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

Abstract

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.

Authors:
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)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1491958
Alternate Identifier(s):
OSTI ID: 1491959; OSTI ID: 1506394
Grant/Contract Number:  
AC02-05CH11231; AC02‐05CH11231; SC0014079; SC0014395
Resource Type:
Published Article
Journal Name:
New Phytologist
Additional Journal Information:
Journal Volume: 222; Journal Issue: 2; Journal ID: ISSN 0028-646X
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Brachypodium distachyon; metabolomics; model ecosystem; reproducibility study; rhizosphere processes; root exudates; root morphology; soil extract

Citation Formats

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., and Northen, Trent R. Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass. United States: N. p., 2018. Web. doi:10.1111/nph.15662.
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. Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass. United States. doi:10.1111/nph.15662.
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., and Northen, Trent R. Wed . "Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass". United States. doi:10.1111/nph.15662.
@article{osti_1491958,
title = {Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass},
author = {Sasse, Joelle and Kant, Josefine and Cole, Benjamin J. and Klein, Andrew P. and Arsova, Borjana and Schlaepfer, Pascal and Gao, Jian and Lewald, Kyle and Zhalnina, Kateryna and Kosina, Suzanne and Bowen, Benjamin P. and Treen, Daniel and Vogel, John and Visel, Axel and Watt, Michelle and Dangl, Jeffery L. and Northen, Trent R.},
abstractNote = {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.},
doi = {10.1111/nph.15662},
journal = {New Phytologist},
number = 2,
volume = 222,
place = {United States},
year = {2018},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1111/nph.15662

Citation Metrics:
Cited by: 2 works
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Figures / Tables:

Figure 1 Figure 1: Experimental setup of the reproducibility experiment. Illustration of the reproducibility experiment: EcoFABs, Brachypodium distachyon seeds, growth media (yellow, 0.59 Murashige & Skoog (MS); red, 0.59 MS-P; blue, soil extract), and light/temperature sensors were distributed to the participating laboratories. Each laboratory germinated the seeds, transferred seedlings to sterilized EcoFABs,more » and grew the plants for 21 d. Root and shoot tissue as well as root exudates were sampled for downstream analysis.« less

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