to gain a fundamental and comprehensive understanding of how the ocean ecosystems “work” and to predict the biogeochemical state of the future ocean.