Contact Professor Wilfred Otten
Areas of expertise
- Digital Agriculture
- Soil Resources
Wilfred Otten joined Cranfield University in May 2016 as Professor of Soil Biophysics. Before that he worked 9 years at Abertay University in Dundee as Chair of Biophysics of Soil Ecosystems and co-Director of the Scottish Informatics Mathematics Biology and Statistics Centre where he developed innovative methods to characterize soil structure. Prior to that he worked for 16 years in the Epidemiology and Modeling Group of the Department of Plant Sciences at Cambridge University working on invasion and persistence of soil borne fungal plant diseases. He has a degree in Agricultural Engineering with special reference to Soil Science and Fertilizer Use (Wageningen University, The Netherlands) and a PhD degree in Horticultural Sciences, focusing on closed fertigation systems (Wageningen University, The Netherlands). He was the President of the British Society of Soil Science (2017-2018), and is a Fellow of the Institute of Soil Science (F.I. Soil Sci.).
Professor Otten has a general research interest in physical, biological and chemical processes in soil. His current and past research has equipped him with multidisciplinary expertise in soil physics, soil chemistry, soil microbiology, epidemiology and mathematical, modelling. He is expert in the characterisation of micro habitats in soil. Research techniques include soil physical methods including the use of X-ray CT to characterise internal pore geometries and root growth. He applies this expertise to develop a quantitative, integrative and predictive approach that forwards our understanding of soil processes to enable sustainable management. A selection of recent projects includes:
FUSED - Functionality of Urban Soils supporting Ecosystem service Delivery. Sponsor: NERC (2019-2022).
This project in partnership with the University of Essex will examine the links between the physical and chemical structure of urban soil, the biodiversity it contains, the ecosystem processes and functions this supports and the delivery of four key ecosystem services (nutrient cycling, carbon sequestration, waste detoxification, and primary productivity). To achieve this we will focus on existing gradients of urbanisation in SE England which provides the full catalogue of urban soil types.
Resilience of belowground fungal communities: a mechanistic and trait based approach. Sponsor: NERC (2018-2019).
Soil structure holds the key to life in soil, regulates many ecosystem services and ultimately underpins sustainable life on Earth. This project integrates biological, physical and chemical processes into a theoretical framework that predicts biodiversity and links this to ecosystem functioning, exemplified by fungi and evolution of CO2, respectively. This framework will provide new insights how resilient soils are in maintaining diversity and functioning and what can be done to enhance this resilience.
Using roots to bioengineer soils. Sponsor: BBSRC 2018-2021.
Cover crops are a way for UK growers to improve soil health by maintaining minimum soil cover, thus minimising the land management required to limit erosion and maintain organic matter levels. They are fast-growing species, planted between two cash crops, which have the ability to boost soil health and reduce the negative impact of agro-management on the environment. In this BBSRC funded project we ask the question how best to exploit root traits of cover crops to improve soil health. A series of root properties (e.g. rooting depth, root hair density) will be carefully determined for 7 cover crops, and we use a DNA technique, qPCR, to determine the proportions of root biomass of each species within a plant community to determine which mixture of cover crops offers most benefits to ecosystem services.
Phenotyping and soil health to address industrial challenges. Sponsors: IUK and industry (2021-2022).
Using our cutting edge Agri-Tech funded Phenotyping and Soil Health Facilities I work directly with stakeholders to develop and test innovative technologies to improve soil and crop health. The assets are able to control the soil and weather variability that often complicates the interpretation of field trial results and offer unique pilot scale facilities to industrial partners. Projects range from using sensors to detect the early onset of plant diseases; testing the use of ultra-fine nano-bubbles in agriculture to reduce inputs; reducing variability in dissipation studies; and optimising soil profiles to redesign landscapes.
Research funding has been obtained from a variety of sources including BBSRC, NERC, EPSRC, IUK, ANR and industry.
Articles In Journals
- Juyal A, Otten W, Baveye PC & Eickhorst T (2020) Influence of soil structure on the spread of Pseudomonas fluorescens in soil at microscale, European Journal of Soil Science, 72 (1) 141-153. Dataset/s: 10.17862/cranfield.rd.11854239
- Portell X, Verheecke-Vaessen C, Torrelles-Ràfales R, Medina A, Otten W, Magan N & García-Cela E (2020) Three-dimensional study of F. graminearum colonisation of stored wheat: post-harvest growth patterns, dry matter losses and mycotoxin contamination, Microorganisms, 8 (8) Article No. 1170. Dataset/s: 10.17862/cranfield.rd.12771347
- McCloskey CS, Otten W, Paterson E, Ingram B & Kirk GJD (2020) A field system for measuring plant and soil carbon fluxes using stable isotope methods, European Journal of Soil Science, Available online 21 June 2020.
- Masters-Clark E, Shone E, Paradelo M, Hirsch PR, Clark IM, Otten W, Brennan F & Mauchline TH (2020) Development of a defined compost system for the study of plant-microbe interactions, Scientific Reports, 10 (1) Article No. 7521.
- Juyal A, Otten W, Falconer R, Hapca S, Schmidt H, Baveye PC & Eickhorst T (2019) Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales, Geoderma, 334 (January) 165-174. Dataset/s: 10.17862/cranfield.rd.6860717
- Kravchenko A, Otten W, Garnier P, Pot V & Baveye PC (2019) Soil aggregates as biogeochemical reactors: Not a way forward in the research on soil‐atmosphere exchange of greenhouse gases, Global Change Biology, 25 (7) 2205-2208.
- Darmovzalova J, Boghi A, Otten W, Eades IJ, Roose T & Kirk GJD (2019) Uranium diffusion and time-dependent adsorption–desorption in soil: a model and experimental testing of the model, European Journal of Soil Science, 71 (March) 215-225. Dataset/s: 10.17862/cranfield.rd.7093574/
- Otten W, Haygarth PM & Baggs EM (2018) A profile of 70 years of soil research [Editorial], European Journal of Soil Science, 69 (1) 21-22.
- Soufan R, Delaunay Y, Vieublé L, Shor L, Garnier P, Otten W & Baveye PC (2018) Pore-scale monitoring of the effect of microarchitecture on fungal growth in a two-dimensional soil-like micromodel, Frontiers in Environmental Science, 6 (July) Article No. 68.
- Juyal A, Eickhorst T, Falconer R, Baveye PC, Spiers A & Otten W (2018) Control of pore geometry in soil microcosms and its effect on the growth and spread of Pseudomonas and Bacillus sp., Frontiers in Environmental Science, 6 Article No. 73.
- Portell X, Pot V, Garnier P, Otten W & Baveye P (2018) Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: Insights from computer simulations, Frontiers in Microbiology, 9 Article No. 1583. Dataset/s: 10.17862/cranfield.rd.6744158
- Baveye PC, Otten W, Kravchenko A, Balseiro Romero M, Beckers E, Chalhoub M, Darnault C, Eickhorst T, Garnier P, Hapca S, Kiranyaz S, Monga O, Mueller CW, Nunan N, Pot V, Schlüter S, Schmidt H & Vogel HJ (2018) Emergent properties of microbial activity in heterogeneous soil microenvironments: different research approaches are slowly converging, yet major challenges remain, Frontiers in Microbiology, 9 (August) Article No. 1929.
- Houston AN, Otten W, Falconer R, Monga O, Baveye PC & Hapca SM (2017) Quantification of the pore size distribution of soils: assessment of existing software using tomographic and synthetic 3D images, Geoderma, 299 (August) 73-82.
- Roose T, Keyes S, Daly K, Carminati A, Otten W, Vetterlein D & Peth S (2016) Challenges in imaging and predictive modeling of rhizosphere processes, Plant and Soil, 407 (1-2) 9-38.
- Schnee LS, Knauth S, Hapca S, Otten W & Eickhorst T (2016) Analysis of physical pore space characteristics of two pyrolytic biochars and potential as microhabitat, Plant and Soil, 408 (1-2) 357-368.
- Falconer R, Battaia G, Schmidt S, Baveye P, Chenu C & Otten W (2015) Microscale heterogeneity explains experimental variability and non-linearity in soil organic matter mineralisation, PLoS ONE, 10 (5) Article No. e0123774.
- Hapca S, Baveye P, Wilson C, Lark R & Otten W (2015) Three-dimensional mapping of soil chemical characteristics at micrometric scale by combining 2D SEM-EDX data and 3D X-Ray CT images, PLoS ONE, 10 (9) Article No. e0137205.
- Falconer R, Otten W & White N (2015) Toward modeling the resistance and resilience of "Below-ground" fungal communities: a mechanistic and trait-based approach, Advances in Applied Microbiology, 93 1-44.
- Downie H, Adu M, Schmidt S, Otten W, Dupuy L, White P & Valentine T (2015) Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis, Plant, Cell and Environment, 38 (7) 1213-1232.
- Archer N, Otten W, Schmidt S, Bengough A, Shah N & Bonell M (2015) Rainfall infiltration and soil hydrological characteristics below ancient forest, planted forest and grassland in a temperate northern climate, Ecohydrology, 9 (4).
- Monga O, Garnier P, Pot V, Coucheney E, Nunan N, Otten W & Chenu C (2014) Simulating microbial degradation of organic matter in a simple porous system using the 3-D diffusion-based model MOSAIC, Biogeosciences, 11 (8) 2201-2209.
- Downie H, Valentine T, Otten W, Spiers A & Dupuy L (2014) Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo, Plant Signaling and Behavior, 9 (10).
- Baveye P, Palfreyman J & Otten W (2014) Research efforts involving several disciplines: Adherence to a clear nomenclature is needed, Water, Air, and Soil Pollution, 225 (6).
- Houston A, Otten W, Baveye P & Hapca S (2013) Adaptive-window indicator kriging: A thresholding method for computed tomography images of porous media, Computers and Geosciences, 54 239-248.
- Hallett PD, Karim KH, Bengough AG & Otten W (2013) Biophysics of the vadose zone: From reality to model systems and back again, Vadose Zone Journal, 12 (4).
- Houston A, Schmidt S, Tarquis A, Otten W, Baveye P & Hapca S (2013) Effect of scanning and image reconstruction settings in X-ray computed microtomography on quality and segmentation of 3D soil images, Geoderma, 207-208 (1) 154-165.
- Hapca S, Houston A, Otten W & Baveye P (2013) New local thresholding method for soil images by minimizing grayscale intra-class variance, Vadose Zone Journal, 12 (3).
- Poggi S, Neri F, Deytieux V, Bates A, Otten W, Gilligan C & Bailey D (2013) Percolation-based risk index for pathogen invasion: Application to soilborne disease in propagation systems, Phytopathology, 103 (10) 1012-1019.
- Cazelles K, Otten W, Baveye P & Falconer R (2013) Soil fungal dynamics: Parameterisation and sensitivity analysis of modelled physiological processes, soil architecture and carbon distribution, Ecological Modelling, 248 165-173.
- Wellington E, Boxall A, Cross P, Feil E, Gaze W, Hawkey P, Johnson-Rollings A, Jones D, Lee N, Otten W, Thomas C & Williams A (2013) The role of the natural environment in the emergence of antibiotic resistance in Gram-negative bacteria, Lancet Infectious Diseases, 13 (2) 155-165.
- Juarez S, Nunan N, Duday A, Pouteau V, Schmidt S, Hapca S, Falconer R, Otten W & Chenu C (2013) Effects of different soil structures on the decomposition of native and added organic carbon, European Journal of Soil Biology, 58 81-90.
- Schmidt S, Bengough A, Gregory P, Grinev D & Otten W (2012) Estimating root-soil contact from 3D X-ray microtomographs, European Journal of Soil Science, 63 (6) 776-786.
- Downie H, Holden N, Otten W, Spiers A, Valentine T & Dupuy L (2012) Transparent soil for imaging the rhizosphere, PLoS ONE, 7 (9).
- Falconer RE, Houston AN, Otten W & Baveye PC (2012) Emergent behavior of soil fungal dynamics: Influence of soil architecture and water distribution, Soil Science, 177 (2) 111-119.
- Perez-Reche FJ, Taraskin SN, Otten W, Viana MP, Costa L & Gilligan CA (2012) Prominent effect of soil network heterogeneity on microbial invasion, Physical Review Letters, 109 (9).
- Ludlam JJ, Gibson GJ, Otten W & Gilligan CA (2012) Applications of percolation theory to fungal spread with synergy, Interface, 9 (70) 949-956.
- Otten W, Pajor R, Schmidt S, Baveye PC, Hague R & Falconer RE (2012) Combining X-ray CT and 3D printing technology to produce microcosms with replicable, complex pore geometries, Soil Biology and Biochemistry, 51 53-55.
- Neri FM, Bates A, Fuchtbauer WS, Perez-Reche FJ, Taraskin SN, Otten W, Bailey DJ & Gilligan CA (2011) The effect of heterogeneity on invasion in spatial epidemics: From theory to experimental evidence in a model system, PLoS Computational Biology, 7 (9).
- Hapca SM, Wang ZX, Otten W, Wilson C & Baveye PC (2011) Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils, Geoderma, 164 (3-4) 146-154.
- Lubbers IM, Brussaard L, Otten W & Van Groenigen JW (2011) Earthworm-induced N mineralization in fertilized grassland increases both N2O emission and crop-N uptake, European Journal of Soil Science, 62 (1) 152-161.
- Koza A, Moshynets O, Otten W & Spiers AJ (2011) Environmental modification and niche construction: Developing O2 gradients drive the evolution of the Wrinkly Spreader, ISME Journal, 5 (4) 665-673.
- Baveye PC, Rangel D, Jacobson AR, Laba M, Darnault C, Otten W, Radulovich R & Camargo FAO (2011) From dust bowl to dust bowl: Soils are still very much a frontier of science, Soil Science Society of America Journal, 75 (6) 2037-2048.
- Kravchenko A, Falconer RE, Grinev D & Otten W (2011) Fungal colonization in soils with different management histories: Modeling growth in three-dimensional pore volumes, Ecological Applications, 21 (4) 1202-1210.
- De Bartolo S, Otten W, Cheng Q & Tarquis AM (2011) Preface "Modeling soil system: Complexity under your feet", Biogeosciences, 8 (11) 3139-3142.
- Lin H, Fluhler H, Otten W & Vogel HJ (2010) Editorial. Soil architecture and preferential flow across scales, Journal of Hydrology, 393 (1-2) 1-2.
- Pajor R, Falconer R, Hapca S & Otten W (2010) Modelling and quantifying the effect of heterogeneity in soil physical conditions on fungal growth, Biogeosciences, 7 (11) 3731-3740.
- Baveye PC, Laba M, Otten W, Bouckaert L, Dello Sterpaio P, Goswami RR, Grinev D, Houston A, Hu Y, Liu J, Mooney S, Pajor R, Sleutel S, Tarquis A, Wang W, Wei Q & Sezgin M (2010) Observer-dependent variability of the thresholding step in the quantitative analysis of soil images and X-ray microtomography data, Geoderma, 157 (1-2) 51-63.
- Young IM, Crawford JW, Nunan N, Otten W & Spiers A (2008) Microbial distribution in soils: Physics and scaling, Advances in Agronomy, 100 81-121.
- Jeger MJ, Lamour A, Gilligan CA & Otten W (2008) A fungal growth model fitted to carbon-limited dynamics of Rhizoctonia solani, New Phytologist, 178 (3) 625-633.
- Cook AR, Otten W, Marion G, Gibson GJ & Gilligan CA (2007) Estimation of multiple transmission rates for epidemics in heterogeneous populations, Proceedings of the National Academy of Sciences, 104 (51) 20392-20397.
- Gibson GJ, Otten W, Filipe JAN, Cook A, Marion G & Gilligan CA (2006) Bayesian estimation for percolation models of disease spread in plant populations, Statistics and Computing, 16 (4) 391-402.
- Otten W & Gilligan CA (2006) Soil structure and soil-borne diseases: using epidemiological concepts to scale from fungal spread to plant epidemics, European Journal of Soil Science, 57 (1) 26-37.
- Otten W, Filipe JAN & Gilligan CA (2005) Damping-off epidemics, contact structure, and disease transmission in mixed-species populations, Ecology, 86 (7) 1948-1957.
- Otten W, Filipe JAN & Gilligan CA (2004) An empirical method to estimate the effect of soil on the rate for transmission of damping-off disease, New Phytologist, 162 (1) 231-238.
- Otten W, Bailey DJ & Gilligan CA (2004) Empirical evidence of spatial thresholds to control invasion of fungal parasites and saprotrophs, New Phytologist, 163 (1) 125-132.
- Filipe JAN, Otten W, Gibson GJ & Gilligan CA (2004) Inferring the dynamics of a spatial epidemic from time-series data, Bulletin of Mathematical Biology, 66 (2) 373-391.
- Otten W, Harris K, Young IM, Ritz K & Gilligan CA (2004) Preferential spread of the pathogenic fungus Rhizoctonia solani through structured soil, Soil Biology and Biochemistry, 36 (2) 203-210.
- Harris K, Young IM, Gilligan CA, Otten W & Ritz K (2003) Effect of bulk density on the spatial organisation of the fungus Rhizoctonia solani in soil., FEMS Microbiology Ecology, 44 (1) 45-56.
- Otten W, Filipe JAN, Bailey DJ & Gilligan CA (2003) Quantification and analysis of transmission rates for soilborne epidemics, Ecology, 84 (12) 3232-3239.
- Harris K, Crabb D, Young IM, Weaver H, Gilligan CA, Otten W & Ritz K (2002) In situ visualisation of fungi in soil thin sections: problems with crystallisation of the fluorochrome FB 28 (Calcofluor M2R) and improved staining by SCRI Renaissance 2200., Mycological Research, 106 (Part 3) 293-297.
- 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 (2) 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 (5) 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 (3) 535-544.
- Otten W, Gilligan CA, Watts CW, 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 (13) 1803-1810.
- Otten W & Gilligan CA (1998) Effect of physical conditions on the spatial and temporal dynamics of the soil-borne fungal pathogen Rhizoctonia solani, New Phytologist, 138 (4) 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 (7) 730-736.
- Falconer RE, Houston AN, Portell X & Otten O (2019) Hardware acceleration of reaction-diffusion systems: A guide to optimisation of pattern formation algorithms using OpenACC. In: 2019 Spring Simulation Conference (SpringSim 19), Tucson, 29 April - 2 May 2019.
- Otten W, Harris K, Hall D, Young IM, Ritz K & Gilligan CA (2003) Impact of structural heterogeneity on growth of Rhizoctonia solani in soil.. In: BES Soil Biodiversity and Ecosystem Function,, Lancaster, U.K., 1 January 2003.
- Otten W, Harris K, Hall D, Young IM, Ritz K & Gilligan CA (2002) The heterogeneous soil environment: are there preferential pathways for fungal spread?. In: Influence of Abiotic and Biotic Factors on Biocontrol Agents: 7th Meeting of the IOBC/OILB Working Group on Biological Control of Fungal and Bacterial Plant Pathogens, Kusadasi, Turkey, 1 January 2002.
- Otten W, Harris K, Young IM, Ritz K & Gilligan CA (2002) Soil structure, fungal exploration and consequences for biocontrol. In: Influence of Abiotic and Biotic Factors on Biocontrol Agents: 7th Meeting of the IOBC/OILB Working Group on Biological Control of Fungal and Bacterial Plant Pathogens, Kusadasi, Turkey, 1 January 2002.
- Harris K, Ritz K, Young IM, Gilligan CA & Otten W (2001) Effect of soil bulk density on growth and spatial organisation of pathogenic fungi. In: ISME 9 Interactions in the Microbial World, Amsterdam, Netherlands, 1 January 2001.