Abstract:The hydrosphere includes oceans, lakes, rivers, glaciers, wetlands, groundwater, etc. It is home to over half of the microorganisms, such as bacteria, archaea, fungi, algae, viruses, on the Earth, and therefore harbors the largest environmental microbiome. Studies show that microorganisms in hydrosphere are the key drive in biogeochemical cycling of important elements on the Earth. Nevertheless, it remains to be fully understood as to how microorganisms serve the drive role (a key scientific issue of research on microbiome in hydrosphere). Recently, National Natural Science Foundation of China (NSFC) launched a Major Research Initiative titled ‘Mechanisms Underlining Elemental Cycling on the Earth by Microorganisms in Hydrosphere’ or ‘Microbes in Hydrosphere’ in short. This Initiative calls for systematic investigation into microbial community structures and their interaction with the environments, mechanisms of microbial transformation of substances and energy, and the ecological functions and contributions of microbial activities in representative habitats in hydrosphere. The ultimate goal of the Initiative is to offer a clear view on the mechanisms underlining carbon, nitrogen, and sulfur cycling on the Earth by microorganisms in hydrosphere. This article briefly reviews the background, major scientific questions, and implementation plan of the Initiative.