2.18 Plant Respiration Tech Note edits

doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst

@@ -2,81 +2,87 @@
 
 Plant Respiration
 =================
-CLM5 includes changes to plant respiration including
- - A new leaf respiration algorithm based on Atkin et al. (2016)
- - A lower growth respiration coefficient, based on Atkin et al. (2017)
 
 Autotrophic Respiration
 ----------------------------
 
-The model treats maintenance and growth respiration fluxes separately, even though it is difficult to measure them as separate fluxes (Lavigne and Ryan, 1997; Sprugel et al., 1995). Maintenance respiration is defined as the carbon cost to support the metabolic activity of existing live tissue, while growth respiration is defined as the additional carbon cost for the synthesis of new growth.
+The model treats maintenance and growth respiration fluxes separately, even though it is difficult to measure them as separate fluxes (:ref:`Lavigne and Ryan 1997 <LavigneRyan1997>`; :ref:`Sprugel et al. 1995 <Sprugeletal1995>`). Maintenance respiration is defined as the carbon cost to support the metabolic activity of existing live tissue, while growth respiration is defined as the additional carbon cost for the synthesis of new growth.
 
 Maintenance Respiration
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Atkin et al. (2016) propose a model for leaf respiration that is based on the leaf nitrogen content per unit area (:math:`NS_{narea}` , gN m\ :sup:`-2` leaf), with an intercept parameter that is PFT dependant, and an acclimation term that depends upon the average temperature of the previous 10 day period :math:`t_{2m,10days}`, in Celsius.
+Maintenance respiration is calculated separately for leaves, live stems, live coarse roots, and fine roots. For leaf maintenance respiration (:math:`CF_{mr\_ leaf}`; gC m\ :sup:`-2` s\ :sup:`-1`), :ref:`Atkin et al. (2015)<Atkinetal2015>` propose a model that includes an intercept parameter that is PFT-dependent (:math:`i_{atkin,pft}`; see :numref:`Table Atkin leaf respiration model intercept values` for values), a term for leaf nitrogen content per unit area (:math:`NS_{narea}`; gN m\ :sup:`-2` leaf), and an acclimation term that depends on the average temperature of the previous 10 day period (:math:`t_{2m,10days}`; °C). Leaf maintenance respiration carbon flux is calculated as:
 
 .. math::
    :label: 17.46)
 
    CF_{mr\_ leaf} =  i_{atkin,pft} + (NS_{narea}  0.2061) - (0.0402 (t_{2m,10days}))
 
-The temperature dependance of leaf maintenance (dark) respiration is described in Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`.
+The temperature dependence of leaf maintenance (dark) respiration is described in Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`. 
+
+Live stem (:math:`CF_{mr\_ livestem}`; gC m\ :sup:`-2` s\ :sup:`-1`), live coarse root (:math:`CF_{mr\_ livecroot}`; gC m\ :sup:`-2` s\ :sup:`-1`), and fine root (:math:`CF_{mr\_ froot}`; gC m\ :sup:`-2` s\ :sup:`-1`) maintenance respiration are calculated as the product of a nitrogen-scaled base respiration rate and a Q10-based temperature scaling. :math:`MR_{base}` (gC gN\ :sup:`-1` s\ :sup:`-1`) represents the base respiration rate per unit nitrogen, :math:`MR_{Q10}` (= 1.5) is the temperature sensitivity for maintenance respiration, and :math:`T_{2m}` (°C) is the air temperature at 2m height. :math:`NS_{livestem}` (gN m\ :sup:`-2` live stem), :math:`NS_{livecroot}` (gN m\ :sup:`-2` live coarse root), and :math:`NS_{froot}` (gN m\ :sup:`-2` fine root) represent nitrogen content per unit area for live stem, live coarse root, and fine root, respectively. Finally, fine root respiration is calculated as the sum of contributions from each soil level *j*. :math:`rootfr_{j}` represents the fraction of fine roots distributed in soil level *j* and :math:`Ts_{j}` (°C) is the soil temperature at level *j*. Thus,
+
+Live stem maintenance respiration carbon flux is calculated as:
 
 .. math::
    :label: 17.47)
 
    CF_{mr\_ livestem} =NS_{livestem} MR_{base} MR_{Q10} ^{(T_{2m} -20)/10}
 
+Live coarse root respiration carbon flux is calculated as:
+
 .. math::
    :label: 17.48)
 
    CF_{mr\_ livecroot} =NS_{livecroot} MR_{base} MR_{Q10} ^{(T_{2m} -20)/10}
 
+Fine root maintenance respiration carbon flux is calculated as:
+
 .. math::
    :label: 17.49)
 
    CF_{mr\_ froot} =\sum _{j=1}^{nlevsoi}NS_{froot} rootfr_{j} MR_{base} MR_{Q10} ^{(Ts_{j} -20)/10}
 
-where :math:`MR_{q10}` (= 2.0) is the temperature sensitivity for maintenance respiration, :math:`T_{2m}` (°C) is the air temperature at 2m height, :math:`Ts_{j}`* (°C) is the soil temperature at level *j*, and :math:`rootfr_{j}` is the fraction of fine roots distributed in soil level *j*.
+The total maintenance respiration cost (:math:`CF_{mr}`; gC m\ :sup:`-2` s\ :sup:`-1`) is then calculated as the sum of leaf (:math:`CF_{mr\_ leaf}`), fine root (:math:`CF_{mr\_ froot}`), live stem (:math:`CF_{mr\_ livestem}`), and live coarse root (:math:`CF_{mr\_ livecroot}`) components:
+
+.. math::
+   :label: 17.50)
+
+   CF_{mr} =CF_{mr\_ leaf} +CF_{mr\_ froot} +CF_{mr\_ livestem} +CF_{mr\_ livecroot}
+
+
+.. _Table Atkin leaf respiration model intercept values:
 
 .. table:: Atkin leaf respiration model intercept values.
 
  ========================  =============
  Plant functional type     :math:`i_{atkin}`
  ========================  =============
- NET Temperate                       1.499
- NET Boreal                          1.499
- NDT Boreal                          1.499
- BET Tropical                        1.756
- BET temperate                       1.756
- BDT tropical                        1.756
- BDT temperate                       1.756
- BDT boreal                          1.756
- BES temperate                       2.075
- BDS temperate                       2.075
- BDS boreal                          2.075
- C\ :sub:`3` arctic grass            2.196
- C\ :sub:`3` grass                   2.196
- C\ :sub:`4` grass                   2.196
+ NET Temperate                       1.5
+ NET Boreal                          1.42
+ NDT Boreal                          1.22
+ BET Tropical                        1.93
+ BET temperate                       1.82
+ BDT tropical                        1.5
+ BDT temperate                       1.64
+ BDT boreal                          1.41
+ BES temperate                       2.07
+ BDS temperate                       2.07
+ BDS boreal                          2.07
+ C\ :sub:`3` arctic grass            2.2
+ C\ :sub:`3` grass                   2.35
+ C\ :sub:`4` grass                   2.2
  ========================  =============
 
-Note that, for woody vegetation, maintenance respiration costs are not calculated for the dead stem and dead coarse root components. These components are assumed to consist of dead xylem cells, with no metabolic function. By separating the small live component of the woody tissue (ray parenchyma, phloem, and sheathing lateral meristem cells) from the larger fraction of dead woody tissue, it is reasonable to assume a common base maintenance respiration rate for all live tissue types.
+Note that, for woody vegetation, maintenance respiration costs are not calculated for dead stem and dead coarse root components. These components are assumed to consist of dead xylem cells with no metabolic function. By separating the small live component of the woody tissue (ray parenchyma, phloem, and sheathing lateral meristem cells) from the larger fraction of dead woody tissue, it is reasonable to assume a common base maintenance respiration rate for all live tissue types.
 
-The total maintenance respiration cost is then given as:
-
-.. math::
-   :label: 17.50)
-
-   CF_{mr} =CF_{mr\_ leaf} +CF_{mr\_ froot} +CF_{mr\_ livestem} +CF_{mr\_ livecroot} .
 
 .. _Growth Respiration:
 
 Growth Respiration
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Growth respiration is calculated as a factor of 0.11 times the total carbon allocation to new growth (:math:`CF_{growth}`, after allocating carbon for N acquisition, Chapter :numref:`rst_FUN`.) on a given timestep, based on construction costs for a range of woody and non-woody tissues, with estimates of the growth respiration flux revised downswards following (Atkin et al. 2017). For new carbon and nitrogen allocation that enters storage pools for subsequent display, it is not clear what fraction of the associated growth respiration should occur at the time of initial allocation, and what fraction should occur later, at the time of display of new growth from storage. Eddy covariance estimates of carbon fluxes in forest ecosystems suggest that the growth respiration associated with transfer of allocated carbon and nitrogen from storage into displayed tissue is not significant (Churkina et al., 2003), and so it is assumed in CLM that all of the growth respiration cost is incurred at the time of initial allocation, regardless of the fraction of allocation that is displayed immediately (i.e. regardless of the value of :math:`f_{cur}`, section 13.5). This behavior is parameterized in such a way that if future research suggests that some fraction of the growth respiration cost should be incurred at the time of display from storage, a simple parameter modification will effect the change. [1]_
+Growth respiration is calculated as a factor of 0.11 times the total carbon allocated to new growth (:math:`CF_{growth}`) after allocating carbon for N acquisition (see Chapter :numref:`rst_CN Allocation`) on a given timestep, based on construction costs for a range of woody and non-woody tissues. Estimates of the growth respiration flux were revised downward following :ref:`Atkin et al. (2017)<Atkinetal2017>`. For new carbon and nitrogen allocation that enters storage pools for subsequent display, it is not clear what fraction of the associated growth respiration should occur at the time of initial allocation, and what fraction should occur later, at the time of display of new growth from storage. Eddy covariance estimates of carbon fluxes in forest ecosystems suggest that the growth respiration associated with transfer of allocated carbon and nitrogen from storage into displayed tissue is not significant (:ref:`Churkina et al. 2003 <Churkinaetal2003>`), so it is assumed in CLM that all of the growth respiration cost is incurred at the time of initial allocation, regardless of the fraction of allocation that is displayed immediately (i.e. regardless of the value of :math:`f_{cur}`, section :numref:`Carbon Allocation to New Growth`). This behavior is parameterized in such a way that if future research suggests that some fraction of the growth respiration cost should be incurred at the time of display from storage, a simple parameter modification will effect the change. [1]_
 
 .. [1]
-   Parameter :math:`\text{grpnow}` in routines CNGResp and CNAllocation, currently set to 1.0, could be changed to a smaller value to transfer some portion (1 - :math:`\text{grpnow}` ) of the growth respiration forward in time to occur at the time of growth display from storage.
-
+   Parameter :math:`\text{grpnow}` in routines CNGRespMod.F90 and CNAllocationMod.F90, currently set to 1.0, could be changed to a smaller value to transfer some portion (1 - :math:`\text{grpnow}` ) of the growth respiration forward in time to occur at the time of growth display from storage.

doc/source/tech_note/References/CLM50_Tech_Note_References.rst

@@ -63,13 +63,13 @@ Asner, G.P., Wessman, C.A., Schimel, D.S., and Archer, S. 1998. Variability in l
 
 Axelsson, E., and Axelsson, B. 1986. Changes in carbon allocation patterns in spruce and pine trees following irrigation and fertilization. Tree Phys. 2:189-204.
 
-.. _Atkin2016:
+.. _Atkinetal2015:
 
-Atkin OK, Bloomfield KJ, Reich PB, Tjoelker MG, Asner GP, Bonal D et al (2015) Global variability in leaf respiration in relation to climate, plant functional types and leaf traits. New Phytologist 206:614–636
+Atkin O.K., Bloomfield K.J., Reich P.B., Tjoelker M.G., Asner G.P., Bonal D. et al. 2015. Global variability in leaf respiration in relation to climate, plant functional types and leaf traits. New Phytologist 206:614–636
 
-.. _Atkin2017:
+.. _Atkinetal2017:
 
-Leaf Respiration in Terrestrial Biosphere Models. In Plant Respiration: Metabolic Fluxes and Carbon Balance, Advances in Photosynthesis and Respiration 43, G. Tcherkez, J. Ghashghaie (eds.) Springer International Publishing AG 2017
+Atkin O.K., Abdul Bahar N., Bloomfield K., Griffin K.L., Heskel M.A., Huntingford C., Martinez-de la Torre A., Turnbull, M.H. 2017. Leaf Respiration in Terrestrial Biosphere Models. In Plant Respiration: Metabolic Fluxes and Carbon Balance, Advances in Photosynthesis and Respiration 43, G. Tcherkez, J. Ghashghaie (eds.) Springer International Publishing AG 2017
 
 .. _BadgerandDirmeyer2015: