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Carbon and Nitrogen allocation

The 3D-CMCC-FEM considers, for deciduous tree species, the length of the vegetative period by the variables Tstart and MinDayLength for the beginning and the end of it. The amount of new biomass at the end of each day is partitioned and allocated among the main tree carbon compartments: leaf, fine and coarse root, stem, branch and fruit. The woody compartments are furthermore subdivided into sapwood and hearthwood and live and dead wood. Another pool is represented by Non-Structural-Carbon (NSC, starch and sugar) that is stored in the whole tree. This pool is used as a carbon reserve pool which is used during periods of negative carbon balance (for example during the dormant season, periods of stress or natural or artificially induced defoliation episodes) where NSC is remobilized and transported from the sites of phloem loading, while during periods of positive carbon balance plants preferentially allocate recently assimilated carbon to replenish NSC (Collalti et al. 2020; D'Andrea et al. 2020, 2021; Merganičová et al. 2019).

Allocation of assimilates to the other C pools is done at daily scale and is strongly regulated by the model phenological scheme which is temperature- and photoperiod-dependent (Collalti et al. 2016, 2018; Marconi et al. 2017).


The 3D-CMCC-FEM, for deciduous species, considers five phenological transitions (being just four in the previous versions: bud burst, peak LAI, leaf fall period and dormancy) that drive the seasonal progression of vegetation through phases of dormancy/quiescence, bud-burst, maximum growth, active growth and senescence as in the following:

1. Leaf onset starts from quiescence when thermic sum (the sum of the Tday air temperatures exceeding the threshold Tbase value of 5 °C) exceeds a species- and site-specific temperature threshold value and when the LAI value reaches LAI = max(LAI) × 0.5. The costs of expanding buds during this period of high carbon demand are supported by NSC.

2. During the budburst phase, carbon and NSC are allocated to the foliage and fine root pools, as long as the balance between GPP and autotrophic respiration is positive.


3. During the succeeding maximum growth phase and lasting up to peak LAI, carbon is allocated into foliage and fine-root pools, based on the pipe model theory, to optimize photosynthesis; otherwise, no growth occurs and NSC is used.

4. Successively, the full growing phase lasts up to the day when day length (in hours) is shorter than a species-specific threshold value. In this phase carbon is allocated into stem, fine and coarse roots, branch and bark, and into NSC pools in order to refill the reserves for the next years.

5. Finally, during the leaf fall (i.e. yellowing or senescence) phase, lasting until the leaf fall (assumed linear) is complete, the total positive carbon balance is allocated to the NSC pool.

Outside the growing season (dormancy) trees consume NSC for fueling maintenance respiration (Merganičová et al. 2019).

For evergreen species the model follows a similar but much more simplified approach simulating a first maximum growth phase, when the model allocates NSC to foliage and fine roots up to reach peak LAI, and a second full growing phase, when the model allocates to the other pools.

The partitioning of carbon within pools is based on species-specific parameters that are dynamically regulated by limiting factors (i.e. radiation and water availability).


where εSx , εRx , εLx are species-specific parameter, ωx controls the ‘sensitivity’ of allocation to changes in fSW and L, as ωx increases allocation which is controlled to a greater extent by fSW and L, for the limiting case of ωx = 0 constants allocation fractions are obtained. The scalars index fSW represents the soil water modifier (Landsberg and Waring, 1997) and L is the unabsorbed light (varying between 0 and 1) by the species x with diameter y, height z, and age k (Collalti et al. 2014).

The carbon that is allocated daily into woody tissues (i.e. branch, stem and coarse root) is considered as sapwood. Heartwood is considered as the difference between total woody and sapwood biomass. Before senescence a fixed fraction (i.e. 10%) of carbon in leaves and fine roots is re-mobilized into the overall NSC pool. In deciduous species two species-specific parameters control budburst (i.e. leaf onset) and leaf offset which are triggered by thermic sum and day length as generally assumed by many other models.


The N pools in biomass are updated daily according to fixed C:N ratios for each pool, based on the relative amount of C within each pool. The daily leaf area index (LAI) is based on the amount of C allocated to the leaves, the specific leaf area (as the branch and bark fractions which vary based on age) and the single tree canopy coverage.


Maximum annual attainable LAI is computed at the beginning of each year of simulation based on the current sapwood area and is controlled by the pipe-model theory. The amount of sapwood that is converted to heartwood, as well as the amount of living ‘respiring’ cells (a fraction of sapwood mass) that die or are retained and renewed, are parameterized at annual level but are computed and updated at daily time-step during the vegetative period.


Example of 3D-CMCC-FEM daily carbon allocation for different tree C-pools based on daily NPP and NSC-usage at Sorø site (Denmark), Fagus sylvatica L.


Example of 3D-CMCC-FEM daily carbon allocation for different tree C-pools based on daily NPP and NSC-usage at Hyytiala site (Finland), Pinus sylvestris L.

More info about the 3D-CMCC-FEM can be found at PUBLICATIONS page

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