DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Journal Article · · New Phytologist
DOI: https://doi.org/10.1111/nph.15662 · OSTI ID:1491958
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [1];  [3]; ORCiD logo [2]; ORCiD logo [4];  [1];  [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1];  [1]; ORCiD logo [1];  [5]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Forschungszentrum Jülich, Jülich (Germany)
  3. Univ. of North Carolina, Chapel Hill, NC (United States)
  4. ETH Zürich, Zürich (Switzerland)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Merced, CA (United States)

There is a dynamic reciprocity between plants and their environment: soil physiochemical properties influence plant morphology and metabolism, and root morphology and exudates shape the environment surrounding roots. Here, we investigate the reproducibility of plant trait changes in response to three growth environments. We utilized fabricated ecosystem (EcoFAB) devices to grow the model grass Brachypodium distachyon in three distinct media across four laboratories: phosphate-sufficient and -deficient mineral media allowed assessment of the effects of phosphate starvation, and a complex, sterile soil extract represented a more natural environment with yet uncharacterized effects on plant growth and metabolism. Tissue weight and phosphate content, total root length, and root tissue and exudate metabolic profiles were consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct, with root hairs four times longer than with other growth conditions. Further, plants depleted half of the metabolites investigated from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures, but also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high interlaboratory reproducibility, demonstrating their value in standardized investigations of plant traits.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231; AC02‐05CH11231; SC0014079; SC0014395
OSTI ID:
1491958
Alternate ID(s):
OSTI ID: 1491959; OSTI ID: 1506394
Journal Information:
New Phytologist, Vol. 222, Issue 2; ISSN 0028-646X
Publisher:
WileyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 36 works
Citation information provided by
Web of Science

References (73)

Influence of vegetation on low-molecular-weight carboxylic acids in soil solution—a review journal February 2001
Plant-in-chip: Microfluidic system for studying root growth and pathogenic interactions in Arabidopsis journal June 2011
Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? journal January 2018
GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems journal August 2015
Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases journal July 2015
Bacillus megaterium Rhizobacteria Promote Growth and Alter Root-System Architecture Through an Auxin- and Ethylene-Independent Signaling Mechanism in Arabidopsis thaliana journal February 2007
Stimulation of root hair elongation in Arabidopsis thaliana by low phosphorus availability journal May 1996
Evolution of the Crop Rhizosphere: Impact of Domestication on Root Exudates in Tetraploid Wheat (Triticum turgidum L.) journal December 2017
Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly journal March 2018
Assay of inorganic phosphate, total phosphate and phosphatases book January 1966
A Novel Image-Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture journal July 2011
Structure, variation, and assembly of the root-associated microbiomes of rice journal January 2015
Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection journal June 2017
Root exudation of sugars, amino acids, and organic acids by maize as affected by nitrogen, phosphorus, potassium, and iron deficiency journal December 2010
Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development journal March 2016
Monosaccharide Absorption Activity of Arabidopsis Roots Depends on Expression Profiles of Transporter Genes under High Salinity Conditions journal October 2011
Dealing with the unknown: Metabolomics and Metabolite Atlases journal September 2010
Direct comparison of MRI and X-ray CT technologies for 3D imaging of root systems in soil: potential and challenges for root trait quantification journal January 2015
Ascorbic acid metabolism and functions: A comparison of plants and mammals journal July 2018
Amino-acid influx at the soil-root interface of Zea mays L. and its implications in the rhizosphere journal June 1994
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy journal November 2016
Root hair formation in rice ( Oryza sativa L.) differs between root types and is altered in artificial growth conditions journal March 2016
Transkingdom signaling based on bacterial cyclodipeptides with auxin activity in plants journal April 2011
The story of phosphorus: Global food security and food for thought journal May 2009
Unraveling Root Developmental Programs Initiated by Beneficial Pseudomonas spp. Bacteria journal March 2013
Dual-flow-RootChip reveals local adaptations of roots towards environmental asymmetry at the physiological and genetic levels journal November 2017
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 journal June 1993
Metabolite profiling of non‐sterile rhizosphere soil journal August 2017
Signaling in the Rhizosphere journal March 2016
The shoot and root growth of Brachypodium and its potential as a model for wheat and other cereal crops journal January 2009
Alteration of nutrient allocation and transporter genes expression in rice under N, P, K, and Mg deficiencies journal November 2011
Exometabolite niche partitioning among sympatric soil bacteria journal September 2015
Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice journal February 2018
Formation of xanthine and the use of purine metabolites as a nitrogen source in Arabidopsis plants journal November 2008
Root developmental adaptation to phosphate starvation: better safe than sorry journal August 2011
Cluster roots – an underground adaptation for survival in extreme environments journal April 2002
Influx and efflux of organic acids across the soil-root interface of Zea mays L. and its implications in rhizosphere C flow journal June 1995
Chemical characterization of root exudates from rice (Oryza sativa) and their effects on the chemotactic response of endophytic bacteria journal February 2003
Correction: Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions journal August 2013
High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation journal July 2017
Plant growth-promoting rhizobacteria and root system functioning journal January 2013
The art of growing plants for experimental purposes: a practical guide for the plant biologist journal January 2012
Metabolic Adaptations of Phosphate-Starved Plants journal May 2011
Plant chip for high-throughput phenotyping of Arabidopsis journal January 2014
Folate biofortification in food crops journal April 2017
The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface journal November 2017
Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI) journal September 2007
Modulation of plant chemistry by beneficial root microbiota journal January 2018
Brachypodium distachyon and Setaria viridis : Model Genetic Systems for the Grasses journal April 2015
Probing the Reproducibility of Leaf Growth and Molecular Phenotypes: A Comparison of Three Arabidopsis Accessions Cultivated in Ten Laboratories journal March 2010
Do longer root hairs improve phosphorus uptake? Testing the hypothesis with transgenic Brachypodium distachyon lines overexpressing endogenous RSL genes journal January 2018
Root microbiota drive direct integration of phosphate stress and immunity journal March 2017
Untargeted soil metabolomics methods for analysis of extractable organic matter journal January 2015
High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3 journal November 2007
Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism journal March 2016
Structure and Functions of the Bacterial Microbiota of Plants journal April 2013
Re-sorption of organic compounds by roots of Zea mays L. and its consequences in the rhizosphere: III. Characteristics of sugar influx and efflux journal January 1996
Enterobacter hormaechei as Plant Growth-Promoting Bacteria for Improvement in Lycopersicum esculentum journal February 2021
Root microbiota drive direct integration of phosphate stress and immunity text January 2017
Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? text January 2018
Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI) journal September 2007
Dealing with the unknown: Metabolomics and Metabolite Atlases journal September 2010
Signaling in the Rhizosphere journal March 2016
Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development journal March 2016
Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? journal January 2018
Root microbiota drive direct integration of phosphate stress and immunity journal March 2017
Root hair formation in rice ( Oryza sativa L.) differs between root types and is altered in artificial growth conditions journal March 2016
Metabolic Adaptations of Phosphate-Starved Plants journal May 2011
Unraveling Root Developmental Programs Initiated by Beneficial Pseudomonas spp. Bacteria journal March 2013
Dual-flow-RootChip reveals local adaptations of roots towards environmental asymmetry at the physiological and genetic levels journal November 2017
Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice journal February 2018
Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases journal July 2015
Formation of xanthine and the use of purine metabolites as a nitrogen source in Arabidopsis plants journal November 2008

Cited By (1)

Dynamics in plant roots and shoots minimize stress, save energy and maintain water and nutrient uptake journal August 2019

Figures / Tables (5)