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

Abstract

Summary 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 (Eco FAB ) 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 Eco FAB s utilized here generated high interlaboratory reproducibility, demonstrating their value in standardized investigations of plant traits.

A Crosstalk Between Brachypodium Root Exudates, Organic Acids, and Bacillus velezensis B26, a Growth Promoting Bacterium

“…The use of inert substrates such as glass beads or sand instead of soil or clay that strongly absorbs a variety of metabolites may affect exudation and metabolite profiles. Notably, root exudation studies of Brachyodium grown under sterile hydroponic systems resulted in similar metabolite profiles of exudates in sand or glass beads ( Kawasaki et al, 2016 ; Sasse et al, 2019 ). The most common organic acids released from Brachypodium roots were malate, citrate, succinic, fumarate, and oxalate ( Kawasaki et al, 2016 ).…”

Crop Improvement from Phenotyping Roots: Highlights Reveal Expanding Opportunities

“…EcoFABs are 3D printed, scalable, and axenic, allowing multiple soil factors to be tested individually and in combination. Right: the EcoFABs showed that root hair development is influenced by filtered soil extracts differently to P supply [109]. Abbreviations: E, root epidermis; n, nucleus; rh, roothair.…”

“…But how can the large number of variables in the rhizosphere be systematically combined for the understanding of processes? An exciting multi-lab approach has been initiated, using repeatable, 3D printed microcosms called Eco-Fabs ( Figure 5C) [109]. Bespoke phenotyping platforms are available globally in fixed locations with highly specialized operators for researchers, breeders, and prebreeders [46].…”

A 3D Print Repository for Plant Phenomics

“…As 3D printer technology becomes more affordable and accessible worldwide, there is an opportunity to use this to facilitate research coordination and scientific reproducibility. The EcoFAB project has shown great promise at coordinating research across multiple groups with each printing the same 3D printable growth system and following defined protocols with reproducible results [ 2 , 10 ]. A hurdle for reproducibility of lab protocols is having accessibility to the respective lab equipment.…”