微生物生态学是研究微生物之间及与环境相互作用的学科，既包括真核细胞也包括原核细胞。

在地球上，微生物无所不在，在整个生物圈中都可发现。除非最为极端的环境，它们在酸性湖泊、深海、冰冻的地方和热泉口都能够生存。随着研究的不断深入，微生物在全球物质能量循环中起到的作用被越来越多地认识到，对微生物生态学的研究将对气候、环境研究起到至关重要的作用。

微生物生态学的核心问题包括：

由于环境中只有很小比例的微生物能够在培养基中分离，目前分子生物学方法被普遍采用，即分子生态学。

随着卫星遥感技术的发展，人造卫星照片可以帮助监测全球性的微生物发展变化，提供更准确的信息，如水华的产生。

Microbial ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses.

Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 7030500000000000000♠5.0×10 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms’ key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms’ production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.