Microbial Functional Traits Through the Whole Soil Profile and Their Response to Warming
Authors
Ulas Karaoz1* (ukaraoz@lbl.gov), Ricardo J. E. Alves1, Nikola Tolić2, Rosalie K. Chu2, David W. Hoyt2, Carrie Nicora2, Elizabeth K. Eder2, Jason Toyoda2, Margaret S. Torn1, Eoin L. Brodie1
Institutions
1Lawrence Berkeley National Laboratory, Berkeley, CA; 2Pacific Northwest National Laboratory, Richland, WA
URLs
Abstract
Subsoils contain the majority of global soil organic matter (SOM), whose depolymerization to dissolved organic carbon and mineralization to carbon dioxide (CO2) is fundamentally microbially driven. An overarching goal of the Science Focus Area (SFA) is the development of mechanistic models that represent microbial metabolic, physiological and life history traits in a numerical model that accounts for interactions with plants, minerals, and environmental drivers, including temperature and moisture. Along the soil depth profile, the decreasing effects of plant inputs and rhizosphere interactions are major drivers of variation in SOM composition and transformation by microbes. This variation selects for microbiomes with distinct metabolic, physiological, and cellular traits that may constrain the trajectory and magnitude of the respiration response to warming through the soil profile.
To evaluate microbiomes and their trait distributions across the soil column under the effect of warming in the long-term field experiment at a conifer forest (Blodgett, CA), researchers utilized genome-centric metagenomics and furthermore assessed active metabolisms and SOM transformation pathways using metaproteomics and metabolomics. At the overall community level, soil depth, warming period, and warming treatment explained 41.5, 5.5, and 1.9% of the community variance, respectively, with multiple phyla represented in ~2,300 MAGs underlying these differences. Trait analysis of MAGs showed that denitrification, nitrite oxidation, degradation of complex carbohydrates, and one-carbon metabolism (for both methane and methanol) were prominent and phylogenetically widespread, with several genome representatives detected in the metaproteomes. Methanol and ethanol were highly abundant through the profile, whereas the abundance of more favorable substrates declined strongly. Transformations of alcohols and methyl compounds were among the most frequent potential transformations through the profile and increased with warming only in deeper soils. Together metagenomes, metaproteomes, and metabolomes support a shift from metabolism of thermodynamically favorable plant-derived inputs (amino acids, sugars) to less favorable substrates with increasing depth.