Dr Wilfred Otten

Wilfred OttenSenior Lecturer
Biophysics of Soil Ecosystems

E: w.otten@abertay.ac.uk
T: +44 (0)1382 308533

General Information

3D soil structure. Pore structure of soil from a long term ecological field trial: abandonded from agricultural use in 1989 (top) and no-till corn-soybean wheat rotation (with Michigan State University)

Manipulation of the soil microbial populations remains one of the most elusive goals in soil science and microbial technology. A key  barrier in the exploitation of current knowledge of soil biology has been the absence of predictive and explanatory approaches towards soil-plant-microbe interactions. In particular we need to understand the spatial and temporal dynamics of micro-organisms as they grow, die and spread through a biologically divers and physically heterogeneous and changing environment.

My research interests are to apply principles of physics, experimentation and modelling to develop and test predictive and explanatory approaches towards soil ecosystems functioning. My current research focuses on the following questions:

What is the role of soil micro-heterogeneity in soil ecosystem functioning?

Can we apply network theory to explain sudden changes in soil ecosystems?

Can we integrate physical, biological and chemical techniques to characterise soil micro-habitats?

The research program makes a significant contribution to the objectives of Theme 2 of the Scottish Alliance for Geosciences, Environment and Society (SAGES), and to the SIMBIOS research program on emergent properties of soil ecosystems. The program is conducted with various national and international universities and institutions. Current and past collaborations include Stirling University (SEM-EDX; Dr. C. Wilson), Cambridge University (epidemiology and modelling; Prof. C. Gilligan, Dr S. Taraskin; Dr P. Perez-Reche; Dr. F. Nero), University of Sao Paulo, Brazil (network theory; Dr. L. da Costa), INRA, Rennes France (epidemiology; Dr. D. Bailey), SCRI (Biophysics, Dr. P. Hallet), Michigan State University (biotic interactions; Dr. S. Kravchenko), Agricultural University Wageningen (greenhouse gas emission: Dr J. van Groenigen; miss. I. Lubbers), Bioemco , France (multi-scale modelling and organic matter dynamics; Prof. C. Chenu and Dr. N. Nunan).

network and exclusion. Top: a network that has been derived from real soil data and in which biological invasions can be studied. Bottom: a transect through soil with pores that belong to the same 3D connected cluster in gray.

My current research projects include:

  • To define the micro-environment within soil, and relate this to decomposition of organic matter and emission of greenhouse gases (as part of SAGES, Scottish Alliance of Geoscience, Environment and Society.

  • Linking theory and experimentation on biotic interactions in soil

  • The use of network models for invasion and persistence of harmful and beneficial organisms in heterogeneous soil environments (BBSRC, with Cambridge University)

  • Identifying thresholds for invasion and control of soil-borne pathogens in horticultural systems (with INRA and Cambridge University)

  • Quantification of spatial and temporal dynamics of fungi in soil

  • Integrating physical (X-ray CT) and chemical techniques (SEM-EDX) to characterize soil microhabitats (NERC, with Stirling University).

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    Publications

    1. Harris, J.A., Sizmur, T.P., Tilston, E.L., and W. Otten. 2010. Chapter 7: The impact of land-use practices on soil microbes. In: Soil Microbiology and Sustainable Crop Protection. Ed: G. R. Dixon, E.L. Tilston., submitted.
    2. Kravchenko, A, R. Falconer, D. Grinev, and W. Otten. 2010. Fungal colonization in soils of contrasting managements: modelling fungal growth in 3D pore volumes of undisturbed soil samples. Ecological Applications, submitted.
    3. Pajor, R., Falconer, R., Hapca, S., and W. Otten. 2010. Modelling and quantifying the effect of heterogeneity in soil physical conditions on fungal growth. Biogeosciences Discussion, 7, 3477-3501.
    4. Lubbers, I.M., Brussaard, L., Otten, W., and J.W. van Groenigen. 2010. Earthworm-induced N mineralization in fertilized grassland increases both N2O emission and crop N uptake. submitted to EJSS
    5. Baveye, P.C. Laba, M. Otten, W. Grinev, D. Bouckaert, L. Dello Starpaio, P. Goswami, R.R. Hu, Y. Liu, J. Mooney, S. Pajor, R. Sleutel, S. Tarquis, A. Wang, W. Wei Q. and M. Sezgin. 2010.Observer-dependent variability of the thresholding step in the quantitative analysis of soil images and X-ray microtomography data. Geoderma 157 51-63
    6. Perez-Roche, Taraskin, S.N., F., Neri, F.M. Gilligan, C.A. da Costa, F. Vianna, M.P. Otten W. and D. Grinev. 2009. Biological invasion in soil: complex network analysis. IEEE Xplore: Special issue Digital Signal Processing, 1-7. [doi:10.1109/ICDSP.2009.5201098].
    7. Kleczkowski, A., Bailey, D.J. Otten, W. Grose M. and Gilligan, C.A. 2009 Implications of root spatial relationships in young wheat obtained from CT-scanning for an invasion by fungal pathogens. In: ‘Multitrophic interactions in Soil’. Steinberg, C., Edel-Hermann, V., Friberg, H., Alabouvette, C., and A. Tronsmo (Eds). IOBC wprs 42:109-112.
    8. Otten, W. Binnie, K. Young, I.M. Villot. J. and D. Grinev. 2009.Interconnectivity of habitats in soil: combining X-ray micro tomography and thin sectioning to reveal fungal-soil structure interactions. In: ‘Multitrophic interactions in Soil’. Steinberg, C., Edel-Hermann, V., Friberg, H., Alabouvette, C., and A. Tronsmo (Eds). IOBC wprs 42:131-134.
    9. Young, I.M., Crawford, J.W., Nunan, N., Otten, W., and A. Spiers. 2008. Microbial distribution in soils: physics and scaling. Advances in Agronomy, vol. 100: 81-121.
    10. Jeger, M.J., Lamour, A., Gilligan C.A , and W. Otten. 2008. A fungal growth model fitted to carbon limited dynamics of Rhizoctonia solani. New Phytologist 178: 625-633.
    11. Cook, A.R., Otten, W, Marion, G, G.J. Gibson, and C.A. Gilligan. 2007. Estimation of multiple transmission rates for epidemics in heterogeneous populations. PNAS, vol. 104, no. 51:20392-20397
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    12. Otten, W., and C.A. Gilligan 2006. Soil structure and soil-borne diseases: using epidemiological concepts to scale from fungal spread to plant epidemics European Journal of Soil Science, 57:26-37
    13. Gibson, G.J., W. Otten, J.A.N. Filipe, Cook, A., Marion, G., and C.A. Gilligan 2006. Bayesian estimation for percolation models of disease spread in plant populations. Statistics and Computing, 16:391-402..
    14. Otten, W., J.A.N. Filipe, and C.A. Gilligan. 2005 Damping-off epidemics, contact structure, and disease transmission in mixed species populations. Ecology, 86(7)1948-1957.
    15. Otten, W., Bailey, D.J., and Gilligan, C.A. 2004. Empirical evidence of spatial thresholds to control invasion of fungal parasites and saprotrophs. New Phytologist 163:125-132.
    16. Otten, W, D.J. Bailey, J.J. Ludlam, and C.A.Gilligan. 2004. Can incomplete spatial coverage of control measures prevent invasion of fungal parasites? In: Management of plant diseases and arthropod pests by BCA’s and their integration in agricultural systems, S. Michelle all’Adige, Trentino, Italy, Proceedings of the working group meeting, (eds. Y. Elad, I Pertot and A Engkegaard), IOBC wprs Bulletin vol 27(8), pp 251-254.
    17. Otten, W., A. Bates, and C.A. Gilligan. 2004. Analysis of efficacy of a biocontrol agent to reduce the transmission of infection in damping-off epidemics. In: Management of plant diseases and arthropod pests by BCA’s and their integration in agricultural systems, S. Michelle all’Adige, Trentino, Italy, Proceedings of the working group meeting, (eds. Y. Elad, I Pertot and A Engkegaard), IOBC wprs Bulletin vol 27(8), pp 275-280.
    18. Otten, W., Filipe, J.A.N., and Gilligan, C.A. 2004. An empirical method to estimate the effect of soil on the rate for transmission of damping-off disease. New Phytologist 162: 231-238
    19. Otten, W., Harris, K., Young, I.M., Ritz, K., and Gilligan, C.A. 2004. Preferential spread of the pathogenic fungus Rhizoctonia solani through structured soil. Soil Biology & Biochemistry 36: 203-210
    20. Filipe, J.A.N., Otten, W., Gibson, G.J., and Gilligan, C.A. 2004. Inferring spatial dynamics of epidemics from time-series data. Bulletin of Mathematical Biology 66, 373-391.
    21. Otten, W., Filipe, J.A.N., Bailey, D.J., and Gilligan, C.A. 2003. Quantification and analysis of transmission rates for soil-borne epidemics. Ecology 84:3232-3239.
    22. Harris, K., Young, I.M., Gilligan, C.A., Otten, W., and Ritz, K. 2003. Effect of bulk density on the spatial organisation of the fungus Rhizoctonia solani in soil. FEMS Microbial Ecology, 44:45-56.
    23. Harris, K., Crabb, D., Weaver H, Young IM, Gilligan CA, Otten W, Ritz K. 2002. In situ visualisation of fungi in soil thin sections: problems with crystallisation of the fluorochrome FB28 (Calcoflour M2R) and improved staining by SCRI renaissance 2200. Mycological Research 106: 293-297.
    24. Otten, W. Harris, K. Young, I.M., Ritz, K., and Gilligan, C.A. 2002. Soil structure, fungal exploration and consequences for biocontrol. In: Elad, Y., Kohl, J., Shtienberg, D., (eds.), Influence of Abiotic and Biotic factors on Biocontrol Agents. Proceeding of the Seventh Working Group Meeting. IOBC wprs Bulletin vol. 25 (10), 85-88.
    25. Otten, W. Harris, K., Hall, D., Young, I.M., Ritz, K., and Gilligan, C.A. 2002. The heterogeneous soil environment: are there preferential pathways for fungal spread? In: Elad, Y., Kohl, J., Shtienberg, D., (eds.), Influence of Abiotic and Biotic factors on Biocontrol Agents. Proceeding of the Seventh Working Group Meeting. IOBC wprs Bulletin vol 25 (10), 283-286.
    26. Otten W, Gilligan CA, Hall D, Harris K, Ritz K, Young IM. 2001. Soil physics, fungal epidemiology and the spread of Rhizoctonia solani. New Phytologist 151:459-468.
    27. Otten W., Watts CW, Longstaff, D. 2000. Method to quantify short-term dynamics in carbon dioxide emission following controlled soil deformation. Soil Science Society of America Journal 64:1740-1748.
    28. Bailey DJ, Otten W, Gilligan CA. 2000. Saprotrophic invasion by the soil-borne fungal plant pathogen Rhizoctonia solani and percolation thresholds. New Phytologist 146: 535-544.
    29. Otten W,Gilligan CA, Watts C, Dexter AR, Hall D. 1999. Continuity of air-filled pores and invasion thresholds for a soil-borne fungal plant pathogen, Rhizoctonia solani. Soil Biology and Biochemistry 31: 1803-1810.
    30. Otten W, Raats PAC, Baas R, Challa H, Kabat P. 1999. Spatial and temporal dynamics of water in the root zone environment of potted plants on a flooded bench fertigation system. Neth. Journ. Agric. Science 47:1-15
    31. Otten W, Raats PAC, Kabat P. 1999. Hydraulic properties of root zone substrates used in greenhouse horticulture. In: M. Th van Genuchten, F. Leij and L. Wu (eds.) Proceedings of the International Workshop on Hydraulic Properties of Unsaturated Porous Media. Riverside, California. p. 477-488.
    32. Otten W. and Gilligan CA. 1998. Effect of physical conditions on the spatial and temporal dynamics of the soil-borne fungal pathogen Rhizoctonia solani. New Phytologist 138: 629-637.
    33. Otten W, Gilligan CA, Thornton CR. 1997. Quantification of Fungal Antigens in Soil with a Monoclonal Antibody-Based ELISA: Analysis and Reduction of Soil-Specific Bias. Phytopathology 87: 730-736.
    34. Otten, W. 1994. Dynamics of Water and Nutrients for Potted Plants Induced by Flooded Bench Fertigation: Experiments and Simulation. Thesis, Agricultural University Wageningen, with summary in Dutch. 115p.

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