Pub Date : 2026-01-01Epub Date: 2025-10-01DOI: 10.1016/j.soilbio.2025.109996
Yakov Kuzyakov , Ning Ling , Giacomo Pietramellara , Paolo Nannipieri
In this Perspective, we look into the future and outline the crucial unresolved questions that can define broad directions in soil biology and biochemistry over the next decades. Considering that most of the Grand Questions of Selman A. Waksman have been answered over the last 100 years, we suggest here intriguing fundamental topics of basic research linking soil life with biochemical processes and ecosystem functions necessary for system understanding. We raise the following six question groups: Which level of understanding of microbial communities do we need? What are the emerging (microbial) properties and functions of soil? Are microbial memory and legacy important for soil functions? What defines soil health: pools, fluxes or potentials? Microbial growth and death: Can we identify the state of the soil microbiome and its importance for biochemical cycles? We subdivide each of these groups into narrower questions and briefly discuss the unsolved scientific problems based on previous and recent studies. The unresolved problems are visualized with exciting examples. We hope that this Perspective will stimulate new and broader discussion, as well as provide novel ideas for future research topics in soil biology and biochemistry.
在这一展望中，我们展望了未来，并概述了关键的未解决的问题，这些问题可以确定未来几十年土壤生物学和生物化学的广阔方向。考虑到Selman A. Waksman的大多数重大问题在过去的100年里已经得到了回答，我们在这里提出了将土壤生命与生物化学过程和系统理解所必需的生态系统功能联系起来的基础研究的有趣的基本主题。我们提出以下六个问题组：我们需要对微生物群落的了解达到什么程度？土壤的新兴（微生物）特性和功能是什么？微生物记忆和遗产对土壤功能重要吗？什么定义土壤健康：池、通量还是潜力？微生物的生长和死亡：我们能否确定土壤微生物群的状态及其对生化循环的重要性？我们将这些组细分为更窄的问题，并简要讨论基于以前和最近的研究尚未解决的科学问题。用令人兴奋的例子将未解决的问题形象化。我们希望这一观点能够激发新的和更广泛的讨论，并为未来土壤生物学和生物化学的研究课题提供新的思路。
{"title":"Some new grand questions in soil biology and biochemistry","authors":"Yakov Kuzyakov , Ning Ling , Giacomo Pietramellara , Paolo Nannipieri","doi":"10.1016/j.soilbio.2025.109996","DOIUrl":"10.1016/j.soilbio.2025.109996","url":null,"abstract":"<div><div>In this Perspective, we look into the future and outline the crucial unresolved questions that can define broad directions in soil biology and biochemistry over the next decades. Considering that most of the Grand Questions of Selman A. Waksman have been answered over the last 100 years, we suggest here intriguing fundamental topics of basic research linking soil life with biochemical processes and ecosystem functions necessary for system understanding. We raise the following six question groups: Which level of understanding of microbial communities do we need? What are the emerging (microbial) properties and functions of soil? Are microbial memory and legacy important for soil functions? What defines soil health: pools, fluxes or potentials? Microbial growth and death: Can we identify the state of the soil microbiome and its importance for biochemical cycles? We subdivide each of these groups into narrower questions and briefly discuss the unsolved scientific problems based on previous and recent studies. The unresolved problems are visualized with exciting examples. We hope that this Perspective will stimulate new and broader discussion, as well as provide novel ideas for future research topics in soil biology and biochemistry.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 109996"},"PeriodicalIF":10.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145204035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-10-17DOI: 10.1016/j.soilbio.2025.110016
Alexander Konrad , Diana Hofmann , Jan Siemens , Friederike Lang , Ines Mulder , Kenton P. Stutz
Ligand-bound carboxylic acids are considered a stabilized fraction of mineral-adsorbed carbon in soil. Carboxyl-14C labeled phenylalanine or salicylic acid were adsorbed onto goethite, kaolinite, or illite, and subsequently incubated in both loamy and sandy arable topsoil for three weeks. Contrary to our expectations, more mineral-adsorbed carboxyl-C was mineralized than remaining C in salicylic acid and phenylalanine irrespective of mineral type or soil due to competitive desorption followed by preferential mineralization. Factors that control the desorbability of organic molecules are more important for their stabilization in the soil than sorption strength.
{"title":"Rapid mineralization of mineral-bound carboxyl-carbon of salicylic acid and phenylalanine","authors":"Alexander Konrad , Diana Hofmann , Jan Siemens , Friederike Lang , Ines Mulder , Kenton P. Stutz","doi":"10.1016/j.soilbio.2025.110016","DOIUrl":"10.1016/j.soilbio.2025.110016","url":null,"abstract":"<div><div>Ligand-bound carboxylic acids are considered a stabilized fraction of mineral-adsorbed carbon in soil. Carboxyl-<sup>14</sup>C labeled phenylalanine or salicylic acid were adsorbed onto goethite, kaolinite, or illite, and subsequently incubated in both loamy and sandy arable topsoil for three weeks. Contrary to our expectations, more mineral-adsorbed carboxyl-C was mineralized than remaining C in salicylic acid and phenylalanine irrespective of mineral type or soil due to competitive desorption followed by preferential mineralization. Factors that control the desorbability of organic molecules are more important for their stabilization in the soil than sorption strength.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 110016"},"PeriodicalIF":10.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-10-17DOI: 10.1016/j.soilbio.2025.110013
Kaitlin R. Rempfert , Sheryl L. Bell , Christopher P. Kasanke , Jennifer Kyle , Kirsten S. Hofmockel
There is an emerging consensus that microorganisms are a primary source of persistent, slow-cycling soil organic matter (SOM), however which microbial residues contribute to SOM and what controls their accumulation remains unresolved. Lipids are a commonly overlooked biomolecular pool that could contribute significantly to stable SOM. While current estimates for phospholipid degradation in soils are rapid, lipids are structurally heterogeneous molecules that could turnover at different rates. Through a year-long soil incubation and compound-specific, stable isotope probing (SIP)-lipidomics, we were able to rigorously track the persistence of lipid compounds in silty and sandy switchgrass bioenergy crop soils. We assessed the influence of lipid structure on soil lipid accrual and degradation as moderated by soil texture, since mineral association is presumed to be the primary mechanism for lipid persistence. After rapid incorporation of 13C glucose into microbial biomass, we found 13C label was retained broadly across chemically diverse lipid classes, even after one year. 13C-labeled lipid profiles varied significantly with soil texture; however, we found no difference between sandy and silty soils in lipid retention, suggesting soil texture may only play a minor role in modulating lipid persistence. Only two lipid subclasses were found to be persistent (i.e., retention of 13C label without significant degradation or production): phosphatidylinositol lipids and hydroxyceramide lipids, both of which are negatively charged, possibly facilitating stabilization by mineral complexation. However, several other subclasses displayed substantial ongoing production. In particular, the accumulation of triacylglycerol lipids across soil textures suggests that storage lipids may be an important component of SOC, highlighting a potential target for management strategies to promote C retention by lipid accrual. Overall, the retention for over a year of 13C label in microbial intact lipid biomarkers reveals the importance of efficient biomass production and turnover when considering microbial C contributions to SOM.
{"title":"Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon","authors":"Kaitlin R. Rempfert , Sheryl L. Bell , Christopher P. Kasanke , Jennifer Kyle , Kirsten S. Hofmockel","doi":"10.1016/j.soilbio.2025.110013","DOIUrl":"10.1016/j.soilbio.2025.110013","url":null,"abstract":"<div><div>There is an emerging consensus that microorganisms are a primary source of persistent, slow-cycling soil organic matter (SOM), however which microbial residues contribute to SOM and what controls their accumulation remains unresolved. Lipids are a commonly overlooked biomolecular pool that could contribute significantly to stable SOM. While current estimates for phospholipid degradation in soils are rapid, lipids are structurally heterogeneous molecules that could turnover at different rates. Through a year-long soil incubation and compound-specific, stable isotope probing (SIP)-lipidomics, we were able to rigorously track the persistence of lipid compounds in silty and sandy switchgrass bioenergy crop soils. We assessed the influence of lipid structure on soil lipid accrual and degradation as moderated by soil texture, since mineral association is presumed to be the primary mechanism for lipid persistence. After rapid incorporation of <sup>13</sup>C glucose into microbial biomass, we found <sup>13</sup>C label was retained broadly across chemically diverse lipid classes, even after one year. <sup>13</sup>C-labeled lipid profiles varied significantly with soil texture; however, we found no difference between sandy and silty soils in lipid retention, suggesting soil texture may only play a minor role in modulating lipid persistence. Only two lipid subclasses were found to be persistent (<em>i.e</em>., retention of <sup>13</sup>C label without significant degradation or production): phosphatidylinositol lipids and hydroxyceramide lipids, both of which are negatively charged, possibly facilitating stabilization by mineral complexation. However, several other subclasses displayed substantial ongoing production. In particular, the accumulation of triacylglycerol lipids across soil textures suggests that storage lipids may be an important component of SOC, highlighting a potential target for management strategies to promote C retention by lipid accrual. Overall, the retention for over a year of <sup>13</sup>C label in microbial intact lipid biomarkers reveals the importance of efficient biomass production and turnover when considering microbial C contributions to SOM.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 110013"},"PeriodicalIF":10.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145314684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-10-22DOI: 10.1016/j.soilbio.2025.110022
Wei Wang , Yang Wang , Jian-Ming Li , Meng-Ying Li , Peng He , Yongxing Cui , Sheng-Jun Ji , Wen-Ying Wang , Levis Kavagi , Muhammd Ashraf , Yinglong Chen , Matthias C. Rillig , You-Cai Xiong
Long-term intercropping represents a key strategy to boost productive and ecological benefits. However, its potential to mitigate soil carbon-climate feedbacks remains unclear. Through a decade-long field investigation, we systematically characterized soil organic carbon (SOC) persistence, bioavailability, microbial traits, and soil properties in both intercropping and monoculture systems. Parallel controlled incubation experiments were conducted to quantify the temperature sensitivity (Q10) of SOC decomposition. The relative contributions of these biotic and abiotic factors to Q10 variability were ultimately determined using mixed-effects modeling. We found that cereal-legume intercropping significantly reduced the Q10 on average by 14.1–18.2 %, relative to monocultures, significantly facilitating carbon resilience of agroecosystems. This effect was closely associated with increased SOC persistence driven by both the chemical recalcitrance of SOC (e.g., Alkyl C and Aromatic C) and its chemical protection through mineral associations. Particularly, sustained intercropping was observed to elevate soil microbial abundance (12.0–39.8 %) and α-diversity (2.4–8.9 %), and network complexity mediated by the enrichment of keystone taxa. Mechanistically, both microorganisms and substrates showcased evident positive effects on improving the resilience of microbial networks and carbon stability, thereby reducing carbon loss caused by warming. Therefore, long-term cereal–legume intercropping can act as a scalable strategy to facilitate climate–smart agriculture and Sustainable Development Goals.
{"title":"Long-term intercropping mitigates warming-induced carbon loss via enhancing microbial and substrate resistance","authors":"Wei Wang , Yang Wang , Jian-Ming Li , Meng-Ying Li , Peng He , Yongxing Cui , Sheng-Jun Ji , Wen-Ying Wang , Levis Kavagi , Muhammd Ashraf , Yinglong Chen , Matthias C. Rillig , You-Cai Xiong","doi":"10.1016/j.soilbio.2025.110022","DOIUrl":"10.1016/j.soilbio.2025.110022","url":null,"abstract":"<div><div>Long-term intercropping represents a key strategy to boost productive and ecological benefits. However, its potential to mitigate soil carbon-climate feedbacks remains unclear. Through a decade-long field investigation, we systematically characterized soil organic carbon (SOC) persistence, bioavailability, microbial traits, and soil properties in both intercropping and monoculture systems. Parallel controlled incubation experiments were conducted to quantify the temperature sensitivity (Q<sub>10</sub>) of SOC decomposition. The relative contributions of these biotic and abiotic factors to Q<sub>10</sub> variability were ultimately determined using mixed-effects modeling. We found that cereal-legume intercropping significantly reduced the Q<sub>10</sub> on average by 14.1–18.2 %, relative to monocultures, significantly facilitating carbon resilience of agroecosystems. This effect was closely associated with increased SOC persistence driven by both the chemical recalcitrance of SOC (e.g., Alkyl C and Aromatic C) and its chemical protection through mineral associations. Particularly, sustained intercropping was observed to elevate soil microbial abundance (12.0–39.8 %) and α-diversity (2.4–8.9 %), and network complexity mediated by the enrichment of keystone taxa. Mechanistically, both microorganisms and substrates showcased evident positive effects on improving the resilience of microbial networks and carbon stability, thereby reducing carbon loss caused by warming. Therefore, long-term cereal–legume intercropping can act as a scalable strategy to facilitate climate–smart agriculture and Sustainable Development Goals.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 110022"},"PeriodicalIF":10.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145363841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-10-25DOI: 10.1016/j.soilbio.2025.110021
Si-moussi Sara , Thuiller Wilfried , Galbrun Esther , Decaëns Thibaud , Gérard Sylvain , Marchán Daniel F. , Marsden Claire , Capowiez Yvan , Hedde Mickaël
Earthworms are key drivers of soil function, influencing organic matter turnover, nutrient cycling, and soil structure. Understanding the environmental controls on their distribution is essential for predicting the impacts of land use and climate change on soil ecosystems. While local studies have identified abiotic drivers of earthworm communities, broad-scale spatial patterns remain underexplored. We developed a multi-species, multi-task deep learning model to jointly predict the distribution of 77 earthworm species across metropolitan France, using historical (1960–1970) and contemporary (1990–2020) records. The model integrates climate, soil, and land cover variables to estimate habitat suitability. We applied SHapley Additive exPlanations (SHAP) to identify key environmental drivers and used species clustering to reveal ecological response groups. The joint model achieved high predictive performance (TSS >0.7) and improved predictions for rare species compared to traditional species distribution models. Shared feature extraction across species allowed for more robust identification of common and contrasting environmental responses. Precipitation variability, temperature seasonality, and land cover emerged as dominant predictors of earthworm distribution but differed in ranking across species and functional groups. Species clustering into response groups to climatic, land use and soil revealed distinct ecological strategies including a gradient of sensitivity to precipitation seasonality, differential habitat preferences in terms of vegetation cover and wetness and trade-offs between soil acidity and organic matter quality. Our study advances both the methodological and ecological understanding of soil biodiversity. We demonstrate the utility of interpretable deep learning approaches for large-scale soil fauna modeling and provide new insights into earthworm habitat specialization. These findings highlight land cover and seasonal climate variability as efficient proxies for soil biodiversity, providing actionable indicators for global monitoring initiatives and helping to identify habitat requirements of earthworm species to guide emerging earthworm conservation strategies in the face of global environmental change.
{"title":"Digging deeper: deep joint species distribution modeling reveals environmental drivers of Earthworm Communities","authors":"Si-moussi Sara , Thuiller Wilfried , Galbrun Esther , Decaëns Thibaud , Gérard Sylvain , Marchán Daniel F. , Marsden Claire , Capowiez Yvan , Hedde Mickaël","doi":"10.1016/j.soilbio.2025.110021","DOIUrl":"10.1016/j.soilbio.2025.110021","url":null,"abstract":"<div><div>Earthworms are key drivers of soil function, influencing organic matter turnover, nutrient cycling, and soil structure. Understanding the environmental controls on their distribution is essential for predicting the impacts of land use and climate change on soil ecosystems. While local studies have identified abiotic drivers of earthworm communities, broad-scale spatial patterns remain underexplored. We developed a multi-species, multi-task deep learning model to jointly predict the distribution of 77 earthworm species across metropolitan France, using historical (1960–1970) and contemporary (1990–2020) records. The model integrates climate, soil, and land cover variables to estimate habitat suitability. We applied SHapley Additive exPlanations (SHAP) to identify key environmental drivers and used species clustering to reveal ecological response groups. The joint model achieved high predictive performance (TSS >0.7) and improved predictions for rare species compared to traditional species distribution models. Shared feature extraction across species allowed for more robust identification of common and contrasting environmental responses. Precipitation variability, temperature seasonality, and land cover emerged as dominant predictors of earthworm distribution but differed in ranking across species and functional groups. Species clustering into response groups to climatic, land use and soil revealed distinct ecological strategies including a gradient of sensitivity to precipitation seasonality, differential habitat preferences in terms of vegetation cover and wetness and trade-offs between soil acidity and organic matter quality. Our study advances both the methodological and ecological understanding of soil biodiversity. We demonstrate the utility of interpretable deep learning approaches for large-scale soil fauna modeling and provide new insights into earthworm habitat specialization. These findings highlight land cover and seasonal climate variability as efficient proxies for soil biodiversity, providing actionable indicators for global monitoring initiatives and helping to identify habitat requirements of earthworm species to guide emerging earthworm conservation strategies in the face of global environmental change.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 110021"},"PeriodicalIF":10.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145382552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Microbial-derived carbon plays a crucial role in mitigating climate change by forming stable carbon components through the soil microbial carbon pump. However, related studies have ignored the contribution of extracellular polymeric substances (EPS) as microbial extracellular metabolites to soil organic carbon (SOC), particularly in deeper soils. This study explored the distribution of EPS in six typical soil profiles (0–120 cm) from two parent materials (limestone and shale) and three land use types (dryland, woodland, and paddy land). The contribution of microbial biomass carbon (MBC) to SOC was significantly higher than that of EPS-carbon (EPS-C) in surface soils (0–40 cm), while EPS-C constituted a larger proportion in deeper soils (80–120 cm). The EPS accumulation efficiency (EPS-protein/MBC and EPS-polysaccharide/MBC) gradually increased with soil depth. This accumulation was strongly correlated with the abundance of g_Zixibacteria, g_Zavarzinella, g_Xylohypha, g_Xanthothecium, and g_Xanthagaricus. Data analysis revealed that β-glucosidase (BG) activity and total nitrogen (TN) content had significant negative effects on the EPS/SOC ratio. Additionally, extracellular enzyme analyses confirmed that low nitrogen availability in deeper soils enhanced the EPS accumulation efficiency, thereby increasing the EPS-C/SOC ratio along the soil profile. Overall, this study provides new insights into the composition of deep soil carbon pools and highlights the important role of EPS in deep soil carbon storage.
{"title":"Increased microbial extracellular polymeric substances as a key factor in deep soil organic carbon accumulation","authors":"Mengxi Feng , Ming Zhang , Peng Cai , Yichao Wu , Qingling Fu , Xin Zhang , Fei Miao , Wen Xing , Shuiqing Chen , Ke-Qing Xiao , Yong-Guan Zhu","doi":"10.1016/j.soilbio.2025.109998","DOIUrl":"10.1016/j.soilbio.2025.109998","url":null,"abstract":"<div><div>Microbial-derived carbon plays a crucial role in mitigating climate change by forming stable carbon components through the soil microbial carbon pump. However, related studies have ignored the contribution of extracellular polymeric substances (EPS) as microbial extracellular metabolites to soil organic carbon (SOC), particularly in deeper soils. This study explored the distribution of EPS in six typical soil profiles (0–120 cm) from two parent materials (limestone and shale) and three land use types (dryland, woodland, and paddy land). The contribution of microbial biomass carbon (MBC) to SOC was significantly higher than that of EPS-carbon (EPS-C) in surface soils (0–40 cm), while EPS-C constituted a larger proportion in deeper soils (80–120 cm). The EPS accumulation efficiency (EPS-protein/MBC and EPS-polysaccharide/MBC) gradually increased with soil depth. This accumulation was strongly correlated with the abundance of <em>g_Zixibacteria</em>, <em>g_Zavarzinella</em>, <em>g_Xylohypha</em>, <em>g_Xanthothecium</em>, and <em>g_Xanthagaricus</em>. Data analysis revealed that β-glucosidase (BG) activity and total nitrogen (TN) content had significant negative effects on the EPS/SOC ratio. Additionally, extracellular enzyme analyses confirmed that low nitrogen availability in deeper soils enhanced the EPS accumulation efficiency, thereby increasing the EPS-C/SOC ratio along the soil profile. Overall, this study provides new insights into the composition of deep soil carbon pools and highlights the important role of EPS in deep soil carbon storage.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 109998"},"PeriodicalIF":10.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145229988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-10-04DOI: 10.1016/j.soilbio.2025.109994
Eliana Di Lodovico , Shiyue Yang , Hauke Harms , Maximilian Meyer , Christian Fricke , Gabriele E. Schaumann , Thomas Maskow
Soil, as the largest terrestrial carbon sink, plays a pivotal role in the global carbon cycle. Soil microorganisms are fundamental to all biochemical processes in soil, ensuring its fertility and supporting a balanced ecosystem. Through their metabolic activities, these microorganisms drive energy and matter flows, mineralizing organic matter and releasing heat and CO2, which can be measured via calorespirometry. A key limitation of conventional calorimeters lies in their inability to combine high sample throughput with sufficiently large sample sizes while avoiding oxygen limitation during measurement. In order to overcome these weaknesses, we have developed a multi-channel macrocalorespirometer (CR-12) for soil analysis. To demonstrate its application, agricultural soil (Dikopshof, Luvisol) amended with 12C (unlabeled) and 13C (labeled) glucose was used in four experiments. Comparisons with commercial isothermal microcalorimeters confirmed the suitability of CR-12 for soil systems, providing reliable heat, CO2 measurements and calorespirometric ratios that align with known ranges for the aerobic turnover of carbohydrates. To further investigate the incorporation of carbon into the soil organic matter (SOM), a time series of soil samples amended with 13C-labeled glucose was subjected to mass spectrometric analysis (m/z 44 for 12C–CO2; m/z 45 for 13C–CO2) using thermogravimetry-differential scanning calorimetry-quadrupole mass spectrometry (TG-DSC-QMS). The integration of calorespirometric and mass spectrometric data demonstrated that combining these complementary techniques provides more detailed information on the fate of microbial carbon and energy turnover within SOM.
{"title":"Soil microbial metabolism: Insights from heat, CO2 emission and isotope analysis using a novel macrocalorespirometer","authors":"Eliana Di Lodovico , Shiyue Yang , Hauke Harms , Maximilian Meyer , Christian Fricke , Gabriele E. Schaumann , Thomas Maskow","doi":"10.1016/j.soilbio.2025.109994","DOIUrl":"10.1016/j.soilbio.2025.109994","url":null,"abstract":"<div><div>Soil, as the largest terrestrial carbon sink, plays a pivotal role in the global carbon cycle. Soil microorganisms are fundamental to all biochemical processes in soil, ensuring its fertility and supporting a balanced ecosystem. Through their metabolic activities, these microorganisms drive energy and matter flows, mineralizing organic matter and releasing heat and CO<sub>2</sub>, which can be measured via calorespirometry. A key limitation of conventional calorimeters lies in their inability to combine high sample throughput with sufficiently large sample sizes while avoiding oxygen limitation during measurement. In order to overcome these weaknesses, we have developed a multi-channel macrocalorespirometer (CR-12) for soil analysis. To demonstrate its application, agricultural soil (Dikopshof, Luvisol) amended with <sup>12</sup>C (unlabeled) and <sup>13</sup>C (labeled) glucose was used in four experiments. Comparisons with commercial isothermal microcalorimeters confirmed the suitability of CR-12 for soil systems, providing reliable heat, CO<sub>2</sub> measurements and calorespirometric ratios that align with known ranges for the aerobic turnover of carbohydrates. To further investigate the incorporation of carbon into the soil organic matter (SOM), a time series of soil samples amended with <sup>13</sup>C-labeled glucose was subjected to mass spectrometric analysis (m/z 44 for <sup>12</sup>C–CO<sub>2</sub>; m/z 45 for <sup>13</sup>C–CO<sub>2</sub>) using thermogravimetry-differential scanning calorimetry-quadrupole mass spectrometry (TG-DSC-QMS). The integration of calorespirometric and mass spectrometric data demonstrated that combining these complementary techniques provides more detailed information on the fate of microbial carbon and energy turnover within SOM.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 109994"},"PeriodicalIF":10.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145226709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-10-13DOI: 10.1016/j.soilbio.2025.110015
Jônatas Pedro da Silva , José João Lelis Leal de Souza , Deborah Pinheiro Dick , Rafael da Silva Teixeira , Emanuelle Mercês Barros Soares , Lucas Carvalho Gomes , Carlos Ernesto G.R. Schaefer
Understanding the biochemical composition and stabilization mechanisms of soil organic matter (SOM) is essential for assessing its persistence in rapidly changing polar environments. In this study, we investigated the molecular, elemental, and isotopic characteristics of SOM fractions—particulate (POM) and mineral-associated organic matter (MAOM)—in soils from the Byers Peninsula, Maritime Antarctica. Using δ13C and δ15N isotopic signatures, off-line TMAH thermochemolysis, solid-state 13C NMR spectroscopy, and thermogravimetric analysis (TGA), we identified key pathways of SOM stabilization and origin. Results revealed that lipid-derived compounds dominated both SOM fractions (39–96 %), with lignin detected exclusively in vascular plant residues and only marginally in MAOM. Isotopic signatures indicated multiple organic matter sources, including C3 plant biomass, marine inputs, ornithogenic deposits, and endolithic communities. Soils affected by cryoturbation and located on high and low platforms exhibited the highest carbon and nitrogen stocks, primarily stabilized in the MAOM fraction. Molecular analyses demonstrated significant variation in SOM composition across soil profiles. While most soils exhibited high proportions of labile O-alkyl C compounds, select profiles (notably P2 and P4) showed enriched aryl C and elevated thermostability, indicating advanced humification and greater molecular complexity. These findings highlight the central role of cryoturbation, hydrophobic interactions, and microbial-derived inputs in stabilizing SOM in the absence of lignin-rich vegetation. Overall, our integrated fingerprinting approach revealed that SOM persistence in Maritime Antarctica is governed by both physical protection (via MAOM) and biochemical resistance, offering critical insights into its potential response to ongoing climate-driven changes.
{"title":"Biochemical and molecular fingerprinting of soil organic matter fractions reveals diverse sources and stabilization mechanisms in Maritime Antarctica","authors":"Jônatas Pedro da Silva , José João Lelis Leal de Souza , Deborah Pinheiro Dick , Rafael da Silva Teixeira , Emanuelle Mercês Barros Soares , Lucas Carvalho Gomes , Carlos Ernesto G.R. Schaefer","doi":"10.1016/j.soilbio.2025.110015","DOIUrl":"10.1016/j.soilbio.2025.110015","url":null,"abstract":"<div><div>Understanding the biochemical composition and stabilization mechanisms of soil organic matter (SOM) is essential for assessing its persistence in rapidly changing polar environments. In this study, we investigated the molecular, elemental, and isotopic characteristics of SOM fractions—particulate (POM) and mineral-associated organic matter (MAOM)—in soils from the Byers Peninsula, Maritime Antarctica. Using δ<sup>13</sup>C and δ<sup>15</sup>N isotopic signatures, off-line TMAH thermochemolysis, solid-state <sup>13</sup>C NMR spectroscopy, and thermogravimetric analysis (TGA), we identified key pathways of SOM stabilization and origin. Results revealed that lipid-derived compounds dominated both SOM fractions (39–96 %), with lignin detected exclusively in vascular plant residues and only marginally in MAOM. Isotopic signatures indicated multiple organic matter sources, including C<sub>3</sub> plant biomass, marine inputs, ornithogenic deposits, and endolithic communities. Soils affected by cryoturbation and located on high and low platforms exhibited the highest carbon and nitrogen stocks, primarily stabilized in the MAOM fraction. Molecular analyses demonstrated significant variation in SOM composition across soil profiles. While most soils exhibited high proportions of labile O-alkyl C compounds, select profiles (notably P2 and P4) showed enriched aryl C and elevated thermostability, indicating advanced humification and greater molecular complexity. These findings highlight the central role of cryoturbation, hydrophobic interactions, and microbial-derived inputs in stabilizing SOM in the absence of lignin-rich vegetation. Overall, our integrated fingerprinting approach revealed that SOM persistence in Maritime Antarctica is governed by both physical protection (via MAOM) and biochemical resistance, offering critical insights into its potential response to ongoing climate-driven changes.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 110015"},"PeriodicalIF":10.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145283211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-10-16DOI: 10.1016/j.soilbio.2025.110020
Xin Qin , Weibo Kong , Zhao Peng , Liangchen Guo , Xinyi Feng , Nannan Ge , Liping Qiu , Mingan Shao , Guohua Rong , Xiaorong Wei
Afforestation is acknowledged as a key strategy for increasing carbon (C) and nitrogen (N) sequestration. However, the temporal dynamics and environmental drivers of organic carbon (OC) and N turnover within soil aggregates during afforestation remain poorly understood. Here, we applied a δ13C- and δ15N-based two-endmember isotope mixing model to quantify the proportions, stocks, and decadal average accumulation rates (AARs) of newly derived and legacy OC and N in soil aggregates along a 30-year afforestation chronosequence on China's Loess Plateau, spanning gradients of soil texture and climate. Afforestation substantially altered aggregate-level C and N dynamics, with stocks of newly derived OC and N progressively increasing, whereas legacy pools remained largely stable. The first decade represented a critical window of biogeochemical transformation, during which surface (0–10 cm) macroaggregates (MAs) acted as hotspots for new OC and N accumulation, exhibiting the highest AARs that declined sharply in subsequent decades. Environmental factors (MAP, MAT, pH) strongly controlled early-stage OC and N accumulation, but their influence weakened substantially over time, indicating a gradual shift from climate-driven dynamics to intrinsic soil stabilization processes. Overall, this study reveals the differentiated dynamics of new and legacy OC and N accumulation during afforestation and their environmental controls, underscoring the critical role of early-stage processes in aggregate-level C and N sequestration. The transition from strong early environmental controls to later intrinsic stabilization highlights the necessity of incorporating stage- and depth-specific representations into terrestrial C–N cycling models to better capture the mechanisms underpinning long-term C storage.
{"title":"Temporal dynamics and environmental controls of carbon and nitrogen stabilization in soil aggregates during afforestation on the Loess Plateau","authors":"Xin Qin , Weibo Kong , Zhao Peng , Liangchen Guo , Xinyi Feng , Nannan Ge , Liping Qiu , Mingan Shao , Guohua Rong , Xiaorong Wei","doi":"10.1016/j.soilbio.2025.110020","DOIUrl":"10.1016/j.soilbio.2025.110020","url":null,"abstract":"<div><div>Afforestation is acknowledged as a key strategy for increasing carbon (C) and nitrogen (N) sequestration. However, the temporal dynamics and environmental drivers of organic carbon (OC) and N turnover within soil aggregates during afforestation remain poorly understood. Here, we applied a δ<sup>13</sup>C- and δ<sup>15</sup>N-based two-endmember isotope mixing model to quantify the proportions, stocks, and decadal average accumulation rates (AARs) of newly derived and legacy OC and N in soil aggregates along a 30-year afforestation chronosequence on China's Loess Plateau, spanning gradients of soil texture and climate. Afforestation substantially altered aggregate-level C and N dynamics, with stocks of newly derived OC and N progressively increasing, whereas legacy pools remained largely stable. The first decade represented a critical window of biogeochemical transformation, during which surface (0–10 cm) macroaggregates (MAs) acted as hotspots for new OC and N accumulation, exhibiting the highest AARs that declined sharply in subsequent decades. Environmental factors (MAP, MAT, pH) strongly controlled early-stage OC and N accumulation, but their influence weakened substantially over time, indicating a gradual shift from climate-driven dynamics to intrinsic soil stabilization processes. Overall, this study reveals the differentiated dynamics of new and legacy OC and N accumulation during afforestation and their environmental controls, underscoring the critical role of early-stage processes in aggregate-level C and N sequestration. The transition from strong early environmental controls to later intrinsic stabilization highlights the necessity of incorporating stage- and depth-specific representations into terrestrial C–N cycling models to better capture the mechanisms underpinning long-term C storage.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 110020"},"PeriodicalIF":10.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-09-29DOI: 10.1016/j.soilbio.2025.109993
Yuwen Lin , Xinyu Yi , Chen Ning , Yong Li , Yinghe Peng , Shuguang Liu , Changhui Peng , Xiaoyong Chen , Shuailong Feng , Pengpeng Duan , Yan Liu , Juyang Liao
Methane (CH4) emissions differ between urban and rural wetlands, while the microbial mechanisms associated with these differences have not been clearly identified. Here, we characterized the CH4-cycling microbial communities and their functional metabolic pathways between urban and rural wetlands by using 16S rRNA amplicon sequencing, metagenomes and CH4 flux measurements. Results showed that rural wetlands primarily utilized acetate/CO2-dependent methanogenic pathway and complete carbon oxidation to CO2 in methanotrophic pathway. Whereas, urban wetlands were dominated by the coenzyme M-dependent methanogenic pathway and trimethylamine catabolism, with methanotrophic pathway characterized by enhanced carbon assimilation capacity. In wetland water, while the abundances of methanogens in urban water were 5-fold lower than in rural water, urban water exhibited stronger microbial cooperation and higher metabolic flexibility, which were associated with an 85 % higher water-atmosphere CH4 flux compared to rural counterparts. In wetland soil, key environmental factors (e.g. higher pH and lower organic matter content compared to rural sites) shaped distinct microbial community structures and CH4 metabolic traits. These differences were shown as higher functional gene diversity, more stable co-occurrence networks, and greater metabolic flexibility, which were linked to a 6-fold higher soil CH4 emissions than in rural soil. This study describes the microbial mechanisms underlying CH4 emission differences between urban and rural wetlands, providing insights into microbially mediated CH4 cycling in urban wetland ecosystems.
{"title":"Microbial mechanisms underlying differences of methane emissions between urban and rural wetlands","authors":"Yuwen Lin , Xinyu Yi , Chen Ning , Yong Li , Yinghe Peng , Shuguang Liu , Changhui Peng , Xiaoyong Chen , Shuailong Feng , Pengpeng Duan , Yan Liu , Juyang Liao","doi":"10.1016/j.soilbio.2025.109993","DOIUrl":"10.1016/j.soilbio.2025.109993","url":null,"abstract":"<div><div>Methane (CH<sub>4</sub>) emissions differ between urban and rural wetlands, while the microbial mechanisms associated with these differences have not been clearly identified. Here, we characterized the CH<sub>4</sub>-cycling microbial communities and their functional metabolic pathways between urban and rural wetlands by using 16S rRNA amplicon sequencing, metagenomes and CH<sub>4</sub> flux measurements. Results showed that rural wetlands primarily utilized acetate/CO<sub>2</sub>-dependent methanogenic pathway and complete carbon oxidation to CO<sub>2</sub> in methanotrophic pathway. Whereas, urban wetlands were dominated by the coenzyme M-dependent methanogenic pathway and trimethylamine catabolism, with methanotrophic pathway characterized by enhanced carbon assimilation capacity. In wetland water, while the abundances of methanogens in urban water were 5-fold lower than in rural water, urban water exhibited stronger microbial cooperation and higher metabolic flexibility, which were associated with an 85 % higher water-atmosphere CH<sub>4</sub> flux compared to rural counterparts. In wetland soil, key environmental factors (e.g. higher pH and lower organic matter content compared to rural sites) shaped distinct microbial community structures and CH<sub>4</sub> metabolic traits. These differences were shown as higher functional gene diversity, more stable co-occurrence networks, and greater metabolic flexibility, which were linked to a 6-fold higher soil CH<sub>4</sub> emissions than in rural soil. This study describes the microbial mechanisms underlying CH<sub>4</sub> emission differences between urban and rural wetlands, providing insights into microbially mediated CH<sub>4</sub> cycling in urban wetland ecosystems.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 109993"},"PeriodicalIF":10.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145183198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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