Inoculation withPseudomonas fluorescensUM270 alters the maize root-associated endobiome and interacting networks in a milpa model

Abstract

AbstractThe traditional milpa system is a polyculture originating in Mesoamerica, whose core is maize (Zea maysL.), associated with squash (Cucurbitaspp.) and beans (Phaseolus vulgarisL.). 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 PGPRPseudomonas fluorescensUM270, 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 ofP. fluorescensUM270 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 generaBurkholderiaandPseudomonas(in a monoculture), whereas in the milpa system, the PGPR stimulated a greater endophytic diversity and the presence of genera such asBurkholderia, Variovorax, and N-fixing rhizobia genera, includingRhizobium, MesorhizobiumandBradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi such asRizophagus irregularisandExophiala pisciphilawere detected in the milpa system. In addition, network analysis revealed unique interactions with species likeStenotrophomonassp.,Burkholderia xenovorans, andSphingobium 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.