Nitrogen addition can weaken yield reduction under no-tillage, a fundamental component of conservation tillage. However, the potential long-term benefits of nitrogen addition in enhancing the yield capacity of no-tillage by improving soil quality remain uncertain. Here we investigated the effects of tillage and nitrogen addition on both yield and soil quality through a comprehensive long-term experiment. We found that increased nitrogen inputs resulted in higher yield under no-tillage, particularly in wet years. Over an 18-year period, the rate of yield enhancement attributed to nitrogen addition varied from 8.2% to 24.5%, resulting in the most optimal yield under no-tillage with adequate nitrogen addition. Similarly, soil quality of no-tillage exhibited improvement with nitrogen inputs, especially in terms of organic carbon and the availability of nitrogen and phosphorus, thereby enhancing production potential. This study concluded that adequate nitrogen addition further improved both crop production and the sustainability of no-tillage systems.
How to cite: Li, S., Wu, X., Li, Y., and Zha, Y.: Long-term nitrogen fertilization addition offsets no-tillage induced decrease in crop yield through enhancing soil fertility, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-3898, https://doi.org/10.5194/egusphere-egu25-3898, 2025.
To retain soil fertility and build up soil organic matter, cultivation of nitrogen-fixing legumes is a promising tool in low-nutrient soils in southern Africa. Legumes can potentially improve soil nitrogen (N) status, particularly in the rhizosphere, through N fixation in nodules. This affects soil microbial and enzymatic activities and thus soil organic carbon (SOC) turnover and nutrient availability. During plant growth, legumes provide photosynthetic carbohydrates for bacteria living in the nodules. When legumes reach maturity stage, developmental senescence begins and N-fixing nodules dissolve. This process represents a plant metabolic switch from a C sink to a C and nutrient source for the soil, as nutrients are released. Few studies exist on legume-soil interaction during plant growth and it is unknown if and how nodule senescence contributes to soil nutrient availability and SOC turnover. Therefore, the aim of this study is to investigate spatial and temporal legume-soil interactions in the rhizosphere, regarding nodule development, N release, and soil enzyme activity during legume growth.
We conducted a rhizobox experiment using two different soils from the Kavango (loamy sand) and Omusati (sand) regions in North Namibia. Cowpea (Vigna unguiculata), a common legume in southern Africa, was grown under controlled temperature and water availability. To investigate spatial and temporal C and N release as well as soil enzyme activity, in-situ zymography was conducted at early vegetative stage, flowering development, and one day after nodule senescence. Three enzymes, representing the C (β-glucosidase, Chitinase) and N (Chitinase, Leucine-Aminopeptidase) cycles were investigated. At each plant growth stage, three plants were harvested to identify changes in soil properties, including SOC, N, mineral N, and pH, over time.
Preliminary results indicate that β-glucosidase activity is generally higher in the rhizosphere and around nodules compared to bulk soil in both soils. During plant growth, β-glucosidase activity varied. It decreased from vegetative to flowering stage but slightly increased during nodule senescence in both soils. At nodule senescence, β-glucosidase activity in bulk soil increased by 17% in the loamy sand compared to the early vegetative stage and generally higher than in the sandy soil. With further image analysis, we aim to understand how β-glucosidase, Chitinase, and Leucine-Aminopeptidase activities are interlinked and influence nutrient availability during plant growth in soil.
How to cite: Toth, E. K., Holz, M., and Becker, J. N.: Spatiotemporal distribution of enzyme activities in the rhizosphere of cowpeas (Vigna unguiculata), EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-18853, https://doi.org/10.5194/egusphere-egu25-18853, 2025.
Rivers serve as a vector for pollutant transport, as well as a dispersal agent for invasive plant species. Through flooding events, these stressors can be distributed to areas such as the riparian zone, which may then alter soil microbial community activity and function. To test this, a pot experiment was conducted with pesticide application and plant community as treatment factors. Plant community treatments included control (no plants), native riparian vegetation, and riparian vegetation with the invasive species Impatiens glandulifera. Pots were flooded with either tap water or a pesticide mixture for a period of 7 days. Root-zone porewater was then collected at the base of each plant. Microbial activity and function were assessed by incubating soil with collected porewater and conducting a MicroResp assay, in which different carbon substrates were added, and CO2 evolution (a proxy for microbial activity) was measured. Results showed that porewater from pesticide-exposed pots (regardless of plant community) led to higher microbial respiration compared to porewater from control pots. Conversely, porewater from pots without pesticide exposure resulted in lower respiration, suggesting that plants may mitigate pesticide-induced changes in microbial activity under flooded conditions. Catabolic diversity, however, remained consistent across treatments, indicating that microbial function was unaffected. Total organic carbon analysis of porewater revealed that the quantity remained constant across treatments, suggesting that composition, rather than concentration, influenced microbial activity. Future work will include untargeted analyses of porewater to characterize its chemical composition and targeted analyses for the presence of root exudates to better understand their role in shaping microbial responses.
How to cite: Ferrer, A. S., Muñoz Sepúlveda, K., Mendoza-Lera, C., and Diehl, D.: Plants mitigate microbial response to pesticides in riparian environments, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-13094, https://doi.org/10.5194/egusphere-egu25-13094, 2025.
Although diversified crop rotations raise drought tolerance and system productivity, the underlying mechanisms within the crop–soil system that confer this resilience remain incomplete.
The drought tolerance mechanisms of maize grown under a 20–year field experiment encompassing low, medium, and high crop diversity rotations was evaluated by combining soil zymography and high–throughput sequencing.
Crop diversification increased maize biomass by 56–87% and mitigated the drought stress by 14.1-58.8%. It also reinforced root diameter stability7–2.5 times and drought tolerance 2.2–2.7 times, which linked to drought tolerance of rhizosphere microbiota. The complexity of the rhizosphere bacterial network increased with crop diversification, and the keystone taxa like biofilm–producing Pseudomonas demonstrated bolstered drought tolerance. These microbiota help stabilize niches and habitats under drought, thereby raising rhizosphere’s stress tolerance and the ecosystem's provisioning and regulatory functions. Enzyme activities and hotspot areas decreased in soils with crop diversification, but has minimal changes with drought systems, suggesting that enzymes may not directly control plant drought tolerance.
Crop diversification enrich drought–tolerance soil microbial species that maintain rhizosphere microenvironment stability and facilitate root proliferation, underscoring the significance of optimizing crop–microbe interactions to bolster resilience against soil drought.
How to cite: Jia, R., Chen, M., Zhou, J., Xu, Y., Huang, J., Yang, Y., Razavi, B. S., Zeng, Z., Kuzyakov, Y., and Zang, H.: Diversified crop rotations strengthen maize drought tolerance via rhizosphere microbiota and enzymes activities, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-5121, https://doi.org/10.5194/egusphere-egu25-5121, 2025.
Under current climate change scenarios for temperate ecosystems in Europe, prolonged drought poses a significant threat to barley production necessitating the development of novel strategies to ensure survival under these scenarios. One such approach is to enhance drought resistance through the application of plant-beneficial rhizobacteria. However, studies exploring this strategy for stress mitigation have been limited thus far. To address this, we established a culture collection of rhizosphere bacteria found to be associated with barley hosts under drought stress (drought-tolerant or DT bacteria) and selected a 16-member consortium (drought-tolerant synthetic community/DT-SynCom) based on their relative abundance in the rhizosphere after drought and their in vitro tolerance to osmotic stress. The members of the DT-SynCom include species from Proteobacteria, Firmicutes, and Actinobacteria. Genome analyses revealed the presence of genes associated with plant growth promotion, and in vitro assays confirmed auxin production, ACC deaminase activity, inorganic phosphorus solubilization, and cellulase and chitinase activity in individual consortium members. The DT-SynCom members are non-antagonistic to one another and exhibit either neutral or beneficial effects on barley shoot and root growth in vitro. Pot experiments in three different soil substrates showed that DT-SynCom application reduced the number of wilting leaves and slightly improved barley growth under drought conditions. The results of the research suggest that members of the barley DT-SynCom have beneficial plant traits that result in improved plant growth under drought stress.
How to cite: Rigerte, L., Reitz, T., Heintz-Buschart, A., and Tarkka, M. T.: Synthetic rhizosphere community confers drought tolerance in barley, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-9813, https://doi.org/10.5194/egusphere-egu25-9813, 2025.
Roots are presumed to be key controls on anoxic microsites, which partially regulate nutrient availability and the fate of carbon and contaminants in soils. However, how root activity interacts with edaphic factors to regulate anoxic microsite formation is poorly understood. Here, we sought to define how root exudation interacts with soil texture to alter soil oxygen dynamics around a model plant root. We used reverse microdialysis to deliver 13C-labelled model exudates to soil mesocosms of two distinct textures. Over the course of three diurnal cycles, we mapped the 2D-distribution of oxygen, defined the contribution of exudates to total soil respiration, and measured the production of Fe(II) and fermentation products around our model plant root. We show that root exudation spurs the formation of anoxic microsites by intensifying microbial respiration around the plant root. These effects are lessened during periods of no exudation (“nighttime”) and enhanced in finer textured soils. Additionally, we show that anaerobic Fe-reducing bacteria partially contribute to Fe-oxide dissolution. The transient nature of anoxic microsites in the rhizosphere and the potential for Fe-redox cycling within them raise important questions about prevailing concepts of rhizosphere contaminant availability, nutrient acquisition, and carbon dynamics.
How to cite: Lacroix, E., Van Der Loo, E., Kocsis, L., and Keiluweit, M.: Interactive effect of root exudation and texture on anoxic microsite dynamics in the rhizosphere, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-17733, https://doi.org/10.5194/egusphere-egu25-17733, 2025.
Root exudation plays a critical role in the biogeochemical functioning of wetlands, influencing nutrient cycling, shaping both plant-plant and plant-microbe interactions and affecting soil organic carbon (SOC) decomposition via priming effects. We showed that contrary to most observations in aerated upland soils, glucose inputs can induce strong negative priming effects on anoxic peat. This finding yields important implications for the stability of the vast organic carbon reserves in global wetland soils. However, root exudation dynamics are complex, and the biogeochemical implications of the hundreds of diverse compounds released from roots remain elusive.
Here we present 1) a meta-analysis compiling data on wetland plant root exudates, focusing on both fluxes and compound diversity, and 2) preliminary results from incubation experiments simulating the effects of a typical wetland plant exudate composite on SOC decomposition.
Our meta-analysis elucidates the challenges in cross-study comparison of quantitative root exudate data due to methodological heterogeneity as well as the strong effects of environmental, biological and chemical parameters influencing plant traits. We found organic acids to be the primary compound class released by wetland roots, and organic acids have been assessed by the majority of studies. By contrast, few studies assessed the compound classes of sugars, amino acids, and secondary compounds, representing important knowledge gaps in our understanding of wetland-plant-microbe interaction and C cycling. To understand the complex effects of diverse root exudates on wetland SOC cycling, our ongoing incubation experiments compare the priming effect of a wetland plant exudate composite with that of conventionally used single sugar inputs.
How to cite: Krüger, N., Subrahmaniam, H. J., Knorr, K.-H., and Mueller, P.: Root exudates in wetland soils – compound diversity and priming effect, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-12261, https://doi.org/10.5194/egusphere-egu25-12261, 2025.
The interaction between soil fungi and plant roots crucially depends on proper recognition and communication by both partners. However, the precise determinants of this communication remain to be identified, both in terms of chemical communication and the underlying gene regulation upon recognition and response. Additionally, the beneficial interaction of fungi and plants often depends on the characteristics of the surrounding soil as well as on the variety of plant species, although the molecular basis of this phenomenon is largely unknown.
Trichoderma harzianum is a filamentous ascomycete frequently applied as plant beneficial agent in agriculture. While mycoparasitism and antagonism of Trichoderma spp. against fungal pathogens is well known, early responses of the fungus to the presence of a plant await broader investigation. In this study we analyzed these early stages of plant- fungus communication at the molecular level. We show that T. harzianum B97 is an efficient colonizer of plants. Analysis of chemotropic responses of B97 germlings to a plant extract showed directed hyphal growth. Patterns of secreted secondary metabolites revealed that the fungus chemically responds to the presence of the plant and that the plant secrets a fungus specific metabolite as well. Hence we developed a strategy for omics analysis to simulate the conditions of the early plant recognition eliciting a chemotropic response in the fungus. We found only 102 genes to be regulated, reflecting a very early stage of response, which revealed a general decrease in secondary metabolism upon recognition. In contrast, among these genes, a so far uncharacterized, presumably silent gene cluster was strongly induced upon recognition of the plant. Gene deletion of two genes of this Plant Communication Associated (PCA) cluster showed that they are essential for colonization of soy been roots. Moreover, for part of the gene cluster a DNA motif with palindromic sequence was detected. Phylogenetic analysis indicated that the PCA cluster is only present in the Harzianum clade of Trichoderma and closely related to from Metarhizium spp. Analysis of horizontal gene transfer (HGT) of the cluster genes, revealed that plants likely acquired a subset of the core genes of the cluster from fungi.
We conclude that the plant recognition specific PCA cluster mediates early chemical communication between plant and fungus and is potentially responsible for the high potential of T. harzianum sensu stricto and closely related species for biocontrol applications. Due to the requirement of this cluster for successful plant interaction (i.e. root colonization) we propose regulation of the PCA cluster as a diagnostic feature to delineate soil characteristics and plant genomic features blocking or facilitating beneficial fungal plant interaction and hence plant protection.
How to cite: Schmoll, M., Schalamun, M., Li, G., Hinterdobler, W., and Compant, S.: Interkingdom communication between fungi and plants: induction of a novel silent secondary metabolite cluster required for root colonization, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-10402, https://doi.org/10.5194/egusphere-egu25-10402, 2025.
The mycorrhizosphere is a highly dynamic soil zone characterized by intense interactions among plant roots, arbuscular mycorrhizal fungi (AMF), and associated microbial communities. This biologically active region is pivotal in nutrient cycling, root colonization, and soil sustainability. Despite its ecological importance, the mycorrhizosphere remains poorly understood due to its challenging accessibility. Conventional destructive sampling methods often fail to isolate this specific zone, leading to a limited understanding of its microbial composition. To address these challenges, we employ rhizobox systems designed to maintain the integrity of the mycorrhizosphere. These systems allow precise sampling of the region directly influenced by root exudates and AMF activity. By consistently accessing the zone of inoculation, the rhizobox enables repeated observations and measurements, enhancing our ability to study the microbial dynamics of this elusive soil environment. This study aims to uncover key taxonomic groups within the mycorrhizosphere, focusing on identifying mycorrhiza-helper bacteria (MHB) and fungi (MHF) that could improve mycorrhizal colonization and soil health. The primary objectives of this research are to: i) Characterize Microbial Diversity: Third-generation sequencing technologies (MinIon R10.4.1 V14, Nanoporetech) will be used to profile bacterial and fungal communities within the mycorrhizosphere of Orchard Baby maize (Zea mays). The focus will be on taxonomic identification using genetic markers such as 16S rRNA for bacteria and ITS for fungi; ii) Establish a Controlled Environment: Sterilized rhizobox systems filled with an artificial soil mixture will serve as the experimental framework. Microbial inocula derived from native forest soils, conservation-managed agricultural soils, and intensively managed agricultural soils will be applied in dilution series (10⁻¹, 10⁻³, and 10⁻⁶) to mimic natural microbial gradients. iii) AMF Inoculation: Rhizophagus irregularis (syn. Glomus intraradices), a well-documented AMF species, will facilitate root colonization and provide a controlled environment to evaluate microbial interactions. The study combines molecular sequencing with temporal sampling to examine microbial recruitment by mycorrhizal plants. DNA extraction will occur at three stages (beginning 1 month and 3 months after the start) to capture temporal changes in microbial composition. The focus will be on identifying the dominant taxa in the mycorrhizosphere. Our project seeks to provide the first high-resolution taxonomic profiles of microbial communities in the mycorrhizosphere. We also expected to establish a methodological framework for studying elusive soil zones with high biological activity and to highlight the microbial taxes associated with AMF colonization. Integrating rhizobox systems with advanced sequencing will provide insights into microbial dynamics that can inform sustainable agricultural practices, particularly in enhancing nutrient uptake and soil resilience.
How to cite: Gumiere, T., Herisse, A.-D., and Dessureault-Rompré, J.: Exploring Mycorrhizosphere Microbial Diversity in Sterilized Rhizobox Systems with Third-Generation Sequencing, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-13610, https://doi.org/10.5194/egusphere-egu25-13610, 2025.
Understanding the feedback mechanisms between roots and soil, and their effects on microbial communities, is crucial for predicting carbon cycling processes in agroecosystems. We developed a onedimensional axisymmetric rhizosphere model to simulate the spatially resolved dynamics of microorganisms and soil organic matter turnover around a single root segment to explore soil-root interactions. The model accounts for two functional microbial groups with different life history strategies (copiotrophs and oligotrophs), reflecting trade-offs in functional microbial traits related to substrate utilization and microbial metabolism. The model also considers substrates of different accessibility of soil organic matter, i.e. low and high molecular weight organic carbon compounds (LMW-OC, HMW-OC). The model was conditioned using Bayesian inference with constraint-based parameter sampling, which enabled the identification of parameter sets resulting in plausible model predictions in agreement with experimental evidence. Mimicking the behavior of growing roots, the model assumed 15 days of rhizodeposition for LMW-OC. As expected, the simulations show a decreasing concentration of dissolved LMW-OC away from the root surface. After 15 days, the microbial community close to the root surface (0–0.1 mm) was dominated by copiotrophs. The spatial patterns of functional microbial groups persisted after rhizodeposition ended, indicating a legacy effect of rhizodeposition on microbial communities, particularly on oligotrophic activity. Simulated microbial biomass exhibits a very rapid change within 0–0.2 mm away from the root surface, which points to the importance of resolving soil properties and states at submillimeter resolution. Microbial-explicit rhizosphere modeling thus facilitates elucidating spatiotemporal patterns of microorganisms and carbon turnover in the rhizosphere.
How to cite: Pagel, H., Sırcan, A. K., Schnepf, A., Giraud, M., Lattacher, A., Kandeler, E., Poll, C., and Streck, T.: Trait-based modeling of microbial interactions and carbon turnover in the rhizosphere, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-16819, https://doi.org/10.5194/egusphere-egu25-16819, 2025.
Soil biophysics may be a relatively new term, but research on biological and physical interactions in soil dates back over a century. As we embark on new research today, blessed with a plethora of techniques and computing power that would be fanciful to the pioneers of the discipline, we have plenty to learn from the past. Devoid of techniques to drive their research, the pioneers focussed on big scientific questions, creating new techniques when none were available.
One of the earliest soil biophysics papers was published by Haines in 1923. He measured soil volume changes with moisture content extremely accurately in arguably the first controlled study exploring biological polymer (gelatine) impacts to soil. He concluded that ‘By means of the method the effect of alternate wetting and drying of soil in producing good tilth is illustrated.’ This early work focussed on volume changes, a major biophysical process driving soil structure formation and stabilisation that much present research ignores. While modern research excels at visualizing 3D soil structure (e.g., X-ray CT) and quantifying aggregate stability, it frequently falls short in elucidating the underlying mechanisms. Soil aggregate pioneers like Hénin (1940s) and Monnier (1965) went beyond descriptive analyses, delving into the physics of particle interactions (cohesion, contact angles) to understand the factors governing aggregate stability.
It is time for soil biophysicists to get back to basics, taking inspiration from the ingenuity and inquisitiveness of overlooked papers of their predecessors. With more effort placed on HOW soil biophysics drives structure formation, and less effort on correlating WHAT we see, progress would be less incremental. We have an array of exciting new tools at our disposal, but these need to be used beyond visualisation and correlation to make leaps rather than small steps in understanding.
Haines, W. 1923. The volume-changes associated with variations of water content in soil. Journal of Agricultural Science, 13, 296-310.
Hénin, S. 1943. The influence of imbibition of various liquids on the resistance to disintegration of earthy agglomerations in water. Comptes Rendus Hebdomadaires des Seances de l’Academie Des Sciences, 217, 578-580.
Monnier, G. 1965. Action des matieres organiques sur la stabilite structurale des sols. Annales Agronomiques, 16,471-+.
How to cite: Hallett, P.: Learning from the soil biophysics pioneers, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-17192, https://doi.org/10.5194/egusphere-egu25-17192, 2025.
Viruses have been recognized as abundant but virtually unknown members of the soil microbiome. Early insights into soil viral diversity and distribution patterns over local and global scales will be presented. Using shotgun viral metagenomic (viromic) approaches to recover and sequence the viral size fraction, hundreds of thousands of viral ‘species’ have been recovered from a wide range of soils, consistently indicating high viral diversity across terrestrial ecosystems. Soil viral communities are often strongly spatially structured, even over short distances, and they exhibit reproducible temporal successional patterns following rewetting of dry soil. The emerging paradigm is of a highly active and dynamic soil virosphere with the potential for substantial contributions to bacterial mortality, biogeochemical cycling, and food web dynamics in terrestrial ecosystems.
How to cite: Emerson, J.: Surprisingly active and dynamic viral communities in soil, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-21038, https://doi.org/10.5194/egusphere-egu25-21038, 2025.
Efficient coordination between aboveground (Kab) and belowground (Kbe) hydraulic conductance is crucial for plants to meet evaporative demands in diverse environmental conditions. Despite significant advances in understanding hydraulic traits, the interplay between Kab and Kbe under varying soil moisture levels remains insufficiently explored. This study investigates how maize (Zea mays L.) regulates hydraulic conductance during development in response to optimal (OWC, 25–30% volumetric water content) and water-stressed (SWC, 10–15%) soil conditions.
A controlled greenhouse experiment measured Kab and Kbe at 14, 26, 35, and 55 days after sowing. Kbe was quantified using a pressure chamber, while Kab components were derived from transpiration rates, leaf water potential, and environmental parameters. Results showed that Kbe exceeded Kab by two orders of magnitude and increased consistently with plant age, reflecting root system expansion. Plants under OWC exhibited significantly higher Kbe and Kab compared to SWC, where growth and hydraulic conductance plateaued earlier. Coordination between Kab and Kbe was linear at early stages but diverged as Kbe plateaued under SWC, while Kab continued to increase.
The trajectory of Kab and Kbe coordination was consistent across both treatments, but OWC plants explored a higher hydraulic capacity, indicating superior water uptake and transport. In contrast, SWC plants maintained the same coordination trajectory but operated at a reduced magnitude, reflecting an adaptive response to conserve water. These findings underscore the critical role of water availability in shaping plant hydraulic traits and highlight strategies for improving water use efficiency and resilience in agricultural systems under drought stress.
How to cite: Zare, M., Spinoso Sosa, S., and Hafner, B.: From Root to Shoot: Understanding Plant Hydraulic Regulation Across Different Soil Moistures, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-17287, https://doi.org/10.5194/egusphere-egu25-17287, 2025.
Soil physical structure, a key indicator of soil health and biomass production potential, can be altered by agricultural practices. In South Africa, the intensive and long-term sugarcane (Saccharum officinarum L.) monoculture is known to degrade soil characteristics. The objective of this study was to evaluate the effect of crop residue management practices (mulching, burning with residues scattered or removed) and mineral fertilization (with or without) on soil physical structure and to investigate possible link with soil microbial communities. To this aim, we analyzed soil aggregation and shrinkage curves (SSCs) in a long-term sugarcane trial established in 1939. The SSC provides descriptive structural soil data by differentiating and characterizing two pore systems (plasma and structural pores). We also quantified soil microbial communities’ abundance by qPCR as well as exopolysaccharides (EPS). Residue management and fertilization practices were found to have significant effects both on physical and microbial properties. Partial redundancy analysis showed that residue management practices had a slightly higher effect (19% of total variance) on hydrostructural variables compared with fertilization (12%). Total soil shrinkage, specific volume, and swelling capacity of the plasma were higher in mulched and/or unfertilized plots, indicating that soil was less compact, and shrinkage was more intense, including at the plasma level. The stronger structural dynamics and aggregate stability of the soil were explained by the behavior of the primary aggregates (peds), which were more porous and reactive during the drying process. In addition, swelling capacity of the plasma and the mean weight diameter of aggregates were both correlated to the amount of microbial EPS and the fungal abundance. This study highlights the importance of mulching and limited fertilization to maintain soil structure over the long term through the action of microbial communities.
How to cite: Deeb, M., Z Lerch, T., Grimaldi, M., Aroui, H., Mthimkhulu, S., Van Antwerpen, R., and Podwojewski, P.: The long-term effect of sugarcane crop residues and fertilization on soil physical properties may be mediated by microbial communities, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-1373, https://doi.org/10.5194/egusphere-egu25-1373, 2025.
Much research has evaluated rhizosphere structure as distinct from bulk soil, often attributing these differences to root-induced changes. However, the role of inherent root growth preferences and their interactions with existing soil pore networks remains underexplored. This study investigates the relative contributions of root-induced changes and root growth preferences in shaping rhizosphere porosity gradients and their relationship to rhizosheath development.
Using repeated X-ray computed micro-tomography (µCT), we analyzed rhizosphere macroporosity in intact and sieved soils. For the first time, we distinguished between changes driven directly by root activity and those arising from the inherent reuse of pre-existing macropores. Our findings demonstrate that root growth preferences, such as the utilization of large macropores, are the dominant factor shaping rhizosphere structure. In contrast, direct root-induced changes, including compaction and pore rearrangement, contributed minimally to overall rhizosphere porosity, particularly in intact soils.
We also examined rhizosheath development, traditionally being considered as a representative subsample of the rhizosphere. Contrary to conventional assumptions, our results revealed no correlation between rhizosheath mass and root-soil contact or rhizosphere soil volume derived from µCT analysis. Instead, rhizosheath formation was primarily associated with roots growing into macropores and actively modifying their surroundings. Roots exploring dense soil matrices or biopores showed minimal rhizosheath development.
This study underscores the importance of root growth preferences in rhizosphere structure development and challenges existing assumptions about the relationship between rhizosheath and rhizosphere properties. Our findings highlight the necessity of conducting rhizosphere research in soils with intact structure to fully capture the complex interactions between roots and soil.
How to cite: Geers-Lucas, M., Guber, A., and Kravchenko, A.: Root-pore interactions and their role in shaping rhizosphere structure and rhizosheath development, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-3096, https://doi.org/10.5194/egusphere-egu25-3096, 2025.
Plant growth-promoting rhizobacteria (PGPR) have been shown to mediate drought tolerance by inducing changes in soil physical properties, water retention and flow dynamics. However, PGPR’s potential and mechanisms in mediating salt tolerance through these biophysical controls remain poorly understood. To address this, we conducted saltwater evaporation experiments with Bacillus subtilis FB17 (UD1022, a PGPR) across multiple scales, including microscale (sessile droplets on glass slides and microchannels packed with a thin layer of sand) and mesoscale (columns packed with sand). Evaporation of NaCl solutions (0, 10, and 20 g/kg) mixed with and without UD1022 cells was compared in these systems. Results demonstrated the significant influence of bacterial deposition on water film configuration, air-water interface behavior, and patterns of salt accumulation/precipitation during evaporation. Images of evaporation of sessile droplets showed that bacterial cells pinned the contact line, resulting in salt precipitation along the perimeter, whereas in the absence of UD1022, salt precipitates were concentrated in the droplet center. In microchannel packed with sand particles, salt clusters formed on sand particle surfaces in controls whereas salt precipitation occurred in the pore space between sand particles in UD1022-treated samples, consistent with contact line pinning. The biophysical controls observed at the microscale were reflected in mesoscale column measurements, where UD1022 treatment increased water retention and reduced evaporation at 10 and 20 g/kg salt concentrations compared to controls. Light reflection imaging revealed earlier onset and more salt precipitation in UD1022-treated columns compared to the controls. Mechanistically, bacterial-induced contact line pinning led to (1) earlier onset of salt precipitates resulting in partial blocking of pores and thus increased capillary connection and evaporation at the early stage, and (2) complete pore blocking thus reduced evaporation at the later stage. The sequential processes contributed to the observed overall reduction in evaporation and higher water retention.
How to cite: Jin, Y., Yan, J., Zheng, W., Knight, B., and Bais, H.: Bacillus subtilis Changes Salt Precipitation Patterns and Affects Saltwater Evaporation via Contact Line Pinning, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-14483, https://doi.org/10.5194/egusphere-egu25-14483, 2025.
Soil temperatures are expected to increase with climate change, which will likely affect soil bioturbation by earthworms. While the ecophysiological response of earthworms to soil temperature has been studied previously, several questions remain, such as whether earthworm species from different geographical origins respond differently to environmental stress. In this study, we used A. caliginosa individuals from two contrasting European climatic zones (i.e. central Sweden and southern France), and measured their energy use (via heat dissipation using isothermal calorimetry) and their burrowing activity (i.e. burrow volume and cast volume, quantified using X-ray imaging) at five different soil temperatures (i.e. 8, 12, 16, 20 and 24 °C).
In general, heat dissipation in earthworms increased with soil temperature, and body mass-normalized heat dissipation was about 20% higher in earthworms from France. Moreover, the increase in heat dissipation with increasing temperature was stronger at high than at low temperatures. However, there was one important exception from these general trends: earthworms from Sweden showed a distinct and absolute peak in heat dissipation at intermediate temperature (16 °C). Burrow volumes created by earthworms increased with soil temperature up to 16-20 °C, after which it decreased. The high levels of heat dissipation in combination with reduced burrowing activity at 24 °C suggest high stress in such warm conditions. The volumes of burrows created by Swedish earthworms were about 50% higher than those created by French earthworms.
As a consequence of the higher heat dissipation and lower burrow volumes, the specific energy costs for burrowing (i.e., heat dissipation per unit burrow volume) was 2-3-fold higher in French earthworms than Swedish earthworms, which suggests that Swedish earthworms are more “efficient”. In general, French A. caliginosa were smaller in size and mass compared to Swedish A. caliginosa, and these differences may be a result of adaptation to distinct climates. While Swedish earthworms had a distinct activity peak at 16 °C, we could not find such an activity peak in French earthworms. Measurements with higher temperature resolution (e.g., measurements every 1 °C) might be needed.
Our data indicate that the geographical origin of earthworms plays a role in the earthworm's ecophysiological responses to environmental stressors such as soil temperature. The findings provide quantitative data on how earthworm burrowing activity is affected by soil temperature, which helps us better understand how earthworms may adapt to climate change and what the consequences on soil processes are.
How to cite: Arrazola Vasquez, E. M., Capowiez, Y., Herrmann, A. M., and Keller, T.: Does geographical origin matter? A study on the effects of soil temperature on the energy costs of burrowing in Aporrectodea caliginosa from Sweden and France, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-3817, https://doi.org/10.5194/egusphere-egu25-3817, 2025.
Soil respiration is a significant driver of climate change and is anticipated to intensify extreme weather events. This type of respiration is associated with soil microorganisms and is a by-product of the global carbon cycle, known for decomposing organic matter. While several parameters impact the respiration rate, soil moisture content has been identified as the most significant abiotic facto, with one of its negative impacts being the appearance of diffusion-limiting effects. This diffusion of nutrients across the soil profile is believed to be crucial as the bound microorganisms depend on nutrients circling towards them across water-connected pores. However, uncertainties persist regarding the relationship between diffusion and soil moisture content, primarily due to the difficulties of capturing the soil respiration across the entire scale of the soils and the destructive nature of traditional respiration and the destructiveness associated with soil water content analyses. Due to this, geophysical tools, including electrical conductivity measurements, have started to be applied to attempt to capture moisture contents as, similarly to the respiration rates, electrical conductivity (EC) relies on the aqueous phase as both solids and gases are isolators. In the present study, we applied various matric suctions and measured the associated soil respiration flux and electrical conductivity, respectively, to validate our hypothesis that there will be a correlation between both respiration and EC. This fascinating relationship would allow us to find a new methodology to capture the respiration rate without reaching invasive steps. The samples were composed of natural and sieved soils from different types of cultivation, as well as top and subsoils. Our findings revealed a strong positive correlation between respiration rates and EC across varying matric potentials. The optimal matric potential (-250 hPa) demonstrated peak respiration rates, coinciding with the combination of the presence of pore connectedness and oxygen availability. Beyond this threshold, respiration rates and EC declined with decreasing soil water content, particularly in sieved samples, where homogenised pore sizes amplified this effect. These findings suggest EC could serve as a proxy for measuring the optimal conditions of microbial activity, offering a non-invasive tool to study soil respiration across diverse conditions. Future research could further refine this approach, enhancing our understanding of microbial processes and their environmental implications.
How to cite: Fülöp, O., Nunan, N., Gueye, M., and Jougnot, D.: Electrical conductivity measurements as a proxy for diffusion-limited microbial activity in soils, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-10876, https://doi.org/10.5194/egusphere-egu25-10876, 2025.
O2 deficiency is a main prerequisite for denitrification promoting N2O formation in soils. Increased microbial activity in the rhizosphere of growing plants promotes microbial respiration, which together with root respiration contributes to high O2 demand and consumption in the rhizosphere creating favorable conditions for denitrification.
To understand the effect of root growth on N2O formation in the rhizosphere, we developed a novel rhizobox design allowing to monitor soil O2 concentrations and N2O fluxes at high spatial and temporal resolution. Rhizoboxes were filled with 2.2 kg of arable soil with silty loam texture and maize (Zea mays L.) was grown for 3-6 weeks. Soil moisture was kept between 70 and 80 % water-filled pore space. The ‘window side’ of the rhizoboxes was equipped with an O2-sensitive optode, allowing monitoring of O2 concentrations in the developing rhizosphere and surrounding soil at high spatial and temporal resolution. Root growth was monitored by photographing roots and analyzed using RootPainter software. Surface N2O fluxes were determined every two to three days using transparent chambers and a LI-COR Trace Gas Analyzer. N2O concentrations in the soil profile were measured with N2O microsensors by piercing through the O2 optode at selected sites in the rhizosphere and bulk soil. On the last day of the experiment, we sampled regions of interest (ROI, 1.6 cm diameter) from the window site of the rhizoboxes and analyzed them for mineral N, total C and N, and the abundance of N cycling genes involved in denitrification and N2O reduction. Afterwards, the remaining soil was sampled in layers of 5 or 10 cm and analyzed for mineral N and dissolved organic C (DOC).
Soil water content decreased with increasing root length (R²=0.39). Soil O2 concentrations were positively correlated with root length (R²=0.80), but negatively with soil water content (R²=0.64). Surface N2O flux rates differed strongly between replicates, yet the overall flux patterns were similar. Root growth and soil moisture were the main controls of N2O fluxes as confirmed by a linear mixed effect model including an interaction between total root length and soil water content as fixed factors and replicate as random factor.
Analyses of soil sampled at the end of the experiment showed that NO3- and DOC content were highest in the uppermost 5 cm of the rhizoboxes and strongly decreased with depth. Similarly, abundance of bacterial 16S rRNA genes, reflecting the overall size of the bacterial community, and genes for denitrification (nirK) and N2O reduction (nosZII) decreased with increasing sampling depth, which was associated with the lower resource availability (NO3-, DOC) in deeper layers.
N2O concentrations measured with microsensors in soil ranged between 0 and 100 µmol N2O L-1 confirming very high heterogeneity of N2O formation in soils. Highest N2O concentrations were found in the direct vicinity of roots. Overall, minimum N2O concentrations were negatively correlated with maximum O2 concentrations and maximum N2O concentrations were positively correlated with total N availability indicating that O2 controlled the onset of denitrification while N availability controlled its magnitude.
How to cite: Rummel, P. S., Rasmussen, M. R., Merl, T., Saghaï, A., Hallin, S., Mueller, C. W., and Koren, K.: Identifying hotspots of N2O formation in the rhizosphere of young maize plants by combining O2 optodes and N2O microsensors, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-5886, https://doi.org/10.5194/egusphere-egu25-5886, 2025.
Denitrification is the sequential reduction of nitrate to dinitrogen. The greenhouse gas nitrous oxide (N2O) is thereby produced as an intermediate and denitrifiers are thus recognized as a major source N2O in soils. Denitrification is stimulated by organic carbon, oxygen limitation and nitrate availability. Such edaphic factors are spatially variable in soils and impacted by soil pores. Thus, we addressed the question, whether denitrifiers exhibit spatial patterns relative to variations in distance to soil pores. Undisturbed soil cores were extracted from two agricultural model soils and subsamples of known distance to soil macropores were extracted by the help of an X-ray computed tomography guided strategy. Spatial variability of genetic and process level denitrification potentials was generally high with a minimal impact of pore distance. A minor increase of process level denitrification potentials with distance to pores was observed for one of the soils only. Quantification of genetic denitrification potentials after short incubations were not significantly different among samples. The minor impact of macropore distance on genetic and process-level denitrification potentials suggests that macropores are not the major source of spatial heterogeneity impacting denitrifiers in soils, implying that there is no need to explicitly consider such a parameter for modelling denitrification in soils.
How to cite: Horn, M. A., van Dijk, H., Lucas, M., Henjes, S., Rohe, L., Vogel, H.-J., and Schlüter, S.: Denitrification potentials in soils are only marginally impacted by distance to air-filled macropores, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-19651, https://doi.org/10.5194/egusphere-egu25-19651, 2025.
Posters on site: Mon, 28 Apr, 14:00–15:45 | Hall X3
Green manure strongly affects saline-alkali soil organic carbon (SOC) sequestration. The mechanism by which green manure influences the contribution of plant and microbial-derived carbon (C) to SOC in wheat-green manure cropping system remains unclear. Herein, plant residue C (PRC), microbial, bacterial, and fungal necromass C (MNC, BNC, and FNC), enzyme activity and microbial community were determined under wheat fallow after harvest (CK), green manure roots return (GMR), and green manure shoots and roots return (GMRS) in a five-year field experiment. Compared with CK, GMR and GMRS increased SOC content by 12% and 11% at 0-20 cm, respectively. Specifically, GMR accelerated the lignin biotransformation by increasing the relative abundance of K-strategy fungi, caused a reduction in the contribution of plant residues to SOC by 16-31%. While GMR increased MNC, especially BNC by 1.6-2.8 times, which was the primary driver of SOC sequestration. Comparatively, GMRS increased the relative abundance of r-strategy bacteria by 12-13%, and C- and Nacquisition enzymes by 12-17% and 56-68% compare to CK. This in turn, increased the accumulation of PRC, but decreased MNC (especially FNC) contribution to SOC. Overall, green manure return strategies altered the contribution of plant residues and microbial necromass to SOC by regulating microbial life strategies. MNC (especially FNC) contributed more to SOC than PRC. Therefore, green manure specially root return is a viable option to drive SOC accumulation via microbial necromass formation in wheat-green manure cropping system in saline-alkali soils.
How to cite: Yuyi, L., Wu, X., Zha, Y., and Li, S.: Soil organic carbon sequestration of green manure in saline-alkali land, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-5352, https://doi.org/10.5194/egusphere-egu25-5352, 2025.
The poor soil structure caused by salinization is a major factor affecting crop growth and soil structure will further affect hydrological function. Biochar is widely used to improve soil physical structure because of its special porous material. However, the mechanism of soil pore structure on hydrological function (e.g., soil saturated hydraulic conductivity, plant available water, least limiting water range) after biochar incorporation in saline soil remains unclear. Therefore, the present study examined the response of soil structural properties of different biochar addition in saline clay loam, and subsequently assessed how the pore structure influence soil hydrological function. The study involved four treatments: CK (Control)、C1 （7.5 t ha−1 biochar）、C2 (15 t ha−1 biochar)、C3 (30 t ha−1 biochar). Soil aggregate stability increased from 15% to 30% when the amount of biochar addition increased from 7.5 t ha−1 to 30 t ha−1. The highest connectivity index (2.36) and the highest fractal dimension (2.56) were found at the biochar addition of 30 t ha−1. Biochar addition reduced the proportion of small pores (<50 µm pore size) at both soil depths of 0–10 cm and 10–20 cm, whereas increased the proportion of large pores (>300 µm pore size). Biochar amendment reduced the soil penetration resistance, with the soil saturated hydraulic conductivity, plant available water and the least limiting water range were measured 46%, 27% and 40% greater in rate of 30 t ha-1 biochar addition as compared with those of the CK, respectively. Person correlation analysis and redundancy analysis revealed that the soil saturated hydraulic conductivity was positively correlated with large pores (diameter >300 μm) and pore connectivity (p < 0.05). The lowest least limiting water range of the CK was primarily constrained by a relatively higher penetration resistance. The improved pore connectivity and elongated pore structures were the key responsible for the reduced penetration resistance in biochar-amended soil, which subsequently increase.
How to cite: Wu, X., Li, Y., Zha, Y., and Li, S.: Biochar's Impact on Soil Structure and Hydrological properties in Saline Land, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-5342, https://doi.org/10.5194/egusphere-egu25-5342, 2025.
Soil microorganisms, in association with mangrove trees, play an important role in supporting the foundation of the ecosystem functions. Understanding the microbial contributions to mangrove ecosystem function and stability is essential for effective conservation and management. Currently, mangroves face heightened vulnerability to the repercussions of global warming. Factors such as elevated temperatures, rising sea level, increased flooding frequency and duration, and salinity fluctuations impact microbial diversity within these ecosystems. Identification and understanding of the core microbiota and mangrove microbial biodiversity remains scarce, specifically in the arid region. This research aims to provide insights into microbial strategies for coping with environmental change, contributing to sustainable mangrove management and ecosystem resilience in the United Arab Emirates (UAE) and beyond.
The UAE government has initiated extensive mangrove afforestation efforts to safeguard coastal environments, yet comparisons between afforested and reforested strategies in terms of microbial community dynamics remain sparse. Considration of microbial communities in mangrove restoration projects is an important key enhance establishment, growth and stress tolerance of mangrove trees as well as enhance the success of the initiatives. In this study, two afforested sites (Ras Al Khor wildlife sanctuary and Jebel Ali wildlife sanctuary, Dubai) and a reforested site (Khor Al Beidah, Umm Al Quwain) in the UAE were selected, with their forest ages approximately >30, <10, and >14 years, respectively. Topsoil samples were collected from grey mangrove (Avicennia marina) forests and surrounding non-vegetated area and salt marshes for two seasons.
Current findings revealed that Jebel Ali site (<10 years) had sandy coarse textured soil, less soil organic matter, and more fluctuating pH with seasonal changes in comparison to the other older sites. This research hypothesizes that age, conservation efforts and physiochemical properties of soil in afforested and reforested mangrove sites are the primary determinants of microbial biodiversity in the soils. We present a comparative study of the microbiota against the physiochemical characteristics of the soils. It is predicted that specific microbial communities will be found across different tidal zones (seaward and landward), and seasons. Along the environmental gradient, specific microbiota are expected to be associated with and adapted to the environmental conditions.
How to cite: Salman, A. Z., Al Mahmoudi, H., Matsuoka, S., Ookami, T., Kang, H., and Tateno, R.: Understanding the role of microbial community in afforested and reforested mangrove ecosystems in the United Arab Emirates, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-7060, https://doi.org/10.5194/egusphere-egu25-7060, 2025.
Plant diversity promotes soil organic carbon (SOC) gains through intricate changes in root-soil interactions and their subsequent influence on soil physical and biological processes. The goal of this study was to assess SOC and pore characteristics of soils under a range of switchgrass-based plant systems, representing a gradient of plant diversity with species richness ranging from 1 to 30. We focused on the structure of biopores, assumed to represent a legacy of root activities, and its relationships with SOC accumulation in the studied systems.
Our findings reveal that plant diversity enhances SOC through biopore-mediated mechanisms, with plant functional richness accounting for 29% of bioporosity variation and bioporosity explaining 32% of the variation in SOC. While a positive correlation between plant diversity and SOC accumulation was observed across all studied systems, a two-species mixture of switchgrass (Panicum virgatum L.) and ryegrass (Elymus canadensis) exhibited the highest bioporosity and achieved SOC levels comparable to those of the systems with 6 and 10 plant species, and inferior only to the system with 30 species. The findings suggest the potential for identifying specific plant combinations that efficiently foster biopore formation and promote SOC sequestration.
How to cite: Kim, K. and Kravchenko, A.: Optimizing soil carbon sequestration: The role of biopores in plant diversity and strategic species combinations, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-18741, https://doi.org/10.5194/egusphere-egu25-18741, 2025.
Despite an importance of organic N for plant growth, it is uncertain how spatial distribution of the hotspots of organic N is affected by root development. We visualized amino-N content and leucine aminopeptidase (LAP) activity in seminal and lateral roots of maize (Zea mays L.) at the 4- and 6-leaves phases. Amino-N and LAP hotspots were strongly overlapped at seminal roots and root tips of maize. The intensity of amino-N hotspots was fertilization-, growth phase- and root-specific. Amino-N content decreased in seminal root tips at the 6- versus the 4-leaves phase irrespective of fertilization levels, while it increased in seminal roots and lateral root tips under full fertilization with root growth. This suggests a potential functional differentiation of seminal and lateral root tips in the N-acquisition strategy in the course of plant growth.
How to cite: Blagodatskaya, E., Shen, G., and Guber, A.: Spatial distribution of organic N in the course of Zea mays L. roots development , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-12061, https://doi.org/10.5194/egusphere-egu25-12061, 2025.
Microbial denitrification is a critical process in soils, driving nitrogen cycling and organic carbon turnover. While traditionally considered an anaerobic process, denitrification has been observed in oxic environments, suggesting the presence of anoxic microsites that facilitate anaerobic metabolism within otherwise oxygen-rich surroundings. These microsites often evade detection by bulk oxygen measurements, leaving their spatiotemporal dynamics and contribution to denitrification poorly understood. This knowledge gap largely stems from the methodological challenges of observing coupled oxygen and microbial dynamics at the microscale (microns to millimeters) in natural subsurface environments.
To address these challenges, we simulated the wetting of sandy soil using a microfluidic device integrated with a transparent planar oxygen sensor. Wide-field and fluorescent time-lapse microscopy were employed to track the spatially heterogeneous growth of a facultative denitrifier (P. veronii 1YdBTEX2) alongside oxygen concentration dynamics. Additionally, nitrate concentrations in the device outflow were analyzed to quantify the overall denitrification rate in the microfluidic device, indicating anaerobic respiration.
Our results revealed that microbial colonization closely correlated with the formation of oxygen-depleted zones. Despite the pore space remaining oxic at the bulk scale throughout the experiment (72 hours), oxygen-depleted "hot-moments" occupied up to 10% of the pore space, providing conditions suitable for anaerobic nitrate respiration. Remarkably, nitrate concentrations in the effluent decreased from 0.5 mM to nearly zero after 50 hours, demonstrating efficient denitrification despite the limited spatial extent of anoxic zones. Contrary to conceptual models predicting reduced activity in previously oxic regions, our findings showed that denitrification peaked during maximum oxygen consumption. This suggests that simultaneous increases in aerobic and anaerobic volumes promote the persistence of anoxic microsites and sustain denitrification in oxic soils.
How to cite: Ceriotti, G., Borisov, S. M., and Berg, J.: Anaerobic Respiration in Oxic Soils: Visualizing Denitrification hot-moments with Microfluidics, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-15041, https://doi.org/10.5194/egusphere-egu25-15041, 2025.
Enhancing plants' ability to deal with climate change consequences requires adopting new measures to improve soil viability. Using beneficial bacteria to enhance plant resilience is a promising approach. Understanding the interplay between bacterial biofilm and water flow and distribution after drainage is crucial to achieving sustainable positive effects. However, the impact of soil structure and various biofilm extracellular components on water flow is still largely unknown. Here, we study the effects of biofilm characteristics and porous medium structure on water retention during drainage. We use microfluidic porous medium devices with prescribed structures and inoculate them with a common soil bacterium, Bacillus Velezensis. We use a wild-type strain and two mutants – a ΔtasA strain mutant in extracellular protein fibers formations and a ΔepsH mutant in forming extracellular sugar polymers. The model porous medium microfluidic devices are fabricated with PDMS and contain an array of circular pillars in a rectangular channel. The porous medium structure is controlled by two parameters: the pillar diameter distribution variance and their spatial correlation. The distribution variance controls the pore-scale heterogeneity of the porous medium, while the spatial correlation controls its macroscopic heterogeneity. We begin our experiments by inoculating the porous medium with a bacterial culture solution. Then, we inject nutrient broth into the microfluidic chip at a constant flow rate while periodically capturing images of biofilm development using a microscope in Brightfield mode. We also compare the biofilm images to a numerical solution of pore-scale velocity by solving Stokes flow in OpenFOAM for the specific geometry of the microfluidic cell. Preliminary results show biofilm accumulates in a heterogeneous porous medium in regions of narrower pore apertures with lower flow velocities. In contrast, biofilm accumulation is not preferential to specific areas in a homogeneous porous medium. Using ΔtasA and Δepsh mutants resulted in reduced biofilm accumulation. In the next stage, we will perform drainage experiments to assess the simultaneous effect of structure and biofilm on water retention and distribution. The fundamental understanding gained from this study will help facilitate upscaled experiments that could indicate the preferred saturation conditions for increasing plant-available water content under different structural and biological soil features.
How to cite: Oren, L., Tzipilevich, E., and Borgman, O.: The interplay between porous medium structure and bacterial biofilms in a microfluidic flow cell, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-10887, https://doi.org/10.5194/egusphere-egu25-10887, 2025.
Understanding microorganism growth in porous soils is vital for a wide range of applications, from bioremediation to industrial processes. In this study, we employ 4D X-ray microscopy (XRM) to track how the growth of the fungus Schizophyllum commune, a wood-decaying basidiomycete, alters the pore space structure of a column experiment. By capturing high-resolution 3D scans at different time intervals (i.e., 4D imaging), we visualize the dynamic interaction between fungal mycelium and the soil substrate, revealing how mycelial growth impacts soli porosity, pore connectivity, and permeability. The results show that the fungal growth induces a complex combination of pore occlusion, pore enlargement, and the creation of new channels through the substrate, which in turn affects the fluid flow through the soil column. Using AI-driven image analysis and segmentation techniques, we can automate the detection and quantification of these structural changes, providing insights into the relationship between microorganism activity and soil properties at a unique level of detail. This approach opens new possibilities for understanding how fungi influence the microstructure of soils and sediments, with potential implications for fields such as bioremediation and material design. The integration of artificial intelligence (AI) with advanced imaging modalities, such as X-ray microtomography (XRM), enables the experimental quantification and computational estimation of permeability. The integration of artificial intelligence (AI) with advanced imaging techniques, such as X-ray microtomography (XRM), facilitates both the experimental quantification and computational estimation of permeability. In this study, the small column system exhibits a reduction in permeability, which may result from both physical and microbiological factors. This synergistic approach enables comparative analysis and predictive modeling of microbial activity within complex systems, thereby enhancing the ability to predict and control its influence on system dynamics.
Keywords: 4D X-ray microscopy, Schizophyllum commune, fungal growth, pore space structure, artificial intelligence, image analysis, microbial impacts, material science, bioremediation.
How to cite: Loewe, A., Sadeghnejad, S., Herold, M., Kothe, E., and Schäfer, T.: Monitoring the Influence of Schizophyllum commune Growth in Pore Space Structure using 4D X-ray Microscopy, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-17940, https://doi.org/10.5194/egusphere-egu25-17940, 2025.
In order to better understand soils heterogenous nature, we can apply chemical imaging to visualize microscale spatiotemporal dynamics of important soil parameters such as oxygen or pH in real-time. However, the use of chemical imaging with planar optodes is mostly limited to laboratory experiments, due to practical constraints of the current applied equipment.
To address these challenges, we have developed a novel and low-cost multi analyte real time in-situ imaging system (MARTINIS)[1]. Specifically designed for operating in-situ or in mesocosm applications. MARTINIS significantly downscales imaging components, fitting them into a 25 cm in diameter and 70 cm long transparent tube. The system can be deployed into the soil profile with planar optodes attached to the tube’s exterior to create an interface for direct chemical imaging in the field. We show how we developed our proof-of-concept system by applying low-cost, off the shelf components and 3d printing, while maintaining high spatial (< 100 um) and temporal resolution (≥ minutes). To demonstrate the functionality of MARTINIS we have deployed the system in various in-situ environments and mesocosm applications in soil or sediments to obtain “panoramic” imaging of oxygen, pH and temperature dynamics. By incorporating a simplified temperature planar optode directly to the imaging system we are able to compensate for soil temperature changes along depth gradients when measuring oxygen or pH.
In one application, MARTINIS operated semi-autonomously over three months to monitor 2D soil oxygen conditions in a 16 cm deep soil profile. The system captured dynamic changes in oxygen levels linked to specific rainfall events and demonstrated reliable performance across various weather conditions, from snow to sun. In another application for short-term deployment, we measured heterogeneous soil pH gradients in wildfire-affected remote locations, highlighting the systems portability and adaptability. Deployment versatility was extended to waterlogged sediments in a mesocosm setup to observe the effect of bioturbation on oxygen dynamics. Measuring 2D oxygen and pH dynamics directly in the field is crucial, as these parameters drive many biogeochemical processes in soils and are tightly linked to rapidly changing environmental conditions. Conditions, which are often impossible to replicate in the laboratory. Enabling in-situ chemical imaging can be especially valuable in agricultural settings, where microscale soil oxygen dynamics leads to “hot spots” or “hot moments” of greenhouse gas production such as N2O.
With MARTINIS we present a proof-of-concept system that aims to overcome current barriers of applying planar optodes in-situ and increase accessibility to researchers by applying low-cost equipment, a modular platform and user-friendly software.
[1] M. R. Rasmussen et al., "A novel, standalone and low-cost system for in-situ chemical imaging with planar optodes in soils," Sensors and Actuators B: Chemical, vol. 424, p. 136894, 2025/02/01/ 2025, doi: https://doi.org/10.1016/j.snb.2024.136894.
How to cite: Reinhard Rasmussen, M., Butterbach-Bahl, K., and Koren, K.: A Novel, Standalone and Low-cost System for In-Situ Chemical Imaging with Planar Optodes, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-16535, https://doi.org/10.5194/egusphere-egu25-16535, 2025.
