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[hal-04611927] Response to Čapek and Šantrůčková’s comment to “Liming effects on microbial carbon use efficiency and its potential consequences for soil organic carbon stocks” [Soil Biology and Biochemistry 194: 109437]
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ano.nymous@ccsd.cnrs.fr.invalid (Julia Schroeder) 14 Jun 2024
https://hal.science/hal-04611927v1
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[hal-04611923] Carbon stabilization in soil after organic amendment application -A comparison of two biomass use scenarios
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ano.nymous@ccsd.cnrs.fr.invalid (Tobias Bölscher) 14 Jun 2024
https://hal.science/hal-04611923v1
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[hal-04557988] Liming effects on microbial carbon use efficiency and its potential consequences for soil organic carbon stocks
The allocation of metabolised carbon (C) between soil microbial growth and respiration, i.e. C use efficiency (CUE) is crucial for SOC dynamics. The pH was shown to be a major driver of microbial CUE in agricultural soils and therefore, management practices to control soil pH, such as liming, could serve as a tool to modify microbial physiology. We hypothesised that raising soil pH would alleviate CUE-limiting conditions and that liming could thus increase CUE, thereby supporting SOC accrual. This study investigated whether CUE can be manipulated by liming and how this might contribute to SOC stock changes. The effects of liming on CUE, microbial biomass C, abundance of microbial domains, SOC stocks and OC inputs were assessed for soils from three European long-term field experiments. Field control soils were additionally limed in the laboratory to assess immediate effects, accounting for lime-derived CO2 emissions (δ13C signature). The shift in soil pHH2O from 4.5 to 7.3 with long-term liming reduced CUE by 40%, whereas the shift from 5.5 to 8.6 and from 6.5 to 7.8 was associated with increases in CUE by 16% and 24%, respectively. The overall relationship between CUE and soil pH followed a U-shaped (i.e. quadratic) curve, implying that in agricultural soils CUE may be lowest at pHH2O = 6.4. The immediate CUE response to liming followed the same trends. Interestingly, liming increased microbial biomass C in all cases. Changes in CUE with long-term liming contributed to the net effect of liming on SOC stocks. Our study confirms the value of liming as a management practice for climate-smart agriculture, but demonstrates that it remains difficult to predict the impact on SOC stocks due its complex effects on the C cycle.
ano.nymous@ccsd.cnrs.fr.invalid (Julia Schroeder) 24 Apr 2024
https://hal.science/hal-04557988v1
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[hal-04526056] Beyond growth: The significance of non-growth anabolism for microbial carbon-use efficiency in the light of soil carbon stabilisation
Microbial carbon-use efficiency (CUE) in soils captures carbon (C) partitioning between anabolic biosynthesis of microbial metabolites and catabolic C emissions (i.e. respiratory C waste). The use of C for biosynthesis provides a potential for the accumulation of microbial metabolic residues in soil. Recognised as a crucial control in C cycling, microbial CUE is implemented in the majority of soil C models. Due to the models' high sensitivity to CUE, reliable soil C projections demand accurate CUE quantifications. Current measurements of CUE neglect microbial non-growth metabolites, such as extracellular polymeric substances (EPS) or exoenzymes, although they remain in soil and could be quantitatively important. Here, we highlight that disregarding non-growth anabolism can lead to severe underestimations of CUE. Based on two case studies, we demonstrate that neglecting exoenzyme and EPS production underestimates CUE by more than 100% and up to 30%, respectively. By incorporating these case-specific values in model simulations, we observed that the model projects up to 34% larger SOC stocks over a period of 64 years when non-growth metabolites are considered for estimating CUE, highlighting the crucial importance of accurate CUE quantification. Our considerations outlined here challenge the current ways how CUE is measured and we suggest improvements concerning the quantification of non-growth metabolites. Research efforts should focus on (i) advancing CUE estimations by capturing the multitude of microbial C uses, (ii) improving techniques to quantify non-growth metabolic products in soil, and (iii) providing an understanding of dynamic metabolic C uses under different environmental conditions and over time. In the light of current discussion on soil C stabilisation mechanisms, we call for efforts to open the ‘black box’ of microbial physiology in soil and to incorporate all quantitative important C uses in CUE measurements.
ano.nymous@ccsd.cnrs.fr.invalid (Tobias Bölscher) 29 Mar 2024
https://hal.science/hal-04526056v1
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[hal-04430943] Liming effects on microbial carbon use efficiency and its potential consequences for soil organic carbon stocks
Climate-smart agriculture aims amongst others at protecting and increasing soil organic carbon (SOC) stocks. The allocation of metabolised carbon (C) between soil microbial growth and respiration, i.e. C use efficiency (CUE) is crucial for SOC dynamics. We hypothesised that raising soil pH would alleviate CUE-limiting conditions and that liming could thus increase CUE, thereby supporting SOC accrual. This study investigated whether CUE can be manipulated by liming and how this might contribute to SOC stock changes. The effects of liming on CUE, microbial biomass C, abundance of microbial domains, SOC stocks and OC inputs were assessed for soils from three European long-term field experiments. Field control soils were additionally limed in the laboratory to assess immediate effects. The shift in soil pH H2O from 4.5 to 7.3 with long-term liming reduced CUE by 40 %, whereas the shift from 5.5 to 8.6 and from 6.5 to 7.8 was associated with increases in CUE by 16 % and 24 %, respectively. The overall relationship between CUE and soil pH followed a U-shaped (i.e. quadratic) curve, implying that in agricultural soils CUE may be lowest at pH H2O = 6.4. The immediate CUE response to liming followed the same trends. Changes in CUE with long-term liming contributed to the net effect of liming on SOC stocks. Our study confirms the value of liming as a management practice for climate-smart agriculture, but demonstrates that it remains difficult to predict the impact on SOC stocks due its complex effects on the C cycle.
ano.nymous@ccsd.cnrs.fr.invalid (Julia Schroeder) 01 Feb 2024
https://hal.science/hal-04430943v1
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[hal-04468177] Gibbs energy or enthalpy—What is relevant for microbial C‐turnover in soils?
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ano.nymous@ccsd.cnrs.fr.invalid (Matthias Kästner) 20 Feb 2024
https://hal.science/hal-04468177v1
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[hal-04257607] Beyond Growth: The Significance of Non-Growth Anabolism for Microbial Carbon-Use Efficiency in the Light of Soil Carbon Stabilisation
Microbial carbon-use efficiency (CUE) in soils captures carbon (C) partitioning between anabolic biosynthesis of microbial metabolites and catabolic C emissions (i.e. respiratory C waste). The use of C for biosynthesis provides a potential for the accumulation of microbial metabolic residues in soil. Recognized as a crucial control in C cycling, microbial CUE is implemented in the majority of soil C models. Due to the models’ high sensitivity to CUE, reliable soil C projections demand accurate CUE quantifications. Current measurements of CUE neglect microbial non-growth metabolites, such as extracellular polymeric substances (EPS) or exoenzymes, although they remain in soil and could be quantitatively important. Here, we highlight that disregarding non-growth anabolism can lead to severe underestimations of CUE. Based on two case studies, we demonstrate that neglecting exoenzyme and EPS production underestimates CUE by more than 100% and up to 30%, respectively. Using these values in model simulations, we observed that the model projects up to 34% larger SOC stocks when non-growth metabolites are considered for estimating CUE. Our considerations outlined here challenge the current ways how CUE is measured. Research efforts should focus on (i) advancing CUE estimations by capturing the multitude of microbial C uses, (ii) improving techniques to quantify non-growth metabolic products in soil, and (iii) providing an understanding of dynamic metabolic C uses under different environmental conditions and over time. In the light of current discussion on soil C stabilization mechanisms, we call for efforts to open the ‘black box’ of microbial physiology in soil and to incorporate all quantitative important C uses in CUE measurements.
ano.nymous@ccsd.cnrs.fr.invalid (Tobias Bölscher) 25 Oct 2023
https://hal.science/hal-04257607v1
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[hal-04489623] Can we manage microbial carbon use efficiency via liming?
Microbial transformation of organic matter is thought to stabilise carbon in soil. When soil microbes have a high carbon use efficiency (CUE), a high proportion of the metabolised carbon is incorporated into the microbial biomass, thereby promoting this in-vivo stabilisation of carbon. Managing CUE could therefore become a strategy to support C sequestration. Soil pH was shown to be a major driver of microbial CUE in agricultural soils and therefore, management practices to control soil pH, such as liming, could serve as a tool to modify microbial physiology. However, the potential to actively manage CUE via liming is unclear. To address this question, the long-term effect of liming on CUE was investigated on soils from three European long-term field experiments (Versailles Bare Fallow ‘42 Parcelles’, Store Jyndevad ‘P and liming experiment’and Dürnast ‘Kalkversuch 016’). In addition, control soils were limed in the laboratory to investigate direct liming effects on CUE by accounting for lime-derived CO2 losses (δ13C signature). Preliminary results suggest that the long-term effect of liming on CUE is dependent on the pH range in which changes occur. Direct liming led to an increase in soil pH, but did not increase CUE in short-term. We will present effects of long-term liming and direct liming on soil microbial CUE and highlight the potential of manipulating CUE via liming.
ano.nymous@ccsd.cnrs.fr.invalid (Julia Schroeder) 05 Mar 2024
https://hal.science/hal-04489623v1
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[hal-04489641] Calorimetric approaches to investigate soil organic matter decomposition
Soil organic matter is the largest carbon pool in terrestrial ecosystems. Consequently, even small changes of soil organic carbon dynamics may have significant impacts on feedbacks to global climate. The fate of soil organic matter in ecosystems is determined during its decomposition by microbial metabolic activity. A driving force of microbial activity in soil is the need of microorganism to acquire energy from organic matter. Thermodynamic limitations and energetic properties of organic matter can hamper microbial activity. Despite the central role of energy in soil organic matter decomposition, energetic approaches have long been peripheral in soil organic matter research. Early uses of calorimetry to investigate microbial activity in soil date back to the 1980s, but only within the last 15 years have calorimetric approaches come slowly back on the research agenda. Currently calorimetric approaches gain momentum in soil organic matter research. This presentation aims to give an (incomplete) overview on how calorimetry is used to investigate organic matter decomposition in soil. The use of calorimetry reaches from isothermal microcalorimetry – to investigate microbial activity and energy use efficiencies – over differential scanning and bomb calorimetry – to analyse energetic properties of organic matter – to calorespirometry, providing insights into microbial physiology during decomposition.
ano.nymous@ccsd.cnrs.fr.invalid (Tobias Bölscher) 05 Mar 2024
https://hal.science/hal-04489641v1
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[hal-04093388] Soil organic carbon models need independent time-series validation for reliable prediction
Abstract Numerical models are crucial to understand and/or predict past and future soil organic carbon dynamics. For those models aiming at prediction, validation is a critical step to gain confidence in projections. With a comprehensive review of ~250 models, we assess how models are validated depending on their objectives and features, discuss how validation of predictive models can be improved. We find a critical lack of independent validation using observed time series. Conducting such validations should be a priority to improve the model reliability. Approximately 60% of the models we analysed are not designed for predictions, but rather for conceptual understanding of soil processes. These models provide important insights by identifying key processes and alternative formalisms that can be relevant for predictive models. We argue that combining independent validation based on observed time series and improved information flow between predictive and conceptual models will increase reliability in predictions.
ano.nymous@ccsd.cnrs.fr.invalid (Julia Le Noë) 10 May 2023
https://hal.science/hal-04093388v1
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[hal-04488430] Post-drought root exudation defines soil organic matter stability in a temperate mature forest
Forest soils are crucial for many ecosystem services that rely on soil organic matter (SOM) stability. Carbon allocated to roots and released as exudates to the rhizosphere plays a key role in SOM stabilization. Under periodic drought, elevated root exudation and SOM accumulation have been reported. Yet, whether root exudates control SOM formation and stability in mature forests once the drought ends is largely unknown. We examined whether root exudates from P. abies and F. sylvatica trees relate to SOM formation and stability in soil depth profiles one year following five years of experimental drought (Kroof experiment, Germany). We collected root exudates throughout the rooting zone and combined the data with thermogravimetric analysis of SOM in the rhizosphere and non-rooted soil. We found that the rhizosphere of both species was characterized by stable SOM fractions that did not decrease post-drought, suggesting potential protection of SOM due to rhizodeposition and root exudates. In contrast, stable SOM fractions decreased relative to controls in non-rooted topsoil below P. abies, indicating a loss of stabilized SOM from drought-affected and re-wetted soil. Our measurements provide valuable insights into post-drought SOM formation and mechanisms of SOM stabilization in forest ecosystems under climate change.
ano.nymous@ccsd.cnrs.fr.invalid (Melanie Brunn) 04 Mar 2024
https://hal.inrae.fr/hal-04488430v1
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[hal-04489594] Beyond growth? The significance of microbial maintenance for carbon-use efficiency in the light of soil carbon storage
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.
ano.nymous@ccsd.cnrs.fr.invalid (Tobias Bölscher) 12 Mar 2024
https://hal.science/hal-04489594v1
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[hal-04489565] Chemical complexity matters: differential mobilization of mineral-associated organic matter driven by functionally distinct rhizodeposits
Purpose Protective mineral-organic associations are the quantitatively most important soil carbon storage mechanism, but their vulnerability to environmental change is largely uncertain. While it is well established that root growth can promote (or “prime”) the microbial decomposition of organic matter (OM), our mechanistic knowledge of the ability of roots to destabilize OM protected within mineral-organic associations remains limited. Here we examined how the composition of root-derived compounds (rhizodeposits) affects the stability of mineral-organic associations. Methods In model systems, we tested the ability of functionally distinct low-molecular weight compounds (ligands, reductants, simple sugars) commonly observed in the rhizosphere to cause the mobilization and mineralization of isotopically labeled OM from different mineral types (Fe and Al hydroxides). Results Our results showed that all compounds stimulated mobilization and mineralization of previously mineral-associated OM. However, OM bound to Al hydroxide was less susceptible to mobilization than OM bound to Fe hydroxide. In batch solution without soil, the strong ligand oxalic acid mobilized more mineral-associated OM than the reducing agent catechol or the simple sugar glucose. This finding was in line with our initial hypotheses. In model soil, however, glucose (sugar) and catechol (reductant) revealed a greater mobilization potential than oxalic acid (ligand) for both mineral types, suggesting that OM mobilization in soils may be microbially mediated, rather than driven by direct mineral dissolution. Conclusion Together, our results suggest a strong mechanistic linkage between the composition and functionality of rhizodeposits and their ability to destabilize mineral-associated OM.
ano.nymous@ccsd.cnrs.fr.invalid (Tobias Bölscher) 05 Mar 2024
https://hal.science/hal-04489565v1
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[hal-04490230] Rediscovering microbial metabolism in terrestrial ecosystems – A bioenergetics approach
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ano.nymous@ccsd.cnrs.fr.invalid (Anke M Herrmann) 05 Mar 2024
https://hal.science/hal-04490230v1
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[tel-04121789] Decomposition of Soil Organic Matter under a Changing Climate
Soil organic matter is the largest carbon (C) pool in the terrestrial C cycle, and soil CO 2 emissions surpass anthropogenic emissions from fossil fuel combustion by a factor of nine. Therefore, mechanisms controlling C stabilisation in soils and its feedback to climate change are widely debated. During decomposition, microbial substrate-use efficiency is an important property because it determines the allocation of substrate C to biosynthesis and respiratory losses. High efficiency values indicate that C primarily remains in soils while low efficiency implies that C is primarily lost into the atmosphere. Despite empirical evidence that efficiency is temperature sensitive, traditional Earth system models treat this property as a constant. The aim of this thesis was to improve our mechanistic understanding of drivers regulating substrate-use efficiency with special consideration to climate change. It investigated the impacts of (i) temperature, (ii) microbial community composition and (iii) substrate quality on substrate-use efficiency. Within the thesis, a microbial energetics approach was applied and further developed using isothermal calorimetry. Further, the thesis compared common approaches for measuring microbial substrate- use efficiency, and the implications of the resultant empirical data for projected C stocks were tested using a modelling approach. Substrate-use efficiency was generally temperature sensitive and decreased with increasing temperature. The observed temperature responses were non-linear and varied across land use management systems. The changes in substrate-use efficiency with temperature were driven rather by changes in microbial physiology than by shifts in active microbial communities. Nevertheless, fungi and Gram-negative bacteria tended towards relatively higher efficiencies. Efficiencies varied among utilised substrates, but substrate quality per se was a poor proxy for efficiency. Projected losses from soil C stocks varied across land use management systems and were up to 39 % and 15 % for grassland and forest systems, respectively. Results from the modelling approach confirmed that substrate-use efficiency is one of the factors to which soil C stocks react most sensitively. Findings from this thesis emphasise the importance of furthering our understanding of substrate-use efficiency for reliable climate projections.
ano.nymous@ccsd.cnrs.fr.invalid (Tobias Bölscher) 08 Jun 2023
https://hal.inrae.fr/tel-04121789v1
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[hal-04489784] Revisiting the terrestrial carbon cycle: New insights into microbial metabolism
Energy is continuously transformed in environmental systems through the metabolic activities of living organisms. In terrestrial ecosystems, there is a general consensus that the diversity of microbial metabolic processes is poorly related to overall ecosystem function because of the inherent functional redundancy that exists within many microbial communities. Here, we propose a conceptual ecological model of microbial energetics in various terrestrial ecosystems (e.g. Scandinavian arable systems or temporarily flooded systems in South East Asia). Using isothermal calorimetry, we show that direct measures of energetics provide a functional link between energy flow and the composition of belowground microbial communities at a high taxonomic level. In contrast, this link is not apparent when carbon dioxide (CO2) was used as an aggregate measure of microbial metabolism. Our results support the notion that systems with higher relative abundances of fungi have more efficient microbial metabolism. Furthermore, we suggest that the microbial energetics approach combined with spectroscopic and aqueous chemical measurements is a viable approach to determine the effect of energy release from organic matter on metal(loid) mobility in soils and sediments under anaerobic conditions. We advocate that the microbial energetics approach provides complementary information to soil respiration for investigating the involvement of microbial communities in belowground carbon dynamics. Our results indicate that microbial metabolic processes are an essential constituent in governing the terrestrial carbon balance and that microbial diversity should not be neglected in ecosystem modeling. Quantification of microbial energetics incorporates thermodynamic principles and our conceptual model provides empirical data that can feed into carbon-climate based ecosystem feedback modeling. Together they disentangle the intrinsically complex yet essential carbon dynamics of soils to address important issues such as climate change.
ano.nymous@ccsd.cnrs.fr.invalid (Anke M Herrmann) 05 Mar 2024
https://hal.science/hal-04489784v1
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[hal-04489715] Revisiting the terrestrial carbon cycle: New insights from isothermal microcalorimetry
Energy is continuously transformed in environmental systems through the metabolic activities of living organisms. In terrestrial ecosystems, there is a general consensus that the diversity of microbial metabolic processes is poorly related to overall ecosystem function because of the inherent functional redundancy that exists within many microbial communities. Here, we propose a conceptual ecological model of microbial energetics in various terrestrial ecosystems (e.g. Scandinavian arable systems or temporarily flooded systems in South East Asia). Using isothermal microcalorimetry, we show that direct measures of energetics provide a functional link between energy flow and the composition of belowground microbial communities at a high taxonomic level. In contrast, this link is not apparent when carbon dioxide (CO2) was used as an aggregate measure of microbial metabolism. Our results support the notion that systems with higher relative abundances of fungi have more efficient microbial metabolism. Furthermore, we suggest that the microbial energetics approach combined with spectroscopic and aqueous chemical measurements is a viable approach to determine the effect of energy release from organic matter on metal(loid) mobility in soils and sediments under anaerobic conditions. We advocate that the microbial energetics approach provides complementary information to soil respiration for investigating the involvement of microbial communities in belowground carbon dynamics. Our results indicate that microbial metabolic processes are an essential constituent in governing the terrestrial carbon balance and that microbial diversity should not be neglected in ecosystem modeling. Quantification of microbial energetics incorporates thermodynamic principles and our conceptual model provides empirical data that can feed into carbon-climate based ecosystem feedback modeling. Together they disentangle the intrinsically complex yet essential carbon dynamics of soils to address important issues such as climate change.
ano.nymous@ccsd.cnrs.fr.invalid (Anke M Herrmann) 05 Mar 2024
https://hal.science/hal-04489715v1
