Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

Abstract

A geographically isolated maize landrace cultivated on nitrogen-depleted fields without synthetic fertilizer in the Sierra Mixe region of Oaxaca, Mexico utilizes nitrogen derived from the atmosphere and develops an extensive network of mucilage-secreting aerial roots that harbors a diazotrophic microbiota. Targeting these diazotrophs, we selected nearly 600 microbes from a collection isolated from these plants and confirmed their ability to incorporate heavy nitrogen (15N2) metabolites in vitro. Sequencing their genomes and conducting comparative bioinformatic analyses showed that these genomes had substantial phylogenetic diversity. We examined each diazotroph genome for the presence of nif genes essential to nitrogen fixation (nifHDKENB) and carbohydrate utilization genes relevant to the mucilage polysaccharide digestion. These analyses identified diazotrophs that possessed canonical nif gene operons, as well as many other operon configurations with concomitant fixation and release of >700 different 15N labeled metabolites. We further demonstrated that many diazotrophs possessed alternative nif gene operons and confirmed their genomic potential to derive chemical energy from mucilage polysaccharide to fuel nitrogen fixation. These results confirm that some diazotrophic bacteria associated with Sierra Mixe maize were capable of incorporating atmospheric nitrogen into their small molecule extracellular metabolites through multiple nif gene configurations while others were able to fix nitrogen without the canonical (nifHDKENB) genes. Data SummaryGenetic resources, including biological materials and nucleic acid sequences, were accessed under an Access and Benefit Sharing (ABS) Agreement between the Sierra Mixe community and the Mars Corporation, and with authorization from the Mexican government. An internationally recognized certificate of compliance has been issued by the Mexican government under the Nagoya Protocol for such activities (ABSCH-IRCC-MX-207343-3). Any party seeking access to the nucleic acid sequences underlying the analysis reported here is subject to the full terms and obligations of the ABS agreement and the authorization from the government of Mexico. Individuals wishing to access nucleic acid sequence data for scientific research activities should contact Mars Incorporated Chief Science Officer at CSO@effem.com.