Soil microbial carbon use efficiency (CUE), defined as the ratio of organic C allocated to growth over organic C taken up, strongly affects soil carbon (C) cycling. Despite the importance of the microbial CUE for the terrestrial C cycle, very little is known about how it is affected by nutrient availability. Therefore, we studied microbial CUE and microbial biomass turnover time in soils of a long-term fertilization experiment in a temperate grassland comprising five treatments (control, PK, NK, NP, NPK). Microbial CUE and the turnover of microbial biomass were determined using a novel substrate-independent method based on incorporation of 18O from labeled water into microbial DNA. Microbial respiration was 28-37% smaller in all three N treatments (NK, NP, and NPK) compared to the control, whereas the PK treatment did not affect microbial respiration. N-fertilization decreased microbial C uptake, while the microbial growth rate was not affected. Microbial CUE ranged between 0.31 and 0.45, and was 1.3- to 1.4-fold higher in the N-fertilized soils than in the control. The turnover time ranged between 80 and 113 days and was not significantly affected by fertilization. Net primary production (NPP) and the abundance of legumes differed strongly across the treatments, and the fungal:bacterial ratio was very low in all treatments. Structural equation modeling revealed that microbial CUE was exclusively controlled by N fertilization and that neither the abundance of legumes (as a proxy for the quality of the organic matter inputs) nor NPP (as a proxy for C inputs) had an effect on microbial CUE. Our results show that N fertilization did not only decrease microbial respiration, but also microbial C uptake, indicating that less C was intracellularly processed in the N fertilized soils. The reason for reduced C uptake and increased CUE in the N-fertilization treatments is likely an inhibition of oxidative enzymes involved in the degradation of aromatic compounds by N in combination with a reduced energy requirement for microbial N acquisition in the fertilized soils. In conclusion, the study shows that N availability can control soil C cycling by affecting microbial CUE, while plant community-mediated changes in organic matter inputs and P and K availability played no important role for C partitioning of the microbial community in this temperate grassland.
", "keywords": ["FUNGAL", "2. Zero hunger", "106022 Mikrobiologie", "Nitrogen addition", "BACTERIAL", "NITROGEN DEPOSITION", "GROWTH EFFICIENCY", "FOREST FLOOR", "Nutrients", "04 agricultural and veterinary sciences", "15. Life on land", "Stoichiometry", "ORGANIC-MATTER", "RESPIRATION", "106026 \u00d6kosystemforschung", "13. Climate action", "Nutrient limitation", "Microbial growth yield", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries", "Mean residence time", "STOICHIOMETRIC CONTROLS", "ENZYME-ACTIVITY", "106026 Ecosystem research", "COMMUNITY STRUCTURE"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2016.03.008"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2016.03.008", "name": "item", "description": "10.1016/j.soilbio.2016.03.008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2016.03.008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2021.108400", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:25Z", "type": "Journal Article", "created": "2021-08-24", "title": "The mechanisms underpinning microbial resilience to drying and rewetting \u2013 A model analysis", "description": "Abstract Soil moisture is one of the most important factors controlling the activity and diversity of soil microorganisms. Soils exposed to pronounced cycles of drying and rewetting (D/RW) exhibit disconnected patterns in microbial growth and respiration at RW. These patterns differ depending on the preceding soil moisture history, leading to contrasting amounts of carbon retained in the soil as biomass versus that respired as CO2. The mechanisms underlying these microbially-induced dynamics are still unclear. In this work, we used the process-based soil microbial model EcoSMMARTS to offer candidate explanations for: i) how soil moisture can shape the structure of microbial communities, ii) how soil moisture history affects the responses during D/RW, iii) what microbial mechanisms control the shape, intensity and duration of these responses, and iv) what carbon sources sustain the increased biogeochemical rates after RW. We first evaluated the response to D/RW in bacterial communities previously exposed to two different stress histories (\u2018moderate\u2019 vs \u2018severe\u2019 soil moisture regimes). We found that both the history of soil moisture and the harshness of the dry period preceding the rewetting shaped the structure and physiology of microbial communities. The characteristics of these communities determined the harshness experienced and the nature of the responses to RW obtained. Modelled communities exposed to extended severe conditions showed a resilient response to D/RW, whereas those exposed to moderate environments exhibited a more sensitive response. We then interchanged the soil moisture regimes and found that the progressive adaptation of microbial physiology and structure to new environmental conditions resulted in a switch in the response patterns. These microbial changes also determined the contribution of biomass synthesis, osmoregulation, mineralization by cell residues, and disruption of soil aggregates to CO2 emissions.", "keywords": ["2. Zero hunger", "Water stress", "Birch effect", "Soil respiration", "04 agricultural and veterinary sciences", "15. Life on land", "Agriculture", " Forestry and Fisheries", "Microbial growth", "01 natural sciences", "Ecological strategies", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Jordbruk", " skogsbruk och fiske", "Soil moisture", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2021.108400"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2021.108400", "name": "item", "description": "10.1016/j.soilbio.2021.108400", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2021.108400"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-11-01T00:00:00Z"}}, {"id": "10.1073/pnas.2107668118", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:38Z", "type": "Journal Article", "created": "2021-11-19", "title": "Energetic scaling in microbial growth", "description": "SignificanceUnderstanding the principles underlying microbial growth is paramount to the cycle of carbon and nutrients in the biosphere, bioremediation technologies, and biochemical engineering, as well as to natural selection and evolution. Yet, fundamental questions remain on the links between mass and energy balances in microbial metabolism and growth. Guided by a nonequilibrium thermodynamics framework, we interpret extensive literature data on microbial growth. The analysis reveals how mass and energy conversion are tightly coupled by scaling laws relating the thermodynamic efficiency to the electron donor uptake rate and the growth yield. Most importantly, these results appear to be universal, in that they apply across microbial species and metabolic pathways, and pave the way for a general thermodynamic theory of microbiological systems.Microorganisms function as open systems that exchange matter and energy with their surrounding environment. Even though mass (carbon and nutrients) and energy exchanges are tightly linked, there is a lack of integrated approaches that combine these fluxes and explore how they jointly impact microbial growth. Such links are essential to predicting how the growth rate of microorganisms varies, especially when the stoichiometry of carbon- (C) and nitrogen (N)-uptake is not balanced. Here, we present a theoretical framework to quantify the microbial growth rate for conditions of C-, N-, and energy-(co-) limitations. We use this framework to show how the C:N ratio and the degree of reduction of the organic matter (OM), which is also the electron donor, availability of electron acceptors (EAs), and the different sources of N together control the microbial growth rate under C, nutrient, and energy-limited conditions. We show that the growth rate peaks at intermediate values of the degree of reduction of OM under oxic and C-limited conditions, but not under N-limited conditions. Under oxic conditions and with N-poor OM, the growth rate is higher when the inorganic N (NInorg)-source is ammonium compared to nitrate due to the additional energetic cost involved in nitrate reduction. Under anoxic conditions, when nitrate is both EA and NInorg-source, the growth rates of denitrifiers and microbes performing the dissimilatory nitrate reduction to ammonia (DNRA) are determined by both OM degree of reduction and nitrate-availability. Consistent with the data, DNRA is predicted to foster growth under extreme nitrate-limitation and with a reduced OM, whereas denitrifiers are favored as nitrate becomes more available and in the presence of oxidized OM. Furthermore, the growth rate is reduced when catabolism is coupled to low energy yielding EAs (e.g., sulfate) because of the low carbon use efficiency (CUE). However, the low CUE also decreases the nutrient demand for growth, thereby reducing N-limitation. We conclude that bioenergetics provides a useful conceptual framework for explaining growth rates under different metabolisms and multiple resource-limitations.
", "keywords": ["0301 basic medicine", "0303 health sciences", "denitrification", "660", "nitrogen limitation", "microbial growth", "Biological Sciences", "bioenergetics", "Microbiology", "QR1-502", "stoichiometry", "DNRA", "thermodynamics", "03 medical and health sciences", "Geovetenskap och relaterad milj\u00f6vetenskap", "Microbiology (Microbiology in the medical area to be 30109)", "Biologiska vetenskaper", "Bioenergy", "Earth and Related Environmental Sciences", "energy limitation"]}, "links": [{"href": "https://pub.epsilon.slu.se/28342/1/chakrawal-a-et-al-220615.pdf"}, {"href": "https://doi.org/10.3389/fmicb.2022.859063"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2022.859063", "name": "item", "description": "10.3389/fmicb.2022.859063", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2022.859063"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-17T00:00:00Z"}}, {"id": "2309129852", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:27:06Z", "type": "Journal Article", "created": "2016-03-26", "title": "Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland", "description": "Soil microbial carbon use efficiency (CUE), defined as the ratio of organic C allocated to growth over organic C taken up, strongly affects soil carbon (C) cycling. Despite the importance of the microbial CUE for the terrestrial C cycle, very little is known about how it is affected by nutrient availability. Therefore, we studied microbial CUE and microbial biomass turnover time in soils of a long-term fertilization experiment in a temperate grassland comprising five treatments (control, PK, NK, NP, NPK). Microbial CUE and the turnover of microbial biomass were determined using a novel substrate-independent method based on incorporation of 18O from labeled water into microbial DNA. Microbial respiration was 28-37% smaller in all three N treatments (NK, NP, and NPK) compared to the control, whereas the PK treatment did not affect microbial respiration. N-fertilization decreased microbial C uptake, while the microbial growth rate was not affected. Microbial CUE ranged between 0.31 and 0.45, and was 1.3- to 1.4-fold higher in the N-fertilized soils than in the control. The turnover time ranged between 80 and 113 days and was not significantly affected by fertilization. Net primary production (NPP) and the abundance of legumes differed strongly across the treatments, and the fungal:bacterial ratio was very low in all treatments. Structural equation modeling revealed that microbial CUE was exclusively controlled by N fertilization and that neither the abundance of legumes (as a proxy for the quality of the organic matter inputs) nor NPP (as a proxy for C inputs) had an effect on microbial CUE. Our results show that N fertilization did not only decrease microbial respiration, but also microbial C uptake, indicating that less C was intracellularly processed in the N fertilized soils. The reason for reduced C uptake and increased CUE in the N-fertilization treatments is likely an inhibition of oxidative enzymes involved in the degradation of aromatic compounds by N in combination with a reduced energy requirement for microbial N acquisition in the fertilized soils. In conclusion, the study shows that N availability can control soil C cycling by affecting microbial CUE, while plant community-mediated changes in organic matter inputs and P and K availability played no important role for C partitioning of the microbial community in this temperate grassland.
", "keywords": ["FUNGAL", "2. Zero hunger", "106022 Mikrobiologie", "Nitrogen addition", "BACTERIAL", "NITROGEN DEPOSITION", "GROWTH EFFICIENCY", "FOREST FLOOR", "Nutrients", "04 agricultural and veterinary sciences", "15. Life on land", "Stoichiometry", "ORGANIC-MATTER", "RESPIRATION", "106026 \u00d6kosystemforschung", "13. Climate action", "Nutrient limitation", "Microbial growth yield", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries", "Mean residence time", "STOICHIOMETRIC CONTROLS", "ENZYME-ACTIVITY", "106026 Ecosystem research", "COMMUNITY STRUCTURE"]}, "links": [{"href": "https://doi.org/2309129852"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2309129852", "name": "item", "description": "2309129852", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2309129852"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "3194398606", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:27:47Z", "type": "Journal Article", "created": "2021-08-24", "title": "The mechanisms underpinning microbial resilience to drying and rewetting \u2013 A model analysis", "description": "Abstract Soil moisture is one of the most important factors controlling the activity and diversity of soil microorganisms. Soils exposed to pronounced cycles of drying and rewetting (D/RW) exhibit disconnected patterns in microbial growth and respiration at RW. These patterns differ depending on the preceding soil moisture history, leading to contrasting amounts of carbon retained in the soil as biomass versus that respired as CO2. The mechanisms underlying these microbially-induced dynamics are still unclear. In this work, we used the process-based soil microbial model EcoSMMARTS to offer candidate explanations for: i) how soil moisture can shape the structure of microbial communities, ii) how soil moisture history affects the responses during D/RW, iii) what microbial mechanisms control the shape, intensity and duration of these responses, and iv) what carbon sources sustain the increased biogeochemical rates after RW. We first evaluated the response to D/RW in bacterial communities previously exposed to two different stress histories (\u2018moderate\u2019 vs \u2018severe\u2019 soil moisture regimes). We found that both the history of soil moisture and the harshness of the dry period preceding the rewetting shaped the structure and physiology of microbial communities. The characteristics of these communities determined the harshness experienced and the nature of the responses to RW obtained. Modelled communities exposed to extended severe conditions showed a resilient response to D/RW, whereas those exposed to moderate environments exhibited a more sensitive response. We then interchanged the soil moisture regimes and found that the progressive adaptation of microbial physiology and structure to new environmental conditions resulted in a switch in the response patterns. These microbial changes also determined the contribution of biomass synthesis, osmoregulation, mineralization by cell residues, and disruption of soil aggregates to CO2 emissions.", "keywords": ["2. Zero hunger", "Water stress", "Birch effect", "Soil respiration", "04 agricultural and veterinary sciences", "15. Life on land", "Agriculture", " Forestry and Fisheries", "Microbial growth", "01 natural sciences", "Ecological strategies", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Jordbruk", " skogsbruk och fiske", "Soil moisture", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/3194398606"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3194398606", "name": "item", "description": "3194398606", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3194398606"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-11-01T00:00:00Z"}}, {"id": "3211355757", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:27:49Z", "type": "Journal Article", "created": "2021-11-19", "title": "Energetic scaling in microbial growth", "description": "SignificanceUnderstanding the principles underlying microbial growth is paramount to the cycle of carbon and nutrients in the biosphere, bioremediation technologies, and biochemical engineering, as well as to natural selection and evolution. Yet, fundamental questions remain on the links between mass and energy balances in microbial metabolism and growth. Guided by a nonequilibrium thermodynamics framework, we interpret extensive literature data on microbial growth. The analysis reveals how mass and energy conversion are tightly coupled by scaling laws relating the thermodynamic efficiency to the electron donor uptake rate and the growth yield. Most importantly, these results appear to be universal, in that they apply across microbial species and metabolic pathways, and pave the way for a general thermodynamic theory of microbiological systems.Understanding the principles underlying microbial growth is paramount to the cycle of carbon and nutrients in the biosphere, bioremediation technologies, and biochemical engineering, as well as to natural selection and evolution. Yet, fundamental questions remain on the links between mass and energy balances in microbial metabolism and growth. Guided by a nonequilibrium thermodynamics framework, we interpret extensive literature data on microbial growth. The analysis reveals how mass and energy conversion are tightly coupled by scaling laws relating the thermodynamic efficiency to the electron donor uptake rate and the growth yield. Most importantly, these results appear to be universal, in that they apply across microbial species and metabolic pathways, and pave the way for a general thermodynamic theory of microbiological systems.Microorganisms function as open systems that exchange matter and energy with their surrounding environment. Even though mass (carbon and nutrients) and energy exchanges are tightly linked, there is a lack of integrated approaches that combine these fluxes and explore how they jointly impact microbial growth. Such links are essential to predicting how the growth rate of microorganisms varies, especially when the stoichiometry of carbon- (C) and nitrogen (N)-uptake is not balanced. Here, we present a theoretical framework to quantify the microbial growth rate for conditions of C-, N-, and energy-(co-) limitations. We use this framework to show how the C:N ratio and the degree of reduction of the organic matter (OM), which is also the electron donor, availability of electron acceptors (EAs), and the different sources of N together control the microbial growth rate under C, nutrient, and energy-limited conditions. We show that the growth rate peaks at intermediate values of the degree of reduction of OM under oxic and C-limited conditions, but not under N-limited conditions. Under oxic conditions and with N-poor OM, the growth rate is higher when the inorganic N (NInorg)-source is ammonium compared to nitrate due to the additional energetic cost involved in nitrate reduction. Under anoxic conditions, when nitrate is both EA and NInorg-source, the growth rates of denitrifiers and microbes performing the dissimilatory nitrate reduction to ammonia (DNRA) are determined by both OM degree of reduction and nitrate-availability. Consistent with the data, DNRA is predicted to foster growth under extreme nitrate-limitation and with a reduced OM, whereas denitrifiers are favored as nitrate becomes more available and in the presence of oxidized OM. Furthermore, the growth rate is reduced when catabolism is coupled to low energy yielding EAs (e.g., sulfate) because of the low carbon use efficiency (CUE). However, the low CUE also decreases the nutrient demand for growth, thereby reducing N-limitation. We conclude that bioenergetics provides a useful conceptual framework for explaining growth rates under different metabolisms and multiple resource-limitations.