Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation

• DOI: 10.1128/msystems.01616-24
• Publication Date: 2025-02-24T14:00:43Z
• Authors: Josué Rodríguez-R...; Natalie Sadler; Elias K. Zegeye; Yuliya Farris; Samuel Purvine; Sneha Couvillion; William C. Nelson; Kirsten S. Hofmockel
• Keywords: Microbial Metabolism

ABSTRACT Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, soil connectivity. However, accurately representing the environment establishing a tractable community that limits confounding variables is difficult. Here, we use reduced-complexity consortium grown in glass bead porous media amended with chitin to test effects of structural matrix on phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, metabolomes, saw our significantly altered phenotypes compared liquid incubations, denoting importance incorporating pores surfaces for understanding soils. These phenotypic shifts were mainly driven differences expression Streptomyces Ensifer , which included significant decrease overall degradation between liquid. Our findings suggest success likely related its ability repurpose carbon via glyoxylate shunt amidst lack byproducts while potentially using polyhydroxyalkanoate granules C source. We also identified traits expressed others, including motility, stress resistance, conservation, influence metabolic profiles observed across treatments. Together, these results demonstrate incubations promote structure-induced are better proxy conditions than culture systems. Furthermore, they emphasize encompass not only multi-enzyme pathways involved but include complex interactions other members. IMPORTANCE critical shaping metabolism. laboratory experiments remains challenging frontier. Through reduced complexity experiment media, reveal predicting from gene-based alone often falls short capturing intricate cellular interactions. highlight affect decomposition, environmental (i.e., beads) shifting towards tolerance, resource acquisition, increased ultimately invoking unique strategies evident cultures. Moreover, find evidence changes relate regarding transporters, biofilm formation, degradation. Ultimately, showcase how communities can be informative present useful alternative cultures studying