Different strategies for colonization and prevalence after inoculation with plant growth-promoting rhizobacteria revealed by a monitoring method

It is critical to monitor plant growth-promoting rhizobacteria (PGPR) in soils after inoculation. Among common PGPR, the Azospirillum sp. strains TSA2s and TSH100 have the ability to mitigate nitrous oxide (N2O) emissions from agricultural soils; however, their mechanism by which they successfully colonize and achieve beneficial effects in plants remains poorly understood. Here, a simple and robust procedure was developed to design strain-specific primers based on the whole-genome sequences of these two strains. After evaluating their specificity and amplification efficiency, three primer pairs were screened for each Azospirillum sp. strain. Quantification of these two strains in the rhizosphere soils of red clover revealed distinct inoculant dynamics for each strain under greenhouse conditions. Specifically, 22, 34, and 41 days after inoculation with TSA2s, the population size of the inoculant was notably greater than that in the non-inoculated control, and reached a maximum at day 34. In contrast, the population size of the TSH100 inoculant was largest at day 22, then decreased dramatically from 34 days after inoculation. These results suggest that different PGPR may have different strategies for colonization and prevalence after inoculation. Of the 31 rhizosphere carbon sources added to the Biolog Eco Micro plate to simulate plant root exudates, TSA2s utilized 14 whereas TSH100 utilized only one. TSA2s utilized more diverse root exudates of red clover, indicating better colonization and prevalence than TSH100 after inoculation. Therefore, this study presents a method of monitoring PGPR after inoculation. Furthermore, this method can screen PGPR with a better ability to survive and colonize, enabling the development of efficient, stable, and standardized biofertilizers.