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

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

doi:10.1002/ppj2.20028

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

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

Research output: Contribution to journal › Article › peer-review

14 Scopus citations

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.

Original language	English
Article number	e20028
Journal	Plant Phenome Journal
Volume	5
Issue number	1
DOIs	https://doi.org/10.1002/ppj2.20028
State	Published - 2022

Funding

This work was funded by the Center for Bioenergy Innovation, a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science, Oak Ridge National Laboratory is managed by UT‐Battelle, LLC under Contract DE‐AC05‐00OR22725 with the U.S. Department of Energy to L.M.Y., J.R.C, U.C.K., Y.P., A.J.R., A.M.; the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE‐SC0018409 to A.T., G.B., A.L., L.K.T, D.K.K.; the DOE Joint BioEnergy Institute supported by the U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE‐AC02‐05CH11231 between Lawrence Berkeley National Laboratory and the U. S. Department of Energy to H.V.S., L.W., J.H.D.; the DOE Center for Advanced Bioenergy and Bioproducts Innovation, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award number DE‐SC0018420 to A.C.V.H., E.B.B., A.F., A.G., N.G.C., C.A.H., A.K., S.R., W.H.Y.; a Laboratory Directed Research Development (LDRD) LBNL grant to J.H.D; and the Microbial Community Analysis and Functional Evaluation in Soils Program at Lawrence Berkeley National Laboratory DE‐AC02‐05CH11231 to T.R.N and P.F.A. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the U.S. Department of Energy. This manuscript has been authored by UT‐Battelle, LLC, under contract DE‐AC05‐00OR22725 with the US Department of Energy (DOE). The US government retains and the publisher, by accepting the article for publication, acknowledges that the US government retains a nonexclusive, paid‐up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for US government purposes. DOE will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan ( http://energy.gov/downloads/doe‐public‐access‐plan ). We would like to thank Chelsea Mamott and the GLBRC communications team for the figures. This work was funded by the Center for Bioenergy Innovation, a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science, Oak Ridge National Laboratory is managed by UT-Battelle, LLC under Contract DE-AC05-00OR22725 with the U.S. Department of Energy to L.M.Y., J.R.C, U.C.K., Y.P., A.J.R., A.M.; the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0018409 to A.T., G.B., A.L., L.K.T, D.K.K.; the DOE Joint BioEnergy Institute supported by the U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U. S. Department of Energy to H.V.S., L.W., J.H.D.; the DOE Center for Advanced Bioenergy and Bioproducts Innovation, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award number DE-SC0018420 to A.C.V.H., E.B.B., A.F., A.G., N.G.C., C.A.H., A.K., S.R., W.H.Y.; a Laboratory Directed Research Development (LDRD) LBNL grant to J.H.D; and the Microbial Community Analysis and Functional Evaluation in Soils Program at Lawrence Berkeley National Laboratory DE-AC02-05CH11231 to T.R.N and P.F.A. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the U.S. Department of Energy. This manuscript has been authored by UT-Battelle, LLC, under contract DE-AC05-00OR22725 with the US Department of Energy (DOE). The US government retains and the publisher, by accepting the article for publication, acknowledges that the US government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for US government purposes. DOE will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). We would like to thank Chelsea Mamott and the GLBRC communications team for the figures.

Funders	Funder number
Chelsea Mamott
DOE Center for Advanced Bioenergy and Bioproducts Innovation	DE‐SC0018420
DOE Public Access Plan
U.S. Department of Energy Bioenergy Research Center
U.S. Department of Energy	DE‐AC02‐05CH11231
Office of Science	DE‐SC0018409
Biological and Environmental Research
Oak Ridge National Laboratory	DE‐AC05‐00OR22725
Lawrence Berkeley National Laboratory
Laboratory Directed Research and Development
Center for Bioenergy Innovation
Great Lakes Bioenergy Research Center
UT-Battelle

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1002/ppj2.20028

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York, L. M., Cumming, J. R., Trusiak, A., Bonito, G., von Haden, A. C., Kalluri, U. C., Tiemann, L. K., Andeer, P. F., Blanc-Betes, E., Diab, J. H., Favela, A., Germon, A., Gomez-Casanovas, N., Hyde, C. A., Kent, A. D., Ko, D. K., Lamb, A., Missaoui, A. M., Northen, T. R., ... Yang, W. H. (2022). Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production. Plant Phenome Journal, 5(1), Article e20028. https://doi.org/10.1002/ppj2.20028

@article{8efb9eb6d2644894ab714a082cd5f861,

title = "Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production",

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.",

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

note = "Publisher Copyright: {\textcopyright} 2022 Oak Ridge National Laboratory, managed by UT-Battelle, LLC. The Plant Phenome Journal published by Wiley Periodicals LLC on behalf of American Society of Agronomy and Crop Science Society of America.",

year = "2022",

doi = "10.1002/ppj2.20028",

language = "English",

volume = "5",

journal = "Plant Phenome Journal",

issn = "2578-2703",

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York, LM, Cumming, JR, Trusiak, A, Bonito, G, von Haden, AC, Kalluri, UC, Tiemann, LK, Andeer, PF, Blanc-Betes, E, Diab, JH, Favela, A, Germon, A, Gomez-Casanovas, N, Hyde, CA, Kent, AD, Ko, DK, Lamb, A, Missaoui, AM, Northen, TR, Pu, Y, Ragauskas, AJ, Raglin, S, Scheller, HV, Washington, L & Yang, WH 2022, 'Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production', Plant Phenome Journal, vol. 5, no. 1, e20028. https://doi.org/10.1002/ppj2.20028

TY - JOUR

T1 - Bioenergy Underground

T2 - Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production

AU - York, Larry M.

AU - Cumming, Jonathan R.

AU - Trusiak, Adrianna

AU - Bonito, Gregory

AU - von Haden, Adam C.

AU - Kalluri, Udaya C.

AU - Tiemann, Lisa K.

AU - Andeer, Peter F.

AU - Blanc-Betes, Elena

AU - Diab, Jonathan H.

AU - Favela, Alonso

AU - Germon, Amandine

AU - Gomez-Casanovas, Nuria

AU - Hyde, Charles A.

AU - Kent, Angela D.

AU - Ko, Dae Kwan

AU - Lamb, Austin

AU - Missaoui, Ali M.

AU - Northen, Trent R.

AU - Pu, Yunqiao

AU - Ragauskas, Arthur J.

AU - Raglin, Sierra

AU - Scheller, Henrik V.

AU - Washington, Lorenzo

AU - Yang, Wendy H.

N1 - Publisher Copyright: © 2022 Oak Ridge National Laboratory, managed by UT-Battelle, LLC. The Plant Phenome Journal published by Wiley Periodicals LLC on behalf of American Society of Agronomy and Crop Science Society of America.

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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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U2 - 10.1002/ppj2.20028

DO - 10.1002/ppj2.20028

M3 - Article

AN - SCOPUS:85145898102

SN - 2578-2703

VL - 5

JO - Plant Phenome Journal

JF - Plant Phenome Journal

IS - 1

M1 - e20028

ER -

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

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UN SDGs

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