## 2.25.5. Aerenchyma Transport[¶](#aerenchyma-transport "Permalink to this headline")
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Aerenchyma transport is modeled in CLM as gaseous diffusion driven by a concentration gradient between the specific soil layer and the atmosphere and, if specified, by vertical advection with the transpiration stream. There is evidence that pressure driven flow can also occur, but we did not include that mechanism in the current model.

The diffusive transport through aerenchyma (_A_, mol m\-2 s\-1) from each soil layer is represented in the model as:

(2.25.8)[¶](#equation-24-8 "Permalink to this equation")\\\[A=\\frac{C\\left(z\\right)-C\_{a} }{{\\raise0.7ex\\hbox{$ r\_{L} z $}\\!\\mathord{\\left/ {\\vphantom {r\_{L} z D}} \\right.}\\!\\lower0.7ex\\hbox{$ D $}} +r\_{a} } pT\\rho \_{r} ,\\\]

where _D_ is the free-air gas diffusion coefficient (m2 s\-1); _C(z)_ (mol m\-3) is the gaseous concentration at depth _z_ (m); \\(r\_{L}\\) is the ratio of root length to depth; _p_ is the porosity (-); _T_ is specific aerenchyma area (m2 m\-2); \\({r}\_{a}\\) is the aerodynamic resistance between the surface and the atmospheric reference height (s m\-1); and \\(\\rho \_{r}\\) is the rooting density as a function of depth (-). The gaseous concentration is calculated with Henry’s law as described in equation [(2.25.7)](#equation-24-7).

Based on the ranges reported in [Colmer (2003)](https://escomp.github.io/ctsm-docs/versions/master/html/tech_note/References/CLM50_Tech_Note_References.html#colmer2003), we have chosen baseline aerenchyma porosity values of 0.3 for grass and crop PFTs and 0.1 for tree and shrub PFTs:

(2.25.9)[¶](#equation-24-9 "Permalink to this equation")\\\[T=\\frac{4 f\_{N} N\_{a}}{0.22} \\pi R^{2} .\\\]

Here \\(N\_{a}\\) is annual net primary production (NPP, mol m\-2 s\-1); _R_ is the aerenchyma radius (2.9 \\(\\times\\)10\-3 m); \\({f}\_{N}\\) is the belowground fraction of annual NPP; and the 0.22 factor represents the amount of C per tiller. O2 can also diffuse in from the atmosphere to the soil layer via the reverse of the same pathway, with the same representation as Equation [(2.25.8)](#equation-24-8) but with the gas diffusivity of oxygen.

CLM also simulates the direct emission of CH4 from leaves to the atmosphere via transpiration of dissolved methane. We calculate this flux (\\(F\_{CH\_{4} -T}\\); mol m\\({}^{-}\\)2 s\-1) using the simulated soil water methane concentration (\\(C\_{CH\_{4},j}\\) (mol m\-3)) in each soil layer _j_ and the CLM predicted transpiration (\\(F\_{T}\\) ) for each PFT, assuming that no methane was oxidized inside the plant tissue:

(2.25.10)[¶](#equation-24-10 "Permalink to this equation")\\\[F\_{CH\_{4} -T} =\\sum \_{j}\\rho \_{r,j} F\_{T} C\_{CH\_{4} ,j} .\\\]

