Bio-printed microbial habitats for high-throughput, in situ metaphenomics
EMSL Project ID
60067
Abstract
Outside of laboratory cultures microorganisms live in micro-structured environments which provide non-competitive spatial niches critical to maintaining genotypic and phenotypic diversity in the community. Bio-printing, an emerging technology that enables the creation of living 3D structures, can augment microbiome research by mimicking native microbial habitats, like soil and tissue, thereby facilitating the emergence of naturally occurring meta-phenomes. Employing the inherent automation of bio-printing for the high-throughput fabrication of structured microbial communities, we will demonstrate the physical and chemical tunability of bio-inks (i.e. bio-compatible hydrogels) to probe microbial interactions and test the compatibility of these bio-printed communities with EMSL’s advanced imaging and multi-omics technologies. Ultimately, our proposed work will facilitate a high-throughput phenotyping pipeline channeling in situ measurements to integrated data streams for EMSL users and will generate standard operating procedures that guide EMSL users through the process of bio-printing their organisms of choice to obtaining multi-omics and imaging data from their hydrogel habitats. We will first demonstrate that bioprinting can be used to create a diverse array of microbial habitat mimics for environments that are of interest to EMSL users including soil, plant, and mammalian tissue. Validated designs will then be used to test the compatibility and survival of microorganisms representing a broad range of growth strategies so that users can easily identify whether bioprinting is amenable toward their target microbe. Species that are viable within the hydrogels will be used in subsequent experiments to test the integration of the hydrogel habitats with EMSL’s multi-omics capabilities. Lastly to demonstrate the value of these hydrogel habitats to the user community, we will conduct a proof-of-concept experiment that examines key microbial interactions underlying chitin degradation processes in the soil by measuring the hydrodynamic exchange of chitin hydrolysis products (e.g. N-acetylglucosamine, glucosamine) between spatially separated soil aggregate communities. Although our proof-of-concept will focus on chitin degradation, the bioprinting capability has extended applications in areas that align with user interests and DOE goals. A few examples include bioprinting engineered biofilms for the study of biogeochemical transformations like lignin and cellulose degradation, microplastics biodegradation, bioremediation of environmental contaminants, bioproduct synthesis, and uranium sensing. Hydrogel structures can also be printed on diverse substrates including submerged in liquid and, conceivably, could print microbes directly onto plant tissues as a microbiome transplant. The basic workflows established by this project will lay the foundation for future work that could incorporate “smart hydrogels” with embedded colorimetric reagents or activity-based probes to sense and visualize in situ and spatially resolved microbial interactions in target ecosystem mimics.
Project Details
Start Date
2021-04-15
End Date
2021-11-08
Status
Closed
Released Data Link
Team
Principal Investigator
Co-Investigator(s)
Team Members
Related Publications
Smercina, D., Zambare, N., Hofmockel, K., Sadler, N., Bredeweg, E. L., Nicora, C., ... & Aufrecht, J. (2022). Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics. Microorganisms, 10(5), 944.
Smercina, D.; Zambare, N.; Hofmockel, K.; Sadler, N.; Bredeweg, E.L.; Nicora, C.; Markillie, L.M.; Aufrecht, J. Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics. Microorganisms 2022, 10, 944. https://doi.org/10.3390/microorganisms10050944