Soil microbe-predator model with enzymes (1.0.0)

We developed agent-based models patterned after the equation-based models developed by Schimel and Weintraub (2003) to explore the influence of microbial-derived extracellular enzymes on carbon (C) dynamics. The models featured spatial arrangements of detritus as either randomly-spaced particles (rain) or as root-like structures (root), detritus input intervals (continuous vs. pulsed) and rates (0-5000 units in 500 unit intervals), trophic structures (presence or absence of predators preying on microbes), and extracellular enzymes with different half-lives (1, 10, 100, and 1000 time steps). We studied how these features affected C dynamics and model persistence (no extinctions). Models without predators were more likely to persist than those with predators, and their C dynamics could be explained with energetics-based arguments. When predators were present, two of the four model configurations – root-continuous and rain-pulsed –were more likely to persistent. The root-continuous models were more likely to persist at lower detritus input rates (500-3500 units), while the rain-pulsed models were more likely to persist at intermediate detritus input rates (2000-3500 units). For both these model configurations, shorter extracellular enzymes half-lives increased the likelihood of persistence. Consistent with the results of Schimel and Weintraub (2003), C dynamics were governed by extracellular enzyme production activity and loss. Our results demonstrated that extracellular enzymes control of C dynamics depends on the spatial arrangement of resources, the input rate and input intervals of detritus and trophic structure.

Release Notes

The model described here is the first to be released to the public.

Associated Publications

Moore, J.C., R.B. Boone, A. Koyama, and K. Holfeder. In press. Enzymatic and detrital influences on the structure, function, and dynamics of spatially-explicit model ecosystems. Biochemistry