Heterotrophic microorganisms decompose soil organic matter to assimilate organic compounds that provide energy and carbon for growth and maintenance. The growth of microbial communities is thus at the heart of the carbon cycle, and understanding how microbial growth is controlled is arguably of paramount importance for understanding global carbon cycling in the present and future climate. 

Most information on microbial growth comes from work with pure cultures (population level) or from studies of microbial community growth, while understanding the growth of individual microbial taxa in natural communities is poorly studied and understood. However, with the advent of new stable isotope probing techniques based on ¹⁸O from labelled water, it is now possible to look beyond the community level to the growth of individual populations of microorganisms in complex soil communities. In addition, recent advances in labelling growing microbial taxa without the addition of liquid water, the so-called ‘vapor qSIP', allow us to analyze microbial growth in complex communities without changing environmental conditions, a prerequisite for studying the behavior of microbial communities in climate change experiments.

We report here on two climate change experiments in which we performed taxon-resolved growth measurements under different environmental conditions. Our results show the following:

(1) Contrary to our expectations, changing environmental conditions (e.g., soil warming and drought) led to a change in the number of actively growing bacterial taxa, but not in their growth rates. Among other things, this challenges the paradigm developed from a plethora of measurements of microbial community growth that microbial physiology is accelerated by higher temperatures.

(2) Many microbial taxa were only actively dividing in specific climate change treatments, i.e., under specific environmental conditions. We conclude that the realized ecological niche of bacteria appears to be much smaller than community growth measurements suggest. Testing, for example, the temperature niche of individual populations (with presumably different functional traits) may therefore lead to very different predictions of soil functions in a future climate.

(3) Compared to estimates of total soil microbial community composition (e.g., amplicon sequencing of the 16S rRNA gene), the actively growing community is more sensitive to changes in environmental conditions, allowing a more accurate prediction of community structure in a future climate and its functional roles in biogeochemistry.

Overall, measuring taxon-resolved population growth rates of complex communities provides a novel, more nuanced and sophisticated picture of soil ecosystems, which may help to develop better predictions of structural and functional changes in microbial ecosystems in a future climate.

How to cite: Richter, A., Metze, D., Canarini, A., Fuchslueger, L., Schmidt, H., and Kaiser, C.: What taxon-specific growth measurements reveal about microbial growth strategies in natural soil communities, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-21168, https://doi.org/10.5194/egusphere-egu24-21168, 2024.

Soil microbes perform important functions in the soil organic carbon (SOC) cycle and soil microbial decomposition activity is a major determinant of the carbon budget of a soil. It is well-established that soil microbial physiology is directly affected by temperature and moisture. However, it is less clear to what extent the environmental setting (i.e. long-term climatic conditions, soil physicochemistry) vs. the microbial actors (i.e. soil bacterial and fungal community composition) control the cycling of SOC in the absence of strong direct physiological constraints such as temperature and moisture limitation.

To address this knowledge gap, we used 35 grassland topsoils (0 – 10 cm) from 10 WRB major soil groups along a north-south transect in Chile, which ranged from arid steppe to tundra. We compiled climatic data and relevant physicochemical soil properties, together with an in depth characterization of OM quality. We then incubated the soils for 1 week in conditions favorable for microbial activity (20 °C, 50 % of water holding capacity). After incubation, we quantified soil microbial carbon and nitrogen, enzyme kinetics of three groups of relevant extracellular enzymes, basal heterotrophic respiration as well as microbial growth rates and carbon use efficiencies by incorporation of ¹⁸O into DNA. In addition, we characterized the microbial actors by DNA extraction and Illumina barcoding of a region of the 16S rRNA gene (bacteria) and a section of the ITS region (fungi). Finally, to investigate how strongly the measured microbial SOC functions were linked with the environmental setting vs. the microbial actors, we applied three different cross-validated regression approaches.

The resulting data highlights the links between environment, microbial community composition and SOC cycle functions under conditions without direct temperature and moisture limitation. Our findings show that the environmental setting controlled the amount of microbial biomass, and in extension biomass dependent SOC cycle functions such as heterotrophic respiration. In  contrast, microbial community composition was a better predictor of SOC cycle functions that are independent of microbial biomass such as carbon use efficiency and relative microbial growth rates. These insights help to disentangle the roles of the environmental setting and the microbial actors in the context of microbial SOC cycle functions.

How to cite: Wasner, D., Schnecker, J., Han, X., Frossard, A., Zagal Venegas, E., and Doetterl, S.: Insights into the role of the environmental setting versus microbial actors for soil carbon cycling, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-8685, https://doi.org/10.5194/egusphere-egu24-8685, 2024.

Arctic climate warming will affect microbially-controlled nutrient cycling through elevated nutrient availability and changes in vegetation productivity and composition. Plant-derived C inputs will serve as a microbial energy and C source, while the inorganic N released from soil organic matter (SOM) could . Albeit controlled by different mechanisms, increased C and N availability may each stimulate microbes to degrade more SOM, creating positive climate change feedbacks. Simultaneously, microbes provide the main pathway to sequester and stabilize C and N in SOM through growth and subsequent necromass formation, termed the “microbial pump”, generating a negative climate change feedback. Combining estimates of microbial growth, biomass, and biogeochemical rates allows for the calculation of Carbon Use Efficiency (CUE) and Nitrogen Use Efficiency (NUE). Analyzing NUE relative to CUE may elucidate microbial resource limitation. Resultantly, NUE exceeding CUE indicates microbial N-limitation, and suggests that microbes sequester N in SOM. Conversely, CUE exceeding NUE suggests microbial C-limitation and points towards microbial C sequestration in SOM. In addition, the strength of the microbial C and N pumps can be estimated by assessing microbial growth along with microbial C and N retention times, providing insights into how long resources will be retained in the microbial biomass. These tools contribute to a comprehensive understanding of whether resources will be liberated through decomposition or sequestered via the microbial pump.

Here, we investigated microbial responses to changes in resource availability associated with future climate change in a subarctic tundra heath. We used additions of mineral N and litter in the field to mimic the effects of elevated nutrient availability and shrubification on microbial growth rates (radio-isotope tracing), C and gross N mineralisation rates (gas chromatography and ¹⁵N pool dilution methods, respectively), and microbial community size was estimated with phospholipid fatty acids.

We found that field N-fertilization generally decreased microbial NUE, and that the resulting NUE/CUE ratio was close to 1, thereby pointing towards alleviated microbial N-limitation. Field N-fertilization also accelerated N-cycling but had no significant effects on C retention times. Conversely, litter addition in the field led to NUE exceeding CUE, implying the induction of microbial N-limitation, and it slowed C turnover times, but had no significant effect on N turnover times. When N and litter were applied together, similar CUE and NUE values, but accelerated C and N turnover times were observed. Overall, fungal contribution to resource cycling diminished across all field treatments, evident from a reduced fungal-to-bacterial growth ratio compared to the control treatment.

These findings highlight that changes in nutrient availability impact microbial C and N cycling independently and emphasize that the microbial resource limitation may be altered by the substrate stoichiometry. Additionally, our results suggest that while microbial N cycling is likely to accelerate, thus weakening the microbial N pump, microbial C cycling may be impeded and microbial C pump strengthened. Overall, these observations align with projections of more fertile and productive subarctic ecosystems in the future, and underscore the potential for microbial C sequestration even under altered resource availability. 

How to cite: Rzepczynska, A., Rousk, J., and Hicks, L.: Changes in the microbial control of C and N cycling in future subarctic tundra soils, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-15875, https://doi.org/10.5194/egusphere-egu24-15875, 2024.

Comprehending the factors influencing microbial carbon use efficiency (CUE), and where CUE is most optimal to soil organic carbon (SOC) storage, are crucial for managing microbial roles in SOC sequestration and model prediction. Yet, establishing a direct mathematical relationship between CUE and SOC might be challenging, with global distributions and controls remaining unresolved, particularly in response to various global changes. Here, we leverage a global synthesis of CUE measurements by ¹⁸O-microbial DNA growth, and observed an average CUE across all biomes at 0.3, with the highest in temperate grasslands and deeper soils, and the lowest in tropical forests. Random forest analysis identified climates (aridity index and mean annual temperature: MAT) and soil properties (pH, bulk density and soil C:N ratio) as primary drivers influencing CUE. However, microbial biomass size overall exhibited a smaller effects on CUE, despite its substantial impact in each land use type. We then review how these drivers affecting CUE values may be altered by warming, soil fertilization, altered precipitation and elevated carbon dioxide. Notably, nitrogen additions plays a big role in increasing CUE and promoting SOC contents, while warming effects depend on time-scale, with long-term warming potentially leading to SOC losses with a lower CUE and growth. Moreover, we found that the CUE–SOC relationship varies across different climates, greatly driven by MAT and soil properties. Higher CUE promots SOC per fine fraction (clay+silt) across the major data points, contrasting with a negative relationship in a subarctic study, where pH is the primary determinate. Consequently, there might be no simple linear relationship between CUE and C in microbial biomass and soil. We conclude by discussing the integration of CUE into SOC models and the necessity of incorporating interactions between CUE and individual drivers for predicting soil carbon-climate change scenarios. Our study underscores the importance of considering microbial CUE and other microbial processes for improving projections of SOC dynamics.

How to cite: Bi, Q.-F., Ahrens, B., Wutzler, T., Reichstein, M., and Schrumpf, M.: Global distribution and drivers of microbial carbon use efficiency for projecting soil organic carbon fates under a changing climate: A meta-analysis, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-19075, https://doi.org/10.5194/egusphere-egu24-19075, 2024.

Soil organic matter is the largest carbon (C) pool in terrestrial ecosystems, and it is largely composed of microbial necromass. Microbes contribute to the long-term C storage in soils by incorporating C from plants into their biomass and, consequently, microbial necromass becomes stabilized mostly in mineral associated organic matter. So far, most studies have focused on tracing microbial necromass using amino sugar biomarkers, while plant contributions to soil organic matter are predominantly traced using lignin or long-chain alkanes. Glucosamine and muramic acid are amino sugars commonly used as biomarkers of fungal and bacterial necromass, respectively. Amino acids, such as D-enantiomers and non-proteinogenic amino acids have also been used though rarely as microbial and/or plant necromass tracers. For instance, meso(D,L)-diaminopimelic acid can be found in the peptidoglycan peptide chain of gram-negative bacteria, while hydroxyproline is commonly found in glycoproteins of plant cell walls. Currently, only very few studies have measured amino sugars alongside primary and secondary amino acids as biomarkers of plant and microbial necromass. In this study, we propose a new method that allows the simultaneous exploration of microbial and plant residue biomarkers using a single run via 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) derivatization, followed by ultra-high performance liquid chromatography (UHPLC) and Orbitrap high resolution mass spectrometry. For this, we analysed 121 species of archaea, bacteria, fungi and plants. We were able to quantify amino acids and amino sugar biomarkers in the biomass of all taxonomic groups, as well as compare how these biomarker contents varied between broad taxonomic groups. We confirmed the biomarker potential of non-proteinogenic amino acids and amino sugars using indicator species analysis as well as supervised multivariate approaches, such as random forest and partial least squares discriminant analysis (PLS-DA). Our results showed that hydroxyproline is a biomarker specific for plants, while L,L-diaminopimelic acid can be used alongside muramic acid as biomarkers specific for bacteria. Talosaminuronic acid represents a biomarker specific for archaea, while glucosamine was a biomarker indicative of archaea, bacteria and fungi, being absent in plants. Our results showcase an unparalleled approach to trace both plant and microbial contributions to soil organic matter which will help improve our understanding of how different organic matter sources contribute to soil carbon formation and stabilization. This approach also allows the quantitation of plant versus microbial contributions to the continuum from litter decomposition to soil organic matter formation though microbial processing, the contribution of plant, fungal and bacterial organic matter to mineral-associated organic matter (MaOM) versus particulate organic matter (POM), and to soil macro- and microaggregate formation.

How to cite: Salas, E., Gorfer, M., Bandian, D., Eichorst, S. A., Schmidt, H., Horak, J., Rittmann, S. K.-M. R., Schleper, C., Reischl, B., Pribasnig, T., Jansa, J., Kaiser, C., and Wanek, W.: Quantifying amino acid and amino sugar biomarkers in a single approach to estimate necromass from soil archaea, bacteria, fungi, and plants, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-5432, https://doi.org/10.5194/egusphere-egu24-5432, 2024.

Alpine biomes experience harsh environmental conditions and short growing seasons, which necessitate interspecific and intraspecific interactions among plants and soil microbes to ensure the stability of diversity and ecosystem multifunctionality. With strong seasonal dynamics in alpine regions, including snow cover, snowmelt, and drought, “hot moments” of biogeochemical activity occur when pulses of nutrients dictate microbial processes across the biome. However, within the rhizosphere, microbial processes are promoted or deterred during phases of plant growth, senescence, and nutrient allocation, leading to a more nuanced seasonal pattern of soil microbes. Indeed, these factors lead to a general microbial phenology of soil processes and community composition. Yet, shifted climatic regimes due to warming likely cause these relationships to be strained, potentially resulting in physiological stress among plants and microbes. Therefore, our research focuses on the coupling or decoupling of plant and microbial parameters across seasonal changes in the Austrian Alps by assessing stoichiometric ratios of shared nutrients such as carbon (C), nitrogen (N) and phosphorus (P), along with microbial diversity. 

Using elevation gradients, the corresponding influence of plants, soil chemistry, and environmental conditions upon microbial phenology can be assessed in two different biomes: undeveloped subnival zones and nutrient-rich alpine meadows.  Furthermore, by combining methods for assessing biological soil parameters, such as chloroform fumigation extraction, enzymatic assays, and respiration measurements, with amplicon DNA sequencing, we can observe broad microbial community responses such as increased biomass (C_mic) in different seasons related to plant-specific interactions while identifying microbial taxa (fungal and bacterial) that indicate nutrient limitations in conjunction with ratios of enzymatic activity. Additionally, by measuring plant nutrient concentrations in distinct plant organs, we can infer which physiological processes among plant species most closely correspond with changes in broad microbial parameters and rhizosphere diversity.

Therefore, we propose that certain aspects of microbial phenology are generalizable, such as increased N cycling during winter and spring months, while the temporal optima for C cycling is more plant-specific. Furthermore, we present results from the rarely studied snow-covered winter months, in which the mineralization of C, P, and chitin degradation are highest. In total, these studies demonstrate a thorough analysis of plant-microbial interactions in alpine ecosystems which are subject to significant change within the coming decades.

How to cite: Ruka, A. T., Schweichhart, J., Doležal, J., Čapková, K., Meador, T. B., Angel, R., Calvillo Medina, R. P., Chlumská, Z., Lanta, V., Praeg, N., Illmer, P., and Řeháková, K.: Microbial phenology in high-alpine environments: the influence of plant dynamics and physiological stress in a changing climate. , EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-19954, https://doi.org/10.5194/egusphere-egu24-19954, 2024.

Bacterial communities that degrade chitin in soils often exhibit “social” behavior, where different strains fulfill different functional roles. “Degraders” produce extracellular enzymes that attack and cleave the complex biopolymer, releasing the monomer N-acetylglucosamine (NAG) as a public good. This compound can be readily taken up by both degraders and “exploiters”. The latter do not contribute directly to the degradation process but might in turn produce different substances that can be utilized by other members. “Scavengers” do not utilize NAG themselves but live mostly off metabolites secreted by the other strains. Our work aimed to investigate what effect the addition of a readily available C compound, like NAG, has on these interactions in such a system. Based on the results of a wet-lab experiment using a model bacterial consortium, we hypothesized that adding labile C leads to domination of the exploiter-strain though competitive exclusion. This in turn results in the breakdown of positive interactions, and a loss of diversity and functionality of the community. To further investigate this, we designed an ordinary differential equation (ODE) consumer-resource model, consisting of different linked pools representing the experiment. By parametrizing this model based on our respiration measurements and simulating the system over time, we were able to reproduce most of the observed experimental patterns in silico. When there was no NAG added to the system, the model matched the measured respiration when we included several positive interactions (such as crossfeeding or division of labor). This resulted in a more diverse community that degraded chitin more efficiently than the degrader-strain in monoculture. When NAG was added, the exploiter-strain outcompeted the other strains quickly, resulting in a loss of their potential function for the community. Through this combined experimental and modelling approach, our work shows that the addition of excess labile C to degrader communities in soil can alter interactions between bacteria, possibly leading to a loss of biodiversity and function.

How to cite: Mohrlok, M., Guseva, K., Alteio, L., Berger, J., Kaufmann, L., Mor Galvez, J., Sirbu, D., and Kaiser, C.: Labile substrate availability affects interactions and function in degrader communities: Insights from a combined experimental and modelling approach, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-15343, https://doi.org/10.5194/egusphere-egu24-15343, 2024.

Intracellular storage of carbon (C) by soil micro-organisms is emerging as a key process that influences soil biogeochemical cycling and the broader function of terrestrial ecosystems. One likely role of intracellular C storage is to serve as a stoichiometric buffer against nutritional imbalances in the microbial substrate. Such a function would make storage compounds vital to the long-term function of ecosystems associated with strongly weathered, low fertility soils, yet there have been few studies of intracellular carbon storage in such ecosystems. We examined the dynamics of two putative storage compounds (triacylglycerol [TAG] and polyhydroxybutyrate [PHB]) across two natural soil fertility gradients in eastern Australia. Across all sites and samples, absolute quantities of storage compounds ranged from 0 to 173 µg C g soil^-1 in the case of TAG and 0 to 56 µg C g soil^-1 for PHB. When standardized to total soil organic C, quantities of storage compounds tended to be markedly higher than those observed in prior studies of temperate and/or agricultural soils. Allocation to storage compounds followed strong trends across natural gradients of soil fertility and tended to peak in phosphorus-deficient and/or retrogressive ecosystems. Across soils of differing parent material, allocation to C storage was highest in infertile soils derived from phosphorus-depleted sandstone and ironstone compared to soils derived from shale and basalt. Likewise, allocation to C storage increased throughout ~700k years of soil development across a strongly weathered podzolic dune chronosequence. Dynamics of community-level C storage allocation were evidently underpinned by a combination of assemblage-level processes, most notably changes in the relative abundance of TAG-rich, C-limited fungal taxa, and physiological plasticity on the level of individual P-limited bacterial cells. Our findings are largely consistent with the surplus/reserve storage framework and highlight the importance of storage compounds for the function of oligotrophic ecosystems and as a major pool of C in soil.

How to cite: Butler, O., Manzoni, S., and Warren, C.: Dynamics of soil microbial carbon storage compounds in low fertility landscapes, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-17226, https://doi.org/10.5194/egusphere-egu24-17226, 2024.

Electron transfer reactions are central to the transformation of energy in the environment and play an important role in biogeochemical element cycling. In soils, one of the main drivers of carbon cycling is the activity of organisms that utilize the energy stored in soil organic matter by extracting electrons from organic carbon and transferring them to various electron acceptors. Yet, our understanding of this process is incomplete and the response of the soil carbon pool to climate change remains one of the primary sources of uncertainty in projections of atmospheric carbon dioxide concentrations.

Here, I discuss how we can track electron transfer reactions in soil and relate them to bioenergetic descriptors to elucidate controls on soil heterotrophic respiration. I will use two examples from my research to illustrate this:  first, I show how to characterize the redox properties of solid phase electron acceptors on the basis of reaction thermodynamics. I focus on iron minerals which are abundant solid phase electron acceptors in many soils. Using mediated electrochemistry, I quantified differences in the reactivity and energetics of synthetic iron minerals and variations in mineral redox properties during microbial mineral reduction. Second, I demonstrate how we can assess effects of mineral redox reactivity on anaerobic microbial respiration in a redox-dynamic floodplain soil. To this end, I link the kinetics of electron transfer to electron acceptors to the rate of microbial carbon dioxide production in a series of soil incubations. These two examples provide inspiration on how to integrate the redox reactivities and energetics of electron acceptors into bioenergetic frameworks.

How to cite: Aeppli, M.: Electron transfer reactions and their role in soil carbon cycling, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-10556, https://doi.org/10.5194/egusphere-egu24-10556, 2024.

Microbial turnover of organic substrates is a key process in soil organic matter formation and turnover. As microorganisms require both carbon and energy for growth and maintenance, carbon and energy fluxes in soils are tightly coupled. On the level of cellular metabolism, the substrates have to be allocated to catabolism and anabolism according to the requirements of the cells. In the soil system, additional processes have to be considered such as multiple substrate use, recycling of biomass components, interaction between different organisms and abiotic processes. As most of the energy flux in catabolism is created by the reduction of the terminal electron acceptors, the availability of the electron acceptors strongly affects carbon use efficiency and energy use efficiency. Here, we present a thermodynamic concept that combines experimental approaches of calorimetry and turnover mass balances paving the way for a better understanding of microbially mediated organic matter turnover and stabilization in soil.

Mass balances in soil systems need to be set up for exemplary substrates using isotope labelled compounds. They should be combined with information on energy fluxes, which can be obtained using calorimetric methods for thermodynamic calculations. Recently, calorimetric methods have been introduced into soil studies, e.g. differential scanning calorimetry or isothermal reaction calorimetry. Alternatively, enthalpies of combustion or formation must be known or estimated, e.g. based on the nominal oxidation state of the substrates and reaction products. All of these methods have their strengths and weaknesses, which need to be considered when assessing and interpreting the results. From a thermodynamic perspective, it is crucial to define the system boundaries and to use thermodynamic state variables such as reaction enthalpy, entropy and Gibbs free energy. If applied properly, the predictive power of thermodynamics can be fully utilized for process evaluation. In particular, this approach will enable us to identify whether a particular process is thermodynamically feasible or not under the given conditions.

In summary, linking mass balances and thermodynamics will allow us to better understand and predict soil organic matter turnover and sequestration.

How to cite: Miltner, A., Kästner, M., Maskow, T., Lorenz, M., and Thiele-Bruhn, S.: Thermodynamic control of microbial turnover of organic substrates in soils, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-8948, https://doi.org/10.5194/egusphere-egu24-8948, 2024.

Metabolic flux analysis is an integrated experimental and computational approach for quantitative understanding of biochemical reaction networks with particular relevance in systems biology. Mass and energy flows through soil microbial metabolism are subject to the laws of thermodynamics. Carbon (C) allocation through central metabolic pathways (e.g. glycolysis, pentose phosphate, and Entner-Doudoroff) can be reconstructed by ¹³C-labelling coupled to metabolic flux analysis (¹³C-MFA) by tracing specific C atoms from within substrate molecules into metabolic products such as carbon dioxide (CO₂) or fatty acids. However, mass flow calculated via ¹³C-MFA alone cannot fully characterise microbial carbon use. Here, we took the novel approach of coupling MFA with microcalorimetry, to also take bioenergetic constraints into account. We coupled energetics and mass flow on a metabolic level by selecting optimal sets of isotopomer tracers. Fifteen position-specific or uniformly ¹³C-labelled isotopomers - four alanine, seven glucose, and four glutamic acid ones – were added to a Luvisol (in total 4 folds of the microbial biomass C), and we analyzed substrate-derived ¹³CO₂ fluxes as well as heat dissipation via isothermal microcalorimetry.

Our results demonstrate that the temporal dynamics of catabolic CO₂ release resembles that of the heat dissipation, i.e. peak respiration and peak heat dissipation were reached approximately 18 h after substrate addition, irrespective of whether the substance entered the central metabolic pathway at the monosaccharide level (glucose), at the pyruvate level (alanine) or in the citric acid cycle (glutamic acid). This indicates that heat dissipation in the initial growth period was strongly dominated by catabolic processes. However, whereas ¹³CO₂ release leveled off during the 36 hours of incubation, the heat dissipation remained above its original level, suggesting that anabolic processes increasingly contribute to the heat dissipation in the later phases of incubation. Glucose isotopomer utilization indicated dominance of the pentose phosphate and Entner Douderoff pathways over glycolysis, suggesting a high activity of fast-growing organisms with considerable C allocation to anabolism. The dominance of this anabolic C use in the later stage of the incubation was confirmed by the isotopomer utilization of alanine and glutamic acid. This study shows that the heat dissipation of growing microbial communities under high C supply is closely linked to their catabolic CO₂ release, whereas slow, potentially recycling-based growth after resource depletion releases energy more via anabolic reactions. We furthermore demonstrated that coupled MFA and calorespirometry provides a powerful tool to differentiate among metabolic contributions to the energy use of soil microbial communities in different growth phases.

How to cite: Shao, G., Xu, X., Banfield, C. C., Shi, L., Mason-Jones, K., Wu, W., and Dippold, M. A.: Using metabolic flux modeling to disentangle anabolic and catabolic contributions to soil heat dissipation, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-18651, https://doi.org/10.5194/egusphere-egu24-18651, 2024.

Soil microbes obtain carbon (C), energy and nutrients from their environment to grow and to sustain themselves. Some of the matter and energy entering microbial metabolism leaves the soil system, e.g., as CO₂ and heat, while some is recycled via microbial death and turnover. All these matter and energy flows are intimately coupled according to stoichiometric relationships and the laws of thermodynamics, and unraveling the details of this coupling is essential for our understanding of soil functions mediated by microbes such as nutrient cycling and carbon storage.

The ratio of heat to CO₂ release, the so-called Calorespirometric Ratio (CR), obtained from soil incubation experiments with substrate amendment has been shown to hold valuable information about the major active metabolic pathways of the microbial community and the C and energy use efficiency. However, due to the complex and obscure nature of the soil system, measured CR values always require mechanistic models of the underlying processes for proper interpretation.

Here, we illustrate both the potential and the limitations of simple dynamic bioenergetic models for explaining experimental CR data and formulating testable hypotheses. For example, we highlight how such models may reveal shifts in metabolic pathways during growth and give clues about the dominant microbial sources of CO₂ and heat in the absence of easily degradable C substrates, e.g., during maintenance and turnover, based on observed temporal CR patterns.

At the same time, the CR framework and associated models face important challenges. First, the CR represents the black box sum of all heat and CO_2­ producing processes, and this complication can lead to different conclusions being drawn from the same data. Based on experiments with glucose amended soil, we explain how the CR pattern observed during the retardation phase after glucose depletion might be interpreted as resulting from either the decomposition of SOM or the formation of necromass or a combination of both. While this challenge prevents a definitive interpretation based on CO_{2 ­}and heat data alone, it can nonetheless play a vital role in informing and designing future experiments.

Second, evaluating the temporal patterns of the CR relies on synchronous measurements of heat and CO₂. In contrast, these two quantities are often measured separately in experiments, and their different diffusion rates may also cause a delay of CO₂ relative to heat in the case of simultaneous measurement. We demonstrate that even small shifts in the relative timing can cause a characteristic artificial pattern in observed CR data, with initially high CR values followed by a pronounced drop. We finally indicate how this issue may be accounted for in the structure of the dynamic models.

In summary, we present two major challenges – the black box nature of CR and shifts in relative timing – that arise from the interpretation of experimental rates of heat and CO₂ release using mechanistic dynamic models, and we show how these issues may be addressed, and even leveraged, to advance our understanding of microbial processes in soil.

How to cite: Endress, M.-G., Dehghani, F., Blagodatskaya, E., and Blagodatsky, S.: The potential and challenges of dynamic models for investigating microbial processes in soil using the Calorespirometric Ratio, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-7984, https://doi.org/10.5194/egusphere-egu24-7984, 2024.

The preservation of soil services and functions is sustained by the catalytic activity of microbial communities. These communities use energy and carbon – especially for microbial growth – from the transformation of organic matter (OM).  A fraction of this OM is assimilated as carbon source for growth (anabolism). Another fraction is oxidized and the resulting electrons are transferred to various terminal acceptors to derive the energy for growth (catabolism). The distribution of carbon and energy into anabolism and catabolism determines carbon use efficiency (CUE) and energy use efficiency (EUE). Accurate quantification of the relationships between carbon and energy fluxes relies on key parameters like the metabolic heat (Q_m),  calorespirometric ratio (CR), carbon dioxide evolution rate (CER), the apparent specific growth rate (μ_app), and the degree of anaerobicity (η_A).

However, determining these parameters faces challenges at technical (sample size and instrument sensitivity) and experimental (thermal disturbance, sample aeration) levels impacting the precise quantification of energy and carbon flux relationships. To address these challenges under controlled conditions, we examined microbial turnover processes in a model arable soil amended with a readily metabolizable substrate (glucose). We utilized three commercial isothermal microcalorimeters (IMC)  with volume-related thermal detection limits (LOD_V) ranging from 0.05 to 1 mW L^-1.

Comparison between three IMCs were conducted to figure out the influence of LOD_V on measuring accuracy. Calorimetric experiments (half ampoules were closed and half were aerated for 5 minutes on selected days) were compared to explore the effect of oxygen limitation and thermal perturbation on the calorimetric signal. CER was monitored by measuring the additional heat resulting from CO₂ absorption in NaOH solution used as CO₂ trap. The range of errors associated with calorimetrically derived μ_app, Q_m, and CR was determined experimentally and compared with the requirements for quantifying CUE and η_A from a theoretical perspective.

Significant differences in Q_m and µ_app were observed between IMCs which have the lowest and highest LOD_V. IMC with the lowest LOD_v provided the most accurate results. Opening ampoules for gas exchange did not significantly impact Q_m. However, regular ampoule opening during calorimetrically derived CER measurements led to notable measurement errors for CER due to strong thermal perturbation of the signal. If established models are used to calculate CUE and η_A from CR, unrealistically high values are obtained and the accuracy of CR do not fit to the requirements.

There are two ways to cope with this problem. On the one hand, new thermodynamic balance models need to be developed that dispense with the error-prone CR value. On the other hand, new calorespirometric methods must be developed to determine the CR value more reliably. Initial results for both approaches will be presented. 

How to cite: Maskow, T., Yang, S., Di Lodovico, E., Rupp, A., Fricke, C., Miltner, A., and Kästner, M.: Expanding Understanding: Investigating the Information Value of Calorespirometric Ratio in Dynamic Processes of Soil Microbial Growth Using Calorimetry, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-6520, https://doi.org/10.5194/egusphere-egu24-6520, 2024.

We developed a new concept of soil organic matter (SOM) formation and microbial utilization of organic carbon (C) and energy: microorganisms use most of the organics entering the soil as energy rather than as a C source, while SOM accumulates as a residual by-product because the microbial energy investment in its decomposition exceeds the energy gain. So, the energy use efficiency (EUE) is at least as important as the carbon use efficiency (CUE). The microbial EUE depends on the nominal oxidation state of carbon (NOSC) of organic compounds, which is the exact proxy of energy content: The energy content per C atom (enthalpy of combustion) increases by 108 kJ mol⁻¹ C per one NOSC unit. The NOSC in litter remaining by decomposition decreases, and the energy content increases. Consequently, the NOSC of the remaining compounds drops to −0.3 units, and the oxidation decreases due to the residual accumulation of aromatic and aliphatic compounds, and entombment of the necromass. Preferential recycling of energy-rich reduced (lipids, aromatics, certain amino acids, amino sugars) and the microbial degradation of oxidized compounds (carboxylic acids) enrich energy content in remaining SOM. This explains why SOM is not fully mineralized (thermodynamically unfavorable). Energy from litter activates decomposers to mine nutrients stored in SOM (the main function of priming effects) because the nutrient content in SOM is 2–5 times higher than that of litter. Thus, the energy captured by photosynthesis is the main reason why microorganisms utilize organic matter, whereby SOM is merely a residual by-product of nutrient storage and a mediator of energy fluxes. For the first time we assessed the NOSC of microbial biomass in soil (−0.52) and calculated the corresponding energy content of −510 kJ mol⁻¹ C, whereas bacteria contain less energy per unit of C than fungi. We linked CUE and EUE considering the NOSC of microbial biomass and element compositions of substrates utilized by microorganisms. The microbial EUE is always lower than CUE. This is one of the reasons why microbial growth is more limited by energy than by C. Based on the comparison of processes of C and energy utilization for cell growth and maintenance, we concluded that the two main mechanisms behind lower EUE versus CUE are: (i) microbial recycling: C can be microbially recycled, whereas energy is always utilized only once, and (ii) chemical reduction of organic and inorganic compounds: Energy is used for reduction, which is ongoing without C utilization.

Gunina A, Kuzyakov Y 2022. From energy to (soil organic) matter. Global Change Biology 28 (7), 2169-2182
Wang C, Kuzyakov Y 2023. Energy use efficiency of soil microorganisms: Driven by carbon recycling and reduction. Global Change Biology 29, 6170-6187

How to cite: Kuzyakov, Y., Wang, C., and Gunina, A.: From energy to soil organic matter, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-11690, https://doi.org/10.5194/egusphere-egu24-11690, 2024.

Mechanistic simulation models are essential tools for predicting soil functions such as nutrient cycling, water filtering and storage, productivity, and carbon storage as well as the complex interactions between these functions. Most soil functions are driven or affected by soil microorganisms. Yet, biological processes are often neglected in soil function models or only implicitly considered in form of unspecific, effective rate parameters. This can be explained by the high complexity of the soil ecosystem with its dynamic and heterogeneous environment, and by the range of temporal and spatial scales at which these processes take place.

We integrated different microbial processes and feedbacks into our systemic soil model BODIUM (König et al., 2023) and tested the sensitivity of soil functions such as productivity and nutrient cycling to these microbial aspects at the scale of soil profiles. This includes flexible C:N ratios, carbon use efficiency, nitrogen fixation, feedback with root exudation, and the dynamics of different functional groups such as fungi and bacteria. We observed a high sensitivity of our simulation outcomes to microbial parameters related to the microbial component, such as the exudation rate or fungal/bacterial resistance to environmental conditions. This shows the high relevance of microbial processes for soil functions at the field scale, but also indicates that the process description should be further improved.  In process-based models, a high sensitivity of parameters is often a sign for an instable process description relying too much on site-specific calibration instead of mechanistic understanding.

We will discuss how to improve this, but also further extensions, including an approach that accounts for the spatial distribution of microorganisms within the pore space.

König, S., Weller, U., Betancur-Corredor, B., Lang, B., Reitz, T., Wiesmeier, M., Wollschläger, U., & Vogel, H.-J. (2023). BODIUM—A systemic approach to model the dynamics of soil functions. European Journal of Soil Science, 74(5), e13411. https://doi.org/10.1111/ejss.13411

How to cite: König, S., Weller, U., Reitz, T., Diel, J., Wollschläger, U., and Vogel, H.-J.: It’s the little things that count – how microbial dynamics affect simulation results of the systemic soil model BODIUM, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-9988, https://doi.org/10.5194/egusphere-egu24-9988, 2024.

Understanding the turnover and stabilization of soil organic matter (SOM) is the key to highly productive agriculture and to climate change mitigation. Understanding and predicting biogeochemical matter and energy flows in soil systems is challenging due to persisting knowledge gaps regarding biological and energetic controls of SOM turnover and limited knowledge integration of informative data with process-based models. We present modeling concepts of microbially explicit soil organic matter models and shed light on integrating trait-based ecological frameworks in process-based models and the use of advanced data-model fusion approaches. We highlight some insights from applying process-based models and challenges we need to address to acquire robust predictions.

How to cite: Pagel, H., Streck, T., Sircan, A., and Manzoni, S.: Prospects and challenges of simulating organic matter turnover and stabilization in soil systems, EGU General Assembly 2024, Vienna, Austria, 14–19 Apr 2024, EGU24-16811, https://doi.org/10.5194/egusphere-egu24-16811, 2024.