**Abstract**

Rhizobiota are involved in plant protection through plant development facilitation and plant defense against stress factors. Pressures of global change either as abiotic or biotic stress factor could modify rhizobiota abundance, community structure, or functioning. Such change could result in anomalies of plant development. Human and veterinary medicines are widely used pharmaceuticals. Their active ingredients are not fully adsorbed and metabolized by living organisms and are therefore excreted unmodified. As current technologies of wastewater treatment plants are not designed to remove these contaminants, pharmaceuticals may be discharged into the environment and reach the soil in multiple ways. At present, there are no standard procedures or methodologies that could be easily applied and cover pharmaceuticals impact on soil microbiota. Besides that, available molecular and genetic approach through which soil microdiversity abundance, structure, and functions are evaluated involves high and expensive technology, which is not easily available to laboratories widespread. In this chapter, we propose an effortless way to address this issue by using gas chromatography–mass spectrometry (GC–MS) approaches to assess soil microbiota responses to commonly used pharmaceuticals. The chapter will refer to gas chromatographic techniques applied in assessment of soil microbiota diversity structure, abundance, and health status.

**Keywords:** microorganisms, volatile organic compounds, anthropogenic stress
