Professor Wilfred Otten
Chair of Biophysics of Soil Ecosystems
Director of The SIMBIOS Centre
T: +44 (0)1382 308533
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.
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
What is the role of soil micro-heterogeneity in soil ecosystem functioning?
we apply network theory to explain sudden changes in soil ecosystems?<
we integrate physical, biological and chemical techniques to
characterise soil micro-habitats?
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. F. Nero), JHI ( Dr T. Velentine and Dr L. Dupuy). University of Aberdeen (Dr P.
Perez-Reche);University of Sao Paulo, Brazil (network
theory; Dr. L. da Costa), INRA, Rennes France (epidemiology; Dr. D.
Bailey), University of Aberdeen (Biophysics, Dr. P. Hallet), Michigan State University
(biotic interactions; Dr. S. Kravchenko), Agricultural University
Wageningen (greenhouse gas emission: Dr J. van Groenigen; miss. I.
(multi-scale modelling and organic matter dynamics; Prof. C. Chenu and
Dr. N. Nunan).
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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- Palfreyman,J, Otten, W., and P. Baveye. (**). Critical reflection on a suitable framework and policies to promote interdisciplinary research in universities and research centres. Research Policy. Submitted.
- Hallet, P. D, Karim, K. H., Bengough, G., and W. Otten.(**) Biophysics of the vadose zone: from reality to model systems and back again. Vadoze Zone, submitted
- Poggi, S., F.M. Neri, V. Deytieux, A. Bates, W. Otten, C.A. Gilligan, D.J. Bailey. 2013. Percolation-based risk index for pathogen invasion: application to soil-borne diseas in propagation systems. Phytopathology, accepted.
- Houston, A.N., S. Schmidt, W. Otten, P. Baveye, S. Hapca. 2013. Effect of scanning and image reconstruction settings in X-ray computed tomography on soil image quality and segmentation performance. Geoderma, 207-208 (2013) 154–165.
- Houston, A.N. W. Otten, P. baveye, and S. Hapca. 2013. Thresholding of Computed Tomography Images of Heterogeneous Porous Media by Adaptive-Window Indicator Kriging. Computers and Geosciences. Doi: 10.1016/j.cageo.2012.11.016.
- Juarez, S., N. Nunan, V. Pouteau, A. Duday, S. Schmidt, S. Hapca, R. Falconer, W. Otten, C. Chenu. 2013. To what extent is microbial decomposition of organic carbon resistant to experimental modifications of soil structure? European Journal of Soil Biology, accepted.
- Hapca, S, M, Houston, A. N., Otten, W., and P. Baveye. 2013. New objective segmentation method based on minimizing locally the intra-class variance of grayscale images. Vadoze zone, doi:10.2136/vzj2012.0172.
- Wellington, EMH., Boxall, A, Cross, P., Feil, E., Gaze, W, Hawkey, P, Johnson-Rollings, A.S., Jones, Lee, N.M., Otten, W., D, Thomas, C, and A. P. Williams. 2013. The role of the natural environment in the emergence of antibiotic resistance in Gram-negative bacteria. The Lancet ID, vol 1: 155-65.
- Cazelles, K., W. Otten, P.C. Baveye, and R.E. Falconer. 2013. Soil fungal dynamics: Parametrization and sensitivity analysis of modelled physiological processes, soil architecture and carbon distribution. Ecological Modelling. in press.
- Perez-Reche, F.J., S.N. Taraskin, W. Otten, M.P. Viana, L. da F. Costa, and C.A. Gilligan. 2012. Prominent effect of soil network heterogeneity on microbial invasion. 2012. Physical Review Letters, 109, 098102.
- Downie; H., N. Holden, W. Otten, A. Spiers, T. Valentine; L.X. Dupuy. 2012. Transparent soil sheds light on root bacteria interactions. PLoS ONE, 7(9): e44276.
- Otten, W, R. Pajor, S. Schmidt, P. Baveye, R. Hague and R. Falconer. 2012. Combining X-ray CT and 3D printing technology to produce microcosms with replicable, complex pore geometries. Soil Biology and Biochemistry. 51: 53-55.
- Schmidt, S., Bengough, A.G., Gregory, P.J., Grinev, D.V., and W. Otten. 2012. Estimating root-soil contact from 3-D X-ray microtomography. Eur. Journal. Soil Science. DOI: 10.1111/j.1365-2389.2012.0148
- Falconer, R., Houston, A., Otten, W., and P. Baveye. 2012. Emergent behaviour of fungal dynamics: influence of soil architecture and moisture distribution. Soil Science, 177(2):111-119.
- Ludlam, J., Gibson, G., Otten, W., and Gilligan, C.A. 2012. Applications of percolation theory to fungal spread with synergy. Journal Royal Society Interface: doi: 10.1098/rsif.2011.0506.
- Baveye, P., Range, D., Otten, W., Jacobson, A.R., and F.O.Camargo. 2011. From Dust Bowl to Dust Bowl: Soils are still very much a frontier of science. Anniversary paper Soil Science Society of America Journal, vol. 75: no 6. 2037- 2048. Also published in CSA News, December 2011: 4-11.
- De Bartolo, S., Otten, W., Cheng, Q., and A.M. Tarquis. 2011. Modelling soil system: complexity under your feet. Preface. Biogeosciences, 8, 3139 – 3142.
- Neri F. M., Bates, A. Füchtbauer, W. S., Pérez-Reche, F. J., Taraskin, S. N., Otten, W., Bailey, D. J. Gilligan, C. A. 2011. The effect of heterogeneity on invasion in spatial epidemics: from theory to experimental evidence in a model system. Computational Biology. Vol 7. issue 9. e1002174. doi:10.1371/journal.pcbi.1002174
- Hapca S.M, Wang, Z.X., Otten, W., Wilson, C, Baveye, P.C. 2011. Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils. Geoderma vol 164, issue 3-4 pp 146-154. doi: 10.1016/ j.geoderma. 2011.05.018.
- Kravchenko, A, R. Falconer, D. Grinev, and W. Otten. 2011. Fungal colonization in soils of contrasting managements: modelling fungal growth in 3D pore volumes of undisturbed soil samples. Ecological Applications, Vol 21.4 pp: 1202-1210. doi:10.1890/10-0525.1.
- Tilston, E.L. Sizmur, T.P., W. Otten, and J.A. Harris. 2010. Chapter 7: The impact of land-use practices on soil microbes. In: Dixon and Tilston (eds.) Soil Microbiology and Sustainable Crop Production, DOI 10.1007/978-90-481-9479-7_7. Springer Science + Business Media B.V.
- 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, 7, 3731-3740.
- Koza, A. Moshynets, E, Otten, W. And A. Spiers.2010. Environmental modification and niche construction: Developing O2 gradients drive the evolution of the Wrinkly Spreader. ISME, ISME J 5: 665-673; advance online publication, October 21, 2010; doi:10.1038/ismej.2010.156.
- Lin, H., Fluhler, H., Otten, W. and H. Vogel. 2010. Soil architecture and preferential flow. Editorial Journal of Hydrology. Editorial Journal of Hydrology. 393: 1-2.
- Kravchenko A, Falconer R, Grinev D, Otten W. 2010. Effect of soil management on pore geometry and the implication for fungal invasion and interactions. In: Gilkes RJ, Prakongkep N, editors. Proceedings of the 19th World Congress of Soil Science; Soil Solutions for a Changing World; ISBN 978-0-646-53783-2; Published on DVD; http://www.iuss.org; 2010 Aug 1-6. Brisbane, Australia: IUSS; 2010, pp. 33- 36
- Otten W, Grinev D, Baveye P, Wang Z, Hapca S, Wilson C. 2010. Integrating physical and chemical techniques to characterise soil microsites. In: Gilkes RJ, Prakongkep N, editors. Proceedings of the 19th World Congress of Soil Science; Soil Solutions for a Changing World; ISBN 978-0-646-53783-2; Published on DVD; http://www.iuss.org; 2010 Aug 1-6. Brisbane, Australia: IUSS; 2010, pp. 60- 63
- Otten W, Grinev D, Perez-Reche F, Neri F, da Costa L, Biana M, Gilligan C, Taraskin S. 2010. Resilience of soil to biological invasion: analysis of spread on networks. In: Gilkes RJ, Prakongkep N, editors. Proceedings of the 19th World Congress of Soil Science; Soil Solutions for a Changing World; ISBN 978-0-646-53783-2; Published on DVD; http://www.iuss.org; 2010 Aug 1-6. Brisbane, Australia: IUSS; 2010, pp. 68- 71.
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. Eur. J. Soil Science. Vol 62. Issue 1: 152-161. DOI: 10.1111/j.1365-2389.2010.01313.x
- 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.
variability of the thresholding step in the quantitative analysis of
soil images and X-ray microtomography data. Geoderma 157 51-63
- 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.
- 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
- 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
- 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.
- 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.
- 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>
- 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
- 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..
- Otten, W., J.A.N. Filipe, and C.A. Gilligan. 2005 Damping-off epidemics, contact structure, and disease transmission in mixed species populations. Ecology,
- 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.
- 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.
- 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.
- 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
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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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