Table 1.

Glossary of techniques used to study plant–microbe interactions.

Techniques	Descriptions
Nucleic acid amplification and fingerprinting	DNA is amplified by polymerase chain reaction (PCR) while cDNA is synthesized from the extracted RNA. The amplicons can be analysed with fingerprinting techniques such as denaturing gradient gel electrophoresis, terminal restriction fragment analysis, amplified rDNA restriction analysis and BOX‐PCR.
Real‐time PCR (RT‐PCR)	RT‐PCR is based on the monitoring of PCR reaction using fluorescent reporter molecules. Particularly, analysis of the exponential curve of the PCR reaction allows the determination of the amount of starting material. Different detections methods have been developed such as SYBR green I, a fluorescent dye binding double‐stranded DNA, and Taqman probes.
Sequencing	Determination of nucleotides sequence in single‐stranded DNA or cDNA using Sanger or Pyrosequencing methods.
Chromatography	Chromatography allows for separation and isolation of chemical mixture by suspending compounds in solvent and separating mobile fraction from stationary fraction through a column. The proportions of the mixture provide quantitative information, and the separated fractions can be used for further analysis. Several types of chromatography have been described: thin layer chromatography, liquid chromatography, gas chromatography, high‐performance liquid chromatography, ultra high‐pressure liquid chromatography.
Mass spectrometry (MS)	MS identifies the chemical composition of molecules based on the mass‐charge ratio of charged particles. Stable Isotope Probing with MS is being used to track a stable isotope atom from a particular plant substrate into microbial cells in situ. Electron‐spray‐ionization‐MS is a technique for measuring chemical speciation in root exudates metabolomics. Quadrupole time‐of‐flight hybrid MS consists of both analysers resulting in high sensitivity in product ion scanning.
Phospholipid fatty acid (PLFA)	PLFA identifies phospholipids in cellular membranes that are esterified to fatty acids. GC is used to identify the fatty acids, and information regarding microbial biomass, metabolic status and community composition can be obtained.
Microscopy	The use of microscopy for visualization of plant‐associated microbes provides useful spatial information that can be used to determine the functional relationships. Confocal laser scanning microscopy is used to obtain high‐resolution optical sectioning images of fluorescent samples. Transmission electron microscopy bombards ultra‐thin specimens with electrons in order to obtain images at higher resolution than light microscopes.
Fourier transform infrared spectroscopy (FTIR)	FTIR generates an infrared absorption spectrum specific for a type of chemical bond thus allowing for the identification of molecules.
Genetic modifications	Manipulating specific genes by both genetic engineering and mutation is used to validate previous observations regarding gene functions. Transgenic plants and recombinant microbes have been used.
Nuclear magnetic resonance	The technique measures physical resonance and is used to determine the structure of the chemical.