From teosinte to modern maize: domestication and crop improvement reshape the endophytic microbiome

Plant-associated microbiomes contribute essential functions related to plant nutrition, stress tolerance, and disease resistance, yet the effects of domestication and host genetic variation on these associations remain poorly understood. We characterized bacterial (16S rRNA) and fungal (ITS2) endophytic communities in leaves and roots of maize ( Zea mays L.) across a domestication gradient including teosinte, traditional landraces, improved lines, and a landrace × improved hybrid grown under common greenhouse conditions using the same soil substrate. Microbial richness differed among maize groups, with teosinte and landraces generally harboring richer endophytic communities than modern cultivars, particularly for fungi. The PT×B73 hybrid also exhibited elevated fungal richness, suggesting an influence of hybridization and host genetic background on microbiome assembly. Plant compartment was the strongest determinant of community composition, with root and leaf microbiomes forming clearly distinct assemblages. Differential abundance analyses revealed shifts from bacterial taxa commonly associated with nutrient cycling and plant growth promotion in teosinte and landraces toward communities enriched in taxa typical of managed agroecosystems in improved cultivars. Fungal communities showed a comparable transition, with modern lines enriched in genera including Trichoderma, Fusarium, and Colletotrichum. Functional inference further suggested shifts in microbial ecological potential across the domestication gradient. Together, our results indicate that domestication and crop improvement reshape the diversity, composition, and predicted functional potential of maize endophytic microbiomes, while wild relatives and traditional landraces remain important reservoirs of microbial diversity for microbiome-informed crop improvement and sustainable agriculture.