In this session we present research exploring microbial dynamics from individuals to complex communities with a focus on their impact on soil carbon and nutrient cycling. Contributions provide a broad overview on latest developments in the field of soil microbial ecology, ranging from studies under controlled conditions with microbial isolates, to assessments of soils from various ecosystems using advanced analytical tools (e.g. -omics, microscopy, spectroscopy or isotope labeling). We present empirical and theoretical studies that investigate the resistance, resilience, and adaptation of soil microbial community structure, activity, and function, in response to single and multi-factorial climatic disturbances and research on the interactions between soil microorganisms, plants and fauna.
Soil organic matter represents the largest active reservoir of organic carbon in terrestrial ecosystems, playing a critical role in atmospheric carbon capture and climate change mitigation. Recent studies have demonstrated that mycelial residues, also known as fungal necromass, contribute significantly to fungal necromass stocks in soils. While the magnitude and distribution of fungal necromass stocks are increasingly well documented, the processes driving their formation remain poorly understood. Specifically, the transformation of recently senesced mycelial residues into stabilized soil organic matter during the early stages of decomposition is not fully elucidated. These residues form an ephemeral resource patch of energy and nutrients for soil microbial decomposers, with the unique aspect that the microorganisms responsible for producing them also serve as their primary decomposers, contrasting with the decay of plant residues. Thus, new concepts, theories, and approaches are needed to understand fungal necromass decomposition. Here, we assess the intrinsic drivers of necromass decay by evaluating how the physiological status of fungi at the time of death influences decomposition processes, and explore extrinsic drivers by characterizing the biodiversity and functional traits of microbial decomposer communities—including fungi and protists. Our goal is to develop a refined conceptual and research framework for microbial residue decomposition and promote the integration of these processes into soil biogeochemical models.
How to cite: Maillard, F., Beatty, B., Lopes Ramos, D., Klinghammer, F., Hammer, E., Tunlid, A., and Kennedy, P.: Intrinsic and extrinsic controls on the decomposition of fungal necromass, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-9458, https://doi.org/10.5194/egusphere-egu25-9458, 2025.
Nitrogen (N) availability influences aboveground productivity, yet the mechanisms governing the retention and release of soil N remain poorly understood. In high latitude regions, N availability often limits decomposition, though this critical factor is rarely integrated into existing decomposition models, which predominantly focus on carbon quality and accessibility. To address this gap, we developed a process-based model of litter decomposition to investigate the effect of low N availability on decomposition. Distinct from most decomposition models, our model explicitly features mechanisms of resource reallocation within the fungal mycelium. Fungal biomass is divided into three fractions: 1) cytoplasmic cells active in decomposition, 2) vacuolised cells with a lower N content and without decomposition capacity, and 3) dead cells (necromass). The model can predict mass loss trajectories of a variety of litter types with different N content based on a single parameter set. The fungal mycelium responds to N limitation by increasing the proportion of vacuolised, inactive cells with a low N content, reducing decomposition rates. Under N limitation, N accumulates in the necromass pool. To predict the observed patterns of N immobilization and release, the rate of fungal necromass decomposition has to be slow and close to that of lignin. Moreover, we found that slow mycelial growth facilitates exploitation of low N resources, whereas fast growth intensifies N-limitation. Our model disentangles the interplay between N availability, mycelial dynamics, and decomposition, pointing towards the potentials of more explicit incorporation of fungal traits in models of N-limited ecosystems.
How to cite: Ghersheen, S., Manzoni, S., Spohn, M., and Lindahl, B.: Modelling nitrogen-limited litter decomposition with fungal dynamics, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-3637, https://doi.org/10.5194/egusphere-egu25-3637, 2025.
Nitrogen (N) limitation can have contrasting consequences on carbon (C) and N cycling in soils, depending on how soil microbes regulate their use of C and N. If microbes respond to N limitation by respiring or excreting more C (overflow hypothesis), C losses from the soil increase with decreasing N availability. In contrast, if under N limitation microbes use N more efficiently and rely less on the scarce available N, C and N can remain in the soil and possibly be stabilized. Efficient N use can be achieved by fungi via resorption of N from senescing mycelium, and in general via local recycling of N when cells die. Here we use a minimal model of litter decomposition to assess how microbes use C and N in litter types with contrasting N contents. The model is fitted to about 500 litter decomposition datasets to estimate microbial C use efficiency (CUE, defined as ratio of growth over C uptake) or N resorption efficiency. Model variants assuming that microbes regulate either their CUE or their N resorption can capture N accumulation and release well, but the latter variants have higher overall performance. This indicates that N resorption can be a fundamental mechanism to cope with N limitation. Moreover, N resorption efficiency as estimated from model fitting decreases with increasing initial litter N content or during decomposition as litter becomes enriched in N. This result implies that N resorption regulation can occur both across litter types with contrasting N contents, and during decomposition within a certain litter cohort. We conclude that N resorption is an ecologically more meaningful strategy to grow in N limited conditions compared to C overflow.
How to cite: Manzoni, S., Siegenthaler, M., Ghersheen, S., Lindahl, B., and Spohn, M.: Do microbes regulate CUE or nutrient recycling to cope with nutrient limitation?, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-3829, https://doi.org/10.5194/egusphere-egu25-3829, 2025.
The nitrogen (N) and phosphorus (P) limitations in soil microorganisms have profound implications for key soil functions such as organic matter decomposition and soil carbon (C) sequestration. However, the extent and magnitude of microbial N and P limitation in soils worldwide remain largely unknown compared to N and P limitation in plants. Moreover, the spatial variability of microbial N and P limitation may lead to disproportionate responses of microbially driven soil processes and functions to global change factors along environmental gradients. Thus, better understanding of global patterns and drivers of microbial N and P limitation is urgently needed for predicting changes in soil functions and their consequences for terrestrial ecosystem functioning. Herein, we evaluated global patterns of microbial N and P limitation by combining profiles of extracellular enzymes (i.e. ecoenzymes; 5,259 observations) with multiple sets of observational and experimental data from natural (i.e. outside of agricultural and urban areas) terrestrial ecosystems. Our analyses reveal widespread indications of microbial P and N limitation (65 and 40% of observations, respectively) in soils worldwide, with unexpectedly frequent N and P co-limitation in the tropics. This co-limitation could be attributable to elevated microbial N demand for the synthesis of P-acquiring enzymes under P limitation, and thus likely as a secondary N limitation resulting from the inherent P deficiency in tropical soils. Upscaling prediction (0.1 × 0.1° spatial resolution) further indicated certain regions such as the Amazon Basin, Tibetan Plateau, and Siberian regions, which harbor substantial soil organic C, showed signs of strong N and P limitation in soil microorganisms, suggesting a high sensitivity of soil C cycling in these regions to nutrient perturbations. As the first global assessment of spatial variation in microbial N and P limitation, these findings provide clues to explain the long-standing “Tropical N Paradox” (i.e. the apparent up-regulation of ecosystem N cycling processes, such as biological N fixation, despite primary P limitation and high soil N levels in tropical ecosystems) and could be useful for understanding and predicting soil biogeochemical cycles in a changing world. [This study is a work that will be published in PNAS (revised stage)].
How to cite: Cui, Y., Peng, S., Rillig, M. C., Camenzind, T., Delgado-Baquerizo, M., Terrer, C., Xu, X., Feng, M., Wang, M., Fang, L., Zhu, B., Du, E., Moorhead, D. L., Sinsabaugh, R. L., Peñuelas, J., and Elser, J. J.: Global patterns of nutrient limitation in soil microorganisms, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-3616, https://doi.org/10.5194/egusphere-egu25-3616, 2025.
Movement of organisms plays a crucial role in microbial ecology, yet little is known about how, when and at what speeds soil microorganisms move. Literature offers conflicting lines of evidence, even regarding whether single-celled organisms can move at all under typical soil conditions. We review the literature on microbial movement in the context of soil physicochemical complexity, to establish its likelihood and its prerequisite conditions. Our focus is on movement at the spatial and temporal scales relevant for microbiota (µm to cm, seconds to days), with particular attention to bacteria and fungi. We synthesize experimental data for bacteria to show that unicellular movement can occur in moderately moist soils, although it is suppressed under dry conditions. By integrating current knowledge of microbial physiology and soil physics, we propose underlying mechanisms that may overcome the challenging conditions of soil, including non-flagellar surface movements (pili, in particular) and the role of biosurfactants. Our energetic analysis also shows that movement is possible, even under moderately oligotrophic conditions. Movement modes are entirely different for filamentous microorganisms like fungi, however, which are not restricted by water connectivity, grow much slower than prokaryotic movement, and must contend with the great tortuosity of the soil habitat. However, once a fungal network is established, cytoplasmic streaming can translocate resources and even the entire fungal cytoplasm at speeds comparable to bacteria (5 µm/s). Fungal hyphae also provide physical connections and favorable conditions to support prokaryotic movement along their surfaces. Hitchhiking, in which one organism is transported by the movement and energy of another, is also likely to be important in soil. A diverse array of movement possibilities emerges from our analysis, suggesting that soil microorganisms may be much more mobile than often appreciated. These also indicate substantial implications of movement for the ecology and ecological functions of soil microbiota. However, many key unknowns remain to be addressed and hypotheses experimentally tested, and we propose an ambitious roadmap to a comprehensive understanding of microbial movement in soil, and its relevance for biogeochemical cycling.
How to cite: Mason-Jones, K., Schluter, S., Guseva, K., Chirol, C., Dupuy, L., Erktan, A., Hu, J., Engelhardt, I., Zou, H., Bickel, S., Lu, J.-Z., Pett-Ridge, J., Otten, W., Schmidt, H., Nunan, N., Hammer, E., Baveye, P., Camenzind, T., and Wick, L. Y.: And yet they move: microbial movement in soil habitats, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-15464, https://doi.org/10.5194/egusphere-egu25-15464, 2025.
Data obtained in pure cultures of the different microbial groups offers a wide range of information of each specific strain, yet how many of those patterns are present in natural environments remains unclear. On the other hand, measurements of soil functions in field or laboratory settings are packed with unhandled parameters that are likely to explain most of the unexplained variation encountered. There is hence the need for approaches that handle at the same time the control and resolution permitted in pure culture settings but with the parameters present in natural microbiomes at the relevant scale. With the use of microfluidics, fluorescence microscopy, and genomic tools, we explored two examples of the implications of soil characteristics on bacterial interactions in pairwise and in community level.
We tested how does the interaction between the two mutually exclusive soil bacterial strains Pseudomonas putida and Bacillus subtilis, holds in microenvironments of various levels of complexity. In low-complexity environments both species showed lower growth than when growing by themselves, which differed from a well-mixed liquid environment where Pseudomonas putida outperformed and inhibited Bacillus subtilis. Fragmented mazes, however, allowed not only the coexistence of both strains, but in the right frequencies permitted them to reach higher yields than when growing separately, thus turning competition into collaboration. Spatial analysis of the space within the mazes indicates that complex mazes allowed colocalization and that the level of such colocalization was linked to the yield of both strains.
Extrapolating patterns from pairwise studies to entire communities can be challenging yet necessary. What we intended in the next set of experiments was to evaluate how does community function depends on its diversity and how these two are linked to spatial characteristics of the microenvironment. A natural soil inoculum was subjected to a series of dilutions to obtain an array of inoculums with decreasing levels of diversity. Each community was then incubated within microenvironments with different levels of complexity where their capacity for substrate enzymatic degradation was measured. We expected variance between replicates of each maze to increase in inoculums of lower levels of diversity, as the founder effect would become more important than in robust entire communities. We found, however, that the enzymatic degradation of the inoculum decreased below detection limits after the third dilution (0.01X). Also, enzymatic degradation of the entire community and the 0.1-fold dilutions depended on the maze type but was consistent in the trend of higher complexity leading to higher degradation. Metagenomic quantification revealed that diluting the initial inoculum effectively reduced the diversity of it and its composition resembled more the one from the last day of incubation experiments. Hence it is apparent that the most abundant bacteria are not the ones responsible for the evaluated function, which complement recent findings which show that high abundant taxa grow slower than low abundant ones by adding that low abundance and fast grower taxa might be the drivers of the entire soil functions.
How to cite: Arellano, C.: The Interplay of physical and community complexity in soil systems, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-12446, https://doi.org/10.5194/egusphere-egu25-12446, 2025.
Soil microorganisms are essential to the processes and cycles that sustain terrestrial ecosystems. They mediate the decomposition of fresh organic matter derived from plant material, driving its transformation into a complex array of microbial products that ultimately form stable soil organic matter. Despite their central role, the extent to which microbial community composition and interactions within these communities shape the transformations of organic matter remains poorly understood.
In this study, we analyse the relationship between the structure of microbial communities and the degradation state of organic matter in individual millimeter-sized soil aggregates sampled from a Beech forest. Microbial communities were characterized by sequencing the 16S rRNA gene (bacteria and archaea) and the ITS region (fungi). Using co-occurrence network analysis and relating microbial composition to biogeochemical parameters (such as C, N, δ15N, and δ13C), we were able to determine three groups of bacteria: generalists, whose abundance does not depend on the degradation state of organic matter, and two groups of specialists – one abundant in soils that are rich in fresh organic matter, and the other abundant in soils that are dominated by more recycled organic matter. While generalists are abundant in all aggregates, the relative abundance of specialists alternates in samples across the gradient of carbon availability. This pattern observed for bacteria is less clear for fungi, for them we distinguish generalists that appear in all samples independent on carbon availability from specialists that are abundant in carbon rich samples. Our findings reveal that the structure of microbial communities in millimeter-sized soil aggregates is closely linked to specific states of carbon recycling. Moreover, this pattern remains consistent across different seasons of the year. Our study highlights the interplay of spatial and temporal complexity of microbial dynamics within soil ecosystems, and the utility of co-occurrence analysis.
How to cite: Guseva, K., Simon, E., and Kaiser, C.: Microbial co-occurrence analysis reveals community restructuring during organic matter degradation in millimeter-sized soil aggregates, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-5177, https://doi.org/10.5194/egusphere-egu25-5177, 2025.
Restoring functional ecosystems through rewilding has become a popular nature restoration strategy. The introduced keystone species are often large herbivores or carnivores due to their ability to shape ecosystem processes top-down. Much less focus has been given to restoring soil engineering, despite being a fundamental natural process in most ecosystems, not least in grasslands. I will present initial results from a field study of the role of bioturbation on soil carbon, nitrogen and phosphorous stocks in a large scale prairie restoration programme with bison reintroductions, the American Prairie in Central Montana, US. We show that, on average, the topsoil carbon stocks are almost doubled on prairie dog colonies in grazed prairie sites compared to grazed sites with no active prairie dog colonies. Further, we show that nearby sites without bovids for at least a century have substantially reduced carbon stocks, despite having higher clay content. This is driven by severely decreased soil bulk density, which we suspect may be partly due to high abundances of ground-dwelling spiders known to be sensitive to trampling. We show how important soil-dwelling animals can be for shaping the carbon and nutrient landscapes of the Great Plains. This belowground perspective deepens our understanding of what a fully functional prairie ecosystem looks like and should be considered in future restoration efforts.
How to cite: Kristensen, J. A., Georgiou, K., and Welti, E.: Effects of bioturbation on soil carbon and nutrient stocks: Insights from the American Prairie, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-8977, https://doi.org/10.5194/egusphere-egu25-8977, 2025.
Soils store large amounts of carbon (C), and even minor changes in C stocks can have profound impact on climate. Microorganisms play a critical role in regulating C stocks by processing soil organic matter (SOM), which forms and stabilises SOM but also releases greenhouse gases such as CO2 into the atmosphere. Despite their key role, microbial processes are generally not explicitly included in decomposition models to predict respiration rates and soil C turnover times. In these models, decomposition rates are only affected by environmental drivers, such as temperature, soil moisture, plant litter inputs and existing SOM content. In addition—and possibly interacting with the environmental drivers—it is theorized that increased microbial diversity would contribute to accelerating decomposition rates, but this relationship needs to be explored with empirical data. We use data from the HoliSoils project (Holistic management practices, modelling, and monitoring for European forest soils; https://holisoils.eu/) collected from managed forest sites across Europe. In this dataset, microbial diversity data, micrometeorological data and soil respiration rates from trenched (providing estimates of microbial respiration) and untrenched plots (including autotrophic respiration) were collected following the same experimental design. First, we fit a non-linear model to capture the effects of temperature and soil moisture on respiration at these sites, allowing the fitting parameters to vary across forest management treatments. We then explore differences across sites and managements in the fitted model parameters such as activation energy, base respiration and moisture sensitivity in light of the different management practices and microbial diversity for each site. These results can be particularly useful for the development and parametrization of microbially explicit SOM decomposition models.
How to cite: Pallandt, M., Guasconi, D., Aleinikovienė, J., Behling, D., Filipek, S., Lehtonen, A., Martinovic, T., Ťupek, B., and Manzoni, S.: Can we disentangle climate and microbial diversity effects on soil respiration in managed forests?, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-8110, https://doi.org/10.5194/egusphere-egu25-8110, 2025.
Quantifying the influence of drought on microbial processes in soil and its consequences for carbon cycling is hindered by the lack of underlying mechanistic understanding. Drought affects soil microbes directly by causing physiological stress but also affects indirectly by influencing substrate transport and diffusion. Another indirect effect is through changes in plant litter chemistry which impacts microbial resource acquisition strategies. Here we present a theoretical framework to study the effects of drought as well as the ecosystem feedbacks that are generated due to the complex interactions of above-ground and below-ground processes. We classify microbial life history strategies into high yield (Y), resource acquisition (A) and stress tolerance (S), or Y-A-S along two main axes of environmental variation: resources and abiotic stress. We propose the use of this framework that incorporates trait-based ecology to link drought-impacted microbial processes to rates of soil carbon decomposition and stabilisation. We also present empirical evidence in plant litter microbial communities from a decade-long precipitation manipulation experiment in the field in Mediterranean grass and shrub ecosystems in Southern California. Using metagenome-assembled genomes (MAGs), we demonstrate trade-offs in stress tolerance and resource acquisition traits in bacterial populations in grass litter which arise due to selection of certain taxa by drought as the environmental filter. Through taxonomic and MAGs analyses across four time points over 18 months, we observed the dominance of fungi at the start of the litter decomposition process. These fungal pioneers by secreting extracellular enzymes likely enable the survival of drought tolerating bacteria with reduced decomposition capabilities. The indirect effect of drought on plant litter chemistry was examined by FTIR analysis of litter linked to microbial Carbohydrate-Active Enzyme (CAZyme) gene abundance for different substrates which shows subtle shifts in plant litter chemistry and associated changes in microbial resource acquisition traits that were linked to community succession during the decomposition process. We also observed signatures of recycling of fungal and bacterial necromass. Litter decomposition rates measured as mass loss using litter bags were unaffected by drought in shrub ecosystems but showed trends of reduction in grass ecosystems. The integrated knowledge from these studies demonstrates the various mechanisms by which microbial ecophysiology influences decomposition rates under drought and highlights the need for such scaling up of microbial response to climate change factors from individual soil microbes to collective communities to ecosystems.
How to cite: Malik, A., Chung, B., Fu, Y., Bouskill, N., and Allison, S.: Scaling the impact of microbial ecophysiology on ecosystem-level decomposition rates under drought, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-14984, https://doi.org/10.5194/egusphere-egu25-14984, 2025.
Aim: Summer droughts are increasing in frequency and severity in Europe with detrimental effects on forests. Reducing the number of trees per area through thinning has been found to improve tree performance during and after drought, but little is known about what happens to the soil. Here, we studied the effects of intense summer drought on soil microbial communities and their functioning, and whether thinning can alter their responses to drought. Methods: We simulated a summer drought using rain-out shelters within a replicated block design of different thinning intensities in Dutch Pinus sylvestris stands. Soil samples were collected before, during and after drought to track changes in fungal community composition, total and ectomycorrhizal fungal biomass, and extracellular enzymatic activities. Throughout the growing season, soil respiration was regularly measured and litter bags were sequentially harvested to monitor decomposition rates. Results: Generally, effects of thinning were larger than those of drought, and drought responses did not differ between harvest intensities. Fungal biomass was not affected by drought, but was lower for heavy thinning and clearcutting compared to unharvested control and light thinning. Respiration and decomposition rates were slower for heavy thinning and clearcutting, and drought also lowered process rates overall. Moreover, soil respiration was still affected by drought after a few months of recovery, as was decomposition of litter incubated over the entire growing season. We will further explore how the fungal community composition responded to drought, honing in on differences between ectomycorrhizal and saprotrophic fungi. Conclusions: We found no evidence that light thinning mitigates the short-term impact of summer drought on soil microbial communities in Pinus sylvestris forests.
How to cite: de Goede, S., Hannula, E., de Hoog, D., van der Putten, W., Sterck, F., and Veen, C.: Combined effects of drought and forest thinning on soil microbial community composition and functioning, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-9423, https://doi.org/10.5194/egusphere-egu25-9423, 2025.
Soil microbial communities are known to drive key processes such as carbon and nutrient cycling. These microbes have developed physiological and metabolic adaptations to cope with the constraining conditions found in soils. However, their responses to climate change, such as increased temperatures and drought, remain uncertain. In addition, the physiological adaptations, interactions, and feedback mechanisms within microbial communities during such perturbations, as well as the mechanisms driving the temporal dynamics of microbial responses and recovery remain understudied.
To address these gaps, we assessed soil microbial responses in an outdoor mesocosm experiment, where warming and drought are simultaneously manipulated. We characterized microbial community composition, and we quantified extracellular enzyme activity and microbial biomass, at four time points over the course of a year: before drought (early-growing season), immediately after drought (peak of the growing season), one month after drought (peak of the growing season), and three months after drought (end of the growing season), on 4 different temperature regimes. We further associate both soil biotic (e.g., microbial diversity and composition) and abiotic variables (e.g., organic matter quality) to better understand enzymatic shifts due to warming and drought.
Our results reveal distinct post-drought recovery patterns in fungal and bacterial diversity under various warming scenarios. Fungal diversity seems more resistant to drought and warming than bacterial diversity. The activity of soil microorganisms declined immediately following drought, with recovery varying based on the type of enzymatic substrate. Oxidative enzymes were highly sensitive to the combined effects of warming and drought, and drought hindered their activity in soils exposed to periodic heatwaves 3 months after drought. On the other hand, constant warming enhanced the recovery of hydrolytic enzymes 3 months after drought, but this recovery was obstructed by periodic heatwaves. These findings suggest that hydrolytic enzymes seem to recover after drought likely due to fungal and bacterial diversity recovery.
These results suggest that soil microbial activity may recover after drought in the short term under warming, but repeated periodic heat waves could disrupt this recovery, by changing microbial community composition and potentially leading to shifts in functional capabilities, having detrimental impacts on carbon and nutrient cycling. By examining drivers such as soil organic matter quality, moisture, and nutrient availability, we aim to obtain critical insights into the stability of soil microbial activity under the combined effects of warming and drought, with implications for predicting and mitigating ecosystem changes in a warming world.
How to cite: Lopez Montoya, I., Ofiti, N. O. E., and Thakur, M. P.: Interactive effects of warming and drought on seasonal dynamics of soil microbial communities and functions , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-843, https://doi.org/10.5194/egusphere-egu25-843, 2025.
One the biggest challenges today is the environmental disruption caused by climate change. Climate change is particularly important in arctic environments which are warming faster than the global average. This can result in a thicker and warmer active layer of the tundra soil and increased microbial activity, resulting in the release of vast quantities of stored carbon and nitrogen in form of greenhouse gases into the atmosphere, depending on mainly water content. Despite its importance, we currently have a limited understanding of how warming can affect arctic microbes and only a few studies that have examined fungi and bacteria at the same time or compared the total and active communities.
We show the effect, after one year, of simulated warming using open-top chambers and snow fences on a soil microbial community in Greenland, using a multifactorial study design that considers bacteria and fungi, the total (DNA-based) and active (RNA-based) community and changes over the course of a growing season. We observed a significant increase in soil temperature at the treated sites as well as changes in the environmental variables of carbon:nitrogen, total organic carbon, microbial carbon, microbial nitrogen, microbial carbon:nitrogen and loss on ignition.
The microbial communities of both bacteria and fungi were highly variable across replicates with sampling site accounting for the majority of variation explained in community composition for both bacteria (16.9%) and fungi (27.5%). While warming had an effect on the communities, it accounted for only a small proportion of variation (2.6% for bacteria, 4.9% for fungi) and few specific taxa were identified as differentially abundant. The bacterial community showed a clear split between the total and active community that accounted for 10.5% of the total variation, however there was no difference in the fungal community. We also observed changes in the community throughout the season but these differences were small and accounted for a similar amount of variation as the treatment (4.2% for bacteria, 3.6% for fungi). The majority of fungi (65%) could not be assigned to a guild, however, we found that the abundance of saprotrophs increased in response to warming.
Our results show only minor changes to the composition of an arctic soil microbial community in response to climate manipulation. This suggests that climate change will primarily influence the activity of microbes rather than the community composition.
How to cite: Bosch, J., Gilman, F. R., Blok, D., Jacobsen, C. S., Holben, W. E., Michelsen, A., Elberling, B., Priemé, A., and Voříšková, J.: Effect of Warming on Arctic Tundra Microbes, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-842, https://doi.org/10.5194/egusphere-egu25-842, 2025.
Urbanization fundamentally reshapes terrestrial environments, leading to significant alterations in soil microbial communities which play crucial roles in ecosystem functioning. This comprehensive study utilizes amplicon sequencing and GeoChip arrays to assess how urbanization and tree functional types impact the composition and functional capacity of soil microbiota across various climatic zones, including boreal (Lahti, Finland), moderate (Baltimore, USA) and tropical regions (Singapore). By comparing urban parks with varying ages and vegetation types to reference forests, the research provides a nuanced understanding of how urban settings influence microbial dynamics.
Our analysis revealed that urban parks host unique microbial communities, distinct from those found in semi-natural forests. Notably, these communities display a surprising functional redundancy with their forest counterparts, suggesting that urban microbiota maintain essential ecosystem processes despite altered environmental conditions. However, the degree of microbial community homogenization differs by microbial type; bacterial communities showed greater homogenization effects than fungal ones. This differential response highlights inherent differences in ecological strategies between bacteria and fungi, with bacteria more readily adapting to the environmental constraints imposed by urban landscapes.
Furthermore, the type of vegetation significantly influences these patterns. Soils under trees producing recalcitrant litter harbored richer fungal communities compared to those with labile litter types. In contrast, lawns—despite their simplicity—supported unexpectedly high diversities of both bacterial and fungal species. These findings emphasize that both the quality of plant-derived organic matter and the structure of plant communities are critical in shaping soil microbial diversity and function in urban environments.
This study underscores the complex interplay between urbanization, vegetation diversity, and microbial community dynamics, highlighting the resilience of soil microbiota to urban stresses. The implications of these findings are significant for urban ecology and biogeochemistry, providing insights into maintaining biodiversity and ecosystem services in rapidly urbanizing regions.
How to cite: Zheng, B.: Functional redundancy and community homogenization: Effects of urbanization and vegetation on soil microbiota across climatic zones, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-1891, https://doi.org/10.5194/egusphere-egu25-1891, 2025.
Arbuscular mycorrhizal (AM) fungi form symbiosis with most terrestrial plants, facilitating nutrient and water uptake while contributing to ecosystem services such as nutrient cycling, soil carbon sequestration, and plant resilience to abiotic stressors. As such, these fungi hold significant potential in advancing climate-change-resilient agriculture. However, their effectiveness in supporting agricultural resilience depends on their own responses to global change, which remain poorly understood due to species-specific and context-dependent variability across agricultural systems and climate scenarios.
To address this knowledge gap, we investigated AM fungal community responses at the Global Change Experimental Facility (GCEF) in Bad Lauchstädt, Germany. Established in 2014, the experiment consists of 5 blocks assigned to ambient climate and 5 to a future climate scenario, simulating the expected climate in Central Germany for 2070-2100, based on the consensus of several climate models. The future climate scenario simulates changes in temperature and precipitation patterns. Within each block, we focused on two distinct land-use types, extensive mowing or grazing, typically used for supporting livestock production. The meadows were mown or grazed one to three times annually, depending on plant biomass production. AM fungal community data from 160 soil samples, collected across eight time points spanning two years (mid-2020 to mid-2022) and differentiated by the two land-use types, were analysed using DNA metabarcoding. Additionally, plant biomass and nutrient concentrations were assessed.
Hierarchical Modelling of Species Communities (HMSC) revealed that, across land-use types and climate scenarios, seasonality was the dominant driver of AM fungal variance in the abundance and occurrence model. Plant growing season spring was the primary influence on AM fungal responses, particularly regarding alpha indices and phylogeny. In addition, Glomeraceae abundance increased in spring (p: 0.043), potentially highlighting its role in providing fast nutrient supply for host plants. However, future climate scenarios dampened these seasonal patterns, particularly in mowed systems, suggesting a shift in the dynamics of AM symbiosis. Additionally, we observed plant functional group-specific effects: under future climate, phosphorus uptake by grasses (p: 0.11) and forbs (p: 0.027) correlated with AM fungal phylogenetic clustering, while legumes exhibited an opposite pattern, with phosphorus uptake correlating with phylogenetic dispersion (p: 0.021). We speculate that this might be due to the dual symbiosis of legumes with AM fungi and nitrogen-fixing bacteria. Thus, these findings contribute to providing insight into the functional roles of AM fungal communities under future climate and suggest that considering plant functional group composition may become more critical for managing these systems in the future.
How to cite: Heuck, M. K., Reitz, T., Rioscher, C., Powell, J. R., Birnbaum, C., Kath, J., Philipp, L., Stoltenburg, R., Hoffmann, P., Harpole, W. S., and Frew, A.: Seasonality drives arbuscular mycorrhizal (AM) fungal community responses while future climate alters AM fungi-mediated phosphorus uptake in plant functional groups, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-10089, https://doi.org/10.5194/egusphere-egu25-10089, 2025.
Climate warming can stimulate soil microbial degradation of organic matter, leading to increases in both microbial growth and CO₂ release into the atmosphere. If microbial growth or respiration outpaces the other in response to warming, it can alter the carbon-use efficiency, potentially leading to either increased carbon storage or release. Understanding the temperature-adaptive responses of soil decomposer microbes is thus essential, as they may significantly influence the balance of C between soil and atmosphere. In this study, we used a “space-for-time” substitution to test the impact of environmental temperature change on microbial carbon cycling in soils from a tropical elevation gradient in Chirripó, Costa Rica, using an in situ reciprocal 7-month transplant experiment to low and high elevation. We hypothesized (H1) that the transplantation of samples will shift microbial thermal traits. Specifically, we expected cold transplants to shift the traits of microbes from warm soils toward cool-adapted traits, while warm transplants would shift the traits of microbes from cold soils toward warm-adapted traits. Additionally, warming accelerates microbial use of organic matter (OM), depleting high-quality soil carbon, while cooling slows it, preserving carbon quality. This shift in carbon quality should increase microbial growth in warm soils under cold conditions and decrease growth in cold soils under warm conditions at a standard temperature (H2). Furthermore, based on the carbon-quality temperature (CQT) hypothesis we expected that the cold transplant will reduce temperature sensitivity (Q10) for microbes from warmer soils, while the warm transplant would increase Q10 for microbes from colder soils (H3).
To estimate microbial thermal traits, microbial growth (bacterial growth and fungal growth) and respiration were estimated at 10 different temperature conditions (0, 5, 10, 15, 20, 25, 30, 35, 40 and 45 °C). We found a significant cool-shift in microbial growth thermal traits after the cold transplant and warm-shifted thermal traits after the warm transplant. These changes led to a marked shift in thermal traits along the elevation gradient, indicating a strong legacy effect of ecosystem differences in temperature and a relatively minor influence of the 7-month transplant experiment. However, the warm transplant had a pronounced influence, driving the microbial growth traits of all samples closer to those of microbes with a warm-ecosystem origin. For respiration thermal traits, the transplant experiment did not alter thermal traits but did affect the respiration rate. The cold transplant reduced microbial respiration in soils with a history of warm temperatures, whereas the warm transplant increased respiration in soils with a history of colder temperatures. We did not find a significant effect of the transplants on bacterial growth and fungal growth rates, but total microbial growth rates tended to increase with MAT. In support of the CQT hypothesis, we observed a decrease in Q10 for bacterial growth following the cold transplant in soils with a history of warmer temperature, and a strong increase in Q10 for both bacterial growth and respiration.
How to cite: Dumontel, H. and Rousk, J.: Using tropical heat to investigate adaptive responses of microbial thermal traits and carbon cycling in an in situ translocation experiment , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-19426, https://doi.org/10.5194/egusphere-egu25-19426, 2025.
The methane-cycling microbiomes in Arctic permafrost-affected soils play crucial roles in the production and consumption of this important greenhouse gas. However, little is known about the distributions of Arctic methanogens and methanotrophs across the regional scale and along the vertical soil profile, as well as their responses to the widespread permafrost thaw. Using a unique sample set from nine different locations across the pan-Arctic, we identified methanogen and methanotroph phylotypes in 729 datasets of 16S rRNA gene amplicons.
In 621 samples of intact permafrost soils across the pan-Arctic, only 22 methanogen and 26 methanotroph phylotypes were identified. Relative abundances of both functional groups varied significantly between sites and soil horizons. Only four methanogen phylotypes were detected at all locations, with the hydrogenotrophic Methanobacterium lacus dominating. Remarkably, the permafrost soil methane filter was almost exclusively comprised of a few phylotypes closely related to the obligate methanotrophic species Methylobacter tundripaludum.
In degraded permafrost sites in Alaska, M. tundripaludum also dominated the methanotroph microbiome in the wet site. However, in dry, water-drained former permafrost site, Methylocapsa phylotypes, closely related with the atmospheric methane oxidizing bacteria, were exclusively found and dominant, indicating a massive restructuring of the methanotroph guild that consequently resulted in functional changes from a soil methane filter to an atmospheric methane sink.
This study provides first insights into the identity and intricate spatial distribution of methanotrophs and methanogens in permafrost soils at a pan-Arctic scale and their responses to different water status after permafrost degradation. These findings point towards a few key microbes particularly relevant for future studies on Arctic CH4 dynamics in a warming climate and that under future dry conditions more atmospheric CH4 uptake in Arctic upland soils might happen.
How to cite: Wang, H., Lindemann, E., Liebmann, P., Varsadiya, M., Svenning, M., Waqas, M., Petters, S., Richter, A., Guggenberger, G., Barta, J., and Urich, T.: The methane-cycling microbiome in intact and degraded permafrost soils of the pan-Arctic, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-19512, https://doi.org/10.5194/egusphere-egu25-19512, 2025.
It is well known that microbes run soil biogeochemistry. Despite a century of progress in microbial ecology, translating microbial ecology into consequences for the atmosphere-soil carbon balance remains elusive. I posit that the solution to this problem is to assume the vantage point of the organisms whose functions we seek to understand: what is it that microbes want to achieve? Organisms ‘want to’ grow. Achieving growth defines both evolutionary fitness and ecological success. Thus, the complex coordination of a physiology matched to the environment, targeting resources that can be tapped, and outmanouvering any other organism that could get in your way, altogether defining growth presents a metric that integrates an organism’s response traits, and thus can be used to predict its performance and response to change. Simultanously, rates of growth capture the metabolism which is the engine that runs global biogeochemistry. As such, we can quantify an organism’s effect trait that can be used to estimate ecosystem fluxes of elements.
Using temperature as a case study, I will show how sensitive estimates of growth can be used to generate microbial community trait distributions that can be used to capture how microbial processes depend on temperature, and will respond to change (response traits). I will show how microbial thermal trait distributions vary along both latitudinal and altitudinal gradients in environmental temperatures, and how they respond to warming in field experiments, and how they respond to reciprocal transplant experiments from warm to cool sites, and vice versa. I will also show how microbial thermal trait distributions dynamically change over the course of a heatwave, revealing that it is the rate of community turnover (defined by several interacting environmental drivers including temperature and moisture) that determines its rate of change.
Finally, I will show how thermal traits determined with sensitive estimates of microbial growth can be accurately modelled with simple mathematical functions which enable integration into representations of the soil carbon cycle in Earth system models. I will demonstrate how this integration of microbial ecology via estimates of growth will allow us to capture long-term ecosystem changes in carbon stocks in warming soils, and can be upscaled to predict the biosphere’s feedback to ongoing climate change.
How to cite: Rousk, J.: Microbial growth is the key to predict biogeochemistry from ecology, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-5782, https://doi.org/10.5194/egusphere-egu25-5782, 2025.
Posters on site: Tue, 29 Apr, 08:30–10:15 | Hall X4
Enhanced rock weathering (ERW) has been considered a new technology to mitigate climate change. Organic acids exuded from plant roots and microbes, e.g., oxalate, gluconate, and citrate, can enhance the rates of rock weathering. Additionally, cations released from rock dust to the soil environment will require ionic neutrality, which is mainly balanced by bicarbonate in soil. This process increases carbon sequestration, and the carbon can be long-term stored either in the form of carbonate minerals or bicarbonate. The first stage of this study is to demonstrate whether microbes (Streptomyces sp.) can enhance rock weathering.
Streptomyces sp. are filamentous bacteria capable of decomposing organic matter and therefore very important in the soil environment. Three Streptomyces strains were isolated from the surfaces of weathered dolerite and screened for their ability to mobilize potassium (K) from rock dusts. All three strains, Mid SCVA3, Mid SCVA1 and MO AIA1, can grow on synthetic minimum medium agar with rock dust as K source. The rock dusts used in this study were nepheline-bearing rocks, Bo Phloi alkaline basalt (ABP), refined nepheline syenite (RNS) and nepheline syenite tailings (NST). Nepheline is a fast-weathering mineral under Earth’s surface conditions. There is 3 to 25% of K substitution in the position of the sodium ion, so nepheline-bearing rocks are a natural and sustainable alternative K source for crop nutrition. An amount of rock dust correlating to 250 ppm K was applied to a weathering experiment. Results show that growth rates of strains using rock dust as a sole source of nutrients were different, referred from glucose consumption. MO AIA1 was the best-growing strain, followed by Mid SCVA1 and Mid SCVA3 for all treatments. NST inoculum showed the highest glucose consumption, followed by RNS and ABP. In contrast, looking at elemental releases, Mid SCVA1 was the best strain mobilizing K from all rock treatments, while MO AIA1 and Mid SCVA3 presented similar rates of K releases. However, K release concentration in all inoculums was distinctively higher than abiotic control, supporting that microbes can increase weathering rates of rock dust. Significantly higher concentrations of K were released from ABP than NST and RNS, respectively. For agronomic purposes, ABP will be the best source of K nutrition, and bioaugmentation of Mid SCVA1 will assist in mobilizing more K from the rock. Next step, we will further investigate carbon removal related to ERW in plant growth experiment, using Streptomyces sp. to enhance rock weathering.
How to cite: Wacharapornpinthu, P.: Microbial mediation of nepheline-bearing rock weathering releases nutrients for crop growth , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-1328, https://doi.org/10.5194/egusphere-egu25-1328, 2025.
Microbial carbon use efficiency (CUE) is a fundamental metric in understanding carbon (C) dynamics in ecosystems, particularly in soils. CUE quantifies the balance between the carbon microorganisms assimilate into their biomass and the carbon they lose as CO2 through respiration, thus providing insights into the accumulation and loss of soil organic matter (SOM). Despite its importance, traditional measurements of CUE often fail to account for the significant variations in microenvironmental conditions within soils, which are known to strongly influence microbial activity. Soil microbial communities inhabit a complex three-dimensional pore network, where the physical structure of the soil, particularly pore size and connectivity, shapes microhabitats and constrains microbial distribution, resource access, and activity. Aerobic bacteria and fungi dominate larger pores, whereas micropores can host both aerobic and anaerobic microbes. These spatial and functional heterogeneities are further influenced by agricultural practices, such as tillage, which alter pore size distribution and connectivity. We measured CUE across different pore sizes using short incubation times, minimizing the confounding effects of carbon recycling. To overcome the limitations of single-substrate studies and better capture the functional diversity of microbial communities, we employed a mixture of six 13C-labeled substrates. We evaluated the effect of different agricultural management systems and pore sizes on respiration and CUE, providing new insights into the interplay between soil physical structure and microbial carbon dynamics.
Our findings indicate that higher respiration rates in larger pores are linked to their lower CUE, driven by the prevalence of fast-growing copiotrophic communities. These microbes rapidly utilize carbon during periods of resource availability but exhibit lower efficiency in carbon use due to the favorable environmental conditions, such as greater aeration and nutrient mobility. In contrast, smaller pores host oligotrophic microbes adapted to resource-limited environments, which maximize carbon recycling and exhibit higher CUE due to constrained nutrient availability and reduced mineralization. We also demonstrate that agricultural practices significantly influence CUE by shaping nutrient dynamics, microbial community composition, and pore connectivity. For instance, grassland systems have favoured microbial communities adapted to stable resource availability and with higher CUE. These findings underscore the importance of tailoring management practices to optimize soil structure, enhance carbon retention, and mitigate greenhouse gas emissions.
How to cite: Maestrali, M., Nunan, N., and Raynaud, X.: How is microbial carbon use efficiency distributed throughout the soil pore network?, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-4301, https://doi.org/10.5194/egusphere-egu25-4301, 2025.
Soil organic matter (SOM) dynamics under long-term warming are critical to understanding how climate change may impact carbon cycling. This study investigates the effects of century scale soil warming on SOM dynamics and microbial communities in a subarctic deciduous forest near the Takhini Hot Springs in Yukon Territory, Canada. Utilizing a natural geothermal gradient, we examine changes in soil microbial community composition and functional potential as carbon use efficiency. Initial findings indicate that warming increases microbial decomposition of litter and native SOM, with significant substrate preference of plant-derived particulate organic matter to microbially-derived compounds, particularly in deeper soil layers. We hypothesize that warming enhances microbial activity, leading to increased decomposition and altered SOM composition. As a result, microbial communities adapt to relatively oligotrophic conditions, observable as an increase in traits associated with a high carbon use efficiency (CUE), like higher codon use bias, as it enhances translational efficiency and reduces metabolic costs.
Our methodology incorporates the 18O-CUE method to measure microbial CUE by tracking microbial growth using 18O-labeled water under steady-state conditions. Incubation experiments will quantify CUE across different temperatures, testing the mechanisms of temperature adaptation in the soil microbial communities. Additionally, exoenzyme analysis, of enzymes involved in SOM decomposition, e.g. N-acetyl glucosaminidase, β-glucosidase, along the same temperature gradients will be performed to connect changes in soil properties to soil functions. To decouple the immediate effects of temperature on enzyme activity from the sustained impacts of long-term warming, we will use Arrhenius plots as a framework.
This research will enhance our understanding of the link between SOM dynamics under climate change and microbial adaptation, providing a framework for predicting long-term ecological responses in subarctic ecosystems. The outcomes will inform broader ecological models and potential mitigation strategies for climate change impacts on soil health and carbon cycling.
How to cite: Peter, A., Kehr, J., Finn, D., Poeplau, C., and Tebbe, C. C.: Impact of Century-Scale Soil Warming on Soil Organic Matter Dynamics and Microbial Communities in a Subarctic Ecosystem, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-8692, https://doi.org/10.5194/egusphere-egu25-8692, 2025.
Soil extracellular polysaccharides (EPSac) are essential biopolymers in terrestrial ecosystems, playing key roles in soil aggregation, water retention, nutrient cycling, and carbon sequestration. These polysaccharides are produced by a wide range of organisms, including archaea, bacteria, fungi, plants, and soil fauna. However, their complex composition and low yet largely unknown abundance in environmental samples present significant challenges for their identification and quantification. In this study, we will culture and collect EPSac samples from various organisms (archaea, bacteria, fungi, algae, higher plants, and soil fauna) across different phyla. The extraction methods will be tailored to the specific sample types, such as cation exchange resin extraction for microbial cells and water extraction for plant roots and soil fauna. Dissolved extracellular polysaccharides will be separated from soil metabolites by ultrafiltration or precipitation before biochemical analysis. Plant samples will be cultivated hydroponically from seeds to minimize soil and microbial contamination of fine roots. To identify and quantify the monomeric composition of the polymers, we will employ an optimized acid hydrolysis method in combination with 1-phenyl-3-methyl-5-pyrazolone (PMP) derivatization, followed by analysis using ultra-high-performance liquid chromatography with high-resolution Orbitrap mass spectrometry (UPLC-Orbitrap MS). EPSac-specific monomers will be seeked for that do not occur in other known cell wall-based and/or storage polysaccharides of prokaryotes and eukaryotes. Multivariate analysis, such as non-metric multidimensional scaling (NMDS) and partial least squares discriminant analysis (PLS-DA), will be utilized to assess the variability of EPSac compounds across different taxonomic groups. Additionally, Indicator species analysis will be performed to evaluate the biomarker potential of these compounds. Finally, these biomarkers will be applied to various soil types (cropland, grassland, and forest soils) to assess their contributions to microbial metabolic and soil carbon cycling. This study aims to identify EPSac-specific and organism-specific biomarkers and precisely quantify these key EPSac monomers, advancing our understanding of soil biogeochemical processes and their role in ecosystem functioning and nutrient dynamics.
How to cite: Li, T., Li, Y., Hodgskiss, L. H., Salas, E., Shi, K., and Wanek, W.: Identification and quantification of extracellular polysaccharide biomarkers across soil organisms and plants, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-12164, https://doi.org/10.5194/egusphere-egu25-12164, 2025.
Since the discovery of microbes, microbial carbon metabolism has been a central research focus, with significant progress in understanding their metabolic pathways under different carbon sources. However, most studies have primarily examined metabolic mechanisms and gene regulation, while how microbes allocate absorbed carbon to growth, respiration, and extracellular metabolism has rarely been quantified in its entirety. There is strongly rising interest in understanding and modeling soil microbial carbon use efficiency (CUE), but results are currently only based on data of growth and respiration, not accounting for extracellular product formation and total substrate uptake. This therefore potentially ignores a large fraction of stress- and resource-limited (extra)cellular metabolism. This gap limits a comprehensive understanding of microbial carbon allocation and its environmental adaptability, highlighting the need for innovative approaches to address this critical aspect.
To this end, we are currently developing high throughput methodology to measure growth, respiration, and the excretion of extracellular enzymes (EE), extracellular polysaccharides (EPs) and extracellular metabolites (EM) in Bacillus subtilis, Escherichia coli and Saccharomyces cerevisiae cultures. In response to carbon concentration, carbon: nutrient stoichiometry, temperature, and oxygen stress, we will assess microbial carbon allocation of three representative microbial species. For this regard, substrate uptake, growth, respiration, extracellular protein and extracellular polysaccharide production will be quantified in a microtiter plate format assay. The growth use efficiency of Bacillus subtilis cultured at 28°C with 0.4% glucose was determined to range between 20% and 30% with this assay. This study addresses a major gap in microbial carbon allocation research, revealing how environmental factors influence anabolic and catabolic transitions, and affect intracellular and extracellular metabolism, and providing important insights into microbial adaptation and ecological roles.
How to cite: Li, Y., Li, T., and Wanek, W.: Development of a high-throughput method for investigating carbon allocation in microbial pure cultures, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-12266, https://doi.org/10.5194/egusphere-egu25-12266, 2025.
Temperature on the Tibetan Plateau (TP) is rising at a rate higher than the global average, and the frequency of extreme climate events is predicted to increase, making the TP a region of critical importance for understanding the consequences of climate change on ecosystems and its feedbacks. The TP hosts the largest alpine pastoral ecosystem in the world: the Kobresia grasslands, dominated by the sedge species Kobresia pygmaea. These ecosystems store most of the terrestrial carbon (C) on the plateau, primarily in the felty root mat. With continuous warming, the carbon captured by Kobresia grasslands may become increasingly vulnerable to decomposition. Our study, therefore, focuses on the soil microbial community’s response to long-term exposure to warming, grazing, and snow addition in a Tibetan alpine pasture, thus reflecting major environmental changes.
We conducted our study at the Nam Co Observation and Research Station for Multisphere, CAS. The fully factorial experiment includes a combination of treatments: warming using open-top chambers, grazing by yaks three times a year (June, July, and August), and spring snow addition using snow cakes measuring 1 m in diameter and 0.5 m in height. Bulk and rhizosphere soil samples were collected for bacterial (16S rRNA) and fungal (ITS1 rRNA) sequencing. Functional genes involved in the carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycles were quantified using the high-throughput quantitative-PCR-based Quantitative Microbial Elemental Cycling chip.
Results showed no significant effects of the treatments on microbial fungal or bacterial diversity, community composition, structure, or functional potential for bulk soils. Rhizosphere soils exhibited higher bacterial diversity from plots with warming + grazing treatment. Furthermore, the abundance of genes related to microbial functional potential for C and P degradation was significantly higher in rhizosphere soil than in the bulk soil. Samples from the plots subjected to both warming and grazing treatments showed a higher relative abundance of predominant genes. These findings suggest that the synergistic effects of warming and grazing significantly enhance rhizosphere microbial diversity and functional potential compared to individual treatments, highlighting the complex interactive effects of environmental factors on soil microbial communities.
How to cite: Urbina Malo, C., Maurischat, P., Bi, Q.-F., Anslan, S., Klein, J., Dorji, T., and Guggenberger, G.: Impact of experimental soil warming, snow addition, and grazing on soil microbial community diversity and functional potential in Tibetan Kobresia grasslands, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-15244, https://doi.org/10.5194/egusphere-egu25-15244, 2025.
Soil is Earth's most biodiverse habitat, harboring unparalleled microbial densities and diversities. These conditions have driven the evolution of diverse microbial interactions, ranging from synergistic to antagonistic. However, studying these interactions is challenging due to the opaque nature of soil and the microscopic scale at which they occur. Understanding these processes is critical for advancing knowledge of ecosystem functions and soil biology.
Fungal hyphae-mediated transport (FHMT) of bacteria is a pivotal yet underexplored mechanism that enables bacterial translocation across nutrient-depleted regions, facilitating microbial movement and interactions within soil. The MICOL-FUNTRANS project investigates the microbial ecology of FHMT as a driving force in soil colonization and structure formation.
To study FHMT-driven belowground soil colonization, specialized soil columns were developed for field use. These columns, designed to either allow fungal hyphae colonization or exclude it, were filled with uncolonized sediment from glacier margins and buried in topsoil along chronosequences in glacier forefields. Field sites include Greenland (Lyngmarksbræen, Disko Island), Iceland (Langjökull), and Austria (Klein Fleiß Kees). After one year, the columns will be harvested to analyze the colonizing microbial communities under field conditions.
In parallel, laboratory microcosms were designed to simulate FHMT processes under controlled conditions. Sterile quartz sand was colonized by source soils from glacier forefields, allowing us to quantify bacterial colonization rates and identify key microbial players involved in targeted translocation processes.
This project provides the first comprehensive insights into FHMT-driven bacterial colonization in field conditions, underscoring its ecological significance and advancing our understanding of soil microbial dynamics.
How to cite: Keuschnig, C., Biswas, R., Amjar, M., Feord, H., Rossel, P. E., Bahl, C., and Benning, L. G.: MICOL-FUNTRANS: Exploring Fungal Hyphae-Mediated Transport in soil colonization, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-16195, https://doi.org/10.5194/egusphere-egu25-16195, 2025.
Functions and productivity of fungal communities in soil are affected by interspecies interactions and competition for resources, which, in turn, affects biogeochemical cycles and fluxes of CO2 from soil. Specifically, saprotrophic and ectomycorrhizal (ECM) fungi compete for limiting nutrients with great effects on overall decomposition rates. Macroscale observations are inconsistent: decomposition can be suppressed (‘Gadgil effect’), typically, in nutrient poor ECM dominated forests, or exacerbated (‘priming’) by ECM fungi foraging for nitrogen in organic matter or introducing labile carbon to soil. Gaining deeper insight into the mechanisms affecting mycelial and hyphal scale processes among the competing fungi could increase understanding of the reasons for these inconsistencies and better predict the direction of overall decomposition rates.
We investigated changes in growth and anabolic metabolism of an ECM fungus (Suillus luteus) interacting with a saprotrophic fungus (Gymnopus confluens) cultured in different concentrations and types of carbon and nitrogen sources on agar plates and inside microfluidic soil chips. The metabolism analysis was performed using stable-isotope labelling (SIP) combined with Raman microspectroscopy in the chips. At the mycelium scale, S. luteus grown in co-culture plates formed denser mycelium and demonstrated increased competitiveness under changing nitrogen concentrations. G. confluens increased its elongation rates and dominated under changing carbon conditions. Supplied with equal amounts of glucose and complex carbon (carboxymethylcellulose, CMC), G. confluens facilitated the growth of S. luteus, which exhibited increased density and elongation rates in co-cultures. Microstructures of the soil chips further affected the growth of S. luteus: while its growth rates in terms of elongation were typically smaller in agar plates, they increased and surpassed those of G. confluens in the chips in all nutrient treatments. This demonstrates the impact of both the nutritional and the physical environment on the outcome of fungal interactions. Furthermore, similar as in the agar plates, C. confluens facilitated growth of S. luteus in chips supplied with both glucose and CMC. To investigate this further, we are setting up an experiment, where deuterium labelled glucose source (glucose-d7) is used and traced as it is incorporated into the fungal hyphae growing in the chips using Raman microspectroscopy. Enrichment of fungal biomass with deuterium is detected via appearance of C-D functional group related spectral bands in the Raman spectra. We expect that this will allow us to determine whether the presence of CMC decreases competitiveness of G. confluens vs S. luetus as it directs its metabolism towards CMC degradation, and whether the carbon released in the process is uptaken by S. luteus as well.
How to cite: Pucetaite, M., Sara Beckman, N., Gonzalez Oliveros, Y. G., Pla-Ferriol, M., and Aleklett Kadish, K.: Growth and metabolism of interacting ectomycorrhizal and saprotrophic fungi: effects on mycelial to hyphal scale, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-17468, https://doi.org/10.5194/egusphere-egu25-17468, 2025.
Warming increases soil microbial respiration which leads to significant soil C loss. However, it has been shown that the initial increase in soil respiration tends to level off in the long term, sometimes even returning to pre-warming levels. Two main hypotheses explain this short-lived thermal respiration increase: (i) The concentration of C substrate in soils declines due to increased microbial activity, becoming a limiting factor and leading to reduced overall respiration, or (ii) Microbial physiology adjusts to higher temperatures to improve fitness under new environmental conditions. The latter concept of a physiological thermal acclimation predicts that microbes in soils exposed to long-term warming will exhibit lower mass-specific growth and respiration rates at a given temperature compared to those at ambient levels. The main objective of this study was to separate the roles of microbial acclimation and substrate limitation in reducing the response of soil respiration to long-term warming.
We examined the microbial respiration and growth rates along long-term (>50 years) geothermal warming gradients in Iceland (ForHOT experiment). Soils collected at multiple temperature steps between ambient temperature and +15 °C field warming were incubated in the laboratory at their respective field temperatures. In addition, soils collected from the ambient sites were incubated the same temperatures as the field-warmed soils. Soils were labelled with deuterium-enriched water during incubation, followed by extraction of phospholipid fatty acids (PLFAs). Analyzing the 2H incorporation into PLFAs by Gas Chromatography coupled to isotope ratio mass spectrometry (GC-IRMS) allowed us to estimate group-specific microbial growth rates.
When incubated at the same temperatures, soils exposed to long-term warming exhibited lower overall respiration rates (per gram of soil) compared to ambient soils. However, the respiration rate per unit of microbial biomass remained comparable between warmed and ambient. This suggests that the reduction in total respiration is likely due to carbon depletion and a subsequent decrease in overall microbial biomass, rather than a thermal acclimation. Interestingly, at long-term warmed field sites, mass-specific growth rates were considerably higher than those observed in ambient soils subjected to short-term warming at the same temperature. This finding also contradicts the thermal acclimation hypothesis, indicating that prolonged warming does not diminish the temperature response of microbial activity. Instead, our results demonstrate that – on a per unit of microbial biomass basis – long-term microbial temperature response is even more pronounced compared to immediate warming. The disparity between long-term and short-term temperature responses varied among microbial groups. While Firmicutes displayed similar growth responses to warming in both scenarios, fungi and gram-negative bacteria showed significantly higher mass-specific growth rates in long-term warmed plots compared to ambient soils exposed to corresponding levels of short-term warming. These results demonstrate that changes in microbial community function and composition following warming run counter to the typical concept of thermal acclimation.
How to cite: Taft, T., Darcy, S. R., Guseva, K., Jenab, K., Rottensteiner, C., Gorka, S., Fuchslueger, L., Ranits, C., Canarini, A., Sigurdsson, B. D., Richter, A., and Kaiser, C.: Elevated mass-specific soil microbial growth rates and no sign of thermal acclimation at a long-term warming gradient, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-21632, https://doi.org/10.5194/egusphere-egu25-21632, 2025.
Soil microbial communities, including bacteria and fungi, play a crucial role in nutrient cycling processes such as carbon sequestration, nitrogen transformation, and phosphate mobilization. Despite their importance, the dynamics of microbial communities in tropical soils remain poorly understood. This study investigates the composition, functional potential, and nutrient profiles of microbial communities across various land-use types, including forests, agricultural farms, parks, and golf courses. Soil samples were analyzed to assess microbial abundance, diversity, and nutrient content.
Bacterial abundances were significantly higher than fungal abundances across all soil types, with agricultural soils showing bacterial abundances that were one order of magnitude greater than those in other soil types. Fungal diversity was influenced by land use, with forest soils dominated by decomposers such as Basidiomycota and Ascomycota, which enhance organic matter turnover and contribute to soil carbon dynamics. In contrast, agricultural soils were enriched in Zygomycota, known for their roles in nutrient cycling and plant growth promotion under conditions of elevated nutrient availability.
Distinct clustering of bacterial communities was observed using principal coordinate analysis, with agricultural soils forming unique clusters separate from other soil types. Organic farming practices were found to support bacterial and fungal communities more similar to natural ecosystems compared to conventional farming. Agricultural soils exhibited higher nutrient levels and microbial biomass due to intensive fertilization, while the forest, park and golf course soils displayed variability in microbial diversity and nutrient content driven by vegetation maturity and management practices. Mature forest soils were characterized by signature taxa such as Gaiella (bacteria) and Trichoderma (fungi), indicative of healthy soil ecological conditions, while agricultural soils were dominated by Bacillus and Paenibacillus, associated with nutrient cycling and pathogen suppression.
These findings highlight the influence of land use and management practices on microbial and fungal community composition, functional potentials, and nutrient cycling. The implications are significant for understanding nutrient concentration in runoff and their impacts on water quality, particularly under climate change scenarios involving temperature increases and intensified rainfall and length of dry periods.
How to cite: Te, S. H., Senaratna, K. Y. K., Fatichi, S., and Gin, K. Y.-H.: Microbial and Fungal Dynamics in Tropical Urban Environments and Their Impact on Soil Health and Nutrient Cycling, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-7800, https://doi.org/10.5194/egusphere-egu25-7800, 2025.
The relevance of studying Arctic regions is growing rapidly due to the sensitive response of fragile ecosystems under climate change and increasing anthropogenic pressures. Under the urbanization impact, there is a significant transformation of abiotic and biotic properties of ecosystems, which affects the ecosystem services provided and can lead to disservices such as the emergence and accumulation of microbial species hazardous to health, including microfungi. Pathogenic and opportunistic fungal species are becoming increasingly important with the growing recognition of chronic diseases and the number of patients with severe immunodeficiencies. However, studies of opportunistic microfungi in Arctic cities are sporadic. In this case, the opportunistic microfungi of Murmansk, the largest Arctic city in the world, was studied in comparison with a background area of natural forest tundra. Mycological analysis was carried out for different components of urban ecosystems: soil cover, atmospheric air, water and lake bottom sediments.
In urban soil and bottom sediments of urban lakes there was an increase in the diversity and number of opportunistic species of microfungi from 30% in background soil/lake to 50-60% in urban soil and 50-100% in bottom sediments of urban lakes. In the air and water, the content of species harmful to human health did not differ from the background level. This emphasizes the high indicative value of buffer components of ecosystems - soil and bottom sediments, as compared to transit components - air and water, in determining the level of long-term anthropogenic load on ecosystems. The most dangerous identified species were fungi Paecilomyces variotii, Aspergillus flavus and Aspergillus fumigatus, capable of causing pulmonary infections, otitis, sinusitis, endocarditis, osteomyelitis, keratitis, traumatic mycoses, peritonitis, onychomycosis. The fact of Paecilomyces variotii dominance in water and bottom sediments of lakes used for recreational purposes is alarming.
How to cite: Korneykova, M. and Soshina, A.: Opportunistic fungi in urban soil and bottom sediments of largest polar city (Murmansk), EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-7158, https://doi.org/10.5194/egusphere-egu25-7158, 2025.
Soil microbiomes are fundamental to carbon cycling, organic matter decomposition, and greenhouse gas regulation, making them essential for maintaining ecosystem stability. In coastal wetlands, which store large amounts of carbon and act as major sources of methane emissions, these microbial communities play an especially crucial role. This study examines the impacts of elevated CO2 and warming on soil microbial communities over a six-year chronosquence in a C3 plant-dominated salt marsh. Results showed that bacterial community structure was primarily influenced by seasonal variability, with distinct clustering patterns driven by temporal shifts rather than treatment effects. In contrast, bacterial diversity and network characteristics responded strongly to climate factors. Elevated CO2 alone increased bacterial diversity, while warming alone caused a reduction. However, their combined effects led to a synergistic decline in bacterial diversity, reducing it to 80% of ambient conditions by year six. Network analysis further revealed that the combined treatment caused substantial disruptions to microbial networks, including reduced size, connectivity, and clustering, along with increased modularity. These findings highlight the vulnerability of soil microbiomes to the compounded effects of climate change factors, with potential consequences for the stability and functionality of coastal wetland ecosystems. Incorporating these interactive effects into predictive models is essential for accurately forecasting future carbon cycling dynamics and for guiding the effective management of coastal wetland ecosystems under future climate scenarios.
How to cite: Yang, Y.: Combined effects of elevated CO2 and warming threaten soil microbial diversity and network stability over a six-year chronosequence, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-5328, https://doi.org/10.5194/egusphere-egu25-5328, 2025.
