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  Modeling ecosystem-scale carbon dynamics in soil: The microbial dimension

  In predicting how soil C fluxes and stocks will change with the environment, models are a critical tool for integrating datasets with theory. Models developed in the 1980's were based on 1st order kinetics of C-pools defined by turnover time. However, new models generally include microbes as decomposers although they vary in the number and nature of microbial pools. They don't, however, integrate modern omics-based datasets because models have coarse resolution and need to function even in the absence of community data—geographically or into the future. There are several issues new models must address to be valuable for large-scale synthesis. First, how to incorporate microbes and their activities—how many pools of organisms? How should they be defined? How should they drive C-cycling? Should their synthesis of degradative enzymes be treated implicitly or explicitly? Second, carbon use efficiency (CUE)—the partitioning of processed C between respiration and re-synthesis into biomass. This term is critical because the size of the biomass influences its rate of organic matter processing. A focus has been on CUE's temperature sensitivity—most studies suggest it declines as temperature rises, which would limit decomposition and organic matter loss. The final novel modeling element I discuss is “priming”—the effect of fresh inputs on decomposition of native organic matter (OM). Priming can either repress or accelerate the breakdown of native OM. But whether, and how, to capture priming effects in soil organic matter models remains an area of exploration.
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  Priming mechanisms providing plants and microbes access to mineral-associated organic matter

  Mineral-associated organic matter (MAOM) is considered a stable reservoir for soil nutrients that influences long-term soil carbon (C) and nitrogen (N) dynamics. However, recent experimental and theoretical evidence shows that root exudates may mobilize MAOM, thereby providing plants and microbes access to a large and N-rich pool. Given the mechanisms underlying MAOM C and N mobilization remain largely untested, we examined direct and indirect pathways by which root exudates destabilize this nutrient pool in laboratory mesocosms. We simulated root exudation with 13C-labeled oxalic acid to test whether root exudates are directly capable of mobilizing MAOM from mineral surfaces; and with 13C-labeled glucose to test whether indirect stimulation of microbial and extracellular enzyme activity leads to MAOM decomposition. We also tested the potential for oxalic acid and glucose to mobilize MAOM in an additional subset of sterilized soils to clarify the potential for non-microbial pathways of MAOM destabilization. Over the course of the 12-day MAOM incubation with and without simulated exudates, we measured C cycling (CO2 respiration rates, 13C–CO2 efflux), N cycling (inorganic N pools, gross N mineralization) and related microbial processes (enzyme activities and microbial community composition via phospholipid fatty acid analysis). Both of the simulated root exudates enhanced MAOM-C mineralization, with cumulative respiration increasing 35–89% relative to the water-only control. Likewise, glucose additions enhanced the production of an exo-cellulase and a chitinase by up to 130% and 39%, respectively, while oxalic acid enhanced oxidative enzyme activities up to 91% greater than control rates. We observed a positive association between glucose-induced shifts in enzyme activities, MAOM-C mineralization, and gross ammonification. Oxalic acid additions were associated with initial increases in fungal relative abundance and in sterile soils appeared to stimulate the release of metals and dissolved organic nitrogen into exchangeable pools. Our results indicate that common root exudates, like glucose and oxalic acid, can significantly increase the turnover and potential release of C and N from MAOM through indirect (e.g., enzyme induction) and direct (e.g., mobilization of metal oxides) mechanisms.