Prof. Michaela Dippold, Jun-Prof. Dr. Kyle Mason-Jones,  Dr. Lingling Shi,Dr. Callum C. Banfield, Dr. Guodong Shao

Soil microorganisms are the principal actors in soil organic matter turnover, and determine the fate of carbon in soils. Their energetic and material efficiency therefore greatly influence soil health and the global climate. However, microbial diversity, and the myriad possible interactions between these organisms, challenge our ability to relate community structure to carbon and energy-use efficiency (CUE and EUE). This project investigates the cooperative interactions that are increasingly recognized as crucially important in microbial communities. We target two specific cases in soil: “Metabolic cross-feeding” refers to one microorganism consuming a metabolic intermediate produced by another. “Enzyme sharing” occurs when extracellular enzymatic depolymerization releases resources that are then also available to other community members, which do not synthesize that enzyme themselves. 

Our overarching hypotheses are that (a) cross-feeding increases CUE and EUE by reducing the need for a broad portfolio of intracellular enzymes to carry out all metabolic pathways within each cell. Instead, individual taxa can specialize in particular metabolic pathways and thereby achieve higher efficiencies; and (b) enzyme sharing increases CUE and EUE by reducing the need for multiple extracellular isoenzymes that degrade the same complex, polymeric resources. Instead, each polymer is degraded by a small range of highly efficient enzymes. The project will proceed through five work packages (WPs). 

This project will provide unprecedented insight into the relationship between microbial interactions and carbon cycling in soil. This will contribute a focused yet integrative ecological perspective to the SPP, while generating results of wide significance to the understanding and steering of microbiome function in and beyond soil ecosystems.

 Prof. Michaela Dippold,  PhD students Steven Senabulya, Nipuna Withanage

Climate change has increased the simultaneous occurrence of crop abiotic and biotic stress, creating a major threat to global food production. While many modern cultivars show tolerance to individual stresses, their responses are often optimised for single-stress conditions, limiting performance during multiple concurrent stresses. Crop response to mitigate stresses requires photosynthetically-derived carbon (C) investment, which reshapes energy allocation within the plant, creating a trade-off between above and belowground processes. These interactions can be additive (i.e., equal to the sum of the single-stress effects), synergistic (i.e., higher than expected) or antagonistic (i.e., lower than expected) effects that vary among genotypes, influencing tolerance.

The project characterises phenotypes of the selected maize genotypes and their responses to individual and multiple stresses in temperate and tropical climates. Phenotypic traits are analysed in relation to gene expression profiles using mRNA sequencing to uncover inherent molecular mechanisms. The primary focus of this work is to assess the interactive effects of abiotic stresses (drought and N deficiency) and biotic stresses (Setosphaeria turcica and maize stem borer) on plant productivity, C allocation, nutrient uptake and root-zone processes as affected by genotype. 

We test the hypothesis that (1) although abiotic and biotic stresses reduce photosynthetic C assimilation, maize shifts C allocation to belowground in response to nutrient or water limitation, even if overall assimilation decreases due to the stress exposure, and (2) during multiple stresses, root biomass, mucilage secretion, rhizosphere N mining by extracellular enzymes, and arbuscular mycorrhizal fungi colonisation will decrease compared to single stress exposure, negatively impacting drought and N deficiency tolerance. Our findings are to provide an improved scientific basis for a field-scale mechanistic Multitrees crop model that explains how multiple stresses influence C allocation, root rhizosphere processes, and resource use efficiency across spatial scales, ultimately leading to breeding more stress-tolerant maize varieties. 

 Prof. Michaela Dippold,Rozy Munene,  PhD student Yuxuan Zhang 

Biological nitrification inhibition (BNI) is a significant process with potential benefits to agriculture and the environment. By slowing the conversion of ammonium to nitrate, BNI reduces nitrogen (N) losses through leaching and denitrification, enhancing nitrogen use efficiency (NUE) and reducing the emission of harmful nitrous oxide (N₂O) in plant production. Biological nitrification inhibition (BNI) by Plantago lanceolata offers a promising strategy for enhancing NUE and mitigating greenhouse gas emissions in agriculture by reducing (de-)nitrification processes in soils. This study explores the potential of various P. lanceolata genotypes with nitrification-inhibiting properties as an intercropping species in maize cultivation at two distinct locations. The primary objective is to elucidate the mechanisms of nitrification and denitrification inhibition by P. lanceolata; with nitrification-inhibiting properties secondary metabolites, focusing on their effects on the soil microbiome's composition, functional potential, and key N-transforming processes. The specific objectives include: i) determining the relationship between nitrifier and denitrifier abundance and N substrates/products, ii) distinguishing between transcriptional and abundance-based inhibition of key nitrification and denitrification genes, and iii) evaluating the effects of P. lanceolata metabolites on key enzyme activities related to nutrient cycling and microbial turnover. The study employs field and laboratory experiments to measure microbial activity, gene expression, and greenhouse gas emissions, complemented by advanced molecular analyses. Expected outcomes include identifying the inhibitory pathways of P. lanceolata metabolites, assessing their persistence in soil, and understanding their broader ecological effects. This research contributes to optimizing P. lanceolata as a BNI crop and offers insights into sustainable strategies for mitigating agricultural N losses and greenhouse gas emissions.

Prof. Michaela Dippold, Dr. Iryna Loginova

This project is complementary by innovative impulses to the original DFG project Are interactions of labile substrates with biochars the key process explaining C stabilization by biochars? A proof of concept by isotopic approaches (DI 2136/15-1). It is aimed to verify the extent to which soil chemical and biological processes on the surface of biochar can be used not only to stabilize carbon, but also for the efficient storage and control of phosphorus (P) mobilization in line with plant requirements.

As a result of an extremely fast rate of phosphate rock mining along with environmental risks associated with ongoing application of high P rates, current P management has to be thoroughly revised and new approaches require not only a more detailed understanding of mechanisms of P mobilization and solubilization, but also should jointly be designed with an elaborated management of soils as C sinks. Therefore, an improved understanding on using biochar application to enhance the P use efficiency of fertilizer P is of key importance.

The aim of this work is to improve mechanistic understanding of the biochar effect on the availability of applied P and soil P especially during the early plant P uptake. Strategies for large areas of arable land considering biochar require the application of much lower rates (less than 1-2 Mg ha-1), which then can, besides their C stabilizing nature, be used as nutrient carrier to increase nutrient use efficiency (NUE) and decrease nutrient losses from agroecosystems. The band application concentrates biochar and P in the zone reached rapidly by the seedlings and may unfold its positive effects on plant nutrition even without, yet, showing a general effect on the bulk soil. Fluid formulation of biochar allows adjustment of different characteristics and impregnation with beneficial additives, such as nutrients or microorganisms. Although, understanding mobilizing and immobilizing processes for soil P and fertilizer P need to be disentangled and a mechanistic, process-based understanding for direct and indirect interaction of biochar with P in interaction with the growing root need to be gained.

Prof. Michaela Dippold, Dr. Kyle Mason-Jones (Netherlands Institute of Ecology), Dr. Weichao Wu (Shanghai Ocean University), Dr. Callum C. Banfield, Prof. Dr. Anke Herrmann (Swedish University of Agricultural Sciences),  Dr. Lingling Shi, Dr. Guodong Shao

The fundamental channels of matter and energy in soils are the reactions of microbial metabolism, which conform to thermodynamic principles such as negative Gibbs free energy change. Consequently, catabolic exergonic reactions are needed to fuel the energy-demanding reactions of biomass synthesis in addition to extracellular enzymes to access substrates. Therefore, bioenergetic and cell economic principles will underlie the thermodynamic-metabolic approach developed by EcoEnergeticS. We aim at understanding microbial use of simple and complex substrates in soils by characterizing five proxies of microbial efficiency: 1) substrate use efficiency, 2) carbon use efficiency, 3) biochemical efficiency, 4) calorespirometric ratio, and 5) thermodynamic efficiency. We expect a trade-off between the efficiency of biomass growth on diverse monomeric precursors that require little metabolic conversion, and the inefficiencies of producing complex enzyme systems to liberate these monomers from diverse polymers. We therefore hypothesize an optimum of microbial efficiency at intermediate substrate complexity, modulated by the cooperative functional diversity of microbial communities and their soil habitats’ boundary conditions. By extension, we hypothesize that the complexity of microbial necromass accounts for its entombing in SoilSystems.In WP1, we implement thermodynamic constraints in soil metabolic flux analysis (MFA) to analyze and model microbial growth on chemically diverse substrates entering central C metabolism at different levels. The impact of monomer diversity on microbial growth and use efficiencies will be quantified in WP2, considering the advantages of precursor ratios that meet the demand of biosynthetic pathways for cell replication. WP3 investigates an alternative substrate use – storage compound formation – as an energy storing strategy under energetically unfavorable growth conditions. In WP4 we shed light on the additional costs of exoenzyme production arising from the predominance of polymers as C sources in soils, using MFA and enzyme economic approaches. Cooperative energy gains by “exoenzyme sharing” among functionally diverse microbial communities will be targeted in WP5. WP6 implements spatio-temporal boundary conditions of microbial habitats as crucial factors of exoenzyme economics, coupling the bioenergetic dimension of substrate use to the joint CERES experiment on various levels of soil complexity as predictors of matter and energy-use channels. Summarizing, a systems-ecology-based bioenergetic concept on substrate use and channeling in soils will be developed, resolving matter and energy fluxes down to the level of biochemical pathways. Thermodynamic constraints of microbial metabolism will be linked with resource economy, considering complex factors of habitat boundary conditions in soils. Thus, this project will provide a unifying concept of bioenergetics and resource economics to SoilSystems.

Dr. Nataliya Bilyera

Transformation of matter and energy in soils depends on the activity state of microorganisms and their metabolism. Microbial mining of phosphorus (P) may be driven not only by P, but also carbon (C) and energy limitation, as high-energy phosphoester bondings serve as major energy-transfer and storage molecules in cells. In this project we will deepen the thermodynamic-metabolic approach developed within ‘EcoEnergeticS’ towards the bioenergetics of P mining from organic sources. We aim to evaluate the energy costs of enzyme production for P mining to acquire C, energy and nutrients from substrates of contrasting complexity. We aim to combine the parameters of microbial P immobilization (Pmic formation), ATP level, dynamics of storage compound (PHBs), PLFA and DNA contents and ratios and enzyme activity with heat dissipation and CO2 emission as proxies of metabolic activity. We hypothesize that energy costs of P-hydrolyzing enzyme production by microorganisms increase with increasing substrate complexity. Besides, at either C or P limitation, microorganisms utilize compounds with high-energetic phosphoester bonds (e.g. ATP) rather as a source of either C or P, respectively. In the absence of P limitation, C from ATP can be accumulated to storage compounds (i.e. PHB) to save the energy, while hydrolyzed P is released to the soil. In WP1, we will assess the investment of microorganisms into enzyme production to mine energy and nutrients from organic P substances of various complexity, that requires hydrolysis by one or several phosphatases (phosphomono- and phosphodiesterases, phytases). Further in WP2, we will disentangle the energy costs of i) inorganic P uptake and anabolic use, ii) mineralization of organic P compounds of increasing complexity. The fate of high energy, C and P-containing organo-phosphoesters used by microorganisms with nutrient and/or energy limitation will be investigated in WP3. Specifically, we aim to define ATP incorporation into cell components as an indicator of the metabolic state of cell being able to differentiate i) energy limited, ii) C limited or iii) P limited microbial communities in soils. Overall, this project will investigate how nutrient deficiencies and the requirement of phosphatase formation is interfering with energy and C storage and how the microbial activity state of microorganisms affects the control of these P and C pathways. The understanding of these mechanisms will help to increase the microbial efficiency in P transformation from SOM especially considering the future P crisis.

Dr. Callum C. Banfield, Dr. Kyle Mason-Jones (Netherlands Institute of Ecology), Prof. Michaela Dippold, PhD student – Yang Ding

Soil microorganisms are important players in terrestrial carbon and nutrient cycles. Many microorganisms produce intracellular storage compounds (PHB, trehalose, glycogen, triacylglycerides), but the implications of storage for microbial growth and C turnover are unknown. Our project investigates microbial storage compounds in soil to understand their occurrence, roles, and drivers in the context of a temperate pasture.

Laboratory incubation experiments and field sampling will be carried out with isotopic labelling and compound-specific chemical analyses to reveal microbial storage dynamics. Experimental results will be combined with stoichiometric modelling to integrate the findings into a broad understanding of soil carbon cycling.

Prof. Michaela Dippold, Dr. Callum C. Banfield,  PhD student Henrik Füllgrabe

Organic farming systems traditionally consider subsoil resources for crop production. As increasing drought frequencies and intensities will reduce nutrient availability in dry topsoils, future conventional agriculture has to manage subsoils as valuable water and nutrient sources. This project aims at optimization of deep rooting winter cover crop mixtures as a strategy for fast access to subsoil resources by root channel re-use in conventional cropping systems. The niche complementarity principle will be used by combining a shallow and a deep-rooting species of one functional cover crop group (Brassicaceae, grasses, legumes) to form deep-reaching root channels even during short winter growing season. Species-specific root-channel re-use of cover crop mixtures by maize will be quantified.

(Physico-)chemical and microbiological characterization of cover crop root channels and their interactions with the maize rhizosphere will explain the preferential use of species-specific root channels by the cash crop maize. Tracer approaches (13C, 15N, D2O, Cs, Rb, Sr) will unravel the fast and efficient access of maize to subsoil nutrients and water using cover crop root channels. Drone-based thermography will allow upscaling of water and nutrient use by maize to the field scale. Implementation of these data in crop models will allow prediction of maize yield depending on cover crop management. The relevance of cover cropping as subsoil-exploring management practice will be determined depending on two key factors: 1) Soil properties by conducting experiments on the three key agricultural soil types in Germany and 2) Soil water supply by simulated drought events by rainout shelters. We will deliver clear recommendations on soil type-specific cover crop mixtures for maize cultivation facing increasing drought risks. We will bring these outcomes to practice by direct cooperation with cover crop seed suppliers and professional agricultural organizations.

Dr. Guodong Shao, Prof. Dr. Michaela Dippold, Dr. Callum C. Banfield, Dr. Lingling Shi, exchange PhD student – Xiaohui Han

The "4 per 1000" Initiative of the United Nations Climate Change Conference 2015 now even politically claims the essential demand for an increase of carbon (C) stabilization in agricultural soils for both – the mitigation of climate change and the increase in soil fertility combating the global food crisis. The meanwhile widely accepted concept of the microbial C pump states that the major pathway forming persistent organic C in soils is the transformation of plant residues to microbial biomass, which after cell death becoming microbial necromass is prone to stabilization by its intense interaction with mineral surfaces in soils. However, this process of stabilization as well as the process in opposite direction – the priming effect (PE = microbially enhanced soil organic matter mineralization) are strongly controlled by the availability of N in the soil solution. Thus, post-harvest N levels might not only be key in controlling the potential stabilization of residue C but they are also a relatively easy to manipulate parameter in cropland management. Therefore, this proposal aims to generate an improved understanding on how post-harvest N levels affect microbial transformation of plant residue-C to soil microbial necromass and the physiological control of the priming affect. Laboratory incubations with highly enriched 13C litter C will allow tracing of the 13C in microbial groups and pools as well as key microbial functions of the microbial C pump under the influence of increasing soil N solutions. Thus, we will provide important knowledge promoting agricultural practices towards increasing C sequestration in agricultural soils.

Dr. Nataliya Bilyera in cooperation with Jun-prof. Dr. Kyle Mason-Jones, Prof. Michaela Dippold, Dr. Ilonka Engelhardt

Phosphorus (P) is a growth-limiting nutrient for plants and microorganisms. Microbial transformations of P in soils plays an important role in increasing its availability for plants and reducing leaching of P as an environmental pollutant, while reducing the dependence on mining nonrenewable phosphate rocks for P fertilizer. Rhizosphere microorganisms are the key drivers of these transformations, but their activity depends on the carbon (C) from root exudates and the prevailing moisture conditions. Microbial activity can be assessed as microbial growth by applying 18O-labelled water to soil, which results in incorporation 18O into all newly synthetized DNA. However, until recently this labeling method has necessarily involved a disturbance of the moisture conditions to introduce the label. The recent development of diffusive 18O labeling makes it possible to apply this method in both moist and dry soil without disturbance. This promising approach has not yet been applied to the rhizosphere. In this proposal we intend to conduct experiments within two working packages (WPs). WP1 will adapt diffusive 18O labeling for rhizosphere studies and verify that it can be combined with 13CO2 plant labelling. WP2 will implement the new technique in combination with 13C labeling of root exudates and potential enzyme activity measurements to relate C utilization, microbial growth and enzymatic transformation of organic P in the rhizosphere. This work will deliver a powerful new method and novel insights into rhizosphere P transformations. Furthermore, the methodological advancement will establish the basis for coupling 18O rhizosphere labelling to DNA sequencing in a subsequent proposal, with the ultimate aim of identifying responsive organisms active in rhizosphere P solubilization.

Prof. Dr. Michaela Dippold, Dr. Ilonka Engelhardt, PhD student Moses Ngugi , Prof. Dr. Kira Rehfeld (Climatology and the Biosphere), Jun-Prof. Dr. Andreas Schweiger, University Hohenheim), External collaborators: Dr. Kevin Mganga, Utrecht University, Prof. Dr. Gerhard Rambold (NGO ITCER in Kenya)

Grasslands are ecologically as well as agronomically of key importance for African countries. Their restoration is essential to combat desertification and maintaining their productivity is essential for mitigating the food crisis of the African continent. For both purposes, their productivity needs to be ensured, often under conditions of multiple abiotic stresses (droughts, unfertile soils, heat stress, etc.).

The project aims to study two already intensively (and ongoingly) monitored grassland trials in Eastern and Western Kenya which are already characterized for their aboveground traits and species composition.

In Eastern Kenyan University (SEKU) Restoration Trial will be established to study 1) the relevance of rooting depth and root traits associated with resource conservation for biomass production grown in monoculture and 2) the influence of rhizosphere traits such as high microbially-mediated nutrient mobilization along with acquisitive root traits for the competition effects of grasses grown in mixtures.

In Western Kenyan Experiment on Use Intensity of native grasslands 1) the effect of trimming frequency on plant biodiversity and by that diversity in belowground traits; 2) the effect of belowground diversity (in root and rhizosphere traits) on drought stress tolerance.

This project establishes a new collaboration between Hohenheim and Tübingen and also serves as a basis for a long-term collaboration with SEKU (South Eastern Kenyan University) and ITCER, where existing experimental platforms and infrastructure can be the basis for future projects.