describes the study of microbes in their natural habitats and the relationships between the microbes and that habitat.

The study of microbes in their natural habitat and their relationship with each other and their environment is termed as Microbial ecology. It mainly constitutes of Viruses, Eukaryotes ,Bacteria and Archaea as its living entities.

Being omnipresent in the biosphere they impact the other life-forms up to a significant extent.

They also help maintaining biogeochemical cycle by nitrogen fixation, sulfur metabolism and methane metabolism. Microbes also play a vital role of availing energy in the ecosystems where sunlight is scarce and hence photosynthesis is not good means of energy trapping, in such ecosystems the microbes actively engage in fundamental ecological processes including production, decomposition, and fixation inside the host organism.