Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production

York, Larry M.; Cumming, Jonathan R.; Trusiak, Adrianna; Bonito, Gregory; von Haden, Adam C.; Kalluri, Udaya C.; Tiemann, Lisa K.; Andeer, Peter F.; Blanc‐Betes, Elena; Diab, Jonathan H.; Favela, Alonso; Germon, Amandine; Gomez‐Casanovas, Nuria; Hyde, Charles A.; Kent, Angela D.; Ko, Dae Kwan; Lamb, Austin; Missaoui, Ali M.; Northen, Trent R.; Pu, Yunqiao; Ragauskas, Arthur J.; Raglin, Sierra; Scheller, Henrik V.; Washington, Lorenzo; Yang, Wendy H.

doi:10.1002/ppj2.20028

Title: Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production

Journal Article · 11 February 2022 · Plant Phenome Journal

DOI: https://doi.org/10.1002/ppj2.20028 · OSTI ID:1844820

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Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN 37831 USA, Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN 37831 USA, Dep. of Natural Sciences Univ. of Maryland Eastern Shore Princess Anne MD 21853 USA
Great Lakes Bioenergy Research Center (GLBRC) Michigan State Univ. East Lansing MI 48824 USA
Great Lakes Bioenergy Research Center (GLBRC) Michigan State Univ. East Lansing MI 48824 USA, Dep. of Plant, Soil and Microbial Sciences Michigan State Univ. East Lansing MI 48824 USA
Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA, Institute for Sustainability, Energy, and Environment Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA
Environmental Genomics and Systems Biology Lawrence Berkeley National Lab Berkeley CA 94720 USA
Environmental Genomics and Systems Biology Lawrence Berkeley National Lab Berkeley CA 94720 USA, Joint BioEnergy Institute Emeryville CA 94608 USA
Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA, Dep. of Natural Resources &, Environmental Sciences Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA
Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA, Program in Ecology, Evolution, and Conservation Biology Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA
Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA, Dep. of Natural Resources &, Environmental Sciences Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA, Program in Ecology, Evolution, and Conservation Biology Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA
Great Lakes Bioenergy Research Center (GLBRC) Michigan State Univ. East Lansing MI 48824 USA, DOE Plant Research Lab Michigan State Univ. East Lansing MI 48824 USA
Great Lakes Bioenergy Research Center Texas A&,M College Station TX 77843 USA, Dep. of Biochemistry Texas A&,M College Station TX 77843 USA
Center for Bioenergy Innovation Univ. of Georgia Athens GA 30602 USA, Dep. of Crop and Soil Sciences and Institute of Plant Breeding Genetics and Genomics Univ. of Georgia Athens GA 30602 USA
Environmental Genomics and Systems Biology Lawrence Berkeley National Lab Berkeley CA 94720 USA, Joint BioEnergy Institute Emeryville CA 94608 USA, The DOE Joint Genome Institute Lawrence Berkeley National Lab Berkeley CA 94720 USA
Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN 37831 USA, Dep. of Chemical &, Biomolecular Engineering Univ. of Tennessee Knoxville TN 37996 USA, Dep. of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon Univ. of Tennessee Institute of Agriculture Knoxville TN 37996 USA
Environmental Genomics and Systems Biology Lawrence Berkeley National Lab Berkeley CA 94720 USA, Joint BioEnergy Institute Emeryville CA 94608 USA, Dep. of Plant and Microbial Biology Univ. of California Berkeley Berkeley CA 94720 USA
Joint BioEnergy Institute Emeryville CA 94608 USA, Dep. of Plant and Microbial Biology Univ. of California Berkeley Berkeley CA 94720 USA
Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA, Institute for Sustainability, Energy, and Environment Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA, Dep. of Plant Biology Dep. of Geology Univ. of Illinois at Urbana‐Champaign Urbana IL 61801 USA

Abstract 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.

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Research Organization:: Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States); Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC05-00OR22725; SC0018409; SC0018420

OSTI ID:: 1844820

Journal Information:: Plant Phenome Journal, Journal Name: Plant Phenome Journal Journal Issue: 1 Vol. 5; ISSN 2578-2703

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: United States

Language:: English

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Matching the Expression of Root Plasticity with Soil Moisture Availability Maximizes Production of Rice Plants Grown in an Experimental Sloping Bed having Soil Moisture Gradients Kameoka, Emi; Suralta, Roel Rodriguezc; Mitsuya, Shiro Plant Production Science, Vol. 18, Issue 3 https://doi.org/10.1626/pps.18.267	journal	January 2015
Soil and root carbon storage is key to climate benefits of bioenergy crops Yang, Yi; Tilman, David Biofuel Research Journal, Vol. 7, Issue 2 https://doi.org/10.18331/brj2020.7.2.2	journal	June 2020
Root Effects on Soil Organic Matter Decomposition Cheng, Weixin; Kuzyakov, Yakov Roots and Soil Management: Interactions between Roots and the Soil, Volume 48 https://doi.org/10.2134/agronmonogr48.c7	book	October 2015
Biomass and Carbon Partitioning in Switchgrass Frank, A. B.; Berdahl, J. D.; Hanson, J. D. Crop Science, Vol. 44, Issue 4 https://doi.org/10.2135/cropsci2004.1391	journal	January 2004
Tracing Root vs. Residue Carbon into Soils from Conventional and Alternative Cropping Systems Kong, Angela Y. Y.; Six, Johan Soil Science Society of America Journal, Vol. 74, Issue 4 https://doi.org/10.2136/sssaj2009.0346	journal	January 2010
Plant growth and phosphorus accumulation of wild type and two root hair mutants of Arabidopsis thaliana (Brassicaceae) Bates, Terence R.; Lynch, Jonathan P. American Journal of Botany, Vol. 87, Issue 7 https://doi.org/10.2307/2656994	journal	July 2000
Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud Mons, Barend; Neylon, Cameron; Velterop, Jan Information Services & Use, Vol. 37, Issue 1 https://doi.org/10.3233/ISU-170824	journal	March 2017
The rhizosphere revisited: root microbiomics Bakker, Peter A. H. M.; Berendsen, Roeland L.; Doornbos, Rogier F. Frontiers in Plant Science, Vol. 4 https://doi.org/10.3389/fpls.2013.00165	journal	January 2013
Integration of root phenes for soil resource acquisition York, Larry M.; Nord, Eric A.; Lynch, Jonathan P. Frontiers in Plant Science, Vol. 4 https://doi.org/10.3389/fpls.2013.00355	journal	January 2013
Root traits contributing to plant productivity under drought Comas, Louise H.; Becker, Steven R.; Cruz, Von Mark V. Frontiers in Plant Science, Vol. 4 https://doi.org/10.3389/fpls.2013.00442	journal	January 2013
Pseudomonas fluorescens Transportome Is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings under Nutrient Stress Shinde, Shalaka; Cumming, Jonathan R.; Collart, Frank R. Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.00348	journal	March 2017
Pitfalls in Root Trait Calculations: How Ignoring Diameter Heterogeneity Can Lead to Overestimation of Functional Traits Rose, Laura Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.00898	journal	May 2017
Influence of Root Diameter and Soil Depth on the Xylem Anatomy of Fine- to Medium-Sized Roots of Mature Beech Trees in the Top- and Subsoil Kirfel, Kristina; Leuschner, Christoph; Hertel, Dietrich Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.01194	journal	July 2017
Arbuscular Mycorrhiza Improves Substrate Hydraulic Conductivity in the Plant Available Moisture Range Under Root Growth Exclusion Bitterlich, Michael; Franken, Philipp; Graefe, Jan Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.00301	journal	March 2018
Bioethanol Potential of Energy Sorghum Grown on Marginal and Arable Lands Tang, Chaochen; Li, Songbo; Li, Meng Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.00440	journal	April 2018
Root Differentiation of Agricultural Plant Cultivars and Proveniences Using FTIR Spectroscopy Legner, Nicole; Meinen, Catharina; Rauber, Rolf Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.00748	journal	June 2018
Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli Canarini, Alberto; Kaiser, Christina; Merchant, Andrew Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00157	journal	February 2019
Plasticity of Fine-Root Traits Under Long-Term Irrigation of a Water-Limited Scots Pine Forest Brunner, Ivano; Herzog, Claude; Galiano, Lucía Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00701	journal	June 2019
Should Root Plasticity Be a Crop Breeding Target? Schneider, Hannah M.; Lynch, Jonathan P. Frontiers in Plant Science, Vol. 11 https://doi.org/10.3389/fpls.2020.00546	journal	May 2020
Biological Nitrification Inhibition (BNI): Phenotyping of a Core Germplasm Collection of the Tropical Forage Grass Megathyrsus maximus Under Greenhouse Conditions Villegas, Daniel; Arevalo, Ashly; Nuñez, Jonathan Frontiers in Plant Science, Vol. 11 https://doi.org/10.3389/fpls.2020.00820	journal	June 2020
Lectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell Surface Sun, Yali; Qiao, Zhenzhen; Muchero, Wellington Frontiers in Plant Science, Vol. 11 https://doi.org/10.3389/fpls.2020.596301	journal	December 2020
Ecological Implications of Plant Secondary Metabolites - Phytochemical Diversity Can Enhance Agricultural Sustainability Clemensen, Andrea K.; Provenza, Frederick D.; Hendrickson, John R. Frontiers in Sustainable Food Systems, Vol. 4 https://doi.org/10.3389/fsufs.2020.547826	journal	November 2020
Root Traits and Phenotyping Strategies for Plant Improvement Paez-Garcia, Ana; Motes, Christy; Scheible, Wolf-Rüdiger Plants, Vol. 4, Issue 2 https://doi.org/10.3390/plants4020334	journal	June 2015
Bioeffectors as Biotechnological Tools to Boost Plant Innate Immunity: Signal Transduction Pathways Involved Martin-Rivilla, Helena; Garcia-Villaraco, Ana; Ramos-Solano, Beatriz Plants, Vol. 9, Issue 12 https://doi.org/10.3390/plants9121731	journal	December 2020
RhizoVision Crown: An Integrated Hardware and Software Platform for Root Crown Phenotyping Seethepalli, Anand; Guo, Haichao; Liu, Xiuwei Plant Phenomics, Vol. 2020 https://doi.org/10.34133/2020/3074916	journal	February 2020
An Analysis of Soil Coring Strategies to Estimate Root Depth in Maize ( Zea mays ) and Common Bean ( Phaseolus vulgaris ) Burridge, James D.; Black, Christopher K.; Nord, Eric A. Plant Phenomics, Vol. 2020 https://doi.org/10.34133/2020/3252703	journal	November 2020
Phosphorus disequilibrium in the tripartite plant-ectomycorrhiza-plant growth promoting rhizobacterial association Cumming, J. R.; Zawaski, C.; Desai, S. Journal of soil science and plant nutrition, Issue ahead https://doi.org/10.4067/s0718‐95162015005000040	journal	January 2015
EZ-Rhizo software: The gateway to root architecture analysis Armengaud, Patrick Plant Signaling & Behavior, Vol. 4, Issue 2 https://doi.org/10.4161/psb.4.2.7763	journal	February 2009
Phosphate solubilizing bacteria stimulate wheat rhizosphere and endosphere biological nitrogen fixation by improving phosphorus content Li, Yongbin; Li, Qin; Guan, Guohua PeerJ, Vol. 8 https://doi.org/10.7717/peerj.9062	journal	January 2020

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