The ecosystem is a dynamic network in which important materials are constantly consumed and recycled, with biogeochemical cycles governing their systemic movement in order to support the environment. Microorganisms play a major role in this process, driving the conversion and biotransformation of these components, from the ubiquitous carbon and nitrogen cycles to the more minute elements: sulphur, phosphorus, and potassium cycles, which are handled by specially adapted microorganisms. These minute organisms use various methods for the conversion of these elements: Cyanobacteria help plants fix atmospheric CO2 during photosynthesis; Rhizobium fix nitrogen in the root nodules of plants; as well as the reductive activities (assimilatory and dissimilatory fixation) of microbes in these cycles and others. It has become necessary to study the roles of these microbes in ensuring the continuation of these cycles, as their processes are important for scientific developments in various areas, including for sustainable agricultural practice to achieve sustainable development goals (SDGs) such as that of “Zero Hunger”. Next-generation sequencing has emerged as a valuable tool for researching microbial activities, especially with the role of whole-genome sequencing aided by machine learning—allowing tremendous depth of research of entire microbiomes. Finally, the recycling of nutrients throughout the ecosystem depends on microbial communities’ activities in reservoirs and sinks. Beyond ecological applications, these microbial capabilities have the potential for novel applications, such as enhancing medicine and drug discovery advancements.