Interactions between Earth's spheres, particularly between deep Earth and surface processes or within the surface system between sea, land and the atmosphere, are a critical issue in Earth system science. Such a large-scale geological process could be recorded by tiny microbes preserved in the fossil record. Triggered by volcanic activities during the Permian-Triassic transition and in the Late Ordovician, the bloom of nitrogen-fixation bacteria including cyanobacteria and the subsequent expansion of eukaryotes including algae, radiolarians and foraminifers clearly reflected a volcanism-induced shift from prokaryotes to eukaryotes. Furthermore, it has been shown that microbial activity could lead to banded iron formations to trigger Pre-Cambrian volcanic activity and even initiate plate movement in the early Earth. These data demonstrated the critical interaction between volcanic activity and the microbial community impacting carbon cycling. Microbes could also trace the complex interaction between sea, land, and the atmosphere and its associated long-range material transport process. Using microbial proxies for hydroclimate we identified the tri-pole mode of spatial variability of dry/wet status in eastern China on different time scales, as well as the extreme drought events in northwestern China triggered by the upper-ocean thermal condition in the tropical western Pacific Oceans. The spatiotemporal variations in dry/wet status reflected in the microbial records are due to variations in sea-land-atmosphere interactions between high- and low-latitude environments. The carbon- and water cycle-associated cross-sphere processes reflected in microbial fingerprints only represent a small portion of Earth sphere interactions. The great contribution of the microbial community in shaping the habitable Earth has yet to be fully deciphered. With research advancement and technical/methodological innovation in geobiology more questions can be addressed, including the interaction between geomicrobiological and deep Earth processes, microbial contribution to the major paleoclimatic shifts and paleoenvironmental changes, and impact of the microbial community on ecological evolution.