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Abstract Background and AimsNitrogenous fertilizers provide a short-lived benefit to crops in agroecosystems, but stimulate nitrification and denitrification, processes that result in nitrate pollution, N₂O production, and reduced soil fertility. Recent advances in plant microbiome science suggest that genetic variation in plants can modulate the composition and activity of rhizosphere N-cycling microorganisms. Here we attempted to determine whether genetic variation exists inZea maysfor the ability to influence the rhizosphere nitrifier and denitrifier microbiome under “real-world” conventional agricultural conditions. MethodsTo capture an extensive amount of genetic diversity within maize we grew and sampled the rhizosphere microbiome of a diversity panel of germplasm that included ex-PVP inbreds (Z. maysssp.mays), ex-PVP hybrids (Z. maysssp.mays), and teosinte (Z. maysssp. mexicanaandZ. maysssp.parviglumis). From these samples, we characterized the microbiome, a suite of microbial genes involved in nitrification and denitrification and carried out N-cycling potential assays. ResultsHere we are showing that populations/genotypes of a single species can vary in their ecological interaction with denitrifers and nitrifers. Some hybrid and teosinte genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbred genotypes stimulated/did not inhibit these N-cycling activities. These potential differences translated to functional differences in N₂O fluxes, with teosinte plots producing less GHG than maize plots. ConclusionTaken together, these results suggest thatZeagenetic variation can lead to changes in N-cycling processes that result in N leaching and N₂O production, and thereby are selectable targets for crop improvement. Understanding the underlying genetic variation contributing to belowground microbiome N-cycling into our conventional agricultural system could be useful for sustainability. 

Plants have a surprising capacity to alter their environmental conditions to create adequate niches for survival and stress tolerance. This process of environmental transformation, commonly referred to as “extended phenotypes” or “niche construction”, has historically been studied in the domain of ecology, but this is a process that is pervasive across the plant kingdom. Furthermore, research is beginning to show that plants’ extended phenotypes shape the assembly and function of closely associated microbial communities. Incorporation and understanding the role that plant-extended phenotypes play in agriculture may offer novel, bioinspired methods to manage our arable soil microbiomes. Here, we review the challenges agriculture faces, the plant extended phenotypes we know to shape the microbiome, and the potential utilization of this knowledge to improve the environmental impact of agriculture. Understanding how plant extended phenotypes shape microbial communities could be a key to creating a sustainable future with both plants and microbiomes in consideration.