Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

Sasse, Joelle; Kant, Josefine; Cole, Benjamin J.; Klein, Andrew P.; Arsova, Borjana; Schlaepfer, Pascal; Gao, Jian; Lewald, Kyle; Zhalnina, Kateryna; Kosina, Suzanne; Bowen, Benjamin P.; Treen, Daniel; Vogel, John; Visel, Axel; Watt, Michelle; Dangl, Jeffery L.; Northen, Trent R.

doi:10.1111/nph.15662

Title: Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

Journal Article · 24 January 2019 · New Phytologist

DOI: https://doi.org/10.1111/nph.15662 · OSTI ID:1491958

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^[4]; Gao, Jian ^[1]; Lewald, Kyle ^[1];

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^[1]; Treen, Daniel ^[1];

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Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA, Joint Genome Institute 2800 Mitchell Drive Walnut Creek CA 94598 USA
Institut für Bio‐ &, Geowissenschaften Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
Department of Biology Howard Hughes Medical Institute University of North Carolina Chapel Hill 250 Bell Tower Drive Chapel Hill NC 27599 USA
Institute of Molecular Plant Biology ETH Zürich Universitätsstrasse 2 8092 Zürich Switzerland
Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA, Joint Genome Institute 2800 Mitchell Drive Walnut Creek CA 94598 USA, School of Natural Sciences University of California Merced CA 95343 USA

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231; SC0014079; SC0014395

OSTI ID:: 1491958

Journal Information:: New Phytologist, Journal Name: New Phytologist Journal Issue: 2 Vol. 222; ISSN 0028-646X

Publisher:: WileyCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (56)

Root exudation of sugars, amino acids, and organic acids by maize as affected by nitrogen, phosphorus, potassium, and iron deficiency Carvalhais, Lilia C.; Dennis, Paul G.; Fedoseyenko, Dmitri Journal of Plant Nutrition and Soil Science, Vol. 174, Issue 1 https://doi.org/10.1002/jpln.201000085	journal	December 2010
Re-sorption of organic compounds by roots of Zea mays L. and its consequences in the rhizosphere: II. Experimental and model evidence for simultaneous exudation and re-sorption of soluble C compounds Jones, D. L.; Darrah, P. R. Plant and Soil, Vol. 153, Issue 1 https://doi.org/10.1007/BF00010543	journal	June 1993
Amino-acid influx at the soil-root interface of Zea mays L. and its implications in the rhizosphere Jones, D. L.; Darrah, P. R. Plant and Soil, Vol. 163, Issue 1 https://doi.org/10.1007/BF00033935	journal	June 1994
Influx and efflux of organic acids across the soil-root interface of Zea mays L. and its implications in rhizosphere C flow Jones, David L.; Darrah, Peter R. Plant and Soil, Vol. 173, Issue 1 https://doi.org/10.1007/BF00155523	journal	June 1995
High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3 Vogel, John; Hill, Theresa Plant Cell Reports, Vol. 27, Issue 3 https://doi.org/10.1007/s00299-007-0472-y	journal	November 2007
Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI) Sumner, Lloyd W.; Amberg, Alexander; Barrett, Dave Metabolomics, Vol. 3, Issue 3 https://doi.org/10.1007/s11306-007-0082-2	journal	September 2007
Alteration of nutrient allocation and transporter genes expression in rice under N, P, K, and Mg deficiencies Cai, Jin; Chen, Lu; Qu, Hongye Acta Physiologiae Plantarum, Vol. 34, Issue 3 https://doi.org/10.1007/s11738-011-0890-x	journal	November 2011
Assay of inorganic phosphate, total phosphate and phosphatases Ames, Bruce N. Methods in Enzymology, p. 115-118 https://doi.org/10.1016/0076-6879(66)08014-5	book	January 1966
Influence of vegetation on low-molecular-weight carboxylic acids in soil solution—a review Strobel, Bjarne W. Geoderma, Vol. 99, Issue 3-4 https://doi.org/10.1016/S0016-7061(00)00102-6	journal	February 2001
Cluster roots – an underground adaptation for survival in extreme environments Neumann, Günter; Martinoia, Enrico Trends in Plant Science, Vol. 7, Issue 4 https://doi.org/10.1016/S1360-1385(02)02241-0	journal	April 2002
Folate biofortification in food crops Strobbe, Simon; Van Der Straeten, Dominique Current Opinion in Biotechnology, Vol. 44 https://doi.org/10.1016/j.copbio.2016.12.003	journal	April 2017
Ascorbic acid metabolism and functions: A comparison of plants and mammals Smirnoff, Nicholas Free Radical Biology and Medicine, Vol. 122 https://doi.org/10.1016/j.freeradbiomed.2018.03.033	journal	July 2018
The story of phosphorus: Global food security and food for thought Cordell, Dana; Drangert, Jan-Olof; White, Stuart Global Environmental Change, Vol. 19, Issue 2 https://doi.org/10.1016/j.gloenvcha.2008.10.009	journal	May 2009
Dealing with the unknown: Metabolomics and Metabolite Atlases Bowen, Benjamin P.; Northen, Trent R. Journal of the American Society for Mass Spectrometry, Vol. 21, Issue 9 https://doi.org/10.1016/j.jasms.2010.04.003	journal	September 2010
Untargeted soil metabolomics methods for analysis of extractable organic matter Swenson, Tami L.; Jenkins, Stefan; Bowen, Benjamin P. Soil Biology and Biochemistry, Vol. 80 https://doi.org/10.1016/j.soilbio.2014.10.007	journal	January 2015
Root developmental adaptation to phosphate starvation: better safe than sorry Péret, Benjamin; Clément, Mathilde; Nussaume, Laurent Trends in Plant Science, Vol. 16, Issue 8 https://doi.org/10.1016/j.tplants.2011.05.006	journal	August 2011
Signaling in the Rhizosphere Venturi, Vittorio; Keel, Christoph Trends in Plant Science, Vol. 21, Issue 3 https://doi.org/10.1016/j.tplants.2016.01.005	journal	March 2016
Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development Verbon, Eline H.; Liberman, Louisa M. Trends in Plant Science, Vol. 21, Issue 3 https://doi.org/10.1016/j.tplants.2016.01.013	journal	March 2016
Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? Sasse, Joelle; Martinoia, Enrico; Northen, Trent Trends in Plant Science, Vol. 23, Issue 1 https://doi.org/10.1016/j.tplants.2017.09.003	journal	January 2018
Chemical characterization of root exudates from rice (Oryza sativa) and their effects on the chemotactic response of endophytic bacteria Bacilio-Jiménez, Macario; Aguilar-Flores, Sara; Ventura-Zapata, Elsa Plant and Soil, Vol. 249, Issue 2, p. 271-277 https://doi.org/10.1023/A:1022888900465	journal	February 2003
Root microbiota drive direct integration of phosphate stress and immunity Castrillo, Gabriel; Teixeira, Paulo José Pereira Lima; Paredes, Sur Herrera Nature, Vol. 543, Issue 7646 https://doi.org/10.1038/nature21417	journal	March 2017
Exometabolite niche partitioning among sympatric soil bacteria Baran, Richard; Brodie, Eoin L.; Mayberry-Lewis, Jazmine Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9289	journal	September 2015
Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly Zhalnina, Kateryna; Louie, Katherine B.; Hao, Zhao Nature Microbiology, Vol. 3, Issue 4 https://doi.org/10.1038/s41564-018-0129-3	journal	March 2018
The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface Helliwell, J. R.; Sturrock, C. J.; Mairhofer, S. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-14904-w	journal	November 2017
Plant chip for high-throughput phenotyping of Arabidopsis Jiang, Huawei; Xu, Zhen; Aluru, Maneesha R. Lab Chip, Vol. 14, Issue 7 https://doi.org/10.1039/C3LC51326B	journal	January 2014
Modulation of plant chemistry by beneficial root microbiota Etalo, Desalegn W.; Jeon, Je-Seung; Raaijmakers, Jos M. Natural Product Reports, Vol. 35, Issue 5 https://doi.org/10.1039/C7NP00057J	journal	January 2018
Plant-in-chip: Microfluidic system for studying root growth and pathogenic interactions in Arabidopsis Parashar, Archana; Pandey, Santosh Applied Physics Letters, Vol. 98, Issue 26 https://doi.org/10.1063/1.3604788	journal	June 2011
The shoot and root growth of Brachypodium and its potential as a model for wheat and other cereal crops Watt, Michelle; Schneebeli, Katharina; Dong, Pan Functional Plant Biology, Vol. 36, Issue 11 https://doi.org/10.1071/FP09214	journal	January 2009
The art of growing plants for experimental purposes: a practical guide for the plant biologist Poorter, Hendrik; Fiorani, Fabio; Stitt, Mark Functional Plant Biology, Vol. 39, Issue 11 https://doi.org/10.1071/FP12028	journal	January 2012
Transkingdom signaling based on bacterial cyclodipeptides with auxin activity in plants Ortiz-Castro, R.; Diaz-Perez, C.; Martinez-Trujillo, M. Proceedings of the National Academy of Sciences, Vol. 108, Issue 17 https://doi.org/10.1073/pnas.1006740108	journal	April 2011
Structure, variation, and assembly of the root-associated microbiomes of rice Edwards, Joseph; Johnson, Cameron; Santos-Medellín, Christian Proceedings of the National Academy of Sciences, Vol. 112, Issue 8 https://doi.org/10.1073/pnas.1414592112	journal	January 2015
Monosaccharide Absorption Activity of Arabidopsis Roots Depends on Expression Profiles of Transporter Genes under High Salinity Conditions Yamada, Kohji; Kanai, Motoki; Osakabe, Yuriko Journal of Biological Chemistry, Vol. 286, Issue 50 https://doi.org/10.1074/jbc.M111.269712	journal	October 2011
Root hair formation in rice ( Oryza sativa L.) differs between root types and is altered in artificial growth conditions Nestler, Josefine; Keyes, Samuel David; Wissuwa, Matthias Journal of Experimental Botany, Vol. 67, Issue 12 https://doi.org/10.1093/jxb/erw115	journal	March 2016
Bacillus megaterium Rhizobacteria Promote Growth and Alter Root-System Architecture Through an Auxin- and Ethylene-Independent Signaling Mechanism in Arabidopsis thaliana López-Bucio, José; Campos-Cuevas, Juan Carlos; Hernández-Calderón, Erasto Molecular Plant-Microbe Interactions, Vol. 20, Issue 2 https://doi.org/10.1094/MPMI-20-2-0207	journal	February 2007
Probing the Reproducibility of Leaf Growth and Molecular Phenotypes: A Comparison of Three Arabidopsis Accessions Cultivated in Ten Laboratories Massonnet, Catherine; Vile, Denis; Fabre, Juliette Plant Physiology, Vol. 152, Issue 4 https://doi.org/10.1104/pp.109.148338	journal	March 2010
Metabolic Adaptations of Phosphate-Starved Plants Plaxton, William C.; Tran, Hue T. Plant Physiology, Vol. 156, Issue 3 https://doi.org/10.1104/pp.111.175281	journal	May 2011
A Novel Image-Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture Lobet, Guillaume; Pagès, Loïc; Draye, Xavier Plant Physiology, Vol. 157, Issue 1 https://doi.org/10.1104/pp.111.179895	journal	July 2011
Unraveling Root Developmental Programs Initiated by Beneficial Pseudomonas spp. Bacteria Zamioudis, Christos; Mastranesti, Parthena; Dhonukshe, Pankaj Plant Physiology, Vol. 162, Issue 1 https://doi.org/10.1104/pp.112.212597	journal	March 2013
Stimulation of root hair elongation in Arabidopsis thaliana by low phosphorus availability Bates, T. R.; Lynch, J. P. Plant, Cell and Environment, Vol. 19, Issue 5 https://doi.org/10.1111/j.1365-3040.1996.tb00386.x	journal	May 1996
High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation Koebernick, Nicolai; Daly, Keith R.; Keyes, Samuel D. New Phytologist, Vol. 216, Issue 1 https://doi.org/10.1111/nph.14705	journal	July 2017
Dual-flow-RootChip reveals local adaptations of roots towards environmental asymmetry at the physiological and genetic levels Stanley, Claire E.; Shrivastava, Jagriti; Brugman, Rik New Phytologist, Vol. 217, Issue 3 https://doi.org/10.1111/nph.14887	journal	November 2017
Do longer root hairs improve phosphorus uptake? Testing the hypothesis with transgenic Brachypodium distachyon lines overexpressing endogenous RSL genes Zhang, Chunyan; Simpson, Richard J.; Kim, Chul Min New Phytologist, Vol. 217, Issue 4 https://doi.org/10.1111/nph.14980	journal	January 2018
Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection Hsia, Mon Mandy; O'Malley, Ronan; Cartwright, Amy The Plant Journal, Vol. 91, Issue 3 https://doi.org/10.1111/tpj.13582	journal	June 2017
Metabolite profiling of non‐sterile rhizosphere soil Pétriacq, Pierre; Williams, Alex; Cotton, Anne The Plant Journal, Vol. 92, Issue 1 https://doi.org/10.1111/tpj.13639	journal	August 2017
Brachypodium distachyon and Setaria viridis : Model Genetic Systems for the Grasses Brutnell, Thomas P.; Bennetzen, Jeffrey L.; Vogel, John P. Annual Review of Plant Biology, Vol. 66, Issue 1 https://doi.org/10.1146/annurev-arplant-042811-105528	journal	April 2015
Structure and Functions of the Bacterial Microbiota of Plants Bulgarelli, Davide; Schlaeppi, Klaus; Spaepen, Stijn Annual Review of Plant Biology, Vol. 64, Issue 1 https://doi.org/10.1146/annurev-arplant-050312-120106	journal	April 2013
Direct comparison of MRI and X-ray CT technologies for 3D imaging of root systems in soil: potential and challenges for root trait quantification Metzner, Ralf; Eggert, Anja; van Dusschoten, Dagmar Plant Methods, Vol. 11, Issue 1 https://doi.org/10.1186/s13007-015-0060-z	journal	January 2015
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy Djoumbou Feunang, Yannick; Eisner, Roman; Knox, Craig Journal of Cheminformatics, Vol. 8, Issue 1 https://doi.org/10.1186/s13321-016-0174-y	journal	November 2016
Correction: Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions Chaparro, Jacqueline M.; Badri, Dayakar V.; Bakker, Matthew G. PLoS ONE, Vol. 8, Issue 8 https://doi.org/10.1371/annotation/51142aed-2d94-4195-8a8a-9cb24b3c733b	journal	August 2013
Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice Edwards, Joseph A.; Santos-Medellín, Christian M.; Liechty, Zachary S. PLOS Biology, Vol. 16, Issue 2 https://doi.org/10.1371/journal.pbio.2003862	journal	February 2018
Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism Thijs, Sofie; Sillen, Wouter; Rineau, Francois Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00341	journal	March 2016
Plant growth-promoting rhizobacteria and root system functioning Vacheron, Jordan; Desbrosses, Guilhem; Bouffaud, Marie-Lara Frontiers in Plant Science, Vol. 4 https://doi.org/10.3389/fpls.2013.00356	journal	January 2013
Evolution of the Crop Rhizosphere: Impact of Domestication on Root Exudates in Tetraploid Wheat (Triticum turgidum L.) Iannucci, Anna; Fragasso, Mariagiovanna; Beleggia, Romina Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.02124	journal	December 2017
Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases Yao, Yushu; Sun, Terence; Wang, Tony Metabolites, Vol. 5, Issue 3 https://doi.org/10.3390/metabo5030431	journal	July 2015
Formation of xanthine and the use of purine metabolites as a nitrogen source in Arabidopsis plants Brychkova, Galina; Fluhr, Robert; Sagi, Moshe Plant Signaling & Behavior, Vol. 3, Issue 11 https://doi.org/10.4161/psb.6304	journal	November 2008
GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems Rellán-Álvarez, Rubén; Lobet, Guillaume; Lindner, Heike eLife, Vol. 4 https://doi.org/10.7554/eLife.07597	journal	August 2015

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59 BASIC BIOLOGICAL SCIENCES
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root exudates
root morphology
soil extract

Title: Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

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References (56)

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