Rhizosphere Microbiomes in a Historical Maize-Soybean Rotation System Respond to Host Species and Nitrogen Fertilization at the Genus and Subgenus Levels.

Root-associated microbes are key players in plant health, disease resistance, and nitrogen (N) use efficiency. It remains largely unclear how the interplay of biological and environmental factors affects rhizobiome dynamics in agricultural systems. In this study, we quantified the composition of rhizosphere and bulk soil microbial communities associated with maize (Zea mays L.) and soybean (Glycine max L.) in a long-term crop rotation study under conventional fertilization and low-N regimes. Over two growing seasons, we evaluated the effects of environmental conditions and several treatment factors on the abundance of rhizosphere- and soil-colonizing microbial taxa. Time of sampling, host plant species, and N fertilization had major effects on microbiomes, while no effect of crop rotation was observed. Using variance partitioning as well as 16S sequence information, we further defined a set of 82 microbial genera and functional taxonomic groups at the subgenus level that show distinct responses to treatment factors. We identified taxa that are highly specific to either maize or soybean rhizospheres, as well as taxa that are sensitive to N fertilization in plant rhizospheres and bulk soil. This study provides insights to harness the full potential of soil microbes in maize and soybean agricultural systems through plant breeding and field management. IMPORTANCE Plant roots are colonized by large numbers of microbes, some of which may help the plant acquire nutrients and fight diseases. Our study contributes to a better understanding of root-colonizing microbes in the widespread and economically important maize-soybean crop rotation system. The long-term goal of this research is to optimize crop plant varieties and field management to create the best possible conditions for beneficial plant-microbe interactions to occur. These beneficial microbes may be harnessed to sustainably reduce dependency on pesticides and industrial fertilizer. We identify groups of microbes specific to the maize or to the soybean host and microbes that are sensitive to nitrogen fertilization. These microbes represent candidates that may be influenced through plant breeding or field management, and future research will be directed toward elucidating their roles in plant health and nitrogen usage.