Inoculation with Pseudomonas fluorescens UM270 alters the maize root-associated endobiome and interacting networks in a milpa model

The traditional milpa system is a polyculture originating in Mesoamerica, whose core is maize (Zea mays L.), associated with squash (Cucurbita spp.) and beans (Phaseolus vulgaris L.). In recent years, milpa-type crops have decreased owing to climate change, rapid population growth, and the excessive use of agrochemicals; therefore, the application of plant growth-promoting rhizobacteria (PGPR) to counteract these negative effects has been little explored. In this study, a maize crop in a milpa system was fertilized with the PGPR Pseudomonas fluorescens UM270, and the endophytic root microbiome (endobiome) of maize was assessed by 16S rRNA and internal transcribed spacer regions (ITS) sequencing. The results showed that UM270 the rhizosphere inoculation of P. fluorescens UM270 did not increase alpha diversity in either monoculture or the milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas in the milpa system, the PGPR stimulated a greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax, and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium and Bradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi such as Rizophagus irregularis and Exophiala pisciphila were detected in the milpa system. In addition, network analysis revealed unique interactions with species like Stenotrophomonas sp., Burkholderia xenovorans, and Sphingobium yanoikuyae, which would potentially be playing a beneficial role with the plant. To the best of our knowledge, this is the first study in which the root microbiome of maize growing under a milpa model was assessed by bio-inoculation with PGPRs.