Bioenergy production often focuses on the aboveground feedstock production for conversion to fuel and other materials. However, the belowground component is crucial for soil carbon sequestration, greenhouse gas fluxes, and ecosystem function. Roots maximize feedstock production on marginal lands by acquiring soil resources and mediating soil ecosystem processes through interactions with the microbial community. This belowground world is challenging to observe and quantify; however, there are unprecedented opportunities using current methodologies to bring roots, microbes, and soil into focus. These opportunities allow not only breeding for increased feedstock production but breeding for increased soil health and carbon sequestration as well. A recent workshop hosted by the USDOE Bioenergy Research Centers highlighted these challenges and opportunities while creating a roadmap for increased collaboration and data interoperability through standardization of methodologies and data using F.A.I.R. principles. This article provides a background on the need for belowground research in bioenergy cropping systems, a primer on root system properties of major U.S. bioenergy crops, and an overview of the roles of root chemistry, exudation, and microbial interactions on sustainability. Crucially, we outline how to adopt standardized measures and databases to meet the most pressing methodological needs to accelerate root, soil, and microbial research to meet the pressing societal challenges of the century.

Bioenergy could help limit global warming to 2°C above pre‐industrial levels while supplying almost a fourth of the world's renewable energy needs by 2050. However, the deployment of bioenergy raises concerns that adoption at meaningful scales may lead to unintended negative environmental consequences. Meanwhile, the full consolidation of a bioenergy industry is currently challenged by a sufficient, resilient, and resource‐efficient biomass supply and an effective conversion process. Here, we provide a comprehensive analysis of how stable isotope approaches have accelerated the development of a robust bioeconomy by advancing knowledge about environmental sustainability, feedstock development, and biological conversion. We show that advances in stable isotope research have generated crucial information to (1) gain mechanistic insight into the potential of bioenergy crops to mitigate climate change as well as their impact on water and nutrient cycling; (2) develop high‐yielding, resilient feedstocks that produce high‐value bioproducts in planta; and (3) engineer microbes to enhance feedstock conversion to bioenergy products. Further, we highlight knowledge gaps that could benefit from future research facilitated by stable isotope approaches. We conclude that advances in mechanistic knowledge and innovations within the field of stable isotopes in cross‐disciplinary research actions will greatly contribute to breaking down the barriers to establishing a robust bioeconomy.

The agricultural imprints on soil microbial processes manifest at various timescales, leaving many temporal patterns to present slowly. Unfortunately, the lack of long-term continuous agricultural field sites in North America has left gaps in our understanding of agricultural management on biogeochemical processes and their controlling microbiota. Nitrification, ammonium oxidation by bacteria and archaea, is a critical control point in terrestrial nitrogen fluxes by oxidizing cationic ammonium to anionic nitrate, promoting nitrate leaching. Moreover, nitrous oxide is produced during nitrification, contributing to massive nitrous oxide emissions from fertilized agroecosystems. Nitrification is sensitive to many macro and micro-ecological filters, as nitrifiers are obligate aerobes and are sensitive to numerous non-growth substrates and metal ions. This study sought to understand the long-term implications of various rotation and fertilizer regimes on nitrification potential and nitrifying bacterial communities in the Morrow Plots (Urbana, IL). The Morrow Plots was established in 1876 and are the longest continuous field experiments in North America, making it the only site in America capable of assessing the impact of over 140 years of agricultural management on nitrification. The Morrow Plots contrasts fertilizer (manure, inorganic, unfertilized) and rotation (continuous corn, corn-soy, corn-oat alfalfa), allowing us to explore how conventional vs. regenerative agriculture practices impact nitrifier communities. The results of this study suggest that fertilizer and rotation interact to promote distinct bacterial nitrifier communities. Nitrification potential is highest in manure corn-oat-alfalfa plots, suggesting ammonium availability is not solely responsible for active nitrifier communities. Various soil chemical variables, like CEC, Mg, and Ca, significantly influenced nitrifier community beta-diversity, using 16S rRNA amplicon sequencing, suggesting long-term accumulation of specific cations diverge microbial community assembly. While this study only uses nitrification potential enzyme activity instead of isotope analyses, it sheds light on the importance of various physiochemical drivers on nitrification potential and communities. The results support the need for a more precise exploration of the mechanisms controlling field-scale nitrification rates over large temporal scales. Put together, this study supports the importance of long-term field sites for understanding agricultural manipulations of microbial biogeochemical cycling and sheds light on the micronutrients influencing nitrifier communities and potential activity.