We welcome submissions seeking to understand soil microbial metabolism, growth and death, encompassing the diverse transformations and interactions these involve. Topics of interest include characterization of microbial activity and turnover using advanced methods (e.g., isotope tracing, calorimetry, metagenomics), microbial ecophysiology and stoichiometry, physiological responses to (micro)environmental changes, carbon and energy-use efficiency, alongside approaches to understand microbial functional responses (e.g. dynamic modelling, artificial intelligence). We aim to stimulate interdisciplinary discussions to advance our understanding of soil biology at scales from the mechanistic understanding of biogeochemical processes to global change.
We are excited to have Prof. Michaela Dippold and Dr. Nataliya Bilyera as invited speakers for the session.
Orals: Mon, 4 May, 14:00–18:00 | Room 0.11/12
The pivotal role of the soil microbiome in global biogeochemical cycles is undisputed. The subsequent demand for simplified quantitative descriptions of its functions in modelling approaches resulted in transferring the pure-culture based microbial yield concept into microbial carbon use efficiency (CUE) – a “one-number” approach to partition C input to soils and to describe the physiological efficiency of the microbiome.
The holy grail lost its sanctity once our challenges to reliably determine it became evident. The method comparison of Geyer et al. (2019) identified which critical assumptions underly the contrasting outcomes in CUEs derived from these methods. Our own data just underline this: While substrate-based CUE has a temporal and substrate dependency, 18O-based and metabolic CUE remain often unaffected by substrate addition but cover, with either DNA-replication or anabolic precursor-based upscaling of biomass C formation contrasting physiological processes of microbial cells.
Such divergent findings highlight that despite decades of research, current methods do not allow an unambiguous quantification of microbial substrate use in soils, owing to two overlapping methodological challenges: 1) Neither extracting microbial biomass nor predicting it from de-novo formed DNA can deliver a reliable quantitative estimation of the newly formed microbial biomass carbon; and 2) Whatever we add as substrate to soils does not reflect what microbes use for growth under native conditions. Our progress in quantitatively covering an increasing number of cellular pools (e.g. also considering cell walls and membranes), the increased consideration of storage, and first concepts on how to integrate secreted extracellular carbon offer perspectives to tackle the first of the two challenges. However, experimentally representing the incredible diversity of organic molecules accessible to microbes for consumption in soils is yet rather avoided, although Lehmann et al (2020) postulated compound diversity as a central factor determining the fate of carbon in soils. Comparing incubations with individual compounds to those of complex monomer mixture revealed that the microbial use of an individual compounds is significantly affected by the presence or absence of other compounds, i.e. the molecular diversity in soil solution. This can readily be explained by viewing microbes through the lens of their metabolic capacities, which impose fundamental constraints on their functioning. Formation of microbial biomass requires a defined ratio of precursor building blocks, which are products of distinct pathways of the basic carbon metabolism. De-novo production requires expression and formation of all pathway-related enzymes, while direct precursor uptake from soil solution allows for “saving” this energy. Therefore, we postulate that monomer diversity would positively affect microbial efficiency. This may be contrasting for polymer diversity, where extracellular enzyme costs exceed those of intracellular de-novo formation and thus a low diversity may be bioenergetically favorable. Thus, substrate diversity-efficiency relationships may centrally underlie deviations between our current CUE approaches. We recommend microbial ecologists to whenever possible replace CUE by the actual processes of interest, i.e. the ecophysiological response and subsequent changes in microbial pools (metabolome, growth) and fluxes (fluxome). This would provide parameters allowing for quantitative upscaling to pools and fluxes required for higher scale soil system models.
How to cite: Dippold, M. A., Shao, G., Zhou, R., and Shi, L.: The carbon use efficiency paradox: why what we measure is not what we need, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-20487, https://doi.org/10.5194/egusphere-egu26-20487, 2026.
The extent to which microbial processes control soil organic carbon (SOC) dynamics remains uncertain. Carbon use efficiency (CUE)—the fraction of assimilated carbon allocated to growth—has been used as a key parameter, but its relationship with SOC reflects carbon partitioning rather than the absolute magnitude of microbial fluxes. Microbial growth rate could provide a more mechanistic link to SOC accumulation, as it quantifies biomass production and reflects necromass formation. Here we combine a global ¹⁸O–H2O dataset (n = 268 paired observations) with outputs from four land surface models to test whether growth rate predicts SOC more strongly than CUE. In the incubation experiments, growth rates are more closely associated with SOC than CUE, although soil properties and climate explain equal or greater variance. Models reproduce the stronger role of growth rate over CUE but tend to underestimate the abiotic controls. The models also emphasize CUE as the main predictor of the SOC/NPP ratio, in contrast to observations, which indicates the soil’s capacity to retain plant carbon inputs. Together, these findings identify microbial growth rate as a diagnostic that can help bridge models with empirical data and guide a more balanced representation of microbial and mineral controls in SOC projections.
How to cite: He, X., Marmasse, G., Hu, J., Varney, R. M., Manzoni, S., Ciais, P., Wang, Y.-P., Cui, Y., Bai, E., Abramoff, R. Z., Abs, E., Schmidt, E., Zhang, H., and Goll, D. S.: Microbial growth rate is a stronger predictor of soil organic carbon than carbon use efficiency, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-4089, https://doi.org/10.5194/egusphere-egu26-4089, 2026.
Microbial carbon use efficiency (CUE) represents the proportion of carbon consumed by microbes that is accumulated in biomass instead of respired, and is important for understanding carbon cycling and storage in soils. Existing methods for quantifying CUE rely on additions of isotopically labeled material and/or incubations in laboratory settings, which may differ from in situ conditions. We propose an alternative strategy to study microbial growth and metabolism using hydrogen isotopes of microbial phospholipid fatty acids (δ2HPLFA).
In bacterial monocultures, δ2HPLFA values are strongly influenced by central metabolism. In particular, the most 2H-depleted PLFAs produced by heterotrophic bacteria are those with precursors derived from the Embden-Meyerhof-Doudoroff (EMP) and pentose phosphate pathways. When glycolysis proceeds through the Entner-Doudoroff (ED) pathway, fatty acids are significantly enriched in 2H. However, the highest δ2HPLFA values are from cultures grown on precursors from the tricarboxylic acid (TCA) cycle as the sole carbon source. These naturally occurring differences in δ2HPLFA values in cultures are one to two orders of magnitude greater than spatial and temporal variability soil water δ2H values. Therefore, δ2HPLFA values offer the opportunity to detect relative changes in TCA activity by soil microbes. As the TCA cycle is typically associated with higher respiration and lower CUE, and specific PLFAs are primarily derived from distinct microbial groups, δ2HPLFA values have potential as indicators of CUE for different groups of soil microbes.
Soil communities are inherently more diverse and dynamic than monocultures. As a first step to assess the utility of δ2HPLFAs as indicators of group-specific metabolism, we established a two-species system using a gram-negative bacteria (Pseudomonas sp.) and gram-positive bacteria (Bacillus sp.). These taxa produce distinct PLFAs from each other and utilize distinct pathways for glycolysis. We grew monocultures and co-cultures in a minimum media (M9) with either glucose or succinate as the sole carbon source. We harvested cultures at mid-exponential phase and measured δ2H values of extracted fatty acids.
First, we confirmed the results of previous monocultures with different strains of Pseudomonas and Bacillus. When grown on glucose, Bacillus, which uses the EMP pathway, produced fatty acids with an average δ2H value of -184 ± 12 ‰, while Pseudomonas, using the ED pathway, produced fatty acids with an average δ2H value of -20 ± 2 ‰. When they were grown on succinate and thereby forced to rely on the citric acid cycle, both bacteria produced fatty acids that were much more enriched in 2H (δ2H = +24 ± 5 ‰ for Bacillus and +192 ± 5 ‰ for Pseudomonas). When grown in co-cultures on glucose, δ2H values for PLFAs produced by Bacillus were similar to when it was grown alone on glucose (-189 ± 8 ‰), but δ2H values for PLFAs produced by Pseudomonas increased to +58 ± 18 ‰, indicating an increase in TCA cycle activity due to consumption of acetate secreted by Bacillus. These results demonstrate how metabolic changes driven by community interactions can be detected through δ2HPLFA values and provide a foundation for applications in more complex systems.
How to cite: Ladd, N., Amacker, N., Wijker, R., Meredith, L., and Nelson, D.: Hydrogen isotopes of lipids as a proxy for central metabolism and carbon use efficiency in soil microbes, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-11278, https://doi.org/10.5194/egusphere-egu26-11278, 2026.
While soil biotic and abiotic processes control carbon emissions and storage in terrestrial ecosystems, biotic processes are key for understanding the future fate of carbon. The faster the rate of decomposition and the lower the fraction of decomposed carbon that is converted to new biomass, the more carbon released to the atmosphere. Despite this known pathway, quantifying this control is uncertain in models. Microbial implicit models capture general environmental controls, but omit direct controls of microbial biomass and its interactions with organic matter. Microbial explicit models account for key processes, but are prone to instability and parameter identifiability issues. This leads to the question, is there an alternative approach that blends simplicity and sufficient process representation? Here, we test whether metabolic theory of ecology (MTE) can be used for predictions of soil carbon fluxes and storages. MTE captures key features of biological processes at the individual level by considering both body size and temperature effects on metabolic rates, and can be used to scale up controls to a community or ecosystem level. Motivated by the need to explain variations in soil carbon fluxes and storages with intermediate-complexity, robust models, MTE is shown to explain scaling relations between respiration rates and microbial biomass, microbial growth rates and temperature, and between the contents of soil organic carbon and microbial biomass. This presents an opportunity to compare scaling relations in observational data and models, and potential to provide insight into global scale parameterising of microbial explicit models. This may help to reduce uncertainties in the future carbon feedback in the soil.
How to cite: Varney, R. M., Schwarz, E., He, X., and Manzoni, S.: Global control of both temperature and microbes on soil carbon, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-13129, https://doi.org/10.5194/egusphere-egu26-13129, 2026.
Soil microorganisms control organic matter cycling and, to a large extent, determine how soil systems can cope with and mitigate climate change and environmental threats. Integrating them explicitly into process-based soil models is critical for predicting how soil carbon (C) flows and stocks change in ecosystems with time. Models are critical tools for integrating datasets with theory. However, integrating information from modern omics-based datasets is a challenge due to the nonlinear relationship between genomes and the actual function microbes express in their local environment. Functional traits can be defined and inferred from these genomic datasets to better leverage their information and better understand the complexity of the soil microbiome. Integrating trait information with process-based microbially explicit models provides an opportunity leverage genomic data for an improved soil carbon prediction.
We present a hybrid modeling framework that uses a data-driven neural network approach to derive microbial parameters of process-based models from metagenome inferred functional traits, leveraging information from metagenomic and DNA sequencing datasets. We combine a neural network (multi-layer perceptron) with a process-based soil model to set up a hybrid model. The neural network uses genomic trait data as the input and predicts biokinetic parameters of the process-based model. We trained the hybrid model with synthetic genomic trait datasets of varying complexity and time series of state variables of the process-based model (e.g. carbon dioxide production) to demonstrate the approach. Using trait inference from genomes, the model can learn several biokinetic parameters such as growth rates, dormancy rates, affinities to organic matter, growth yields or decay rates. The training uses a complex constraint-based loss function, informing the model from ecological theory and literature data, ensuring the realistic behavior of every non observed state variable during training such as active and dormant microbial pools. Compared to a ‘naïve’ hybrid model, the use of a more complex loss function reduces model equifinality and ensure realistic behavior of the non-observed state variables. Naïve loss function cannot efficiently learn the behavior of non-observed state variables and fail to predict realistic microbial dynamics. We present i) the concept of the hybrid soil modelling framework, ii) the constraint-based loss function approach, iii) the performance of constrained versus naïve hybrid models after training with different synthetic datasets.
How to cite: Collart, P., Gall, J., Schnepf, A., Doorenbos, L., and Pagel, H.: Constrained hybrid modelling to predict microbial dynamics and organic matter turnover in soil systems, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-8161, https://doi.org/10.5194/egusphere-egu26-8161, 2026.
Tropical forest soils are important carbon stocks, despite often being highly weathered and depleted in mineral nutrients. In these soils, microbial communities play a crucial role in carbon, nitrogen and phosphorus cycling, and contribute largely to the soils’ nutrient pools. However, as tropical primary forests are remote, and deep soil layers are difficult to access, little is still known about the role of microbial activity affecting carbon cycling beyond the more frequently studied top layers.
We conducted a carbon and nutrient stock inventory in soils down to two meters at the experimental site of the AmazonFACE program, located in Central Amazonia, near Manaus, Brazil. Additionally, we investigated microbial community composition with phospholipid fatty acids (PLFA) and measured microbial respiration and potential extracellular enzyme activity rates in short-term incubations.
We found that the Amazon FACE site harbors 180.0 (±6.50) Mg C ha-1 in the upper two meters of soil, with almost 60% already being stored in the first 50 cm. Below the organic upper 5 cm of soil, C:N ratios remained constant at around 14.5, however, δ13C signatures of soil organic carbon increased, indicating more often turned-over carbon at deeper layers. We found a faster decrease in fungal than bacterial PLFA markers with depth, and no 16:1w5 markers (representing arbuscular mycorrhizal fungi) below 20 cm of soil. In contrast, our results showed less strong declines in microbial respiration rates.
Overall, our data shows that the upper 50 cm of soil have a crucial function in forest carbon storage and turnover, likely related to plant nutrient inputs by roots, facilitating higher microbial activity, making these upper layers more prone to environmental changes. As in deeper soil layers fine root biomass and microbial activity are relatively low, these layers can play an important role in forest resilience. However, normalized by microbial biomass, carbon mineralization is still high in deeper layers, suggesting that they are not static and could be sensitive to climate change.
How to cite: Fuchslueger, L., Pires Martins, N., Figueiredo Lugli, L., Souza, C. C., Santana, F., Marinho, N., Pires, M., Hartley, I., Norby, R., and Quesada, C. A. and the AmazonFACE team: Going deeper underground – unravelling microbial activity and carbon cycling in deep soils in the Central Amazon, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-21795, https://doi.org/10.5194/egusphere-egu26-21795, 2026.
Root exudates are key drivers of microbial activity and carbon cycling in the rhizosphere, but their transient and localised nature makes microbial responses hard to measure. We used reverse microdialysis to deliver glucose as a root exudate analogue and trace microbial synthesis and carbon allocation. Deuterated water (D₂O) quantified baseline rates of synthesis in unamended soil, while 13C-glucose traced microbial synthesis fuelled by C from localised glucose input. Over 72 hours, we quantified incorporation of 2H and 13C into metabolites, membrane lipids, and storage compounds. Glucose perfusion significantly increased microbial respiration and synthesis rates, particularly for polyhydroxybutyrate (PHB) and triacylglycerols (TG), indicating strong stimulation of intracellular carbon storage. The rapid incorporation of 2H and 13C into diacylglycerols (DGs), coupled with slow turnover, suggests DGs may function in intracellular carbon storage or as membrane lipids rather than solely as transient metabolic intermediates. Glucose perfusion also increased membrane lipid synthesis, with differences in 13C incorporation among membrane lipids indicating differential growth among microbial groups. In contrast to larger increases in synthesis of intracellular C storage and membrane lipids, synthesis and turnover of compatible solutes such as trehalose and mannitol were largely unaffected by glucose perfusion, implying their roles are independent of carbon supply and tied to metabolic regulation in well-watered soil. Our results highlight the utility of reverse microdialysis and dual isotope labelling for disentangling effects of root exudates on microbial metabolism. This approach provides new insights into how localized carbon inputs shape microbial function and community dynamics, and emphasises intracellular carbon storage as a key microbial response for coping with transient resource availability in the rhizosphere.
How to cite: Warren, C.: Reverse Microdialysis and Isotope Labelling Reveal Microbial Strategies for Carbon Storage in the Rhizosphere, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-2294, https://doi.org/10.5194/egusphere-egu26-2294, 2026.
Microbial necromass carbon (MNC) is 15-80% of SOC and is controlled by necromass production (microbial growth and death), stabilisation (minerals and aggregates), and consumption (recycling and destabilisation). Microbial traits (i.e., quantitative measures that capture differences in life strategies or niche segregation among taxa) provide a step-change in understanding the interactions between microbes and soil organic carbon (SOC) cycling, particularly regarding the contribution of MNC. However, it remains unclear which traits consistently inform MNC and its relationship with SOC in cropland soils. Here, we address this gap by collecting soil samples from 22 farm fields spanning 4 soil types in Luxembourg, then we inferred genomic bacterial traits using representative genomes available in the Genome Taxonomy Database (GTDB) and the Bacterial Diversity Metadatabase (BacDive) and correlated them with SOC and MNC stocks.
Our preliminary results suggest that soil-type selects traits linked to resource acquisition and high-yield microbial strategies, including genome size, GC content, 16S rRNA copy number, and motility. We also observed positive or negative correlations between the traits themselves, suggesting possible trade-offs in community-level life history strategies, with potential implications for carbon derived from microbes. However, these traits or trade-offs had no direct links with bulk SOC stocks. Our ongoing analysis will instead link these traits and trade-offs directly to MNC stocks, to assess whether genome-derived traits can be useful for informing the necromass cycle. If this microbial trait relationship with MNC stocks holds true, the results and method will be useful for better understanding the MNC cycle in cropland soils and for improving next-generation SOC models.
How to cite: Buckeridge, K., Sousa Rocha, A. V., and Herold, M.: Microbial traits are shaped by soil type with potential implications for microbial necromass carbon cycling, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-20400, https://doi.org/10.5194/egusphere-egu26-20400, 2026.
Soil organic carbon (SOC) sequestration is closely linked to the functioning of microbial communities present in soil microenvironments. However, it is unclear how the distribution of microbial communities or carbon resources within soil pore space influences the formation and long-term storage of microbial necromass. Using a cellular automaton simulating the exploration of pore space by bacterial cells, we estimated the relative production of necromass in different soil pore sizes, taking into account (i) the initial distribution of carbon resources used by microbial cells, (ii) soil moisture, and (iii) the microbial biomass recycling threshold. We show that carbon resources located in macropores are consumed more rapidly than those located in narrow pores. Microbial mobility appears to be highly dependent on the pore context: it is advantageous in connected macropores but becomes costly and inefficient in confined micropores, reducing carbon-use efficiency. Necromass tends to accumulate preferentially in small pores, where reduced connectivity limits its recycling. These results highlight the importance of soil spatial organization and water status in regulating microbial carbon fluxes and suggest that explicit integration of pore heterogeneity and microbial functional traits is essential for improving soil carbon dynamics models.
How to cite: Maestrali, M.: How do pore size and microbial mobility shape necromass distribution in soils ?, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-10654, https://doi.org/10.5194/egusphere-egu26-10654, 2026.
Microbial life in soils is highly heterogeneous in space and time, as the intensity of microbial activities and processes depends strongly on the availability of nutrients and water, as well as a wide range of environmental factors. Identifying these hotspots requires high-resolution approaches, which can be achieved using advanced soil imaging techniques. In parallel, molecular methods provide powerful tools to characterize the microbial community structure and functional potential within these regions.
In this talk, I will present the opportunities and challenges associated with soil zymography for detecting microbial hotspots by mapping the activity of enzymes directly in soil over time and space. Additionally, I will demonstrate how molecular techniques, such as DNA sequencing, can be employed to identify the dominant microbial species inhabiting particular hotspots and determine which microorganisms are active and what functions they perform. Finally, I will discuss how co-localizing different imaging approaches combined with molecular methods can help to distinguish between microbial strategies for acquiring nutrients, offering new insights into how soil microbes drive key ecosystem processes.
How to cite: Bilyera, N.: Seeing the Invisible: Opportunities and Challenges in Studying Microbial Life in Hotspots, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-5080, https://doi.org/10.5194/egusphere-egu26-5080, 2026.
Microbial metabolism represents the major pathway for both the formation and the decomposition of soil organic matter, as carbon (C) consumed by microbes is either respired during catabolism and leaves the soil system as CO2 or is incorporated into new biomass compounds during anabolism and eventually becomes stabilized as microbial necromass. The partitioning of C between these two metabolic branches, also known as the microbial carbon use efficiency (CUE), depends on the complex interplay of many factors such as the quality of the carbon substrate and the availability of nutrients such as nitrogen (N) and phosphorus (P).
In this contribution, we combined measurements of soil respiration, DNA and RNA content with highly temporally resolved metatranscriptomics and dynamic modeling to study microbial activity and community changes in an arable soil after batch input of glucose as a labile C source and further factorial addition of N and P sources in mineral form. While the respiration results indicated a strong N limitation in the studied soil, we observed similar short-term changes in the bacterial, fungal and protist communities regardless of nutrient addition, with an expansion of copiotrophic taxa in all three groups. Notably, while the resulting communities were comparable after two days, these shifts occurred at a faster rate in treatments that received additional N. These observations suggest that glucose stimulated the growth of the same species in the soil under both nutrient-rich and nutrient-poor conditions, with N availability modulating the kinetics and the efficiency of copiotroph growth instead of stimulating a distinct group of specialists adapted to nutrient limitation. This interpretation is also supported by the observed ratio of RNA to DNA as a metric of microbial activity status as well as by a simple dynamic model of microbial growth, both of which reveal a faster activation and more efficient growth in nutrient-rich treatments.
Overall, our findings demonstrate that the input of a labile C source determines a relatively small subset of actively growing copiotrophs in the bacterial, fungal and protist communities, whereas the stoichiometric availability of other nutrients such as N only controls the rate and efficiency with which
these species are able to grow.
How to cite: Endress, M.-G., Kang, L., El Kouche, N., Dumack, K., Blagodatsky, S., and Bonkowski, M.: Temporally resolved microbial community dynamics reveal the parallel proliferation of copiotrophic bacteria, fungi and protists after labile substrate addition irrespective of nitrogen availability, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-2809, https://doi.org/10.5194/egusphere-egu26-2809, 2026.
Similar to human settlements, soil bacteria are distributed into numerous cell clusters whose sizes encode their function and environmental context. We show that bacterial cell cluster size distributions follow log-normal patterns, predicted by proportionate growth (Gibrat’s law). This log-normal distribution of cell cluster sizes is robust across biomes spanning a wide range of resource availabilities. Importantly, we show how characteristic cluster sizes vary with soil carrying capacity and transport limitations. In soils with high bulk cell density, cell cluster size distribution gives rise to rare but disproportionately large, ‘mega’ communities, that, in turn, disproportionately drive metabolism leading to anoxic microsites in largely oxic soils. A cursory evaluation of the statistical features of soil bacterial microgeography suggests that standard bulk soil sampling conflates many small, endemic clusters with a few dominant mega clusters. Consequently, accurate assessment of diversity and composition requires “unmixing” of genetic information across the likely original distributions and bacterial cluster size spectrum. We outline an analytical and modeling framework that translates soil carrying capacity into expected community size heterogeneity based on the observed cell cluster size distributions with heavy tails. We combine global soil and microbiome data sets to model putative community size structures across different ecosystems. Our approach reframes soil microbiomes as size-structured meta-communities and provides testable predictions for diversity-function relationships under changing moisture and carbon regimes.
How to cite: Bickel, S., Berg, G., and Or, D.: Unmixing soil bacterial diversity considering community microgeography, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-18524, https://doi.org/10.5194/egusphere-egu26-18524, 2026.
Salinity stress is a major factor limiting microbial activity in soils, as it can impair enzymatic processes by destroying microbial cells and disrupting root exudation. In contrast, biochar, through the improvement of soil physicochemical properties, may stimulate microbial growth and functionality. However, the response of soil enzymes to the simultaneous presence of biochar and salinity stress has been scarcely investigated. In the present study, we assessed the effects of two salinity levels (0 and 150 mM NaCl) under two biochar treatments (0 and 2%) on spatial distribution and kinetic parameters of leucine aminopeptidase (LAP) activity in the rhizosphere of wheat by combining zymography with enzyme kinetics.
In the presence and absence of biochar, salinity reduced the hotspots of LAP activity by 15.8% and 15.7% compared to the respective control, respectively. In contrast, at both biochar levels, salinity increased the rhizosphere extent of LAP compared to the respective control. Biochar nearly doubled hotspots of LAP activity compared to its absence, yet it simultaneously reduced the rhizosphere extent of LAP at both salinity levels. Generally, the highest LAP activity hotspots and the lowest rhizosphere extent of LAP were observed in the of 2% biochar treatment under non-saline condition. The analysis of enzyme kinetics (Vmax, Km) in the hotspots showed salinity caused an increase in enzyme affinity for substrate (Km decreased by 37.9% to 97.2%) at both levels of biochar. In contrast, biochar decreased enzyme affinity for the substrate (as indicated by a 1.1- to 2.2-fold increase in Km) under both salinity levels. Biochar increased potential enzymatic activity (Vmax) in the hotspots, reaching 1.9 times higher than without biochar. Conversely, under salinity conditions, this activity decreased relative to optimal conditions at both biochar levels. Overall, the 2% biochar treatment under non-saline condition showed the highest Vmax and Km, whereas the non-biochar treatment under saline condition indicated the lowest.
These patterns collectively indicate that salinity and biochar exert contrasting controls on rhizosphere enzymatic functioning by modifying both microbial physiology and microhabitat conditions. Salinity imposes physiological stress and reduces root-derived substrates, driving microbial communities toward more dispersed activity and the production of high-affinity enzymes optimized for resource scarcity. In contrast, biochar enhances microhabitat quality, stimulating microbial activity and catalytic capacity despite reducing enzyme affinity, likely due to changes in community composition or enzyme–biochar interactions. Overall, biochar strengthens rhizosphere functioning but cannot fully offset the inhibitory effects of salinity on microbial metabolism and enzymatic efficiency.
How to cite: Hozhabri, T., Halajnia, A., Lakzian, A., and Hosseini, S. S.: Biochar Modulates Leucine Aminopeptidase Hotspots and Kinetics under Salinity Stress in the Wheat Rhizosphere, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-1300, https://doi.org/10.5194/egusphere-egu26-1300, 2026.
The spatial distribution of soil organic matter (OM) and its accessibility to microbial decomposers are key regulators of microbial functioning and soil carbon dynamics. However, how the interactions between soil pore sizes and mineral surfaces shape microbial activities remain unclear. In this study, we conducted a 21-day incubation experiment using ceramic microcosms with soil-like pore networks, coated with different mineral surfaces (illite and goethite). We selectively distributed 13C-labelled organic matter into distinct pore size classes (<10 μm and >20 μm). By monitoring carbon mineralization and microbial carbon use efficiency (CUE), we elucidated the interplay between microbial microenvironments and metabolic activities. We compared a simple mix of organic low-molecular-weight compounds with water-extractable OM of wheat root, to determine the role of different types of OM on microbial metabolism and OM decomposition. Mean comparisons for microbial respiration, fraction of added carbon respired, microbial biomass, and CUE were performed using linear models with pore size, mineral surface and OM type as fixed factors, allowing us to identify the dominant drivers of microbial OM decomposition across distinct microenvironments. Post-incubation NanoSIMS analyses were used to quantify pore-scale patterns of the incorporation and spatial retention of freshly added OM across mineral surfaces and pore size classes. Our findings provide insights on how localized interactions between microbes and their organo-mineral microenvironments within pores modulate the persistence and turnover of soil organic carbon.
How to cite: Wu, H., Maestrali, M., Raynaud, X., Nunan, N., and Schweizer, S.: The role of mineral surfaces in soil organic carbon dynamics across soil pores , EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-18977, https://doi.org/10.5194/egusphere-egu26-18977, 2026.
Soil carbon persistence under climate warming depends critically on how microbial processes regulate the transformation and stabilization of organic inputs. In cold alpine ecosystems, low temperatures constrain microbial metabolism, and warming has the potential to reshape microbial carbon processing with long-term consequences for soil organic carbon (SOC) storage. Using a 14-year in situ warming experiment in an alpine meadow on the Qinghai–Tibetan Plateau, we examined how sustained temperature increases alter microbially mediated SOC fractions across soil depths. Warming did not change particulate organic carbon (POC), but led to a pronounced accumulation of mineral-associated organic carbon (MAOC), increasing by 11% in surface soils and 6% in subsoils. This enrichment was driven by enhanced formation of iron- and aluminum-associated organic carbon in topsoil and calcium-associated organic carbon in deeper layers. Notably, MAOC stocks were tightly linked to fungal biomass and fungal-derived necromass carbon, indicating that warming preferentially stimulates fungal pathways that channel microbial residues into mineral-stabilized carbon pools. In contrast, the stability of POC under warming likely reflects counteracting effects of increased plant inputs and accelerated microbial breakdown. Together, these findings demonstrate that long-term warming reorganizes SOC through microbially driven mineral associations rather than bulk carbon inputs, highlighting microbial necromass formation and organo–mineral interactions as key mechanisms governing carbon stabilization in cold-region soils under climate change.
How to cite: Chen, J., Sun, S., Zhou, J., Zhang, Y., Chen, X., Liu, S., Liu, L., and Chen, Y.: Accumulation of mineral-associated organic carbon under decade warming on the Tibetan Plateau, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-12541, https://doi.org/10.5194/egusphere-egu26-12541, 2026.
Forest degradation is widely assumed to drive a monotonic decline in belowground functioning, yet plant-soil feedbacks may transiently buffer stress. We tested this idea by quantifying the rhizosphere effect (RE), the percent difference between rhizosphere and bulk soil, for soil carbon (C), nitrogen (N) and phosphorus (P) pools, enzymatic activities, and microbial biomass across four degradation stages in three types of shelterbelt forests. We found that RE generally increased or remained stable from undegraded to mild-moderate degradation stage and then declined sharply at severe degradation stage. This pattern was consistent across species but differed in amplitude, with Populus thevestina showing the largest early increases, Populus alba maintaining RE longer before decline, and Populus popularis sustaining higher RE for N-acquiring enzymes at early degradation stages. Early positive RE coincided with lower pH and higher water-soluble organic carbon (WSOC), soil water content (SWC), NH₄+, and NO₃⁻ in rhizospheres, conditions that stimulate microbial activities and nutrient turnover. As degradation intensified, RE contracted toward zero or negative values, reflecting reduced root exudation and weaker plant-microbe feedbacks. Random-forest and redundancy analyses highlighted rhizosphere P, rhizosphere N, bulk soil WSOC, rhizosphere SWC, and bulk-soil stoichiometry as the most influential factors, consistent with a transition from compensatory stimulation to functional collapse beyond a tipping zone. Our study provides the first field evidence that rhizosphere functioning responds nonlinearly to forest degradation. Recognizing this transient compensatory phase advances our understanding of ecosystem belowground resilience and can inform the intervention windows for dryland forest restoration.
How to cite: Wang, G., Xiao, H., Shi, L., Liu, T., Xin, Z., Yang, C., and Li, J.: From Buffering to Collapse: A Hump-shaped Rhizosphere Response to Shelterbelt Forest Degradation, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-8645, https://doi.org/10.5194/egusphere-egu26-8645, 2026.
Pyrogenic carbon (PyC), commonly applied as biochar in agricultural soils, is widely promoted as a stable carbon pool for climate mitigation. However, this passive framing overlooks the central role of microbial metabolism and turnover in governing PyC-associated carbon cycling. Here, our study reveal that biochar should be conceptualized not as an inert carbon reservoir but as a dynamic microbial interface that actively regulates soil carbon turnover through coupled heterotrophic and autotrophic processes. Drawing on incubation experiments, microbial functional profiling, and field-scale analyses, we show that biochar–microbe interactions are driven by integrated physical, chemical, and biological mechanisms. Biochar restructures microbial habitats through pore-mediated colonization, nutrient retention, and pH buffering, while simultaneously enabling extracellular and interspecific electron transfer that mediates redox-sensitive metabolic pathways. These processes directly regulate microbial metabolic activity, community structure, and functional assembly, positioning biochar as an active regulator of soil biogeochemical function. Biochar-induced priming effects on native soil organic carbon (SOC) arise primarily from shifts in microbial metabolic strategies rather than from carbon recalcitrance alone. Biochar promotes SOC persistence by stabilizing soil physicochemical conditions and selectively enriching microbial consortia associated with reduced heterotrophic disturbance and efficient secondary metabolite turnover. These findings identify microbial accessibility and functional redundancy as key determinants of carbon turnover and persistence in biochar-amended soils. Critically, biochar also activates an overlooked autotrophic carbon input pathway. We demonstrate that biochar substantially alters Calvin cycle–mediated CO₂ fixation by regulating the abundance, activity, and community structure of cbbL- and cbbM-containing autotrophic microorganisms. The rhizosphere emerges as a hotspot of biochar-enhanced CO₂ assimilation. This autotrophic CO2 fixation is tightly coupled with essential elemental cycling in soil, integrating PyC-driven microbial metabolism into broader soil biogeochemical networks. Our study supports a conceptual shift from passive PyC stabilization to microbially regulated carbon turnover, highlighting microbial metabolism and turnover as central controls on long-term soil carbon sequestration and soil function.
How to cite: Zhu, X.: From heterotrophic priming to autotrophic CO₂ fixation: biochar-driven shifts in microbial turnover of soil carbon, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-17741, https://doi.org/10.5194/egusphere-egu26-17741, 2026.
Pulses of labile substrate, as for example exuded by plant roots, have been shown to accelerate decomposition of complex Soil Organic Matter (SOM), with strong implications for soil carbon balance and the global carbon cycle. Despite its importance, the mechanisms behind this so-called priming effect’ are still not fully clear. Most studies to date focus on investigating priming effects at the bulk soil scale. However, as this effect is caused by the action of soil microbes, it can be assumed that it fundamentally emerges from microscale processes. Observing the activities of microbial decomposers at the microscale could thus be the key for a better mechanistic understanding of the priming effect, but this has been hampered by technical challenges of microscale in-situ observations in soil so far.
Here, we present a novel approach to study the priming effect on scales relevant to its main actors. We developed a microfluidic model system and image analysis pipeline that allows us to track microbes living on transparent agarose patches containing carboxymethylcellulose (CMC) with time-resolved fluorescence microscopy. Using this system, we exposed fluorescently tagged cellulose-degrading soil bacteria (Bacillus subtilis) to pulses of labile substrate at different concentrations. Total CMC decomposition was finally assessed by Congo Red staining of the substrate patches.
After 42 days of incubation with periodic observations, we observed a positive priming effect in our system: Increased decomposition of CMC upon addition of enough labile substrate. Our image analysis suggests that different mechanisms caused decomposition at different substrate concentrations: In chips supplied with the highest concentration of labile substrate, decomposition was associated with microbial biomass, which peaked shortly after the substrate pulse but then quickly declined, possibly due to depletion of essential nutrients or waste accumulation. On the contrary, a lower but more sustained and spatially organized biomass at intermediate concentration led to the same amount of decomposition. Additionally, we found that motility was transiently increased in the bacterial population after the pulse, suggesting that substrate pulses can facilitate the colonization of soil microhabitats.
Our approach, albeit strongly simplifying the microbial environment in soils, allows novel insights into fundamental microbial mechanisms at the microscale that could play a role during rhizosphere priming.
How to cite: Mohrlok, M. and Kaiser, C.: Microscale mechanisms behind the priming effect - Insights from a novel experimental model system, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-18157, https://doi.org/10.5194/egusphere-egu26-18157, 2026.
Posters on site: Mon, 4 May, 08:30–10:15 | Hall X3
The adoption of biodegradable plastics, such as poly (butylene adipate-co-terephthalate) (PBAT), in agriculture is promoted as a sustainable alternative to conventional polyethylene (PE) mulching. However, concerns persist regarding their incomplete degradation into microplastics (MPs) and their long-term impact on soil ecosystems. Based on a multi-year field experiment initiated in 1998 with a completely randomized design comparing three treatments: no mulching (NoMul), continuous PE mulching (PolyMul), and a transition from 15 years of PE to 11 years of biodegradable film (PBAT) mulching (BioMul). We evaluated the effects of mulch transition on soil carbon dynamics, microbial communities, and MPs accumulation.
Results show that soils under BioMul accumulated a higher load of MPs than those under PolyMul, with the presence of finer particles and unique polymer intermediates indicating ongoing degradation. Despite MPs accumulation, BioMul increased total soil organic carbon (SOC) and the mineral-associated organic carbon (MAOC) fraction throughout the soil profile (0–100 cm). In surface soil (0–30 cm), SOC under BioMul was 4.0–13.0% higher than under PolyMul or NoMul. This carbon accrual was accompanied by an increase in avtive carbon pools, with dissolved organic carbon (DOC) and microbial biomass carbon (MBC) showing higher concentrations under BioMul in 0–30 cm and 60–100 cm depths. Microbial alpha diversity was decreased, while community composition shifted toward a more functionally integrated structure, characterized by the enrichment of bacterial phyla such as Proteobacteria and Bacteroidetes, and increased fungal (Ascomycota) participation. Co-occurrence network analysis further revealed that BioMul formed a more connected and robust microbial network with stronger bacterial-fungal associations, indicating improved functional synergy within the soil microbiome.
Our findings demonstrate that long-term biodegradable film mulching can increase both stable carbon pools, while fostering a cooperative and functionally integrated microbial community, despite the accumulation of MPs. This study provides field evidence that PBAT mulch supports key aspects of soil ecological function and highlights the importance of management practices in realizing the environmental benefits of biodegradable plastics in agriculture.
How to cite: Jiang, R. and Wang, K.: Biodegradable Film Mulching Increases Soil Carbon Sequestration and Microbial Network Complexity in a Long-Term Field Study, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-4455, https://doi.org/10.5194/egusphere-egu26-4455, 2026.
Microorganisms metabolize soil organic carbon (C) as a source of energy and biosynthetic precursors. Conventional metabolic flux analysis (MFA), coupled to 13C-labelling, can reconstruct C allocation through central metabolic pathways, but only reflects mass flow and not the thermodynamics of metabolism. We coupled metabolic energetics (13C), mass flow (18O) and calorespirometry in soil using an optimal set of isotopomer tracers. Fifteen position-specific or uniformly 13C-labelled isotopomers - four for alanine, seven glucose, and four glutamic acid – were added to a Luvisol, and substrate-derived 13CO2 fluxes along with microbial use efficiencies (CUE and SUE) were quantified as well as heat dissipation via isothermal microcalorimetry. Our results demonstrate that the temporal dynamics of catabolic CO2 release resemble that of heat dissipation, with both peaking approximately 18 h after substrate addition, irrespective of whether the tracer enters the central metabolic pathway at the monosaccharide level (glucose), at the pyruvate level (alanine) or the citric acid cycle (glutamic acid). This indicates that heat dissipation during the growth phase was strongly dominated by the microbial metabolic processes. Heat dissipation declined disproportionally compared to C mineralization after multiplicative growth, resulting in a lower calorespirometric ratio. Substrate-derived microbial biomass C (13C-MBC) pools showed that amino acids were incorporated, and retained in the biomass with intensive recycling, whereas glucose gets taken up, incorporated but ongoingly consumed, which leads to the peak biomass. This suggests that sugar may be a good tracer for metabolism. Glucose isotopomer utilization indicated dominance of the pentose phosphate and Entner Douderoff pathways over glycolysis, suggesting high activity of fast-growing organisms with considerable C allocation to anabolism. While calorespirometric ratio declined stepwise from 2426 kJ mol-1 , SUE and EUE were close to 100% during initial stage after the addition and declined when substance respiration started. In contrast, neither 18O-water- nor 13C-MFA-based CUE were altered by substrate supply, indicating that exogeneous substrate did not alter the microbial utilization and microbial quick regulation. Therefore, substrate mixtures do not induce a major shift in metabolic pathways during growing on them, leaving overall CUE largely unaffected. This study shows that the heat dissipation of growing microbial communities under high C supply is closely linked to their catabolic CO2 release. Consumption of easily-available carbon does not alter CUE (i.e. metabolic and physiological state of the soil microbiome), but strongly reduces SUE and EUE during ongoing substrate use. We furthermore demonstrated that coupled MFA and calorespirometry provides a powerful tool to understand in-situ microbial C and energy use in soils.
How to cite: Shi, L., Shao, G., Banfield, C. C., Xu, X., Wu, W., Mason-Jones, K., and Dippold, M. A.: Consumption of easily-available carbon does not alter microbial carbon use efficiency in soils, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-9990, https://doi.org/10.5194/egusphere-egu26-9990, 2026.
Microbial processes are known to substantially influence carbon dynamics in soil, which can be altered by changes in community structure. However, the explicit representation of soil microbial diversity in ecosystem models is still in need of improvement. Model-based estimates are crucial to quantify links between functional diversity of soil microbes and ecosystem functioning, in particular soil carbon turnover and storage.
Incorporating functional diversity is well established in vegetation models and is the methodological basis for the presented approach. Trait-based modelling is used here to directly connect community structure to corresponding carbon fluxes and thereby enable implications for the marsh soils of the Elbe estuary, which represent an important carbon sink. Modelled microbial diversity is based on multiple functional types that vary in key traits related to carbon cycling. The simulated microbial community develops population dynamics based on the environmental conditions, leading to selection of certain functional types. This allows predictions of the abundances and potential shifts in the community structure resulting in altered soil carbon dynamics. Parameter values for the microbial model are derived from empirical data and a specifically developed experimental approach that investigates microbial growth and uptake kinetics. We assess the impact of functional diversity on carbon dynamics in marsh soils by comparing soil carbon fluxes in the model with and without explicitly modelled microbial functional diversity. The findings of the study are expected to enhance projections of soil organic carbon storage in wetland ecosystems as well as emphasizing the role of microbial functional diversity for ecosystem carbon dynamics.
How to cite: Schimmel, M., Dumnitch, A., Streit, W., and Porada, P.: Estimating Effects of Microbial Functional Diversity on Marsh Ecosystem Carbon Balance , EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-16596, https://doi.org/10.5194/egusphere-egu26-16596, 2026.
Microorganisms play a key role in the cycling of elements in soil systems by driving organic matter decomposition and regulating nutrient availability. Biomarkers provide an effective approach to studying microbial communities and their functions. In this study, phospholipid fatty acids (PLFAs) and amino sugars (ASs) are used as complementary indicators of short- and long-term microbial processes involved in the cycling and storage of carbon and nitrogen. While PLFA and amino sugar analyses are not interchangeable, their combined application allows for a clear distinction between living microbial biomass and accumulated microbial residues.
The study is set at two chronosequences using heaps of various stages of soil development, differing in type of reclamation (alder reclamation vs. spontaneous succession), at post-mining sites in northwestern Czech Republic. Carbon and nitrogen cycling during soil development are tightly coupled through microbial activity, particularly via the formation and persistence of microbial biomass and necromass. These microbially derived pools form an important link between microbial activity and biogeochemical processes during soil development.
The aim of this study is to monitor changes in PLFA and amino sugar concentrations along two chronosequences and to evaluate how microbial processes contribute to the long-term storage of carbon and nitrogen in soil. By combining biomarkers of living microbial biomass and microbial necromass across different successional pathways, this study improves our understanding of microbial community development during soil formation.
How to cite: Čápová, K., Vindušková, O., Frouz, J., and Jandová, K.: Microbial carbon and nitrogen dynamics during soil development in post-mining sites, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-19135, https://doi.org/10.5194/egusphere-egu26-19135, 2026.
Soil microorganisms regulate fundamental biogeochemical processes, including carbon sequestration and nutrient cycling, yet their activity and growth are frequently constrained by the availability of limiting resources. Microbial resource limitation is highly dynamic and context dependent, shaped by interacting biotic and abiotic drivers such as soil organic carbon, nutrient availability, land-use, and pedo-climatic conditions. Despite its central role for ecosystem functioning, we still lack a comprehensive and mechanistic understanding of how microbial resource limitation emerges and shifts along soil development gradients, largely due to the confounding nature of multiple co-varying environmental factors in natural ecosystems.
Post-mining chronosequences offer a powerful framework to disentangle such drivers, as they share highly comparable initial soil conditions while differing in time since reclamation. We used a 66-year post-mining chronosequence at the open-cast lignite mine Inden (Western Germany) to investigate patterns of soil microbial resource limitation along a pronounced soil organic carbon gradient. Soils originated from a standardized loess-based substrate and encompassed two land-use systems: reclaimed arable fields under conventional management and adjacent, unmanaged field margins. Topsoil samples (0–15 cm) spanning SOC contents from 0.6-4.0% were subjected to multifactorial carbon, nitrogen, and phosphorus additions, followed by measurements of microbial biomass growth and heterotrophic respiration.
Across both land-use systems, microbial growth and respiration responded most strongly to treatments receiving carbon, either alone or combined with nitrogen and phosphorus, indicating a prevailing state of microbial carbon limitation along the chronosequence. Microbial biomass responses to carbon amendments declined exponentially with increasing soil organic carbon, revealing a critical soil organic carbon threshold around 1-1.5%, below which strong carbon limitation prevailed and above which carbon limitation was progressively alleviated. In arable soils with low soil organic carbon, evidence for carbon and nitrogen co-limitation emerged, while high-soil organic carbon soils - particularly field margins - showed indications of phosphorus co-limitation in respiratory responses. Extrapolation of the observed response functions suggests that even soils with substantially higher soil organic carbon contents may retain a measurable, albeit diminishing, degree of microbial carbon limitation.
Overall, our results highlight soil organic carbon as a dominant regulator of microbial resource limitation during early to intermediate soil development and emphasize the value of post-mining chronosequences for advancing a mechanistic understanding of microbial constraints on soil biogeochemical functioning.
How to cite: Rosinger, C., Bonkowski, M., and Kaul, H.-P.: Soil microbial resource limitation along a postmining chronosequence, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-20812, https://doi.org/10.5194/egusphere-egu26-20812, 2026.
Biodegradable plastics have been proposed as an alternative to mitigate the environmental persistence of conventional petroleum-based plastics, however, securing bacterial resources capable of degradation is essential to achieve stable biodegradation under treatment conditions such as composting. Although bacteria that can degrade biodegradable plastics have been reported, there remains a need to obtain degrader resources applicable across different plastic types and diverse environmental conditions. Conventional approaches based on strain isolation followed by degradation activity tests are labor-intensive and time-consuming, which limits efficient screening and isolation of target degraders. To address these limitations, we introduced a network-based analytical framework that leverages metagenomic information from enrichment cultures and functional gene information to identify candidate bacteria contributing to biodegradable plastic degradation. Two composts were used as inocula, and enrichment cultures were conducted for 100 days at mesophilic (35 °C) and thermophilic (58 °C) conditions using Polylactic acid (PLA) or Polybutylene adipate terephthalate (PBAT) as the sole carbon source. Bacterial community structure was characterized across 20 enrichment cultures using 16S rRNA gene amplicon sequencing. To evaluate functional potential related to biodegradable plastic degradation, predicted functional gene profiles were inferred at the KEGG Orthology (KO) level using PICRUSt2. Co-occurrence network analysis was then performed to link changes in genus-level dominance with shifts in predicted functional gene abundances and to explore candidate bacterial resources with high degradation potential for PLA and PBAT. As a result, genera whose dominance increased over time and showed positive associations with predicted secondary-metabolism–related functional genes (K10804, K01432, K15739, and K00467)—processes involved in polymer breakdown to lower-molecular-weight compounds and/or transformation and accumulation of intermediates such as lactate—were highlighted as candidate degraders, including Pseudoxanthomonas, Thermoflavifilum, and Thermopolyspora. This study provides microbiological insights for inoculum design and process optimization for composting-based biodegradation, and demonstrates that a network analysis approach integrating community and predicted functional gene information can be applied to explore diverse microbial resources in future studies.
Keywords
Biodegradable plastics, Bacterial resource, Metagenome, Functional genes, Network analysis
Acknowledgement
This research was supported by Particulate Matter Management Specialized Graduate Program through the Korea Environmental Industry & Technology Institute (KEITI) funded by the Ministry of Environment (MOE), and by the Ministry of Trade, Industry and Energy (MOTIE) (RS-2025-07902968).
How to cite: Hwang, S., Lee, S. Y., Cho, I., and Cho, K.-S.: Network-Based Exploration of Candidate Biodegradable Plastic-Degrading Bacteria Using Metagenomic and Functional Gene Data from Enrichment Cultures, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-21930, https://doi.org/10.5194/egusphere-egu26-21930, 2026.
Phosphorus (P) is essential for life but is often poorly available to plants, limiting biological processes in ecosystems. Microbial transformations increase P availability through enzymatic hydrolysis of organic P compounds; however, these processes are metabolically and energetically costly and occur predominantly in microbial hotspots, such as the rhizosphere and other microsites with elevated microbial activity. Microorganisms invest cellular energy, primarily in the form of ATP, to produce phosphatase enzymes required for P mineralisation.
This study aimed to quantify the energetic and metabolic costs of enzymatic hydrolysis of organic P compounds of increasing complexity within microbial hotspots. We hypothesized that (i) energy investment for enzyme production increases with substrate complexity and its interaction with soil minerals, and (ii) enzyme-mediated P mineralization requires higher energy input than direct P uptake. To test these hypotheses, a soil–sand mixture was incubated with different P substrates while measuring heat dissipation (microcalorimetry), enzyme activities, soil ATP content, and available P.
Four treatments were applied: inorganic P (control), glycerol phosphate, DNA, and phytic acid (phytate). Heat release increased with substrate complexity, from phosphomonoester to DNA, indicating higher energetic investment. Microorganisms invested more energy in enzyme production than in P uptake, and phosphomonoesterase activity increased with substrate complexity. In contrast, phosphodiester hydrolysis was constrained by low phosphodiesterase activity, reflecting higher metabolic costs.
These results demonstrate that microbial hotspot activity governs the energetic efficiency of organic P transformations in soils, highlighting the importance of microscale processes for soil P cycling.
Acknowledgments and Funding: This work was funded by the German Research Foundation (DFG, BI 2570/1-1), project number 525137622.
How to cite: Bilyera, N., Sun, N., Banfield, C. C., Feng, G., Turner, B. L., Kuzyakov, Y., and Dippold, M. A.: Energetic and Metabolic Costs of Organic Phosphorus Mineralization in Microbial Hotspots, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-20639, https://doi.org/10.5194/egusphere-egu26-20639, 2026.
At the microscale, soil organic matter (OM) and the mineral matrix are highly heterogeneous, shaping microbial activity and nitrogen (N) transport within soils and thereby influencing detritusphere formation. Although native soil OM determines the stabilization of new organic inputs in bulk soil, it is unclear whether the native soil OM is also controlling processes at the microscale, within the detritusphere. Here, using Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS), we examine the microscale spatial expression of native soil OM effects on detritusphere formation through direct isotopic mapping. Intact soil macroaggregates (1–2 mm) from topsoil and subsoil differing only in native OM content and containing occluded 15N-labelled straw were analysed by NanoSIMS (30 µm fields of view; ~120 nm lateral resolution) after 51 days of incubation. Two-dimensional mosaic images show that litter-derived N is redistributed into the surrounding soil matrix as discrete, micrometre-scale hotspots extending up to 150 µm from particulate OM. In both topsoil and subsoil, the size, spatial separation, and persistence of these hotspots are consistent with biologically structured transfer pathways, potentially moving along the saprotrophic fungal hyphae and through micropores within macroaggregate. Hotspots were more abundant in subsoil than in topsoil, consistent with more mineral binding sites and greater microbial acquisition of scarce N resources in low-OM subsoils. The observed microscale heterogeneity in the redistribution of litter-derived N within the mineral matrix of the detritusphere illustrates the importance of spatially explicit biological processes and soil architecture in governing soil N dynamics within macroaggregates.
How to cite: Lima Barroso, W., Poirier, V., Chagnon, P.-L., Hoeschen, C., Schweizer, S., Harrington, G., K. Whalen, J., Angers, D., and Basile-Doelsch, I.: Tracing litter-derived soil organic nitrogen across the intact soil structure at microscale, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-14188, https://doi.org/10.5194/egusphere-egu26-14188, 2026.
Microbial processes play a key role in soil organic matter turnover and stabilisation, by controlling both matter and energy fluxes. While carbon cycling has been intensively studied, microbial energy fluxes - and their conservation during soil biogeochemical processes - remain insufficiently explored. Existing thermodynamic concepts and calorimetric approaches provide important insights, but they often rely on oversimplified representations of microbial metabolism and do not sufficiently account for soil heterogeneity, redox dynamics, and the simultaneous occurrence of multiple turnover processes
This study aims to develop a solid thermodynamic framework for assessing microbial energy turnover in soils by linking calorimetric heat flux measurements with carbon-fluxes (CO2 evolution, substrate consumption, biomass formation, etc.) within an enthalpy-based balance approach, using cellobiose turnover as an example.
The framework will be explored in controlled soil experiments covering a range of redox conditions, availability of biomass building blocks, and the abundance of the microbial catalysts. A key focus will be the quantitative reliability of thermodynamic balances derived from current experimental methods. To address this, we are initiating a calorimetric interlaboratory comparison. Furthermore, we will outline first concepts for extending the framework toward Gibbs energy changes, entropy production, and energy conservation in complex soil systems.
The poster presents the conceptional framework and experimental approaches, together with initial results demonstrating how calorespirometric and C-flux data can be integrated to quantify microbial energy turnover in soils.
[1] M. Kästner et al., Assessing energy fluxes and carbon use in soil as controlled by microbial activity – a thermodynamic perspective, Soil Biology & Biochemistry, 193, 109403 (2024).
How to cite: Du, Y., Ohls, S., Miltner, A., Kastner, M., and Maskow, T.: Thermodynamic quantification of microbial energy turnover in soils using calorespirometry , EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-11679, https://doi.org/10.5194/egusphere-egu26-11679, 2026.
Microbial growth drives carbon mineralization, nutrient turnover, and nearly all biogeochemical cycling. Accurately quantifying (in-situ) microbial growth rates is therefore fundamental for linking microbial activity to soil processes and ecosystem functioning, not only in soils but across ecosystems. Numerous methods have been developed for this purpose. Microbial growth varies across soil properties (e.g., soil type, substrate quantity and quality, pH) and microbial life-history strategies (e.g. oligotrophic vs. copiotrophic lifestyles). At the same time, methodological differences, whether or not they depend on soil and microbial characteristics, make it difficult to compare microbial growth rate across studies, with community-level estimates frequently spanning several orders of magnitude.
Here, we aim to benchmark commonly used microbial growth measurements in soil to enable meaningful comparison of in situ microbial growth rates and ultimately improve our understanding of microbial contributions to soil carbon and nutrient dynamics. We conducted a systematic comparison of four widely applied growth methods across contrasting soils and depths. These included two substrate-free stable isotope probing (SIP) approaches: ¹⁸O–DNA-SIP (incorporation of labelled water into DNA) and 2H–FAME-SIP (incorporation of labelled water into phospholipid fatty acids), as well as two radioactive isotope approaches using labeled organic substrates: the ¹⁴C-leucine method (incorporation of labelled leucine into protein) and ³H-thymidine method (incorporation of thymidine into DNA). Soils were collected from four forest sites around Vienna, spanning sandy to clay-rich textures, at two depths. Incubation experiments were initiated under identical conditions with sieved soil in the lab.
Across all four methods, consistent patterns were observed: topsoils exhibited higher microbial growth rates and respiration than subsoils, with higher moisture and organic matter availability. Despite these shared trends, substantial methodological divergence was observed in estimated specific growth rates within the same soils. This divergence is expected, as the four methods target distinct cellular processes and macromolecular pools (DNA, protein, lipids). Comparability among methods implicitly assumes balanced growth, where all cellular components are synthesized at a given rate, that doesn’t change with external conditions. In natural environments, however, microorganisms frequently experience unbalanced growth, where cell division and synthesis of storage compounds or other metabolic processes become decoupled from each other. In addition, radiotracer approaches rely on extraction of microbes from soil and use of carbon-substrates that may not be taken up at the same rate by all microbial taxa, whereas SIP methods are applied directly to intact soils without substrate addition, introducing further variability in growth estimates. Consequently, carbon use efficiencies (CUE), derived by the four methods, were significantly different.
In summary, our study provides the first controlled comparison of four widely used methods to measure in situ soil microbial growth. Our results demonstrate how methodological choices shape apparent microbial growth rate estimates and identify systematic sources of variation among approaches. By deriving empirically based conversion factors between methods, our work facilitates cross-study comparisons and synthesis, ultimately advancing our understanding of microbial growth and its role in soil ecosystem functioning.
How to cite: Luo, Y., Prommer, J., Stein, L., and Richter, A.: Different methods, different growth rates: disentangling in situ microbial growth quantification, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-7494, https://doi.org/10.5194/egusphere-egu26-7494, 2026.
Posters virtual: Thu, 7 May, 14:00–18:00 | vPoster spot 1a
EGU26-2885 | ECS | Posters virtual | VPS15
Vegetation and microtopography drive microbial necromass carbon sequestration in wetland soilsThu, 07 May, 14:12–14:15 (CEST) vPoster spot 1a
Floodplain wetlands are important carbon sinks, yet drought-induced water level declines threaten this function by triggering mudflat-to-meadow transitions that alter soil organic carbon (SOC) stocks and stability. Microtopography shapes wetland hydrology and vegetation productivity; however, its interactive effects with vegetation on microbial necromass carbon (MNC)—the main component of stable SOC derived from microbial death—remain unknown. Combining amino sugar biomarkers, amplicon and metagenomic sequencing, we investigated MNC distribution and drivers across vegetation covers (meadow and mudflat) and microtopographic units (dish-shaped depressions, delta slopes, and riparian slopes) up to 30 cm depth in Poyang Lake floodplains. In the top 10 cm, MNC pool shifted from bacterial (BNC) to fungal necromass carbon (FNC) dominance from mudflats to meadows, with FNC/BNC ratio increasing from 0.5 to 1.7. This shift was driven by drainage that stimulated plant growth and C input belowground as well as oxygenation, thereby enriching fungal saprotrophic and symbiotrophic guilds, cellulose-hydrolyzing enzymes, and genes responsible for aerobic lignin-degradation. Conversely, lower meadow pH suppressed bacterial richness and functions critical for carbon, nitrogen, and sulfur cycling. Microtopography further mediated MNC/SOC ratio following vegetation effects. In the top 10 cm, delta meadow soil had higher FNC/SOC than dish-shaped and riparian meadows, driven by recalcitrant dissolved organic matter that enriched saprotrophic fungi. Aerated riparian mudflat had higher BNC/SOC than other mudflats due to efficient nitrogen turnover and reduced CO2 emissions. Below 10 cm, BNC exceeded FNC owing to oxygen limitation for fungi. Delta meadow and riparian mudflat also maintained higher BNC/SOC than other microtopography units, primarily driven by clay-silt mineral protection. Overall, drought-induced meadow expansion restructured topsoil microbial communities, shifting microbial carbon sequestration pathway from bacterial toward fungal dominance. Slope wetlands mitigate climate change more effectively than depressions through greater SOC stability, mediated by depth-dependent drivers of microbial necromass—substrate availability in the top 10 cm and mineral protection below. These findings reveal that the impact of microbial life-and-death processes on long-term carbon sequestration and stability is regulated by the hotspot-specific conditions created by vegetation, microtopography, and soil depth, highlighting the need for hotspot-differentiated wetland management strategies.
How to cite: Zhang, X., Kuzyakov, Y., Zhao, D., and Zeng, J.: Vegetation and microtopography drive microbial necromass carbon sequestration in wetland soils, EGU General Assembly 2026, Vienna, Austria, 3–8 May 2026, EGU26-2885, https://doi.org/10.5194/egusphere-egu26-2885, 2026.
