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Growth and Defence in Plants pp 335–353Cite as

Mechanistic Modelling of Soil–Plant–Atmosphere Systems

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Part of the book series: Ecological Studies ((ECOLSTUD,volume 220))

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.

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References

  • Abrahamsen P, Hansen S (2000) Daisy: an open soil-crop-atmosphere system model. Environ Model Softw 15:313–330

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Aumann CA, Ford DE (2002) Modeling tree water flow as an unsaturated flow through a porous medium. J Theor Biol 219:415–429

    Article  PubMed  Google Scholar 

  • Bailey JE, Ollis DF (1986) Biochemical engineering fundamentals. McGraw-Hill, New York

    Google Scholar 

  • 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

    Google Scholar 

  • Campbell GS (1985) Soil physics with BASIC, transport models for soil-plant systems, vol 14, Developments in soil science. Elsevier, New York

    Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • Clausnitzer V, Hopmans JW (1994) Simultaneous modeling of transient three-dimensional root growth and soil water flow. Plant Soil 164:299–314

    Article  CAS  Google Scholar 

  • Cowan IR (1965) Transport of water in the soil-plant-atmosphere system. J Appl Ecol 2:221–239

    Article  Google Scholar 

  • Cruizat P, Cochard H, Améglio T (2002) Hydraulic architecture of trees: main concepts and results. Ann Forest Sci 59:723–752

    Article  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Google Scholar 

  • Engel T, Klöcking B, Priesack E, Schaaf T (1993) Simulationsmodelle zur Stickstoffdynamik. Verlag Eugen Ulmer, Stuttgart

    Google Scholar 

  • Farquhar GD, Caemmerer S, Berry JA (1980) A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149:78–90

    Article  CAS  PubMed  Google Scholar 

  • Feddes RA, Kowalik PJ, Zaradny H (1978) Simulation of field water use and crop yield, Simulation monographs. Pudoc, Wageningen

    Google Scholar 

  • Früh T, Kurth W (1999) The hydraulic system of trees: theoretical framework and numerical simulation. J Theor Biol 201:251–270

    Article  PubMed  Google Scholar 

  • Gardner WR (1960) Dynamic aspects of water availability to plants. Soil Sci 89:63–73

    Article  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Google Scholar 

  • Goudriaan J, van Laar HH (1994) Modelling potential crop growth processes. Textbook with exercises. Kluwer, Dordrecht

    Book  Google Scholar 

  • Grote R, Pretzsch H (2002) A model for individual tree development based on physiological processes. Plant Biol 4:167–180

    Article  Google Scholar 

  • Herms DA, Mattson WJ (1992) The dilemma of plants: to grow or defend. Q Rev Biol 67:283–335

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Hund F (1996) Geschichte der physikalischen Begriffe. Spektrum, Heidelberg

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  Google Scholar 

  • Jones CA, Kiniry JR (1986) CERES-Maize: a simulation model of maize growth and development. Texas A&M University Press, Temple, TX

    Google Scholar 

  • Kumagai T (2001) Modeling water transportation and storage in sapwood: model development and validation. Agric Forest Meteorol 109:105–115

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Lacointe A, Minchin PEH (2008) Modelling phloem and xylem transport within a complex architecture. Funct Plant Biol 35:772–780

    Article  Google Scholar 

  • Laughlin RB (2006) A different universe: reinventing physics from the bottom down. Basic, New York

    Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Meier U (1997) Growth stages of mono- and dicotyledonous plants, BBCH-monograph. Blackwell, Berlin

    Google Scholar 

  • Monod J (1949) The growth of bacterial cultures. Annu Rev Microbiol 3:371–394

    Article  CAS  Google Scholar 

  • Munteanu A, Solé RV (2006) Phenotypic diversity and chaos in a minimal cell model. J Theor Biol 240(3):434–442

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • Penning de Vries FWT, Jansen DM, ten Berge HFM, Bakema A (1989) Simulation of ecophysiological processes of growth in several annual crops. Pudoc, Wageningen

    Google Scholar 

  • Pretzsch H (2009) Forest dynamics, growth and yield. Springer, Berlin

    Google Scholar 

  • Priesack E (2006) Expert-N Dokumentation der Modell-Bibliothek. Hieronymus, München

    Google Scholar 

  • 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

    Chapter  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  Google Scholar 

  • Schröder U, Richter O (1993) Parameter estimation in plant growth models at different levels of aggregation. Model Geobiosph Process 2:211–226

    Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Thornley JHM, Johnson IR (1990) Plant and crop modelling. A mathematical approach to plant and crop physiology. Clarendon, Oxford

    Google Scholar 

  • 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

    Google Scholar 

  • Tyree MT, Zimmermann MH (2002) Xylem structure and the ascent of sap, 2nd edn, Springer series in wood sciences. Springer, Berlin

    Book  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Yin X, van Laar HH (2005) Crop systems dynamics. Wageningen Academic, Wageningen

    Book  Google Scholar 

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Author information

Authors and Affiliations

  1. Institute of Soil Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany

    E. Priesack & S. Gayler

  2. Center for Applied Geoscience, Water & Earth System Science Competence Cluster, c/o University of Tübingen, 72074, Tübingen, Germany

    S. Gayler

  3. Chair of Forest Growth and Yield Science, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany

    T. Rötzer, T. Seifert & H. Pretzsch

  4. Forest and Wood Science, Stellenbosch University, X1, 7602, Matieland, South Africa

    T. Seifert

Authors
  1. E. Priesack
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  2. S. Gayler
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  3. T. Rötzer
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  4. T. Seifert
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  5. H. Pretzsch
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Corresponding author

Correspondence to E. Priesack .

Editor information

Editors and Affiliations

  1. Chair of Ecophysiology of Plants, Technical University of Munich Chair of Ecophysiology of Plants, Freising, Germany

    Rainer Matyssek

  2. Chair of Grassland Science, Technische Universität München, Freising, Germany

    Hans Schnyder

  3. Chair of Phytopathology of Woody Plants, Technische Universität München, Freising, Germany

    Wolfgang Oßwald

  4. Institute of Biochemcial Plant Biology, Helmholtz-Zentrum München, Neuherberg, Germany

    Dieter Ernst

  5. Institute of Soil Ecology, Helmholtz-Zentrum München, Neuherberg, Germany

    Jean Charles Munch

  6. LS Waldwachstumskunde, TU München LS Waldwachstumskunde, Freising, Germany

    Hans Pretzsch

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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

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