Environmental Transformations and Interactions
3D Printing a Home for Microbes
Novel technique gives scientists a new tool to study soil microbes quickly and easily
Scientists discovered a way to 3D-print soil habitats, allowing them to bypass the difficulties of using natural soil and study microbes in rarely seen detail. (Image by Andrea Starr, Pacific Northwest National Laboratory)
The Science
Studying soil microbes in their natural habitat can be tricky. The microbes are tiny. The soils are opaque, making it hard to see through them, and they include a complex cocktail of chemicals that can vary by location, rainfall, and other factors. Now scientists have discovered a way to print a three-dimensional (3D) habitat that mimics aspects of natural soil, only more transparent and with predefined chemicals. These synthetic soils can be used to grow and study microbes down to their molecular biochemistry.
The Impact
Microorganisms in the soil are key players in the environment, underlying everything from growing plants to moving carbon dioxide into the atmosphere. But making the link between how microbes function and why the environment changes has proven challenging. With synthetic soil habitats, scientists can change factors like pore structure, water, and chemistry. This level of control could help researchers forge a never-before-seen detailed understanding of the interplay between environmental properties and microbial ecology.
Summary
Scientists sought to bypass the challenges of studying microbial dynamics in natural soils. Borrowing a state-of-the-art technique from medicine, they used rapid 3D bioprinting at EMSL, the Environmental Molecular Sciences Laboratory, a Department of Energy (DOE) Office of Science User Facility. They created bio-inks by embedding microbes into a translucent and porous hydrogel that mimicked the physical structure of natural soil. They then characterized the printed microbes by analyzing their genes, metabolites, proteins, and lipids. They found that the synthetic soil allowed them to study the microbes’ community structure, properties, and processes more easily compared to natural soil. In the future, the synthetic soil could also be amended with other compounds, such as plant litter or minerals, to simulate different nutrient inputs, mimic soil hotspots, and study microbe–mineral interactions.
PM Contact
Paul Bayer
BER Earth and Environmental Systems Sciences Division
301-903-5324
Contacts
Pacific Northwest National Laboratory darian.smercina@pnnl.gov
Environmental Molecular Sciences Laboratory jayde.aufrecht@pnnl.gov
Funding
This research was conducted using resources at EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility. A portion of the work was funded through the Laboratory Directed Research and Development program at Pacific Northwest National Laboratory. Three of the researchers were supported by the Linus Pauling Distinguished Postdoctoral Fellowship.
Publications
D. Smercina, et al., “Synthetic soil aggregates: Bioprinted habitats for high-throughput microbial metaphenomics.” Microorganisms 10, 944 (2022). [DOI: 10.3390/microorganisms10050944]