Plant-Microorganism-Soil interactions in the rhizosphere: from chemical, biological, and physical perspectives to an interlinked understanding of processes

The rhizosphere is regarded as the soil compartment with the highest level of nutrient flux through a multitude of interactions between plants, soil, and (micro)biota. Roots and associated (micro)organisms interact with heterogeneous soil environments that provide habitats for biota on various scales. High metabolic activity and nutrient cycling can be observed from single root tips to whole root systems which makes the rhizosphere of central importance for ecosystem functioning.
The main knowledge-gaps in rhizosphere research are related to the difficulty in mechanistically linking the physical, chemical and biological processes, taking place at different scales (nm to cm) in the rhizosphere and to the challenge of upscaling these processes to the scale of the root system and the soil profile. The key for overcoming these knowledge gaps is to understand rates of matter flux, and to link the spatial arrangement of the different interconnected components of the rhizosphere with their temporal dynamics. This requires concerted efforts to combine methods from different disciplines like plant genomics, imaging, soil physics, chemistry and microbiology.
We welcome experimental and modelling studies on rhizosphere functioning that aim at revealing spatial gradients of e.g. functional biodiversity of microorganisms, uptake and release patterns by roots, soil structure modification by root growth (and vice versa) as well as feedbacks between those processes in order to improve our mechanistic understanding of emerging properties like water acquisition, nutrient cycling, plant health, soil structure development and feedbacks among them.

Convener: Evgenia Blagodatskaya | Co-conveners: Carsten W. Mueller, Steffen Schlüter, Hannes SchmidtECSECS
vPICO presentations
| Tue, 27 Apr, 13:30–15:00 (CEST)

vPICO presentations: Tue, 27 Apr

Chairpersons: Evgenia Blagodatskaya, Carsten W. Mueller, Hannes Schmidt
Yelena S. Pájaro-Esquivia, Yamileth Domínguez-Haydar, Clara Tinoco-Ojanguren, Sergio E. Lozano-Baez, Mirko Castellini, and Simone Di Prima

There is a lack of knowledge on the grow requirements for most endangered plant species in tropical ecosystems. The interdisciplinary field of the “critical zone” provides an opportunity to understand the plant-soil interactions, allowing the development of strategies for species propagation and restoration. Aspidosperma polyneuron is a Tropical Dry Forest native species, currently categorized as “endangered” in Colombia and the neotropics.  In this study, we evaluated the intrapopulation differences in the morphological and plastic responses of A. polyneuron seedlings along an experimental gradient of light and water. We collected seedlings from two locations of the same population at the department of Atlántico (Colombia) and exposed them to three levels of light (100, 55 and 10%) and two different levels of water (field capacity, 60% and dry conditions, 20%). We allowed these seeds to grow for six months in an experimental 3 x 2 x 2 m random factorial design. In addition, we measured 16 morphological and growth traits associated to their performance. Results showed that medium-light treatment produced the most favorable outcome when facing drought conditions, while low light aggravated negative performance effects when facing drought conditions. The seedlings origin was a significant factor influencing the morphological responses of most traits. Regarding plasticity, there were differences in the pattern and magnitude of the traits according to the locality they were collected from. The influence of water gradient prevailed over the light gradient in the phenotypic responses. The results showed differences in the response mechanism of the two groups of seedlings, indicating intrapopulation differentiation processes between both groups.

How to cite: Pájaro-Esquivia, Y. S., Domínguez-Haydar, Y., Tinoco-Ojanguren, C., Lozano-Baez, S. E., Castellini, M., and Di Prima, S.: Effects of hydric and light combined stresses on the morphological and plastic responses of Aspidosperma polyneuron Müll. Arg. Seedlings (Apocynaceae), EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-44,, 2021.

Emily Solly, Astrid Jäger, Matti Barthel, Johan Six, and Martin Hartmann

Worldwide tree species have been observed to be suffering from extended periods of water limitation, for example due to warmer climate that increases soil evaporation and plant transpiration. These conditions likely do not only affect the growth and vitality of trees but may also feed back on the cycling of carbon and nitrogen at the interface between roots and soils.

In September 2019, we established a mesocosm experiment to mechanistically study on a seasonal basis how the interactions between plants and soil biotic and abiotic resources are altered during events of drought. The mesocosms feature young Scots pine (Pinus sylvestris L.) trees and soil collected from a drought-affected natural forest in the Rhone valley, Switzerland; and are treated with three different levels of water availability (control, sufficient water; intermediate drought, 40% reduction; severe drought, 75% reduction). One year after the start of the experiment an isotopic labelling campaign with 13CO2 was conducted to trace the natural pathway of photosynthetic assimilates into above- and belowground carbon pools and fluxes.

During the first growing season of the experiment, severe drought more than doubled the growth of fine roots when compared to the control treatment. In turn, the mean diameter of the fine roots significantly decreased by 22%, and fewer ectomycorrhizal root tips were observed. These findings suggest that trees exposed to drought invest more in within-plant carbon maintenance and in the growth of root systems, rather than in the allocation of carbon to sustain the biology in the rhizosphere for nutrient acquisition. Moreover, post-label soil pore 13CO2 concentrations and total soil CO2 concentrations were lower under severe drought compared to intermediate and control treatments, indicating a generally reduced carbon metabolism. By tracking the fate of 13C assimilates into fine roots, soils and microbial communities over time we now investigate whether there is a threshold at which Scots pine trees stop investing in providing carbon to the rhizosphere and rather succumb to drought.

How to cite: Solly, E., Jäger, A., Barthel, M., Six, J., and Hartmann, M.: Enhanced root growth but reduced belowground carbon allocation are the initial responses to water limitation in model Scots pine-soil systems, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-1125,, 2021.

Chaoqun Wang, Maxim Dorodnikov, Evgenia Blagodatskaya, and Michaela Dippold

Soil enzymes produced by microorganisms and plants are very sensitive to the variations in microclimate, e.g. aeration, and respond quickly to the induced changes. The majority of the enzyme assays are conducted under normal (temperature and air) conditions irrespectively of the origin of the environmental samples. However, it remains unclear how conditions of assays may affect results in anaerobic systems. In the present study, we have clarified this key gap in current methods by measuring the kinetics of phosphatase, β-glucosidase, and leucine aminopeptidase in paddy soil under aerobic and anaerobic conditions by means of a glovebox. Specifically, we quantified Vmax and Km in soil from three compartments in a rhizobox (top bulk (2-5 cm), rhizosphere, and bottom bulk (15-18 cm)) during rice growth. We demonstrate that the activities of three tested enzymes were significantly lower under aerobic conditions compared to anaerobic conditions at three consecutive dates of rice growth. Lower Vmax values for phosphatase in top bulk soil and rhizosphere soil and β-glucosidase in top bulk soil, rhizosphere soil, and bottom bulk soil confirmed that aerobic conditions limited enzyme activities. For leucine aminopeptidase, although the difference in Vmax values between anaerobic and aerobic conditions was not significant, the values always increased under anaerobic conditions compared to aerobic conditions. Compared with anaerobic conditions, the Km values for phosphatase under aerobic conditions decreased by 10.11-22.78%. The maximum difference in the Km values for β-glucosidase and leucine aminopeptidase between aerobic and anaerobic conditions was 30.93% and 40.53%, respectively. We conclude that enzyme activities of samples taken from the anaerobic or low-redox environment have to be assayed under anoxic conditions to avoid 10-40% underestimation (for Vmax) due to suppression by oxygen.

How to cite: Wang, C., Dorodnikov, M., Blagodatskaya, E., and Dippold, M.: An improved method for extracellular enzyme assays in paddy soil: a comparative study under aerobic and anaerobic conditions, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-2180,, 2021.

Martin Lohse, Rebecca Haag, Thorsten Reemtsma, and Oliver Lechtenfeld

The rhizosphere is an important hotspot for microbial activity, organic carbon input, and carbon turnover in soils. The interplay of these rhizosphere components results in small scale gradients of organic molecules in the zone around a root. Mass spectrometric imaging (MSI) can reveal the spatial distribution of individual plant metabolites in the soil, which cannot be achieved using bulk analysis. Using non-fragmenting ionization techniques such as laser desorption ionization (LDI) allows for the detection of intact molecules without the need for labeling with e.g. fluorescent tags.

Direct MSI for the chemical imaging of intact molecules of the rhizosphere has been recognized as a still existing analytical gap. Here we present a novel method allowing mass spectrometric molecular rhizosphere imaging directly in a complex soil matrix.

Our novel approach consists of sampling the roots and the surrounding soil of Zea mays plants in either field- or lab-scale experiments using small metal cylinders. After excavation, the loam soil pellets were embedded in gelatin and cryosectioned to 100 µm sections. After selecting regions of interest on the soil section, the root and the soil surrounding the root was analysed using ultra-high resolution laser desorption ionization Fourier-transform ion cyclotron resonance mass spectrometry (LDI-FT-ICR-MS).

Given the large background of soil-derived organic carbon, the high mass resolution and sensitivity of FT-ICR-MS allow distinguishing root-derived molecules from soil organic matter based on their exact masses. We show that our method is capable to recover rhizosphere gradients of a dihexose (C12H22O11, e.g. sucrose, maltose) directly in the soil with a spatial resolution of 25 µm.

Molecular gradients for the dihexose showed a high abundance of this metabolite in the root and a strong depletion of the signal intensity within 150 µm from the root surface. Analysing several sections from the same soil pellet allowed to recover 3D molecular gradients from one root segment. Utilizing the potential to easily change the mass window a variety of potential metabolites can be analysed in the same region around the root. Thus the chemical diversity of potential root exudates can be revealed.

Our workflow enables the study of root-derived organic carbon with high spatial resolution directly in a soil context. For the first time, direct molecular imaging of the rhizosphere via LDI-FT-ICR-MS will allow for a non-target or targeted analysis of complex soil samples.

Visualizing the root structure via X-ray computed tomography in a soil sample before the embedding would enable a guided sampling approach to analyse molecular distributions at certain parts of the root. Moreover, the molecular LDI-MSI results could be correlated with elemental imaging via laser ablation – inductively coupled plasma – mass spectrometry directly at the same sample position - allowing for an even more detailed insight into chemical processes in the rhizosphere.

How to cite: Lohse, M., Haag, R., Reemtsma, T., and Lechtenfeld, O.: Direct Imaging of Plant Metabolites in the Rhizosphere using Laser Desorption Ionization Ultra-high Resolution Mass Spectrometry, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-2450,, 2021.

Fengxian Chen, Zeev Ronen, and Gilboa Arye

Azospirillum brasilense Sp7 and Azospirillum brasilense Cd are two plant growth-promoting bacteria (PGPB). Traditional inoculation methods with PGPB are seed inoculation, seedling root inoculation and soil inoculation. Although these methods are simple to use, they are limited to apply at a specific plant growth stage. Therefore, PGPB inoculation by drip irrigation has been suggested as a means to deliver PGPB directly to the root zone during the plant growth stages. To quantify the intrinsic transport characteristics of two A. brasilense strains following point source inoculation, the properties of A. brasilense Sp7 and A. brasilense Cd (e.g., cell size, hydrophobicity, and zeta potential) and the adsorption characteristics on fine sand were measured. The transport and fate of the two strains were examined under transient water flow conditions with three soil inoculation regimes: (i) surface irrigation (ii) subsurface irrigation and (iii) soil premixing. The water content, bromide, and bacteria distribution in the soil profile were measured after 2 and 48 hours. The measured data were described using the attachment/detachment model using the Hydrus 2/3D code. The result showed that even though A. brasilense Sp7 and Cd exhibit similar hydrophilicity and zeta potential their adsorption and/or straining in the soil profile were differed. A. brasilense Cd has a smaller cell size, less adsorption and less straining than A. brasilense Sp7, thus its vertical movement is deeper. However, both strains accumulated at the vicinity of the water source. The results of this study will be presented and the pros and cons of three inoculation regimes will be discussed.

How to cite: Chen, F., Ronen, Z., and Arye, G.: Vertical movement of A. brasilense Sp7 and strain Cd in soil under different inoculation regimes, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-4252,, 2021.

Negar Ghaderi, Andrey Guber, Sajedeh Khosrozadeh, Vusal Guliyev, and Evgenia Blagodatskaya

Alive plants and soil microorganisms are the influential sources of extracellular enzymes facilitating decomposition of polymeric organic compounds. Enzyme activities are especially intensive and spatially heterogeneous in the rhizosphere, where microorganisms are stimulated by rhizodeposition. Two-dimensional activity distribution of hydrolytic enzymes participating in transformation of soil organics in the distance gradients from the root can be visualized under UV light by zymography - by placing a fluorogenic substrate-saturated membrane on the soil surface. Functional traits of enzymes can be co-localized with spatial distribution of enzymatic activity by precise micro-sampling based on zymography. We used rhizobox experiment to visualize activity of β-glucosidase, leucine aminopeptidase, and phosphatase in the rhizosphere of wild type and root hairless mutant of Zea mays L. cultivated for 3 weeks. After precise micro-sampling, we determined kinetic parameters of enzymes: max potential activity and affinity to substrate in the rhizosphere gradients. Finally, we compared the correspondence of enzymatic activity determined by zymography and by kinetic approach. This work was conducted within the framework of the priority program 2089, funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project number: 403664478. Seeds of the maize were provided by Caroline Marcon and Frank Hochholdinger (University of Bonn).

Keywords: zymography, enzyme kinetic, maize, rhizosphere gradients

How to cite: Ghaderi, N., Guber, A., Khosrozadeh, S., Guliyev, V., and Blagodatskaya, E.: Functional traits of hydrolytic enzymes and visualized enzymatic activity in the rhizosphere gradients of Zea mays L. , EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-5841,, 2021.

Lioba Rüger, Feng Kai, Dumack Kenneth, Chen Yan, Sun Ruibo, Deng Ye, Hochholdinger Frank, Vetterlein Doris, and Bonkowski Michael

This study was conducted within the framework of the DFG project SPP2089 “Rhizosphere Spatiotemporal Organization – a Key to Rhizosphere Functions”.

Different plant species select for individual subsets of bulk soil microbial communities within root systems. The fast variability of root environments implies that roots constitute highly dynamic habitats. Rapid root elongation, combined with widely varying quality and quantity of rhizodeposition between different root regions, lead to continuously changing conditions for colonizing microorganisms. As the microbiome concept implies a rather static outcome of the microbial assembly, it raises the question as to where and how the dynamic transition of a microbial bulk soil community into a plant species-specific rhizosphere microbiome is taking place.

To investigate the assembly of communities of prokaryotes and their microbial predators (Cercozoa, Rhizaria; protists) along the longitudinal root axis of maize (Zea mays L.), plants were grown in an agricultural loamy soil. Rhizosphere soil was sampled at distinct locations along roots. Diversity and co-occurrence of rhizosphere microbiota along the root axis were tracked by high-throughput sequencing, diversity measures and network analyses.

High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Deterministic processes of community assembly were revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their microbial predators. Deterministic processes were most robust in regions with fully developed lateral roots, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is of crucial importance.

How to cite: Rüger, L., Kai, F., Kenneth, D., Yan, C., Ruibo, S., Ye, D., Frank, H., Doris, V., and Michael, B.: Assembly patterns of the rhizosphere microbiome along the longitudinal root axis of maize (Zea mays L.), EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7196,, 2021.

Minh Ganther, Lioba Rüger, Michael Bonkowski, Anna Heintz-Buschart, and Mika Tarkka

This study was conducted within the framework of the DFG project SPP2089 “Rhizosphere Spatiotemporal Organization – a Key to Rhizosphere Functions” (project number 403641192).

As plant roots grow into the soil, the formation of biological gradients occurs at different spatial scales. It has been shown that plants recruit specific subsets of the soil bacterial community at their roots through excretion of mucilage at root tips and exudates at the sites of root hair formation. The promotion of or defense against certain bacterial taxa is also reflected in the composition of the protist communities that feed on bacteria.

Using high-throughput sequencing methods, we investigated emerging patterns in root gene expression in relation to bacterial and protozoan community structures. We found highly distinct root region specific patterns relating to differential root gene expression relating to growth, defense and transporter activity, as well as bacterial and protist (cercozoan) diversity. Root cap removal led to differently composed microbial communities, as well as a regulation of root genes relating to stress and defense. The lack of root hairs was only reflected in the amount of microbial carbon in soil and a small number of differentially expressed genes involved in cell wall processes.

We could show that the rhizosphere microbiome, is as dynamic as its environment. Root regions differentially affect microbial communities, which is also reflected in the expression of plant genes of categories relating to defense, immunity and stress. Our findings will further enhance our understanding of microbial root interactions at single root scale.

How to cite: Ganther, M., Rüger, L., Bonkowski, M., Heintz-Buschart, A., and Tarkka, M.: Integrated analysis of plant gene expression and bacterial and protozoan community composition reveals changes related to root zonation, root cap and root hair formation, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7518,, 2021.

Christoph Tebbe, Damini Damini, Damien Finn, Nataliya Bilyera, Minh Ganther, Márton Szoboszlay, Mika Tarkka, and Bahar S. Razavi

The deposition of energy rich carbon sources released by plant roots during their growth fuels microbially driven ecosystem processes in soil, but there is a lack of understanding how microorganisms interact and collaborate. The objective of this research was therefore to characterize microbial networks as they assemble under the influence of plant roots. To identify the specific importance of root hairs, we compared the impact of a maize wild-type to a root-air defective mutant (rth3; (1).

The microbial community structure was analyzed by qPCR and 16S rRNA gene amplicon sequencing from soil DNA. In order to increase the probability of detecting truly interacting microbial partners as a basis for network analyses, we first evaluated a new protocol to obtain DNA from as little as 1 mg instead of the usual 250 mg soil samples, thereby approaching the aggregate level (2). While the diversity of bacterial 16S rRNA gene amplicons of 250-mg samples taken from the same soil was not distinct, DNA analyses from individual aggregates clearly differed from each other underlining that soil aggregates represent distinct microbial habitats.

Soil column experiments with maize grown in a loam soil (3) revealed distinct communities between rhizosphere and bulk soil. The community composition of individual aggregates showed more differences in bulk soil compared to rhizosphere. Less elaborated networks were seen in bulk soil and a profound effect of root hairs could be unravelled. Null model testing demonstrated that Actinobacteria were equally important for network connectivity independent of the root hair mutation, but for networks of the wildtype, Acidobacteria were essential for synergistic interactions and overall network structure. In contrast, Proteobacteria and Firmicutes connectivity became more important. The observed differences in community composition and interactions suggests carbon cycling, and perhaps other microbially-driven functions, are markedly affected by the presence of root hairs.

Utilizing maize root soil microcosms for studying soil zymography in the rhizosphere allowed to obtain soil samples from regions with distinct specific enzyme activities. In order to enhance the detection of actively metabolizing bacterial community members, we studied rRNA sequences and compared it to rRNA gene sequences from the same samples. Currently the data are under analysis.


(1) Wen, T-J, Schnable PS (1994) Analyses of mutants of three genes that influence root hair development in Zea mays (Gramineae) suggest that root hairs are dispensable. Am. J. Bot. 81, 833–842.

(2) Szoboszlay M, Tebbe CC (2020) Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates. Microbiol. Open, e1144. DOI: 10.1002/mbo3.1144

(3) Vetterlein D et al. (2020) Experimental platforms for the investigation of spatiotemporal patterns in the rhizosphere – laboratory and field scale. J. Plant Nutr. Soil Sci., 000, 1–16 DOI: 10.1002/jpln.202000079

How to cite: Tebbe, C., Damini, D., Finn, D., Bilyera, N., Ganther, M., Szoboszlay, M., Tarkka, M., and Razavi, B. S.: Soil aggregate-based nucleic acid analyses of the impact of maize roots and their root hairs on the structural diversity of microbial communities, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7620,, 2021.

Bunlong Yim, Minh Ganther, Anna Heintz-Buschart, Mika Tarkka, Doris Vetterlein, and Kornelia Smalla

Plants interact with the rhizosphere microbiome via root exudates that consist of numerous metabolites serving as energy or carbon sources for microbial growth and as modulators of the uncountable rhizosphere interactions. The rhizosphere microbiome plays also an important role in plant health, growth, and productivity. Different drivers are known to shape the rhizosphere microbiome, but limited investigation exists whether there is a spatial variability in the microbiome along the root system (depth). The present study aimed to assess effects of potentially different drivers such as soil substrates, soil compartments (rhizosphere, and bulk soil), depths, and plant genotypes on bacterial/archaeal communities associated with two maize genotypes, root hair defective mutant (rth3), and the corresponding wild-type (WT). Experiments using maize genotypes rth3 and WT, grown on soil substrates loam, and sand under growth chamber, and field conditions were performed. Under growth camber conditions, the rhizosphere samples were harvested at twenty-two days after sowing the maize seeds from three different soil depths at 4.5 – 6.1 (GD1), 9.0 – 10.6 (GD2), and 13.5 – 15.1 (GD3) cm from soil surface. Under field conditions, analyses were carried out using both rhizosphere, and bulk soil samples taken at three developmental growth stages BBCH14, -19, and -59 of the maize plants; each from two depths at (0 – 20) FD1, and FD2 (20 - 40) cm from soil surface, except the BBCH14 (only samples from D1 were available). Bacterial/archaeal communities were analyzed by MiSeq Illumina sequencing of 16S rRNA gene fragments amplified from total community DNAs.

Under growth chamber conditions, we observed shifts in bacterial/archaeal diversity of maize rhizosphere at different depths as plant genotype- and soil substrate-dependent effects. Depth-dependent effects of maize rhizosphere (rth3/WT) on bacterial/archaeal compositions displayed high differences between GD1, and the GD3 on both soil substrates. The relative abundances of the bacterial phylum Proteobacteria were significantly higher at GD3 than GD1 for both plant genotypes on sand, but not on loam. Overall, the factor soil substrate was the strongest driver of bacterial/archaeal maize rhizosphere, followed by depth, and maize genotype.

Under field conditions, depths affected the rhizosphere bacterial/archaeal diversity only at the BBCH59 for WT grown on sand. Lower bacterial/archaeal diversity in soil substrates sand than loam was observed at both FD1 and FD2 in the rhizosphere, but not in bulk soil at all developmental growth stages of maize. The bacterial/archaeal diversity of both maize genotypes was not affected by developmental growth stages of maize on both soil substrates, and soil compartments. Depth gradients of bacterial/archaeal community composition in rhizosphere, and bulk soil displayed at BBCH59 on both soil substrates, and they were relatively higher on sand than loam (rhizosphere). Differences in relative abundances of the bacterial phyla Proteobacteria, and Actinobacteria between soil compartments, developmental growth stages of maize were observed mainly at FD1. Overall, factor soil compartment is the strongest driver of bacterial/archaeal communities followed by soil substrates, developmental growth stages and sampling depths for maize grown under field conditions.

How to cite: Yim, B., Ganther, M., Heintz-Buschart, A., Tarkka, M., Vetterlein, D., and Smalla, K.: Spatiotemporal organization of bacteria/archaea in maize rhizosphere, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7890,, 2021.

Yaarao Oppenheimer-Shaanan, Gilad Jakoby, Maya Laurenci Starr, Romiel Karliner, Gal Eilon, Maxim Itkin, Sergey Malitsky, and Tamir Klein

Root exudates are thought to play an important role in plant-microbial interactions. In return, soil bacteria can increase the bioavailability of soil minerals, which is typically decreasing in situations such as drought. Here we describe an exudate-driven microbial priming on Cupressus saplings grown outside in forest soil in custom-made rhizotron boxes. A 1-month imposed drought and inoculations with Bacillus subtilis and Pseudomonas stutzeri, bacteria species forest soil isolation, were applied in a factorial design. We revealed that both bacteria associated with Cupressus roots and were more abundant in rhizosphere than in bulk soil. Moreover, root exudation rate increased in inoculated trees under drought with >100 first identified metabolites from Cupressus roots. Among these metabolites, phenolic acid compounds, quinate, and others, were used as carbon and nitrogen sources by both bacterial species. Furthermore, soil phosphorous bioavailability was maintained only in inoculated trees, where a drought-induced decrease in leaf phosphorus and iron was prevented. We provide evidence that changes in exudation rate and composition under drought and bacteria inoculation, support the idea of root recruitment of beneficial bacteria. In turn, trees secreted further carbon source to the rhizosphere and hosted more bacteria, benefited from improved nutrition.

How to cite: Oppenheimer-Shaanan, Y., Jakoby, G., Starr, M. L., Karliner, R., Eilon, G., Itkin, M., Malitsky, S., and Klein, T.: A dynamic rhizosphere interplay between tree roots and soil bacteria under drought stress, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8069,, 2021.

Itamar Shabtai, Johannes Lehmann, and Taryn Bauerle

Plants allocate an estimated 11% of the C that they fixate as root exudates, a complex mixture of compounds that helps engineer the plant’s subterranean habitat. Root exudates stabilize soil aggregates, improve water retention, and shape rhizosphere microbial community composition. Exudates are also thought to contribute to the formation of stable mineral-associated organic matter. However, the function and fate of exudates along the soil profile may differ. We hypothesize that in topsoils with highly active microbial populations and mineral surfaces saturated with organic matter, root exudates may be rapidly intercepted and assimilated by soil microbes, and later adsorbed to surfaces as microbial necromass. But in subsoils with low microbial activity, exudates may directly adsorb on unsaturated mineral surfaces. The magnitude of these divergent pathways can shape the role of root exudates in rhizosphere C cycling. However, little is known about how adsorption vs. decomposition processes at the root-soil interface control i) the chemical transformations of C occurring along the root-microbe-mineral pathway, and ii) the spatial distribution and heterogeneity of exuded and processed exudate C. Our objective was to investigate the effect of microbial activity, and reactive mineral surfaces on the spatial distribution and functional group chemistry of root exudates at the root-microbe-mineral interface.

We packed samples from O, A, B, and C horizons collected from a grassland Mollisol, into individual microcosms, and installed a porous microdialysis membrane which served as an artificial root. Through this root, we injected either root exudates collected from maize plants, or dissolved organic carbon extracted from plant litter collected at the site. This comparison allowed us to study the dynamics of organic inputs entering the soil profile from the litter layer vs. directly from the roots. We destructively sampled the microcosms and obtained intact cross sections containing the artificial root and surrounding mineral/pore structures at different time points throughout the experiment. Here, we will present results obtained using synchrotron-radiation FTIR-microscopy of the temporal evolution, and spatial distribution of organic matter functional group chemistry in an artificial rhizosphere.

How to cite: Shabtai, I., Lehmann, J., and Bauerle, T.: Investigating the chemical and spatial distribution of root carbon along the root-microbe-mineral pathway, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8525,, 2021.

Francesco De Mastro, Andreina Traversa, Gennaro Brunetti, and Evgenia Blagodatskaya

Soil enzymes respond rapidly to changes in soil managements, and therefore are used as early and sensitive indicators of alteration in soil properties induced by tillage and additions of fertilizers. The aim of this work was to compare the effects of different tillage (no, minimum, and conventional tillage), fertilization and soil depth (0-30, 30-60 and 60- 90 cm) on the microbial biomass, enzyme activity and their relationship with soil nutrients in a semiarid Mediterranean agro-ecosystem. Growing and total microbial biomass decreased with depth together with the activities of β-glucosidase and N-acetyl-β-glucosaminidase presumably because of the reduced carbon and oxygen content in the deeper layers of soils. The fertilization stimulated fast-growing microorganisms with low affinity of enzyme systems to substrate, enhanced the growing microbial biomass and facilitated the turnover rate of soil organics. Under no tillage, all enzymes showed higher potential activity in top layers of fertilized plots as compared with non-fertilized ones. The minimum tillage practice increased the growing microbial biomass, and stimulated N- and P-acquiring enzymes due to  increased nutrients limitation. Parameters of microbial growth and enzyme kinetics are suitable indicators of microbial activity in semiarid Mediterranean agroecosystems.

How to cite: De Mastro, F., Traversa, A., Brunetti, G., and Blagodatskaya, E.: Enzymatic and microbial activities as influenced by tillage and fertilization in a semi-arid Mediterranean agroecosystem, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8646,, 2021.

Andrey Guber, Evgenia Blagodatskaya, and Alexandra Kravchenko

Plant roots and soil microorganisms produce hydrolytic extracellular enzymes to acquire nutrients via transformation of organic matter. Microorganisms inhabit hydraulically active pores, being attached to their surfaces or to organic and mineral colloids in soil solution. Therefore, diffusion of enzymes due to Brownian motion is constrained by their interactions with the surfaces of soil particles dispersed in the solution. It is generally unknown to which extent the extracellular enzymes are associated with solid and liquid soil phases and whether enzyme motility is affected by the movement of colloids occurring in soil solution. Therefore, the goal of our study was to quantify enzyme transport in soils with contrasting properties. Transport of ß-glucosidase, acid-phosphatase, xylosidase and cellobiohydrolase was studied in undisturbed non-sterile columns of soils with three contrasting textures: sandy, sandy loam and loam. The colloids, microorganisms, and enzymes inherent for each soil were applied via soil suspensions to the tops of the undisturbed columns. The suspensions were prepared by dispersing 1 g of each soil in 100 ml of de-ionized water, followed by 30 min sedimentation. Approximately 2.5 pore volumes of the applied suspensions were passed through the columns with continuous collection of the effluent from the bottom of the columns. The effluent was analyzed for colloid contents and enzyme activities before and after removal of soil particles of size 1-10 μm by centrifugation. From 7 to 49% of applied colloids recovered from the columns with higher colloid retention capacity in finer textured soils. The enzyme activity and colloid content were the highest in the first portions of the effluent and decreased as more suspension passed the columns, suggesting presence of enzymes and colloids in soil pores readily available for convective transport. Removal of soil particles of size 1-10 μm from the effluents by centrifugation reduced enzyme activity by factors 2-5, which was much larger than reduction in the enzyme solutions free of colloids centrifuged at the same settings (24- 30%). Our results indicated that most enzymes are present and transported through soil pores convectively while attached to soil colloids. Support for this research was provided by the USDA NIFA Program (Award # 2019-67019-29361), by the NSF LTER Program (DEB 1027253) at the Kellogg Biological Station, by USDA NC1187 project, by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0018409.

How to cite: Guber, A., Blagodatskaya, E., and Kravchenko, A.: Convective transport of enzymes through soil columns, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-9001,, 2021.

Alexandra Kravchenko and Andrey Guber

Soil microorganisms preferably occupy intermediate-sized pores, which are the arena for most biochemical reactions due to high nutrient contents and beneficial air and water regimes in these pores. Extracellular enzymes produced by microorganisms for organic matter transformations are assumed to reside in the same pores. However, there is a lack of direct experimental evidence of enzymatic activity being associated with pores of particular sizes. In this study we measured activity of ß-glucosidase in soil pores Ø<14 μm, 14<Ø<164 μm and Ø<164 μm. Undisturbed soil cores (5 cm Ø, 5 cm height) were taken at continuous sorghum (G2), switchgrass (G5) and restored prairie (G10) treatments of KBS Great Lakes Bioenergy Research Center's Biofuel Cropping System Experiment. Soil cores were drained at 500 kPa, and undisturbed subsamples (0.8 cm Ø, 1 cm height) were taken from them and placed at ceramic plates connected to a vacuum system. The same quantities of 4-Methylumbelliferyl β-D-glucoside were applied to soil subsamples at vacuum corresponded to saturation of the three studied groups of pores and kept in soil for 30 min. Produced 4-methylumbelliferone (MUF) was then extracted from the soil. The results demonstrated that the enzyme activity increased in all groups of pores in the order G2<G5<G10, but was significantly different only between G2 and G10 treatments for Ø<14 μm pores (p<0.05). The enzyme activity was lower in Ø<14 μm pores than in the 14<Ø<164 and Ø<164 μm pores (p<0.05), with only numerically higher activity in Ø<164 μm compared to the 14<Ø<164 μm pores. Interconnectivity of pores drained at different matrix pressures likely results in an overestimation of the enzyme activity associated with Ø<14 μm pores and an underestimation of that associated with 14<Ø<164 μm pores, hence the observed differences among the pore sizes are likely smaller than the actual pore effects. Thus, the results support our earlier observations and confirm that the activity of extracellular enzymes is higher within intermediate-sized pores than within fine pores. Support for this research was provided by the USDA NIFA Program (Award # 2019-67019-29361), by the NSF LTER Program (DEB 1027253) at the Kellogg Biological Station, by USDA NC1187 project, by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0018409.

How to cite: Kravchenko, A. and Guber, A.: Whether enzyme activity is the same in different soil pores, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-9009,, 2021.

Chiththaka Chaturanga D B Imihami Mudiyanselage, Matthias Schmidt, Yalda Davoudpour, Hryhoriy Stryhanyuk, Hans Richnow, and Niculina Musat

Studying the spatial distribution of bacteria and characterizing the soil chemistry (i.e., elemental, isotopic and molecular composition) underpins the comprehensive understanding of rhizosphere associated processes. During the past decades, several stand-alone methods have been developed to investigate soil chemistry, nutrient cycling and plant nutrition. However, individual approaches as stand-alone are not capable of providing an overall rhizosphere processes involving soil, root and microbes in a spatial context, as there is no common sample preparation method available to satisfy individual needs of each technique. Here, we present i) a sample preparation method, which includes soil embedding, sectioning and ii) a correlative imaging and image registration workflow, which allows for characterization of minerals, roots and microbes by different high-resolution imaging and microanalytical techniques. This allows for conducting rhizosphere studies on different scales, focusing on root-soil-microbe interfaces with spatial resolution of nano-meter scale. Hydrophilic, immunohistochemistry compatible, low viscosity LR White resin was used to embed and stabilize the soil and make it ultra-high vacuum compatible. We employed water-jet cutting as a novel approach to slice the embedded samples, and, by doing so, avoided polishing of the surface which often leads to translocation of sample material (smearing). The quality of this embedding was analyzed by and Helium Ion Microscopy (HIM). Epifluorescence microscopy in combination with Catalyzed Reporter Deposition-Fluorescence in-situ Hybridization (CARD-FISH) was employed to accurately identify and determine the spatial distribution of bacteria in the embedded sample, thus avoiding ambiguities from high levels of auto-fluorescence emitted by soil particles and organic matter. Chemical mapping of the rhizosphere was acquired by SEM/EDX, ToF-SIMS, nanoSIMS for elemental, molecular and isotopic characterization, respectively, and µ-Raman microscopy for specific identification of minerals.

In summary, we demonstrate that LR White embedding and water-jet cutting of soil in combination with CARD-FISH and a correlative microscopic workflow, allows for a comprehensive characterization of biotic and abiotic components in the rhizosphere. The developed sample preparation method can facilitate the various requirements of involved microscopy techniques and individual workflows for imaging and image registration to analyze data. We foresee that this approach will establish an excellent platform to study various soil processes and synergistic understanding of complex rhizosphere processes.

How to cite: Imihami Mudiyanselage, C. C. D. B., Schmidt, M., Davoudpour, Y., Stryhanyuk, H., Richnow, H., and Musat, N.: High-Resolution Chemical Mapping and Identifying Spatial Distribution of Microbes in the Zea mays Rhizosphere using Correlative Microscopy, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-12160,, 2021.

Sarah Bereswill, Nicole Rudolph-Mohr, and Sascha E. Oswald

Root respiration constitutes a major contribution to the CO2 efflux from vegetated soils. Amongst temperature, soil moisture is a key environmental variable determining respiration in soils, because it affects the amount of oxygen available for respiration as well as the CO2 gas transport within the soil pore space.

Non-invasive imaging techniques facilitate the in situ observation of the complex respiration patterns in the rhizosphere. We applied planar optodes (80x100 mm²) to map the CO2 and O2 concentration in the rhizosphere of white lupine plants (Lupinus albus) grown in slab-shaped glass rhizotrons (150x150x15 mm³) in sandy soil under P-deficient conditions. Respiration was measured daily for 19 days after planting at constant soil moisture content as well as during a drying-rewetting experiment, during which soil volumetric water content varied between 0.1 and 0.3 cm³ cm-3.

During their development, the plants exhibited a heterogeneous spatial pattern of root respiration; the highest CO2-concentrations were measured at the root tips and along younger parts of the root system. Heterogeneity in CO2 and O2 patterns was most pronounced in the drying-rewetting experiment: Distinct hotspots of CO2-release and oxygen consumption emerged 30 to 60 minutes after watering. The hotspot-regions correlated with the location of cluster roots growing close to the optodes, where up to three times increased CO2 concentrations occurred. Overall CO2 concentrations in the bulk soil increased as CO2 accumulated over time as gas diffusion in the wet soil was limited.

Our results highlight the strong spatial and temporal variability of root respiration throughout the growth and development of the root system, and particularly in response to an increase in soil moisture. Further experiments aim to combine CO2 and O2 optode measurements with neutron computed laminography, a tomographic imaging method suited to capture the 3D root system architecture of plants grown in laterally extended rhizotrons in order to link root respiration to root branching order, diameter and functional type.

How to cite: Bereswill, S., Rudolph-Mohr, N., and Oswald, S. E.: Non-invasive imaging of CO2 and O2 concentration reveals hotspots of root respiration , EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13279,, 2021.

James Moran, Vivian Lin, Ying Zhu, Allison Thompson, Samuel Purvine, Nikola Tolic, Joshua Rosnow, and Mary Lipton

Extensive spatial variability combined with analytical challenges associated with soil sampling complicate efforts to elucidate plant-microbe interactions within the rhizosphere, changes in these relationships over time, and the impacts of shifting microenvironmental conditions on microbial community membership and activity. Proteomics analysis of root or soil samples can provide insights to the taxonomy and functional capability of microbial populations and be used to augment various genomic and imaging techniques. Historically, however, proteomics relies on bulk level sampling by removing rhizosphere over relatively large lengths of root surface and is, therefore, neither spatially specific nor non-destructive. We are employing spatially resolved, non-destructive harvesting of mobile proteins onto a membrane to enable both two-dimensional protein mapping and proteomic analysis within rhizosphere while preserving the sample for either timeseries measurements or complementary, destructive techniques.

We are using rhizoboxes planted with switchgrass (variety Cave-in-rock) and constructed with natural soil (Kellogg Biological Station, Hickory Corners, Michigan, USA) to develop the approach. We are coupling membrane extraction with specialized sample digestion, purification, and analysis to enable proteomic interpretation. Through its non-destructive nature, this approach permits timeseries analyses for tracking specific taxa and, in some cases, functions associated with rhizosphere processes before and after a system perturbation or over plant growth phases during a growing season. The method’s high sensitivity enables spatial analysis at the up to two-millimeter diameter scale along the rhizobox sampling plane and samples can be manually selected based on proximity to specific root structure, metabolic hotspots, or other parameters of choice. We are using this analysis to track statistically significant shifts in plant and microbe contributions to rhizosphere proteome associated with roots at different growth stages. We are also linking this approach to a 13C tracer to identify specific taxonomic groups having the closest metabolic association with a host plant to identify shifts in plant-microbe interactions associated with nutrient availability. For instance, we are using a split root rhizobox approach to monitor the plasticity of plant-microbe C exchange associated with P availability. Combined, the spatial and 13C tracer components of this proteomic technique can help illuminate understanding of the complex inter-kingdom interactions within the rhizosphere and the implications these interactions have on driving C cycling and plant performance.

How to cite: Moran, J., Lin, V., Zhu, Y., Thompson, A., Purvine, S., Tolic, N., Rosnow, J., and Lipton, M.: Assessing plant-microbe interactions in the rhizosphere using spatially resolved proteomics , EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13838,, 2021.

Patrick Duddek, Mutez Ahmed, Nicolai Koebernick, Luise Ohmann, Goran Lovric, and Andrea Carminati

Due to global warming, future agriculture will have to face increasing temperatures, more frequent and extreme drought events and consequently water and nutrient scarcity. Thus, it is necessary to improve our understanding of how plants deal with dry conditions. Since there is still a lack of knowledge concerning below ground feedbacks of plants to drought, we are particularly interested in the response of below ground organs to soil drying.

Hence, the objective of our study was to determine morphological responses of roots and root hairs to soil drying in situ.
For this purpose, we have grown maize plants (Zea maize wildtype) in seedling holder microcosms for 8 days before harvesting and performing high-resolution synchrotron X-ray CT in order to visualize root compartements as well as the elongated root hairs (Koebernick et al. 2017). The segmented images served as basis for the quantification of our observations.

The results revealed that not only roots (Carminati et al. 2012) but also root hairs lose turgidity under dry soil conditions. This shrinkage of hairs occurs at high soil water potentials and reduces the surface and soil contact area of roots tremendously. Root hair shrinkage is the first step in a sequence of responses to progressive soil drying. The follow up processes within this sequence are the formation of cortical lacunae and root shrinkage resulting in air filled gaps at the root-soil interface. Severe cavitation within the xylem was not observed at the corresponding soil water potentials meaning that xylem embolism occurs at even lower potentials. This leads to the conclusion that there is a severe loss of root-soil contact and consequently of hydraulic conductivity at the root-soil interface before xylem cavitates and reduces water as well as nutrient fluxes in the radial root direction.
As not only roots but also root hairs take up nutrients and release exudates (Holz et al. 2017), they are assumed to be an important trait of the rhizosphere for both nutrient uptake and microbial activity. Furthermore, they increase the radial extent of the rhizosphere and although it is not yet clear if shrunk root hairs are inactive in exudation and nutrient uptake, their enormous shrinkage due to soil drying might limit rhizosphere processes.

In summary, losses of root-soil contact due to root and particularly root hair shrinkage are profound and occur at high water potentials.



  • Carminati, A., Vetterlein, D., Koebernick, N., Blaser, S., Weller, U., & Vogel, H.-J. (2012). Do roots mind the gap? Plant and Soil, 367(1–2), 651–661.
  • Holz, M., Zarebanadkouki, M., Kuzyakov, Y., Pausch, J., & Carminati, A. (2017). Root hairs increase rhizosphere extension and carbon input to soil. Annals of Botany, 121(1), 61–69.
  • Koebernick, N., Daly, K. R., Keyes, S. D., George, T. S., Brown, L. K., Raffan, A., Cooper, L. J., Naveed, M., Bengough, A. G., Sinclair, I., Hallett, P. D., & Roose, T. (2017). High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation. New Phytologist, 216(1), 124–135.


How to cite: Duddek, P., Ahmed, M., Koebernick, N., Ohmann, L., Lovric, G., and Carminati, A.: Loss of root-soil contact due to root and root hair shrinkage, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-15913,, 2021.