Abstract
Based on the concepts of mechanistic mathematical modelling the foundations of plant growth models are explained and some examples provided. It is illustrated how model modularity can be helpful to describe more complex eco-systems and how mechanistic plant growth models can be based on a multitude of sub-models that describe the important eco-physiological processes needed to determine plant growth dynamics. Modelling concepts for the simulation of phenological development, of photosynthesis, of nutrient allocation and of water and solute transport within the soil–plant continuum are presented. Moreover, two newly developed mechanistic plant growth models will be introduced. One model is the individual-based model PLATHO, which focuses on the description of the plant internal regulation of carbon allocation and nutrient uptake, and the other model is the stand model BALANCE, which in particular considers allocation strategies of trees in dependence on competition within the canopy.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Abrahamsen P, Hansen S (2000) Daisy: an open soil-crop-atmosphere system model. Environ Model Softw 15:313–330
Arbogast T, Obeyesekere M, Wheeler MF (1993) Numerical methods for the simulation of flow in root-soil systems. SIAM J Numer Anal 30:1677–1702
Aumann CA, Ford DE (2002) Modeling tree water flow as an unsaturated flow through a porous medium. J Theor Biol 219:415–429
Bailey JE, Ollis DF (1986) Biochemical engineering fundamentals. McGraw-Hill, New York
Bohrer G, Mourad H, Laursen TA, Drewry D, Avissar R, Poggi D, Oren R, Katul GG (2005) Finite element tree crown hydrodynamics model (FETCH) using porous media flow within branching elements: a new representation of tree hydrodynamics. Water Resour Res 41:W11404. doi:10.1029/2005WR004181
Campbell GS (1985) Soil physics with BASIC, transport models for soil-plant systems, vol 14, Developments in soil science. Elsevier, New York
Cárdenas ML, Letelier J-C, Gutierrez C, Cornish-Bowden A, Soto-Andrade J (2010) Closure to efficient causation, computability and artificial life. J Theor Biol 263:79–92
Chuang YL, Oren R, Bertozzi AL, Phillips N, Katul GG (2006) The porous media model for the hydraulic system of a conifer tree: linking sap flux data to transpiration rate. Ecol Model 191:447–468
Clausnitzer V, Hopmans JW (1994) Simultaneous modeling of transient three-dimensional root growth and soil water flow. Plant Soil 164:299–314
Cowan IR (1965) Transport of water in the soil-plant-atmosphere system. J Appl Ecol 2:221–239
Cruizat P, Cochard H, Améglio T (2002) Hydraulic architecture of trees: main concepts and results. Ann Forest Sci 59:723–752
Daudet FA, Lacointe A, Gaudillère JP, Cruiziat P (2002) Generalized Münch coupling between sugar and water fluxes for modelling carbon allocation as affected by water status. Journal of Theoretical Biology 214:481–498
De Pury DGG, Farquhar GD (1997) Simple scaling of photosynthesis from leaves to canopies without the errors of big-leaf models. Plant Cell Environ 20:537–557
Doussan C, Pagès L, Pierret A (2003) Soil exploration and resource acquisition by plant roots: an architectural and modelling point of view. Agronomie 23:419–431
Doussan C, Pierret A, Garrigues E, Pages L (2006) Water uptake by plant roots: II. Modelling of water transfer in the soil root-system with explicit account of flow within the root system – comparison with experiments. Plant Soil 283:99–117
Dunbabin VM, Diggle AJ, Rengel Z (2002) Simulation of field data by a basic three-dimensional model of interactive root growth. Plant Soil 239:39–54
Engel T, Priesack E (1993) Expert-N, a building block system of nitrogen models as a resource for advice, research, water management and policy. In: Eijsackers HJP, Hamers T (eds) Integrated soil and sediment research: a basis for proper protection. Kluwer, Dordrecht, pp 503–507
Engel T, Klöcking B, Priesack E, Schaaf T (1993) Simulationsmodelle zur Stickstoffdynamik. Verlag Eugen Ulmer, Stuttgart
Farquhar GD, Caemmerer S, Berry JA (1980) A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149:78–90
Feddes RA, Kowalik PJ, Zaradny H (1978) Simulation of field water use and crop yield, Simulation monographs. Pudoc, Wageningen
Früh T, Kurth W (1999) The hydraulic system of trees: theoretical framework and numerical simulation. J Theor Biol 201:251–270
Gardner WR (1960) Dynamic aspects of water availability to plants. Soil Sci 89:63–73
Gayler S, Priesack E (2007) PLATHO – A dynamic plant growth model considering competition between individuals and allocation to carbon-based secondary compounds. In: Fourcaud T, Zhang XP (eds) PMA06 – Plant growth modeling and applications. IEEE Computer Society, Los Alamitos, CA, pp 85–92
Gayler S, Grams TEE, Heller W, Treutter D, Priesack E (2008) A dynamical model of environmental effects on allocation to carbon-based secondary compounds in juvenile trees. Ann Bot 101:1089–1098
Génard M, Dauzat J, Franck N, Lescourret F, Moitrier N, Vaast P, Vercambre G (2008) Carbon allocation in fruit trees: from theory to modelling. Trees 22:269–282
Goudriaan J, van Laar HH (1978) Calculation of daily totals of the gross CO2 assimilation of leaf canopies. Neth J Agric Sci 26:373–382
Goudriaan J, van Laar HH (1994) Modelling potential crop growth processes. Textbook with exercises. Kluwer, Dordrecht
Grote R, Pretzsch H (2002) A model for individual tree development based on physiological processes. Plant Biol 4:167–180
Herms DA, Mattson WJ (1992) The dilemma of plants: to grow or defend. Q Rev Biol 67:283–335
Hölttä T, Vesala T, Nikinmaa E, Perämäki M, Siivola E, Mencuccini M (2005) Field measurements of ultrasonic acoustic emissions and stem diameter variations. New insight into the relationship between xylem tensions and embolism. Tree Phys 25:237–243
Hölttä T, Vesala T, Sevanto S, Perämäki M, Nikinmaa E (2006) Modeling xylem and phloem water flows in trees according to cohesion theory and Münch hypothesis. Trees 20:67–78
Hund F (1996) Geschichte der physikalischen Begriffe. Spektrum, Heidelberg
Hutson JL, Wagenet RJ (1992) LEACHM: Leaching estimation and chemistry model: a process-based model of water and solute movement, transformations, plant uptake and chemical reactions in the unsaturated zone. Version 3.0. Cornell University, Ithaca, NY
Janott M, Gayler S, Gessler A, Javaux M, Klier C, Priesack E (2011) A one-dimensional model of water flow in soil-plant systems based on plant architecture. Plant and Soil 341:233–256
Javaux M, Schröder T, Vanderborght J, Vereecken H (2008) Use of a three-dimensional detailed modeling approach for predicting root water uptake. Vadose Zone J 7:1079–1088
Jones CA, Kiniry JR (1986) CERES-Maize: a simulation model of maize growth and development. Texas A&M University Press, Temple, TX
Kumagai T (2001) Modeling water transportation and storage in sapwood: model development and validation. Agric Forest Meteorol 109:105–115
Lacointe A (2000) Carbon allocation among tree organs: a review of basic processes and representation in functional-structural tree models. Ann Forest Sci 57:521–533
Lacointe A, Minchin PEH (2008) Modelling phloem and xylem transport within a complex architecture. Funct Plant Biol 35:772–780
Laughlin RB (2006) A different universe: reinventing physics from the bottom down. Basic, New York
Le Roux X, Lacointe A, Escobar-Gutiérrez A, Le Dizèsa S (2001) Carbon-based models of individual tree growth: a critical appraisal. Ann Forest Sci 58:469–506
Letelier J-C, Soto-Andrade J, Guíñez Abarzúa F, Cornish-Bowden A, Cárdenas ML (2006) Organizational invariance and metabolic closure: analysis in terms of (M, R) systems. J Theor Biol 238:949–961
Leuning R, Kelliher FM, De Pury DGG, Schultze E-D (1995) Leaf nitrogen, photosynthesis, conductance and transpiration: scaling from leaves to canopies. Plant Cell Environ 18:1183–1200
Matyssek R, Agerer R, Ernst D, Munch JC, Oßwald W, Pretzsch H, Priesack E, Schnyder H, Treutter D (2005) The plant’s capacity in regulating resource demand. Plant Biol 7:560–580
Meier U (1997) Growth stages of mono- and dicotyledonous plants, BBCH-monograph. Blackwell, Berlin
Monod J (1949) The growth of bacterial cultures. Annu Rev Microbiol 3:371–394
Munteanu A, Solé RV (2006) Phenotypic diversity and chaos in a minimal cell model. J Theor Biol 240(3):434–442
Nimah MN, Hanks RJ (1973) Model for estimation of soil water, plant, and atmospheric interrelations: I. Description and sensitivity. Soil Sci Soc Am Proc 37:522–527
Penning de Vries FWT, Jansen DM, ten Berge HFM, Bakema A (1989) Simulation of ecophysiological processes of growth in several annual crops. Pudoc, Wageningen
Pretzsch H (2009) Forest dynamics, growth and yield. Springer, Berlin
Priesack E (2006) Expert-N Dokumentation der Modell-Bibliothek. Hieronymus, München
Priesack E, Gayler S (2009) Agricultural crop models: Concepts of resource acquisition and assimilate partitioning. In: Lüttge UE, Beyschlag W, Murata J (eds) Progress in botany, vol 70. Springer, Heidelberg, pp 195–222
Ritchie JT (1991) Wheat phasic development. In: Hanks J, Ritchie JT (eds) Modeling plant and soil systems. ASA, CSSA, SSSA, Madison, WI, pp 31–54
Ritchie JT, Godwin DC, Otter-Nacke S (1987) CERES-Wheat - A simulation model of wheat growth and development Texas A&M University Press, College Station, TX, pp. 185
Rötzer T, Seifert T, Pretzsch H (2009) Modelling above and below ground carbon dynamics in a mixed beech and spruce stand influenced by climate. Eur J Forest Res 128:171–182
Schröder U, Richter O (1993) Parameter estimation in plant growth models at different levels of aggregation. Model Geobiosph Process 2:211–226
Somma F, Hopmans JW, Clausnitzer V (1998) Transient three-dimensional modeling of soil water and solute transport with simultaneous root growth, root water and nutrient uptake. Plant Soil 202:281–293
Thornley JHM, Johnson IR (1990) Plant and crop modelling. A mathematical approach to plant and crop physiology. Clarendon, Oxford
Thompson MV, Holbrook NM (2003) Application of a single-solute non-steady-state phloem model to the study of long-distance assimilate transport. Journal of Theoretical Biology 220:419–455
Tyree MT, Zimmermann MH (2002) Xylem structure and the ascent of sap, 2nd edn, Springer series in wood sciences. Springer, Berlin
Vrugt JA, van Wijk MT, Hopmans JW, Simunek J (2001) One-, two-, and three-dimensional root water uptake functions for transient modeling. Water Resour Res 37:2457–2470
Wang Y-P, Leuning R (1998) A two-leaf model for canopy conductance, photosynthesis and partitioning of available energy I: model description and comparison with a multi-layered model. Agric Forest Meteorol 91(1–2):89–111
Yin X, Struik PC (2009) C3 and C4 photosynthesis models: an overview from the perspective of crop modelling. NJAS Wageningen J Life Sci 57:27–38
Yin X, van Laar HH (2005) Crop systems dynamics. Wageningen Academic, Wageningen
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Priesack, E., Gayler, S., Rötzer, T., Seifert, T., Pretzsch, H. (2012). Mechanistic Modelling of Soil–Plant–Atmosphere Systems. In: Matyssek, R., Schnyder, H., Oßwald, W., Ernst, D., Munch, J., Pretzsch, H. (eds) Growth and Defence in Plants. Ecological Studies, vol 220. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30645-7_15
Download citation
DOI: https://doi.org/10.1007/978-3-642-30645-7_15
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-30644-0
Online ISBN: 978-3-642-30645-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)