SSS4.7 | Microbial growth, turnover and functioning in soils: modelling and experimental advances
EDI
Microbial growth, turnover and functioning in soils: modelling and experimental advances
Co-organized by BG3
Convener: Sergey Blagodatsky | Co-conveners: Albert C. Brangarí, Minsu KimECSECS, Hanbang Zou, Ksenia GusevaECSECS, Kyle Mason-Jones
Orals
| Mon, 24 Apr, 08:30–12:25 (CEST), 14:00–15:40 (CEST)
 
Room K2
Posters on site
| Attendance Mon, 24 Apr, 16:15–18:00 (CEST)
 
Hall X3
Orals |
Mon, 08:30
Mon, 16:15
Soil microorganisms decompose organic substrates to maintain their metabolic requirements and support growth. For growth and anabolic reactions, they require not only C and energy, but various nutrients (e.g., N and P) in stoichiometric relationships. Transformation of soil organic compounds therefore couples energy and matter flows via complex mechanisms dependent on environmental conditions and the intensity and efficiency of microbial metabolism. This coupling can be investigated from the perspective of microbial carbon use efficiency (CUE=ratio of biomass production to carbon substrate consumption), ecological stoichiometry, and microbial metabolic pathways. Elucidating the governing principles of energy and matter coupling is advancing through experimental work as well as modelling, with coupled matter and energy turnover now considered an essential feature of C cycling models.
This session invites experimental and modelling studies to understand how soil microbial life governs transformations of organic matter and the associated energy flows, with particular interest in growth, death, maintenance metabolism and necromass formation. In this context, this session also presents contributions on carbon and energy use efficiency as an indicator of microbial metabolism. These include CUE estimation in soil using advanced methods – isotope labelling, kinetic studies, isothermal calorimetry, and approaches disclosing the effect of microbial community composition and activity on CUE. We welcome innovative and interdisciplinary studies that are advancing the field of soil ecology from the understanding of biogeochemical processes to addressing global sustainability issues.

Orals: Mon, 24 Apr | Room K2

Chairpersons: Minsu Kim, Hanbang Zou
Spatial and temporal patterns of soil microbial activity
08:30–08:50
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EGU23-13193
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solicited
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On-site presentation
Naoise Nunan, Hannes Schmidt, Claire Chenu, Valerie Pouteau, and Xavier Raynaud

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.

08:50–09:00
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EGU23-8678
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On-site presentation
Oskar Franklin, Mark T.L. Bonner, Shun Hasegawa, and Torgny Näsholm

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.

09:00–09:10
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EGU23-13715
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ECS
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On-site presentation
Nelly Sophie Raymond, Federica Tamburini, Astrid Oberson, Jakob Magid, and Carsten Müller

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.

09:10–09:20
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EGU23-16359
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On-site presentation
Dmytro Yakovenko and Svitlana Korsun

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.

09:20–09:30
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EGU23-4445
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ECS
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On-site presentation
Nataliya Bilyera, Callum C. Banfield, and Michaela A. Dippold

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.

09:30–09:40
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EGU23-11025
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ECS
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On-site presentation
Peter Chuckran, Mary Firestone, Alexa M. Nicolas, Ella T. Sieradzki, Jennifer Pett-Ridge, and Stephen Blazewicz

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.

09:40–09:50
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EGU23-3290
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ECS
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On-site presentation
Rob A. Schmitz, Nikola Obradović, Martin H. Schroth, and Michael Sander

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 (POMox) 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 POMox 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 POMox 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 POMox 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.

09:50–10:00
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EGU23-4559
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On-site presentation
Hojeong Kang and Chris Freeman

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.

10:00–10:10
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EGU23-10879
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ECS
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On-site presentation
Gabriel Reuben Smith, Johan van den Hoogen, Kabir Peay, Manuel Delgado-Baquerizo, Robert Jackson, Kailiang Yu, and Thomas Crowther and the Soil Organisms Team

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.

Coffee break
Chairpersons: Albert C. Brangarí, Ksenia Guseva
Microbial models in soil science
10:45–11:05
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EGU23-2918
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solicited
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On-site presentation
Stefano Manzoni, Arjun Chakrawal, and Glenn Ledder

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.

11:05–11:15
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EGU23-1751
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On-site presentation
Yiqi Luo

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.

11:15–11:25
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EGU23-5249
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On-site presentation
Thomas Wutzler, Bernhard Ahrens, and Marion Schrumpf

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.

11:25–11:35
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EGU23-5847
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ECS
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On-site presentation
Swamini Khurana, Rose Abramoff, Elisa Bruni, Bertrand Guenet, Boris Tupek, and Stefano Manzoni

The factors governing stability of soil organic carbon vary from chemical characteristics to physical occlusion from either biotic (such as plant roots, soil fauna and microorganisms) or abiotic agents (such as water). By mediating the decomposition potential, microbial community diversity and structure may play an important role in the fate of soil organic carbon. In this theoretical study, we aim to understand the role of the microbial community diversity and composition in soil organic carbon storage and decomposition. 

We constructed a model describing a microbial process network incorporating diverse organic matter compounds and microbial groups. The microbial groups varied from each other with respect to their affinity to depolymerise, take-up, metabolise and assimilate organic compounds. We allowed for adaptation of microbial communities to available carbon, and competition among microbial groups.  We tested this process network with functionally diverse microbial communities which were subjected to varying carbon availability. This framework allowed us to explore organic carbon decomposition rates and their temporal evolution under different conditions of microbial diversity and carbon availability, as well as the tendency of a soil microbial system to store carbon. 

We found that the microbial community functional diversity is a good predictor of organic carbon decomposition rates. This result suggests that an  organic carbon decomposition rate modifier could be defined based on functional diversity and then included in soil carbon models. Furthermore, we observed that organic carbon decomposition by functionally similar communities in carbon poor conditions slowed down after approximately half of the initial carbon was consumed. In the same conditions, functionally diverse communities with a higher number of biotic agents allowed a more complete decomposition. However, with increasing initial carbon availability, the functional diversity of the microbial community ceased to play a role in soil carbon storage. These results link microbial community diversity and carbon availability to decomposition potential and thus organic carbon stability in soils.

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.

11:35–11:45
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EGU23-10998
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ECS
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On-site presentation
Katerina Georgiou, Ksenia Guseva, Jennifer Pett-Ridge, and Christina Kaiser

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.

11:45–11:55
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EGU23-14428
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On-site presentation
Annette Dathe, Laurel Lynch, Dominic Woolf, and Johannes Lehmann

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.

11:55–12:05
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EGU23-9924
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On-site presentation
Nicholas Bouskill, Bill Riley, Zhen Li, and Zelalem Mekonnen

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.

12:05–12:15
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EGU23-6112
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ECS
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On-site presentation
Marleen Pallandt, Bernhard Ahrens, Marion Schrumpf, Holger Lange, Sönke Zaehle, and Markus Reichstein

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 = Vmax * [S] *  [B]/(kMB + [B]). The maximum reaction velocity, Vmax, is temperature sensitive and follows an Arrhenius function. Also, a positive correlation between temperature and kMB-values of different enzymes has been empirically shown, with Q10 values ranging from 0.71-2.80 (Allison et al., 2018). Q10 kMB-values for microbial depolymerization of microbial residues would be low compared to those of a (lignified) litter pool. An increase in kMB 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 Vmax and kMB?” 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.

12:15–12:25
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EGU23-14803
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ECS
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On-site presentation
Edith Hammer, Pelle Ohlsson, and Hanbang Zou

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.

Lunch break
Chairpersons: Kyle Mason-Jones, Sergey Blagodatsky
Microbial growth and turnover in soils
14:00–14:10
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EGU23-7550
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ECS
|
solicited
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On-site presentation
Tobias Bölscher, Melanie Brunn, Tino Colombi, Luiz A. Domeignoz-Horta, Anke M. Herrmann, Katharina H.E. Meurer, Folasade K. Olagoke, and Cordula Vogel

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.

14:10–14:20
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EGU23-7245
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ECS
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On-site presentation
Erik Schwarz, Salim Belyazid, and Stefano Manzoni

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.

14:20–14:30
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EGU23-7901
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ECS
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On-site presentation
|
Julia Schroeder, Florian Schneider, Christoph C. Tebbe, and Christopher Poeplau

The efficiency by which soil microbes direct metabolised carbon to their growth, i.e. the microbial carbon use efficiency (CUE), is hypothesised to be driven by soil pH, nutrient stoichiometry and the microbial community composition (e.g. Fungi-to-Bacteria ratio). Despite extensive research it remains difficult to identify general trends in how these drivers affect CUE and results of individual studies often point in different directions. To unravel general trends, we aggregated a unique data set of samples analysed using the 18O-labelling technique - all derived from the same laboratory - to gain deeper insights into the relationship between CUE and pH, CN ratio and the relative abundance of domains (based on 16S and ITS gene copy numbers by qPCR). To date, the growing data set comprises 685 observations of 18O-CUE, including samples from 41 individual sites under three different land use types (forest, managed grassland, cropland) from tropical to subarctic climate. A Random Forest model and a linear mixed-effects model approach were used to analyse the data. Preliminary results on a filtered and aggregated subset (n= 221; aggregated to reduce the heterogeneity of the data set structure) suggest that the CUE is strongly dependent on soil pH, following a U-shaped curve. The relationship between CUE and pH was found negative for pH < 5.5 and positive for pH ≥ 6.5, while overall the CUE was found to be negatively correlated to soil C:N ratio. Additional data on climate (MAT, MAP), soil texture, and soil microbial community will complement the analysis.

How to cite: Schroeder, J., Schneider, F., Tebbe, C. C., and Poeplau, C.: General drivers of microbial carbon use efficiency in soils, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-7901, https://doi.org/10.5194/egusphere-egu23-7901, 2023.

14:30–14:40
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EGU23-2882
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On-site presentation
Shang Wang, Bahar Razavi, Sandra Spielvogel, and Evgenia Blagodatskaya

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.

14:40–14:50
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EGU23-5268
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ECS
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On-site presentation
Martin-Georg Endress, Ruirui Chen, Evgenia Blagodatskaya, and Sergey Blagodatsky

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.

14:50–15:00
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EGU23-12332
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ECS
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On-site presentation
|
Moritz Mohrlok, Lauren Alteio, Ksenia Guseva, Julia Mor Galvez, Erika Salas Hernández, and Christina Kaiser

Chitin decomposition involves different extracellular enzymes and intermediate products, giving rise to complex social dynamics within chitin-degrading communities. These communities are therefore an ideal model system to investigate how complex organic matter is decomposed in soil, and what effect microbial interactions have on the decomposition process. We used a synthetic consortium consisting of three unrelated, potentially chitin-degrading soil bacterial strains (Paenibacillus alginolyticus, Paraburkholderia xenovorans and Solirubrobacter soli) to investigate how their interactions affect the decomposition of chitin, and how the availability of labile carbon influences these interactions.

The strains were grown in monoculture and in all possible combinations on three different substrates (2% chitin, 2% n-acetylglucosamine (NAG, the monomer of chitin) and a mixture of 1% chitin and 1% NAG). Cumulative respiration as a community performance metric was measured over the course of two weeks using the MicroResptm system. We measured the concentration of chitin oligomers (chitobiose and chitotriose) at the endpoint using PMP-derivatisation and UPLC-Orbitrap MS. The final microbial community composition was assessed via 16s Amplicon sequencing and the 16s gene copy number was measured with droplet-digital PCR.

Depending on the substrate, each strain showed distinct respiration patterns in monoculture, indicating different functionalities. We found both competitive and synergistic interactions in the strain combinations, depending on the involved species and available substrate. P. xenovorans dominated the other strains whenever the labile substrate (NAG) was added. The relative abundance of the less competitive strains (P. alginolyticus and S. soli) was however increased in the treatment containing only chitin compared to the NAG-treatments. Chitin was degraded a lot more when all three strains were included, as shown by both the maximum respiration and chitobiose concentration. All three strains were still detectable in this treatment, which was not the case when NAG was present from the beginning.

Based on these results we assume that energy limitation forces synergistic interactions in this model community, increasing the chitin decomposition efficiency. Adding labile substrate alters these interactions, leading to the exclusion of less competitive strains. Our results emphasize how interacting bacteria of different functional groups can result in increased decomposition of complex soil organic matter and how the relationships between different species in a microbial community at a soil microsite might change based on the available substrate.

How to cite: Mohrlok, M., Alteio, L., Guseva, K., Mor Galvez, J., Salas Hernández, E., and Kaiser, C.: Labile substrate availability shapes interactions in a synthetic chitin-degrading soil bacterial community, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-12332, https://doi.org/10.5194/egusphere-egu23-12332, 2023.

15:00–15:10
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EGU23-802
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ECS
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On-site presentation
Rebecca Millington, Francisca C. García, and Gabriel Yvon-Durocher

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.

15:10–15:20
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EGU23-14657
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ECS
|
On-site presentation
Christoph Gall, Lucia Fuchslueger, Hannes Schmidt, Andrea Söllinger, Mathilde Borg Dahl, Alexander Tveit, Bjarni Sigurdsson, Stephanie Eichorst, Ben Roller, and Andreas Richter

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.

15:20–15:30
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EGU23-11477
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ECS
|
On-site presentation
Fatemeh Dehghani Mohammad Abadi, Thomas Reitz, Steffen Schlüter, and Evgenia Blagodatskaya

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.

15:30–15:40
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EGU23-16487
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On-site presentation
Tessa Camenzind, Kyle Mason-Jones, India Mansour, Matthias C. Rillig, and Johannes Lehmann

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.

Posters on site: Mon, 24 Apr, 16:15–18:00 | Hall X3

X3.76
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EGU23-6453
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ECS
|
Enrico Balugani, Simone Pesce, Celeste Zuliani, and Diego Marazza

The last decade has seen an increase of innovative soil carbon models that takes explicitly into account the microbial community interaction with the soil organic matter, and various state of protection of the soil organic matter itself. This proliferation is fuelled by (a) the recognition that microbial ecology is the main determinant of soil organic carbon mineralization, and (b) that soil organic matter can be protected from microbial degradation in various ways. Of particular interest is the interaction of the organic matter with the mineral fraction of the soil, which can lead to mineral adsorbtion and the formation of soil aggregates. However, the uncertainties about soil microbial ecology and organic matter – mineral fraction have led to the formulation of various soil microbial models, each one modelling some of the aspects of the complex net of interacting processes, but not other. These models often use different assumptions, model structures, and pool definitions. The lack of comparability among models, and the low comparability of models with measurable data, makes it hard to discriminate among them and to use them to assess the driving processes relevant for soil carbon dynamics depending on climatic, soil and vegetation conditions.

A first attempt to compare some of these models has been presented in Sulman et al. (2018); however, the lack of a harmonization framework for the models, and the use of lumped model pools/flows such as soil respiration and bulk soil organic carbon, have led to the conclusion that the uncertainties are too elevated to discriminate among the models.

Here, we propose a framework to harmonize five different soil microbial models among them (MEND, CORPSE, MIMIC, DEMENT, RESOM), and harmonize them with measurable soil organic matter fraction widely recognized as related to processes of interaction with the soil mineral fraction (aggregates, mineral associated organic matter, dissolve organic matter, and particulate organic matter). We reformulated the five models based on this framework, and analysed them on the same parameter space to understand in which regions of said space the models gave results that were substantially different.

The results show that: (a) the model can be clearly distinguished in most regions of the parameters space, (b) it is possible to calculate an index of robustness of the models. This information can help in design specific experiments to test the models and, this way, get insights about the driving processes in certain conditions (different climates, soils, vegetations); moreover, the robustness index can give indication about their applicability to different conditions, which is of utmost importance if they are to inform Earth System Models.

How to cite: Balugani, E., Pesce, S., Zuliani, C., and Marazza, D.: Numerical comparison of five soil microbial models, in relation to measurable soil organic matter fractions, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-6453, https://doi.org/10.5194/egusphere-egu23-6453, 2023.

X3.77
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EGU23-7231
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ECS
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Denise Vonhoegen, Ubaida Yousaf, and Sören Thiele-Bruhn

Recent studies of soil organic matter formation focus on energy and matter fluxes and their linkage to broaden the understanding of the processes and drivers underlying microbial turnover of organic carbon substrates in soil. In this study, which is part of the DriverPool project in the SoilSystems priority program, the energy and mass balances of organic matter turnover are investigated with special reference to the soil microbial community by testing selected hydrocarbon substrates with different properties.

In a first incubation experiment the effect of substrate size was investigated by comparing the turnover of glucose (180 Da) and α-1,4-maltoteraose (666.6 Da). We hypothesize that exoenzymatic activity is required for substrates exceeding a size of 600 Da; thus, resulting in a different process type (adaptation-oriented process) compared to the intracellular turnover of  glucose (growth-oriented process). From a batch microcosm experiment, subsamples were collected after different incubation periods to determine microbial pools (biomass, necromass) and the incorporation of the C13-labeled substrates. Enzymatic activity of exoenzymes (α- and β-glucosidase, N-acetyl-glucosaminidase, sulfatase, phosphatase, fungal peroxidase) and endoenzymatic activity (dehydrogenase) were assessed to elaborate the understanding of metabolic pathways. To analyze shifts in the microbial community and to identify a bacterial- or fungal-dominated use channel for each substrate, substrate induced alteration in phospholipid fatty acid (PLFA) patterns of the harvested samples will be studied as well. First results show differences in enzyme activity pattern for glucose and maltotetraose.

How to cite: Vonhoegen, D., Yousaf, U., and Thiele-Bruhn, S.: Microbial enzyme activities and use channels during microbial turnover of organic carbon substrates in soil , EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-7231, https://doi.org/10.5194/egusphere-egu23-7231, 2023.

X3.78
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EGU23-9060
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ECS
Katherine Shek and Adam Wymore

Soil microbes govern biogeochemical processes such as carbon and nutrient cycling, but the microbial controls on soil nutrient stoichiometry vary under different environmental contexts. Recent evidence suggests that microbial genomic traits such as GC content and genome size correlate with soil pH and soil C: N ratios, but how this pattern relates to the fate of soil organic carbon (SOC) and in which microbial groups this occurs is inconclusive. The rapid generation of environmental metagenomic datasets presents a unique and relatively untapped resource that can be used to examine microbial niche breadth, or soil resource use and reuse, and how specific groups of microbes respond to environmental gradients. Metagenome assembled genomes (MAGs) for soil microbes can describe the functional potential of populations, serving as valuable descriptors of niche breadth for soil microbial communities.  Here, we aimed to identify the ecological factors structuring microbiological nutrient cycling functions, and how they vary with microbial traits and functional groups by harmonizing soil metagenome datasets with soil nutrient measurements across space and time. We applied the Hutchinsonian niche hypervolume concept to examine relationships between microbial functional niche and environmental resource space. We expect that comparative analysis of MAGs across diverse environments varying in soil organic C and N can identify specific functional and/or taxonomic groups of microbes contributing to SOC dynamics, such as fungal saprotrophs. Biotic and abiotic controls such as climate and vegetation that influence these groups of microbes can then be identified using large-scale amplicon sequence datasets that represent broad spatiotemporal scales.

How to cite: Shek, K. and Wymore, A.: Microbial niche breadth as a tool to identify controls on carbon and nutrient cycling across environmental gradients, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-9060, https://doi.org/10.5194/egusphere-egu23-9060, 2023.

X3.79
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EGU23-9585
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ECS
Alexander König, Christoph Rosinger, Katharina Keiblinger, Sophie Zechmeister-Boltenstern, Anke Herrmann, and Erich Inselsbacher

Sequestering atmospheric CO2 into soil organic matter through changes in agricultural practices is an appealing idea to improve soil ecosystem services and to improve global change mitigations. The old view of carbon (C) stability in soil, based on the intrinsic properties of the organic matter inputs (e.g. lignin content), would lead policy towards greater percentages of recalcitrant organic matter content in crops. Recent research suggests otherwise and that managing how the soil microbiome process C inputs is a more fruitful approach (Sokol et al., 2019, Poeplau et al., 2019). It is therefore to decipher and evaluate the link between the aboveground plant community and the complex belowground diversity of the microbiome and their metabolic processes that mediate C sequestration. Lehmann et al. (2020) proposed a theoretical framework in which the persistence of C in soil can be understood as the outcome of interactions between the molecular variability of organic matter input and spatio-temporal microbial heterogeneities of the soil system.

Within the EnergyLink framework we therefore investigate various microbial markers to illuminate possible physiological changes across several European agricultural field sites with different cover crop management types. Specifically, for detecting shifts in microbial necromass composition and quantity we target amino-sugars (galactosamin, gluctosamine, mannosamine and muramic acid), for evaluating effects on growth rates we measure 14C incorporation into ergosterol for fungi and 14C-leucine incorporation for bacteria and to grasp changes in uptake strategies we test extra cellular enzyme activities for different nutrient classes. Additionally, we determine C:N:P ratio for bulk soil, microbial biomass and above ground plant biomass to estimate stoichiometric imbalances. Here we present results from our first sampling campaign and discuss implications of diversified cover crops on soil carbon properties on a European scale.

How to cite: König, A., Rosinger, C., Keiblinger, K., Zechmeister-Boltenstern, S., Herrmann, A., and Inselsbacher, E.: Linking soil microbial carbon sequestration to cover crop diversification in agricultural soil systems across Europe, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-9585, https://doi.org/10.5194/egusphere-egu23-9585, 2023.

X3.80
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EGU23-11989
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ECS
Ubaida Yousaf, Denise Vonhoegen, and Sören Thiele-Bruhn

Recent research indicates that soil microbes play a significant role in the formation and turnover of soil organic matter (SOM). Thus, OM is metabolized by microorganisms through intracellular and extracellular enzymatic activity, with one portion of it being converted into biomass and another being respired for energy. This causes an energy and matter flux that is adjusted and slowed down by ongoing recycling of the matter and residual energy. Matter and energy are conserved as much as possible throughout repeating microbial growth cycles, resulting in an "energy use channel," and/or storage as necromass. Soil fertility and several other soil functions depend on the activity of diverse soil microbial populations and, consequently, on continual energy and carbon flows within the soil system. Fluxes and stoichiometry concerns must be considered for the maintenance of microbial diversity and ecosystem activities in soil, including C storage. To comprehend C turnover and sequestration in terrestrial ecosystems, further knowledge of the relationship between element cycling and energy fluxes is required. In this project, we present a conceptual overview of microorganisms as mediators of SOM production, we do that by investigating seven carbon substrates with varying complexity with the same model soil (fertilized Dikopshof) in five different incubation experiments.

In the first experiment, we study the effect of substrate size (Glucose — 180 Da, α — 1,4-maltotetraose — 666,6 Da). We hypothesize that exoenzymes would be required to degrade any substrate greater in size than 600 Da, meaning different CUE/EUE due to a change in the process type from growth-oriented processes — high energy flux for glucose degradation to the adaption-oriented processes for the larger substrate, i.e., maltotetraose in this case. The substrates were labelled with 13C to determine various carbon pools in the samples. Destructive sampling was used to obtain subsamples from 6 different time points. Aminosugars and acids were used as markers of microbial biomass/necromass. Chloroform fumigation extraction was performed to determine microbial biomass of carbon and nitrogen. In combination with further data to calculate the microbial quotient (Cmic/OC), the respiratory quotient (qCO2= resp./Cmic), and CUE. Gas flux sampling and isotope selective CO2 analysis to determine the differences in the turnover of the substrates (Energy consumption respiration) The energy accumulation includes the formation of additional biomass, necromass, and metabolites. Analysis of C, H, N, S, O, and P to calculate the stoichiometry of OM. 

 

How to cite: Yousaf, U., Vonhoegen, D., and Thiele-Bruhn, S.: Chemical and microbial mass balances in microbial turnover of two easily degradable carbon substrates, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-11989, https://doi.org/10.5194/egusphere-egu23-11989, 2023.

X3.81
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EGU23-12021
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ECS
Magdalena Rath, Ksenia Guseva, and Christina Kaiser

Microbial decomposition of soil organic matter is one of the major drivers of nutrient and carbon cycling in terrestrial ecosystems. Soils are spatially heterogeneous habitats built up hierarchically from µm- to mm-sized aggregates that provide a complex pore system. An enormous diversity of microbes occupies this physically and chemically heterogeneous pore space. Although, in recent decades the consensus has largely been established, that microbial processes are strongly affected by the architecture of the soil pore space and the patchiness of the substrate distribution within it, still, the integration of pore network characteristics in models of microbial activity is scarce. 

We use an individual-based modelling approach to address the following questions:

  • How does pore network architecture affect the efficiency of microbial organic matter decomposition?
  • How do pore network properties like average node degree, shortest path length, and clustering coefficient affect the efficiency of organic matter decomposition?
  • What is the effect of additional heterogeneity in pore sizes or distribution of substrate between pores on microbial efficiency?

To incorporate the spatial structure the soil pore space that forms microhabitats is modelled as nodes of a network. Specific attributes are assigned to the nodes to describe their physical and biochemical conditions. Microbes inhabit a certain fraction of microhabitats (nodes) of the network and degrade organic matter that is available to them. Depending on microbial growth neighboring pores can be invaded  through the connecting links.
 We were able to identify a number of network properties that affect the spread of microorganisms trough the network and the subsequent decomposition efficiency of the total substrate available in the system. While high clustering of nodes enables nearly complete decomposition of substrate, the presence of highly connected nodes (hubs) can decrease the efficiency of decomposition and lead to higher amount of substrate that remains undegraded. Regarding microbial growth parameters, the system shows a threshold behaviour. If microbial growth stays below a certain threshold value, microbes live only in the initially occupied pores and are not able to invade new pores. When the substrate concentration or the growth rate reaches the threshold value, there is a jump to large-scale invasion of all reachable pores in the network and much higher efficiency in the decomposition. In addition, high heterogeneity in substrate concentration or pore sizes lead to lower invasion efficiency, lower decomposition rate and a higher amount of substrate that is left at the end. Overall, we found that the spatial structure of the pore network had a more pronounced effect on microbial decomposition efficiencies than microbial physiological parameters, such as maximum microbial growth rates or extracellular enzyme kinetics.
 Our findings allow for better understanding of the impact of soil pore network architecture on microbial processes. This is of high relevance when modelling the response of soil microbial communities to climate change.

How to cite: Rath, M., Guseva, K., and Kaiser, C.: Effect of pore network architecture on the efficiency of microbial soil organic matter decomposition, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-12021, https://doi.org/10.5194/egusphere-egu23-12021, 2023.

X3.82
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EGU23-16018
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ECS
Alejandro Javier Criado Monleon, Jan Knappe, Celia Somlai, Carolina Ospina Betancourth, Muhammad Ali, Thomas P. Curtis, and Laurence William Gill

There has been a large output of genomic data in ecological studies of centralised wastewater treatment plants over the past number of years. One significant collaboration of Danish and Swedish research institutions lead to the development of the Microbes of Activated Sludge and Anaerobic Digesters (MiDAS 4) global taxonomic database. The database has been an effective tool in understanding centralised systems, however, there has been no known application of this tool in understanding the ecology of organisms in the on-site wastewater treatment systems. The growth of microbial mats or "biomats" has been identified as an essential component in the attenuation of pollutants within the soil treatment unit (STU) of conventional on-site wastewater treatment systems (OWTSs). Two research sites were employed to determine the influence of the pre-treatment of raw-domestic wastewater on these communities. The STUs at each of the two sites were split, whereby half received effluent directly from septic tanks, and half received more highly treated effluents from packaged aerobic treatment systems [a coconut husk media filter on one site, and a rotating biodisc contactor (RBC) on the other site]. Effluents from the RBC had a higher level of pre-treatment [~90% Total Organic Carbon (TOC) removal], compared to the media filter (~60% TOC removal).  These sites' biomat were sampled two-dimensionally in respect of distance and depth, to configure ecological data with changes in the volumetric water content values which had been used successfully as an indicator of the location of the biomat. A total of 92 samples were obtained from both STU locations and characterized by MiDAS taxonomic database. Our study has shown that the biomats receiving primary or untreated effluent have less pronounced increases in denitrifiers compared to the biomats receiving treated or partially treated effluent. but biomats receiving primary effluents have been found to be capable of removing six times the amount of total nitrogen. This suggests that the increases in functional richness within the STU are secondary to bioclogging, as metabolic rates could be limited by hydraulic conductivity.

How to cite: Criado Monleon, A. J., Knappe, J., Somlai, C., Ospina Betancourth, C., Ali, M., Curtis, T. P., and Gill, L. W.: Successful characterisation of on-site wastewater treatment system biomats using the Microbes of Activated Sludge and Anaerobic Digesters (MiDAS) taxonomic database, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-16018, https://doi.org/10.5194/egusphere-egu23-16018, 2023.

X3.83
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EGU23-16479
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ECS
Hanbang Zou, Pelle Ohlsson, and Edith Hammer

Microfluidics is a multidisciplinary platform that integrates microfabrication, physical chemistry analysis, automation, and microscopy. It has the advantages of precise liquid manipulation, rapid measurements, and real-time visualization at the microscale, which is especially of interest and benefit to microbial studies. Soil Chips are microfabricated microfluidic devices typically made of glass and polydimethylsiloxane (PDMS), designed to mimic the real soil network and allow real-time visualization and characterization of microbial activity at the micro-scale. They have so far been used to investigate microbial activities, interactions, community composition, and distribution under different conditions in soil analog systems. Challenge comes when working with natural soil samples. Due to mineral aggregates and debris, valuable information such as the abundance of individuals, cell morphology, and the relationship between bacteria and their geochemical and physical environment are difficult to extract via a simple thresholding method. Since microorganisms and microfluidic structures have distinct features from the noisy background that can be easily picked up by our eyes, a biologically inspired convolutional neural network model for object detection is the most suitable tool for this task.
We used a small part of data from three different experiments to train a well-developed object detection and segmentation algorithm Mask RCNN and implemented further analysis of bacteria abundance, spatial distribution, and morphological characterization. We are able to plot the distribution of all the detected bacteria including clusters in terms of abundance, size, shape, and index of aggregation. A distinct difference in bacteria characteristics can be observed in the samples acquired from three locations (Greenland, Sweden, and Kenya). We are now planning to extend the classification library to include other microbial groups including fungi, protists, invertebrates, and micro arthropods.

How to cite: Zou, H., Ohlsson, P., and Hammer, E.: Deep learning-based object detection for soil bacterial community analysis in microfluidics, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-16479, https://doi.org/10.5194/egusphere-egu23-16479, 2023.

X3.84
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EGU23-9238
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ECS
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Marialina Tsinidis and Manolis Simigdalas

The present experiment investigates the behavior of marine actinobacteria in the International Space Station (ISS). More specifically, the aim of the experiment is to examine the growth rate and antibiotic production of the actinobacteria and as a result the correlation between the growth rate and the viscosity of the liquid (mix of actinobacteria and nutrient agar). The experiment is performed in cooperation with Nanoracks and launched via Falcon 9, Space – X and remained in the ISS for a 90-day time period under constant temperature (4 degree Celsius), being stirred by the astronauts on a weekly basis. There is a medical and pharmacological interest since marine actinobacteria are a source of bioactive natural and antibiotic products, beneficial for the human organism, producing a variety of secondary metabolites. The experiment in the ISS indicates growth similar to the experiment on Earth, with slightly higher values showing that the bacteria survived the microgravity conditions. The viscosity is slightly greater in the ISS, potentially due to the change in the density of the liquid, following the growth of the bacteria.

 

How to cite: Tsinidis, M. and Simigdalas, M.: Investigation of the growth rate and antibiotic production of Marine Actinobacteria in the International Space Station, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-9238, https://doi.org/10.5194/egusphere-egu23-9238, 2023.