Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions

Gao, Jian; Sasse, Joëlle; Lewald, Kyle M; Zhalnina, Kateryna; Cornmesser, Lloyd T.; Duncombe, Todd A.; Yoshikuni, Yasuo; Vogel, John P.; Firestone, Mary K.; Northen, Trent

doi:10.3791/57170-v

Cited by 13 publications

(15 citation statements)

References 14 publications

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“…The MS medium used to cultivate B. distachyon contains major salts and trace metals. Fabricated ecosystems (EcoFABs; Gao et al, 2018) were sterilized, and seedlings were transferred to EcoFABs 5 d after germination. The EcoFABs were filled with 4 ml of 0.29 MS medium and incubated in a 16 h : 8 h, light : dark regime at 24°C with 150 lmol m À2 s À1 light intensity for 5 d before further processing.…”

Section: Brachypodium Distachyon and M Vaginatus Growth Conditionsmentioning

confidence: 99%

Conservation of beneficial microbes between the rhizosphere and the cyanosphere

Zheng,

Hu,

Kosina

et al. 2023

New Phytologist

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Summary Biocrusts are phototroph‐driven communities inhabiting arid soil surfaces. Like plants, most photoautotrophs (largely cyanobacteria) in biocrusts are thought to exchange fixed carbon for essential nutrients like nitrogen with cyanosphere bacteria. Here, we aim to compare beneficial interactions in rhizosphere and cyanosphere environments, including finding growth‐promoting strains for hosts from both environments. To examine this, we performed a retrospective analysis of 16S rRNA gene sequencing datasets, host–microbe co‐culture experiments between biocrust communities/biocrust isolates and a model grass (Brachypodium distachyon) or a dominant biocrust cyanobacterium (Microcoleus vaginatus), and metabolomic analysis. All 18 microbial phyla in the cyanosphere were also present in the rhizosphere, with additional 17 phyla uniquely found in the rhizosphere. The biocrust microbes promoted the growth of the model grass, and three biocrust isolates (Bosea sp._L1B56, Pseudarthrobacter sp._L1D14 and Pseudarthrobacter picheli_L1D33) significantly promoted the growth of both hosts. Moreover, pantothenic acid was produced by Pseudarthrobacter sp._L1D14 when grown on B. distachyon exudates, and supplementation of plant growth medium with this metabolite increased B. distachyon biomass by over 60%. These findings suggest that cyanobacteria and other diverse photoautotrophic hosts can be a source for new plant growth‐promoting microbes and metabolites.

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Section: Brachypodium Distachyon and M Vaginatus Growth Conditionsmentioning

confidence: 99%

Conservation of beneficial microbes between the rhizosphere and the cyanosphere

Zheng,

Hu,

Kosina

et al. 2023

New Phytologist

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“…These systems are less easily transferred to other labs because of the need for specialised equipment and facilities as well as the knowhow to operate them. Simpler fabrication techniques such as that proposed by EcoFAB have been demonstrated 32,33 . With our framework we showed that such fabrication techniques can be expanded to combine features that allow for the control of water in the microcosms created (fluxes, content and heterogeneity), which is critical in the study of plant responses to their environment.…”

Section: Resultsmentioning

confidence: 99%

Microcosm Fabrication Platform for Live Microscopy of Plant-Soil Systems

Liu,

Patko,

de le Mata

et al. 2024

Preprint

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Biological processes in soil pores are critical to crop nutrition and productivity, but live observations of these processes at that scale have been difficult to accomplish. To address this challenge, we have developed new techniques for the fabrication of microcosms dedicated to live imaging of the rhizosphere which incorporate the ability to control water content in transparent soil. Chambers were assembled using poly(dimethyl siloxane) (PDMS) parts fabricated by injection moulding and subsequently joined to glass slides. The control of liquid fluxes in the microcosm was achieved by syringes passing through the PDMS parts or through custom made PDMS sponges. We then tested various low refractive index materials for the fabrication of transparent soils and carried out live microscopy using Fluorescence Light Sheet microscopy. The proposed fabrication techniques are modular and enabled the construction of a wide range of experimental systems, including split chamber systems for the control of water content in soil, heterogeneous distribution of water content, monitoring of dye tracers, and live observation of plant roots. Using the techniques, we show how plant roots increase water infiltration through increased permeability of dry soil layers. This study therefore establishes that material property control and microfabrication in model rhizosphere systems can greatly enhance our understanding of plant-soil interactions.

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“…The 155 annotated features belonged to diverse biosynthetic pathways according to the NPClassifier: amino acids-peptides (53), carbohydrates (39), alkaloids (27), shikimates-phenylpropanoids (22), fatty acids (8), no classification (4), terpenoid (1), and polyketides (1) (fig. S4).…”

Section: Root Exudation Changes With Nitrogen Supplymentioning

confidence: 99%

Reproducible growth ofBrachypodiumin EcoFAB 2.0 reveals that nitrogen form and starvation modulate root exudation

Novak,

Andeer,

Bowen

et al. 2024

Sci. Adv.

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Understanding plant-microbe interactions requires examination of root exudation under nutrient stress using standardized and reproducible experimental systems. We grew Brachypodium distachyon hydroponically in fabricated ecosystem devices (EcoFAB 2.0) under three inorganic nitrogen forms (nitrate, ammonium, and ammonium nitrate), followed by nitrogen starvation. Analyses of exudates with liquid chromatography–tandem mass spectrometry, biomass, medium pH, and nitrogen uptake showed EcoFAB 2.0’s low intratreatment data variability. Furthermore, the three inorganic nitrogen forms caused differential exudation, generalized by abundant amino acids–peptides and alkaloids. Comparatively, nitrogen deficiency decreased nitrogen-containing compounds but increased shikimates-phenylpropanoids. Subsequent bioassays with two shikimates-phenylpropanoids (shikimic and p -coumaric acids) on soil bacteria or Brachypodium seedlings revealed their distinct capacity to regulate both bacterial and plant growth. Our results suggest that (i) Brachypodium alters exudation in response to nitrogen status, which can affect rhizobacterial growth, and (ii) EcoFAB 2.0 is a valuable standardized plant research tool.

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Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions

Cited by 13 publications

References 14 publications

Conservation of beneficial microbes between the rhizosphere and the cyanosphere

Conservation of beneficial microbes between the rhizosphere and the cyanosphere

Microcosm Fabrication Platform for Live Microscopy of Plant-Soil Systems

Reproducible growth ofBrachypodiumin EcoFAB 2.0 reveals that nitrogen form and starvation modulate root exudation

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