PINEL

A nutrient cycling model in managed pine forests

USER’s MANUAL 2007

General Model Information

(as registered in the Register of Ecological Models (REM) http://eco.wiz.uni-

kassel.de/ecobas.html)

Name: PInus sylvestris: Nutrient cycling modEL

Acronym: PINEL

Main medium: terrestrial

Main subject: biogeochemistry, forestry

Organization level: Population

Type of model: ordinary differential equations, static-algebraic equations

Main application: research, decision support/expert system, simulation/optimization tool

Keywords: Pinus sylvestris, Spain, Whole-tree removal, Thinning, Forest harvesting, Nitrogen,

Phosphorus, Mediterranean pine forest, sustainable forest management

Contact:

Dr. Federico J. Castillo

Departamento de Ciencias del Medio Natural, Edificio los Olivos, Universidad Publica de

Navarra, Pamplona, Navarra, Spain., E-31006.

Phone: +34 948 169 115

Fax: +34 948 168 930

email: federico.castillo@unavarra.es

Alternative contact:

Dr. Juan A. Blanco

Department Forest Sciences, Faculty of Forestry, University of British Columbia.

2424 Main Mall, Vancouver, B.C., Canada, V6T 1Z4

Phone: +1 604 822 8876

Fax: +1 604 822 9133

Email: juan.blanco@ubc.ca

Author(s):

J.A. Blanco: conceptual model, mathematical development, technical development, user manual.

M.A. Zavala: conceptual model, mathematical development.

J. B. Imbert: conceptual model.

F.J. Castillo: conceptual model.

Abstract:

Forest harvesting may interfere with long-term ecosystem structure and function and different

harvesting methods will differ in their effects on soil fertility (e.g. whole-tree harvesting versus

stem removal). In the case of thinning, effects of thinning intensity, rotation length and site

quality must be assessed in order to formulate sustainable management practices. Assessment of

the relative impact of these practices is difficult, however, given the long temporal scales

involved. In this study, we implement a process-based model of nutrient cycling to evaluate

temporal changes in ecosystem nutrient dynamics of managed and non-managed forest stands.

The model was specifically designed to asses differences between two contrasting site-quality

Pinus sylvestris L. stands in the western Pyrenees (Navarre, Spain) managed under two thinning

intensities. The model describes the main nutrient fluxes in the stand: litterfall, decomposition,

resorption, root uptake and management type, and it was parameterized and verified with 3 years

of field data. After model verification we examined the effects of thinning intensity, thinning

frequency and harvesting method (whole-tree versus stem removal) on potential nutrient losses.

The results suggest that in this heterogeneous region, sustainability of forestry practices is

strongly site dependent. N and P were particularly sensitive to overexploitation and in no case

could whole-tree removal be recommended as it may have a strong negative effect on nutrient

reserves. In relation to previous nutrient cycling models, our model offers a satisfactory

compromise between simplicity, biological realism and predictability, and it proved to be a

useful tool to predict short-term changes in nutrient reserves as well as to evaluate possible

negative effects of applying current thinning prescriptions on long-term sustainability of

managed forests in the western Pyrenees.

II. Technical Information

II.1 Executables:

Operating System(s): STELLA Research v 7

II.2 Source-code:

Programming Language(s): STELLA Research v 7

II.3 Input

Nutrient concentrations in Pinus sylvestris tissues. Nutrient concentrations in Pinus sylvestris

litterfall.l Decomposition rates. Type of thinning (stem-only or whole-tree, stand age for the first

thinning, % Basal area removed)

II.4 Output

Accumulated nutrient losses over rotation

III. Manual

III.1 General features

What PINEL is:

• PINEL is a mass balance model. It was developed to predict the evolution of different

nutrient pools and nutrient fluxes in forests of Pinus sylvestris in the western Pyrenees.

• PINEL is based on SILVES (Del Rio and Montero 2001), a Growth & Yield model

developed for Pinus sylvestris in Spain. PINEL calculates biomass from SILVES by

using Allometric equations, and then PINEL calculates nutrient mass by using nutrient

concentration in different pools.

• PINEL starts all the simulation in a mature Pinus sylvestris stand, 40 years old. All the

years calculated for the simulation must be increased by this amount to have the real

stand age.

What PINEL is not:

• PINEL is not a model of forest growth. PINEL takes the growth pattern from another

model: SILVES.

• PINEL is not a model of forest climate. There are no climate variables in the model.

This manual explains the version developed to study nitrogen fluxes at the southern

Mediterranean site Aspurz (see Blanco 2004, Blanco et al. 2005). In addition, there is some

comments about the version developed to study biomass fluxes. During the work by Blanco

(2004), there were version for the northern continental site of Garde and for four other nutrients

(phosphorus, potassium, calcium and magnesium), for a total of ten different versions of this

model. However, all the versions were similar, with differences only in the calibration values.

For this reason, in this manual only one version is explained.

III.2 The control panel

PINEL has been developed in STELLA, and therefore it has three different levels, starting with

the main control panel (Figure 1).

In the up left hand corner, there is a simplified diagram of the model, showing it as a two-part

model (tree and soil), with mass fluxes (blue arrows) and interactions (red arrows) between both.

There are three main boxes in the control panel.

Figure 1. PINEL control panel.

The box entitled MODEL OUTPUT contains the results of the simulation, divided in several

sectors.

• Under the label NUTRIENT POOLS there are two figures, which show the evolution of

different nutrient pools in the ecosystem during the simulation. In the graph labelled as

Tree, nutrient pools are roots, stems, leaves and branches. In the graph labelled as Soil,

nutrient pools are woody debris, forest floor and mineral soil. In the table labelled as N in

the system, there are two variables displayed in tabular form: total aboveground N and

mineral soil N.

• Under the label FLUXES there are two figures, which show the evolution in the nutrient

fluxes in both aboveground and belowground. The aboveground fluxes are N in leaves

growth (amount of N in the new leaves created every year), N in branches growth, N in

stems growth and N in roots growth. In the belowground fluxes, the graphs show the

evolution of N in mineralization of leaves, N taken by trees, available N, N in roots killed

by thinning and accumulated available N.

• Under the label MANAGEMENT there are a graph that shows the amount of N in the

leaves in the residues produced by thinning, the pool of N in harvested timber and the

amount of N in branches in thinning residues.

• The three small boxes show the amount of accumulated leaching during the simulation

(in kg / ha), the accumulated timber harvested by thinning (in tons /ha) and the

accumulated N outputs by thinning (in kg / ha). The harvested timber showed here is only

harvested during the thinning operations. The timber harvested in the final cut is not

account for in this graph.

The box entitled MODEL INPUT contains the values needed to carry out the simulation.

• Under the label entitled NUTRIENT CONCENTRATION, there are four slider devices to

introduce the concentration (mg / g) of N in green leaves, in senesced leaves, in branches

and in stems (timber).

• Under the label entitled THINNING PLAN there is a slider that defines thinning intensity

(in percentage of basal area removed). This value is constant for all thinning operations

during the simulation. The bolt entitled “Years between thinning” defines the time

between a thinning operation and the next one (in years) and the bolt marked as “Year of

first thinning” defines the stand age when the first thinning is carried out.

The box entitled MODEL INITIALIZATION defines the initial values for several variables

• Under the label NUTRIENT POOLS INITIAL VALUES there are six bolts, which define

the initial amount of N (in kg / ha) in alive leaves, branches and stems, and in woody

debris, forest floor and mineral soil.

• Under the label EXTERNAL CYCLE there is a slider to define nutrient inputs from

external sources (such as atmospheric deposition or mineral weathering) in kg / ha per

year. This amount remains constant during the whole simulation.

III.3 Variables

PINEL is the translation into STELLA of the processes described in Blanco et al. (2005), and it

was calibrated with values gathered during the PhD thesis of the main author (Blanco 2004). The

model is subdivided in two modules.

The TREE MODULE is the most developed one (Figure 2). This module is organized following

aboveground nutrient fluxes. In this module, the Stocks are:

• N IN LEAVES: This reservoir accounts for the total amount of N in leaves. The initial

value is set in the control panel by the bolt.

• N IN BRANCHES: As before, but for branches.

• N IN STEMS: As before, but for stems.

• N IN ROOTS: Total amount of N in roots. The initial value of this reservoir is not

connected to a bolt in the control panel because it is calculated through the above /

belowground biomass ratio (see below).

• N IN LEAVES IN THINNING RESIDUES: This reservoir accumulates the amount of N

in leaves than have been removed from the canopy by thinning. The initial value is zero.

• N IN BRANCHES IN THINNING RESIDUES: As before, but for branches.

• N IN HARVESTED TIMBER: As before, but for stems.

The Flows in this module are:

• N IN RESORPTION: Amount of N resorpted from senescent leaves every year. It is

calculated as:

leavesgreeninionConcentrat

leavesdryinionConcentratleavesgreeninionConcentratlittefallleafinN

___

_________

−×

• N IN LEAVES RESIDUES: This flow simulates the amount of N removed from the

leaves reservoir by thinning. The value is zero if there is no thinning. If some thinning is

applied, the value is calculated as a percentage of the reservoir removed. This percentage

is calculated trough an empirical relationship established by field data (see Blanco 2004).

This relationship is a linear regression of observed percentage of N in leaves removed

versus thinning intensity.

• N IN LEAVES LITTERFALL: This flow simulates the amount of N removed from the

leaves reservoir by natural litterfall every year. This amount is calculated as the product

of the reservoir size and the percentage of the reservoir that falls every year (see below).

• N IN LEAVES GROWTH: This flow simulates the amount of N added to the reservoir

every year to cover the losses by resorption and litterfall and to account for the growth of

leaves. The yearly growth is calculated by multiplying the concentration of leaves by an

empirical relationship (linear regression) between stem growth and leaf biomass.

• N IN BRANCHES GROWTH: As before, but for branches and without considering

nutrient resorption from branches.

• N IN BRANCHES IN RESIDUES: As for leaves, but for branches.

• N IN BRANCHES LITTERFALL: As for leaves, but for branches.

• N IN STEMS GROWTH: As for leaves, but for stems and without considering nutrient

resorption from stemwood.

Figure 2. Tree module

• N IN HARVESTED STEMS: This flow simulates de amount of N in harvested stems by

thinning. It is calculated as the product of N concentration in stemwood by the value of

the converter of harvested volume into harvested stem biomass (see below).

• N IN ROOTS GROWTH: This flow accounts for the amount of N in the new root

biomass. It is calculated as the difference between the current amount of N in the roots

reservoir and the amount of N needed to keep the aboveground/belowground biomass

ratio.

• N IN UPTAKE: This flow simulates the amount of N that must be taken from the mineral

soil to cover the demands for N in branches, leaves, roots and stems growth, minus the N

recycled from leaves by resorption.

The tree module uses a number of Converters to link several processes. These converters are:

• CONCENTRATION IN DRY LEAVES: This is an empirical data provided by the user

through the bolt in the control panel.

• CONCENTRATION IN GREEN LEAVES: As before, but for green leaves.

• CONCENTRATION IN BRANCHES: As before, but for branches.

• CONCENTRATION IN STEMS: As before, but for stemwood.

• N IN LEAF LITTERFALL PREVIOUS YEAR: This converter keeps the value of the

flow N in leaves litterfall from the previous year.

• LEAVES LITTERFALL: This is an empirical data for the percentage of leave biomass

that becomes litterfall every year. It is calculated with a empirical linear regression to the

thinning intensity.

• N ABOVEGROUND: This converter calculates the combined amount of N in the leaves,

N in Branches and N in Stems stocks.

• RATIO ABOVE BELOWGROUND: This is a single value from bibliography that

provides the ratio between aboveground tree biomass and belowground tree biomass.

• N TO ROOTS: This converter calculates the root biomass needed to be in the N in Roots

stock to keep the above/belowground ratio, and its associated amount of N.

• N TO ROOTS PREVOIUS YEAR: This parameter keeps the value of the converter N to

roots from the previous year.

• YEAR: This converter keeps track of the simulation year.

• STEM GROWTH: This converter calculates the annual stem growth as a equation

derived from the SILVES model (Del Río and Montero 2001) for plots as the one in the

Aspurz site, corrected by the influence of thinning.

• CORRECTION BY THINNING: This converter calculates the correction in stem growth

due to thinning, depending on stand age. The relationship is derived from the results

obtained with SILVES (Del Río and Montero 2001).

• COMBINATION: This is a mathematical operator to include stand age in the correction

by thinning of stem growth.

• HARVESTER TIMBER: This converter calculates the amount of harvested timber given

the amount of N removed by harvesting and the concentration of N in stemwood.

• BRANCHES LITTERFALL: Empirical value that accounts for the percentage of branch

biomass that becomes litterfall every year.

• N IN BRANCHES LITTERFALL PREVIOUS YEAR: This converter keeps the value of

the flow N in branches litterfall from the previous year.

• CONVERTER BA TO VOL: This operator converts the amount of removed stemwood

volume to percentage of basal area removed by thinning.

• THINNING PLAN: This converter produces a thinning event, as defined by the

following converters.

• YEAR OF FIRST THINNING: The year when the first thinning is applied is defined by

the user by using the bolt in the control panel.

• THINNING INTENSITY: The percentage of basal area removed in each thinning event

is defined by the user with the slider in the control panel. This intensity is constant during

the whole simulation.

• YEARS BETWEEN THINNINGS: The time in years between one thinning event and the

next one is defined by the user with the bolt in the control panel. This time is constant

during the simulation.

• INITIAL N IN ROOTS: This converter calculates the initial amount of N in the N in

roots stock, taking into consideration the initial values for the stocks n in Leaves, N in

Branches and N in Stems and the above/belowground ratio.

The SOIL MODULE is more simplified than the Tree Module, and the main objective is to

simulation decomposition of leaves and woody debris (Figure 3). In this module, the Stocks are:

• MINERAL SOIL: This stock simulates the amount of nutrient in the mineral soil. The

initial value is selected by the user with the bolt in the control panel.

• N IN BRANCH LITTERFALL: This stock accounts for the amount of N in the fallen

branches, either from natural litterfall of from thinning. This flow is just a crossing point

for the natural and artificial flow of N in branches. The value is zero after every iteration

of the model.

• WOODY DEBRIS: This stock simulates the amount of N in decomposing woody debris

(either from stems or from branches). The initial amount is fixed by the user with the bolt

in the control panel. This value is calculated by running the model starting from a soil

without forest floor and without thinning for 30 years. See Blanco et al (2005) for a

deeper explanation of this procedure.

• N IN LEAVE LITTERFALL: This stock is equivalent to N in branch litterfall but for

leaves.

• FOREST FLOOR: This stock is equivalent to Woody debris but for decomposing leaves.

The initial value is defined by the user, following a procedure similar to the one for

woody debris.

• ACCUMULATED LEACHING: The amount of N that exceeds tree uptake is

accumulated in this stock. The initial value is zero.

• ACCUMULATED AVILABLE N: This stock accounts for the total N available during

the whole simulation.

In the soil module, the flows are defined as follows:

• N IN ROOT MINERALIZATION: This flow is the amount of N that goes into the

mineral soil every year as result of root decomposition. It is calculated as a fraction of the

stock N in roots.

• N IN THINNED ROOTS: This flow is the amount of N mineralized from the roots killed

by thinning. The flow is proportional by the above/belowground ratio to the amount of N

in stems, branches and leaves fallen by thinning.

• N IN BRANCH LITTERFALL: This flow simulates the amount of N that gets into the

Woody debris stock every year, from both natural litterfall and thinning residues (if any).

• THINNING WOODY DEBRIS: This flow simulates de amount of N that goes to the soil

as a result of a thinning event, if the thinning plan does not prescribe whole-tree thinning.

• N IN WOODY DEBRIES MINERALIZATION: This is the flow of mineralized N from

decomposing woody debris that gets into the mineral soil every year. The flow is

regulated by the woody debris decomposition ate and the amount of N in woody debris.

• N IN LEAVES MINERALIZATION: Equivalent to the previous flow, but for

decomposing leaves.

• N IN LEAF LITTERFALL: Amount of N that gets into the forest floor every year from

fallen leaves, either from natural litterfall or thinning.

• LEAVES RESIDUES: flow of N coming from leaves fallen down by thinning, if the

whole-tree option is deactivated.

• YEARLY LEACHING: Amount of N that is leached from the soil, calculated as the

difference between Nutrient uptake and N available (see below).

• YEARLY N AVIAILABLE: Amount of N that is available every year, as calculated by

the converter N available (see below).

• INPUTS: This flow simulates N inputs from external sources, such as mineral

weathering, rainfall or atmospheric deposition.

In this module, the Converters are:

• ROOT MINERALIZATION RATE: Percentage of roots that decompose every year,

from bibliographical sources.

• THINNED ROOTS: This converter calculates the amount of roots that are killed by

thinning, supposing that this value keeps the above/belowground biomass ratio with the

stems, branches and leaves fallen by thinning.

• WHOLE TREE HARVESTING?: This converter turns on/off the option of whole-tree

harvesting, leaving thinning residues (branches and leaves) in the forest floor or not, as

decided by the user when using the switch in the control panel.

• N IN WOODY DEBRIS: This converter adds up the amount of N calculated by the

following three converters.

• N1 IN WOODY DEBRIS: This converter calculates the amount of N in the 35 youngest

cohorts of fallen branches, taking into account the time since falling down and the woody

debris decomposition rate.

• N2 IN WOODY DEBRIS: As before, but for the cohorts fallen from 36 to 70 years ago.

Figure 3. Soil module.

• N3 IN WOODY DEBRIS: AS before, but for the cohorts fallen from 71 to 105 years ago.

• WOODY DEBRIS DECOMP RATE: Olson’s decomposition rate for woody debris,

taken from bibliography. See Blanco et al. (2005) for more info.

• N IN FOREST FLOOR: This converter adds up the amount of N calculated by the

following three converters.

• N1 IN FOREST FLOOR: This converter calculates the amount of N in the 35 youngest

cohorts of fallen leaves, taking into account the time since falling down and the leaf

decomposition rate.

• N2 IN FOREST FLOOR: As before, but for the cohorts fallen from 36 to 70 years ago.

• N3 IN FOREST FLOOR: AS before, but for the cohorts fallen from 71 to 105 years ago.

• LEAVES DECOMP RATE: Olson’s decomposition rate for woody debris, determined

empirically. See Blanco (2004) and Blanco et al. (2005) for more info about how this rate

was calculated.

• SOIL N: This converter calculates the total amount of N in the soil, adding up the stocks

Mineral soil, Woody debris and Forest floor.

• LEACHING: This converter calculates the N leached every year, as the difference

between the N available and the N in tree uptake.

III.4 PINEL biomass

PINEL BIOMASS is a simplified version of PINEL designed to simulate the amounts of biomass

in different stocks and flows (Figure 4). This version of PINEL does not simulate nutrient fluxes,

only biomass fluxes, and therefore the inputs are lower. Only the definition of the thinning plan

is needed. As before, this version of PINEL is calibrated for the Mediterranean site of Aspurz

(Blanco et al. 2005) using the growth and yield data provided for the site by SILVES (Del Río

and Montero 2001).

III.5 Use of PINEL

The use of PINEL is easy. Before running the simulation, the user has to select the values for the

concentrations of nutrients in several pine tissues (stemwood, branches, green leaves and dry

leaves). After that, the user has to decide the thinning plan to be applied. This plan will be

constant during the simulation. The plan is defined by the thinning intensity (percentage of basal

area removed), year of first thinning and years between two consecutive thinning events. In

addition, the user must choose between removing the whole tree after thinning (whole-tree

harvesting) or leaving thinning residues (leaves and branches) in the stand and removing only

stems. Finally, the user must define the initial nutrient pools in six different stocks (leaves,

branches, stems, forest floor, woody debris and mineral soil) and the input of nutrient from the

exterior. The outputs can be get by clicking in the graphs and tables in the Model output section.

Figure 4. PINEL BIOMASS control panel.

IV. References

Blanco J.A., Zavala M.A., Imbert J.B., and Castillo F.J. 2005. Sustainability of forest

management practices: Evaluation through a simulation model of nutrient cycling. Forest

Ecology and Management 213(1-3), 209-228.

Blanco J.A., Zavala M.A., Imbert J.B., and Castillo F.J. 2004. Sostenibilidad de las prácticas

forestales en masas de Pinus sylvestris L. en el Pirineo navarro. Evaluación mediante un modelo

de proceso (in Spanish). Cuadernos de la Sociedad Española de Ciencias Forestales 18, 39-44.

Blanco J.A. 2004. La práctica de las claras forestales y su influencia en el ciclo interno de

nutrientes en dos bosques de pino silvestre de Los Pirineos navarros (in Spanish). PhD

Dissertation. Universidad Pública de Navarra, Pamplona, Spain, 315 pp.

Del Río, M., Montero, G., 2001. Modelo de simulación de claras en masas de Pinus sylvestris L.

Monografías I.N.I.A. Forestal No. 3, Madrid. 50 pp.

V. Credits

PINEL

Grupo de Ecología de la Universidad Pública de Navarra.

Life Science Programming Ltd. Ecocast Ltd.

Departamento de Ciencias del Medio Natural, Edificio los Olivos, Universidad Publica de

Navarra, Pamplona, Navarra, Spain., E-31006.

Phone: +34 948 169 115 Fax: +34 948 168 930 E-Mail: Federico.castillo@unavarra.es

Copyright

PINEL model copyright 2005 Grupo de Ecología de la Universidad Pública de Navarra.

Manual Copyright 2007 J Grupo de Ecología de la Universidad Pública de Navarra.

License Agreement

The enclosed software programs are licensed by Grupo de Ecología de la Universidad Pública de

Navarra to customers for their non-exclusive right to use the PINEL files on a single computer,

unless a site license is obtained by writing to Grupo de Ecología de la Universidad Pública at the

address given above. You may not copy, modify, sublicense, rent, lease or in any way alter the

software without the express consent of the developers.

Limited Warranty

These files are provided without warranty of any kind, either expressed or implied. The entire

risk as to the results and performance of the software, any conclusions you may draw from use of

the software, and decisions or actions taken on the basis of the software or your conclusions from

its use, is assumed by you, the user. PINEL is calibrated for a particular type of forest on western

Pyrenees, Navarre, Spain. The developers are not responsible for, and do not warrant the

performance of the software with respect to forests in different ecological zones and site types.

We do not guarantee that the software is error-free, or that the results are directly applicable to

any particular forest that you have in mind.

Acknowledgments and Credits

Funding for the software development that created the foundation form which the PINEL

ecosystem management simulation model was developed was provided by Departamento de

Educación de la Diputación de Navarra and by Universidad Pública de Navarra. All these

sources of support are gratefully acknowledged.

Credits

Concept and design

J.A. Blanco, M.A. Zavala, F.J. Castillo, J.B. Imbert

Programming

J.A. Blanco

User’s Manual

J.A. Blanco