Heterogeneity (spatial, temporal chemical and biological) is a fundamental property of soils. Although it is rarely explicitly accounted for in models of soil microbial functioning, it is a determinant of microbial access to substrate and therefore of microbial activity. Microbial adaptation to heterogeneity is also likely to play a significant role in determining microbial activity and therefore C persistence in soil. A more developed understanding of heterogeneity and how microbial communities interact with their heterogenous environment can help us better understand the mechanisms that regulate microbial activity and soil C dynamics, as well as offer potential avenues for upscaling. In this presentation I will show how microbial communities have adapted to spatial and molecular heterogeneity at the microbial scale and, through the use of a spatial explicit model, how spatial and molecular heterogeneity interact to reduce decomposition. Pore scale heterogeneity affects the distribution of both decomposers and organic matter. Using a stable isotope approach, I will show that, although there does not appear to be a clear relationship between microbial decomposer composition and pore size, a simple relationship emerges between pore size and microbial decomposition of organic substrate. As the pore size distribution of soils can be deduced from pedo-transfer functions, this relationship may provide a more mechanistic basis for the representation of moisture effects on C dynamics in larger scale models.

How to cite: Nunan, N., Schmidt, H., Chenu, C., Pouteau, V., and Raynaud, X.: Heterogeneity and C dynamics in soil, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-13193, https://doi.org/10.5194/egusphere-egu23-13193, 2023.

Here we present a novel model supplementing existing theories of soil organic matter (SOM) decomposition, based on evolutionary-ecological principles rather than chemical or physical limitations to decomposition. We argue that decomposition of some substrates, in particular nitrogen-rich non-hydrolyzable matter (NHLS), may be constrained by spatial competition from opportunists (Bonner et al., 2022). Our model is based on two linked hypotheses: (1) From an evolutionary point of view, microbes should optimise their enzyme production to maximise the net fitness gain (F), and they should only decompose NHLS if the uptake of decomposition products (S) brings a net fitness gain (F > 0) in terms of growth minus costs of enzyme production. (2) F strongly depends on the fraction of decomposition products absorbed by the decomposer, i.e. the return on enzyme investment, which depends on the distance to the substrate and the competition from opportunistic bacteria. A minimum ‘safe’ distance for oxidative decomposition is included, based on the idea that cost of oxidative stress to the decomposer will surpass potential gain from decomposition when the activity is too close. Although the model predictions have not been tested directly against observations, they provide proof-of-concept that substrate can be spared decomposition and accumulate even when it is physically and chemically accessible. Due to the spatial competition effect, it is not profitable for either bacteria or decomposer fungi to decompose NHLS under certain conditions.  Our framework can help explain a variety of SOM dynamics, including priming and the suppression of decomposition by nitrogen addition.

Reference

Bonner MTL, Franklin O, Hasegawa S, Näsholm T. 2022. Those who can don't want to, and those who want to can't: An eco-evolutionary mechanism of soil carbon persistence. Soil Biology and Biochemistry 174: 108813.

How to cite: Franklin, O., T.L. Bonner, M., Hasegawa, S., and Näsholm, T.: A spatial microbial competition mechanism of soil carbon persistence, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-8678, https://doi.org/10.5194/egusphere-egu23-8678, 2023.

Farming practices affect soil structure and aggregate formation. The addition of organic fertilizers, such as cow manure, is a practice that can affect soil aggregation and can foster the formation of macroaggregates, which resemble high contents of rather labile soil organic carbon (SOC). Soil aggregates, known to be hotspots for microbial activity, can also be assumed to be hotspots for microbial nutrient cycling. Within the soil system, microorganisms play an active key role in the cycling of phosphorus (P) by: 1) storing P within their biomass, 2) mineralizing non-plant available organic P, and 3) solubilizing inorganic P forms. Microorganisms are thus a key driver in the cycling of P in soil. However, P cycling through the microbial biomass is often limited by SOC availability. The use of organic fertilizers may provide the OC required for microorganisms to cycle P, especially in SOC rich maccroaggregates. The main objective of the present work is to better understand how soil microorganisms’ habitat and P-cycling is affected by the addition of cow manure and how it affect the P cycling through microbial biomass. We collected soils from a long term field trial consisting of different organic soil amendments (Taastrup, Denmark), namely a soil amended with cow manure and a soil amended with mineral fertilizer (nitrogen, potassium and P). We determined soil aggregate size distribution as well as macroaggregate stability, soil C, N and P contents and microbial biomass C, N and P within aggregate size fractions We are able to demonstrate that the application of organic fertilizer has clearly affected soil macroaggregation and stability, as well as the nutrient distribution and content within the aggregates. As large macroaggregates between 2 and 8 mm dominated the sampled soils (49-79 % of the soil mass), we selected these macroaggregates as a functional unit to evaluate the effect of the organic fertilizer on microbial P cycling. We suggest that the addition of cow manure alleviates microorganisms’ OC limitation and thus stimulate P cycling through microbial biomass. The better understanding of soil microorganisms activity and organic fertilizer interaction at the aggregate scale is providing a better understanding of plant-P availability which will benefit the development of future sustainable cropping systems.

How to cite: Raymond, N. S., Tamburini, F., Oberson, A., Magid, J., and Müller, C.: Organic fertilizer amendment affect soil aggregates during crop growth: a hotspot for microbial phosphorus turnover?, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-13715, https://doi.org/10.5194/egusphere-egu23-13715, 2023.

Nowadays, the integral indicators of soil health in agrocenoses are the crop yield and the quality of raw material. In order to achieve efficient use of soil in the field, it is necessary to understand its physical, chemical and biological properties. It is essential to consider the possibilities of improving of the soil health and plant nutrition using different types of biofertilizers, especially of microbial origin. The standard indicators included in the agrochemical certificate describe various physical and chemical properties: humus content, granulometric composition, soil density, productive moisture, acidity, salinity degree, content of mobile or hydrolyzed nutrients – N, P, K, and microelements as well as different contaminants - mobile forms of cadmium, lead, pesticide residues, etc. For the microbial analysis, it is suggested to evaluate biological indicators by the number of microorganisms and the ratio of certain physiological groups. Principle of soil condition assessment according to the research conducted includes main groups of microorganisms: oligotrophs, pedotrophs, microorganisms that use different nitrogen compounds (mineral – organic), nitrogen-fixing bacteria; different groups of fungi: saprotrophs or pathogens.

The results of conducted experiments showed that before and after application of a complex of PGPR (Groundfix®) at a rate 1 l/ha, the soil indicators had a tendency to improve. The content of mobile phosphorus compounds increased by 49.3% and potassium increased by 55.8% respectively. This efficiency was achieved due to the microorganisms that contribute to the release of phosphorus and potassium from hard-to-reach compounds. Statistical data analysis showed that humus content and hydrolyzed nitrogen dependent were high during both the first soil sampling in May and the next one in August (204.4 mg/kg and 207.2 mg/kg). This stability was provided by the high number of microorganisms that transform organic compounds contributing to both the destruction of light organic matter of plant residues and the synthesis of humus substances. According to the results of the soil analysis, the bacteria could affect the acidity of the soil. Another important fact to discover was increase in the diversity of saprophytic fungi from two to five genera, including fungi genus Trichoderma, counting 15% from the total number of fungi. These changes could be explained by the activation of the indigenous agronomically valuable microbiota in the soil. Therefore, application of the product Groundfix affected the number of microorganisms of certain physiological groups. The ratio between these groups showed that in the soil there is a predominance of synthesis over destruction processes. The number of Azotobacter bacteria increased by 2.4 times, which confirms the high level of soil fertility.

Contrary to what has often been assumed, the efficacy of PGPR bacteria usage in soil health improvement has confirmed by multiple analyses and statistical data. Our finding indicate that this complex of bacteria not only activate other beneficial groups of organisms but also make P and K more available for plants uptake. As a result, farmers get more rich harvest on their fertile soil.

How to cite: Yakovenko, D. and Korsun, S.: Use of PGPR (GROUNDFIX®) to Improve Soil Health, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-16359, https://doi.org/10.5194/egusphere-egu23-16359, 2023.

Soil imaging visualizes and quantifies processes in soil hotspots across space and time involving microorganisms, roots and carbon and nutrient sources, thereby helping to elucidate mechanisms. A wide range of individual approaches exists to determine spatial distributions of soil pH (optodes), root exudation and pesticides (¹⁴C phosphor imaging), fertilizers (³³P phosphor imaging), nutrient fluxes (DGT), etc.

Since processes and mechanisms are clearly multi-factorial, combining individual approaches is key for any real understanding of soil processes. Multi-imaging comes with a set of challenges as firstly, scales need to be bridged as imaging methods operate at different spatial scales from cm to nm. Secondly, their time scales vary from minutes to days. Thirdly, the sequence of method application needs careful consideration as some methods leave behind chemicals, which may interfere with other measurements.

Imaging methods were initially developed for laboratory-controlled conditions, and only several were already adapted for field conditions. We will present the challenges for application soil imaging techniques in the field and problems related to sequential application. We will suggest a workflow for multi-imaging, which includes suggestions on coupling methods to study defined soil process, the sequence of the methods application, image alignment, hotspot thresholding and analysis, co-localization of images and quantitative image analysis. The perspectives, advantages and challenges of multi-imaging approaches will be comprehensively discussed.

How to cite: Bilyera, N., Banfield, C. C., and Dippold, M. A.: Perspectives and methodological challenges of imaging soil hotspots and coupling soil images of different origin in multi-imaging approach, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-4445, https://doi.org/10.5194/egusphere-egu23-4445, 2023.

In drought affected ecosystems, a large portion of the annually respired CO₂ from soil may occur in the short period following the first rain event after drought. This process, where the rewetting of dry soil results in a pulse of CO­₂, is commonly known as the Birch Effect. This pulse of activity influences the stability and persistence of soil carbon which, considering the large and growing extent of dryland and drought-impacted ecosystems, may have far reaching implications. It’s been shown that the consumption of the compounds driving the Birch Effect varies temporally and that different taxa grow over the course of wet-up; however, the transcriptional response of specific taxa during wet-up, and their associated characteristics, has not been fully explored.  In this study we map metatranscriptomes against metagenome-assembled genomes (MAGs) in order to assess the transcriptional response of taxa to wet-up at 0, 3, 24, 48, 72, and 168 h post rewetting. We found distinct temporal response patterns that were often conserved on the family-level. Based on response patterns, we grouped genomes into early, mid, and late responders. The average transcriptional profile of MAGs within these different response types did not vary substantially from each other. Instead, for a majority of MAGs, we found shifts in the transcriptional profile of functional genes over time. Together, these findings suggest that much of the temporal dynamics of microbial transcription during the Birch Effect are controlled by differences in within-taxa response time as opposed to stark differences in functional gene transcription between response groups.

How to cite: Chuckran, P., Firestone, M., Nicolas, A. M., Sieradzki, E. T., Pett-Ridge, J., and Blazewicz, S.: Tracking transcription in soil microbial communities during the Birch Effect, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-11025, https://doi.org/10.5194/egusphere-egu23-11025, 2023.

Northern peatlands store approximately 500 Pg carbon in the form of peat particulate organic matter (POM). Ombrotrophic bogs are peatlands that only receive water and nutrients through precipitation, creating anoxic, water-logged soils deprived of inorganic terminal electron acceptors (TEAs). In the absence of suitable TEAs for anaerobic respiration, methanogenesis prevails as final step in the degradation of organic matter and is expected to result in equimolar CO₂:CH₄ production ratios. However, field and laboratory studies revealed higher CO₂:CH₄ production ratios than expected based on low concentrations of canonical inorganic TEAs, suggesting the presence of a previously unrecognized TEA used in anaerobic microbial respiration. It has been hypothesized that oxidized particulate organic matter (POM_ox) functions as TEA, explaining elevated CO₂:CH₄ production ratios. Through seasonal water table fluctuations, POM gets re-oxidized abiotically, creating a microbial hotspot at the oxic-anoxic interface. To investigate these processes, incubation studies linking CO₂ and CH₄ production to the reduction of POM_ox are indispensable. Here, we present data strongly indicating that POM collected from ombrotrophic bogs in Sweden functions as TEA in anaerobic respiration, suppressing methanogenesis. We ran anoxic incubations with various initial ratios of oxidized and reduced POM and hence a range of starting electron accepting capacities, which we quantified using a novel spectrophotometric assay. Increasing contributions of POM_ox resulted in higher CO₂:CH₄ production ratios and prolonged transition times from anaerobic respiration to methanogenesis. These findings strongly support the use of POM as TEA, suppressing methanogenesis until POM_ox was depleted through respiration. Additionally, we developed an incubation system that allowed amending incubations with ¹³C-labeled substrates to selectively track their conversion to ¹³CO₂ and ¹³CH₄. Using ¹³C-glucose we successfully linked ¹³CO₂ and ¹³CH₄ formation ratios to POM redox state. Our results advance our understanding of microbial carbon turnover in peatlands in the present and future climate.

How to cite: Schmitz, R. A., Obradović, N., Schroth, M. H., and Sander, M.: Particulate organic matter as electron acceptor for microbial respiration in peatlands, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-3290, https://doi.org/10.5194/egusphere-egu23-3290, 2023.

Peatlands are a globally important carbon sink, storing up to 455 Pg C as soil organic carbon. One of the drivers of this immense storage relates to the extremely low rate of peat decomposition, which is ultimately regulated by the bacterial community of these peat soils. Previous studies note that vegetation type (e.g., bog vs. fen), depth of peat, water level and pH may determine bacterial composition in peatlands. However, in terms of global patterns, the key controlling variables remain elusive due to a lack of data synthesis and direct experimental evidence. To identify bacterial community composition in global peatlands and key controlling variables, we conducted a field survey of 7 peatland sites in Korea, a meta-analysis of published data from over 95 peatland sites, and pH-manipulation experiments in the UK, by employing NGS analysis targeting 16sRNA.

Although immense variabilities in bacterial composition among sites were observed, pH appears to be a dominant controlling variable shaping bacterial community structure. For example, high pH is associated with higher relative abundance of Proteobacteria, while low pH appears to be related to the abundance of Acidobacteria. Variations of bacterial composition at different depths or vegetation types in a single site are smaller than those among different locations, suggesting that environmental changes in local conditions such as water level fluctuation and carbon availability may be less critical than the mean temperature or overall pH of a given site. Our study further suggests that the long-term changes in pH may have much greater implications than previously assumed, with peat decomposition likely to accelerate during the current recovery from acidification being experienced by peatlands across the world.

How to cite: Kang, H. and Freeman, C.: Patterns of bacterial composition in global peatlands and their controlling variables, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-4559, https://doi.org/10.5194/egusphere-egu23-4559, 2023.

Soil contains immense stocks of carbon, which may accelerate climate change if released. Soil microbes affect these carbon stocks by producing decomposition-catalyzing enzymes, a capacity varying across different microbial groups. Consequently, establishing links between global variation in microbial communities and functions should substantially enhance future projections of soil carbon. To this end, we here reveal global patterns in soil microbial community function using nearly 13,000 observations of microbial biomass, community structure, and enzyme activities (>100,000 measurements). We find total biomass and fungal and Gram-negative bacterial dominance increase with latitude, whereas Gram-positive bacteria predominate near the equator. Enzyme stoichiometry correspondingly suggests greater nitrogen and carbon limitation at higher latitudes. Comparing microbial and enzyme patterns, fungal biomass indicates nitrogen limitation, whereas Gram-negative bacterial biomass indicates carbon limitation. Together, microbial community structure explains significant variation in enzyme profile uncaptured by climate, soil properties, or landcover. Soil microbial communities dominated by fungi and Gram-negative bacteria exhibit less enzyme activity per unit biomass, with two- to four-fold variation in temperature- and biomass-normalized activity rate observed across the Earth. Significant functional differences thus arise with global turnover in microbial communities, indicating that community structure merits a central position in process-based soil models.

How to cite: Smith, G. R., van den Hoogen, J., Peay, K., Delgado-Baquerizo, M., Jackson, R., Yu, K., and Crowther, T. and the Soil Organisms Team: Global links between soil microbes and biogeochemical functions, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-10879, https://doi.org/10.5194/egusphere-egu23-10879, 2023.

Microbial explicit models are constructed by linking decomposition (the process of organic matter break-down) and substrate uptake to microbial growth, respiration, and mortality. Therefore, the specific choice of the decomposition and/or uptake kinetics affects how in the model microbes grow and die, with consequences for carbon stabilization. There are well-established theories for extracellular enzymatic reactions and for substrate transport and uptake by cells, which allow deriving formulas for the decomposition and uptake kinetics, respectively. These laws account for microbial growth (e.g., in the Monod equation), but implicitly assume that microbial traits encoded in model parameters are static. Yet, microbes adapt to the environmental conditions they experience, resulting in temporally dynamic traits at both population and community levels. Adaptation is a result of natural selection for the fittest organisms. Therefore, we can describe adapted microbes by assuming they maximize their growth for given environmental conditions (e.g., limiting the amount of available resources) and given metabolic tradeoffs (e.g., decreasing efficiency of substrate to biomass conversion at high growth rates). In this contribution, we translate this assumption into a formulation of decomposition as an optimal control problem, where the objective is the maximization of cumulative growth, the constraint is imposed via a substrate mass balance, and the control parameter is the realized substrate uptake rate, assumed to be the outcome of optimally adapted production of extracellular enzymes and cellular uptake capacity. This optimal control problem is solved analytically for a simple case study (one substrate, homogeneous microbial community), leading to optimal decomposition kinetics that scale with the square root of substrate carbon content (different from Monod or Michaelis-Menten equations) and with a strong effect of maintenance respiration. If maintenance respiration is high, the kinetics flattens, and the optimal decomposition rate remains larger than zero even as the substrate is depleted. This means that the optimal decomposition rate approaches zero-order kinetics and exhibits increasingly high values as maintenance costs are increased. Interestingly, a tradeoff emerges between the rate of substrate consumption at the beginning of decomposition and microbial carbon use efficiency (ratio of growth over uptake). At high resource availability, efficient but slow-growing microbes are selected, whereas at low resource availability inefficient but fast-growing microbes are favored because they can more effectively compete for the limited resources. These results suggest that optimization methods offer an alternative way to define decomposition kinetics laws that account for microbial adaptation.

How to cite: Manzoni, S., Chakrawal, A., and Ledder, G.: Decomposition kinetics as an optimal control problem, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-2918, https://doi.org/10.5194/egusphere-egu23-2918, 2023.

Microorganisms catalyze almost all transformation processes of organic carbon in soil and are largely responsible for changes in soil carbon cycle feedback to climate change. To account for the microbial role in regulation of carbon-climate feedback, several dozens of microbial models have been developed in the past decades, mostly based on an idea that microbial biomass or microbial extracellular enzymes control decomposition of soil organic carbon (SOC). However, these idea-based models may or may not be well supported by empirical evidence. This presentation will show how data have been used to develop and test microbial models with three case studies. The first case study is to infer microbial mechanisms from observed patterns of lignin decomposition. Our study indicates that time-dependent growth and mortality of the microbial community, instead Michaelis-Menten kinetics, control microbial decomposition of lignin. The second case is to incorporate observed mechanisms into a carbon cycle model. Our meta-analysis indicates that changes in SOC under experimental warming and nitrogen addition are closely related to changes in microbial oxidative enzyme activities but not in hydrolytic enzyme activities. We directly incorporated this observed mechanism into a terrestrial ecosystem model to predict SOC changes. The third case study is to confront microbial models with nearly 58,000 vertical profiles of SOC over the globe to identify mechanisms underlying global SOC storage. Overall, scientists have developed different microbial models to explore all kind of possibilities while data offer reality. The data-model integration helps identify the most probable mechanisms under a Bayesian inference framework.

How to cite: Luo, Y.: Data-driven approaches to soil microbial modeling, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-1751, https://doi.org/10.5194/egusphere-egu23-1751, 2023.

Describing the coupling of nitrogen (N), phosphorus (P), and carbon (C) cycles of land ecosystems requires understanding microbial element use efficiencies of soil organic matter (SOM) decomposition. These efficiencies are studied by the soil enzyme steady allocation model (SESAM) at decadal scale. The model assumes that the soil microbial community and their element use efficiencies develop in a way that maximizes the growth of the entire community. Specifically, SESAM approximated this growth optimization by allocating resources to several SOM degrading enzymes proportional to the revenue of these enzymes, called the Relative approach. However, a rigorous mathematical treatment of this approximation has been lacking so far. 

Therefore, this study derives explicit formulas of enzyme allocation that maximize total return from enzyme reactions, called the Optimal approach. When comparing predictions across these approaches, we find that the Relative approach is a special case of the Optimal approach valid at sufficiently high microbial biomass. However, at low microbial biomass, it overestimates  allocation to the enzymes having lower revenues.

The model finding that a smaller set of enzyme types is expressed at low microbial biomass provides another hypothesis for why some substrates in soil are preserved over decades although being decomposed within a few years in incubation experiments. This study is another step in integrating a simple representation of an adaptive microbial community into coupled stoichiometric CNP SOM dynamic models. 

How to cite: Wutzler, T., Ahrens, B., and Schrumpf, M.: Stoichiometrically constrained soil microbial community adaptation modeled with SESAM, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-5249, https://doi.org/10.5194/egusphere-egu23-5249, 2023.

How to cite: Khurana, S., Abramoff, R., Bruni, E., Guenet, B., Tupek, B., and Manzoni, S.: Disentangling the effects of microbial functional diversity and carbon availability on soil organic carbon decomposition, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-5847, https://doi.org/10.5194/egusphere-egu23-5847, 2023.

Soil is organizationally complex and spatially heterogeneous with exceptional microbial diversity that varies in time and space. Hotspots of microbial activity are prevalent, yet they are patchy and periodic and it remains intractable to represent this level of detail in macro-scale soil microbial models. Most macro-scale microbial models have, therefore, been focused on exploring theory and capturing select processes in a simplified way. However, effective equations that account for population- and community-level controls may be needed to suitably capture emergent feedbacks at macro-scales. In this study, we explore the effective relationships that emerge between spatially aggregated carbon pools in a micro-scale soil model with competition and space constraints. Specifically, we use an individual-based, spatially explicit model to simulate the response of soil microbes to a range of scenarios with increasing carbon inputs, including spatially-uniform (homogeneous) and spatially-clumped (heterogeneous) increases, where the input flux integrated over the total area is the same in both scenarios. The latter is meant to mimic hotspots of carbon inputs, for example, in the rhizosphere or near preferential flow paths. We find that competition between microbes and the probability of invasion from neighboring microsites plays a critical role in emergent density-dependent dynamics of microbial growth and turnover. Our study elucidates the role of population-level controls on microbial turnover at macro-scales, and motivates careful consideration of scale-dependent model representations. 

How to cite: Georgiou, K., Guseva, K., Pett-Ridge, J., and Kaiser, C.: Modeling population-level controls on soil microbial turnover across scales, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-10998, https://doi.org/10.5194/egusphere-egu23-10998, 2023.

Soil is the largest terrestrial carbon reservoir and processes leading to carbon sequestration play a crucial role in quantifying size as well as changes of this important pool. Microorganisms transform plant residues to smaller organic compounds, and often necromass is assumed to be the main stable end product. The turnover of microbial biomass at end of life, however, is only one pathway by which microorganisms contribute to soil organic matter. As a proof-of-concept, we use a mechanistic modeling approach with Monte Carlo simulation of 10,000 iterations, where input parameters vary according to values derived from literature. Bacterial growth follows a Monod kinetic, and biomass is further transformed to exudates, waste, and exo-enzymes, which vary in their C:N ratios. Assuming abundant N-resources, bacterial necromass contributes with 23.2% (median) of organic carbon only a minor portion to microbially-derived soil organic matter at the end of the simulation of 72 days. Most of the microbially derived organic carbon originates as part of metabolism by a combination of exudation (median 39.0%), wastes such as for osmotic regulation (median 22.4%), and exoenzyme production (median 10.3%). The organic product yields vary by about 300% between anabolic stages six days after substrate additions compared to catabolic stages at the end of the simulation. Predictions and management of soil organic carbon sequestration should therefore be based on carbon input through microbial metabolism rather than assumptions of carbon input solely at end of life.

How to cite: Dathe, A., Lynch, L., Woolf, D., and Lehmann, J.: The importance of bacterial metabolism contribution to soil organic carbon revealed by Monte Carlo simulations, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-14428, https://doi.org/10.5194/egusphere-egu23-14428, 2023.

Ecosystem priming is a critical process contributing to the carbon balance of tundra soils. On one hand, plant exudation of labile organic compounds can stimulate microbial activity inducing the decomposition of more complex organic matter, resulting in soil carbon loss. On the other hand, the efficient processing of plant exudates, and stabilization of microbial necromass in soils, can increase soil carbon stocks, reducing CO₂ emissions to the atmosphere. The divergence between positive and negative priming depends on ecosystem stoichiometry, microbial trait distribution, climate, and non-linear interactions between plants and microbial activity. Here we employ a mechanistic model, ecosys, to examine the role of microbial trait distribution and plant-microbe interactions in determining priming effects on tundra soil carbon stocks. The ecosys model represents distinct functional guilds of bacteria (e.g., heterotrophic decomposers, nitrifiers) and fungi (e.g., mycorrhizae and saprotrophs), and the diversity within, as a function of their traits, including carbon use efficiency (CUE). We examine the role of priming in short- and long-term experiments. We initially benchmarked the ecosys model to well-studied sites in the North American Arctic and explore how diversity in microbial CUE regulates soil carbon stocks under different priming conditions (e.g., a single application of labile carbon vs. semi-continuous exudation conditions) over the course of one year. We then scale up these simulations to the whole of Alaska and examine how plant-microbe interactions alter the priming effect over centennial time scales, with and without warming. We generally observed the attenuation of the priming effect contingent upon elevated nutrient concentrations under warming, which reduced plant exudation to soils. We will discuss these results, and how microbial traits influence the long-term balance of soil carbon in tundra ecosystems. 

How to cite: Bouskill, N., Riley, B., Li, Z., and Mekonnen, Z.: Long-term plant-microbe interactions weaken the rhizosphere priming effect in tundra systems, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-9924, https://doi.org/10.5194/egusphere-egu23-9924, 2023.

Soil organic carbon (SOC) is the largest terrestrial carbon pool, but it is still uncertain how it will respond to climate change. Especially the fate of SOC due to concurrent changes in soil temperature and moisture is uncertain. It is generally accepted that microbially driven SOC decomposition will increase with warming, provided that sufficient soil moisture, and hence enough C substrate, is available for microbial decomposition. We use a mechanistic, microbially explicit SOC decomposition model, the Jena Soil Model (JSM), and focus on the depolymerization of litter and microbial residues by microbes. These model processes are sensitive to temperature and soil moisture content and follow reverse Michaelis-Menten kinetics. Microbial decomposition rate V of the substrate [S] is limited by the microbial biomass [B]: V = V_max * [S] *  [B]/(kM_B + [B]). The maximum reaction velocity, V_max, is temperature sensitive and follows an Arrhenius function. Also, a positive correlation between temperature and kM_B-values of different enzymes has been empirically shown, with Q10 values ranging from 0.71-2.80 (Allison et al., 2018). Q10 kM_B-values for microbial depolymerization of microbial residues would be low compared to those of a (lignified) litter pool. An increase in kM_B leads to a lower reaction velocity (V) and V becomes less temperature sensitive at low substrate concentrations. In this work we focus on the following questions: “how do temperature and soil moisture changes affect modelled heterotrophic respiration through the Michaelis-Menten term? Is there a temperature compensation effect on modelled decomposition rate because of the counteracting temperature sensitivities of V_max and kM_B?” We model these interactions under a mean warming experiment (+3.5 °K) as well as three soil moisture experiments: constant soil moisture, a drought, and a wetting scenario.

How to cite: Pallandt, M., Ahrens, B., Schrumpf, M., Lange, H., Zaehle, S., and Reichstein, M.: Modelling climate-substrate interactions in microbial SOC decomposition, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-6112, https://doi.org/10.5194/egusphere-egu23-6112, 2023.

Empirical soil models reproducing soil characteristics can help to reduce the inherent complexity of soils in experiments. Microengineered or microfluidic soil chips can simulate the soil pore space at microscale in a transparent material that enables direct visual investigation of soil- and soil microbial processes including monitoring of single cells and their interactions in communities. Through the chips it is possible to control and closely monitor microhabitat conditions including oxygen levels and pH, and to single out factors such as spatial relations, pore space structure or resource patch size. They can be designed either close to realistic conditions such as based on µCT measurements, or using simple geometrical patterns that can be frequently replicated and modified within the chip design. They can thus be tailored to fit scenarios of spatially explicit soil computer models and used for iterative in-silico – in-situ experiments. We found amongst others that the geometric shape of a pore space and its connectivity influences bacterial and fungal growth, their interactions and enzymatic activity. We can measure those factors spatially resolved at cellular scale.  We want to initiate a discussion for future collaborations between soil chip experimentalists and computer modelers.

How to cite: Hammer, E., Ohlsson, P., and Zou, H.: Uniting microbial modelling with microfluidic soil chips, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-14803, https://doi.org/10.5194/egusphere-egu23-14803, 2023.

During decomposition of organic matter, soil microbes determine the fate of C. They partition C between anabolic biosynthesis of various new microbial metabolites (i.e. C reuse) and catabolic C emissions (i.e. C waste, mainly through respiration). This partitioning is commonly referred to as microbial carbon-use efficiency (CUE). The reuse of C during biosynthesis provides a potential for the accumulation of microbial metabolic residues in soil. The microbial metabolic performance is a key factor in soil C dynamics, because the vast majority of C inputs to soil will – sooner or later – be processed by soil microorganisms. Soil C inputs will thus be subjected to microbial allocation of C towards reuse or emitted waste, with the former leading to C remaining in soil. Recognized as a crucial control in C cycling, microbial CUE is implemented – implicitly or explicitly – in soil C models, which react highly sensitive to even small changes in CUE. Due to the models’ high sensitivity, reliable soil C projections demand accurate CUE quantifications, capturing unambiguously all metabolic C fluxes.

The current concept of microbial CUE neglects microbial maintenance which could make up considerable parts of the microbially processed C. Commonly, CUE is quantified from C incorporated into biomass or used for growth and C released as CO₂. Extracellular metabolites, such as polymeric substances (EPS), exoenzymes or nutrient mobilizing compounds, as well as intracellular maintenance metabolites, such as storage compounds or endoenzymes, are ignored although they represent microbial metabolic C reuse and thus C remaining in soil.

Based on theoretical considerations and a case study for EPS production, we will demonstrate that neglecting microbial maintenance can have severe impact on estimation of terrestrial C storage. For instance, ignoring measured EPS production (of a quantity of C which equals 37 % of the C used for growth) causes a substantial underestimation of CUE. Here, current approaches of CUE provide an apparent CUE of 0.20 while disregard an actual CUE of 0.25 (i.e. CUE is 25 % higher when maintenance metabolism is considered). Based on our findings, we suggest an adjustment of how we conceptualize and calculate microbial CUE in soils.

How to cite: Bölscher, T., Brunn, M., Colombi, T., Domeignoz-Horta, L. A., Herrmann, A. M., Meurer, K. H. E., Olagoke, F. K., and Vogel, C.: Beyond growth? The significance of microbial maintenance for carbon-use efficiency in the light of soil carbon storage, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-7550, https://doi.org/10.5194/egusphere-egu23-7550, 2023.

Soil microbes are key players in the cycling of soil organic carbon. In the complex soil system, microbes are faced with multiple stresses and trade-offs. In order to build biomass and proliferate, microbes have to mine accessible substrate and simultaneously have to survive abiotic stresses such as dry conditions. How they allocate carbon to the production of microbial biomass, extracellular enzymes, or biomolecules that help resist abiotic stresses is an important control of soil organic carbon fate. High carbon use efficiency fuels the build-up of microbial necromass, while increased production of exoenzymes might accelerate the breakdown of particulate organic matter. Production of additional biopolymers needed to sustain metabolic activity under stress – e.g., the production of osmolytes for maintaining turgor pressure in drying soils – poses an additional carbon cost that trades-off with the production of biomass and extracellular enzymes. Here we propose a conceptual model of soil carbon cycling with an explicit representation of these microbial allocation trade-offs. The model resolves physical processes such as saturation dependent substrate diffusion and is formulated at steady-state. It is based on the premise that microbes are optimally adapted to the environment they inhabit – meaning that the allocation trade-offs between the production of biomass, extracellular enzymes, and biomolecular stress response are adapted to maximize the microbial growth rate under these conditions. Using this conceptual model, we investigate how microbial allocation traits (fraction of carbon taken up and allocated to new biomass, extracellular enzymes, or osmolytes) might vary over a range of environmental conditions. Optimal allocation of carbon leads to increased investment in extracellular enzymes when carbon is scarce, and to progressively higher investment in osmolytes in drier conditions. While these trends are somewhat expected, the model predicts (rather than prescribing) the sensitivity of these allocation traits to changes in soil moisture and available carbon as a consequence of the optimality assumption. We conclude by exploring what implications these results might have for soil organic carbon fate.

How to cite: Schwarz, E., Belyazid, S., and Manzoni, S.: Implications of optimal resource allocation in soil microorganisms, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-7245, https://doi.org/10.5194/egusphere-egu23-7245, 2023.

Climate change is turning soil salinization into a global problem due to the increasing frequency and severity of coastal salt and brackish water ingress. How increasing salinity affects microbial metabolic activity and its consequences for matter and energy turnover under climate warming remain unclear. Thus, we conducted a lab incubation experiment to explore the interactive effects of salinization and warming on microbial and enzymatic functional traits related to the CO₂ (matter) and heat (energy) losses in the course of glucose metabolism.

Soil from coastal grassland was artificially salinized to, middle (2.06 mS cm^-1) and high (3.45 mS cm^-1) levels by gradually adding salt solution, while the soil with ambient salinity (0.49 mS cm^-1) was defined as control. Effect of realistic warming (+2 ℃) on CO₂ emission and heat release from soil amended with glucose was estimated by the respirometer Respicond V and microcalorimeter TAM Air, respectively. Energy and carbon use efficiency, calorespirometric ratio, microbial growth parameters and enzyme kinetics were determined in the salinity gradient.

Despite cumulative CO₂ emission and heat release were not affected by soil salinity, we observed gradual delay in glucose induced respiration (GIR) and heat release with the increasing salinity level. In contrast, warming facilitated both GIR and heat release, and increased the cumulative CO₂ by 8-14%, but had no effect on the cumulative heat.

Before glucose addition, high salinity greatly reduced the C-acquiring enzyme activities (β-D-glucosidase, cellobiohydrolase) by 17-39% compared with control, while an activity of the P-acquiring enzyme (acid phosphomonoesterase) notably increased by 24 and 82% under middle and high salinity, respectively. In soil activated with glucose, high salinity greatly increased the activities of both C- and P-acquiring enzymes up to 74 and 30%, respectively, compared with control. Surprisingly, irrespectively of microbial activation by glucose, the N-acquiring enzyme activity (leucine aminopeptidase) was not affected by salinity.

The interactive effect of soil salinity and climate warming on the fate of soil organic matter, energy and carbon use efficiency, calorespirometric ratio and microbial community will be discussed in our presentation.

How to cite: Wang, S., Razavi, B., Spielvogel, S., and Blagodatskaya, E.: Response of soil organic matter turnover to soil salinization and climate warming, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-2882, https://doi.org/10.5194/egusphere-egu23-2882, 2023.

Soil microorganisms rely on coupled fluxes of carbon and energy from the decomposition of organic substrates to fuel their maintenance and growth requirements. This complex coupling depends on environmental conditions as well as the specific metabolic reactions carried out by the microbial community, but our understanding of the principles governing these dynamics is still limited. The joint analysis of both matter and energy fluxes and in particular the linkage of the microbial carbon and energy use efficiencies (CUE and EUE) during substrate turnover have the potential to elucidate the underlying metabolic pathways. However, such evaluations remain rare.

In this study, we present measurements of heat and CO₂ release from soil after batch input of glucose along with estimates of microbial biomass and community composition. The results reveal a temporal variation in the ratio of heat to CO₂ release (Calorespirometric Ratio, CR) that is inconsistent with simple aerobic decomposition of the substrate. In addition, we find that the dynamics are dominated by the growth of Firmicutes, whose relative abundance increases from 2 percent of initial biomass to almost 50 percent over the course of the incubation.

To interpret these findings, we developed a dynamic model of carbon and energy fluxes during growth on glucose. The model simulates aerobic respiration as well as anaerobic fermentation to lactate and acetate depending on the time-varying availability of O₂ and accounts for activation of the microbial population after initial dormancy. Model simulations capture the complex experimental CR pattern and suggest a gradual depletion of available O₂ and a concurrent shift to anaerobic pathways as the main driver of the dynamics. Given the widespread adaptation to anaerobic conditions found in prevalent members of the Firmicutes, this interpretation is consistent with the observed dominance of the phylum. Notably, model variants of lower complexity that do not include fermentation or increasing microbial activity fail to appropriately reproduce the measured CR and biomass.

These results highlight the potential of the joint analysis of matter and energy fluxes in a combined experimental and modeling approach. The evolution of CR over time revealed the presence of complex dynamics even in the simple case of glucose-amended soil samples and provided constraints on the metabolic processes behind those dynamics that align with the available biomass and community composition estimates. By considering the balance of multiple metabolic pathways as well as the concept of microbial activity, our findings offer a more detailed description of temporal microbial carbon and energy use that goes beyond the assumption of constant CUE and EUE. Such an approach will be essential for the investigation of more complicated transformations of organic matter in soil.

How to cite: Endress, M.-G., Chen, R., Blagodatskaya, E., and Blagodatsky, S.: Using the Calorespirometric Ratio to investigate the metabolism of a growing microbial community dominated by Firmicutes in glucose-amended soil, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-5268, https://doi.org/10.5194/egusphere-egu23-5268, 2023.

Microbial respiration in soils controls a key flux in the global carbon cycle, yet its sensitivity to warming remains uncertain. Respiration rates increase exponentially with rapid warming, but the response is dampened over time. Several possible mechanisms have been suggested to explain the response: taxon-level adaptation, changes to community composition and changes to community biomass. However, the role played by each mechanism has not been resolved. Here, we separate the relative importance of these mechanisms, finding that taxon-level adaptation has a larger role in controlling the dampening of the temperature sensitivity of community respiration rather than changes to community composition. We used a novel dataset of five taxa incubated simultaneously in monoculture and as a community across a range of temperatures in a controlled laboratory environment, which showed the expected dampening of community respiration. Taxon-level adaptation, changes to community composition and changes to community biomass were all observed, with a new mathematical model of taxon-level adaptation revealing that the dampening of taxon-level respiration was due to changes in maintenance respiration and cell mass. The importance of taxon-level adaptation in the dampening of community respiration response to temperature reconciles disagreement from previous studies and provides evidence for a robust representation of microbial processes in carbon cycle models.

How to cite: Millington, R., García, F. C., and Yvon-Durocher, G.: Adaptation dampens the response of microbial community respiration to temperature, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-802, https://doi.org/10.5194/egusphere-egu23-802, 2023.

It is well documented that microbial biomass increases during winter in cold mountain or tundra ecosystems, but the cause and mechanism of such accumulation is unclear. Results from a grassland in Iceland demonstrated that the microbial biomass carbon (MBC, measured by the fumigation-extraction method) increased in winter, while microbial DNA content remained constant. We thus hypothesized that this accumulation of microbial biomass during the cold season is driven by the decrease in temperature, that increases the carbon storage of individual cells, but not by an increase in microbial cell numbers.

To test this hypothesis, we conducted a laboratory incubation experiment with soils from a grassland in Iceland sampled before the onset of winter in early October (around 9 °C). We then exposed the soils to decreasing temperatures (0.5 °C, 3 °C, 6 °C and 9 °C) over five months. We analyzed microbial biomass carbon (MBC) and quantified the DNA content. Over the course of five months, we found higher MBC values at cool temperatures compared to warm conditions. As expected, cooling did not affect the DNA content, leading to a significantly higher MBC to DNA ratio when soils were incubated at 0.5 °C compared to 9 °C. This indicates that numbers of microbial cells did not change across temperatures, but that microbes at lower temperatures stored more carbon. We also found similar patterns in soils collected at different time points in the field. Furthermore, we estimated microbial DNA production, i.e., growth rates, by measuring the incorporation of ¹⁸O from labelled water into DNA. We observed lower microbial growth rates under field conditions in winter, indicating that increasing biomass carbon was not due to increased growth and that growth and turnover was balanced at all temperatures. Instead, we suggest that carbon uptake (which was decreased at lower temperatures) was less affected by cold temperatures than growth, so that microbial carbon could accumulate. We also verified this pattern in growth and carbon uptake rates with decreasing temperatures in the laboratory incubation experiment.

Decreasing growth (cell division) and turnover rates with decreasing temperatures, at a lower but sustained carbon uptake rate, suggest that the cell size of soil microorganisms may increase when exposed to cooling. We will show and discuss first results from measurements with a suspended microchannel resonator (SMR), that, together with microscopic imaging allows to assess the mass (size) of individual cells of microorganisms at different temperatures. 

How to cite: Gall, C., Fuchslueger, L., Schmidt, H., Söllinger, A., Borg Dahl, M., Tveit, A., Sigurdsson, B., Eichorst, S., Roller, B., and Richter, A.: Investigating the effect of temperature on growth and microbial biomass accumulation during winter, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-14657, https://doi.org/10.5194/egusphere-egu23-14657, 2023.

One of the major research foci of modern environmental sciences is the mechanism of carbon sequestration in the course of microbial decomposition of organic compounds in soil. Microorganisms decompose soil organic matter as a source of carbon, energy, and nutrients for their metabolism. The transformation process of various organic compounds in the soil is driven by competition between diverse microorganisms during several successional stages. The number, duration, and amplitude of which are dependent on substrate quality and quantity by regulating the tradeoff between fast but less efficient and slow but more efficient microbial taxa. In the frame of the Priority Program “Soil Systems”, funded by the German Research Foundation (DFG), we aim to study the relationships between substrate turnover rate, CO₂ release, heat production, and efficiency of microbial metabolism at various stages of microbial succession in the course of cellulose decomposition in a fertilized Haplic Cambisol soil. To link metabolism efficiency with microbial functional traits, the kinetic parameter of microbial enzymes and growth parameters are determined at different stages of microbial succession. This research will thus contribute to the elucidation of regulatory mechanisms of energy and matter turnover in soil.

How to cite: Dehghani Mohammad Abadi, F., Reitz, T., Schlüter, S., and Blagodatskaya, E.: Linking heat and matter turnover over microbial successional stages in the soil to substrate quality and quantity, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-11477, https://doi.org/10.5194/egusphere-egu23-11477, 2023.

The last two decades soil organic matter research developed rapidly, uncovering a central role of soil microorganisms in the sequestration and storage of soil organic carbon (C), especially through accumulation of their necromass. However, despite strong evidence that the so-called soil microbial carbon pump is an important process, the direct characterization of microbial necromass in soil is difficult to achieve, leaving the actual chemical composition and formation of necromass unresolved. To fill this knowledge gap, we compiled evidence from microbiological literature on the processes of microbial dying, here referred to as microbial death pathways (MDPs). We discuss how fungi and bacteria die in soil, regarding the causes of death but also the consequences for chemical composition of microbial necromass. Evidence from existing literature clearly shows that MDPs in soil microorganisms represent relevant processes that affect necromass composition and its subsequent fate. Depending on environmental conditions and the relative significance of different MDPs, cell wall : cytoplasm ratios increase, while nutrient contents and easily degradable compounds are depleted. Thus, microbial necromass does not equal microbial biomass. These insights on microbial necromass are relevant for our understanding of mechanisms underpinning biogeochemical processes: (i) the quantity and persistence of microbial necromass is also governed by MDPs, not only the initial  biomass composition; (ii) efficient recycling of nutrients in microbial biomass during MDPs may minimize nitrogen losses during the process of C sequestration; (iii) human-induced disturbances do not only affect microbial activity, but also necromass quantity and composition. We present evidence for this novel concept of MDP, showing that not only microbial growth, but also death drive the soil microbial carbon pump. Additionally, we show some first data on actual experiments with “real” microbial necromass based on these principles, and discuss possibilities to explore this topic in future research studies.

How to cite: Camenzind, T., Mason-Jones, K., Mansour, I., Rillig, M. C., and Lehmann, J.: Microbial necromass ≠ microbial biomass: Microbial death pathways affect soil organic carbon sequestration, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-16487, https://doi.org/10.5194/egusphere-egu23-16487, 2023.