Soil C cycling in a changing world: The role of root-microbe interactions

Franciska de Vries1

1Professor of Earth Surface Science, BBSRC David Phillips Fellow, University of Amsterdam, Institute for Biodiversity and Ecosystem Dynamics, The Netherlands

Soil microbial communities play an important role in ecosystem functioning: they perform important steps in soil nutrient and carbon cycles and feed back to plant performance and community composition. Plants strongly alter the soil environment through root processes and are therefore likely to modify how soil microbial communities, and their functioning, respond to changing environmental conditions. Here, I will present the results from three experiments, ranging from field-based mesocosm, to glasshouse, to growth chamber experiments. Using these case studies, I will highlight different mechanisms through which roots can alter belowground microbial response to changes in plant community composition and drought, and the consequences for ecosystem functioning, including plant growth and community composition.


Franciska de Vries is Professor of Earth Surface Science at the University of Amsterdam. Franciska did her PhD in Wageningen, the Netherlands, and then spent 10 years in the UK at Lancaster University and The University of Manchester, before she returned to her home country for a full professorship at the Institute for Biodiversity and Ecosystem Dynamics in 2019. Her research focusses on the effects of global change on soil organisms and their functioning, and in particular how interactions with plants modify these responses. She is interested in global patterns as well as in disentangling small-scale mechanisms, and uses experimental and observational studies on global and regional scales, field and field-based mesocosm experiments, and pot experiments under controlled conditions. A major aim in her work is to understand the properties that determine ecosystem response to change, and using those for predicting, and managing, future ecosystem functioning. Franciska set up the special interest group Plants-Soils-Ecosystems of the British Ecological Society, and is on the editorial boards of Ecosystems and Journal of Ecology.

Organomineral interactions: Zoom at nanoscale using EXAFS and MET-EELS

Isabelle BASILE-DOELSCH1,2*, Nithavong CAM1, Clément LEVARD1, Emmanuel DOELSCH2, Jérôme ROSE1

1Aix Marseille Univ, CNRS, IRD, INRA, Coll France, CEREGE, Aix-en-Provence, France; 2CSIRO, Gate 4, Waite Road, Urrbrae SA 5064, Australia; 3CIRAD, UPR Recyclage et risque, F-34398 Montpellier, France

Organo-mineral interactions are recognized as a key factor in stabilizing organic matter (OM) in soils and short-range order mineral phases are increasingly considered as key mineral phases in the control of OM dynamics (Rasmussen et al., 2018). Coprecipitation has been recently proposed as one of the main mechanisms involved. A recent conceptual model proposes that coprecipitates form continuously upon soil mineral weathering in contact with organic compounds of the soil solution (Basile-Doelsch et al., 2015). For silicate minerals, this process imply that Si may also take part in the structure of coprecipitates. However, only Fe and Al coprecipitates have been considered as coprecipitating cations in the literature. Experimental work precipitated nanophases from a solution containing ionic Fe, Al, Si, Mg and K, obtained from a biotite weathered leachate. TEM and Fe K-edge EXAFS showed that they were structured mainly by small oligomers of Fe, together with Si and Al (Tamrat et al., 2018). By adding an organic ligand (DOPA, initial M:C≈1), coprecipitates were structured by a loose and irregular 3D network of small oligmers of Fe, Si and Al forming a highly reactive open-structured mineral skeleton on which OM was bond. A conceptual model of the nanometer-scale structure, animated in 3D, has been proposed (Tamrat et al., 2019) and named “nanoCLICs” for “Nanosized Coprecipitates of inorganic oLIgomers with organiCs”. It differs significantly from the previous models presented for ferrihydrite and amorphous Al(OH)3 coprecipitates (Kleber et al., 2015). We will present the main results that lead to the proposition of the nanoCLICs fine structure model, as well as ongoing imaging of nanoCLICS at nanometer scale by TEM, TEM-EELS and STXM.


Dr I. Basile-Doelsch. MSc in Geology (ENSG, Nancy, France), PhD in Geochemistry for paleoclimatic reconstructions (Vostok ice core, Antarctica), Habilitation à Diriger des Recherches in geochemistry of soils and weathering systems in the critical zone. She is specialized in organomineral interactions in soils. She has been an Aix-Marseille University lecturer since 1998 (France), and a junior member of the prestigious “Institut Universitaire de France” from 2011 to April 2015. As of May 2015, she became a Director of Research at the French INRA institute(CEREGE). She recently spent one year as a visiting scientist in Jeff’s Baldock group at CSIRO Adelaide. or

Lateral transport of SOM through landscapes

Prof. Asmeret Asefaw Berhe1

1University Of California, Merced, Merced, United States

Most of the earth’s terrestrial ecosystem is composed of sloping landscapes, where soil organic matter dynamics is partly controlled by the mass movement events that laterally distribute topsoil. Accurate estimation of the global soil carbon stock or the potential of soils to sequester atmospheric carbon dioxide are complicated by the effects of soil redistribution on both net primary productivity and decomposition. In this presentation, I will discuss: (1) why and how soil erosion can constitute a C sink; and how soil erosion is being considered within the context of global climate models; (2) the role of soil erosion on determining spatial distribution and stocks of SOM, stability, and stabilization  mechanisms; (3) emerging understanding of the role of soil erosion in soil nitrogen dynamics; and I will conclude the presentation by highlighting remaining knowledge gaps in our understanding of the  role of soil erosion in  soil phosphorus dynamics, and SOM dynamics in temperate and arctic ecosystems.

Biography: Dr. Asmeret Asefaw Berhe is a Professor of Soil Biogeochemistry at the Department of Life and Environmental Sciences, University of California, Merced. Prof.

Berhe received her Ph.D. in Biogeochemistry from the University of California (UC), Berkeley; M. Sc. in Resource Development (Political Ecology) from Michigan State University, and B. Sc. in Soil and Water Conservation from University of Asmara, Eritrea.

Dr. Berhe was a University of California President’s Postdoctoral Fellow at UC Berkeley and UC Davis, and a NASA Earth System Science Graduate fellow at UC Berkeley.

Prof. Berhe’s research focuses on biogeochemical cycling of essential elements (esp. carbon, nitrogen, and phosphorus) and furthering our understanding of how the soil system regulates atmospheric climate.

Prof. Berhe is a recipient of several awards and honors including the National Science Foundation’s CAREER award, the Young Investigator Award from Sigma Xi, the Hellman Family Foundations award for early career faculty, and is a member of the inaugural class of the US National Academies of Science, Engineering and Medicine’s New Voices in Science, Engineering, and Medicine. Prof. Berhe is the Chair of the US National Committee on Soil Science at the National Academies; serves in the Leadership board of the Earth Science Women’s Network; and currently is an Associate Editor for the Journal of Geophysical Research – Biogeosciences

Quantifying changes in soil carbon stocks of grazed pastures: identifying gains and avoiding losses

Professor Louis Schipper


There is an increasing emphasis on removing carbon dioxide from the atmosphere and storing this carbon in soil to mitigate against predicted trajectories of climate change. While simple in concept facilitating this transformation requires deep understanding of carbon cycling scaling up from fundamental processes of surface chemistry, photosynthesis and respiration and aggregating these up to (agro)ecosystems and their management. I will take the top down approach examining evidence for changes in carbon stocks associated with management of intensively grazed pastures. The timeframe to identify management practices that encourage gains and avoid soil carbon losses mean that traditional soil sampling approaches may take too long to answer these questions. Techniques such as eddy covariance allow us to identify subtleties of carbon cycling at hectare scales to rapidly identify possible management solutions and collaborate across scales from the hectare to the soil surface of soil particles. These management practices need to be practical, maintain food production, decrease greenhouse gas production or at a minimum increase efficiency at producing food per unit of greenhouse gas production


Louis Schipper is a Professor at the University of Waikato investigating soil biogeochemical processes at landscape scales and how they might be manipulated to achieve improved environmental performance. He has led teams determining changes in carbon stocks of pasture soils at paddock to national scales. They have provided data and understanding that has been central to developing a national picture of New Zealand’s carbon budget. They have tested simple soil sampling strategies and eddy covariance approaches to quantify changes in soil carbon stocks associated with landuse change and different management practices. He also has helped develop new theories of temperature dependence of biological processes with a specific focus on soil respiration, scaling from enzymes to ecosystems and the globe. Louis is a principal investigator for the New Zealand Agricultural Greenhouse Gas Research Centre and elected fellow of the New Zealand and American soil science societies.

Wetland blue carbon storage controlled by millennial scale variation in sea-level rise and soil organic matter is influenced by sea level variations

Associate Professor Kerrylee Rogers1

1School of Earth, Atmospheric and Life Sciences, University of Wollongong


The urgent need to mitigate climate change has focussed attention on the extraordinary capacity of coastal and marine ecosystems to sequester and store carbon within living biomass and substrates. Known as blue carbon ecosystems due to their connection with oceans, mangrove and saltmarsh are reported to have amongst the highest carbon stock density and rates of carbon sequestration of all ecosystems. Soil carbon storage is related to vegetative capacity to add organic matter to substrates, and physical processes that enhance to organic matter preservation and/or limit organic matter decomposition; periodic inundation by saline tidal water is crucial for both vegetative additions, and processes favouring preservation over decomposition. Global scale analyses have variably highlighted the role of temperature and precipitation on blue carbon storage, but surprisingly have ignored the critical role of sea level in influencing tidal inundation. The influence of global variation in relative sea level over the past few millennia on soil organic matter and carbon storage within substrates of blue carbon ecosystems is demonstrated. Using a unique study site exposed to rapid relative sea-level rise, the relationship between carbon sequestration and sea-level rise is validated over shorter time scales, confirming the capacity for coastal wetlands to adjust to sea-level rise by storing soil organic matter. Unlike terrestrial ecosystems blue carbon ecosystems do not become carbon saturated and can continue to store organic matter providing vertical and lateral space is provided by sea-level rise. The space available for carbon storage within mangrove and saltmarsh has become increasingly limited for many coastal wetlands where sea level has been stable for the past few millennia, particularly in the southern hemisphere. This paper confirms that sea-level rise will enhance carbon sequestration providing sediment supply to coastal wetlands is sufficient and space for lateral expansion does not become limited by coastal squeeze.


Associate Professor Kerrylee Rogers is a coastal ecogeomorphologist and recent ARC Future Fellow in the School of Earth, Atmospheric and Life Sciences at the University of Wollongong (UOW). Between 2005, when she graduated with PhD from UOW, and 2012 she was appointed as an environmental scientist with the New South Wales Government, before returning as a research associate at UOW in 2012. Her research has largely focused on the response of coastal ecosystems and landscapes to climate change. Particular attention is placed on the role of sea level in shaping coastal ecosystems, with substrate organic matter addition being a critical process that provides dual benefits of facilitating adaptation to sea-level rise, and contributing towards carbon storage and climate change mitigation. She is an active researcher, regarded as a national and emerging global leader in coastal ecosystem research, which is exemplified by her recent work published in Nature demonstrating that coastal wetland carbon storage is related to millennial scale variation in sea level, and that carbon storage may be enhanced should sea-level rise accelerate as projected. In addition to her research, Kerrylee Rogers is a lead co-ordinator for an Asia-Pacific Regional Cooperation Agreement (RCA) project with the International Atomic Energy Agency focussed on building country capacity in the application of radiometric and isotopic techniques for assessing the vulnerability of coasts to sea-level rise. Kerrylee Rogers also co-ordinates the Bachelor of Environmental Science (Honours) degree, teaches geomorphology and project management in environmental science, and shares her passion for coastal sustainability with her husband and two sons.

Soil capital- our last rampart to address climate change, food security & reaping societal challenges

Abad Chabbi

INRA, Ecosys, 78850, Thiverval-Grignon,

INRA, URP3F, 86600 Lusignan, France &

The 21st century has come with drastic environmental, social and economic changes that need real world solutions. By the middle of this century anthropogenic pressures will have caused additional change to the globe and all its inhabitants. While technological changes are occurring at a rapid pace, globalization has brought about both possibilities, but also environmental problems which are reaching or have reached a tipping point. For instance, soil capital resources and sustainability are drastically affected. More than 40% of soil used for agriculture around the world is classed as either degraded or seriously degraded. Because of poor management and intensive conventional farming methods that strip the soil of carbon, soil resources is being lost at between 10 and 40 times the rate at which it can be naturally replenished. There are two key issues. One is the loss of soil productivity (e.g. 30% less food over the next 20-50 years). Second, water will reach a crisis point that will further accentuate tensions among farmers and fuel local conflict, with potential geopolitical subregional implications. Taken together, this is a potent new cocktail, we need to redefine our relationship to the soil system and especially review radically our economic model and wealth indicators. In other words, the concept of exponential growth in a world of finite resources is no longer sustainable. We need to recognize that this is a global problem that would benefit from a global approach. We don’t need to reinvent the wheel in each country, and we don’t have time to do so. We just need to considerer reliable systems as quickly as possible that substantially rewards any effort to preserve the soil capital. Changing the way, the soil is managed, can have a clear influence on the amount of carbon that the soil can hold with big impact on global warming and food security.

Recycled Organic Amendments: Targeting use towards underlying soil constraints

Lynne Macdonald1

1 CSIRO Agriculture & Food, Locked Bag 2, Glen Osmond, SA 5064,

Recycled organic resources have a role to play in supporting soil health and function, food production, and regulating greenhouse gas emissions. Widespread use, however, can be hampered by variable composition, unpredictable results, biophysical barriers, and economic feasibility. There are opportunities to improve uptake through targeting amendment choice according to an understanding of the mode of action and the underlying soil constraints limiting plant growth. Here we discuss the chemical variability in a range of organic amendments, the role of carbon chemistry and nutrient stoichiometry in decomposition dynamics, and expected longevity of effect. Stepping from fundamental research to field based applications, we discuss opportunities and challenges for the use of organic amendments in supporting soil function and agricultural productivity. Highlighting limitations in surface application, we lean on examples from recent field based research aiming to overcome soil constraints through deep soil amelioration.

Biofunctionality of soil organic matter

Ellis Hoffland1, Thom Kuyper1, Rob Comans2, Rachel Creamer1

Wageningen University, The Netherlands

1Soil Biology group

2Soil Chemistry and Chemical Soil Quality group


Soil organic matter serves various functions. Interest in SOM as the source of plant nutrients is ancient. And while mineral fertilizers have, in many agro-ecosystems, replaced the role of SOM as supplier of nutrients, that interest has remained, also because of additional roles of SOM in maintaining or enhancing soil health. Since awareness about global warming grew in the 1980’s, however, the focus within research has somewhat shifted from a soil fertility perspective to C sequestration as an opportunity for climate regulation. Despite a huge body of research, there is lack of knowledge regarding the chemical, biochemical, and biological factors responsible for the various functions of SOM. We propose the term “biofunctionality” to describe the quality of SOM suitable to serve any soil ecosystem function as a result of SOM effects on the decomposer community. In our presentation I will try to link properties of SOM to the functions and ecosystem services that they provide. Apart from scientists, the concept of “biofunctionality” should also guide managers who need instruments to manage SOM for the various purposes that it has.


Ellis Hoffland is from the Soil Biology Group of Wageningen University, The Netherlands. The keyword describing her research is “soil fertility” in a broader sense. She regards soil fertility as the result of biogeochemical cycles of carbon and nutrient elements. Her motivation to study these cycles is their relevance to primary production. Being a biologist by training, her natural bias is towards the biological aspects of these cycles and, more specifically, of soil-plant interactions. She often cooperates with soil chemists because she is convinced that integration of chemical and biological information provides unique opportunities to elucidate feedbacks that are operating in complex environmental systems such as the soil. Ellis has been leading a wide diversity of research projects related to soil organic matter, including effects of mixed cropping on C sequestration and soil fertility, dissolved organic matter as a predictor for SOM mineralisation or as an indicator for disease suppression, biochar, bacterial/fungal ratio effects and cycles of nitrogen, and root exudate to increase micronutrient availability to crops.

Mineral surface area and organic matter accrual

Prof. Dr. Dr. h.c. Ingrid Kögel-Knabner1

1Carl von Linde Senior Fellow at TUM Institute of Advanced Study


Soil is build of a dynamic and hierarchically organized system of various organic and inorganic constituents and organisms, the spatial structure of which defines a large, complex and heterogeneous biogeochemical interface. Recent evidence shows a zonation of fine soil particle surfaces into key sites with high OM sequestration in multi-layered stacked OM patches decoupled from the mineral surface area. We explain why soils, even if they contain less fine minerals and particulate OM than others, can store substantial amounts of stacked OM piled-up through their three-dimensional arrangement. This sustains a coexistence of soil functions provided by mineral surfaces beyond OM sequestration. We provide a new concept for patchy, piled-up OM sequestration in soil microstructures independent from the specific mineral surface area. This opens new perspectives for the potential of soils to sequester organic carbon. A significantly advanced understanding of the structure, dynamics and functioning of the soil architecture holds the promise to explain organic matter stabilizations within a general mechanistic framework and thus will launch the integration of this information into field-scale concepts and models of CO2 sequestration in soils.


Ingrid Kögel-Knabner studied geoecology at the University of Bayreuth, where she also obtained a doctorate in soil science (1987) and habilitation (1992). In 1991 she received a professorship for soil science and soil ecology at the Ruhr-Universität Bochum. Since 1995 she serves at the Chair of soil science of the Technical University of Munich TUM. Since 2011 she is Carl von Linde Senior Fellow at TUM Institute of Advanced Study. She is member of the Editorial Board of several high-impact soil science journals. Since 2015, she has been on the list of “Highly Cited Researchers”, belonging to the most cited scientists in the world.

Ingrid Kögel-Knabner’s work is dedicated to understanding the formation and properties of soil organic matter as a major component of soils, and its central role in the terrestrial carbon cycle. Her work focusses specifically on soil structure and the biogeochemical soil interface formed by the interaction of organic matter with the soil mineral phase. The challenge to be coped with is the transition of methods which have been designed and developed for pure systems to the extremely complex, often amorphous natural materials found in soils. By applying a spectrum of sophisticated techniques (solid-state 13C NMR spectroscopy, chemolytic methods with gas chromatography-mass spectrometry, stable isotopes, radiocarbon dating, scanning electron microscopy SEM, NanoSIMS) the elucidation of soil organic matter structure, interactions and turnover can be brought a step forward.

Soil microbial community and metabolic feedbacks on soil organic matter pools.

Assistant Professor Cynthia Kallenbach1

1McGill University, Quebec, in the Department of Natural Resource Sciences Faculty of Agricultural and the Environmental Science


Soil microbial communities— their structure, biotic and abiotic interactions, and metabolic functions— directly impact both the accumulation and mineralization of soil organic matter. Yet, knowing how microbial communities and their associated traits shape SOM dynamics and the environmental conditions in which they are manifested is a grand challenge. This limits our ability to successfully target or manage microbial communities for SOM processes that facilitate ecosystem services of concern. This presentation will explore, using experimental case studies, how microbial community structure, metabolic tradeoffs, and carbon cycling genes influence SOM transformations from the stable to dissolved pools and considers the feedbacks to crop productivity, drought resiliency, and C sequestration.


Cynthia Kallenbach is an Assistant Professor at McGill University, Quebec, in the Department of Natural Resource Sciences Faculty of Agricultural and the Environmental Science. She received her Ph.D. from the University of New Hampshire in Earth and Environmental Science, M.Sc. degrees in International Agriculture Development and in Soil Biogeochemistry at the University of California-Davis, and her B.A. in Geography from Sonoma State University. Her research integrates soil ecology and biogeochemistry to understand soil organic matter turnover and accumulation and microbial-plant interactions influencing carbon and nutrient cycling under land use management and global change.

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