Orals: Wed, 30 Apr | Room -2.20
Soil microorganisms contribute to the stabilization of organic carbon and nutrients by breaking down organic matter into relatively small compounds that can be stabilized on mineral surfaces (ex vivo pathway) and by building biomass that eventually turns into necromass, which can also be effectively stabilized (in vivo pathway). Which of these pathways is dominant? We answer this question using a model tracing the fate of plant residues into particulate organic matter (POM) and mineral associated organic matter (MAOM). The model allows partitioning ex vivo and in vivo contributions through a small set of parameters that can be estimated using data from incubation of isotopically labelled plant residues. Leveraging a new database of plant-derived POM and MAOM data from these incubations, we estimated the contributions of the two pathways across nearly 40 soils. We found that the in vivo pathway is in general more important than the ex vivo pathway (especially for stabilization of organic nitrogen). Comparing results across soils, we found that the contribution of the in vivo pathway is particularly high in fine-textured soils with low organic matter content, where a larger area of mineral surfaces is available. We conclude that microbial necromass is a key factor for carbon and nitrogen stabilization, especially in soils that have abundant available mineral surfaces.
How to cite: Manzoni, S. and Cotrufo, F.: In vivo vs. ex vivo pathways of carbon and nitrogen stabilization – a model analysis, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-3790, https://doi.org/10.5194/egusphere-egu25-3790, 2025.
Currently, most microbially-explicit biogeochemical models use flexible carbon-use efficiency (i.e., overflow respiration) to balance the mismatch between microbial biomass and litter stoichiometry (e.g. carbon : nitrogen, C:N). However, other known mechanisms might lead to different biogeochemical outcomes. Here we perform a rigorous test of the functional consequences of several mechanisms that aid in solving this mismatch. We used an individual-based, trait-based leaf litter decomposition model that represents microbial functional groups by uptake and extracellular enzyme genes. The original model incorporates overflow respiration and flexible biomass stoichiometry as mechanisms to solve elemental imbalance. We further introduce a novel mechanism of enzyme allocation. We established 4 simulation treatments: overflow, overflow + flexible stoichiometry, overflow + enzyme allocation, and overflow + flexible stoichiometry + enzyme allocation. In each treatment we manipulate initial litter C:N from 10 to 90. We also manipulate the initial community to yield scenarios with high and low functional redundancy based on the number of polymers each “taxon” can degrade. We found that biomass production was greatest when all mechanisms were in operation, followed by enzyme allocation, flexible stoichiometry, and overflow being the lowest. This pattern inverted in the low redundancy scenario. Total respiration decreased with higher litter C:N but was greater for flexible stoichiometry and lowest for enzyme allocation. When enzyme allocation was present, mass loss and nutrient mineralization were consistently decreased. As suggested by other studies, carbon-use efficiency remained high when having alternatives to overflow. This, however, occurs only in the low redundancy scenario. We conclude that current microbially-explicit biogeochemical models might be overestimating carbon losses for high C:N substrates due to an unrealistic increase in respiration rates by overflow. We urge for the quantification of these mechanisms in natural systems.
How to cite: Murúa Royo, J., Bertolet, B., Chávez Rodríguez, L., and Allison, S.: Functional Consequences of Solving Elemental Imbalances, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-4860, https://doi.org/10.5194/egusphere-egu25-4860, 2025.
Growing bacteria, alongside fungi, are the productive core of the soil microbiome. They assimilate soil organic matter and drive biogeochemical transformations. While recent evidence suggests that large parts of the bacterial community are transcriptionally or translationally active, only a subset of bacteria actively divides at any given time. However, the proportion of dividing bacteria and their responses to environmental change remain poorly understood.
Using more than 76,000 taxon-specific growth estimates inferred by 18O-quantitative stable isotope probing from >200 soil samples, we characterized the size and dynamics of the growing fraction of soil bacteria across a range of ecosystems and environmental change treatments (warming, nutrient addition, drought, cooling). We then estimated the percentage of replicating bacterial cells and taxa based on taxon-specific 18O-enrichment, absolute 16S rRNA gene abundances, and predicted gene copy numbers.
Across soils, a significant yet variable proportion of bacterial cells (median: 12%; range: 0.2-65%) were growing, representing about 16% (median; range: 0.9-39%) of the total taxa richness. More than 50% of all taxa were growing exclusively in only 1-2 samples. Environmental change affected the size of the growing community as well as its composition. More than 40% (median; range: 9.7-90%) of the taxa growing at ambient conditions stopped growing when the environment changed, whereas others initiated growth following a shift in conditions.
Our results indicate that the pool of growing bacteria constitutes a significant fraction of the soil microbiome and responds dynamically to changes in the environment through shifts in size and composition with potential implications for soil functioning.
How to cite: Metze, D., Stone, B. W., Hungate, B. A., Séneca, J., Mau, R. L., Hayer, M., Purcell, A. M., Propster, J., Liu, X. J. A., Koch, B. J., Pett-Ridge, J., Schwartz, E., Dijkstra, P., Terrer, C., J. Blazewicz, S., Morrissey, E. M., Hofmockel, K. S., Marks, J., Richter, A., and Kaiser, C. and the Team: How many bacteria are growing in soil?, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-19125, https://doi.org/10.5194/egusphere-egu25-19125, 2025.
Microbial carbon use efficiency (CUE) affects the fate and storage of carbon in terrestrial ecosystems, but its global importance remains uncertain. Accurately modeling and predicting CUE on a global scale is challenging due to inconsistencies in measurement techniques and the complex interactions of climatic, edaphic, and biological factors across scales. The link between microbial CUE and soil organic carbon relies on the stabilization of microbial necromass within soil aggregates or its association with minerals, necessitating an integration of microbial and stabilization processes in modeling approaches. In this perspective, we propose a comprehensive framework that integrates diverse data sources, ranging from genomic information to traditional soil carbon assessments, to refine carbon cycle models by incorporating variations in CUE, thereby enhancing our understanding of the microbial contribution to carbon cycling.
How to cite: He, X.: Emerging multiscale insights on microbial carbon use efficiency in the land carbon cycle, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-55, https://doi.org/10.5194/egusphere-egu25-55, 2025.
A key parameter to understand microbial activity in soil is growth. However, our approaches to measure microbial growth fail to integrate a potential key element for microbial functioning: the spatial structure of soil. In this study we used soil cores together with deuterium-labelling of soil water via vapor exchange to identify growing microbial groups in undisturbed soil compared to sieved soil via the production of (labelled) phospholipid fatty acids (PLFAs). Our results showed comparable measurements of community-level microbial respiration, mass-specific growth rates, and carbon use efficiency in intact and sieved soil. Although soil cores exhibited a larger variability of PLFA biomarker production rates, a high level of overlap was observed among the growing community members in intact and sieved soils. Contrary to our assumption, we conclude that sieving does not necessarily affect quantification of soil microbial growth rates. Importantly, the presented approach enables to identify and to quantify the growing soil microbial subpopulation in experimental conditions close to the field, which opens new avenues for spatial detection of soil microbial growth in situ.
How to cite: Schmidt, H., Canarini, A., Marmasse, G., Fuchslueger, L., and Richter, A.: Microbial growth in intact soil cores assessed by deuterium isotope probing, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-9667, https://doi.org/10.5194/egusphere-egu25-9667, 2025.
Soil microorganisms control organic matter cycling and largely determine how soil systems can cope with and mitigate climate change and environmental threats. Integrating microbial dynamics in process-based soil models is critical for predicting how soil carbon flows and stocks change in ecosystems with time. Functional traits can be inferred from amplicon sequencing data and metagenome assembled genomes to leverage model parameterization. However, informing models using omics-based datasets is challenging due to their large dimensional nature and the nonlinear relationship between genomes and the actual function microbes express. We present a hybrid modeling framework that combines machine learning to analyze metagenomic and DNA sequencing data with a simple microbial explicit process-based model. This hybrid model is conditioned using a convolutional network trained with data from the LUCAS 2018 database (Land Use and Coverage Area frame Survey), which includes soil metagenomes, 16S sequencing data in combination with soil carbon, microbial biomass and soil respiration measurements. 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. We present the concept of the hybrid soil modelling framework and discuss what data is informative for these models and how to best link machine learning with process-based models.
How to cite: Collart, P., Gall, J., Schnepf, A., Sousa Rocha, A. V., Herold, M., Buckeridge, K., and Pagel, H.: Hybrid Soil Microbiome Modeling - Combining process-based models with machine learning to predict microbial dynamics and organic matter turnover in soil systems, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-10523, https://doi.org/10.5194/egusphere-egu25-10523, 2025.
Soil microorganisms utilize organic carbon (C) through catabolic processes to produce the energy required for their metabolic needs and to synthesize microbial biomass via anabolic processes. The fraction of C retained in microbial biomass relative to the total amount of metabolized C is usually termed carbon use efficiency (CUE), which is a key metric for carbon turnover processes in soil. The input of fresh labile substrate in soil typically activates fast-growing microorganisms which are often less efficient than their slow-growing counterparts. However, the microbial succession may differ when utilizing less degradable organic compounds such as plant residues. In addition to the primary C source, newly-formed microbial biomass can subsequently act as a secondary source of C, nutrients, and energy for soil microorganisms. Therefore, the degradation of more complex organic compounds might be sequentially performed by different microbial taxa. However, knowledge of the microbial succession that occurs in the course of degradation of such complex organic compounds remains elusive.
To explore the microbial community changes during the degradation of complex C compounds, we conducted an incubation experiment using arable soil amended with 13C-labeled cellulose as a carbon and energy source. Microbial activity, estimated by respiration and heat release, was continuously determined for 56 days. To calculate CUE, the fraction of 13C transformed into CO2 was quantified via isotope probing techniques. Following DNA extraction at specific time points, 16S rRNA and ITS amplicon sequencing were performed to determine successions in bacterial and fungal community composition. Finally, kinetic parameters of cellobiohydrolase, ß-glucosidase, and phosphatase were measured destructively at specific time points during the incubation. Heat and CO2 release indicated an intensive degradation phase in the first 14 days of incubation. While the Vmax of the enzymes slightly changed during the incubation period, essential changes in bacterial and fungal communities were observed. This study provides insights into the dynamics of microbial communities and their functional roles during cellulose degradation in soils.
How to cite: Dehghani, F., Reitz, T., Schlüter, S., Prada Salcedo, L. D., and Blagodatskaya, E.: Linking microbial community composition and their functions in the course of cellulose degradation in arable soil, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-9807, https://doi.org/10.5194/egusphere-egu25-9807, 2025.
Microbial activity drives soil carbon mineralization, while microbial necromass along with other residues contributes to the stable soil organic carbon pool. Still, precise quantification and characterization of microbial residues remains methodologically challenging in complex soil systems, requiring controlled microbial experiments. We have recently presented the conceptual framework of microbial death pathways in soil, where we hypothesized that different agents of death would lead to varying chemical properties of microbial necromass, with consequences for the fate of microbial necromass carbon in soil.
In the studies presented here, we have now tested these hypotheses experimentally and analysed fungal mycelial residues exposed to diverse agents of death. We investigated the composition of mycelial residues by (i) microscopic live/dead staining, (ii) measurements of carbon, nitrogen and melanin contents, (iii) Raman spectroscopy and (iv) Nanoscale Secondary Ion Mass Spectrometer (NanoSIMS). Using fungal isolates in a controlled experimental design, we found that heat or fungicide exposure led to rapid hyphal death with less chemical transformation of necromass compared to biomass. By contrast, starvation or senescence (ageing of hyphae) allowed mycelia to internally recycle cytosolic components, leading to residues reduced in cytosolic compounds and characterized by wider C:N ratios and increased melanin contents. A litterbag experiment in soil showed that mycelia resembling the chemical properties of biomass are mineralized more rapidly than chemically altered fungal necromass.
We further tested the impact of nitrogen availability on residue formation. Necromass nitrogen contents affect mineralization rates, but also stabilization due to preferential binding of nitrogen-rich compounds to mineral surfaces. Here, fungal residues from nitrogen depleted media showed wide C:N ratios (50-90), resulting from internal recycling of cytosolic compounds but also differential cell wall composition (as indicated by Raman spectroscopy and NanoSIMS analyses). Interestingly, independent of medium nitrogen supply, fungal residues in contact with mineral surfaces (goethite) were strongly nitrogen enriched, indicating preferential binding of nitrogen-rich compounds independent of overall mycelial C:N ratios.
In conclusion, specific microbial death pathways may alter the composition of microbial residues in soil, with consequences for carbon mineralization and stabilization processes. These results further highlight the interaction of carbon and nitrogen cycling via microbial turnover and stabilization, mechanisms that must be integrated in future conceptual and experimental approaches.
How to cite: Camenzind, T., Gawronski, J., Zimmer, A., Höschen, C., Oliva, R. L., Rillig, M. C., Mason-Jones, K., Schweizer, S., and Lehmann, J.: Fungal necromass composition highlights the ecological significance of microbial death pathways in soil, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-16575, https://doi.org/10.5194/egusphere-egu25-16575, 2025.
Soil drying challenges microbial viability and survival, with bacteria employing various mechanisms to respond to shifts in osmolarity, including dormancy or metabolic upregulation of osmoprotectants. However, the extent to which these responses are shaped by an organism’s phylogeny or the climate history of a given environment is poorly understood. This study examines the responses of phylogenetically similar bacteria from semi-arid and humid tropical forest soils to osmotic and matric stress using synchrotron radiation-based Fourier Transform Infrared spectromicroscopy. This non-destructive approach depicts the biochemical phenotype for whole cells under control and stress conditions. We observed that, under osmotic stress, bacteria upregulated cell-signaling pathways, rapidly turned over lipid-storage compounds, and increased osmolyte production. In contrast, matric stress induced a more muted response, typically elevating the production of carbohydrate stress compounds, such as glycine betaine and trehalose. While phylogenetically similar bacteria showed comparable biochemistry under control conditions, climate history played an important role in regulating responses to stress, whereby a stronger metabolic response was observed from semi-arid relative to tropical forest isolates. We conclude that bacterial stress response to drought can be more diverse than previously observed, and regulated by both phylogeny and climate history.
How to cite: Bouskill, N.: Does climate history shape the bacterial metabolic response to drought?, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-7728, https://doi.org/10.5194/egusphere-egu25-7728, 2025.
Agricultural land use intensification has led to loss of soil carbon; restoring soil carbon through regenerative practices offers an opportunity to help mitigate climate change and promote soil health. The soil microbiome is central in transforming plant materials into persistent forms of soil organic carbon. However, there is a poor mechanistic understanding of how microbiomes function, assemble, interact and collectively influence soil carbon changes across land use gradients. Here we present integration of knowledge across scales from field observations and lab experiments to highlight the importance of microbial ecophysiology and their emergent traits in determining the soil carbon balance in multiple paired local contrasts of low and high land use intensity systems in the UK. Across 11 paired contrasts, we observed significantly higher microbial community-level carbon use efficiency (CUE) and increased biomass in low intensity grassland soils compared with high intensity cropland soils. We suggest that less-intensive management practices have more potential for carbon storage through increased microbial CUE. Using proteomics and extracellular enzyme analysis, we demonstrate that reduced CUE in cropland soils was linked to higher microbial investment in stress alleviation and resource acquisition traits. To examine if grassland microbiomes with higher CUE could be recruited to help accumulate soil carbon in cropland soils, in lab mesocosm we reciprocally transferred microbiomes derived from historically undisturbed grassland soil and neighbouring cropland soil into their sterile counterparts from 2 paired contrasts. We fed the microbiomes with plant litter tea and monitored community assembly over 8 months. We observed that soil conditions were more important than inoculum source in determining bacterial assemblage, inoculum source was more important than soil conditions in determining fungal assemblage, whereas both inoculum source and soil conditions mattered equally in shaping the protist assemblage. This highlights the differential response of bacteria, fungi and protists to environmental filtering and raises questions around the persistence and therefore efficacy of microbial inoculations. In terms of soil carbon accumulation, we observed that a grassland microbiome led to positive outcomes in terms of soil carbon changes in cropland soil after 8 months suggesting that the microbial emergent ecophysiology that arises from both initial inoculum as well as the soil conditions matter in determining soil carbon accumulation. Our research highlights the need for careful land management to create the right soil conditions for the promotion of beneficial microbiomes with efficient metabolism for carbon accumulation. This will aid in regenerating degraded soils for sustainable climate-smart agriculture.
How to cite: Malik, A., Cole, L., Goodall, T., Puissant, J., Jehmlich, N., Gubry-Rangin, C., Gleixner, G., and Griffiths, R.: Microbial emergent ecophysiology affects soil carbon accumulation across land use gradients, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-14626, https://doi.org/10.5194/egusphere-egu25-14626, 2025.
Our current agricultural system is non-sustainable due to its negative impact on soil and water quality, and its eroding effect on biodiversity. To promote sustainability while maintaining productivity, we need to explore alternative practices. One such strategy is the extensification of agricultural management, which reduces external inputs while aiming to enhance soil functioning. Nutrient cycling, a key soil function, may improve under extensification due to shifts in abiotic conditions and microbial community interactions. However, the mechanisms by which extensification affects soil microbial communities and their functional interactions in field conditions remain poorly understood. In this study, we investigated how management extensification affects soil nutrient cycling. We assessed nutrient cycling using enzymatic assays, Microresp analysis, and Teabag decomposition, and evaluated the role of abiotic factors (e.g., pH, SOC) and microbial community composition along an agricultural extensification gradient, ranging from conventional productive grasslands to semi-natural grasslands. Microbial interactions were explored using co-occurrence network analysis to assess how management influences the community as a whole. Preliminary results show that fungal communities change with extensification, accompanied by an increase in overall soil nutrient functioning, particularly for decomposition rate. Our results highlight that management choices have implications for soil functioning, and that the validity to use soil parameters to underpin soil nutrient functioning are highly context dependent.
How to cite: Boone, R., Robroek, B., van der Putten, W., and de Kroon, H.: Linking agricultural extensification to soil microbial communities and soil nutrient functioning, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-11138, https://doi.org/10.5194/egusphere-egu25-11138, 2025.
Thriving communities of soil biota are a cornerstone of soil functionality. Intensification of land management with the aim to increase yield changes the biodiversity of soils, which comes at the cost of other soil functions, due to the destructive effect such management can have on soil biodiversity. While more nature-inclusive soil management practices may lead to more balanced soil multifunctionality, the recovery of biodiversity in long-term intensively managed soils is expected to take a long time. Inoculation with healthy soil may provide a jump start in the recovery of degraded soils, but only if the inoculated soil communities can become successfully established. Previous studies have shown that soil transplantation can result in greater recovery of soil communities compared to when single soil species are inoculated, but the effects on soil microbial communities and their contributions to soil functionality are not yet well-understood. Therefore, we used a four-years-old mesocosm experiment in order to test the long-term effects of soil inoculation by soil transplantation on the community composition and functionality of three types of grasslands soils. The experiment is composed of 60 intact soil cores of 95 cm diameter and 1 m depth that have been collected from three high input-output production grasslands on sand, clay, and peat. These grasslands had been exposed to high mowing frequencies, and had low vegetation diversity. At the start of the experiment, the soil cores were inoculated with soil from less intensively managed mid-successional grasslands, containing higher plant diversity than the intensively used grasslands. For half of the soil cores, the inoculate was sterilized beforehand to serve as a control. Bi-yearly measurements of yield, quarterly measurements of greenhouse gas emissions (CO2, CH4, N2O), measurements of soil organic carbon, a vegetation analysis, and results from a recent litter decomposition experiment are combined with a time-series of amplicon sequence data of soil microbial communities. I will present the effects of inoculation on microbial community composition in sand, clay, and peat soils, and show that these inoculations can have functional consequences.
How to cite: Schram, M., Bodelier, P., ten Hooven, F., Chardon, I., Veen, C., and van der Putten, W.: Long-term effects of a single soil inoculation: shifts in soil microbial community composition and functioning after a community coalescence event in sand, clay, and peat grasslands. , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-6267, https://doi.org/10.5194/egusphere-egu25-6267, 2025.
The vegetative mycelium of wood decomposing fungi is indeterminate and ever changing over the course of their lifetime. When it comes to fruiting bodies, we know that there are stark differences between species in terms of how long lasting their fruiting bodies are, with some appearing, ephemerally, for a short moment in the season and others lasting for multiple years. However, for the vegetative mycelium, it is not well known and documented how ephemeral the body of the mycelial network is for the same species.
In this study, we utilized microfluidic chip systems to document, classify and quantify turnover of fungal hyphae in eight different species of basidiomycetes grown with two different carbon sources (glucose or carboxymethylcellulose) to gain a better understanding of how mycelial turnover and potential recycling differs across wood decomposing species.
Our results show that there was a difference between species but not between carbon sources in terms of how quickly and to what degree the mycelium was degenerated. The turnover rate and hyphal persistence of the different species grouped into two distinct clusters. One with low turnover rate and species leaving “skeletonized hyphae” behind and one group that showed a quick and almost full turnover of hyphae (likely through autolysis). These results open up for new questions around species differences in hyphal re-cycling abilities, whether some wood decomposing species could contribute more to carbon sequestration in soils than others and if they have different effects on subsequent succession scenarios due to the different levels of nutrients left behind.
How to cite: Aleklett Kadish, K., van Bokhoven, R.-M. I. J., and Floudas, D.: Quantifying species differences in hyphal persistence between wood decomposing fungi at the microscale, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-21218, https://doi.org/10.5194/egusphere-egu25-21218, 2025.
Soil water dynamics within a highly fragmented soil physical environment constrain soil bacterial dispersion ranges, modulate diffusion and access to patchy resources. We have used a mechanistic modeling framework that integrates soil hydration status with organic carbon inputs to estimate community size distributions and interaction distances of modeled soil bacterial populations. The resulting spatial patterns of bacterial communities is critical for interpreting soil micro-ecological functioning. Experimental data supported by model results show that soil bacterial cluster sizes often follow an exponentially truncated power law with key parameters that vary with mean soil water content and total carbon inputs across biomes. Similar to human settlement size distributions, tree sizes and other spatially fixed systems in which growth rates are defined by their environment independent of object size (city or a tree), bacterial community size distribution is expected to obey the so-called Gibrat’s law (derived analytically for growth rates independent of community size). Results support generalization in soil using positively skewed distributions of soil bacterial community sizes (e.g., log normal). We show that soil bacteria reside in numerous small communities (with over 90% of soil bacterial communities containing less than 100 cells), supported by theoretical predictions of log-normal distribution for non-interacting soil bacterial community sizes with scaling parameters that vary with biome characteristics.
How to cite: Bickel, S. and Or, D.: General Rules for Size and Spatial Distribution of Soil Bacterial Communities, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-15487, https://doi.org/10.5194/egusphere-egu25-15487, 2025.
Defining the links between DNA-derived taxonomic outputs and morphological identifications is an important step in determining the contributions to ecological functioning by soil biotic asslemblages. Here, I present findings from work linking sequence outputs of soil faunal assemblages ( nematodes and springtails) with their inherent ecological and functional traits. These are then linked to experimental manipulations and restoration gradients that can help to unpack these relationships to can provide greater insight into the influence of ecosystem services towards community assemblages. These aspects can greatly accelerate classification of functional traits on seqeuences alone, advancing our understanding of soil communities and their importance to ecosystem functioning.
How to cite: Ross, G.: Verifying molecular sequencing data with morphological data in soil biota to uncover contributions to ecosystem functioning, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-901, https://doi.org/10.5194/egusphere-egu25-901, 2025.
Phosphorus (P) is a growth-limiting nutrient for plants and microorganisms in many natural and agricultural ecosystems. Microbial transformations of P in soils play a crucial role in increasing its availability to plants. Once taken up by microorganisms, P contributes to the energy and nutrient metabolism of microbial cells and often becomes plant-available only after microbial cell death (i.e., through the mineralization of microbial necromass).
The processes of P acquisition and microbial activation require cellular energy, which is often transferred by P-containing substances with high-energy phosphoester bonds, most commonly adenosine triphosphate (ATP). Microbial phosphorus mining from organic phosphorus compounds demands energy for the production of phosphatases. The type and combination of phosphatases required depend on the complexity of the P-containing compound, as these enzymes hydrolyze P into a plant-available form.
This talk will present measurements of the energetic costs microorganisms invest in producing various enzymes to solubilize P from compounds of increasing complexity. Additionally, the energetic costs of microbial P uptake from inorganic sources will be compared to those associated with the enzymatic hydrolysis of organic sources.
Results from incubation experiments revealed that the heat released during organic P hydrolysis increased with the complexity of the substrate, ranging from phosphomonoester bonds in sugar phosphate to six ester bonds in phytate. Furthermore, microorganisms expended significantly more energy on enzyme production than on phosphorus uptake via active cellular transport alone.
These findings provide valuable insights into predicting the hydrolysis of organic P compounds in soil, based on potential enzymatic activities and the energy balance of microorganism-mediated processes.
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.: Microbial energetic costs of phosphorus mining and uptake, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-5260, https://doi.org/10.5194/egusphere-egu25-5260, 2025.
Soil rewetting after a long dry season results in a burst of microbial activity accompanied by succession of both microbial and DNA viral communities. We hypothesized that RNA viruses, like DNA viruses, would exhibit temporal succession following rewetting. Moreover, we expected their response would change with the addition of phosphate, since viral proliferation may lead to phosphorus (P) limitation due to their low C:N:P ratio. We used a replicated time-series of soil metatranscriptomes collected after rewetting to identify parameters affecting RNA viral community composition over three weeks. P amendment led to a decrease in RNA viral community diversity and evenness, significantly impacting beta diversity over time. As has been observed for DNA viruses, the spatial distribution of RNA viruses in dry soil was highly heterogeneous. Most viruses were predicted to infect bacteria or fungi, and a small fraction was predicted to infect protists, plants, and animals. The amount of RNA extracted from phages of the class Leviviricetes increased significantly after one week in P-amended soil, contrasting with unamended soil. This suggests that P availability plays an important role in RNA phage proliferation. We estimate that the number of bacteria infected by RNA phages is on the order of 107–109 per gram soil, comparable to the range of total cells in soil. This implies that RNA phages likely have a profound effect on the bacterial community following soil wet-up when P is not a limiting factor.
How to cite: Sieradzki, E. T., Allen, G. M., Kimbrel, J. A., Nicol, G. W., Hazard, C., Nuccio, E. E., Blazewicz, S. J., Pett-Ridge, J., and Trubl, G.: Phosphate amendment drives bloom of RNA viruses after soil wet-up, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-4171, https://doi.org/10.5194/egusphere-egu25-4171, 2025.
Earthworms play a crucial role in enhancing phosphorus (P) availability in soils by processing organic matter as well as mineral soil particles and associated P. This role could represent a lever to increase agronomic P use efficiency. However, if earthworms are employed to unlock soil P, soils will still need to be replenished with nutrients. This could be accomplished through the application of circular fertilisers. In this context, earthworms could help to mobilize P from emerging mineral fertilisers recovered from waste streams, such as struvite. Despite these potential benefits, the biotic influence of earthworms on P cycling remains poorly understood and the interactions between earthworms and emerging fertilisers are unknown. Here, we present results of two studies aiming at (1) testing an isotopic approach based on the oxygen isotopes ratio in phosphate (PO4) to study the biotic effect of earthworms on soil P cycling in arable soils; and (2) investigating the role of earthworms in mobilizing P from poorly soluble struvite. In a mesocosm experiment using straw and 18O-enriched water in the presence of soil-dwelling earthworms, we found that earthworms have a significant effect on the mineralization of P from organic residues in litter-amended soils with a low PO4 availability. We demonstrated that the 18O-isotopic approach provides a promising method to study the influence of earthworms on PO4 cycling. In a field study using struvite and ryegrass in the presence of multiple combinations of earthworm species, we showed that struvite performs comparably to conventional mineral P fertiliser in terms of plant P uptake, highlighting that struvite could be an efficient P fertiliser. The effect of earthworms on plant P uptake was significant but relatively small. These two studies emphasize that the effect of earthworms on P cycling is highly context dependent (e.g., soil P status and organic matter), with optimal efficiency observed in P-poor soils when a suitable food source is provided.
How to cite: Vidal, A., Burr, A., Ferron, L., Vos, H. M. J., Pistocchi, C., Tamburini, F., Ros, M., Koopmans, G. F., and van Groenigen, J. W.: Disentangling the role of earthworms in soil phosphorus cycling, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-5988, https://doi.org/10.5194/egusphere-egu25-5988, 2025.
Tropical forests often grow on highly weathered soils with rather high nitrogen (N), but low rock-derived phosphorus (P) (and base cation) availability. While the role of P limitation in constraining plant productivity is well established, its impact on heterotrophic microbial communities remains less clear. Specifically, it is crucial to understand how P availability shapes microbial activity, physiology and resource acquisition strategies, but also potential repercussions on organic matter decomposition, nutrient mineralization, and long-term carbon (C) sequestration.
To address this knowledge gap, we studied soil microbial communities in tropical lowland forest soils located in the north-eastern Amazon in French Guiana following three years of N and P additions. We assessed soil microbial biomass, stoichiometry, extracellular enzyme activity potential, and respiration rates. Additionally, we quantified soil microbial growth using a substrate-independent method based on the incorporation of 18O from labelled water into microbial DNA.
Our results showed that soil microbial biomass slightly increased in response to N, but remained unaffected by P additions. In contrast, P additions increased microbial P content (and reduced associated C:P ratios), suggesting that microbes are highly competitive for P and can act as a significant P sink in these soils. Additionally, P additions also increased total and available soil P pools, indicating that both plant and microbial communities are well adapted to naturally occurring low P availability, and may have reached P saturation after multiple years of nutrient enrichment. Despite these changes, microbial biomass-normalized specific respiration- and growth-rates increased with both N and P fertilization, with a stronger response to P, while overall, the C use efficiency of the microbial communities remained unaffected by both.
Our results highlight (i) the pivotal role of soil microbes in C, N and P cycling in tropical forest soil and (ii) the remarkable P storage capacity of microbial communities in highly weathered soils. While microbial C and N dynamics appear tightly coupled, likely due to the similar composition of microbial cell walls, our data demonstrate non-homoeostatic stoichiometric behavior of microbial communities. This underscores the importance of reconsidering assumptions about strict stoichiometric relationships in soil and ecosystem models.
How to cite: Fuchslueger, L., Ranits, C., Figueiredo Lugli, L., Vallicrosa, H., Bréchet, L., Van Langenhove, L., Verryckt, L., Ramirez-Rojas, I., Fernandez, P. R., Courtois, E., Stahl, C., Asensio, D., Peguero, G., Llusia, J., Canarini, A., Martin, V., Verbruggen, E., Peñuelas, J., Richter, A., and Janssens, I.: Phosphorus additions increase microbial phosphorus accumulation and carbon turnover in tropical soils in French Guiana, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-16373, https://doi.org/10.5194/egusphere-egu25-16373, 2025.
Posters on site: Wed, 30 Apr, 10:45–12:30 | Hall X3
Soil microorganisms use various sources of organic matter to meet their carbon (C) and energy needs. Additionally, they require nutrients such as nitrogen (N) in appropriate stoichiometric proportions. Organic sources often have higher C/N ratios than microbial biomass, which influences organic matter decomposability and the fate of C and N in the microbe-soil-plant system. In general, microbial carbon-use efficiency (CUE), the ratio of growth to C uptake, is higher for organic sources with lower C/N, promoting C stabilization in soil. While CUE has received increasing attention, less often microbial C and N transformations are jointly studied.
We collect literature data from studies applying 13C- and 15N-enriched organic sources with variable C/N (e.g., plant litter, microbial necromass, and small organic molecules). Isotope tracing allowed quantification of C and N originating from these sources in soil and microbial biomass. We aim to determine across studies how the recovery of C and N in the microbial biomass over time is impacted by the organic source C/N and system-specific conditions. We hypothesize that high source C/N leads to greater loss of C via respiration and thus higher relative recovery of source N than C in the microbial biomass. In contrast, low source C/N likely results in a reduced difference in the relative recovery of C and N in the microbial biomass. These patterns are likely modified by system-specific conditions such as the presence of plants or inorganic fertilization. Our contribution aims to provide insights into the joint microbial use of C and N related to organic source stoichiometry.
How to cite: Siegenthaler, M. and Manzoni, S.: Microbial use of C and N from organic sources - Insights from isotopic tracer literature data, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-4045, https://doi.org/10.5194/egusphere-egu25-4045, 2025.
Soil microbes play an important role in stabilizing soil organic carbon (C) as microbial residues, a process known as soil ‘microbial C pump’ (MCP). Accurately assessing MCP efficiency is essential for understanding microbial-mediated soil C sequestration. Conventional assessments based on microbial C use efficiency (CUE) hinge on microbial biomass only and do not include microbial necromass, which may not depict MCP efficiency. Here we propose a relatively simple and rapid approach based on 13C-glucose amendment experiment to assess microbial C accumulation efficiency (CAE) as a novel metric for assessing MCP efficiency. We first validated the approach by showing negligible retention of glucose to soils with a wide range of edaphic properties. Glucose-derived 13C may hence be considered to represent microbial C (including biomass and residues) after a few days of addition, given the rapid uptake of glucose by microbes. Microbial CAE may thus be assessed as the recovery of glucose-derived 13C in the soil. By further conducting a meta-analysis of literature data involving isotopically labeled glucose amendment experiments, we revealed distinct variation patterns and influencing factors of microbial CAE and CUE across various terrestrial ecosystems. Compared to CUE which is mainly regulated by factors influencing microbial physiological processes (particularly substrate availability), CAE is jointly regulated by factors that influence microbial growth (e.g., biomass and climate) and residue preservation (e.g., clay content). These findings underscore that CAE is decoupled from CUE. Incorporating CAE into soil C models may provide new insights into future SOC dynamics under climate change.
How to cite: Hu, W., Cai, Y., Li, X., Jia, J., and Feng, X.: Microbial Carbon Accumulation Efficiency: Assessing Microbial Carbon Pump Efficiency based on 13C-glucose Amendment Experiment, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-2276, https://doi.org/10.5194/egusphere-egu25-2276, 2025.
The physical colocation of decomposers and substrates has been proposed as being a determining factor of microbial metabolism in soil, which is also greatly modulated by environmental temperature. Moreover, spatial heterogeneity of insoluble substrates is hypothesized to favor the fungal energy channel, as fungi have a well-developed capacity to translocate resources within their mycelia thus overcoming local resource limitation. Here, the effects of warming, substrate spatial heterogeneity, and fungal translocation on microbial metabolism as indicated by substrate-derived CO2 emission, heat production, and calorespirometric ratio (CR, the ratio of heat production to CO2 emission) were tested, using cylinders with four compartments that either prevent or allow diffusion between compartments.
With increasing spatial heterogeneity, the CO2 emission rate generally declined under ambient temperature. The emission rate was slightly higher when diffusion was not allowed across the compartments, except the second half of incubation in the most heterogeneous treatment (100-0-0-0%). In warming environment, the CO2 emission rates were stimulated, but with diminished effect of spatial heterogeneity. The heat release in the most heterogeneous treatment was lower than the most homogenous (25-25-25-25%) and intermediate heterogeneous (50-0-50-0%) treatments. Under warming condition, the peaks of heat release were heightened, and the peak of the most heterogeneous treatment was brought forward. The heat release was higher when diffusion was not allowed across the compartments under ambient temperature, but insignificant difference among treatments were detected under warming environment. CR decreased rapidly in the first half of incubation, and remained stable during the rest . The difference in CR was mainly detected in the first half of incubation, with CR declining with the decrease of spatial heterogeneity.
Overall, our findings provide detailed information about microbial metabolism in response to substrate spatial heterogeneity and warming climate, and suggest that the degree of substrate spatial heterogeneity is an important boundary condition shaping the energy use channel in this soil compartment.
How to cite: Tian, P., Lorenzen, C., Shao, G., Banfield, C., Dippold, M., Spielvogel, S., and Razavi, B.: The microbial metabolism in a heterogeneous and warming soil environment: A bioenergetic point of view, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-8436, https://doi.org/10.5194/egusphere-egu25-8436, 2025.
The growth of soil microorganisms is limited by scarce substrate availability for most of the time in most soils, interrupted only by comparatively brief bursts of activity following localized pulses of substrate input. During periods of starvation, microbes must persist in a state of inactivity or dormancy to maintain their viability. Given the prevalence of such non-growing microbes, the costs of maintenance metabolism as well as those associated with emergence from and return to dormancy can be expected to play a significant role in soil carbon (C) cycling.
Recent advances have highlighted the utility of bioenergetic modeling based on coupled C and energy fluxes for the analysis of microbial activity in soil. In particular, the calorespirometric ratio (CR) of heat to CO2 production obtained from incubation experiments presents a useful tool for monitoring the bioenergetics of microbial metabolism in a dynamic fashion. However, previous studies have primarily focused on the CR during microbial growth, and the effects of non-growth metabolism are rarely considered.
In this contribution, we present a theoretical analysis of the consequences of non-growth metabolism on temporal patterns of the CR (Fig. 1). Specifically, we employ process-based modeling to show that both exogenous maintenance fueled by the consumption of external substrates and endogenous maintenance fueled by the consumption of biomass have distinct effects on the dynamics of the CR (Fig. 1) as well as on the relationship between CR and microbial C use efficiency (CUE), depending on the energy content of the consumed compounds. To connect these theoretical findings with empirical evidence, we compiled data on the CR measured in unamended soils as well as during the lag and retardation phases of substrate amendment experiments from the literature. The results reveal a wide range of observed CR values consistent with high metabolic diversity of microbial maintenance processes. In addition, we find a strong positive correlation between the non-growth CR and the average SOM energy content in arable soils but observe a weak inverse relationship in forest soils, the causes and implications of which remain to be explored.
Overall, our theoretical findings demonstrate a distinct effect of microbial maintenance metabolism on the coupling between C and energy fluxes in soil, which is supported by existing empirical evidence from incubation experiments.
Fig. 1: Simulated dynamics of CR after addition of labile substrate
both with (red) and without (black) additional utilization of SOM (i.e., priming).
Dotted lines indicate CR calculated from rates of heat and CO2 release (CRrate),
solid lines indicate CR calculated from cumulative release (CRcumu).
How to cite: Endress, M.-G. and Blagodatsky, S.: Exploring the energetics of soil microbial metabolism under substrate limitation, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-9719, https://doi.org/10.5194/egusphere-egu25-9719, 2025.
Microbial growth is a fundamental aspect of microbial life history, underpinning essential ecosystem functions and driving all biogeochemical cycles. While culture-based studies have provided valuable insights into microbial growth, they often fail to capture how microbes grow under natural conditions, which include complex interactions with other organisms and their physical and chemical environments.
Currently, microbial growth is typically defined as the ability of individual cells to replicate. Such a definition, however, overlooks the diverse strategies to survive and thrive in dynamic environments. These strategies reflect how microorganisms allocate carbon they take up to various pathways, including cellular replication, synthesis of storage compounds (e.g., triacylglycerides and polyhydroxyalkanoates), accumulation of osmolytes, and exudation of substances such as extracellular polymeric substances, extracellular enzymes and metabolites like short-chain fatty acids. These strategies are often accompanied by physiological shifts, such as transitioning between active and dormant metabolic states.
Despite the central importance of microbial growth, its in situ measurement remains a significant challenge. This limitation hinders our understanding of the ecological functions of soil microbiomes and our ability to accurately predict carbon use and cycling. Addressing this knowledge gap requires, a multi-faceted approach including the following key considerations:
- Expanding definitions of microbial growth: Microbial growth encompasses more than cell division and DNA replication, particularly under stress conditions, such as nutrient and water scarcity. It includes the synthesis of storage compounds, osmolytes, and extracellular material. A more flexible definition, along with a delineation of growth and activity, is urgently needed.
- Understanding and benchmarking growth methods: To isolate patterns in growth across microbial ecosystems, it is crucial to understand what different growth methods (that target various biomolecules, such as nucleic acids, proteins, and lipids) actually quantify, and how they relate to one another. Emphasis should be placed on substrate-independent methods.
- Developing and improving models: Models should prioritize the exploration of microbial growth strategies in dynamic, non-steady steady-state environments and include robust experimental validation.
By addressing these key considerations, we hope to be able to deepen our understanding of microbial growth in natural systems, enhance ecological modeling, and better predict the role of soil microbiomes in carbon cycling.
How to cite: Luo, Y., Metze, D., Guseva, K., and Richter, A.: Theoretical Considerations Concerning Soil Microbial Growth, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-17846, https://doi.org/10.5194/egusphere-egu25-17846, 2025.
The quantitative understanding of microbial physiological roles in microbial-explicit soil organic carbon (SOC) models has been limited by focusing primarily on microbial carbon use efficiency (CUE) in relation to SOC storage. To improve this understanding, it is essential to explore underlying processes such as microbial respiration and growth, which directly impact SOC loss and sequestration.
Using a global database of CUE measured through 18O-microbial DNA growth, we found that total microbial respiration and growth rates behave differently across various climate zones and land uses. Respiration and growth rates are the highest in temperate grasslands and boreal forests, while no significant differences are observed for specific rates. Moreover, microbial respiration is found to be more sensitive to environmental constraints than microbial growth, although both are ecosystem-dependent. For example, the contrasting relationships between SOC-CUE and microbial biomas C-CUE in temperate grasslands and tropical forests arise from the interplay of C availability, nitrogen limitation, and microbial growth and respiration dynamics. While temperate grasslands maintain a balance between microbial growth and respiration despite nitrogen limitations, tropical forests experience severe inefficiencies due to higher microbial activity and faster nutrient cycling. These differences underscore the ecosystem-specific nature of microbial respiration, growth, and consequently CUE.
How to cite: Bi, Q.-F., Reichstein, M., and Schrumpf, M.: Ecosystem-dependent microbial respiration and growth strategies with consequences for global soil carbon cycling , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-20117, https://doi.org/10.5194/egusphere-egu25-20117, 2025.
Soil microbes are responsible for important ecosystem services such as nutrient cycling and decomposition, and as such their activity is an important contributor to GHG emissions from soils. However, while microbial biomass is known to affect soil C turnover, the role of community composition and diversity is less clear. It has been theorized that microbial functional diversity may be a useful predictor of decomposition rates, but empirical data from natural systems are ambiguous. In addition, the contribution of diversity to decomposition may be affected by the different sensitivity of various fungal and bacterial functional groups to land management. In this study we aim to disentangle the direct effect of forest management on decomposition rates via changes in soil moisture and temperature, from its indirect effects via changes in microbial community composition. We use empirical data collected from multiple forest management experiments across Europe by the HoliSoils consortium (Holistic management practices, modelling and monitoring for European forest soils; https://holisoils.eu/). Preliminary results indicate a significant correlation between microbial diversity and soil respiration, but with significant differences between fungi and bacteria. This suggests that identifying appropriate diversity indicators could improve microbially explicit C turnover models and inform forest management practices for climate impact mitigation.
How to cite: Guasconi, D., Pallandt, M., Aleinikovienė, J., Behling, D., Filipek, S., Lehtonen, A., Martinović, T., Ťupek, B., and Manzoni, S.: Effects of forest management and microbial diversity and community composition on soil respiration, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-8656, https://doi.org/10.5194/egusphere-egu25-8656, 2025.
The role of multitrophic diversity in regulating soil carbon dynamics remains unclear, yet understanding these dynamics is essential for enhancing soil health and carbon storage. This study examines how tree mycorrhizal diversity and soil community complexity influence soil carbon sequestration. We hypothesize that greater soil community complexity and the presence of both arbuscular (AMF) and ectomycorrhizal fungi (EMF) enhance carbon stabilization. To test this, biodiversity was manipulated by (1) pairing tree species associated with AMF, EMF, or both, and (2) establishing four levels of soil complexity: microbes alone, microbes with mesofauna, microbes with mesofauna and macrofauna, and all previous levels with earthworms. Treatments were fully crossed and incubated in ecotrons for 140 days. Soil carbon responses are currently being assessed across free and occluded particulate organic matter and mineral-associated organic matter fractions. Ongoing carbon content analyses may provide valuable insights into how multitrophic biodiversity shapes soil carbon dynamics, with implications for soil management and carbon storage.
How to cite: den Toonder, J., Hines, J., Ganault, P., Eisenhauer, N., and Angst, G.: The Influence of Multitrophic Soil Biodiversity on Carbon Stabilization, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-9770, https://doi.org/10.5194/egusphere-egu25-9770, 2025.
Current efforts to enhance carbon storage and minimize losses in natural and managed soil systems increasingly recognize microbial necromass (i.e., the sum of extracellular microbial products as well as dead cells) as a major contributor to persistent carbon. To date, however, the abiotic and biotic factors controlling necromass formation and persistence in complex and diverse soil microhabitats are poorly understood. Here we combine microfluidics experiments with optical photothermal infrared (OPTIR) spectromicroscopy and fluorescence microscopy to track microbial growth, turnover and necromass production within different microhabitats. The microfluidics approach allows us to create different microenvironments that vary in pore connectivity and, thus, show gradients in substrate, oxygen, and nutrient availability. We inoculated microfluidic plates with bacterial species isolated from a topsoil in Switzerland (21 species; see Čaušević et al., 2022), representing four major phyla: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Using diagnostic infrared spectra along with fluorescence labelling, we can follow the growth dynamics of different bacterial species within synthetic communities as well as their turnover and associated necromass formation. Spectra were obtained for soil bacteria known to differ in essential ecophysiological characteristics, such as EPS production, Gram classification (Gram-positive vs. Gram-negative), and predatory versus non-predatory behaviour. We will report on a first proof-of-concept experiment that highlights the potential for this approach to reveal critical interactions between bacterial traits, microhabitats characteristics, growth dynamics, and necromass formation.
Literature cited:
Čaušević, S., Tackmann, J., Sentchilo, V., von Mering, C., & van der Meer, J. R. (2022). Reproducible propagation of species-rich soil bacterial communities suggests robust underlying deterministic principles of community formation. Msystems, 7(2), e00160-22.
How to cite: Bentvelsen, B., Foley, M., Jamoteau, F., van der Meer, J. R., and Keiluweit, M.: Mapping microbial growth, turnover and necromass formation in soil microhabitats using photothermal infrared spectromicroscopy , EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-19286, https://doi.org/10.5194/egusphere-egu25-19286, 2025.
Soil microbiome is one of the most important components influencing biogeochemical cycles. Changes in the dominance of different microbial functional groups can result in a community that, due to the changes in microbial enzymes, can respond more or less rapidly to decomposition rates, synthesis of organic matter, nutrient availability and soil structure (Brangarí et al., 2021, Wu et al., 2024). The size and composition of soil microbiome is influenced by variables such as plant species, soil moisture and temperature, pH and nutrients availability (Naylor et al., 2022), which in turn are influenced by climate conditions and agronomic practices. Estimating the soil microbiome composition is therefore crucial to deeper understanding processes such as crop development, carbon (C) and nitrogen (N) uptake, soil nutrient retention, drought tolerance and pest resistance (Lutz et al., 2023).
Despite the large importance of soil microbial composition at determining magnitude and patterns of biogeochemical cycles, the majority of crop and biogeochemical models currently existing are not able to well represent this process. For instance, the microbial biomass simulated by STICS (Brisson et al., 1998) and EPIC (Izaurralde et al., 2006) varies according to N availability in the soil organic matter (SOM) decomposition, without considering microbial species dynamics. Similarly, the pools of models such as RothC (Coleman and Jenkinson, 1996), CENTURY (Parton, 1996), APSIM (Probert et al., 1998), DayCent (Parton et al., 1998), FASSET (Berntsen et al., 2003) Report fixed values of C/N ratios.
This poor representation is mainly related to the lack of detailed algorithms to simulate, for example, SOM turnover driven by soil microbial biomass, the partitioning of different incorporation of decomposable C pools (i.e., lignin and cellulose) from crop residues into soils, the effect of N deficiency on SOM decomposition, and gas transport in soils. These processes should be incorporated into process-based biogeochemical models as driven by soil microbiome to provide more reliable estimates of C and N while reducing uncertainties.
To this end, the RothC submodel implemented within the GRASSVISTOCK model (Leolini et al., 2023) has been improved to take into account seasonal evolution of the soil microbiome and the related effect of agronomic practices. Specifically, new mathematical approaches reproducing the response of microbiota activity to soil temperature and water availability numerically quantify the seasonal trend of the enzymatic activity of the soil microbiota communities (Zhao et al., 2024; Babic et al., 2024; Ghodizadeh et al., 2024) will be integrated within the GRASSVISTOCK model and then validated against a measured available data of the grassland test site in Italy.
How to cite: Costafreda-Aumedes, S., Brilli, L., Leolini, L., Moriondo, M., and Gioli, B.: Implementation of a novel soil module that simulates the microbiome species dynamics in grasslands, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-17905, https://doi.org/10.5194/egusphere-egu25-17905, 2025.
Soil health is defined as the ability of a soil to function as a vital, living ecosystem, supporting the growth of plant, animal and humain This capacity is highly dependent on the microorganisms living in the soil due to their role in biochemical cycles linked to the recycling and availability of nutrients such as carbon (C), nitrogen (N), and phosphorus (P). Due to their disruption of the soil microbiome, conventional farming practices negatively affect the long-term health of cultivated soils (Montgomery & Biklé, 2021). The establishment of soil’s health indices is a complex matter due to the grand variability of existing soil’s type, texture, soil physicochemicalcharacteristics, and the variation in crop’s needs. Those three cycle where chosen for their importance in the context of agricultural’s plants needs and those critical process include the fixation of atmospheric nitrogen and the recycling of nitrogen compound from organic matter and the production of acid and alkaline phosphatase by soil’s archeae, bacteria and fungy. Those process are deemed critical by the introduction in a usable form of critical nutriment to plant’s grow that are other wise in a unusable form for the plant. To this end, we observed the impact of 4 different kind of mulches, all with reduced tillage, and a standard treatment with conventional farming practice over a 3 years period, with two sampling per year, one in May and one in August. The obtention of the soil’s microbiome composition was done with the shotgun metagenomic technique using the AVITI plateform. The metagenomic shotgun technique was chosen for its capacity to obtain an overall picture of the population of fungi, bacteria, and archaea composing the soil microbiome in a single sequencing run, thus avoiding PCR bias due to multiple amplicon sequencing on the microbiome's proportions. In this presentation, the observed variation in the soil’s microbiome population du to the treatments and their impacts on the soil critical process will be explored. We hypothesize that the soil under the conventional treatment will have a lower redundancy level compare to the soil under the other treatment.
Lehmann, J., Bossio, D. A., Kögel-Knabner, I., & Rillig, M. C. (2020). The concept and future prospects of soil health. Nature Reviews Earth & Environment, 1(10), 544-553. https://doi.org/10.1038/s43017-020-0080-8
Montgomery, D. R., & Biklé, A. (2021). Soil Health and Nutrient Density: Beyond Organic vs. Conventional Farming [Review]. Frontiers in Sustainable Food Systems, 5. https://doi.org/10.3389/fsufs.2021.699147
How to cite: Gauthier, G., Van Der Heyden, H., Dessureault-Rompré, J., and Gumiere, T.: Metagenomic for a better understanding of cultivated soil health, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-15114, https://doi.org/10.5194/egusphere-egu25-15114, 2025.
In Iceland, unsustainable land use has led to severe land degradation and desertification. Degradation may shape soil microbial communities, which has implications for ecosystem functioning. This study presents for the first time a characterization of the structure and function of soil microbial communities in tundra soils of contrasting stages of degradation in Iceland and shows promise in identifying degradation processes and potentials for recovery. We used shotgun metagenomic sequencing to compare soil microbial communities in a Betula nana heath with erosion spots and a highly degraded desert at two sites, inside and outside the active volcanic zone (Þeistareykir and Auðkúluheiði). The bacterial taxonomic composition of the desert soils with relatively high abundance of Actinobacteria, low respiration (microbial activity) and lower functional diversity reflected a highly degraded state. Heath soils at Þeistareykir had more abundant key ecosystem taxa of the genus Bradyrhizobium, higher taxonomic richness, microbial activity, and functional diversity compared to the heath at Auðkúluheiði, indicating that the heath in Auðkúluheiði is more degraded. Use of the trait-based framework of high yield (Y), resource acquisition (A), and stress tolerance (S) provided a more nuanced picture of the functional microbial roles in each of these soil types.
How to cite: Ólafsdóttir, A. B., Andrésson, Ó. S., Barrio, I. C., Warshan, D., and Jónsdóttir, I. S.: Microbial communities and functionality in degraded tundra soils, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-10195, https://doi.org/10.5194/egusphere-egu25-10195, 2025.
Conservative agricultural practices have been identified as pivotal in mitigating the effects of global warming. These practices are essential to maintain soil fertility and ensure the productivity of crops. Ground cover crops are an example of this practice, which can be readily implemented in orchards. They confer numerous benefits to agrosystems, including the prevention of soil mechanical damage and erosion, the reduction of water evaporation, the enhancement of soil carbon sequestration, the facilitation of weed control, the increase of soil microorganism community stability, the promotion of beneficial specific taxa, and the improvement of soil multifunctionality. This study was conducted within the framework of the LIFE Vida for Citrus project (LIFE18 CCA/ES/001109), which had the primary objective of developing sustainable control strategies to enhance the resilience of citrus orchards under the threat of climate change and to prevent the entry of Huanglongbing (HLB), or citrus greening disease, into the European Union. The objective of the present study was to evaluate the benefits of cover crops under the climatic and edaphic conditions of the Canary Islands (Spain), in the functional diversity of edaphic microbiota in a citrus orchard. In the Canary Islands, areas with little or poor soil depth (normally located below 300 meters above sea level) are usually modified by creating terraces with more fertile soil from higher altitudes (300-700 m.a.s.l.) situated in the northern side of the islands. This practice allows for more favorable cultivation, but degrades the original soil. The cover crops that were evaluated included the grass Lolium arundinaceum (Schreb.) Darbysh and a combination of flowering species, such as Lobularia maritima (L.) Desv., Diplotaxis tenuifolia (L.) DC., Calendula arvensis L., Medicago sativa L., Trifolium repens L., and Petroselinum crispum (Mill.) Fuss. The community level physiological profiles were measured, by the MicroRespTM method, after three years of groundcovers sowing. Total and oxidizable organic matter, as well as total nitrogen content, were also evaluated. The multiple substrate-induced respiration (MSIR) profiles were found to be influenced by the utilization of the cover crop in comparison to the bare soil, which exhibited a substantial impact on the individual respiration rates for 16 of the 18 tested substrates (p < 0.050). The soil under groundcovers exhibited the highest consumption (between 2.2 and 3.0 times higher MSIR) of simple and complex carbohydrates, linear and aromatic carboxylic acids, and amino acids and amino sugars, in comparison to the bare soil (p < 0.050). Additionally, the highest respiratory responses were exhibited after the addition of γ-aminobutyric acid, arabinose and α-ketoglutaric acid, ranging from 0.773 ± 0.370 and 2.34 ± 1.04 μg C-CO2 · g-1 · h−1. The diversity of the soil microbial community is a sensitive means to assess soil health in the implementation of conservative agriculture practices in the citrus orchards.
How to cite: González-González, M., Quintana-González-de-Chaves, M., García-González, M. A., Garzón-Molina, M. S., and Gómez-Jara, A. G.: Impact of cover crops on functional response of soil microbial communities in a citrus orchard in the Canary Islands, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-20563, https://doi.org/10.5194/egusphere-egu25-20563, 2025.
Posters virtual: Fri, 2 May, 14:00–15:45 | vPoster spot 3
EGU25-8569 | Posters virtual | VPS15
Soil microbial communities dynamic in spontaneous afforestation: a comparative analysis between the Casentino Forests and the Julian PrealpsFri, 02 May, 14:00–15:45 (CEST) | vP3.5
In this study we investigate the effects of rewilding, a spontaneous process ongoing since decades after land abandonment at national and European levels, with a focus on the replacement of former grasslands and pastures by tree forest. In particular, we explored the ecological dynamics occurring within the topsoil. The main objectives are: i) to clarify how topsoil physico-chemical properties change along the successional gradient, ii) to provide an overview of soil microbial communities response along the same gradient, and iii) assess causal relationships among soil predictors and microbial response, in terms of community composition and diversity, as well as abundance of bacterial and fungal taxonomic groups. The study areas were the Foreste Casentinesi National Park and the Julian Prealps Regional Park (Italy), In both areas we identified by historical ortophotos (period 1954-2020) five successional stages replicated in four chronosequences: grassland-pasture (G), shrubland (S), early (E), intermediate (I), and late afforestation (L). Replicated topsoil samples (0–10 cm) were analysed for pH, bulk density (BD), and organic carbon (OC), and total nitrogen (N) contents. Microbial communities were assessed from environmental DNA extracted by the fine soil fractions followed by DNA metabarcoding using ITS and 16S markers for fungi and bacteria, respectively. Results showed that as the succession progresses, soil acidification and a reduction in bulk density occur, coupled with an increase in soil organic matter at later stages in mature soils. However, such trends are quantitatively affected by site-specific variability. Bacterial and fungal communities respond differently to secondary grassland afforestation: fungi, mainly Ascomycota and Basidiomycota, exhibit greater specialisation in mature successional stages, while bacteria, dominated by Proteobacteria and Verrucomicrobiota, show more site-specific traits. Comparisons between the two study areas showed a lower variability in microbial diversity in the Casentino National Park, likely due to its more homogeneous environmental conditions, including plant cover. Our study underlines the functional importance of soil biota in enhancing and sustaining carbon storage in forest soils undergoing natural afforestation. On a broader scale, the study highlights the value of nature-based solutions such as rewilding for climate neutrality and biodiversity conservation.
How to cite: Panico, S. C., Alberti, G., Foscari, A., Orzan, L., Piazza, N., Tomao, A., and Incerti, G.: Soil microbial communities dynamic in spontaneous afforestation: a comparative analysis between the Casentino Forests and the Julian Prealps, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-8569, https://doi.org/10.5194/egusphere-egu25-8569, 2025.
