1. General Model Information

Name: Tree Root Architecture and Microbial Ecology Simulation

Acronym: RS2

Main medium: terrestrial
Main subject: population dynamics, forestry, biogeochemistry
Organization level: Organ, Population, Biocoenosis
Type of model: individual-based, not specified (3D)
Main application:
Keywords: tree, root, architecture, morphology, root map, microbial populations, microbial infections, simulation, spatially explicit, object-oriented


Terry N Brown

NRRI, 5013 Miller Trunk Hwy, Duluth, MN 55812, USA
phone: +218 720 4345
fax: +218 720 4219
email: tbrown@sage.nrri.umn.edu

WWW: http://beaver.nrri.umn.edu/~tbrown


Terry N Brown


A simulation scheme to model three-dimensional plant root architecture and the location, growth and interaction of associated microbial communities has been developed. The scheme expands on previous root architecture models by using the mature root system morphology observed in the field as a spatial envelope to model the system's temporal development. The three-dimensional representation allows a uniquely detailed treatment of the spatial development of microbial populations and their interactions with the root system and with each other. Root morphology and microbial populations are described by different types of ``node'', each node records a position in three-dimensional space and other details specific to the feature it represents. For example, ``Branch'' nodes indicate the start of a higher order root, and ``Fungal'' nodes increase or decrease the level of a fungal population on a root's surface. A large number of probability density functions are required to produce the list of nodes that describe each root. A four-dimensional matrix is used as a convenient abstraction for these functions, the dimensions represent tree type, root order, a ``feature'' such as branching or microbial infection, and an ``attribute'' such as length or lifespan. Algorithms for the generation and manipulation of the node lists are given. Specific implementation issues, such as rapid location of roots within the area potentially affected by disease lesion, and visualisation of the simulated root system, are also addressed. Validation of models of complex, irregular entities such as plant root systems is difficult, some techniques, including an objective root distribution index, have been developed and applied in this research. The simulation software includes extensions to allow input and editing of observed root system architectures to simplify the extraction of relevant parameters from such observations.

II. Technical Information

II.1 Executables:

Operating System(s): any system running GNU-C++

II.2 Source-code:

Programming Language(s): C++ , please contact author

II.3 Manuals:


II.4 Data:

Long description of root system architecture is required Examples included

III. Mathematical Information

III.1 Mathematics


III.2 Quantities

III.2.1 Input

Long description of root system architecture is required Examples included

III.2.2 Output

Sequence of infection maps, plant root maps

IV. References

see here

V. Further information in the World-Wide-Web

VI. Additional remarks

Last review of this document by: Terry Brown Fri Oct 23 22:14:20 1998
Status of the document: Contributed by Terry Brown
last modified by Tobias Gabele Wed Aug 21 21:44:48 CEST 2002

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