## 2.16.1. Introduction[¶](#introduction "Permalink to this headline")
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CLM includes a prognostic treatment of the terrestrial carbon and nitrogen cycles including natural vegetation, crops, and soil biogeochemistry. The model is fully prognostic with respect to all carbon and nitrogen state variables in the vegetation, litter, and soil organic matter. The seasonal timing of new vegetation growth and litterfall is also prognostic, responding to soil and air temperature, soil water availability, daylength, and crop management practices in varying degrees depending on a specified phenology type or management for each PFT (Chapter [2.20](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.html#rst-vegetation-phenology-and-turnover)). The prognostic LAI, SAI, tissue stoichiometry, and vegetation heights are utilized by the biophysical model that couples carbon, water, and energy cycles.

Separate state variables for C and N are tracked for leaf, live stem, dead stem, live coarse root, dead coarse root, fine root, and grain pools ([Figure 2.16.1](#figure-vegetation-fluxes-and-pools)). Each of these pools has two corresponding storage pools representing, respectively, short-term and long-term storage of non-structural carbohydrates and labile nitrogen. There are two additional carbon pools, one for the storage of growth respiration reserves, and another used to meet excess demand for maintenance respiration during periods with low photosynthesis. One additional nitrogen pool tracks retranslocated nitrogen, mobilized from leaf tissue prior to abscission and litterfall. Altogether there are 23 state variables for vegetation carbon, and 22 for vegetation nitrogen.

[![Image 1: ../../_images/CLMCN_pool_structure_v2_lores.png](https://escomp.github.io/ctsm-docs/versions/master/html/_images/CLMCN_pool_structure_v2_lores.png)](https://escomp.github.io/ctsm-docs/versions/master/html/_images/CLMCN_pool_structure_v2_lores.png)

Figure 2.16.1 Vegetation fluxes and pools for carbon cycle in CLM5.[¶](#id1 "Permalink to this image")

In addition to the vegetation pools, CLM includes a series of decomposing carbon and nitrogen pools as vegetation successively breaks down to CWD, and/or litter, and subsequently to soil organic matter. Discussion of the decomposition model, alternate specifications of decomposition rates, and methods to rapidly equilibrate the decomposition model, is in Chapter [2.21](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.html#rst-decomposition).

