CV page

Johannes Koestel

Johannes Koestel


Research Interests

Soil is one of the natural resources that is crucial for the existence of a large number of microbial and the vast majority of higher terrestrial life forms, including humanity. Yet, we know surprisingly little about the details of soil functioning. Among the reasons for our lack of knowledge, I want to highlight three: i) soil systems are highly complex, ii) soil systems are highly diverse and they are opaque and iii) large scale observations emerge from small scale processes. Addressing these will be among the main challenges for the future.

i) The longer I am working in this field of research, the more I am becoming convinced that soil physical, chemical and biological processes are all intertwined and cannot be not be fully understood if investigated in an isolated fashion. I am therefore envisioning a future in which researchers from all soil research disciplines are working closely together, providing the expertise needed to recognize all important aspects in a respective research project. 

A white root, illustration.

Figure 1: Displacement of soil matrix due to the radial growth of a dandelion root (Koestel and Schlüter, Geoderma, 2019).

ii) I furthermore hold it for self-evident that a more detailed understanding of soil systems requires more detailed measurements. From such measurements, theories may be validated or new relationships may be derived. One fundamental property of soil systems is that they feature highly complex and diverse, hierarchically organized pore networks. These networks and their evolution are fundamental for all, soil physics, chemistry, biology and ecology. As the soil building materials, i.e. minerals and dead and living organic matter are opaque, these structures are only visible upon destruction or with help of 3-D non-invasive imaging methods. I believe that such imaging methods are required for understanding the creation and evolution of soil pore structure as well as its role in defining soil properties or constraining processes in soil. I am especially advocating combining complementary imaging and point measurement methods.

Blue and red lines, illustration.iii) The detailed knowledge that is obtained at the pore scale needs to be translated to larger scales where the knowledge is most needed by stakeholders. By the rule of thumb, level of detail is lost with increasing scale of measurement. I believe that combined measurements at different scales will be the winning strategy for finding the required scaling and transfer relationships. I likewise am convinced that machine learning and data mining will become more and more important to process the ever increasing amount of collected data.

To the left: Figure 2: Macropore network in a ‘water-saturated’ soil. Blue colours indicate water, red colors air filled pores. The size of the soil block is approximately 3 × 3 × 6 cm.

Ongoing Projects

As Principal Investigator
As co-supervisor
  • Quantifying macropore flow by X-ray tomography to improve model predictions of contaminant leaching in soil (PhD project of Anna Hess)
  • Effects of soil organic carbon fractions on soil structure and preferential solute transport (PhD project of Jumpei Fukumasu)
As co-investigator
  • A combined application of zymography and X-ray imaging to locate regions of high microbial activity in soil (PI: Alexandra Kravchenko)
  • Imaging freezing-thawing processes in porous media using MRI (PI: Michal Snehota)
  • Long-Term Soil Structure Observatory for Monitoring Post-Compaction Evolution of Soil Structure (PI: Thomas Keller)
  • A better understanding and modelling of soil structure effects on the regulation of C mineralization by soil moisture(PI: Elsa Coucheney)
  • Environmental impact of gas ebullition in fiberbank sediments – flux measurements and X-ray tomography for improved remediation strategies (PI: Anna-Karin Dahlberg)
  • Vitmossor (Sphagnum) som klimatvänligt växtsubstrat (PI: Sabine Jordan)
  • Soil structure and soil degradation: improved model tools to meet sustainable development goals under climate and land use change (PI: Nicholas Jarvis)
  • Greenhouse gas emissions in dependence to soil macropore network structures (PhD project of Katrin Rychel)
  • The effect of capillary trapping of air on quasi-saturated hydraulic conductivity of sands (PhD project of Tomáš Princ)


since 2017   
Associate Senior Lecturer, Institute of Soil and Environment, SLU, Uppsala, Sweden.

2012 – 2016 
Forskarassistent, Institute of Soil and Environment, SLU, Uppsala, Sweden.

2009 – 2011 
Postdoc, Institute of Soil and Environment, SLU, Uppsala, Sweden. Research group of Nicholas Jarvis.

PhD in Agricultural Sciences, Forschungszentrum Jülich (Agrosphere) and the Rheinische Friedrich-Wilhelms Universität Bonn, Germany. “Quantitative characterization of solute transport processes in an undisturbed unsaturated soil by means of electrical resistivity tomography (ERT)”, Main supervisor: Harry Vereecken.

German Diploma (corresponds to Master) in Hydrology, Albert-Ludwigs University Freiburg, Germany.


Peer-reviewed publications in international scientific journals

Koestel, J., Schlüter, S., 2019. Quantification of the structure evolution in a garden soil over the course of two years. Geoderma 338, 597-609.

Hellner, Q., Koestel, J., Ulén, B., Larsbo, M., 2018. Effects of tillage and liming on macropore networks derived from X-ray tomography images of a silty clay soil. Soil Use Manage. 34(2), 197-205.

Koestel, J., Dathe, A., Skaggs, T.H., Klakegg, O., Ahmad, M.A., Babko, M., Giménez, D., Farkas, C., Nemes, A., Jarvis, N., 2018. Estimating the Permeability of Naturally Structured Soil From Percolation Theory and Pore Space Characteristics Imaged by X-Ray. Water Resour. Res. 54(11), 9255-9263.

Koestel, J. 2018. SoilJ: An ImageJ Plugin for the Semi-automatic Processing of Three-Dimensional X-ray Images of Soils. Vadose Zone J. 17. doi:10.2136/vzj2017.03.0062.

Kravchenko, A.N., A.K. Guber, M.Y. Quigley, J. Koestel, H. Gandhi and N.E. Ostrom, 2018.X-ray computed tomography to predict soil N2O production via bacterial denitrification and N2O emission in contrasting bioenergy cropping systems. GCB Bioenergy 10(11), 894-909. doi:10.1111/gcbb.12552.

Hansson, L.J., J. Koestel, E. Ring and A.I. Gärdenäs. 2017. Impacts of off-road traffic on soil physical properties of forest clear-cuts: X-ray and laboratory analysis. Scandinavian Journal of Forest Research: 1-12.

Jarvis, N., M. Larsbo and J. Koestel. 2017. Connectivity and percolation of structural pore networks in a cultivated silt loam soil quantified by X-ray tomography. Geoderma 287: 71-79.

Jarvis, N., J. Forkman, J. Koestel, T. Kätterer, M. Larsbo and A. Taylor. 2017. Long-term effects of grass-clover leys on the structure of a silt loam soil in a cold climate. Agriculture, Ecosystems & Environment 247: 319-328.

Jarvis, N., J. Koestel and M. Larsbo. 2017. Reply to 'Comment on "Understanding preferential flow in the vadose zone: Recent advances and future prospects" by N. Jarvis et al.'. Vadose Zone Journal. 16. doi:10.2136/vzj2017.01.0034r.

Keck, H., B.W. Strobel, J.P. Gustafsson and J. Koestel. 2017. Quantitative imaging of the 3-D distribution of cation adsorption sites in undisturbed soil. SOIL 3: 177-189.

Sandin, M., J. Koestel, N. Jarvis and M. Larsbo. 2017. Post-tillage evolution of structural pore space and saturated and near-saturated hydraulic conductivity in a clay loam soil. Soil and Tillage Research 165: 161-168.

Ulén, B., M. Larsbo, J. Koestel, Q. Hellner, M. Blomberg and P. Geranmayeh. 2017. Assessing strategies to mitigate phosphorus leaching from drained clay soils. Ambio. doi:10.1007/s13280-017-0991-x.

Van Looy K., Bouma J., Herbst M., Koestel J., Minasny B., Mishra U., Montzka C., Nemes A., Pachepsky Y., Padarian J., Schaap M., Tóth B., Verhoef A., Vanderborght J., van der Ploeg M., Weihermüller L., Zacharias S., Zhang Y., Vereecken H.  2017, Pedotransfer functions in Earth system science: challenges and perspectives. Reviews of Geophysics 55, 1199-1256, doi: 10.1002/2017RG000581.

Jarvis, N., J. Koestel and M. Larsbo. 2016. Understanding preferential flow in the vadose zone: Recent advances and future prospects. Vadose Zone Journal. 15. doi: 10.2136/vzj2016.09.0075

Larsbo, M., J. Koestel, T. Kätterer and N. Jarvis. 2016. Preferential transport in macropores is reduced by soil organic carbon. Vadose Zone Journal. 15. doi:10.2136/vzj2016.03.0021.

Mossadeghi-Björklund, M., J. Arvidsson, T. Keller, J. Koestel, M. Lamandé, M. Larsbo, N. Jarvis. 2016. Effects of subsoil compaction on hydraulic properties and preferential flow in a Swedish clay soil. Soil and Tillage Research 156: 91-98. doi: 10.1016/j.still.2015.09.013.

Bacher, M., A. Schwen and J. Koestel. 2015, 3-D printing of macropore networks of an undisturbed soil sample, Vadose Zone Journal, 14(2). doi: 10.2136/vzj2014.08.0111.

Jorda, H., M. Bechtold, N. Jarvis and J. Koestel. 2015, Using boosted regression trees to explore key factors controlling saturated and near-saturated hydraulic conductivity, European Journal of Soil Science, 66, 744-756.

Koestel, J. and H. Jorda. 2014, What determines the strength of preferential transport in undisturbed soil under steady-state flow? Geoderma, 217–218, 144-160.

Koestel, J. and M. Larsbo. 2014, Imaging and quantification of preferential solute transport in soil macropores, Water Resources Research, 50, 4357-4378.

Larsbo, M., J. Koestel, N. Jarvis. 2014, Relations between macropore network characteristics and the degree of preferential solute transport, Hydrology and Earth System Sciences, 18, 5255-5269. doi: 10.5194/hess-18-5255-2014.

Jarvis, N., J. Koestel, I. Messing, J. Moeys and A. Lindahl. 2013, Influence of soil, land use and climatic factors on the hydraulic conductivity of soil, Hydrology and Earth System Sciences, 17(12), 5185-5195. doi: 10.5194/hess-17-5185-2013.

Koestel, J., T. Norgaard, N. M. Luong, A. L. Vendelboe, P. Moldrup, N. J. Jarvis, M. Lamandé, B. V. Iversen and L. Wollesen de Jonge. 2013, Links between soil properties and steady-state solute transport through cultivated topsoil at the field scale, Water Resources Research, 49(2), 790-807. doi: 10.1002/wrcr.20079.

Ghafoor, A., J. Koestel, M. Larsbo, J. Moeys and N. Jarvis. 2013, Soil properties and susceptibility to preferential solute transport in tilled topsoil at the catchment scale, Journal of Hydrology, 492, 190-199. doi: 10.1016/j.jhydrol.2013.03.046.

Koestel, J., J. Moeys and N. J. Jarvis. 2012, Meta-analysis of the effects of soil properties, site factors and experimental conditions on solute transport, Hydrology and Earth System Sciences, 16(6), 1647-1665. doi: 10.5194/hess-16-1647-2012.     

Koestel, J., J. Moeys, and N. J. Jarvis. 2011, Evaluation of non-parametric shape-measures for solute breakthrough curves, Vadose Zone Journal, 10(4), 1261-1275. doi: 10.2136/vzj2011.0010.

Garré, S., J. Koestel, T. Günther, M. Javaux, J. Vanderborght, and H. Vereecken. 2010, Comparison of heterogeneous transport processes observed with electrical resistivity tomography in two soils, Vadose Zone Journal, 9(2), 336 – 349.

Koestel, J., R. Kasteel, A. Kemna, O. Esser, M. Javaux, A. Binley and H. Vereecken (2009), Imaging Brilliant Blue stained soil by means of electrical resistivity tomography, Vadose Zone Journal, 8(4), 963-975.

Koestel, J., J. Vanderborght, M. Javaux, A. Kemna, A. Binley, and H. Vereecken (2009), Non-invasive 3-D transport characterization in a sandy soil using ERT I: Investigating the validity of ERT-derived transport parameters, Vadose Zone Journal, 8(3), 711-722.

Koestel, J., J. Vanderborght, M. Javaux, A. Kemna, A. Binley, and H. Vereecken (2009), Non-invasive 3-D transport characterization in a sandy soil using ERT II: Transport process inference, Vadose Zone Journal 8(3), 723-734.

Koestel, J., A. Kemna, M. Javaux, A. Binley, and H. Vereecken (2008), Quantitative imaging of solute transport in an unsaturated and undisturbed soil monolith with 3D ERT and TDR, Water Resources Research, 44, W12411, doi:10.1029/2007WR006755.

Book chapters

Jarvis, N. J., J. Moeys, J. Koestel, and J. M. Hollis. 2012, Preferential flow in a pedological perspective, in Hydropedology: Synergistic Integration of Soil Science and Hydrology, edited by H. Lin, Elsevier, Amsterdam.

Oral contributions to international conferences

Invited talks

Koestel, J. 2018. SoilJ: An ImageJ plugin for the semi-automatic processing of three-dimensional X-ray Images of Soils, MicroSoil 2018 - Workshop on “Elucidating microbial processes in soils and sediments: Microscale measurements and modeling”, Saint-Loup-Lamairé, France, 26-29. June 2018.

Koestel, J. 2017. On the role of structure in PTFs, workshop of the International Soil Modelling Consortium (ISMC) ‘Pedotransfer functions in Earth system sciences; challenges and perspectives’, New Orleans, USA, 10th December 2017.

Jarvis, N, J. Koestel, M. Larsbo, 2017. Preferential flow from pore to landscape scales (J. Koestel held the presentation), American Geophysical Union, Fall Meeting 2017, abstract #H54B-02.

Koestel, J. 2017. Soil structure evolution in an individual soil column over the course of two years, Invited speaker in the framework of the PhD symposium of Steffen Merz, 24th March 2017, University Bonn / Forschungzentrum Jülich, Germany.

Koestel, J. 2016. Unravelling relationships between soil properties, site factors and preferential flow using meta-analyses and X-ray imaging. 3rd International Conference on Hydropedology during August 16-19, 2016 in Beijing Normal University, Beijing, China.

Koestel, J. 2014. A machine learning approach for appraising soils’ susceptibility to preferential flow under steady state irrigation. 16th Fresenius AGRO Conference, Behaviour of Pesticides in Air, Soil and Water, Mainz, Germany, 23-24 June 2014.

Other selected oral presentations

Koestel, J. 2019. SoilJ - A software for the semi-automatic processing and analyses of X-ray images of soil samples. Interpore 2019, 11th Annual Meeting, 6-10 May 2019, Valencia, Spain.

Koestel, J. 2017, Finger-printing breakthrough curves in soils, American Geophysical Union, Fall Meeting 2017, abstract #H44E-04, New Orleans, USA.

Koestel, J., Mats Larsbo, and Nick Jarvis, 2017. Current challenges in quantifying preferential flow through the vadose zone, EGU General Assembly 2017, abstract EGU2017-16617, Vienna, Austria.

Koestel, J., Mats Larsbo, and Nick Jarvis, 2017. Current challenges in quantifying preferential flow through the vadose zone, EGU General Assembly 2017, abstract EGU2017-16617, Vienna, Austria.

Koestel, J. 2015, Monitoring the 3-D Evolution of Soil Macropore Networks Under Natural Boundary Conditions. ASA, CSSA and SSSA International Annual Meetings, Nov. 15-18, Minneapolis, USA.

Koestel, J. and Mats Larsbo, 2014.Imaging and quantification of preferential solute transport in an undisturbed soil, EGU General Assembly 2014, abstract EGU2014-10361, Vienna, Austria.


Koestel, J., 2017. SoilJ, Software, 1.1 MB of JAVA code,


Researcher at the Department of Soil and Environment; Soil and Environmental Physics
Telephone: +4618672410, +46724539153
Postal address:
Box 7014
750 07 Uppsala
Visiting address: Lennart Hjelms väg 9, Uppsala