Microbes in deep sea, deep Earth, deep space and deep time are referred here to four deep microbes (abbreviated as 4D microbes), including bacteria, archaea, fungi, virus, etc. Knowledge about 4D microbes are very limited in comparison with those in Earth surface system. 4D microbes are thus proposed to be one of the key frontiers in geobiology, which helps to understand the origin of life in Earth, to constrain the boundaries of the biosphere, and to promote the cut- edge investigations on geosciences, life science and planetary science. A series of grand engineering projects were launched in recent years in China, providing unique opportunity for Chinese scientists to investigate some critical issues related to the 4D microbes. Some issues to be investigated include the interactions and co- evolution between the 4D microbes and climate and environments, the ecological and biological security of the 4D microbes, and the cryptic biogeochemical processes. The reactive oxygen species (ROS) in cells are paid great attention to in life science. However, ROS in natural environments are needed to be investigated, concerning their impact on molecular, cellular and ecological levels of organisms as well as the whole biosphere turnover and the microbial roles in geological history. Virus is believed to throw great impact on our society in modern days, leading to the occurrence of global pandemic, but the virus in geological times remains to be investigated on their impact on the background extinction and mass extinction in Earth history due to the lack of substantial geological records.