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

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

doi:10.3791/57170

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

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Abstract

Beneficial plant-microbe interactions offer a sustainable biological solution with the potential to boost low-input food and bioenergy production. A better mechanistic understanding of these complex plant-microbe interactions will be crucial to improving plant production as well as performing basic ecological studies investigating plant-soil-microbe interactions. Here, a detailed description for ecosystem fabrication is presented, using widely available 3D printing technologies, to create controlled laboratory habitats (EcoFABs) for mechanistic studies of plant-microbe interactions within specific environmental conditions. Two sizes of EcoFABs are described that are suited for the investigation of microbial interactions with various plant species, including Arabidopsis thaliana, Brachypodium distachyon, and Panicum virgatum. These flow-through devices allow for controlled manipulation and sampling of root microbiomes, root chemistry as well as imaging of root morphology and microbial localization. This protocol includes the details for maintaining sterile conditions inside EcoFABs and mounting independent LED light systems onto EcoFABs. Detailed methods for addition of different forms of media, including soils, sand, and liquid growth media coupled to the characterization of these systems using imaging and metabolomics are described. Together, these systems enable dynamic and detailed investigation of plant and plant-microbial consortia including the manipulation of microbiome composition (including mutants), the monitoring of plant growth,more »« less

Authors:

Gao, Jian ^[1]; Sasse, Joelle ^[1]; Lewald, Kyle M. ^[1]; Zhalnina, Kateryna ^[1]; Cornmesser, Lloyd T. ^[1]; Duncombe, Todd A. ^[2]; Yoshikuni, Yasuo ^[3]; Vogel, John P. ^[3]; Firestone, Mary K. ^[4]; Northen, Trent R. ^[1]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science Policy and Management

Publication Date:: 2018-04-10

Research Org.:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER); LBNL Laboratory Directed Research and Development (LDRD) Program

OSTI Identifier:: 1506304

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

Resource Type:: Accepted Manuscript

Journal Name:: Journal of Visualized Experiments

Additional Journal Information:: Journal Volume: 2018; Journal Issue: 134; Journal ID: ISSN 1940-087X

Publisher:: MyJoVE Corp.

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; environmental sciences; laboratory ecosystems; EcoFAB; plant-microbe interactions; microbiome; root morphology; root exudates; LC-MS; NIMS; metabolomics; microscopic imaging

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                    Gao, Jian, Sasse, Joelle, Lewald, Kyle M., Zhalnina, Kateryna, Cornmesser, Lloyd T., Duncombe, Todd A., Yoshikuni, Yasuo, Vogel, John P., Firestone, Mary K., and Northen, Trent R. Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions.  United States: N. p., 2018. 
Web.  doi:10.3791/57170.

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                    Gao, Jian, Sasse, Joelle, Lewald, Kyle M., Zhalnina, Kateryna, Cornmesser, Lloyd T., Duncombe, Todd A., Yoshikuni, Yasuo, Vogel, John P., Firestone, Mary K., & Northen, Trent R. Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions.  United States.  https://doi.org/10.3791/57170

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                    Gao, Jian, Sasse, Joelle, Lewald, Kyle M., Zhalnina, Kateryna, Cornmesser, Lloyd T., Duncombe, Todd A., Yoshikuni, Yasuo, Vogel, John P., Firestone, Mary K., and Northen, Trent R. Tue .  
"Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions".  United States.  https://doi.org/10.3791/57170.  https://www.osti.gov/servlets/purl/1506304.

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@article{osti_1506304,

  title        = {Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions},

  author       = {Gao, Jian and Sasse, Joelle and Lewald, Kyle M. and Zhalnina, Kateryna and Cornmesser, Lloyd T. and Duncombe, Todd A. and Yoshikuni, Yasuo and Vogel, John P. and Firestone, Mary K. and Northen, Trent R.},

  abstractNote = {Beneficial plant-microbe interactions offer a sustainable biological solution with the potential to boost low-input food and bioenergy production. A better mechanistic understanding of these complex plant-microbe interactions will be crucial to improving plant production as well as performing basic ecological studies investigating plant-soil-microbe interactions. Here, a detailed description for ecosystem fabrication is presented, using widely available 3D printing technologies, to create controlled laboratory habitats (EcoFABs) for mechanistic studies of plant-microbe interactions within specific environmental conditions. Two sizes of EcoFABs are described that are suited for the investigation of microbial interactions with various plant species, including Arabidopsis thaliana, Brachypodium distachyon, and Panicum virgatum. These flow-through devices allow for controlled manipulation and sampling of root microbiomes, root chemistry as well as imaging of root morphology and microbial localization. This protocol includes the details for maintaining sterile conditions inside EcoFABs and mounting independent LED light systems onto EcoFABs. Detailed methods for addition of different forms of media, including soils, sand, and liquid growth media coupled to the characterization of these systems using imaging and metabolomics are described. Together, these systems enable dynamic and detailed investigation of plant and plant-microbial consortia including the manipulation of microbiome composition (including mutants), the monitoring of plant growth, root morphology, exudate composition, and microbial localization under controlled environmental conditions. We anticipate that these detailed protocols will serve as an important starting point for other researchers, ideally helping create standardized experimental systems for investigating plant-microbe interactions.},

  doi          = {10.3791/57170},

  journal      = {Journal of Visualized Experiments},

  number       = 134,

  volume       = 2018,

  place        = {United States},

  year         = {2018},

  month        = {4}

}

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