Soil is arguably the most complicated biomaterial on the planet. It is the largest terrestrial carbon sink, and the most species rich habitat on Earth. Microorganisms driving biogeochemical cycles live and interact in the soil’s intricate pore space labyrinth, but they are difficult to study in their realistic settings because of the soil’s opaqueness. Microfluidic Soil Chips allow us to study the impact of soil physical microstructures on microbes and vice versa, realistic microbial interactions, and microbial impact on biogeochemical cycles live and at the scale of their cells.
Chips can be tailored according to each research question, designing labyrinths or realistic image-based pore spaces, and also microchemical conditions can be varied in a controlled manner. We found that pore space geometry impacted the growth and degradation activity of the two microbial groups - bacteria and fungi - in synthetic communities in opposing ways: fungi were inhibited by increasing spatial complexity of the pore space, while bacteria and their enzymatic activity were enhanced in increasingly intricate pore spaces.
We can study bio-physical interactions throughout processes such as drying, freezing and soil aggregation, and can trace biochemical changes of cells and their environment, including metabolic rates of single fungal hyphae, via Raman microspectroscopy. Inoculating the chips with soil brings a large proportion of the natural microbial community into their inner microstructures, allowing us to study and manipulate interactions among species embedded in their complex food webs. We developed AI-based image analyses for soil bacteria, fungi and protists that aid counting, movement tracking and morphotyping biodiversity, which can complement molecular biodiversity measurements. The soil chips enable us to conduct complex ecological studies, such as testing the effect of predator removal on community composition and bacterial and fungal population and necromass dynamics.
Beyond the scientific potential, the image footage from soil chips can also bring soil ecosystems closer to people,aiming to increase appreciation of their beauty, and engagement in soil health conservation.
How to cite: Hammer, E. C., Zou, H., Arellano, C., Aleklett Kadish, K., and Pucetaite, M.: Expanding toolbox for Microfluidic Soil Chips to study biophysicochemical interactions and microbial community dynamics, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-18324, https://doi.org/10.5194/egusphere-egu26-18324, 2026.
Soil microbial communities drive most biogeochemical processes and create hotspots of nutrient cycling. However, spatial visualization of microorganisms in these soil hotspots at the microscopic scale remains challenging due to the intrinsic fluorescence and opacity of soil matrices. One promising approach to distinguish microbial cells from the heterogeneous soil background is fluorescence lifetime imaging microscopy (FLIM) combined with phasor plot analysis. This technique separates and visualizes distinct photon arrival times on a per-pixel basis, providing information independent of fluorescence intensity. As a result, FLIM overcomes limitations of intensity-based imaging caused by autofluorescence, limited resolution, and photobleaching artifacts associated with minerals and organic matter.
In this study, we determined characteristic fluorescence lifetime profiles of BacLight™ Green–stained Rhodotorula mucilaginosa and Bacillus subtilis using FLIM via confocal laser scanning fluorescence microscopy. Measurements were conducted in phosphate-buffered saline solution (PBS), water, and in natural, autoclaved, glucose-activated soils, as well as soil mineral particles. In pure cultures, fluorescence lifetimes were 1.20 ± 0.2 ns for R. mucilaginosa and 1.30 ± 0.1 ns for B. subtilis in both water and PBS. Fluorescence lifetimes within individual cells were spatially homogeneous for both species, indicating stable photon arrival times and only minor matrix effects under the tested conditions.
Using phasor plot analysis, we observed a clear separation between microbial fluorescence lifetimes (approximately 1 ns) and those of the surrounding soil matrix (0.2–0.7 ns and > 3.6 ns). These findings demonstrate the feasibility of using FLIM to discriminate microbial cells from complex soil backgrounds and suggest strong potential for extending this approach to other soil types and their associated microbiota.
How to cite: Loeppmann, S., Shi, Y., de la Fuente, A. A., Boy, J., Guggenberger, G., Fulterer, A., Fritsch, M., and Spielvogel, S.: Using fluorescence lifetime imaging to disentangle microbes from the heterogeneous soil matrix, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-5487, https://doi.org/10.5194/egusphere-egu26-5487, 2026.
Soil microorganisms decompose a wide range of organic sources to meet their carbon (C) and energy needs. They further require nutrients such as nitrogen (N) in appropriate stoichiometric ratios to C. Organic sources are often N-poor (high C/N) compared to microbial biomass (low C/N). The extent of this stoichiometric imbalance influences organic matter decomposability, microbial C and N turnover, and ultimately C and N stabilization in soil.
Here, we investigate how organic source C/N and system-specific conditions impact the fate of C and N across diverse microbe-plant-soil systems. We synthesized data from 14 published isotope-tracing studies that applied 13C- and 15N-enriched organic sources and quantified the recovery of C and N from these sources in microbial biomass and bulk soil. The applied organic sources included microbial necromass and various plant residues spanning C/N ratios from 4 to 42. Similarly, the soils used in the studies were diverse, with bulk soil C/N ranging from 8 to 35 and pH values from 3 to 13.
The relative recovery of source N generally exceeds that of source C in microbial biomass and bulk soil, following the expected greater losses of C through microbial respiration. Moreover, low source C/N resulted in higher relative recoveries of source C and N in microbial biomass and bulk soil, likely reflecting more efficient microbial processing of sources with a stoichiometry that closely matches microbial needs. In addition, system-specific conditions, such as bulk soil C/N, influence the fate of C and N.
In our contribution, we aim to provide insights into the joint microbial use of C and N related to organic source stoichiometry and discuss how system-specific conditions and experimental design shape the observed patterns across diverse microbe-plant-soil systems.
How to cite: Siegenthaler, M. and Manzoni, S.: Linking microbial carbon and nitrogen use to organic source stoichiometry and system-specific conditions, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-8185, https://doi.org/10.5194/egusphere-egu26-8185, 2026.
Microorganisms drive soil C cycling, yet microbial metabolism is commonly conceptualized as a balance between growth (usually increase in biomass) and respiration. This simplified view neglects substantial microbial investments into non-growth pathways, such as the production of extracellular polymeric substances (EPS), which may strongly influence soil biogeochemical processes. EPS contribute to soil aggregation, resource acquisition, and microbial stress tolerance, but their role in microbial C allocation and soil C cycling remains poorly quantified. In this study, agricultural soils with different fertilization histories were incubated for 70 days with ¹³C-1-glucose and ¹⁵N-U-urea to trace substrate allocation among microbial biomass (MB), EPS, and CO₂ efflux. Our main hypothesis was that even though most substrate C and N would be allocated to MB, a significant portion would be incorporated into EPS. As results, we found that most added substrates were allocated to MB. However, 2 ~ 15% of added C and 10 ~ 15% of added N were recovered in EPS, corroborating our hypothesis that this non-growth pathway can account for a meaningful portion of microbial resource use. Further, we also observed that soil intrinsic characteristics, rather than their fertilization history, had the most significant effects over C and N partitioning in the studied sites. Microorganisms residing in clay-rich soils allocated more substrate to EPS than those in sandy soils. Finally, we also found that the incorporation of labelled C and N correlated positively in both MB and EPS. This supports the hypothesis of a coupled microbial C–N metabolism, in which EPS production accompanies growth rather than occurring independently of it. A larger set of soils is needed to incorporate non-growth C allocation pathways (other than EPS) into conceptual and quantitative models of soil biogeochemistry, in order to improve our understanding of microbial resource allocation for soil C and N stabilization.
How to cite: Leme Oliva, R., Dyckmans, J., and Georg Joergensen, R.: Microbial EPS as a relevant pathway for non-growth C investment: a study in two agricultural soils, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-3882, https://doi.org/10.5194/egusphere-egu26-3882, 2026.
Fungal mycelia constitute a major structural component of soils and play a central role in carbon (C) cycling. Yet, despite their importance, we lack a mechanistic understanding of how variation in mycelial morphology translates into differences in soil C dynamics and stabilization. In particular, the role of intraspecific variation (i.e. the genetic and phenotypic diversity within a single fungal species) remains largely unexplored. This gap represents a critical barrier to predicting the formation and persistence of soil C pools under ongoing environmental change.
This project addresses this challenge by using the model filamentous fungus Neurospora crassa to test how intraspecific variation influences soil C partitioning and respiration. We quantify how morphologically distinct strains of N. crassa differ in their contributions to soil respiration and to the formation of particulate organic matter (POM) versus mineral-associated organic matter (MAOM). Controlled soil microcosm experiments will allow us to directly link fungal traits (e.g. hyphal density, branching architecture) to C fluxes and stabilization pathways.
By leveraging a model organism, this work enables a level of experimental resolution that is difficult to achieve in complex natural communities. This approach allows us to move beyond species-level averages and explicitly test how individual-level variation shapes ecosystem processes in soils. Ultimately, we aim to identify the fungal traits and underlying genetic mechanisms that promote long-term C stabilization in soils.
By uncovering the mechanistic links between fungal intraspecific diversity and soil C dynamics, this project advances a shift from descriptive to predictive soil ecology. The results will provide a foundation for incorporating fungal trait variation into soil C models, thereby improving predictions of soil C permanence and refining our understanding of fungi as precise, trait-driven regulators of the terrestrial carbon cycle.
How to cite: Nieminen, V. and Aguilar-Trigueros, C.: A model-system approach to disentangle the role of intraspecific fungal effects on soil carbon cycling, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-22604, https://doi.org/10.5194/egusphere-egu26-22604, 2026.
A substantial fraction of nitrogen (N) in forest soils is present in mineral-associated proteinaceous compounds. The strong association between proteins and soil minerals protects these compounds from decomposition; however, previous studies have shown that ectomycorrhizal (ECM) fungi can acquire N via extracellular proteolytic enzymes acting on iron oxide mineral-associated proteins. Hydrolysis is accompanied by reductive dissolution of the iron oxides, creating conditions for Fenton chemistry and hence, generation of highly reactive hydroxyl radicals (HO•). Yet, the specific mechanisms employed by ECM fungi to acquire N from these mineral-associated proteinaceous compounds remain largely unresolved. In situ IR spectroscopy was used to monitor the molecular-scale reactions of bovine serum albumin (BSA, as a model protein) with proteases and HO• occurring at iron mineral interfaces. The decomposition of ferrihydrite-associated BSA by the ECM fungus Suillus luteus was followed using optical photothermal infrared (O-PTIR) microspectroscopy at the individual hyphal level. The effects and interplay between the oxidative and hydrolytic mechanisms in degrading and liberating N from mineral-associated BSA were examined using in vitro experiments. Proteolysis and oxidative mechanisms generated distinct, diagnostic IR spectral fingerprints of the mineral-adsorbed BSA. By correlating IR fingerprints with microspectroscopy of the fungal extracellular polymeric substance (EPS) region, we show that S. luteus decomposes mineral-associated proteins through sequentially deployed oxidative and hydrolytic mechanisms. BSA adsorbed on ferrihydrite is susceptible to HO• generated in heterogeneous Fenton reactions, and carboxylates (e.g., oxalate) were generated that occupied adsorption sites on ferrihydrite, which can counteract the suppression of protease activity due to protease adsorption onto the mineral. Moreover, deamination and fragmentation were also observed during the Fenton reaction. Our findings underscore the previously overlooked role of extracellular oxidative chemistry in fungal acquisition of nitrogen from mineral-organic complexes.
How to cite: Zhang, B., Maillard, F., Troein, C., Op De Beeck, M., Zhou, M., Tunlid, A., and Persson, P.: Fungal decomposition of mineral-associated proteins through Fenton-based oxidation and enzymatic hydrolysis, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-5208, https://doi.org/10.5194/egusphere-egu26-5208, 2026.
Ectomycorrhizal (ECM) fungi represent major drivers of soil carbon (C) and nitrogen (N) cycling, as they liberate nutrients by decomposing soil organic matter (OM), especially when labile N is limited. However, in contrast to saprotrophic fungi, knowledge on the decomposition of OM of different origin by ECM fungi remains limited. Here, we investigated the decomposition of fungal necromass and leaf litter by various ECM fungal species under different availabilities of mineral N, using in-vitro stable isotope tracing. We hypothesised that (I) the narrow C/N ratio of fungal necromass enhances decomposition and fungal growth compared to leaf litter, (II) N limitation increases the share of OM-N over mineral N in the fungal biomass, and (III) N limitation enhances respiration.
We grew four different ECM fungal species (Hebeloma cylindrosporum, Paxillus involutus, Laccaria bicolor, Suillus luteus) in the absence of OM, with Agaricus bisporus fungal necromass (C/N = 8) or with leaf litter of Ulmus laevis or Quercus alba (C/N = 29 and 60, respectively) on nutrient medium containing 13C-enriched glucose and two concentrations of 15N-enriched ammonium. We calculated the utilization of OM-C and OM-N for fungal growth and respiration after a minimum growth period of 45 days.
In accordance with hypothesis I, C from fungal necromass was more effectively utilized by ECM fungi (40% of the necromass-C) than C from leaf litter (around 5%). In contrast, the percentage utilization of OM-N was highest for the Q. alba leaf litter (40%). However, due to the narrow C/N of the necromass, this treatment still resulted in the highest absolute amount of OM-N being incorporated into ECM fungal biomass and consequently increased fungal growth. As expected in hypothesis II, the relative share of OM-N in the fungal biomass was higher under mineral N limitation, even if the absolute uptake of N from leaf litter was decreased. We did not find support for hypothesis III as mineral N limitation did not lead to an increased respiration. However, under N limitation, respiration of ECM fungi growing on leaf litter was increased while growth was reduced compared to the controls without OM, suggesting a shift in C and energy investment from growth to decomposition in the presence of OM. Interestingly, the patterns were surprisingly uniform across the tested species.
Our findings show that OM type and mineral N availability control ECM fungal C and N uptake, growth, and respiration across four tested species and highlight fungal necromass as an important source of organic N and C for ECM fungi.
How to cite: Kurbel, V. B., Detiger, M. L., Abdalla, K., Tyborski, N., Frank, A. H., Schwerdtner, U., and Pausch, J.: In-vitro utilization of fungal necromass and plant litter by ectomycorrhizal fungi under contrasting mineral nitrogen availabilities, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-19745, https://doi.org/10.5194/egusphere-egu26-19745, 2026.
Arctic and subarctic regions are warming faster than the global average, yet carbon dynamics in mineral horizons remain comparatively understudied despite large stocks stabilized as mineral-associated organic matter (MAOM). Clarifying how warming alters mineral-associated carbon (C) and nutrient pools, and the soil microbial communities that mediate MAOM formation and destabilization, is therefore critical for predicting Arctic carbon–climate feedbacks. Here, we experimentally warmed subarctic birch forest soil in Abisko, Sweden, using distinct regimes: chronic (year-round) warming and seasonal warming (summer-only or winter-only). To quantify MAOM formation potential, we developed recoverable Mineral Interface Sampling Probes (MISP) consisting of thin films of Fe- and Al-(hydr)oxides (MISP-Fe and MISP-Al) and coupled them with surface-sensitive spectroscopy techniques (X-ray photoelectron spectroscopy, XPS; Fourier-transform infrared spectroscopy, FTIR). Bacterial and fungal community composition and richness were assessed by high-throughput amplicon sequencing (16S rRNA gene and ITS markers), while microbial abundances were quantified by quantitative PCR (qPCR) as marker-gene copy numbers. Warming increased bacterial and fungal gene copy numbers and the fungal-to-bacterial ratio, while reducing richness in both domains, consistent with a community shift toward fewer warming-tolerant taxa. MISPs showed mineral-type-dependent responses in mineral-associated C formation potential (Fe vs Al (hydr)oxides), whereas mineral-associated N formation potential increased consistently under warmed treatments, yielding newly formed MAOM with a lower C:N ratio. Both microbial community shifts and MISP responses were strongest under summer warming, with comparatively weak responses under chronic or winter warming. Overall, summer warming increased microbial abundance and produced newly formed MAOM with a lower C:N ratio, consistent with soil warming shifting MAOM formation toward a microbial necromass-mediated pathway, where organic matter is processed through microbial biomass before stabilization on mineral surfaces. These findings highlight the sensitivity of MAOM pools and microbial communities in subarctic mineral soil horizons to soil warming.
How to cite: Moravcová, A., Gredeby, A., Zhang, B., Dumontel, H., Rousk, J., and François Maillard, F.: Experimental warming reshapes soil microbial communities and mineral-associated organic matter formation dynamics in a subarctic mineral horizon, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-21008, https://doi.org/10.5194/egusphere-egu26-21008, 2026.
The assignment of functional traits to protistan sequence data has become central for understanding how these diverse microorganisms contribute to ecosystem processes, yet current schemes that reduce protists to “phototrophs,” “consumers,” or “parasites” vastly underrepresent their functional diversity and ecological strategies. Because traits directly reflect adaptations to environmental conditions, community‐level trait profiles offer more mechanistic insight into species interactions, niche partitioning, and responses to disturbance than taxonomy alone, especially in highly divergent protist lineages. Recently developed, ontology‑based trait frameworks for major soil protist groups now enable more detailed functional annotation and reveal striking differences in morphology and physiology among phyla such as Cercozoa/Endomyxa, Oomycota, Amoebozoa and testate amoebae, challenging the notion of a single, unified trait set for all protists.
I will first outline the breadth of morphological traits across soil protists and their implications for habitat use and trophic interactions, and then explore novel molecular methods to reveal expressed physiological traits using deeply sequenced transcriptomes of free-living Thecofilosea (Rhizaria: Cercozoa), including 12 Rhogostoma strains, Fisculla terrestris and Katarium polorum. A conserved core of orthogroups supported central carbohydrate and nucleotide metabolism, whereas amino acid and lipid pathways, particularly sterol and branched-chain amino acid metabolism, varied strongly even among closely related strains, indicating divergent resource demands and prey dependencies. Distinct orthogroup repertoires and expression profiles in two Rhogostoma clusters point to specialization in sensory, adhesion and biofilm-related functions that likely modulate interactions with bacterial prey and soil microhabitats. Together, these morphological and transcriptomic perspectives demonstrate that fine-scale trait variation among protists is essential for mechanistic links between microbial community composition and soil biogeochemical processes.
How to cite: Bonkowski, M., Freudenthal, J., Öztoprak, H., Schlegel, M., and Dumack, K.: From Morphology to Metabolism: Trait‑Based Insights into Protist Diversity and Soil Biogeochemical Processes, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-13593, https://doi.org/10.5194/egusphere-egu26-13593, 2026.
The rhizosphere and hyphosphere are critical interfaces for plant-microbe interactions. However, the regulatory impact of long-term fertilization on the functional niche partitioning between these two compartments remains poorly understood. To address this, we conducted a pot experiment with wheat grown in preconditioned soils from a century-old fertilization trial. A 41-μm nylon mesh was used to physically separate the rhizosphere from the hyphosphere, enabling independent measurements of enzyme activities, microbial biomass, and available nutrient concentrations in each compartment. Our results showed that nitrogen (N) availability was the dominant factor among the fertilization regimes influencing plant performance, belowground C, nutrient dynamics, and prokaryote communities. Under N-limited conditions, plant–fungus cooperation was intensified, leading to a larger amount (24-41%) of dissolved organic C than in N-rich treatments. The dissolved organic C enrichment induced in the hyphosphere was 12-16% higher than that induced in the rhizosphere. This is evidenced by the strong positive correlation between arbuscular mycorrhizal fungal colonisation and hyphosphere dissolved organic C enrichment. In the fully mineral-fertilized NPK treatment, C-, N- and P-acquiring enzyme activities were 43-102% higher in the rhizosphere compared to the hyphosphere. Under combined manure and mineral fertilization, the highest overall levels of enzyme activities, nutrient availability, dissolved organic carbon, and microbial biomass carbon were observed in both compartments, but no differentiation between rhizosphere and hyphosphere was evident, reflecting the homogeneity of the microhabitats in these microbial functional traits. Linear discriminant analysis revealed that fertilization regimes significantly shaped microbial community composition, with combined manure and mineral fertilization consistently enriching Nitrososphaeria in both compartments. However, niche differentiation was evident between the two microhabitats: the rhizosphere uniquely recruited Planctomycetota under PK fertilization, whereas the hyphosphere was characterized by an enrichment of Chloroflexi under PK. This suggests that while fertilization drives broad taxonomic shifts, the rhizosphere imposes specific selective filters distinct from the hyphosphere. Together, these findings demonstrate that distinct fertilization regimes restructure the spatial partitioning of dissolved organic C dynamics and microbial functioning in the rhizosphere–hyphosphere by plant mediated cascading effect. Our results underscore the necessity of evaluating the rhizosphere and hyphosphere as distinct compartments to elucidate belowground C–N interactions under varying fertilization regimes. Accordingly, future research should examine these compartments separately to accurately capture fertilization-induced shifts in belowground C–N dynamics.
How to cite: Peng, C., Reitz, T., Blagodatskaya, E., Bouffaud, M.-L., and Tarkka, M.: The legacy of long-term fertilization reshapes functional partitioning of the rhizosphere and hyphosphere through a plant-mediated cascade effect, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-486, https://doi.org/10.5194/egusphere-egu26-486, 2026.
Understanding changes in soil organic matter (SOM) dynamics in response to long-term warming is central to predicting carbon stocks under future climate-change scenarios. This study investigates how century-scale soil warming influences microbial community composition and functional potential using a subarctic deciduous forest located on a geothermal hotspring (Takhini Hot Springs, Yukon Territory, Canada) as a model system. The soils affected by this natural geothermal gradient, which has been documented as being active for at least 100 years, range between 0 and 5°C above ambient surface temperature, with 40 - 60 cm subsoils reaching up to +11°C. Previous analyses of SOM from the study site show a decline in C:N ratios with increasing soil temperature, while nitrogen stocks remain largely unchanged, suggesting long-term alterations in organic matter inputs and decomposition processes. This system provides a unique opportunity to study long-term warming effects under field conditions while avoiding artefacts associated with short-term manipulations.
Topsoil and subsoil microbial community population size, taxonomy and functional gene composition at topsoil mean annual temperatures of 3.5, 4.2 and 5.3 and 8.3°C were assessed using qPCR and whole-genome shotgun sequencing. As soil texture and humic acid content varied along the gradient (e.g., 8.5 % to 25.9 % clay), an adapted extraction protocol optimised for humic-rich soils was used for DNA extraction, together with the use of an internal whole-cell spike-in standard of Gram-positive and negative halophilic extremophiles in all qPCR assays to correct for differential extraction efficiency and PCR inhibition. Metagenomic data is used to characterise microbial community shifts and to identify functional genes related to carbon, nitrogen and phosphorus cycling, as well as traits linked to microbial metabolic strategies. Metagenomic analyses indicate that long-term warming restructures microbial communities in a depth-dependent manner, characterised by increased Actinobacteriota in warmer deep soils, reduced Planctomycetota and Chloroflexi with warming, and higher surface-layer abundance of Amorphea in cooler plots. PCA of phylum-level communities revealed clear depth stratification (p<0.001) and warming effects (p=0.003), with surface and subsoil samples clustering separately and warmer plots diverging along PC1.
By integrating microbial community data with soil physicochemical properties, this study aims to clarify how sustained warming alters microbial functional potential and SOM processing in subarctic soils. Decreases in the relative abundance of eukaryotes (Amorphea) with increasing temperature, and a concomitant increase in Gram-positive Actinobacteriota associated with plant biomass cycling and secondary metabolite production in soils, suggests that temperature-dependent shifts in organisms responsible for SOM cycling may occur under soil warming of > 5 °C. The findings will contribute to improving predictions of climate-driven changes in soil biogeochemistry and the long-term stability of SOM under warming.
How to cite: Peter, A., Kehr, J., Poeplau, C., and Finn, D.: Microbial community composition and functional potential changes along a century-scale geothermally warmed soil temperature gradient , EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-517, https://doi.org/10.5194/egusphere-egu26-517, 2026.
Arsenic contamination in agricultural soils poses a major threat to environmental safety, food security, and sustainable farming systems across South Asia. This study investigates the extent of arsenic accumulation in agricultural soils of Haridwar district, Uttarakhand, and evaluates microbe-assisted remediation as a potential strategy to mitigate arsenic toxicity. Ten soil samples from arsenic-affected sites were analyzed for physicochemical, elemental, and microbial characteristics. The soils were predominantly sandy loam and exhibited moderate ionic strength (EC 316 µS/cm), neutral pH (7.2), reducing redox potential, and low moisture content. CHNS profiles (C/N = 8.83) and (C/H ratios =2.40) indicated nutrient-limited conditions that constrain microbial redox processes. Arsenic concentrations reached 11.4 ppm along with elevated levels of Cu, Zn, Fe, Mn, and Se. Strong positive correlations of As with pH (R2 = 0.904), iron (R2 = 0.808), and manganese (R2 = 0.797) suggested alkaline conditions and Fe–Mn redox cycling are key drivers of arsenic mobilization. High phosphate, calcium, and magnesium further contributed to competitive desorption and enhanced arsenic solubility. Microbial functional assessments using CLPP and enzyme assays revealed suppressed metabolic activity and reduced carbon utilization under metal stress, reflecting ecosystem perturbation. Overall, the findings demonstrate that the interplay of soil geochemistry and microbial activity drives arsenic behavior in agricultural systems. Microbe-assisted approaches focused on modulating redox conditions, stabilizing Fe–Mn phases, and improving nutrient balance offer a promising pathway for reducing arsenic bioavailability and restoring soil health in contaminated agricultural landscapes.
Keywords: Arsenic contamination, Agricultural soils, Soil geochemistry, Microbe-assisted remediation
How to cite: Dixit, S., Maurya, A., Singh, R., Singh, S., and Kumar, M.: Microbe-Assisted Remediation Potential in Arsenic-Impacted Agricultural Soils of Laksar, Uttarakhand, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-811, https://doi.org/10.5194/egusphere-egu26-811, 2026.
The soil microbiome provides indispensable ecosystem services, including nutrient and organic matter cycling, affecting exchange of energy, water, and carbon at the land-atmosphere interface, as well as provisioning an important environmental resilience layer through buffering natural and anthropogenic stressors. We applied generalized additive models (GAMs) to the largest methodologically consistent dataset of soil eDNA at continental scale. Based on colocated eDNA and soil parameter measurements from the LUCAS 2018 soil biodiversity dataset (Labouyrie et al., 2023; Orgiazzi et al., 2022) and ERA5-Land climate reanalysis data (Muñoz Sabater, 2019) for the 30-year period pre-dating sample collection (1988–2017), we (i) identify key drivers shaping the composition of soil bacterial communities, (ii) quantify changes in soil bacterial richness and diversity forced by soil properties, climatic effects, and anthropogenic pressures, and (iii) assess interaction effects between the different drivers. Multiple feature selection methodologies were employed and cross-checked to reduce the number of predictors without conceding prediction accuracy. A GAM including pH, electrical conductivity, and top layer bulk density (0–10 cm) as covariates can explain 73.3% of variance (adjusted R² = 0.727) in the Shannon entropy of samples. While land cover is commonly considered an important categorical determinant of soil bacterial diversity, our results suggest that land cover per se is no immediate factor, but instead land cover types constrain the physicochemical habitats on site, which are in turn the immediate drivers of bacterial diversity.
References
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Orgiazzi, A., Panagos, P., Fernández‐Ugalde, O., Wojda, P., Labouyrie, M., Ballabio, C., Franco, A., Pistocchi, A., Montanarella, L., & Jones, A. (2022). LUCAS Soil Biodiversity and LUCAS Soil Pesticides, new tools for research and policy development. European Journal of Soil Science, 73(5), e13299. https://doi.org/10.1111/ejss.13299
How to cite: Heintze, P., Hassani, A., Or, D., Panagos, P., Orgiazzi, A., Labouyrie, M., Köninger, J., Lebron, I., Robinson, D. A., and Shokri, N.: Generalized additive models confirm pH and emphasize electrical conductivity as key drivers of European soil bacterial diversity, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-1134, https://doi.org/10.5194/egusphere-egu26-1134, 2026.
Enhancing soil carbon (C) storage is critical for climate mitigation, and perennial systems for cereal agriculture have emerged as a promising strategy due to their sustained root-derived C inputs. However, an increased supply of labile C may also lead to a higher demand for nitrogen (N), whereby microbes decompose existing soil organic matter (SOM) to acquire N, termed N-mining, potentially triggering a priming effect that offsets C storage. Whether perennial cropping primarily promotes microbial C assimilation and subsequent production of SOM or accelerates SOM mineralization remains uncertain. Moreover, the stand age of perennial crops can substantially modify root-exudate C, thereby altering microbial C availability and shifing microbial decomposition strategies. But how perennial stand age regulates these coupled plant-soil-microbe processes is still poorly understood.
Here, we examined how converting annual crops to perennial intermediate wheatgrass (Thinopyrum intermedium, Kernza®) influences microbial decomposition dynamics and N-mining. Soils were collected from the annual cropping system, the first-year Kernza stand, and the ninth-year stand. Root-exudate inputs were simulated by semi-continuous additions of ¹³C-glucose over 20 days, applied at the daily exudate-C level of the perennial crop and at a five-fold higher intensity. We quantified the real-time soil organic C mineralization, organic N mineralization with the 15N pool dilution method, and microbial growth and biomass to resolve the balance between C storage and SOC loss, N mining from SOM, and its microbial response underpinning the simulated rhizosphere. We hypothesized that the conversion to perennial crops would enhance microbial N-mining and priming effects, particularly in young stands, whereas older stands progressively shift toward more efficient microbial C utilization and higher SOM stabilization potential. Based on the results, we found that glucose applied at levels matching those in the perennial crop rhizosphere induced fast (within days) and sustained (for weeks) priming response. Across addition levels, young perennial crops exhibited consistently higher cumulative priming than older perennial crops. These temporal patterns best matched responses in bacterial growth, suggesting a bacterial control of the young perennial rhizosphere priming effect and indicating a greater need for bacteria to acquire organic N there.
How to cite: Yang, X., Hicks, L., and Rousk, J.: Can the conversion to perennial cereal crops simultaneously promote SOC formation and stimulate microbial N-mining?, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-1229, https://doi.org/10.5194/egusphere-egu26-1229, 2026.
Deuterated water (2H2O) has been used to investigate changes in the metabolic activity of microorganisms. In contrast to, for example, 13C-labeled compounds, 2H2O acts as a general marker of biosynthetic activity, does not alter the available substrate pool and is more cost-effective than 18O-labeled water. These properties make 2H2O an attractive alternative for stable isotope labeling experiments, ranging from small-scale microcosm incubations with only a few grams of soil to larger-scale and more integrative experimental setups. However, high concentrations of deuterium (2H), introduced via 2H2O, can be toxic to cells, as kinetic isotope effects slow biochemical reaction rates and may therefore inhibit metabolic processes. Consequently, 2H2O-concentration-dependent effects on metabolic activity in the soil microbiome must be investigated to obtain reliable results. In this study, we conducted a microcosm experiment to analyze the effects of different 2H2O concentrations (0, 10, 20, 30, 40, 50, 60 at% of 2H) on nitrogen assimilation in the soil microbial community, using 15N-labeled ammonium sulfate as a tracer. Nanoscale Secondary Ion Mass Spectrometry will be used to derive the metabolic activity of single cells based on the amount of 15N tracer assimilated at the different 2H2O concentrations. Furthermore, metagenomics and metaproteomics will reveal 2H2O-induced shifts in bacterial community composition and functional pathways. Together, these data will provide the range of 2H2O concentrations that ensure the non-inhibited metabolic activity in the soil microbiome, supporting its use as a marker in soil microbiome research.
How to cite: Raab, F., Jehmlich, N., Stryhanyuk, H., and Worrich, A.: Evaluating concentration-dependent effects of deuterated water to optimize its use as marker of metabolic activity in soil microbiomes, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-13248, https://doi.org/10.5194/egusphere-egu26-13248, 2026.
Nitrification is a key control on soil nitrate (NO3−) pools, and yet the dominant microbial taxa driving the process may vary with land use and land management practices. In this study we test whether dominant nitrifiers (eg: autotrophic vs heterotrophic; bacterial vs fungal) differ between heavily managed tropical soils (urban farms, golf courses) and natural tropical forests in Singapore, using machine learning to identify the microbe groups most strongly associated with soil NO3- pools across sites.
We collected soils across multiple sites in each land-use and quantified soil NO3− using ion chromatography. To estimate taxon-level abundances, we combined qPCR-derived total bacterial and fungal abundances (16S/18S) with ribosomal DNA Amplicon sequencing relative abundances, using their product as a proxy for genus-level absolute abundance. We compiled a list of canonical ammonia oxidisers and microbes with reported heterotrophic nitrifying strains, and evaluated their ability to predict spatial variation of NO3− within each land-use type. This was done using three flexible models (generalised additive model, support-vector regression and random forest), where model performance was assessed using R² obtained from leave-one-out and repeated 5-fold cross-validation (200 repeats).
In managed soils, bacterial genera were consistently the strongest predictors of NO3− (across all models), including the canonical AOB genus Nitrosomonas and bacteria with reported heterotrophic nitrifying strains (Paenibacillus, Rhodococcus). Predictive performance was high across all model types (R² ≈ 0.6–0.85). In forests, fungal genera (notably Aspergillus and Fusarium) ranked highest, but overall predictive performance was lower (R² ≈ 0.3–0.5), suggesting that functional groups not captured by the current candidate set (e.g., ammonia-oxidising archaea) might potentially be driving nitrification in these sites. Further analysis on this is currently in progress
Overall, our results suggest that contrasting nitrifier niches exist in different land uses with bacteria-dominated predictors in managed soils and fungal predictors in forests, which highlights how management may restructure microbial pathways that govern nitrate formation in tropical soils.
Acknowledgements
This research grant is funded by the Singapore National Research Foundation under its Competitive Funding for Water Research (CWR) initiative and administered by PUB, Singapore’s National Water Agency. We also acknowledge NParks, for providing us site access to conduct the measurements.
How to cite: Senaratna, K. Y. K., Te, S. H., Fatichi, S., and Gin, K. Y.-H.: Identifying microbial predictors of soil nitrate pools across tropical land uses with machine learning, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-16012, https://doi.org/10.5194/egusphere-egu26-16012, 2026.
Soil biodiversity is increasingly recognized as an important part of the One Health framework. It is known to be pivotal not only for sustaining agricultural productivity, but also as a biological barrier limiting the establishment and persistence of livestock-associated pathogens. While direct transmission pathways between animals and humans are well documented, the role of soil microbial communities in regulating pathogen survival outside hosts remains poorly understood.
We investigate how abiotic soil properties and native microbial biodiversity interact to constrain the environmental persistence of emerging zoonotic pathogens. Enterococci were used as a model for fecal-derived, opportunistic pathogens in agricultural systems. Combining field observations with controlled microcosm experiments, we studied soils from a free-range and a conventional pig farm representing contrasting management practices and soil textures. Enterococcal abundance was quantified using genus-specific qPCR, while bacterial community composition was assessed via 16S rRNA amplicon sequencing to characterize the ecological context of potential pathogen establishment.
Enterococcal DNA was detected across multiple management zones in freshly collected soils, with highest abundances in areas of recent pig activity. However, few viable cells were found across the samples. In sterile soil microcosms, Enterococcus lactis and E. sulfureus proliferated strongly in both sandy and silty soils, demonstrating that abiotic conditions alone do not prevent enterococcal growth. These results indicate that biotic interactions, rather than physicochemical constraints, are likely the dominant factor limiting enterococcal persistence in natural soils.
Ongoing experiments manipulate native microbial diversity gradients to disentangle mechanisms of biotic suppression, while integrated DNA/RNA analyses will distinguish active growth from residual necromass. By linking microbial community composition to pathogen exclusion, our work highlights soil biodiversity as a key ecosystem function contributing to “pathogen-resistant” soils. The experimental framework established here is broadly transferable to other soil-borne or fecal-associated pathogens, supporting risk assessment and sustainable soil management in agricultural landscapes.
How to cite: Borchert, M., Finn, D., and Tebbe, C.: Exploring Establishment and Persistence of Enterococci in Agricultural Soils under Controlled Abiotic and Biotic Conditions, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-18222, https://doi.org/10.5194/egusphere-egu26-18222, 2026.
Soil microorganisms in agricultural fields are an important contributor to soil nutrient cycling. The soil microorganism abundance and diversity are affected by multiple factors, including physical and chemical soil characteristics as well as agricultural farming practices, all of which combine to affect crop growth and crop yield. As organic farming bans the use of synthetic chemical inputs, inducing changes in soil tillage and fertilization types, we expect positive effects on the soil microbial communities compared to conventional farming systems. To test this, soils from 30 farms of both conventional and organic systems were sampled, including small grain cereals (annual crops) and leys (improved sown grassland - perennial crops). Soil chips inoculated with these soils were used to determine microscopically the abundance of different microorganism groups. This was followed by conducting molecular identification of microbial diversity (bacteria, fungi and protists) for fresh soils, lab incubated soils and internal parts of the soil chips. Results showed variable abundances across the microbial groups for both crop types and the agricultural systems. Preliminary molecular results of fresh soils indicate comparable genetic diversity within and between crops and farming systems. Molecular results were compared to soil chip samples resulting in rather small microbial community shifts for lab incubated soils, but with stronger shifts in internal parts of the soil chip. Our results show that microbial group abundances via soil chip microscopy vary for crop type and farming practices, indicating possible effects by specific field treatments. On the other hand, preliminary molecular microbial biodiversity results show comparable microbial diversities for the fresh sampled soils, indicating a rather stable microbial diversity in agricultural soils.
How to cite: Lake, F. B., Bacon, C. D., Carrié, R., Ekroos, J., and Hammer, E. C.: Biodiversity of soil microbial communities in conventional and organic agriculture in Southern Sweden, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-19691, https://doi.org/10.5194/egusphere-egu26-19691, 2026.
Anthropogenic activities are a significant source of pollutants that pose substantial risks to both the environment and human health. Among these, microplastics and persistent organic pollutants (POPs) are of particular concern due to their persistence and long-term impacts. While the environmental presence and effects of these pollutants are well documented, their specific implications for regulating, provisioning, and cultural ecosystem service (ES) supply remain underexplored. Further research on these topics is essential, as they are critical to human wellbeing. The impacts of microplastics and POPs on ES include negative effects on biogeochemical cycles, macro- and microbiological activity, and plant development. These disruptions contribute to soil degradation and initiate a cascade of adverse effects on ES by altering soil physical, chemical, and biological processes. Soil pollution leads to decreased plant cover and diminishes the capacity to regulate erosion, flooding, climate, pollination, and nutrient cycling. Declining soil fertility subsequently affects the provision of timber, medicinal plants, biomass, and water. Additionally, soil and vegetation degradation are associated with reduced landscape aesthetics and the loss of traditional landscapes, particularly in regions subjected to intensive agroforestry activities.
Acknowledgements
This research was funded by the European Union NextGeneration EU through the National Recovery and Resilience Plan, Component 9. I8., grant number 760104/May 23, 2023, code CF 245/November 29, 2022. This work was supported by the project "Sensing, Mapping, Interconnecting: Tools for soil functions and services evaluation" supported by the Romanian Government, Ministry of the Innovation and Digitization through the National Recovery and Resilience Plan (PNRR) PNRR-III-C9-2022-I8, contract no. CF245/29.11.2022.
How to cite: Pereira, P., Kovacs, E., Kovacs, M., Inacio, M., Brevik, E., and Barcelo, D.: Understanding the effects of Microplastics and persistent organic pollutants' on soil ecosystem services supply, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-16725, https://doi.org/10.5194/egusphere-egu26-16725, 2026.
Antimicrobial resistance is on the rise and poses a global public health risk. Livestock manure serves as a primary source of antibiotic resistance in agricultural soils, where the specific agricultural management and climatic factors may influence antimicrobial resistance genes (ARG) levels and diversity. However, the compounded effects of climate change and shifts in land use on the spread of antibiotic resistance from livestock manure to soil microbiomes have not been studied. This study fills this knowledge gap by using soils from the “Global Change Experimental Facility” which investigates the consequences of climate change on ecosystem processes in different land-use types. Soils with four distinct land-use histories reflecting different agricultural management practices (conventional farming, organic farming, intensive grassland, and extensive grassland) were amended with cattle manure and incubated under current and future climate scenarios according to IPCC projections. The antimicrobial resistance genes (the resistome) and the mobile genetic elements (the mobilome) of the soil microbiomes were analyzed via metagenomics, while the abundance of clinically important resistance genes was quantified over time using real‑time quantitative PCR. The metagenomic approach indicates that 56% of the genes are shared among different land-use types, and a similar proportion of ARGs occurs in soils with or without manure additions. While the same ARG classes remain dominant across all treatments, the total ARG counts are consistently higher in grasslands than in croplands. Under conventional farming, future climatic conditions lead to an increase of unique ARGs, whereas organic farming maintains the same number of unique ARGs under both climatic scenarios. In intensive and extensive meadows, future climatic conditions show an increase of the unique ARGs compared to current ambient conditions. The temporal evaluation across all treatments revealed an overall decrease in the counts of the main ARG classes, such that, four months after manure addition, ARG abundances closely resembled the natural levels observed in soils without manure application and a similar ARGs composition. Overall, agricultural management was the main determinant of total ARG abundance, whereas future climatic conditions primarily influenced the occurrence of unique ARGs in a land-use-dependent manner.
How to cite: Prada Salcedo, L. D., Fischer, M. A., and Worrich, A.: Land-use-dependent responses of soil antibiotic resistance to manure input under current and future climates, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-11647, https://doi.org/10.5194/egusphere-egu26-11647, 2026.
Microbial ecology is dependent upon environmental samples collected in the field. However, field trips in remote locations present a number of logistical problems which can compromise sample integrity and lead to unreliable conclusions. Microbial communities continue to live after sample collection and, now under different conditions, may shift their composition. In the laboratory environment, the microbial community can be held constant through techniques such as freezing which may not be available for several days during sampling trips. There are several treatments which claim to preserve samples without refrigeration but most are (1) not designed for soil communities and (2) have not been independently tested.
We compare five treatments—DNA/RNA Shield (Zymo Research), PowerProtect DNA/RNA (Qiagen), Phoenix Protect (Procomcure Biotech), DESS and silica gel packets—on the basis of ease-of-use, cost-effectiveness and preservation effectiveness to make a final recommendation of the best choice for preserving microbial soil communities during field trips. Soil samples were collected, treated with one of the five treatments and incubated at either 5 °C or 22 °C. DNA was isolated from controls at the beginning of the experiment and from the treated samples at 7, 14, 28 and 56 days after sampling. Amplicons of the bacterial 16S ribosomal gene and fungal ITS region were sequenced and analysed to compare how the microbial communities in different treatments changed over time in terms of their richness and overall beta diversity. In addition, we checked for differential abundance of individual taxa.
With this work, we hope to inform researchers about which microbial preservation treatments are most appropriate for soil samples and which taxa might still change despite their use. We hope that this will aid researchers better plan field trips into remote locations and will improve the quality of data produced from such trips.
How to cite: Bosch, J., Olekšák, A., and Voříšková, J.: What is the most effective treatment for maintaining soil microbial community structure during field sampling expeditions?, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-1350, https://doi.org/10.5194/egusphere-egu26-1350, 2026.
Bacteria can disperse along fungal hyphae, using them as “highways” to cross physical discontinuities in soil (e.g. air-filled pores) and potentially to traverse microsites with suboptimal conditions such as oxygen- or nutrient-limited zones. While laboratory studies have resolved mechanistic aspects of hypha-associated bacterial motility, the ecological and resource-dependent context of this interaction, and its relevance for soil C and N dynamics, remains poorly understood. We address this gap by combining (1) laboratory experiments manipulating carbon and nitrogen sources to test how nutrient regime shapes the dispersal of fungal–bacterial co-communities from mid-Arctic glacier forefield soils (Greenland), and (2) a one-year field colonization experiment in glacier forefields of Greenland, Iceland, and Austria, tracking colonization of initially barren sediments in specially designed columns across geologies and soil development stages.
In the laboratory, distinct C/N combinations promoted exploratory growth by different fungi, with communities dominated by Mucor, Actinomortierella, and Syncephalis. Co-dispersing bacterial communities also shifted with nutrient regime, dominated by Flavobacterium, Janthinobacterium and Pseudomonas. Bacterial diversity transported along hyphae increased under inorganic N supply (ammonium or nitrate) relative to cellulose amendment without added N, indicating that fungal nutritional status and N availability can modulate partner recruitment during dispersal. Field observations complemented these results by revealing how hypha-associated colonization unfolds under natural conditions across contrasting forefields.
Together, our findings show that fungal physiology and nutrient status structure hypha-associated bacterial partnerships and suggest that hypha-mediated translocation can influence microbial community assembly during early soil formation, with implications for C/N acquisition strategies in heterogeneous soils.
How to cite: Keuschnig, C., Biswas, R., Deinert, S., and Benning, L. G.: Carbon and nitrogen control hyphae-mediated bacterial dispersal and partner recruitment in glacier forefield soils, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-16750, https://doi.org/10.5194/egusphere-egu26-16750, 2026.
Peatlands store a disproportionally large fraction of global soil carbon, yet their stability is increasingly threatened by climate-driven drying and degradation. One underexplored consequence of peatland drying is the potential colonization of soil fauna, such as earthworms, which have historically been absent from waterlogged peat soils. However, the implications of earthworm colonization for peatland carbon dynamics and vertical soil functioning remain poorly understood. Here, we used intact peat soil columns from alpine peatlands to investigate how increasing earthworm densities affect carbon pools, nitrogen availability, and microbial processes across two soil depths (0–10 cm and 10–20 cm). Earthworm treatments included a low-density and a high-density combination of epigeic and endogeic species, reflecting realistic colonization scenarios under peatland degradation. Earthworm addition substantially altered the vertical distribution of soil carbon. In control soils, total carbon and dissolved organic carbon exhibited pronounced depth stratification, whereas earthworm presence weakened or even reversed these depth patterns. Moreover, earthworms increased dissolved nitrogen concentrations and modified extracellular enzyme activities, indicating changes in nutrient cycling and microbial decomposition pathways. Integrated carbon stability indices further suggested a shift toward more decomposable carbon pools under earthworm treatments. Together, our results demonstrate that earthworm colonization can fundamentally reorganize vertical carbon distribution and biogeochemical functioning in peat soils. These findings highlight soil fauna as an overlooked but potentially critical mediator of peatland carbon destabilization under climate-driven degradation.
How to cite: Zhang, H., Eisenhauer, N., and Chen, H.: Earthworm colonization weakens vertical carbon stratification in alpine peat soils under climate-relevant degradation scenarios, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-17970, https://doi.org/10.5194/egusphere-egu26-17970, 2026.
Regulatory constraints on herbicide use and the spread of herbicide-resistant weeds have increased the interest in mechanical weed control in European agriculture. In this context, autonomous field robots, for which mechanical weeding is currently the dominant application, are receiving growing attention in research and practice.
Mechanical weeding generally affects the upper soil layers compared to conventional tillage. Nevertheless, its higher frequency and timing may impose additional pressures on soil biodiversity through regular habitat disruption, direct damage to soil fauna, or interactions with soil water. While the effects of conventional mechanical weeding on soil biology are sparsely studied, even less is known about the effects of mechanical weeding with autonomous field robots on soil biological parameters. Robotic weed control may affect soils differently from traditional mechanical weed control due to variations in driving speed, working width, and operational frequency.
To assess potential effects on soil fauna, we conducted several field experiments in 2024 and 2025, comparing mechanical weeding by different robots (NaioOZ, FarmDroid FD20, and FarmingGT) with chemical weed control or mechanical weeding using conventional machinery. The experiments were conducted at three sites in Germany and were cropped either with sugar beet (Beta vulgaris) or maize (Zea mays). The first site in Eastern Germany (landscape laboratory patchCROP) is sand dominated (Loamy sand), whereas the soils at the second site in Bavaria and the third site in central Germany have finer textured soils (Silty loams).
Several biological soil indicators were assessed depending on the experimental site, including feeding activity using Von Törne bait lamina sticks placed in consecutive periods starting directly after the last of several weeding operations, carabid beetle and spider abundance collected via pitfall traps in consecutive sampling intervals during and after weeding, and earthworm abundance determined by hand sorting in the autumn following robotic activity in summer. In addition, chemical and physical soil parameters were determined before and after weeding, including pH, soil organic carbon content, bulk density, and aggregate stability indices.
Preliminary results indicate trends towards reduced feeding activities, decreased earthworm biomass, and lower carabid abundance under mechanical weeding with autonomous field robots, highlighting the need for systematic assessment of biological soil responses to robotic field management. We will discuss implications for soil-smart robot implementation with respect to the frequency and intensity of robotic interventions and outline future research directions.
How to cite: Thielemann, L. and Grahmann, K.: Effects of mechanical weeding with lightweight autonomous field robots on soil biological indicators , EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-18561, https://doi.org/10.5194/egusphere-egu26-18561, 2026.
Earthworms play important roles in maintaining soil structure and function, soil aeration, drainage, the moisture holding capacity of soils and the cycling of nutrients. The presence of earthworms in soil can lead to greater plant growth. Evidence suggests that earthworm abundance has been declining over the last several decades, which potentially negatively impacts soil function. Anthropogenic climate change means extreme weather events are becoming more frequent and intense; flooding is particularly relevant for earthworm populations, with increasing flood frequency and duration. Soils become rapidly anoxic when flooded, which threatens earthworm survival. We are investigating whether flooding is likely to change earthworm populations, through changes in abundance, diversity and distribution.
We carried out surveys to sample earthworms, collecting data on abundance and species distributions at field sites with twinned flooding and non-flooding areas and differing soil moistures and flooding histories. In laboratory experiments we have been working with common UK species, such as the lob worm Lumbricus terrestris, the green worm Allolobophora chlorotica, the grey worm Aporrectodea caliginosa, the blue-grey worm Octolasion cyaneum, and the European nightcrawler compost worm Dendrobaena veneta.
To determine moisture preferences of earthworm species we carried out choice chamber experiments, providing standard soils with a gradient of soil moisture contents. All species had similar, but soil specific, moisture preferences, choosing moist, but not waterlogged conditions.
Survival experiments were carried out, exposing earthworms to conditions of restricted oxygen, simulating flood conditions. Species commonly found in wetter or drier soils were found to survive for a similarly short duration of approximately 22 hours in oxygen-depleted water (0.25 mg l-1 dissolved oxygen). This is in contrast to our previous research in which A. chlorotica, a species that is able to aestivate, survived in oxygen-depleted water, whereas L. terrestris did not. Furthermore, A. chlorotica has more oxygen-carrying haemoglobin (0.22 vs 0.125 µmol Hb g-1), and its haemoglobin is more efficient at binding and retaining oxygen than the much larger L. terrestris (4.18 vs 11.47 mmHg P50), which suggests that A. chlorotica may be better adapted to survive in oxygen-depleted conditions resulting from flooding.
We are also monitoring the hatching success of earthworm cocoons exposed to 90 hours of oxygen depletion in simulated flood conditions. Cocoons were subjected to oxygenated conditions of 2 mg l-1 or a treatment restricted to 0.25 mg l-1 of dissolved oxygen for the duration. The majority of cocoons of A. chlorotica and D. veneta remain viable when subjected to reduced oxygen but suffer lower hatching success than those with unrestricted oxygen. A difference was found between species, D. veneta retained higher viability than A. chlorotica, time to hatching was found to be delayed in both species when exposed to low oxygen conditions.
The above evidence is consistent with an increasing frequency of flooding causing changes in earthworm population structure and potentially reducing earthworm abundance, with cocoons being a key component for the survival of earthworm populations after flood events. Our results highlight one possible consequence of climate change on earthworm populations and consequent impacts on soil functionality.
How to cite: Pile, B., Hodson, M., Berenbrink, M., Klaar, M., Daly, K., and Zhu, Q.: Impacts of climate change related flooding on earthworm populations, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-18765, https://doi.org/10.5194/egusphere-egu26-18765, 2026.
Posters virtual: Thu, 7 May, 14:00–18:00 | vPoster spot 1a
EGU26-22253 | Posters virtual | VPS15
Data Mining of ELFA Bioindicators to Assess Soil Threats Across European Biogeoclimatic Regions Using the LUCAS DatasetThu, 07 May, 14:15–14:18 (CEST) vPoster spot 1a
Soil threats, such as pollution, salinity, soil organic carbon (SOC) loss and compaction, are often difficult to quantify or costly to analyze and bioindicator research represents an important approach for their efficient evaluation. Microbial bioindicators can reflect early biological responses to soil degradation processes, offering a sensitive and cost-efficient complement to conventional soil analyses. The identification of microbial clade–specific indicators can be achieved in detail through metabarcoding technologies, although these methods typically require extensive data processing and advanced bioinformatics expertise.
In contrast, ester-linked fatty acid (ELFA) analysis provides an inexpensive biological method capable of quantifying major microbial groups in soil, including bacteria, fungi, Gram-positive, Gram-negative and Actinobacteria. We hypothesize that ELFA analysis can serve as a complementary and alternative technique for soil threat bioindication.
Using LUCAS 2018 soil survey data, we assessed relationships between soil threat proxies (estimated metal and metalloid concentrations, electrical conductivity, SOCmeasured/SOCexpected ratio and bulk density) and ELFA-derived parameters (both raw and ratio-transformed) through random forest modeling and ANOVA. Significant bioindicators (α < 0.05 and β > 0.8) were confirmed using generalized additive model (GAM) regressions across European biogeoclimatic regions (Alpin, Continental, Pannonian, Mediterranean, Boreal and Atlantic).
Our results demonstrate that Actinobacteria/Gram− ratio, fungi-to-bacteria (F/B) ratio, Gram+ and Gram− groups can serve as potential bioindicators for soils enriched in metals (Zn and Cd) and for SOC loss (SOC_observed/SOC_expected) as significantly highlighted by Random Forest, ANOVA and GAM analyses. Some responses were found to be specific to continental, boreal and Mediterranean biogeoclimates.
These findings support the inclusion of ELFA-based microbial metrics in European soil monitoring schemes such as LUCAS or the Soil Monitoring Law. Future research should integrate ELFA data with molecular bioindicators to refine multi-parameter soil threat assessments.
How to cite: Martin, N., Caner, L., Vilhelmsson, O., and Zucca, C.: Data Mining of ELFA Bioindicators to Assess Soil Threats Across European Biogeoclimatic Regions Using the LUCAS Dataset, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-22253, https://doi.org/10.5194/egusphere-egu26-22253, 2026.
