Trait-based models as the nexus between environmental genomics and ecosystem biogeochemistry
In soils and sediments, physical, chemical, and biological components interact intimately to create truly “complex systems”. Microbial engines drive the catalytic potential within these systems, performing a range of critical ecosystem services, such as the regulation of water purification, nutrient flux, and carbon stability. Our understanding of individual components that make up this complexity has improved immensely, with cultivation-independent approaches illuminating microbial functional diversity. The challenge now becomes moving beyond qualitative use of this new knowledge towards a mechanistic quantitative framework. The ability to reconstruct thousands of genomes from microbial populations using metagenomic approaches opens the door to predicting function and fitness traits of organisms from their metabolic blueprints and to investigate how fine-scale physical structure and chemical characteristics of this environment regulate the emergence of microbial functions and biogeochemical processes.
We are developing a trait-based reactive transport model (BioCrunch) model of microbial activity that simulates coupled functional guilds that are parameterized using ‘omic information. We simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. Trait values related to growth are directly estimated from genomic information and key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and nitrogen fixation etc are linked within genomes. Simulations at the continuum scale were carried out to explore abiotic controls on community emergence including identification of the processes regulating aquifer oxygen concentrations during seasonally fluctuating water table regimes at the Rifle floodplain. Simulations and metagenomic/metatranscriptomic observations identified a number of functional guilds with chemolithoautotrophic lifestyles that appear to be important in mediating elemental cycling within aquifer biogeochemical hotspots. We are also developing pore-scale reactive transport simulations in grassland soils using an adaptive mesh and model refinement approach using real pore networks obtained measuring soil microaggregates via sub-micron resolution synchrotron X-ray microCT.