Current opinion and perspectives on the methods for tracking and monitoring plant growth-promoting bacteria

Since the 1980s, plant growth-promoting bacteria (PGPB) have been studied as a sustainable alternative to the use of chemical fertilizers to increase crop yields, and effective PGPB have been isolated from diverse plant (e.g., endosphere and phyllosphere) and soil (e.g., rhizosphere) compartments. Despite the promising plant growth promotion results commonly observed under laboratory and greenhouse conditions, the successful application of PGPB under field conditions has been limited, partly by the lack of knowledge of the ecological/environmental factors affecting the colonization, prevalence and activity of beneficial bacteria on crops. It is generally accepted that the effectiveness of PGPB depends on their ability to colonize a niche and compete with the indigenous plant microbiome under agronomic conditions. However, most studies do not include tracking or monitoring of PGPB in the environment after their application, and the beneficial effects on plants are measured by determining biomass- and physiology-related parameters without confirming bacterial colonization. To date, methods based on reporter genes, immunological reactions and nucleic acids have been applied to track or monitor PGPB in seeds, soils or in planta after inoculation. In this review, we describe, compare and discuss the methods used for tracking and monitoring PGPB, including challenges and perspectives on some novel methods.