ABSTRACT
This chapter presents the methods used to detect specific bacteria in the soil environment. Microscale analyses of bacterial cells colonizing surfaces in the soil, for example, soil colloids, plant roots, or fungal hyphae, are typically carried out for samples that are as intact as possible, as subsequent microscopic analyses can then reveal their localization and any spatial relationships between different cells. Epifluorescence Microscopy is a classical technique for the enumeration of total fluorescent bacterial populations in soil samples, in particular when physical interactions are of interest. The most commonly used marker genes encode auto fluorescent proteins or enzymes involved in the emission of bioluminescence. Flow cytometry and accompanying cell sorting is a technique that provides information at the single-cell level in a fast high-throughput manner. The chapter presents the methodology of qPCR, in its classical form and in the form of digital droplet polymerase chain reaction (PCR), which includes a technological overlay to the classical quantitative PCR.
