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TerraForms: Pore2Chip

Arunima Bhattacharjee holds a micromodel created from X-ray computed tomography images of soil core from Alaska field site using Pore2Chip. Micromodels generated using Pore2Chip are scalable and can be created in different dimensions based on research needs.
Arunima Bhattacharjee holds a micromodel created from X-ray computed tomography images of soil core from Alaska field site using Pore2Chip. Micromodels generated using Pore2Chip are scalable and can be created in different dimensions based on research needs.
3-D model and micromodel created from X-ray computed tomography images of soil core from Alaska field site using Pore2Chip.
3-D model and micromodel created from X-ray computed tomography images of soil core from Alaska field site using Pore2Chip.
rectangular micromodel created with Pore2Chip
Micromodel created with Pore2Chip

The Environmental Molecular Sciences Laboratory (EMSL) offers researchers access and use of a Python package called Pore2Chip, which creates field-representative micromodels and RhizoChips.

Pore2Chip generates two-dimensional (2D) micromodels and RhizoChips using data extracted from three-dimensional (3D) X-ray computed tomography (XCT) images of soil cores. This tool allows researchers to evaluate the soil core pore network by using major metrics of water retention and flow (pore size distributions and pore throat size distributions) and connectivity (pore coordination numbers). The final output from this software is a soil core or aggregate-representative 2D design that can be printed using various methods, including laser etching, 3D printing, and photolithography.

Pore2Chip creates fast, reliable, and scalable replicates of field soil cores for reduced complexity micromodel or RhizoChip platforms, which can be used to design experiments comparable to field experiments. These platforms are also robust and field deployable. Apart from replicating a field site soil core, all previous features of micromodels and RhizoChips are included in these newly printed platforms. Previous features include mineral or organic matter amendment and microbial and plant growth. These new platforms are compatible with the optical and chemical imaging offered at EMSL.

Access Pore2Chip on GitHub.

Research application

Supporting EMSL’s Molecular Observation Network (MONet), EMSL creates reduced complexity micromodels and RhizoChips with XCT images of MONet soil cores.

Supporting the Biogeochemical Transformations Integrated Research Platform, Pore2Chip helps unlock how contaminants move and change in the environment. This essential knowledge can help improve predictive models to anticipate and manage effects on both human and natural systems. EMSL’s microfluidic technologies allow scientists to create synthetic soil habitats to understand and study microbe–mineral interactions.

Supporting the Terrestrial–Atmospheric Processes Integrated Research Platform, TerraForms enables the identification of belowground and aboveground volatile organic compounds.

Supporting the Data Transformations and Systems Modeling Integrated Research Platforms, Pore2Chip allows multiphysics modeling of belowground nutrient flow simulations to inform specific experimental designs. Using recent advances in physics-informed machine learning, Pore2Chip will be developed to inform TerraForms’s experimental data and calibrate multiphysics process models.

Supporting the Rhizosphere Function Integrated Research Platform, these resources help unlock how plant roots and their associated microbiomes exchange metabolites. This essential knowledge can help us improve predictive models for carbon and nutrient cycling underground and help engineers design microorganisms for sustainable agriculture.

Supporting the Biomolecular Pathways Integrated Research Platform, Pore2Chip enables platforms to be built for mapping the molecular pathways of microbial and plant dynamics.

Available instruments

  • A HORIBA Jobin Yvon Raman spectroscopy system with 532 and 632 nm lasers combined with a Nikon Eclipse Ti epifluorescence microscope for mineral and microbe characterization and imaging.
  • The Nikon XTH 320/225 x-ray computed tomography instrument for 3D imaging of soil cores and creating 3D digital pore structure data to be used as input for Pore2Chip creating a representative micromodel.
  • A stand-alone Nikon Eclipse Ti epifluorescence microscope for mineral and microbe characterization and imaging.
  • A Nikon AZ100 multipurpose zoom fluorescent microscope connected to a motorized stage and charge-coupled device (CCD) camera for imaging larger samples at a resolution of 0.8–20 μm.
  • A Class 1000 clean room microfabrication facility with equipment (e.g., mask aligner, plasma dry etch, anodic bonding, etc.) that allows the fabrication of microfluidic pore structures in silicon, polydimethylsiloxane (PDMS), glass, etc.
  • Chemical imaging includes matrix-assisted laser desorption ionization–mass spectrometry imaging (MALDI-MSI), nanospray desorption electrospray ionization mass spectrometry (nanoDESI), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy–energy-dispersive X-ray spectroscopy (SEM-EDX), and secondary-ion mass spectrometry (SIMS).

  • Examples of micromodels generated from field site soil cores using Pore2Chip. Designs are scalable and can be created in any dimension based on experiment needs.

    A model-data-integration (ModEx) workflow is used to generate a Pore2Chip micromodel. Follow these recommended steps:

    1. Submit soil cores/aggregates for XCT analysis

    2. Conduct Pore2Chip analyses for determining soil core characteristics

    3. Generate a 2D micromodel with Pore2Chip

    4. Fabricate micromodels in the EMSL cleanroom

    5. Design experiments

    6. Create modeling based on experiment needs

    7. Upscale pore scale models to ecosystem scale.

    Tips for success

    All Pore2Chip platforms are compatible with mass spectrometry imaging such as matrix-assisted laser desorption ionization mass spectrometry imaging, nanospray desorption electrospray ionization, secondary ion mass spectrometry (SIMS), anoscale secondary ion mass spectrometry (nanoSIMS), and scanning electron microscopy. Request Pore2Chip micromodels and RhizoChips through EMSL proposal calls. Through calls, users can create reduced complexity platforms for investigating spatial metabolites and carbon distribution resulting from microbial and plant growth, or to investigate hotspots and hot moments within a soil-like environment.

    If researchers have XCT images of MONet soil cores, EMSL staff can create micromodels and RhizoChips from that data.

    Contributing teams and resources

    EMSL develops and deploys capabilities for the user program by conducting original research independently or in partnership with others and by adapting/advancing science and technologies developed outside of EMSL. In some instances, EMSL directly deploys mature capabilities developed by others where there is value for the EMSL user community. The following grants/activities, PIs and teams contributed to the development of this capability:

  • Erin Rooney, user proposal # 61069;
    • DOI: Award DOIs: 10.46936/ltds.proj.2024.61069/60012423
  • Maruti Mudunuru, EMSL S&T investments:
    • 10.46936/intm.proj.2023.60674/60008777; 10.46936/intm.proj.2023.60904/60008965

Contacts