Subsoil management in agricultural soil: Visualizing the impacts on soil organic carbon stocks and distribution by hyperspectral imaging and machine learning algorithms

Msc Chris Henke1, Dr Julien Guigue1, Dr Eleanor Hobley1, Pr, Dr Ingrid Kögel-Knabner1

1Technical University of Munich, Freising, Germany

Significant amounts of water and nutrients are stored in deep soil horizons and subsoil management is being considered as an option to sustain high demand in crop productivity. At the same time, subsoils contain a large proportion of total soil organic carbon (SOC) and the dynamics of SOC in subsoils are now receiving more attention, especially given the link of SOC with climate processes. However, subsoils are highly heterogeneous, subsoil SOC contents are low and have longer turnover times, so that detecting SOC changes in subsoils is difficult using classic soil analyses based on sample homogenisation by depth increments.

We analysed soil cores from a field experiment with deep ploughing treatments, with and without compost incorporation, using hyperspectral Vis-NIR imaging spectroscopy. The C distribution within the soil was modelled at a very high spatial resolution (53×53 µm) using random forest and artificial neural network algorithms. The SOC mapping revealed an increase in SOC stocks resulting from deep ploughing (12% relative increase). We hypothesize that, in addition to the added SOC, an increase in rooting densities resulting from lowered bulk density and enhanced nutrient availability in the subsoil are the driving factors for this C accumulation.

Hyperspectral imaging of soil cores is a promising tool for the quantification of SOC stocks and changes in deeper horizons, and allows visualisation of the spatial heterogeneity of soil organic carbon.


Julien Guigue is a Post-Doctoral scientist at Technical University of Munich. He is doing research on soil organic matter dynamics in agricultural ecosystems, more specifically on the effect of agricultural management of subsoils on SOM distribution and stocks.

Stable isotope techniques: Recent developments in tracing changes in C and N cycling and biodiversity using uniformly 13C-labelled plant materials

Dr Ton Gorissen1

1IsoLife, Wageningen, Netherlands

Stable isotopes like 13C have been used in ecology for decades in tracer studies of plant materials in organic environments like natural soils. They are used to study distribution of recently added organic matter amongst SOM fractions, fluxes of C and N between SOM pools, or to unravel biodiversity and food web interactions in complex soil ecosystems.

The stable-isotope labelled plant materials that IsoLife produces have been used in many papers describing the dynamics of SOM. These materials opened up new ways in i) decomposition studies, ii) stable isotope probing studies on trophic interactions and functional relationships in soil ecosystems, and iii) the sensitivity of detection techniques.

  1. i) Decomposition studies have been carried out with uniformly 13C-labelled plant parts or extracted plant materials like lignin or cellulose yielding detailed information about fractions respired, distribution among SOM pools, and SOM transformation. Issues on decomposition efficiency, substrate availability, priming, stabilisation of SOM, and microbial utilisation can be better studied, providing useful data for e.g. carbon sequestration related to climate change.
  2. ii) Stable Isotope Probing enables the detection of functional organisms in complex ecosystems at species level using U-13C substrates and density gradient centrifugation to separate 12C- from 13C-DNA or -RNA. Subsequent sequencing of the 13C-bands reveals the active, functional species. Community structure, biodiversity, and symbiotic associations have been studied with a renewed focus.

iii) Methods for tracing C and nutrient transfer between hosts and organisms can be measured in situ using continuous 13C-labelling at extreme enrichment levels (>97 atom %) or visualised by direct imaging using microscopy techniques such as NanoSIMS or FISH.

During the last few years, many papers have been published based on the use of uniformly 13C-labelled plant materials ( The poster shows an overview of the achievements during the last 3 years of using U-13C-labelled substrates in SOM-studies.

Aluminium-DOM precipitation: A high resolution mass spectrometry (LC-QTOF-MS) study

Mr Olaf Brock1, Mr Rick Helmus1, Prof. Dr. Karsten Kalbitz2, Dr. Boris Jansen1

1University Of Amsterdam (IBED-ELD), Amsterdam, Netherlands, 2Technische Universität Dresden (Soil resources and land use), Dresden, Germany

The interaction of metal cations – iron and aluminium – with dissolved organic matter (DOM) derived from leaf litter leads to the formation of the dark coloured and resistant Bh horizons in podzols. The characteristics of these Bh horizons – especially the effect on water permeability – partly inspired the innovative SoSEAL project (Soil Sealing by Enhanced Aluminium and DOM Leaching). SoSEAL aims at making dykes more stable by reducing water permeability through the dyke body by enhancing metal-DOM precipitation. In order to use metal-DOM interaction for engineering purposes, it is important to identify the molecular characteristics of DOM involved in metal-DOM interaction. This allows us to select suitable DOM sources and be able to better control the formation of metal-DOM flocs. Molecular characterisation of DOM was done with a new non-target screening method using liquid chromatography (LC) coupled to high resolution quadrupole time-of-flight mass spectrometry (QTOF-MS). DOM solutions were prepared from coniferous, deciduous and mixed leaf litter and from HUMIN-P 775, a commercially available leonardite material which dissolves completely in water and has a high number of carboxylic groups. We measured the molecular characteristics of the DOM solutions before and after the addition of aluminium. The amount of precipitation was quantified by measuring aluminium and dissolved organic carbon content. Results show that humin-DOM precipitation is up to twice as high as that of leaf litter DOM. Preliminary results suggest that there is preferential precipitation of larger/heavier compounds and of aromatic compounds. However, we did not observe preferential precipitation of specific compound groups (such as lignin and tannin) and also not of nitrogen poor compounds. These findings mean that we can increase the formation of aluminium-DOM precipitates by selecting a source of DOM with a DOM composition that is more suitable for aluminium-DOM precipitation.


I am a PhD student at the University of Amsterdam (UvA) in the Netherlands. My PhD is part of a larger project in which we are developing a method to reduce water permeability through sandy layers, e.g. in dykes. This method consists of injecting a mixture of dissolved organic matter (DOM) and aluminum that together form flocs or Al-DOM precipitates. These flocs/precipitates block the soil pores, thereby reduce water permeability and inhibit unwanted water flow. In my research I study the role of organic matter in the precipitation process, also known from podzolization.  I conduct this by investigating the molecular composition of different natural and commercially available DOM sources using liquid chromatography coupled to high resolution mass spectrometry (LC-QTOF-MS). I also work on the effect of forest conversion on SOM composition (former master thesis topic). For this pyrolysis-GC–MS was used to study SOM beneath deciduous and (converted) spruce forests, with a focus on lignin and cutin/suberin.

The potential of temperature-dependent carbon differentiation for soil analysis

Dr. Fabian Alt1, Almut Loos1, Dr. Christine Hallgren2, Dr. Lutz Lange1

1Elementar Analysensysteme GmbH, Langenselbold, Germany, 2Elementar Australia Pty Ltd, Sydney, Australia

Detailed information about carbon contents, fractions, and pools in soils are essential for understanding biogeochemical processes and the consequences for land use, waste management, and climate change. The methodological challenge in the determination of carbon fractions is the accurate differentiation of organic, inorganic and in particular elemental carbon. Additionally, it is important to understand the soil organic carbon (SOC) storage and degradation processes. Therefore, knowledge about the SOC stability and association is highly beneficial.

We tested the advantages and drawbacks of a temperature gradient program with different hold times compared to classic direct and indirect methods for the determination of carbon fractions and species (e.g., EN 15936).

The soli TOC® cube of Elementar Analysensysteme GmbH has been used for comparison measurements of different soils, waste as well as pure substances. It offers the opportunity to run a free configurable temperature program due to its dynamic heater and catalytic post combustion. Accordingly, carbon compounds are combusted and transformed to CO2 due to their thermal stability at different temperatures and the CO2 is detected. Also, different carrier gases have been tested for separating elemental and inorganic carbon under oxidative and pyrolytic conditions.

For most soils, the organic carbon fractions determined by the direct procedure, match the sum of elemental and organic carbon according to the temperature ramping program. The differentiation of organic and elemental carbon is  determined by using a temperature of 400°C for splitting these fractions. Furthermore, the flexibility of the temperature gradient offers more opportunities for a reliable and accurate separation of carbon fractions and possibly even species. Consequently, there are more options for special samples and research questions compared to acidification and combustion methods, which use only one temperature above 900°C.


  • Studied Chemistry in Frankfurt and Heidelberg University
    • Diploma Thesis in Environmental Geosciences
  • Dissertation (PhD) at Max-Planck-Institute for Chemistry in Mainz (Germany) and Utrecht University (the Netherlands)
    • Atmospheric Sciences: Exchange processes between the lowermost stratosphere and the upper troposphere.
  • Post Doc at Max Planck Institute for Chemistry in Mainz
  • 2005: Produktmanager at Elementar (Elemental Analysis and IRMS)
  • 2011 Director for R&D and innovation management
  • 2017: Director Global Sales and Marketing
  • August 2019: move to Elementar Australia

Rapid spectral-reflectance-based assessment of soil carbon stratification following full inversion tillage pasture renewal

Dr Roberto Calvelo-Pereira1, Dr Matteo Poggio2, Professor Michael J. Hedley1, Dr Michael Blaschek2, Dr Carolyn Hedley2, Dr Michael H. Beare3, Dr Samuel R. McNally3

1Massey University, Palmerston North, New Zealand, 2Manaaki Whenua-Landcare Research, Palmerston North, New Zealand, 3The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand

Sequestration of soil organic carbon (SOC) is one strategy to reduce atmospheric CO₂ concentrations and limit climate change. Permanently grazed pastures, such as those in New Zealand, accumulate large amounts of SOC because pastures allocate a high proportion of plant-fixed C to root turnover and rhizodeposition. Consequently, these soils show a strong vertical stratification of roots and SOC that limits the topsoil’s ability to sequester any additional carbon. Full inversion tillage at pasture renewal (FIT-renewal) has been proposed as a farm management practice suitable to accelerate SOC storage in pastoral soils showing a high degree of SOC stratification. Using a modified mouldboard plough, a one-off soil inversion event transfers carbon-rich topsoil into the subsoil while low-carbon mineral subsoil is brought to the surface where it is exposed to higher carbon inputs from the new pasture. The potential of increasing SOC stocks after FIT-renewal is under investigation at the field scale in New Zealand. In the North Island, two field trial sites were established, one on an Alfisol and the other on an Andosol. Pasture renewal via FIT involved full cultivation of a summer brassica crop followed by autumn re-grassing by direct drilling compared to other pasture renewal treatments by direct drill and shallow till. The sites were sampled through coring before renewal and after 5 months of crop growth to assess changes in SOC stocks and stratification using either (1) laboratory-based analytical methods or (2) diffuse reflectance spectroscopy. The one-time deep ploughing event redistributed large quantities of soil and soil C into depth (below 10 cm), altering its SOC stratification at varying degrees. The rapid reflectance scanning of the cores allows soil carbon content and stratification to be estimated with greater depth resolution helping researchers to make rapid decisions about the plough settings needed prior to FIT-renewal.


Roberto completed his PhD in Soil Science in 2008, at the University of Santiago de Compostela (Galicia, Spain), joining Massey University (NZ) in 2010. His research focusses on carbon and nitrogen dynamics in pastoral soils, particularly considering farm management practices that could increase the long-term storage of carbon in soils, impacting both fluxes of other greenhouse gases and nutrient cycling. In this context, the deployment of advanced spectroscopic technology (e.g. near and mid-infrared) to track and monitor multiple chemical signatures in soils, as carbon stocks and stratification, as well as trace element content and speciation, is also considered.

Molecular-level investigation into the fractionation of dissolved organic carbon during co-precipitation with ferrihydrite

Dr. Dinesh Adhikari1,2, Dr. Nancy Hess3, Malak Tfaily3,4, Ravi Kukkadapu3, Qian Zhao3, Rosey Chu3, Trent Graham3, Dr Yu Yang1

1University Of Nevada, Reno, Reno, United States, 2Lawrence Livermore National Lab, Livermore, United States, 3Pacific Northwest National Laboratory, Richland, United States, 4University of Arizona, Tucson, United States

Association with minerals, especially poorly crystalline iron (Fe) minerals, plays an important role in the persistence of dissolved organic carbon (DOC). Chemical fraction can occur for DOC upon its association with Fe minerals, however, scant information is available for the fractionation of DOC during co-precipitation with Fe-minerals. Herein, applying Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), we investigated the fractionation of DOC during co-precipitation with ferrihydrite (Fh) in systems with C/Fe molar ratio of 0.5 and 3. Our results showed that high-molecular-weight DOC was preferentially precipitated for system with C/Fe of 3. In addition, a higher fraction of condensed polycyclic aromatic hydrocarbons (98.12%) was co-precipiated compared to unsaturated phenolic (66.25%) and aliphatic (39.01%) DOC. Our findings demonstrated that high-molecular-weight aromatic compounds preferentially co-precipitate with Fh in systems with feed C/F ratio relevant to the natural systems. Results from this study provided valuable information regarding the importance of DOC composition in its association with Fe-minerals and stability in the natural environment.


Yang is an expert in Fe-oxide and OM dynamics and has applied extensive tool sets for molecular-scale analytical determination of soil and solution OM and Fe-oxide chemistry, including application of X-ray absorption spectroscopy, Mössbauer spectroscopy, and state-of-the-art mass spectroscopy (MS) such as Fourier-transform ion cyclotron resonance MS (FT-ICR-MS).

Improved methodologies for SOC measurement, estimation and reporting its density changes in agricultural soils

Dr Mohammad Ibrahim Khalil1, Dr Bruce Arthur Osborne1

1UCD SBES and CRAES-EI, University College Dublin, Dublin 4, Ireland

Reduction of greenhouse gas (GHG) assessment uncertainties and improvement in the quantification of sinks and offsetting mechanisms are required to develop appropriate mitigation measures aimed at keeping global temperature <2oC. The key factors that are needed to fulfil these objectives are a precise, verifiable estimation of soil organic carbon (SOC) and its variation at field scales. For SOC measurements, land use (LU)/soil type-specific and consistent sampling protocols (e.g., method and timing of samplings) together with a consideration of other factors (e.g., soil moisture and carbon) that influence soil mass and volume, are required. For accurate estimations, the determination of SOC by ‘mass by volume’ on an equal soil mass basis, in a defined but adjustable soil layer and reporting is essential. The Intergovernmental Panel on Climate Change proposes proportional (%) approach, as a SOC density (here)/stock change factor (DCF), for application across key agricultural LUs, managements and inputs. Methodologies developed with higher spatial resolution databases, coupled with two-phase modelling and GIS approaches, could provide robust estimates. However, the DCF factors overestimated the SOC density changes for organo-mineral (12-19%) and organo-mineral plus organic soils (33-81%) compared to mineral soils. This resulted in a corresponding increase in national SOC stock estimates by, on average, 14 and 20%. The corrected estimates showed a sequestration rate of 0.04, 0.12 and 0.42 t C ha-1 yr-1 in Irish agricultural soils, and a potential GHG offsetting of 1.20, 2.93 and 5.41 Tg C yr-1 for the 0-10, 0-30 and 0-100 cm soil layers, respectively. These findings suggest the replacement of the apportioning approach, including 4‰ concept, by a ‘mass by area’ (depth-specific) one for more precise estimations. This will include the disaggregation of soil types, and the calculation of country-specific DCFs and weighting factors for individual LUs, management practices and inputs for upscaling to regional/international level.


Dr. M. Ibrahim Khalil is a Sr. Environmental Scientist and Modeler attached with University College Dublin, Ireland, and leading a multi-disciplinary research group (Climate-Resilient Agri-Environmental Systems, CRAES). Dr. Khalil is an agricultural graduate with honours, double masters and PhD in environmental soil science, completed with a Belgian scholarship. He was an awardee of IAEA traineeship and did post-doctoral research with the prestigious fellowships awarded by the Royal Society (UK), Alexander von Humboldt Foundation (Germany) and Japan Society for the Promotion of Science (Japan). Dr. Khalil  has been leading and coordinating a large number of externally-funded research projects, and published more than 150 scientific papers in peer-reviewed journals/book chapters/proceedings; member of editorial board and reviewer  for international journals. He has expertise in the key research areas of Biogeochemistry of Carbon and Nitrogen Cycles, Monitoring, Modelling and Mitigation of Greenhouse Gases/trace gases and SOC density/stocks; Climate Change and Adaptation.

How frequently do Sorghum roots reoccupy the same soil pore spaces?

Miss Ivanah Oliver1, Dr Richard Flavel1, Dr  Oliver  Knox1, Dr Brian  Wilson1,2

1University Of New England, Armidale, Australia, 2NSW Office of Environment and Heritage, Armidale, Australia

X-ray computed tomography (xCT) has enhanced our understanding of how soil structure impacts the spatial distribution of root systems. Pore space characteristics and presence of root channels are two physio-chemical properties of the soil which influence spatial root distribution. Our current understanding of how regularly roots utilise a single pore space seasonally is limited. This in turn has implications for resource depletion (e.g. phosphorus), accumulation of plant products (e.g. root exudates) and physical legacy. This study evaluated the occupancy of an actively growing root system in pre-existing root pore spaces and the potential for root derived microbial and exudate hotspots.

The experiment involved growing Sorghum (Sorghum spp.) in pots for two 8 week growth periods separated by a 12 week decomposition period. At the beginning of the decomposition period plant above-ground biomass was removed and roots were left to decompose naturally. X-ray computed tomography was utilised to image a small section of the pot for determination of the spatial distribution of roots and pore spaces. The images collected at the end of each growth and decomposition period were then overlayed and compared to determine the proportion of roots that reoccupied the pre-existing root pore spaces.

Under the experimental conditions of this study, the sorghum roots did not appear to preferentially occupy the root channels created by the previous crop. The study findings will be utilised to better explain the broader implications for nutrient and water acquisition, microbial and exudate hotspots, and soil physical properties.


Ivanah is a PhD candidate at the University of New England. Her research focus is on root carbon inputs into the soil.

From spectra to decision support and back again: A roadmap to impact for soil spectroscopy

Dr Ryan Farquharson1, Dr Jeff Baldock1, Dr Uta Stockmann2, Dr Lynne Macdonald1, Dr Brendan Malone2, Mrs Seija Tuomi2, Mr David Benn3

1CSIRO Agriculture and Food, Glen Osmond, Australia, 2CSIRO Agricuture and Food, Acton, Australia, 3CSIRO IM&T, Glen Osmond, Australia

Infrared (IR) spectroscopy can provide estimates of the quantities of organic carbon in soil as well as its allocation to fractions isolated and measured by physical and chemical means.  Rapid and cost-effective estimates of a range of soil properties by IR spectroscopy allow more samples to be analysed, making the acquisition of large data sets feasible, as exemplified by the national soil carbon dataset collected by the Australian Soil Carbon Research Program. These data sets open up a number of opportunities for spatial modelling at a range of scales and for monitoring of soil condition, with applications in greenhouse gas accounting and mitigation, and management of resources in agricultural enterprises, for example.  Here we present a roadmap to take this technology out of the research domain and make it available to a range of users.  By combining measurement, prediction and modelling, and creating a system where information flow is circular, synergistic benefits to both end users and technology developers will be realised.  For example, analysis of spectra in real time might identify samples for which current prediction algorithms are unreliable, which can then be further analysed and added to calibration sets, potentially providing the end user with more reliable results.  Land managers make multiple decisions that balance a number of objectives, including productivity, sustainability and profitability.  In the soil organic matter space, we recognise that carbon fractions are just one of many pieces of information that need to be brought together into a decision support framework.  To do so will require a concerted effort involving a range of players including researchers, analytical laboratories, data scientists, software engineers, government departments, advisory bodies, agronomists, grower groups, industry and funding bodies.  We hope that by articulating a roadmap we can bring these players together and expedite the path to impact for soil spectroscopy.


Ryan Farquharson is an Experimental Scientist in the Carbon and Nutrient Cycling group at CSIRO Agriculture and Food.  Based at the Waite Campus in Adelaide since 2002, his research interests include greenhouse gas balances of agricultural systems, modelling approaches for greenhouse gas inventories and life cycle analysis, biological nitrogen fixation by the legume/rhizobium symbiosis and more recently, the use of infrared spectroscopy for a range of applications in soil, including quantifying soil carbon.

Development of a predictive tool for herbicide sorption to soil based on mid-infrared spectrometry

Mr Gavin Styles1, Ms Miguela Martin1, Professor Antonio Patti1, Dr Mick Rose2, Associate Professor Lukas Van Zwieten2

1Monash University, Melbourne, Australia, 2New South Wales Department of Primary Industries, Wollongbar, Australia

Sorption is considered one of the most influential processes on the mobility, bioavailability and rate of degradation of herbicides in soil. Site specific estimates of soil sorption coefficients are therefore a prerequisite for the accurate prediction of herbicide persistence in different soils. The adsorption affinity of a soil for a given herbicide is controlled by a wide variety of factors such as mineralogy, organic matter content, and organic matter speciation. However, direct measurement of sorption requires expensive and laborious construction of adsorption isotherms. The development of an effective predictive model could circumvent this testing, and advance our capabilities to predict herbicide persistence and ecological and agronomic risks.

Mid-infrared spectrometry (MIR) is a cheap, rapid technique that, given adequate calibration, can quantify a wide variety of factors including organic matter content and speciation, particle size distribution and mineralogy. This makes it especially promising for predictive modelling of small organic molecule sorption. There have been previous attempts to use MIR based modelling to predict herbicide adsorption affinity of soils, however, due to a limited dataset; these models have lacked the generality required for wider application.

The aim of this work is build a soils dataset with widely varying properties, and then to develop a compressive model capable of predicting herbicide sorption, based on MIR. By using a larger data set, comprised of 40+ sites from across Australia, a relatively universal model may be produced, capable of predicting adsorption affinity in soils outside of the initial data set. In this work, we assessed the adsorption of glyphosate, clopyralid and imazamox using MIR combined with principle component analysis, partial least squares and principle component regression techniques. Results will be presented in the context of herbicide sorption relationships to soil organic matter and mineralogy.


Gavin Styles is a PhD researcher at Monash University working with the New South Wales Depmartment of Primary Industry. His work focuses on herbicide dynamics and bio availability in the soil, with a particular focus on sorption, preictive modelling, and the development of new testing methods for herbicide presence and bioavailability in soil.


7th International Symposium
Soil Organic Matter

6 – 11 October 2019

Hilton Adelaide

Adelaide, South Australia


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