PNNL

Abstract

Soil moisture and porosity play crucial roles in controlling microbial metabolism by influencing factors such as redox conditions, substrate availability, and soil connectivity. However, the inherent biological, chemical, and physical heterogeneity of soil complicates experimental investigations into microbial metabolism. This difficulty arises from challenges in accurately representing the soil environment and in establishing a manageable microbial community that limits confounding variables. To address these challenges, we utilized a reduced-complexity microbial consortium grown in a soil analog using a glass-bead matrix amended with chitin. From these experiments, we collected long-read and short-read metagenomes, metatranscriptomes, metaproteomes, and metabolomes to investigate how soil environmental matrix and moisture influence chitin degradation across varying moisture contents. Highlighting the importance of the environmental matrix, our soil structure analog system greatly altered microbial expression profiles compared to the liquid-only incubations. These changes were mainly driven by differences in the overall expression of chitin-degrading Streptomyces species and stress-tolerant Ensifer. We hypothesize that the success of Ensifer in a structured environment is likely related to its ability to repurpose carbon via the glyoxylate shunt, while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits like motility, stress resistance, and biofilm formation that underlie the degradation of chitin across our treatments and inform how they may ultimately alter carbon use efficiency.