Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.
Rodríguez-Ramos, Josué A., et al. "Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation." mSystems, vol. 10, no. 3, Feb. 2025. https://doi.org/10.1128/msystems.01616-24
Rodríguez-Ramos, Josué A., Sadler, Natalie C., Zegeye, Elias K., Farris, Yuliya, Purvine, Samuel O., Couvillion, Sneha P., Nelson, William C., & Hofmockel, Kirsten S. (2025). Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation. mSystems, 10(3). https://doi.org/10.1128/msystems.01616-24
Rodríguez-Ramos, Josué A., Sadler, Natalie C., Zegeye, Elias K., et al., "Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation," mSystems 10, no. 3 (2025), https://doi.org/10.1128/msystems.01616-24
@article{osti_2572869,
author = {Rodríguez-Ramos, Josué A. and Sadler, Natalie C. and Zegeye, Elias K. and Farris, Yuliya and Purvine, Samuel O. and Couvillion, Sneha P. and Nelson, William C. and Hofmockel, Kirsten S.},
title = {Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation},
annote = {Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.},
doi = {10.1128/msystems.01616-24},
url = {https://www.osti.gov/biblio/2572869},
journal = {mSystems},
issn = {ISSN 2379-5077},
number = {3},
volume = {10},
place = {United States},
publisher = {American Society for Microbiology},
year = {2025},
month = {02}}
CHItaly '17: 12th Biannual Conference of the Italian SIGCHI Chapter, Proceedings of the 12th Biannual Conference on Italian SIGCHI Chapterhttps://doi.org/10.1145/3125571.3125585