COS 275-1 - Mining ancient genomes for new strategies for nutrient retention in agroecosystems

Abstract: Plant-microbe interactions in the rhizosphere govern availability of nutrients and are a target for improving crop sustainability. However, the ability of modern crops to recruit and structure their microbiome has been altered by domestication and breeding. Selection for crop plants based on aboveground traits in high nutrient environments has inadvertently led to large changes to belowground plant physiology and relationships with the soil microbiome, altering microbiome functions that contribute to sustainability and environmental quality (e.g. nutrient acquisition, nutrient retention, and GHG production). We hypothesized that plant genotypes differ in their ability to recruit microbial functional groups, and ultimately that the functional profile of the microbial community can be treated as a selectable plant phenotype and optimized through plant breeding. We theorized that selection for microbiome-associated phenotypes requires: genetic variation in plant traits that influence the microbiome, microbial diversity that can be shaped by the plant host, and that the plant host and microbiome must interact with common resources.


We surveyed the rhizosphere microbiome of diverse maize genotypes to compare their capability to recruit microbial nitrogen cycling functional groups and examined rates of nitrogen transformations. Significantly different N cycling microbial communities were observed among maize genotypes that represent the endpoints of directed evolution, as well as among germplasm selected under different levels of fertilization. This differential recruitment affected microbiome function as well. Our results showed significantly lower rates of nitrification and denitrification in ancestral lineages of maize (teosinte). Maize-teosinte near isogenic lines were used to narrow down the genetic region associated with these nutrient retention traits to explore the mechanistic basis for these these microbiome-associated phenotypes. We also explored the combinatorial effect of plant-microbe interactions for their ability to both provision (via N fixation) and retain nutrients, which resulted in elevated nutrient acquisition by the crop as well as sustainable environmental outcomes.


Our results link the host-associated microbiome and ecosystem function, and demonstrated the genetic capacity to optimize recruitment of N cycling functional groups and improve crop sustainability. Understanding this relationship will allow breeders and ecosystem scientists to select crop cultivars that interact with the nitrogen cycle in predictable beneficial ways to improve the efficiency and sustainability of agriculture, while protecting environmental quality.