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.

Co-organized by BG3
Convener: Hannes SchmidtECSECS | Co-conveners: Evgenia Blagodatskaya, Carsten W. Mueller, Steffen Schlüter
| Attendance Thu, 07 May, 08:30–10:15 (CEST)

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Chat time: Thursday, 7 May 2020, 08:30–10:15

D2073 |
| solicited
| Highlight
Tiina Roose, Siul Ruiz, Dan McKay Fletcher, Katy Williams, Chiara Petroselli, Callum Scotson, and Arjen van Veelen

We rely on soil to support the crops on which we depend. Less obviously we also rely on soil for a host of 'free services' from which we benefit. For example, soil buffers the hydrological system greatly reducing the risk of flooding after heavy rain; soil contains very large quantities of carbon, which would otherwise be released into the atmosphere where it would contribute to climate change. Given its importance it is not surprising that soil, especially its interaction with plant roots, has been a focus of many researchers. However the complex and opaque nature of soil has always made it a difficult medium to study.

In this talk I will show how we can build a state of the art image based model of the physical and chemical properties of soil and soil-root interactions, i.e., a quantitative, model of the rhizosphere based on fundamental scientific laws.
This will be realised by a combination of innovative, data rich fusion of structural and chemical imaging methods, integration of experimental efforts to both support and challenge modelling capabilities at the scale of underpinning bio-physical processes, and application of mathematically sound homogenisation/scale-up techniques to translate knowledge from rhizosphere to field scale. The specific science questions I will address with these

techniques are: (1) how does the soil around the root, the rhizosphere, function and influence the soil ecosystems at multiple scales, (2) what is the role of root- soil interface micro morphology on plant nutrient uptake, (3) what is the effect of plant exuded mucilage on the soil morphology, mechanics and resulting field and ecosystem scale soil function and (4) how to translate this knowledge from the single root scale to root system, field and ecosystem scale in order to predict how the climate change, different soil management strategies and plant breeding will influence the soil fertility.

How to cite: Roose, T., Ruiz, S., McKay Fletcher, D., Williams, K., Petroselli, C., Scotson, C., and van Veelen, A.: Multimodal Imaging of Plant-Soil Interaction for Better and More Predictive Modelling of Rhizosphere Processes, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-4634, https://doi.org/10.5194/egusphere-egu2020-4634, 2020

D2074 |
Alice Lieu, Alexander Prechtel, Nadja Ray, and Raphael Schulz

A novel, comprehensive modeling approach extending (Ray et al., 2017, Rupp et al., 2018, Rupp et al., 2019) is used to study the interplay between biogeochemical processes in the rhizosphere. Understanding these local interactions is crucial for the habitat as they influence processes in the root-soil system such as the water and nutrient uptake by the roots. The mechanistic model explicitly represents the pore structure and allows for dynamic structural organization of the rhizosphere at the single root scale.

At this microscale, the movement of interacting entities - nutrients, bacteria and possibly charged chemicals - in the fluid is described by means of the diffusion and Nernst-Planck equations with a Henry transmission condition at the liquid/gas interfaces. A biomass phase can develop from agglomerations of bacteria and stabilising sticky agents may grow or decay at the solid surfaces. To take into account specific properties of the rhizosphere, root cells and an explicit phase of exudated mucilage as well as root hairs are included. In addition to solving the continuous partial differential equations, a discrete cellular automaton method (Tang and Valocchi 2013, Ray et al. 2017, Rupp et al., 2019) is used, enabling structural changes in the solid and mucilage phases at each time step. The partial differential equations are discretised with a local discontinuous Galerkin method which is able to handle discontinuities induced by the evolving geometry.

The microscale model is not amenable to large scale computations because of its high complexity. Upscaling techniques enable the incorporation of information from the rhizosphere scale to the macroscale. We apply these techniques to dynamically evolving microstructures taking the spatiotemporal evolution of the rhizosphere into account. Although the setting is periodic, the underlying geometries can be arbitrarily complex. The resulting hydraulic properties (e.g. diffusion coefficient, permeability) are an important input for existing root-water uptake models, involving e.g., the effect of mucilage.

In this study, we use two- and three-dimensional CT scans of maize root, and show how mucilage concentration as well as its distribution in the pore space result in changes of macroscopic soil hydraulic properties. The access of nutrients in small pores for the root is assessed in simulation studies and its effect on effective diffusivity is evaluated.

N. Ray, A. Rupp and A. Prechtel (2017): Discrete-continuum multiscale model for transport, biomass development and solid restructuring in porous media. Advances in Water Resources 107, 393-404.

A. Rupp and K. Totsche and A. Prechtel and N. Ray (2018): Discrete-continuum multiphase model for structure formation in soils including electrostatic effects. Frontiers in Environmental Science, 6, 96.

A. Rupp, T. Guhra, A. Meier, A. Prechtel, T. Ritschel, N. Ray, K.U. Totsche (2019): Application of a cellular automaton method to model the structure formation in soils under saturated conditions: A mechanistic approach. Frontiers in Environmental Science 7, 170.

Y. Tang and A.J. Valocchi (2013): An improved cellular automaton method to model multispecies biofilms. Water Research 47 (15), 5729-5742.

How to cite: Lieu, A., Prechtel, A., Ray, N., and Schulz, R.: A micro-macroscale approach coupling processes that shape rhizosphere diffusivity and permeability, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-7925, https://doi.org/10.5194/egusphere-egu2020-7925, 2020

D2075 |
Eva Lippold, Maxime Phalempin, Steffen Schlüter, Robert Mikutta, and Doris Vetterlein

Root hairs substantially contribute to the acquisition of nutrients and potentially also to water uptake. Hence, they might have a strong impact on plant growth under nutrient- or water-limited conditions. As little information presently exists about differences in matter uptake to plants either with or without root hairs, we hypothesize that the absence of root hairs will be compensated by an increase in root growth to overcome the hair-less handicap. Within the DFG-funded Priority Program 2089, we compare two different genotypes (i.e. Zea mays “Wild Type” and its corresponding hair-less mutant “rth3”) grown in two different substrates (loam and sand) in column experiments. X-ray computed tomography (X-ray CT) was used to investigate the spatial-temporal change of root architecture during growth. Additionally, total root length was measured after destructive sampling at harvest with WinRhizo. Contrary to our expectation, the reduced root surface area available for water and nutrient uptake in case of the hair-less cultivar was not compensated by more intensive root growth. The substrate had a higher impact on root growth than the presence or absence of root-hairs. For shoot growth (shoot biomass), both factors (genotype, substrate) had a significant impact. As a consequence, nutrient uptake efficiency (uptake per unit root length) was clearly increased by the presence of root-hairs, irrespective of the substrate. Water uptake efficiency did not show any difference between genotypes under the well-watered conditions studied. In general, water uptake per unit root length was higher in sand compared to loam. Differences in nutrient uptake efficiency should be reflected in the extent of nutrient depletion gradients around roots. To address such biochemical gradients we develop a new subsampling scheme based on extraction of undisturbed subsamples. Subsamples will be imaged with micro X-ray fluorescence (μXRF) for elemental mapping. The 2D µXRF image will be registered into the 3D X-ray CT image to relate the extent of gradients to the age of the respective root segment.


This project was carried out in the framework of the priority programme 2089 “Rhizosphere spatiotemporal organisation - a key to rhizosphere functions” funded by DFG (project number 403640293).

How to cite: Lippold, E., Phalempin, M., Schlüter, S., Mikutta, R., and Vetterlein, D.: Root system architecture with and without root hairs: Consequences for nutrient and water uptake efficiency and related spatio-temporal patterns, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-8612, https://doi.org/10.5194/egusphere-egu2020-8612, 2020

D2076 |
Scott Buckley, Richard Brackin, Torgny Näsholm, Susanne Schmidt, and Sandra Jämtgård

Plant root exudates are believed to increase root capture of nutrients (including nitrogen) by encouraging development of a rhizosphere root community, and providing them with an energy source to facilitate degradation of litter and soil organic matter. However, observing the consequences of root exudation on nutrient cycling and microbial activity is challenging with current methods, given the small scales involved. We investigated the effect of root exudation on nitrogen (N) availability by simulating root exudation with microdialysis. This novel technique enables continuous release of synthetic solutions of root exudates via diffusion in situ in soil by using a root-sized permeable membrane. Importantly, it also allows for simultaneously monitoring the effects on inorganic N fluxes. To emulate growth of a root tip through a specific soil region, sucrose was released for seven days before substituting sucrose with water for a further 7 days. We investigated boreal forest soils with and without litter amendments (ground pea shoots) to attain different C/N ratios and we used two rates of exudation by retrodialysing with either 0.5 or 5 mM sucrose solution. We observed that pea litter promoted significant N immobilisation, along with greater rates of sucrose release from microdialysis probes - peaking at 90.7 ± 8 µg sucrose m-2 s-1 using the 5 mM sucrose solution after three days. This suggests that greater root exudation may be driven by microbial demand for both C and N, with no short-term nutritional benefit for plant roots, even after exudation has ceased within a specific soil region. Glucose and fructose fluxes (breakdown products of sucrose) were also greatest in the litter treatment, indicating enzyme activity was promoted by the availability of both sucrose and litter. CO2 respiration measurements indicated significant differences between litter and control soils, but there was no detectable effect of sucrose exudation, suggesting that the small amounts of C supplied and the limited area influenced by the diffusion of sucrose had little impact on overall microcosm respiration. We conclude that short-term C exudation presented no immediate benefit for plant nutrition in our experiment. Future studies can benefit from using microdialysis to investigate the influence of more complex root exudate solutions, as well as the mechanistic roles of transpiration-induced mass flow on plant N availability in the rhizosphere.

How to cite: Buckley, S., Brackin, R., Näsholm, T., Schmidt, S., and Jämtgård, S.: The effect of root exudates on soil nitrogen availability - an evaluation using microdialysis, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-14310, https://doi.org/10.5194/egusphere-egu2020-14310, 2020

D2077 |
James Moran, Vivian Lin, Ying Zhu, Nikola Tolic, Samuel Purvine, Joshua Rosnow, and Mary Lipton

Clear elucidation of plant-microbe interactions within the rhizosphere and how these relationships change over time can be confounded by the large microbial biodiversity, shifting microenvironmental conditions, and extensive spatial constraints within these complex systems. Proteomics analysis of root or soil samples, when linked with metagenomic interpretation, can provide key insights to both the taxonomy and functional capability of microbial populations within a sample. Yet, existing proteomic approaches may not always be able to provide the needed temporal and spatial resolution to capture fine-scale and short-term interactions between plants and microorganisms. To remedy this limitation, we are developing a suite of methodological adaptations intended to leverage proteomic analysis to help identify key interactions between rhizosphere microorganisms and their host plant.

First, we are employing 13C tracers coupled with automated data analysis to identify specific organisms consuming both simulated and natural root exudates. We are specifically exploring microcosms constructed from natural soil (Kellogg Biological Station, Hickory Corners, Michigan, USA) and planted with switchgrass as a platform for developing the techniques. Multiple previous studies have linked key interactions between both free-living and epiphytic microbial members with improved performance of a switchgrass host under nutrient-depleted, natural field conditions. Providing evaluation of the amount and taxonomic recipient of switchgrass-supplied carbon under varying conditions may help link key taxonomic groups with improved plant performance and biomass production.

Second, we are leveraging a membrane extraction technique coupled with specialized sample digestion, purification, and analysis to enable non-destructive, spatially-resolved protein extraction from the root-soil interface within our constructed microcosms. Through its non-destructive nature, this approach permits timeseries analysis for tracking specific taxa and, in some cases, functions associated with rhizosphere processes both before and after a system perturbation as well as variations over plant growth phases during a growing season. The high sensitivity of this system enables spatial analysis at the one to two mm scale where samples can be manually selected based on proximity to specific root structure, metabolic hotspots in the system, or other parameter of choice. Spatial analysis can be leveraged to track taxonomic distribution within the rhizospheres associated with roots at different growth stages or levels of maturity.

How to cite: Moran, J., Lin, V., Zhu, Y., Tolic, N., Purvine, S., Rosnow, J., and Lipton, M.: Deciphering taxonomic carbon exchange between plants and microorganisms using proteomics coupled with 13C tracers and spatially resolved protein extraction, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-12304, https://doi.org/10.5194/egusphere-egu2020-12304, 2020

D2078 |
Bahar S. Razavi, Nicole Rudolph-Mohr, and Christoph Tebbe

Soil compaction is a multi-disciplinary problem in which soil, plant, and air operations play an important role and may have dramatic environmental consequences throughout the world. In compacted soils, the increase in bulk density, and the accompanying decrease in porosity hinders the exchange of oxygen, carbon dioxide and other gases, thereby causing hypoxic stress in plant roots. Hypoxic stress can effects root physiological functions, reduce soil enzyme activity, hence reducing soil fertility. For the first time we applied a unique combination of two imaging techniques, zymography and optodes sensors with molecular microbial community analysis to illuminate the rhizosphere self-regulation for amelioration of microbiophysical properties of compacted soil. To this end maize in compacted and uncompacted soil under control condition for 2 weeks was planted.

Soil oxygen map and β-glucosidase activity in compacted maize treatment overlaid with the extracted root system demonstrated more than 65% positive correlation between hotspots of enzymatic activity and localities with high oxygen concentration –which were mostly in association with root. Similarly, extend of rhizosphere for oxygen concentration and enzyme activity across the root of compacted soil was 1mm broader than the uncompacted.

Based on root morphology analysis, compacted maize reduced roots diameter and increased the distribution. Which resulted in 30% higher ratio of rhizosheath mass in compacted than uncompacted soil. Rhizosheath formation changed porosity and aggregation around the root, thus, improved oxygen exchange. Accordingly, bacterial abundance and alpha diversity in hotspots of compacted soils were higher than the one of uncompacted. Thus, microorganisms localized in hotspots (rhizosheath) respond to better aeration, new carbon inputs compared to those inhabiting in the bulk soil. This confirms the distinguished role of rhizosphere-self organization for enzymatic mobilization of nutrients, and point out on the importance of aeration for rhizospheric microbial functionality (such as, enzyme expression for nutrients mining).

How to cite: Razavi, B. S., Rudolph-Mohr, N., and Tebbe, C.: Rhizosphere legacy: amelioration of MicroBioPhysical properties of compacted soil, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-6171, https://doi.org/10.5194/egusphere-egu2020-6171, 2020

D2079 |
Kristian Thorup-Kristensen

Water and nutrients are distributed throughout the soil volume, and their ability to move towards the plant roots is highly restricted, in most cases to a few mm or less. This mean, that unlike the aboveground resources of light and CO2 moving to the plants, roots need to grow towards the resources. Thus, for efficient resource uptake, roots need to be well distributed in the soil, both locally within the root zone and to grow deep to increase the overall volume of soil exploited. In crop production, deep rooting has been shown to be highly important for water and nitrogen use, and deep rooting is expected to contribute specifically to soil C sequestration.

Research into deep rooting and its functions is strongly restricted by the difficulties of studying roots hidden deeply in the soil. It is very laborious to access them, and even more difficult to set up experiments giving frequent and non-destructive measurements of the relevant parameters.  

In previous experiments, we have studied deep rooting of crops and cover crops and its effect on deep nitrogen uptake. By measuring roots and soil nitrogen to 2.5 m depth, we found that deep rooting was a main factor in nitrogen uptake and the reduction of nitrogen leaching loss. This showed how deep rooted species can be used to develop nitrogen efficient cropping systems. Further, it was shown that inclusion of deeper soil layers in the studies were critical for the conclusions to be drawn. Increasing the depth of study from e.g. 1 m to 2.5 m did not just moderate the conclusions and quantitative estimates, in several studies it basically changed conclusions that could be drawn.

Since 2015, we have built three new research platforms dedicated to detailed study of deep root growth and function. We have built a rhizobox facility consisting of 24 rhizoboxes each 4 m deep. The rhizoboxes are equipped with soil water sensors, and give access to observe the roots, take soil and root samples and inject tracers along the whole soil profile. In the field, we have built a platform, aimed at giving similar research possibilities, using long minirhizotrons, soil water sensors and metal access tubes for inserting ingrowth cores, all together giving valuable opportunities, though we cannot achieve the same easy access to the root zone as in the rhizoboxes. Finally, we have built a deep root phenotyping facility, using minirhizotrons to allow screening of 600 plant lines for root growth down to 3 meters depth, and allowing us to measure root activity of the lines by deep placement of isotope tracers.

These new facilities, and the research opportunities they give will be discussed, together with some of the first research results on deep roots we have obtained there.

How to cite: Thorup-Kristensen, K.: Studying deep rooting and its value for crops, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-22488, https://doi.org/10.5194/egusphere-egu2020-22488, 2020

D2080 |
Doris Vetterlein, Susanne Schreiter, Eva Lippold, Maxime Phalempin, Sebastian Blaser, and Steffen Schlüter

A better understanding of how roots explore soil is crucial for plant breeding, yield increase and sustainable agriculture. This requires detailed knowledge about the temporal dynamics of root system architecture under field conditions, which is hard to achieve as sampling of roots with unconstrained growth (no root windows) is very laborious. 
Here we present the results of a major undertaking to sample maize roots in a field experiments at four growth stages in various depths (0-20, 20-40, 40-60 cm) with two different methods: a) destructive sampling with a root corer and root washing vs. b) undisturbed sampling combined with root detection in X-ray CT images. The first method results in root length data with a higher number of technical replicates per depth and plot, whereas the second provides more details of small-scale rooting patterns and plant-soil interactions in intact soil for a smaller number of samples.
The aim of the study was to explore differences in spatio-temporal root growth patterns between two different maize genotypes (wild type vs. root hairless mutant) growing in two different homogenized substrates (sand vs. loam). For disturbed sampling we found that for both genotypes root growth was more vigorous in sand during the entire growing season. This was remarkable since shoot biomass was larger on the loam plot. As drought developed during the growing season, root length density profiles reversed in loam, but not on sandy substrate. For intact cores we find the same trends so that they can now be analyzed towards inter-root distances at shorter scales.
In loam the absence of root hairs and the associated reduction of available surface for water and nutrient uptake resulted in a 50% reduction in shoot biomass, whereas root length profiles did not differ in the root corer data. In sand differences in shoot biomass between genotypes were comparable, but here root length densities were lower for the root hairless mutant in the root corer data. Unexpectedly there was no compensation of lacking root hairs by enhanced root growth. The root length data in intact samples showed higher variation due to smaller sampled volumes which disguised possible trends between genotypes.
In summary, the different hydraulic properties of the substrates had a strong effect on root growth and root distribution with depth, whereas the genotype governed shoot biomass supposedly through differences in nutrient and/or water uptake efficiency mediated by the presence or absence of root hairs. As the next steps, these observations will be underpinned by transpiration and soil moisture monitoring data as well as plant nutrient uptake data.

How to cite: Vetterlein, D., Schreiter, S., Lippold, E., Phalempin, M., Blaser, S., and Schlüter, S.: Spatio-temporal dynamics of root system architecture of maize in a field trial during a growing season, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-5061, https://doi.org/10.5194/egusphere-egu2020-5061, 2020

D2081 |
Maxime Phalempin, Eva Lippold, Doris Vetterlein, and Steffen Schlueter

X-ray computed tomography (CT) is acknowledged as a powerful tool for the study of root system architecture (RSA) of plants grown in soil. The study of the root system properties is however only possible after performing root segmentation, i.e. the binarization of all root voxels. Root segmentation is often regarded as a tedious and difficult task as its success depends on several factors such as the image resolution, the signal to noise during image acquisition and the gray value contrast between the roots and all other surrounding features. Here, we present an improved method for the segmentation of roots from X-Ray computed tomography 3D images. The algorithm Rootine (Gao et al. 2019) does not detect roots by their gray values but by their characteristic tubular shape. This algorithm was further developed in order to improve the root recovery rate and to reduce the number of parameters involved during the segmentation process. This was achieved by adding two key steps: (1) an absolute difference transform and (2) an automatic calculation of the parameters used during the Gaussian smoothing. The first step allows for targeting specific features based on a gray value criteria contained within a user-defined gray value range in order to better distinguish roots from pores whereas the second step allows for targeting root segments of specific diameters. On the benchmark dataset of Gao et al. 2019, the newly called “Rootine v.2” was able to recover 34 % more roots as compared to its preceding version. Moreover, the number of parameters was reduced from 10 down to 5 which allows for a faster calibration and an overall better usability of the algorithm. The presented method also allows for a more reliable estimation of root diameter derived from X-Ray CT images. This work was carried out in the framework of the priority programme 2089 “Rhizosphere spatiotemporal organization - a key to rhizosphere functions” funded by DFG (project number 403640293).

How to cite: Phalempin, M., Lippold, E., Vetterlein, D., and Schlueter, S.: An improved method for the segmentation of roots from X-Ray computed tomography 3D images: Rootine v.2, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-5225, https://doi.org/10.5194/egusphere-egu2020-5225, 2020

D2082 |
Minh Ganther, Marie-Lara Bouffaud, Lucie Gebauer, François Buscot, Doris Vetterlein, Anna Heintz-Buschart, and Mika Tarkka

The complex interactions between plant roots and soil microbes enable a range of beneficial functions such as nutrient acquisition, defense against pathogens and production of plant growth hormones. The role of soil type and plant genotype in shaping rhizosphere communities has been explored in the past, but often without spatial context. The spatial resolution of rhizosphere processes enables us to observe pattern formation in the rhizosphere and investigate how spatial soil organization is shaped through soil–plant–microbiome interactions.

We applied spatial sampling in a standardized soil column experiment with two maize genotypes (wildtype vs. roothairless3) and two different soil textures (loam vs. sand) in order to investigate how in particular functions of the maize roots relating to nutrient/water uptake, immunity/defense, stress and exudation are affected. RNA sequencing and differential gene expression analysis were used to dissect impact of soil texture, root genotype and sampling depth. Our results indicate that variance in gene expression is predominantly explained by soil texture as well as sampling depth, whereas genotype appears to play a less pronounced role at the analyzed depths. Gene Ontology enrichment analysis of differentially expressed genes between soil textures revealed several functional categories and pathways relating to phytohormone-mediated signaling, cell growth, secondary metabolism, and water homeostasis. Community analysis of rhizosphere derived ACC deaminase active (acdS gene including) plant beneficial bacteria, which suppress the phytohormone ethylene production, suggests that soil texture and column depth are the major factors that affect acdS community composition.

From the comprehensive gene expression analyses we aim to identify maize marker genes from the relevant core functional groups. These marker genes will be potentially useful for future experiments; such as field plot experiments for investigation of later-emerging plant properties.

This research was conducted within the research program “Rhizosphere Spatiotemporal Organisation – a Key to Rhizosphere Functions” of the German Science Foundation (TA 290/5-1).

How to cite: Ganther, M., Bouffaud, M.-L., Gebauer, L., Buscot, F., Vetterlein, D., Heintz-Buschart, A., and Tarkka, M.: Spatial sampling approach to unravel the impact of soil texture and root genotype on maize root gene expression profiles, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-9707, https://doi.org/10.5194/egusphere-egu2020-9707, 2020

D2083 |
Riffat Rahim, Adrian Haupenthal, and Eva Kroener

Root exudates stimulate microbial activity and functions as a binding and adhesive agent that increases aggregate stability in the rhizosphere. The exudates produced from plant roots and microorganisms in the rhizosphere play a significant role in the formation of rhizosheath. Rhizosheaths comprises the soil that adheres to the roots with the help of root hair and mucilage even when it is removed from the surrounding soil. Low surface tension and great viscosity stabilize soil aggregates in surrounding root and develop rhizosheath formation. To our knowledge, no investigations are made on the influence of root exudates in soil rhizosheath formation, although it is well documented the formation and stabilization of rhizosheath of maize plants under various soil water contents but the influence of root exudates on the rhizosheath formation associated with other rheological properties is still missing. Such knowledge will greatly enhance the understanding of how rhizosheath is formed under different root and seed exudates and the effect of their physiochemical properties on the adhesion properties of mucilage will be studied in this project.

The aim of this study is to provide the first combined quantitative data on how root and seed exudates of different plants affect rhizosheath formation. We hypothesized that mucilage will contribute to the formation of rhizosheaths.  For this, we will use the mucilage of chia seeds which acts as a modelled plant root mucilage and mix it with soil in five different concentrations. After preparing the soil with mucilage, artificial roots (flax cords) will be incorporated in this soil and after drying and wetting cycles roots will be removed and the mucilage adhesion, simulation and rheological properties will be investigated under various soil water contents, soil texture, soil type, and soil compaction.

Key words:

                   Rhizosheath, mucilage, drying and wetting cycles and soil structure


How to cite: Rahim, R., Haupenthal, A., and Kroener, E.: Implications of root exudates on the formation of rhizosheaths, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-10412, https://doi.org/10.5194/egusphere-egu2020-10412, 2020

D2084 |
Dayong Gan, Jiguang Feng, and Biao Zhu

Interactions among plants, soil and microbiota play an important role in maintaining the function of terrestrial ecosystems, which often occur in rhizosphere. The rhizosphere effect is defined as the difference in soil properties and biogeochemical processes between rhizosphere and root-free bulk soil. Despite its importance in controlling soil biogeochemical cycling, quantitative assessments of the rhizosphere effects of woody plants are still rare. In this study, we synthesized the rhizosphere effects of woody plants on soil physicochemical properties, microbial biomass and community structure, enzyme activities, and carbon (C) and nitrogen (N) mineralization rates. We also explored the controls of rhizosphere effects by functional traits (eg. leaf life form, mycorrhizal type), environmental and experimental variables (eg. soil sampling method).

Our results showed that the rhizosphere effects on most soil physicochemical variables were positive (except pH). For example, the rhizosphere stimulated C mineralization rate by 56.7%, gross N mineralization rate by 57.9%, and net N mineralization by 60.9% on average compared to the root-free bulk soil. Moreover, for enzyme activities and C mineralization rate, the rhizosphere effects were generally higher in shrubs than in trees. For C mineralization rate, the rhizosphere effects of evergreen species were stronger than those of deciduous species. However, the rhizosphere effects did not vary significantly between species associated two mycorrhizal types (arbuscular mycorrhizal, AM vs. ectomycorrhizal ECM), with few exceptions for NO3-, NH4+, bacteria and fungi biomass. Overall, this meta-analysis comprehensively assessed the rhizosphere effects of woody plants (187 species and 29 variables) on global scale and strengthened our understanding of the effect of living roots on soil C and nutrient cycling in the rhizosphere.

How to cite: Gan, D., Feng, J., and Zhu, B.: Rhizosphere effect of woody plants: A meta-analysis, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-6428, https://doi.org/10.5194/egusphere-egu2020-6428, 2020

D2085 |
Vusal Guliyev, Melissa Pfeiffer, Maria Udovenko, Christina Fasching, Thomas Reitz, and Evgenia Blagodatskaya

Fresh input of organic material in soil is continuously transformed and processed by growing microorganisms using this organic input as a substrate. Therefore, the quality and quantity of soil organic C stock is strongly dependent on the intensity of mineralization processes through microbial respiration and growth. We aimed to prove the sensitivity of microbial respiration and growth parameters to indicate an interactive effect of land use and climate warming. For this we used Global Change Experimental Facility in Bad Lauchstädt, UFZ, Halle, Germany. This long-term experiment is designed in 5 land use strategies (Organic Farming, Conventional Farming, Intensive Meadow, Extensive Meadow, and Extensive Pasture) and 2 climate scenarios (ambient and future). We determined basal respiration by CO2 emission, microbial growth parameters by substrate-induced growth respiration (SIGR), and the quality of soil organic matter by Fourier-transformed infrared spectroscopy (FTIR). The effect of biotic (vegetation type) and abiotic (temperature and moisture) factors on microbial attributes and on chemical composition of soil organic matter will be compared.

How to cite: Guliyev, V., Pfeiffer, M., Udovenko, M., Fasching, C., Reitz, T., and Blagodatskaya, E.: Land use effect on microbial growth and respiration under future climate, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-8363, https://doi.org/10.5194/egusphere-egu2020-8363, 2020

D2086 |
Maria Udovenko, Vusal Guliyev, and Evgenia Blagodatskaya

Soil microbiota ensuring sustainable functioning of terrestrial ecosystems is strongly dependent on climatic conditions and vegetation type. Even within the same climatic zone, active land use alters the size, structure and functioning of the microbial community. We hypothesized that land use effect on soil microbial biomass will be more pronounced under impact of global warming. We also tested whether the biomass of specific microbial group (e.g., fungi) is more sensitive to environmental changes than total microbial biomass.

We proved these hypotheses in the experiments based on Global Change Experimental Facility platform, located at the field research station of the Helmholtz-Centre for Environmental Research in Bad Lauchstädt near Halle, Saxon-Anhalt, Germany. Experimental setup included 50 plots, located in 10 blocks (5 plots per block). Five blocks are under ambient climate and the rest 5 blocks are subjected to a realistic climate change treatment (under conditions predicted by several models of climate change in Central Germany for 2050–2080 period). Five land use types were established in every block: conventional farming; organic farming; intensively used meadow, extensively used meadow and extensively used pasture. We determined soil microbial biomass and its fungal component by chloroform fumigation-extraction method and by ergosterol content, respectively. We found that fungal biomass was more sensitive to intensive land use for crop production than to climate change. The possible mechanisms of such a sensitivity will be discussed.

How to cite: Udovenko, M., Guliyev, V., and Blagodatskaya, E.: Interactive effect of vegetation and climate warming on total microbial and fungal biomass in soil, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-8403, https://doi.org/10.5194/egusphere-egu2020-8403, 2020

D2087 |
Stefano Mocali, Loredana Canfora, Flavia Pinzari, and Eligio Malusà

The H2020 project Excalibur will be presented. It has the ambition of making the road to a biodiversity-driven change in the soil management of crops through the acknowledgement of the important role of soil biodiversity conservation and exploitation. The project applies integrated approach of research, development and field implementation to achieve its goals. Excalibur will deploy the knowledge gained by new molecular techniques, such as genomic sequences characteristics to specific groups of microorganisms and functions, in the creation of tools, indicators and evaluation systems. Co- innovation is fostered by collaboration of researchers with farmers and manufacturers, with a mutual exchange of information and feedback. Project’s results will bring new insights and practical solutions to stakeholders, validated by process analysis. For this purpose Excalibur plans to: 1) focus on multiscale plant-soil-microbes interactions be to exploit the potential of multifunctional bio-inocula and bio-effectors; 2) optimize the formulation and the application methods of these products based on native soil biodiversity dynamics; 3) develop a strategy to improve the exploitation of soil biodiversity interactions with bio-effectors and bio-inocula by assessing their impacts on crops and biodiversity under contrasting agricultural management practices (conventional, organic) and biotic/abiotic stress conditions; 4) to build a multi-criteria model to assess soil biodiversity status of cropping systems for a more efficient use of bio-effectors and bio-inocula; 5) develop technical tools to monitor the persistence and dispersion of bio-inocula under field conditions for eco-toxicological and agronomical purposes; 6) evaluate the effects of the new strategy on economy, environment quality and ecosystem functions; 7) disseminate results to all stakeholders with a dynamic and comprehensive methodology and encourage the adoption of best practices derived from the new strategy at local, regional and global level.

How to cite: Mocali, S., Canfora, L., Pinzari, F., and Malusà, E.: The EXCALIBUR project: novel microbial-based bioproducts improving soil biodiversity and the effectiveness of biocontrol and biofertilization practices in horticulture, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-11850, https://doi.org/10.5194/egusphere-egu2020-11850, 2020

D2088 |
Anna Kvitkina

Forests plants affect the biological and chemical properties of the soil through the root exudation, input of leaf and root litter. This study investigates the relationships between the species composition of plant communities, microbial properties and content of elements of the upper soil horizon in boreal forest ecosystems (using NMS analysis).

It is hypothesized that 1) microbial biomass and chemical properties relates to the species diversity of plants, 2) microbial biomass and chemical properties relates to certain plant communities, 3) microbial biomass and chemical properties linked to altitude gradient, 4) types of communities differ due to the composition of the grass cover.

Plots were chosen in the foothills of the Ural Mountains, Russia, in Pechoro-Ilych Nature Reserve, 62-63°N, 58-59°E, to small altitude gradient 250-400 m above sea level. Plant, litter and soil were taken from five spruce - fir forests (Picea obovate together with Abies sibirica) with siberian pine and birch (hereinafter “spruce forest”). The peculiarity of the territory is that in a small area five different grassy communities were formed.  They represented by both species-rich tall grasses forests and poor species, moss and large fern forests.

Types of forests: boreal-tall grass (3 plots), small grass – green moss (3 plots), bilberry-green moss (3 plots), shrub - haircap moss (4 plots) and large fern (3 plots). The plots (10×10 m) were selected for plant biodiversity describing. Topsoil samples (0-5 cm) were taken from sub-plots in July 2018 (n=48). In the collected samples, microbial biomass carbon (MBC), basal respiration (BR), pH and content of elements (S, P, Ca, Mg, K, Si, Ti, Mn) were measured.

We distinguished a group of communities with high microbial biomass (small grass-green moss and boreal-tall grass spruce forests) and a group with low microbial biomass (shrub-long moss, bilberry-green moss, large fern spruce forests). The high biological activity of the soil is weak confined to plant communities.

No strong relationship between MBC, BR, plant species richness and altitude was found.

Microbial biomass is strongly related to species of boreal-tall grasses (Aconitum septentrionale Koelle, Crepispaludosa (L.) Moench, Rubussaxatilis L., Thalictrum minus L., Valerianaofficinalis L., Filipendulaulmaria (L.) common species, Geranium spp. Species L.) albiflorumLedeb., Paris quadrifolia L.). These types of grass indicate an increase in soil pH, increase the content of Ca, Mg and S in the soil, and a decrease the content of Si and Ti. Opposite, the content of Si and Ti increased in the moss communities. K increased in the soil of large fern and boreal-tall grass communities. Thus, the content of microbial biomass, S, Ca, Mg, pH increased together in the direction of boreal tall grass community. The research was financial supported by grant RFBR mol_a No. 18-34-00987.

How to cite: Kvitkina, A.: Plant biodiversity linked with microbial biomass and chemical soil properties in boreal forests, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-10420, https://doi.org/10.5194/egusphere-egu2020-10420, 2020

D2089 |
Natascha Arnauts

Until the early nineteenth century, the Belgian landscape was characterized mainly by the presence of heathland, a typical cultural landscape with important ecosystem services. Since then, urbanisation has led to the conversion of large stretches of heathland to be converted to forest, arable land or cities. Increased concentrations of exhaust gasses result in elevated concentrations of nitrogen (N) in the atmosphere. Through rainfall this N enters the soil and is fixed via precipitation reactions, which in turn leads to higher N soil concentrations. Because Calluna vulgaris (common heather; the dominant plant species in heathlands) thrives on soil containing low nutrient concentrations,  it is now being outcompeted by plant species more suited to these altered nutrient levels. As a result, the heathland is slowly evolving into grassland and, consequently, its ecosystem services and soil nutrient cycling are changing.

Here, we present the preliminary results of our investigation into the influence of grass encroachment on nutrient cycling in heathlands. For this research question, we set up a gradient of 14 plots of increasing grass cover from 0 to 100%. The woody structures of heather contain high concentrations of lignin, consequently the 100% heather plots have a more recalcitrant organic input. It is therefore hypothesized that the nutrient turnover in these plots are lower than in the 100% grass plots since grass has lower lignin concentrations and thus higher litter quality. We set up a series of measurements on pooled and homogenized soil samples of these 14 plots. We measured N mineralization and nitrification, 2 enzymes and relevant soil parameters. Interestingly, there were no significant results found for the N mineralization and nitrification. The measurement of the enzymes chitinase and phosphatase showed a significant correlation, indicating the impact of vegetation on the enzymatic activity, and therefore on the soil nutrient cycle.

How to cite: Arnauts, N.: Influence of grass invasion on soil parameters in a Belgian heathland, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-8330, https://doi.org/10.5194/egusphere-egu2020-8330, 2020

D2090 |
Martin Lohse, Sebastian Blaser, Doris Vetterlein, Steffen Schlüter, Eva Oburger, Thorsten Reemtsma, and Oliver Lechtenfeld

Plant-microbe interplay in the rhizosphere generates multi-faceted chemical gradients. The soil solution is a crucial component of the rhizosphere, where chemical gradients of organic molecules first develop upon growth of roots, introduction of plant-derived carbon and microbial turnover. Studying these gradients requires high resolution both in time and space as well as high chemical specificity to resolve the multitude of compounds. Existing methods to probe the rhizosphere soil solution were mostly limited to bulk chemical parameters, inorganic ions or targeted analysis of organic molecules. However, to decipher organic carbon turnover in the rhizosphere the characterization of the complex pool of soil solution organic matter is needed.

Here we present a novel method that combines time-resolved collection of soil solution samples via micro-suction cups in the rhizosphere with ultrahigh chemical resolution provided by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to unravel developing pattern of soil solution organic matter.

Zea mays plants were grown in soil columns for three weeks and soil solution samples of undisturbed root-soil system were collected once a week. Growth of the root system and hence position of sampling locations in relation to the distance from the root, were followed by X-ray computed tomography (X-ray CT).

The online sample preparation was optimised to extract and desalt the organic matter from a few microliters of soil solution. The downscaling to a nano-liquid chromatography system for the on-line extraction allowed the analysis of only minute amounts of organic carbon within the samples (down to 10 ng). Given the high background concentration of soil-derived organic carbon, the high mass resolution and sensitivity of FT-ICR-MS enabled to distinguish root derived molecules from soil organic matter based on their exact masses. Molecular formulas of the root derived molecules could be calculated showing distinct chemical characteristics as compared to the bulk soil solution. X-ray CT analyses enabled relating the results from the chemical analysis to distance from the root and root age. With increasing influence of the roots higher molecular masses and an increasing degree of oxygenation of the molecules could be observed.

Our method is thus capable to show the changing small scale pattern of soil solution organic matter during the early rhizosphere development, closing the knowledge gap between root exudates, soil chemistry and microbial processes.

How to cite: Lohse, M., Blaser, S., Vetterlein, D., Schlüter, S., Oburger, E., Reemtsma, T., and Lechtenfeld, O.: On-line nano-solid phase extraction Fourier-transform ion cyclotron resonance mass spectrometry workflow to analyse soil solution organic matter gradients in the rhizosphere , EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-21598, https://doi.org/10.5194/egusphere-egu2020-21598, 2020

D2091 |
Pedro Paulo de C. Teixeira, Ana Paula M. Teixeira, Luís Fernando J. Almeida, Luís Carlos Colocho Hurtarte, Ivan F. de Souza, Danilo H. S. da Silva, Carsten W. Mueller, Alix Vidal, and Ivo R. da Silva

There is growing evidence that belowground plant carbon (C) inputs displays a major role for soil organic matter (SOM) dynamics. During the root life-cycle, there is a sequential shift from C inputs from living to dead roots, which might affect the conversion of these specific compound classes to SOM. However, this successional effect has yet not been investigated. In this study, we aimed to evaluate (i) the short-term impacts of living root-derived C on SOM formation and composition and (ii) how the succession between living and dead roots impacts their respective fate in soil. For this purpose, we set up a two-step experiment that simulated the shift between living and dead roots C inputs. In the first step, Eucalyptus spp. plants were cultivated in pots under controlled conditions for 66 days. In order to isolate the living root-derived C, we inserted in each pot 4 cylinders (0.5 cm high, 4.75 cm diameter) capped with a nylon membrane (pore size 5 μm) and filled with soil (clayey Rhodic Ferrasol) at the start of the experiment. Half of the pots were periodically pulse-labeled with 13C-CO2 (10 pulses of 10 h, 0.46 g of 13C plant-1), while the remaining ones were used as controls (unlabeled treatments). After 66 days, all pots were harvested, and one cylinder per pot was used to depict the living root effects on SOM pools. Those cylinders were separated in layers according to the distance from the roots (0-4, 4-8, 8-15 and 15-25 mm) and analyzed for organic carbon, nitrogen, as well as δ13C. We quantified and characterized the microbial communities using phospholipid fatty acid (PLFA), and extracted the pedogenic oxides (iron and aluminum) to highlight potential alterations in organo-mineral complexes and short-range order phases. Using density/size fractionation, we further gained elemental and isotopic information of specific SOM pools, i.e. particulate, occluded and mineral-associated organic matter. The remaining cylinders were incubated for 84 days in two treatments, with and without dead roots. Heterotrophic respiration rates were measured periodically together with the 13C enrichment of the CO2 produced. Carbon derived from living roots was mainly recovered in the first millimeters from the root source, as occluded or mineral-associated SOM. Close to the roots, we detected a shift in the microbial communities and a decrease of organo-mineral complexes and short-range order phases. Carbon derived from living roots was rapidly mineralized and the δ13C from the respired CO2 returned to natural abundance ranges after 84 days of incubation. The presence of dead roots did not affect the mineralization C derived from living roots. Our work highlights the importance of C inputs from living roots for the formation of SOM. However, the compounds deposited by living roots exhibit also a transient nature which challenges the assumption that living root-derived C is necessarely a precursor of stable SOM formation.

How to cite: de C. Teixeira, P. P., Teixeira, A. P. M., Almeida, L. F. J., Colocho Hurtarte, L. C., Souza, I. F. D., Silva, D. H. S. D., Mueller, C. W., Vidal, A., and Silva, I. R. D.: Succession between living and dead roots drives the fate of soil carbon pools, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-10640, https://doi.org/10.5194/egusphere-egu2020-10640, 2020

D2092 |
Natalia Aguilera, Felipe Aburto, Francisco Salazar, Marcela Bustamante, Manuel Acevedo, Marta Gonzalez, Ulrike Schwerdtner, and Yvonne Oelmann

Keywords: Assemblage, Interaction, nutrients

Forest fires can cause a temporary nutrient deficiency or imbalance in the soil. Post fire forest restauration could be enhance by simulating process of vegetation succession taking advantage of beneficial interaction between species (e.g. facilitation and complementarity), which could help coping with nutrient imbalances. To determine the type of interactions and their effects on soil nutrients affected by fires and on the acquisition of nutrients by plants, a meso-cosmos experiment was established under controlled conditions, using surface soils affected by the Cayumanque megafire (Región del Biobio). Seven assemblages of three species with different nutrient acquisition strategies were established: Nothofagus obliqua (mycorrhizae), Lomatia dentata (proteiform roots) and Sophora cassioides (nodules). In a complete factorial design of two blocks (with and without complementary fertilization). The main interactions resulted in competition between N. obliqua from S. cassioides and L. dentata, while S. cassioides was not be significantly affected by the presence of L. dentate, suggesting complementarity. Fertilization did not interact with assemblages or reduce competition, but increased plant growth in all assemblages. Available soil nitrogen (NO3-) increased significantly in the presence of S. cassioides (6.88±3.10) and decreased in the presence of L. dentata (2.67±0.84). Finally, N. obliqua increased its nitrogen acquisition by 44% in the presence of L. dentata and decreased by 5% in the presence of S. cassioides. Although no significant differences were observed in POlsen, the fraction of inorganic phosphorus was significantly lower in the presence of proteacea (122.24±20.99). In addition, enzyme analysis showed no significant differences for microbial biomass and LAP activity. However, the combination of N.O. and L.D. showed significantly high phosphatase activity (16.36±5.57).

Finally, further isotopic and enzymes work is in process to study nutrient pools in plants and soil either of L. hirsuta and N. obliqua individuals growing alone or in combination. Because native Nothofagus spec. forests have been affected by forestry fires and replaced by plantations of exotic tree species throughout Chile, knowledge on interactions among native species affecting tree nutrition is lacking. Therefore, the results of our research support the use of plant assemblages as a potentially effective restoration strategy in post-fire soils with low nutrient content.

Acknowledgement: Special thanks to National forestry institute, BayCEER and Yvonne Oelmann’s laboratory for contribute to this research and make it possible at an international scale.   


How to cite: Aguilera, N., Aburto, F., Salazar, F., Bustamante, M., Acevedo, M., Gonzalez, M., Schwerdtner, U., and Oelmann, Y.: Effect of tree native species assemblages on C, N & P contents of burned soils, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-20202, https://doi.org/10.5194/egusphere-egu2020-20202, 2020

D2093 |
Negar Ghaderi, Andrey Guber, Hannes Schmidt, and Evgenia Blagodatskaya

Enzymes are produced by microorganisms either intracellularly in cell’s cytoplasm and periplasm or extracellularly either as attached to outer surface of cell membranes or released to the soil microhabitats. The distribution of microhabitats in soil is highly heterogeneous with high abundance of microorganisms in the small volume of soil hotspots, e.g., in the rhizosphere - the most important plant-soil interface with very dynamic interactions between roots and microorganisms. Soil zymography is one of the most realistic methods developed to visualize enzyme activity in undisturbed soil at the mesoscale (mm-cm) level using substrate-saturated membranes. However, visualization of enzymatic processes at the micro-scale level remains a challenge. We tested several impregnation strategies of soil sample (e.g., by agarose gel, silicon spray and super transparent silicon mixture) for their suitability for micro-zymography, i.e., for visualization of enzyme activity in undisturbed soil particles at the microscopic level combining fluorogenic substrates with epifluorescence microscopy. The pros- and cons- of various combinations of impregnation and staining of micro-sized soil samples will be discussed.

Keywords: enzyme activity, zymography, fluorogenic substrates

How to cite: Ghaderi, N., Guber, A., Schmidt, H., and Blagodatskaya, E.: Towards soil micro-zymography: comparison of staining and impregnation strategies , EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-5784, https://doi.org/10.5194/egusphere-egu2020-5784, 2020