Microorganisms can be found in unexpected niches, such as thermal ocean vents and fissures in deep rocks. Once a specialized branch of microbiology, microbial ecology now occupies centre stage. The present compendium makes emphasis on environmental approach to biology of microorganisms, first of all bacteria and virus, aiming the wide understanding of the role these organisms in ecosystems sustainability and human practical activity. Clever genetic approaches have been developed to identify genes that are selectively expressed in a particular environment. These approaches have many applications, for example identifying gene products that are essential for a pathogen to survive in a host or in the outside environment. This ecological approach has led to great steps in the identification of novel molecular mechanisms of host–pathogen interactions. This manual can be used by students of wide range of biological specialities.