Soil is one of the main reservoirs of microorganisms on the planet and soil borne microorganisms are one of the earth′s greatest sources of biodiversity. Soil microorganisms play an irreplaceable role in maintaining soil health and quality, contain tremendous economic values in agriculture, chemical, industrial and pharmaceutical industries, and in addition have great potentials in alleviating environmental crises such as global warming and loss of biodiversity. Therefore, the linkage between soil microdiversity and their ecological services, and the comprehensive management of soil microbial resources are considered necessary to maintain the stability of terrestrial ecosystems and to strengthen ecosystems productivity. Herein, we reviewed the improved techniques for detecting and monitoring soil microbes and their applications as a sustainable resource in many areas, predominantly in the enhancement and conservation of soil fertility, in the elimination and regulation of soil obstacles, and in the remediation and control of soil contamination. The field of soil microbiology is continually advancing, and may be generally divided into three sub-disciplines in the near future: soil microbial systematology, soil microbial processology and soil microbial ergology. Soil microbial systematology is to study taxonomy, diversity, phylogenetic relationships and biogeography of soil microorganisms, mainly including two aspects: (1) to establish soil microbial germplasm bank through traditional methods i.e. isolation and pure culture of microbes; and (2) to establish soil microbial genetic information bank through molecular biology techniques. These two sides are combined and provide the basis for the preservation, development and utilization of soil microbial resources. Soil microbial processology, taking microorganisms activities as subjects, is to study microbial metabolic processes, material transformation, energy transfer and information exchange in soils. Physiological processes, biochemical processes and ecological behavior processes are involved in this component. Furthermore the complexity of interactions in the soil, including interactions between microorganisms and interactions between microorganisms and plants or animals needs to be addressed in investigations of soil microbial processology. Soil microbial ergology aims at exploring ecological services of soil microorganisms in terrestrial ecosystems, obtaining knowledge in the coupling of soil microbial diversity and soil ecological functions, and predicting the responses of soil microbes to the environmental changes, and finally regulating soil ecological services actively. This field aims to answer the questions regarding the roles of soil microbes play in driving earth′s biogeochemical cycles, how to maintain and enhance soil fertility and productivity, how to participate in the maintenance of ecological stability when meeting disturbance, and how to restore or rebuild ecosystem services in degraded ecosystems and in contaminated soils. However, considering the impressively large microbial diversity and the highly heterogeneous environment observed in soils, complete description or sequencing of soil microorganisms is virtually impossible with the current technologies, thus the innovation of improved techniques will be another study frontier. With the help of biogeography and bioinformatics, decoding soil ecological functions of specific genes and applying them in the dark aspects of ecosystems will be a major challenge for future work.