Interaction networks reveal highly antagonistic endophytic bacteria in native maize seeds from traditional milpa agroecosystems

Abstract

Milpas are traditional Mesoamerican agroecosystems maintained with ancestral practices. Maize landraces are grown in polyculture, creating highly productive and diverse ecosystems. Recent studies suggest that milpas maintain beneficial plant-microbe interactions that are probably absent in modern agroecosystems; however, direct comparisons of the microbiome of plants between traditional and modern agroecosystems are still needed. Here, we studied seed-endophytic bacterial communities from native maize landraces from milpas and hybrid varieties. First, we quantified the abundance of culturable endophytic microbes; next, we assessed pairwise antagonistic interaction networks between bacterial isolates; finally, we compared bacterial community structure by 16S rRNA amplicon sequencing. We found that seeds from native maize landraces harbour a higher endophytic microbial load, including more bacterial strains with antagonistic activity against soil-borne bacteria, and overall harbour more diverse bacterial communities than the hybrid varieties. Noteworthy, most of the seed-endophytic strains with antagonistic activity corresponded to Burkholderia spp. that were only found in native maize seeds, through both culture-dependent and independent strategies. Altogether, our results support that crop modernization alters the functions and structure of plant-associated microbes; we propose native maize from milpas could serve as a model for understanding plant-microbe interactions and the effect of modernization.