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TerraForms: Pore-Scale Micromodels

The Environmental Molecular Sciences Laboratory’s (EMSL’s) pore-scale micromodels simulate soil porosity and aggregate size distribution on a microfluidic platform. These TerraForms are suitable for microbial (bacterial and fungal) incubations for investigating pore-scale effects on resulting growth. The micromodels have been used to study anaerobic hotspot and hot moment formation by microbial growth, fungal hyphae development, and the effects of carbon sources on extracellular polysaccharide-induced water retention within soil pores.

Mineral-amended micromodels can be created to simulate a specific soil mineralogy. These micromodels have been used to investigate fungal mineral weathering, distribution of microbial exudates around a carbon hotspot, and changes in mineral chemistry resulting from biotic mineral weathering.  

EMSL is home to the pore-scale micromodel flow and transport laboratory, which is part of EMSL's Subsurface Flow and Transport Laboratory. The focus of this laboratory is on coupled (multiphase) flow, diffusion, and reactions processes at the microscopic scale (μm to cm) that affect the fate and transport of contaminants in the subsurface and geological sequestration of CO2. Increasing scientific understanding of such transformations is part of a broader EMSL mission to characterize Earth systems and validate predictive models through biogeochemical studies.

Research application

Supporting the Biogeochemical Transformations Integrated Research Platform, these resources help unlock how contaminants move and change in the environment. This essential knowledge can help us 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 to study microbe–mineral interactions.

Supporting the Terrestrial-Atmospheric Processes Integrated Research Platform, TerraForms enables identifying belowground and aboveground volatile organic compounds for your science.

Supporting the Biomolecular Pathways Integrated Research Platform, TerraForms pore-scale micromodels enables detection of gases and volatile organic compounds using the real time mass spectrometry. 

Available resources

  • 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.
  • 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 CCD camera for imaging larger samples at 0.8–20 μm resolution.
  • A Class 1000 clean room microfabrication facility with equipment (e.g., mask aligner, plasma dry etch, anodic bonding, etc.) that allows fabrication of microfluidic pore structures in silicon, PDMS (polydimethylsiloxane), glass, etc.

pore-scale micromel
Micromodel porosity and aggregate distribution can be customized to a user’s research requirements. C denotes carbon hotspots that a fungus is bridging while weathering minerals embedded within the micromodel platform. (Illustration by Arunima Bhattacharjee)

Tips for success

All pore-scale micromodels 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), nanoSIMS, and scanning electron microscopy. Request pore-scale micromodels to investigate spatial metabolites and carbon distribution resulting from microbial growth, or to investigate hotspots and hot moments within a soil-like environment.

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, PI’s and teams contributed to the development of this capability: 

  • Arunima Bhattacharjee, DE-AC05-76RL01830, Environmental Molecular Sciences Laboratory 
  • Kirsten Hofmockel, FWP 70880, U.S. Department of Energy, Office of Science, Biological and Environmental Research Program

Related publications

 

 

Contacts