Drought induces substitution of bacteria within taxonomic groups in the rhizosphere of native maize from arid and tropical regions

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In Mexico, maize landraces are usually cultivated in milpa polyculture agroecosystems, which are maintained with ancestral practices, i.e. with very low external inputs such as chemicals and without irrigation systems. Several studies have characterized soil and maize-root microbiota from different milpas, however, robust experimental approaches are necessary to understand the relationship between a healthy microbial community structure and the health of milpa plants. We tested the hypothesis that different maize varieties not only differ in the microorganisms enriched in their rhizospheric environment, but also in the responses of these communities to drought. By suspending irrigation, we induced drought experimentally in three varieties of maize: one landrace from an arid milpa, one from a tropical milpa, and a commercial hybrid. The treatment elicited stress symptoms and growth declines in all three maize varieties. Nevertheless, the maize landrace from arid milpa displayed a better performance in biomass accumulation. The drought treatment did not significantly affect bulk soil bacterial communities; in contrast, all three varieties had shifts in their rhizospheric microbiomes, indicating that these responses were related to the presence of plant roots. The varieties differed in their changes of root-associated microbiota in response to drought, with only Paenarthrobacter genus increasing in all three. Responses mainly consisted of increases in the abundance of certain groups (e.g. Verrucomicrobiota) and substitution of strains within groups (e.g. Group 6 Acidobacteriota, family Streptomycetacea, and many others). The landrace from an arid region had the most bacteria substituted under drought, suggesting that a more stringent selection of microorganisms in roots could be part of the response of this landrace to drought. We propose that drought-tolerant maize landraces from arid milpas could be the source of bacterial strains or communities that aid drought-sensitive varieties in coping with reduced water availability expected due to climate change.