Pub Date : 2025-11-21DOI: 10.1016/j.soilbio.2025.110043
Shiyue Yang , Sven Paufler , Hauke Harms , Matthias Kästner , Anja Miltner , Thomas Maskow
Soil, as the largest terrestrial carbon sink, plays a crucial role in carbon sequestration. Within soil systems, microorganisms decompose soil organic matter to generate energy and obtain carbon for growth, concomitantly release heat and CO2 as metabolic byproducts. The calorespirometric (CR) ratio – defined as the ratio of heat production to CO2 evolution, is a key indicator of carbon use efficiency and soil anaerobicity. However, conventional methodologies typically measure heat and CO2 separately, with CO2 often quantified by intermittent sampling. This discontinuous approach, compounded by the inherent heterogeneity of soil, introduces uncertainties in calorespirometric analysis. To address this limitation, an infrared CO2 sensor was mounted onto a stainless-steel calorimetric ampoule, containing soil-glucose mixtures, enabling simultaneous real-time measurements within an isothermal microcalorimeter. The novel configuration permits continuous monitoring of both parameters, validated through comparative analysis with traditional methods. The derived CR ratios aligned with theoretical predictions for carbohydrates metabolism. Furthermore, parallel oxygen measurements enabled quantification of CR ratio based on O2 (heat-to-O2), and the respiratory quotient (CO2-to-O2), offering deeper insight into microbial carbon-energy coupling and turnover in soil systems. This methodological advancement enhances the capacity to interrogate soil biogeochemical processes under dynamic environmental conditions.
{"title":"A novel approach for calorespirometry: Integrating a CO2 sensor into an isothermal microcalorimeter for simultaneous measurement of microbial heat evolution and mineralization","authors":"Shiyue Yang , Sven Paufler , Hauke Harms , Matthias Kästner , Anja Miltner , Thomas Maskow","doi":"10.1016/j.soilbio.2025.110043","DOIUrl":"10.1016/j.soilbio.2025.110043","url":null,"abstract":"<div><div>Soil, as the largest terrestrial carbon sink, plays a crucial role in carbon sequestration. Within soil systems, microorganisms decompose soil organic matter to generate energy and obtain carbon for growth, concomitantly release heat and CO<sub>2</sub> as metabolic byproducts. The calorespirometric (CR) ratio – defined as the ratio of heat production to CO<sub>2</sub> evolution, is a key indicator of carbon use efficiency and soil anaerobicity. However, conventional methodologies typically measure heat and CO<sub>2</sub> separately, with CO<sub>2</sub> often quantified by intermittent sampling. This discontinuous approach, compounded by the inherent heterogeneity of soil, introduces uncertainties in calorespirometric analysis. To address this limitation, an infrared CO<sub>2</sub> sensor was mounted onto a stainless-steel calorimetric ampoule, containing soil-glucose mixtures, enabling simultaneous real-time measurements within an isothermal microcalorimeter. The novel configuration permits continuous monitoring of both parameters, validated through comparative analysis with traditional methods. The derived CR ratios aligned with theoretical predictions for carbohydrates metabolism. Furthermore, parallel oxygen measurements enabled quantification of CR ratio based on O<sub>2</sub> (heat-to-O<sub>2</sub>), and the respiratory quotient (CO<sub>2</sub>-to-O<sub>2</sub>), offering deeper insight into microbial carbon-energy coupling and turnover in soil systems. This methodological advancement enhances the capacity to interrogate soil biogeochemical processes under dynamic environmental conditions.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110043"},"PeriodicalIF":10.3,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145567786","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 : 2025-11-20DOI: 10.1016/j.soilbio.2025.110042
Elisa Karina Albrecht , Maire Holz , Joscha N. Becker
Legume-soil interactions are well recognised for their role in ecosystem nutrient cycling, yet specific mechanisms such as nodule senescence effects on soil nitrogen (N) and carbon (C) cycling remain poorly understood. Here, we investigated the effect of nodule senescence on soil enzyme activity and soil biochemical properties in the rhizospheres of cowpea (Vigna unguiculata) during plant growth. We conducted a rhizobox experiment using soil from the Kavango (loamy sand) and Omusati (sandy soil) regions in Northern Namibia under controlled temperature and optimum water conditions. To investigate spatial and temporal C and N release, in-situ zymography was conducted at early vegetative, flowering, and maturity stage (i.e. one day after the start of nodule senescence) with six replicates per soil. Three enzymes, representing the C (β-glucosidase, chitinase) and N (chitinase, leucine-aminopeptidase) cycle, were investigated. At each plant growth stage, three additional plants per soil were harvested to identify changes in soil properties, including soil organic carbon, total N, mineral N, and pH. Our results showed that enzyme activities did not vary significantly during plant growth in rhizospheres and at nodule and root surfaces. In contrast, enzyme activities significantly increased with plant growth in bulk soil, especially β-glucosidase and chitinase, with a peak at maturity stage. Particularly in the sandy soil, nodule senescence significantly increased enzyme activities. This indicates enhanced organic matter decomposition and nutrient release mainly from the nodule-influenced rhizosphere to the bulk soil and might be attributed to rhizodeposition and microbial responses to substrate availability. We conclude that nodule senescence of legumes is an important driver of enzyme activity and can be a crucial factor for managing soil properties in low-nutrient soils.
{"title":"Spatio-temporal distribution of enzyme activities in cowpea rhizosphere – the role of plant growth stages and nodule senescence","authors":"Elisa Karina Albrecht , Maire Holz , Joscha N. Becker","doi":"10.1016/j.soilbio.2025.110042","DOIUrl":"10.1016/j.soilbio.2025.110042","url":null,"abstract":"<div><div>Legume-soil interactions are well recognised for their role in ecosystem nutrient cycling, yet specific mechanisms such as nodule senescence effects on soil nitrogen (N) and carbon (C) cycling remain poorly understood. Here, we investigated the effect of nodule senescence on soil enzyme activity and soil biochemical properties in the rhizospheres of cowpea (<em>Vigna unguiculata</em>) during plant growth. We conducted a rhizobox experiment using soil from the Kavango (loamy sand) and Omusati (sandy soil) regions in Northern Namibia under controlled temperature and optimum water conditions. To investigate spatial and temporal C and N release, <em>in-situ</em> zymography was conducted at early vegetative, flowering, and maturity stage (i.e. one day after the start of nodule senescence) with six replicates per soil. Three enzymes, representing the C (β-glucosidase, chitinase) and N (chitinase, leucine-aminopeptidase) cycle, were investigated. At each plant growth stage, three additional plants per soil were harvested to identify changes in soil properties, including soil organic carbon, total N, mineral N, and pH. Our results showed that enzyme activities did not vary significantly during plant growth in rhizospheres and at nodule and root surfaces. In contrast, enzyme activities significantly increased with plant growth in bulk soil, especially β-glucosidase and chitinase, with a peak at maturity stage. Particularly in the sandy soil, nodule senescence significantly increased enzyme activities. This indicates enhanced organic matter decomposition and nutrient release mainly from the nodule-influenced rhizosphere to the bulk soil and might be attributed to rhizodeposition and microbial responses to substrate availability. We conclude that nodule senescence of legumes is an important driver of enzyme activity and can be a crucial factor for managing soil properties in low-nutrient soils.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110042"},"PeriodicalIF":10.3,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145554827","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 : 2025-11-20DOI: 10.1016/j.soilbio.2025.110041
Robin Wilgan, Marta Brygida Kujawska, Tomasz Leski
Invasive trees can significantly transform habitats, modify nutrient cycles, and change microbial community composition and assembly processes. Therefore, they pose significant threat to nature conservation and sustainable management. However, the impacts of invasive trees on the trophy and taxonomy of soil mycobiomes in forest ecosystems remain unclear. In this study, we investigated how the invasive tree species – Robinia pseudoacacia, Prunus serotina, and Quercus rubra – influence soil mycobiomes in forest ecosystems. We analysed soil samples taken from an invasive tree density gradient, using 81 study stands in Poland, Central Europe. The soil mycobiome was identified using Next-Generation Sequencing of the ITS2 rDNA barcode region for fungi.
The three invasive tree species had a similar impact on the soil mycobiome. Each invasive tree reduced the relative abundance of root endophytes and increased the relative abundance of pathogens in soil. The response of saprotrophs varied, but they generally showed no negative response to invasive trees. The mycobial community composition and abundance of trophic guilds changed substantially, but taxa richness and diversity indices were weak predictors of disturbances. Robinia pseudoacacia had the most significant impact on the soil mycobiome, and Robinia-invaded stands had significantly higher N–NO3, potassium, and calcium content in soil. It is a major concern given that Robinia is probably the most common invasive tree in Europe. We recommend further investigation of the impact of R. pseudoacacia on soil microbiomes in various types of ecosystems to determine the habitats in which Robinia is most detrimental. This will inform targeted invasive species management.
{"title":"Biological invasions of three different alien tree species has comparable influence in soil mycobiome: increase the abundance of pathogens, and decomposers, but decrease root-associated endophytic symbionts","authors":"Robin Wilgan, Marta Brygida Kujawska, Tomasz Leski","doi":"10.1016/j.soilbio.2025.110041","DOIUrl":"10.1016/j.soilbio.2025.110041","url":null,"abstract":"<div><div>Invasive trees can significantly transform habitats, modify nutrient cycles, and change microbial community composition and assembly processes. Therefore, they pose significant threat to nature conservation and sustainable management. However, the impacts of invasive trees on the trophy and taxonomy of soil mycobiomes in forest ecosystems remain unclear. In this study, we investigated how the invasive tree species – <em>Robinia pseudoacacia</em>, <em>Prunus serotina</em>, and <em>Quercus rubra</em> – influence soil mycobiomes in forest ecosystems. We analysed soil samples taken from an invasive tree density gradient, using 81 study stands in Poland, Central Europe. The soil mycobiome was identified using Next-Generation Sequencing of the ITS2 rDNA barcode region for fungi.</div><div>The three invasive tree species had a similar impact on the soil mycobiome. Each invasive tree reduced the relative abundance of root endophytes and increased the relative abundance of pathogens in soil. The response of saprotrophs varied, but they generally showed no negative response to invasive trees. The mycobial community composition and abundance of trophic guilds changed substantially, but taxa richness and diversity indices were weak predictors of disturbances. <em>Robinia pseudoacacia</em> had the most significant impact on the soil mycobiome, and <em>Robinia</em>-invaded stands had significantly higher N–NO3, potassium, and calcium content in soil. It is a major concern given that <em>Robinia</em> is probably the most common invasive tree in Europe. We recommend further investigation of the impact of <em>R. pseudoacacia</em> on soil microbiomes in various types of ecosystems to determine the habitats in which <em>Robinia</em> is most detrimental. This will inform targeted invasive species management.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110041"},"PeriodicalIF":10.3,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145554828","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 : 2025-11-14DOI: 10.1016/j.soilbio.2025.110039
L. Paillat , P. Cannavo , A. Mouret , E. Metzger , L. Huché-Thélier , F. Barraud , A.S. Azimi , J. Cardenas , C. Banfield , Y. Kuzyakov , M. Dippold , R. Guénon
Organic fertilization is a recognized sustainable practice in agriculture and represents a major nutrient source for microbes and plants in these systems. Microbes produce hydrolytic enzymes to mineralize nutrients from organic forms into mineral forms to satisfy their own needs, and thus can compete with plants for these mineralized nutrients. Thus, interactions between plants and microbes in the rhizosphere determine nutrient availability and flows. We investigated these relations, using a spatial approach that combined zymography with the method of diffusive equilibrium in thin films (DET) to localize enzyme activity and N and P availabilities simultaneously. Basil (Ocimum basilicum L.) was grown in rhizoboxes filled with an organo-mineral crop soil (MS) or 100 % organic peat soil (OS) that was unfertilized or fertilized locally with horn meal for 20 days. In general, enzyme activities were higher in MS than in OS, but the stimulation of leucine aminopeptidase (LAP) activity and associated decrease in nutrient availability was 2 times as strong in OS as in MS. A rhizosphere effect, in which rhizodeposits stimulated enzyme activity, was clearly observed in OS. Fertilization increased LAP activity and nutrient availability near the location of fertilization, which increased basil growth in OS but not in MS. β-glucosidase, acid phosphatase and N-acetyl-glucosaminidase activities responded weakly to fertilization and the rhizosphere. By relating enzyme activities mapped by zymography to nutrient availability mapped by DET, we identified microbial hotspots in the rhizosphere where most nutrient mobilization processes and competition between plants and microbes occurred.
{"title":"Locating enzyme activities and nutrients in the rhizosphere: Combining zymography and DET methods","authors":"L. Paillat , P. Cannavo , A. Mouret , E. Metzger , L. Huché-Thélier , F. Barraud , A.S. Azimi , J. Cardenas , C. Banfield , Y. Kuzyakov , M. Dippold , R. Guénon","doi":"10.1016/j.soilbio.2025.110039","DOIUrl":"10.1016/j.soilbio.2025.110039","url":null,"abstract":"<div><div>Organic fertilization is a recognized sustainable practice in agriculture and represents a major nutrient source for microbes and plants in these systems. Microbes produce hydrolytic enzymes to mineralize nutrients from organic forms into mineral forms to satisfy their own needs, and thus can compete with plants for these mineralized nutrients. Thus, interactions between plants and microbes in the rhizosphere determine nutrient availability and flows. We investigated these relations, using a spatial approach that combined zymography with the method of diffusive equilibrium in thin films (DET) to localize enzyme activity and N and P availabilities simultaneously. Basil (<em>Ocimum basilicum</em> L.) was grown in rhizoboxes filled with an organo-mineral crop soil (MS) or 100 % organic peat soil (OS) that was unfertilized or fertilized locally with horn meal for 20 days. In general, enzyme activities were higher in MS than in OS, but the stimulation of leucine aminopeptidase (LAP) activity and associated decrease in nutrient availability was 2 times as strong in OS as in MS. A rhizosphere effect, in which rhizodeposits stimulated enzyme activity, was clearly observed in OS. Fertilization increased LAP activity and nutrient availability near the location of fertilization, which increased basil growth in OS but not in MS. β-glucosidase, acid phosphatase and N-acetyl-glucosaminidase activities responded weakly to fertilization and the rhizosphere. By relating enzyme activities mapped by zymography to nutrient availability mapped by DET, we identified microbial hotspots in the rhizosphere where most nutrient mobilization processes and competition between plants and microbes occurred.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110039"},"PeriodicalIF":10.3,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145509547","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 : 2025-11-13DOI: 10.1016/j.soilbio.2025.110037
Eduardo Vázquez , Jaanis Juhanson , Sara Hallin , Marie Spohn
Tree productivity in northern regions is limited by low soil nitrogen (N) availability, and biological N2 fixation is a crucial N input to these forests. To enhance forest productivity, N fertilization has been proposed as a strategy although it may negatively affect N2 fixation and the abundance of diazotrophic microorganisms. In contrast to N2 fixation by the cyanobacteria-moss associations, there is limited understanding of non-symbiotic N2 fixation in northern forest soils and the free-living diazotrophs involved. To assess the impact of N fertilization on non-symbiotic N2 fixation and the diazotrophic community in soil, we sampled 15 forest sites along a latitudinal gradient in Sweden that are part of a fertilization experiment. Fertilization started between 41 and 55 years ago, using ammonium nitrate at 100–150 kg N ha−1 every 5th year for the first 25 years and thereafter every 7th year. We measured non-symbiotic N2 fixation in the soil organic layer in laboratory incubations and analyzed the diazotrophic community. Both the abundance and diversity of diazotrophs decreased in response to N fertilization. However, this decline did not translate into significant changes in non-symbiotic N2 fixation rates (22.4 ± 4.2 and 22.5 ± 5.7 ng N g−1 dry weight soil h−1 in the control and N treatments, respectively). Yet, N2 fixation per area increased by 24 % in fertilized plots because of the increase in the organic layer stock caused by higher primary production. Additionally, we observed an influence of fertilization and mean annual temperature on diazotroph community composition across the gradient. Our findings indicate that N fertilization in northern forests strongly affects diazotrophs, the organic layer stock, and N2 fixation. Although N fertilization positively affected the N2 fixation rate per area in this experiment, its negative effect on diazotroph diversity might reduce N2 fixation in the long run.
北方地区的树木生产力受到土壤氮有效性低的限制，而生物固氮是这些森林至关重要的氮输入。为了提高森林生产力，尽管氮肥可能会对固氮和重氮营养微生物的丰度产生负面影响，但仍被提出作为一种策略。与蓝藻-苔藓联合固氮相反，对北方森林土壤中非共生固氮和自由生活重氮营养菌的了解有限。为了评估氮肥对土壤非共生固氮和重氮营养群落的影响，我们在瑞典沿纬度梯度取样了15个森林样地，作为施肥试验的一部分。在41 - 55年前开始施肥，前25年每5年施用100-150 kg N hm -1硝酸铵，此后每7年施用一次。在实验室培养条件下测定了土壤有机层非共生固氮量，并对重氮营养化群落进行了分析。重氮营养体的丰度和多样性随施氮量的增加而降低。然而，这种下降并未转化为非共生固氮率的显著变化（对照和施氮处理分别为22.4±4.2和22.5±5.7 ng N g-1干重土壤h-1）。然而，施肥地块的单位面积固氮量增加了24%，这是由于初级产量增加导致有机层储量增加。此外，我们还观察了施肥和年平均温度对重氮营养菌群落组成的影响。研究结果表明，氮肥对北方森林重氮营养物、有机层储量和氮固定有显著影响。虽然在本试验中，施氮对单位面积固氮率有积极影响，但从长期来看，施氮对重氮养分多样性的负面影响可能会降低氮素的固定。
{"title":"Nitrogen fertilization does not affect non-symbiotic N2 fixation in northern forest soils despite its negative impacts on diazotroph communities","authors":"Eduardo Vázquez , Jaanis Juhanson , Sara Hallin , Marie Spohn","doi":"10.1016/j.soilbio.2025.110037","DOIUrl":"10.1016/j.soilbio.2025.110037","url":null,"abstract":"<div><div>Tree productivity in northern regions is limited by low soil nitrogen (N) availability, and biological N<sub>2</sub> fixation is a crucial N input to these forests. To enhance forest productivity, N fertilization has been proposed as a strategy although it may negatively affect N<sub>2</sub> fixation and the abundance of diazotrophic microorganisms. In contrast to N<sub>2</sub> fixation by the cyanobacteria-moss associations, there is limited understanding of non-symbiotic N<sub>2</sub> fixation in northern forest soils and the free-living diazotrophs involved. To assess the impact of N fertilization on non-symbiotic N<sub>2</sub> fixation and the diazotrophic community in soil, we sampled 15 forest sites along a latitudinal gradient in Sweden that are part of a fertilization experiment. Fertilization started between 41 and 55 years ago, using ammonium nitrate at 100–150 kg N ha<sup>−1</sup> every 5th year for the first 25 years and thereafter every 7th year. We measured non-symbiotic N<sub>2</sub> fixation in the soil organic layer in laboratory incubations and analyzed the diazotrophic community. Both the abundance and diversity of diazotrophs decreased in response to N fertilization. However, this decline did not translate into significant changes in non-symbiotic N<sub>2</sub> fixation rates (22.4 ± 4.2 and 22.5 ± 5.7 ng N g<sup>−1</sup> dry weight soil h<sup>−1</sup> in the control and N treatments, respectively). Yet, N<sub>2</sub> fixation per area increased by 24 % in fertilized plots because of the increase in the organic layer stock caused by higher primary production. Additionally, we observed an influence of fertilization and mean annual temperature on diazotroph community composition across the gradient. Our findings indicate that N fertilization in northern forests strongly affects diazotrophs, the organic layer stock, and N<sub>2</sub> fixation. Although N fertilization positively affected the N<sub>2</sub> fixation rate per area in this experiment, its negative effect on diazotroph diversity might reduce N<sub>2</sub> fixation in the long run.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110037"},"PeriodicalIF":10.3,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145498681","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 : 2025-11-11DOI: 10.1016/j.soilbio.2025.110038
Carolina Voigt , Henri M.P. Siljanen , Carlos Palacin-Lizarbe , Kathryn A. Bennett , Charles Chevrier-Dion , Claudia Fiencke , Christian Knoblauch , Charlotte Marquis , Maija E. Marushchak , Taija Saarela , Evan J. Wilcox , Oliver Sonnentag
Atmospheric methane (CH4) uptake by arctic soils is widespread in dry tundra ecosystems. However, the environmental controls regulating CH4 uptake are poorly understood, particularly such as soil nutrient availability or microbial community composition. Here, we analyzed the relative abundance and community structure of functional gene markers associated with CH4 and mineral nitrogen (N) cycling in two contrasting tundra types in the Western Canadian Arctic using a targeted metagenomics approach. Microbial data were compared to soil properties, macro- and micronutrient concentrations, and CH4 fluxes during an entire growing season (May–August). We find that soil pH was the most important control on gene distribution between the studied microsites. Methanotrophs associated with the upland soil cluster α (USCα) dominated in polygonal tundra (low pH), while USCγ dominated in upland tundra (high pH). Methane uptake rates ranged from −15 to −27 μg CH4–C m−2 h−1 (growing season mean) and increased with higher relative abundances of USCα and USCγ. Although CH4 uptake rates were similar between microsites, our microbial data indicate different mechanisms to cope with N limitation in these nutrient-limited tundra environments: upland tundra was characterized by genes involved in denitrification and N retention, while polygonal tundra contained genes associated with biological N fixation. Our study highlights the need for an integrated view on interactions between CH4 oxidation and N availability for methanotrophs in arctic tundra soils.
{"title":"Contrasting methanotrophic communities between upland and polygonal tundra and their link to nitrogen metabolism and methane uptake in the Western Canadian Arctic","authors":"Carolina Voigt , Henri M.P. Siljanen , Carlos Palacin-Lizarbe , Kathryn A. Bennett , Charles Chevrier-Dion , Claudia Fiencke , Christian Knoblauch , Charlotte Marquis , Maija E. Marushchak , Taija Saarela , Evan J. Wilcox , Oliver Sonnentag","doi":"10.1016/j.soilbio.2025.110038","DOIUrl":"10.1016/j.soilbio.2025.110038","url":null,"abstract":"<div><div>Atmospheric methane (CH<sub>4</sub>) uptake by arctic soils is widespread in dry tundra ecosystems. However, the environmental controls regulating CH<sub>4</sub> uptake are poorly understood, particularly such as soil nutrient availability or microbial community composition. Here, we analyzed the relative abundance and community structure of functional gene markers associated with CH<sub>4</sub> and mineral nitrogen (N) cycling in two contrasting tundra types in the Western Canadian Arctic using a targeted metagenomics approach. Microbial data were compared to soil properties, macro- and micronutrient concentrations, and CH<sub>4</sub> fluxes during an entire growing season (May–August). We find that soil pH was the most important control on gene distribution between the studied microsites. Methanotrophs associated with the upland soil cluster α (USCα) dominated in polygonal tundra (low pH), while USCγ dominated in upland tundra (high pH). Methane uptake rates ranged from −15 to −27 μg CH<sub>4</sub>–C m<sup>−2</sup> h<sup>−1</sup> (growing season mean) and increased with higher relative abundances of USCα and USCγ. Although CH<sub>4</sub> uptake rates were similar between microsites, our microbial data indicate different mechanisms to cope with N limitation in these nutrient-limited tundra environments: upland tundra was characterized by genes involved in denitrification and N retention, while polygonal tundra contained genes associated with biological N fixation. Our study highlights the need for an integrated view on interactions between CH<sub>4</sub> oxidation and N availability for methanotrophs in arctic tundra soils.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110038"},"PeriodicalIF":10.3,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145485831","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 : 2025-11-05DOI: 10.1016/j.soilbio.2025.110036
Alexine Ehlinger , Sara Martinengo , Maria Sofia Lasagna , Fulvia Tambone , Maria Martin , Luisella Celi , Daniel Said-Pullicino
Rice roots represent an important contributor to belowground organic carbon (C) inputs in paddy soils. They have characteristic traits specifically linked to their growth in predominantly anoxic soils, such as the presence of iron plaque (IP) on the roots surfaces and the development of apoplastic barriers through the lignification/suberization of cell wall exteriors. Nevertheless, evidence on how these traits influence microbial decomposition and root C turnover in the detritusphere is still lacking. In this work we evaluated how water management practices, involving rice cropping under continuous flooding (CF) and alternate wetting and drying (AWD), affect coarse and fine root C inputs, their biochemical quality and IP contents. Moreover, by harnessing the difference in natural abundance 13C between C3 rice plant residues added to a C4 maize-cropped soil, we elucidated how these traits affect microbial decomposition, soil organic C (SOC) priming and the contribution of root C to different functional SOC pools over a 90-d microcosm incubation under aerobic conditions. The main findings suggest that growing rice under CF resulted in a lower abundance of fine roots and favoured the accumulation of root-associated IP compared to AWD. This, together with their greater content of aromatic and alkyl C moieties, was mainly responsible for the slower turnover of fine compared to coarse roots, and their slightly greater contribution to mineral-associated OC pools, without considerably affecting native SOC priming. We conclude that evaluating the effects of water management practices, among other parameters, on belowground C inputs and rice root traits may help decipher the root C turnover and contribution to stable SOC in rice paddies.
{"title":"The influence of iron plaque and root traits on organic carbon turnover in the rice root detritusphere","authors":"Alexine Ehlinger , Sara Martinengo , Maria Sofia Lasagna , Fulvia Tambone , Maria Martin , Luisella Celi , Daniel Said-Pullicino","doi":"10.1016/j.soilbio.2025.110036","DOIUrl":"10.1016/j.soilbio.2025.110036","url":null,"abstract":"<div><div>Rice roots represent an important contributor to belowground organic carbon (C) inputs in paddy soils. They have characteristic traits specifically linked to their growth in predominantly anoxic soils, such as the presence of iron plaque (IP) on the roots surfaces and the development of apoplastic barriers through the lignification/suberization of cell wall exteriors. Nevertheless, evidence on how these traits influence microbial decomposition and root C turnover in the detritusphere is still lacking. In this work we evaluated how water management practices, involving rice cropping under continuous flooding (CF) and alternate wetting and drying (AWD), affect coarse and fine root C inputs, their biochemical quality and IP contents. Moreover, by harnessing the difference in natural abundance <sup>13</sup>C between C3 rice plant residues added to a C4 maize-cropped soil, we elucidated how these traits affect microbial decomposition, soil organic C (SOC) priming and the contribution of root C to different functional SOC pools over a 90-d microcosm incubation under aerobic conditions. The main findings suggest that growing rice under CF resulted in a lower abundance of fine roots and favoured the accumulation of root-associated IP compared to AWD. This, together with their greater content of aromatic and alkyl C moieties, was mainly responsible for the slower turnover of fine compared to coarse roots, and their slightly greater contribution to mineral-associated OC pools, without considerably affecting native SOC priming. We conclude that evaluating the effects of water management practices, among other parameters, on belowground C inputs and rice root traits may help decipher the root C turnover and contribution to stable SOC in rice paddies.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110036"},"PeriodicalIF":10.3,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145441531","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 : 2025-11-03DOI: 10.1016/j.soilbio.2025.110028
Chao Wang , Xiaoyi Huang , Jing Yu , Yue Liu , Fangying Qu , Jian Wang , Xu Wang , Edith Bai
Soil biodiversity is declining globally due to human activities and climate change, but the consequences for soil carbon cycling and carbon dioxide (CO2) emissions remain poorly understood. Here, we investigated the relationship between microbial diversity and soil CO2 flux using a microbial dilution-to-extinction approach across three land-use types (forest, grassland and cropland). We find that soil CO2 fluxes respond nonlinearly to diversity loss, increasing initially at moderate diversity loss, then declining sharply at severe loss. Several key microbial physiological properties, including microbial carbon use efficiency (CUE), nitrogen use efficiency (NUE), and turnover rate, exhibit similar hump-shaped responses to declining diversity. Linear mixed-effects models show that microbial turnover and NUE are positively correlated with soil CO2 fluxes, whereas microbial CUE and the interaction between turnover and NUE are negatively correlated with them. Structural equation modeling approaches further demonstrate that indirect effects mediated by microbial physiological properties, especially turnover rate, exert a stronger influence on soil CO2 fluxes than the direct effects of diversity loss. Together, these findings highlight the complexity of biodiversity-function relationships in soils and emphasize the need to incorporate microbial physiological properties into soil carbon cycle models in the context of global biodiversity change.
{"title":"Nonlinear effect of microbial diversity loss on soil carbon flux","authors":"Chao Wang , Xiaoyi Huang , Jing Yu , Yue Liu , Fangying Qu , Jian Wang , Xu Wang , Edith Bai","doi":"10.1016/j.soilbio.2025.110028","DOIUrl":"10.1016/j.soilbio.2025.110028","url":null,"abstract":"<div><div>Soil biodiversity is declining globally due to human activities and climate change, but the consequences for soil carbon cycling and carbon dioxide (CO<sub>2</sub>) emissions remain poorly understood. Here, we investigated the relationship between microbial diversity and soil CO<sub>2</sub> flux using a microbial dilution-to-extinction approach across three land-use types (forest, grassland and cropland). We find that soil CO<sub>2</sub> fluxes respond nonlinearly to diversity loss, increasing initially at moderate diversity loss, then declining sharply at severe loss. Several key microbial physiological properties, including microbial carbon use efficiency (CUE), nitrogen use efficiency (NUE), and turnover rate, exhibit similar hump-shaped responses to declining diversity. Linear mixed-effects models show that microbial turnover and NUE are positively correlated with soil CO<sub>2</sub> fluxes, whereas microbial CUE and the interaction between turnover and NUE are negatively correlated with them. Structural equation modeling approaches further demonstrate that indirect effects mediated by microbial physiological properties, especially turnover rate, exert a stronger influence on soil CO<sub>2</sub> fluxes than the direct effects of diversity loss. Together, these findings highlight the complexity of biodiversity-function relationships in soils and emphasize the need to incorporate microbial physiological properties into soil carbon cycle models in the context of global biodiversity change.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110028"},"PeriodicalIF":10.3,"publicationDate":"2025-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145428042","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 : 2025-11-01DOI: 10.1016/j.soilbio.2025.110027
Min Liu , Xingliang Xu , Peng Jin , Helge Bruelheide , Yakov Kuzyakov , Richard D. Bardgett , Wolfgang Wanek
Plants uptake nitrogen (N) from soils in inorganic forms, such as ammonium (NH4+) and nitrate (NO3−), but also in the form of organic compounds like amino acids. Despite extensive research on terrestrial N cycling, the patterns and underpinning mechanisms of inorganic and organic N uptake by tree species across forest biomes remained very uncertain. To address this knowledge gap, we conducted field-based hydroponic labelling experiments on 34 tree species spanning from temperate to subtropical and tropical climate zones. We assessed uptake rates of nine common amino acids (15N and 13C dual-labelled) alongside with NH4+ and NO3− (15N-labelled) at micromolar concentrations. Root morphological traits, soil chemical properties, soil N pool sizes and microbial N functional genes were determined to assess their role in explaining differential N uptake among tree species and forest biomes. Our results demonstrated stable N uptake rates and preferences across all forest biomes but showed large differences among N forms. Such N uptake was predominantly affected by N intrinsic properties, followed by effects of soil properties and microbial N functional genes on soil N availability, while controls by tree root traits were weakest. Mean uptake rates of single amino acids contributed to 39 % of the total root N uptake, with NH4+ showing the highest (56 %), and NO3− showing the lowest uptake rates (5.0 %). Uptake rates of positively charged and high N% amino acids such as arginine, histidine, and lysine were fastest, i.e., 0.98, 0.81, and 0.78 μg N g−1 d. w. root h−1, respectively. Nitrogen uptake rates were faster when trees have longer and thinner fine roots, in soils with higher pH and phosphorus (P) availability and faster microbial N turnover. Our findings highlight the important role of organic N and NH4+ for tree nutrition and reveal how tree N uptake is influenced (in increasing importance) by tree root morphological traits, soil microbial N functional composition, soil resource availability, and N form intrinsic properties. These findings provide profound quantitative and predictive insights into our understanding of forest N sink processes, offering a scientific foundation for optimizing global forestry N management strategies in the context of environmental change.
植物以无机形式从土壤中吸收氮(N)，如铵（NH4+）和硝酸盐（NO3 -），但也以有机化合物的形式，如氨基酸。尽管对陆地氮循环进行了广泛的研究，但森林生物群系树种对无机氮和有机氮的吸收模式和基本机制仍不确定。为了解决这一知识缺口，我们对34种树种进行了基于田间的水培标记实验，这些树种分布在温带、亚热带和热带气候区。我们评估了九种常见氨基酸（15N和13C双标记）以及NH4+和NO3 - （15N标记）在微摩尔浓度下的吸收率。根系形态特征、土壤化学性质、土壤氮库大小和微生物氮功能基因在不同树种和森林生物群落间氮吸收差异中的作用。我们的研究结果表明，所有森林生物群落的氮素吸收速率和偏好都很稳定，但氮素形态之间存在较大差异。氮素吸收主要受氮素内在特性的影响，其次是土壤特性和微生物氮功能基因对土壤氮素有效性的影响，而根系性状对土壤氮素有效性的影响最弱。单氨基酸的平均吸收率占根系总氮吸收率的39%，其中NH4+吸收率最高（56%），NO3 -吸收率最低（5.0%）。对带正电荷和高N%氨基酸如精氨酸、组氨酸和赖氨酸的吸收速率最快，分别为0.98、0.81和0.78 μg N g-1 d w根h-1。在pH和磷有效度较高、微生物氮周转快的土壤中，树木细根长、细根细的土壤吸收氮速率较高。我们的研究结果强调了有机氮和NH4+对树木营养的重要作用，并揭示了树木对N的吸收如何受到树木根系形态特征、土壤微生物N功能组成、土壤资源有效性以及树木和森林生物群落中N形态固有特性的影响（其重要性日益增加）。这些发现为我们对森林氮汇过程的理解提供了深刻的定量和预测见解，为优化环境变化背景下的全球森林氮管理策略提供了科学依据。
{"title":"Advancing predictive understanding of tree organic and inorganic nitrogen uptake across forest biomes","authors":"Min Liu , Xingliang Xu , Peng Jin , Helge Bruelheide , Yakov Kuzyakov , Richard D. Bardgett , Wolfgang Wanek","doi":"10.1016/j.soilbio.2025.110027","DOIUrl":"10.1016/j.soilbio.2025.110027","url":null,"abstract":"<div><div>Plants uptake nitrogen (N) from soils in inorganic forms, such as ammonium (NH<sub>4</sub><sup>+</sup>) and nitrate (NO<sub>3</sub><sup>−</sup>), but also in the form of organic compounds like amino acids. Despite extensive research on terrestrial N cycling, the patterns and underpinning mechanisms of inorganic and organic N uptake by tree species across forest biomes remained very uncertain. To address this knowledge gap, we conducted field-based hydroponic labelling experiments on 34 tree species spanning from temperate to subtropical and tropical climate zones. We assessed uptake rates of nine common amino acids (<sup>15</sup>N and <sup>13</sup>C dual-labelled) alongside with NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>−</sup> (<sup>15</sup>N-labelled) at micromolar concentrations. Root morphological traits, soil chemical properties, soil N pool sizes and microbial N functional genes were determined to assess their role in explaining differential N uptake among tree species and forest biomes. Our results demonstrated stable N uptake rates and preferences across all forest biomes but showed large differences among N forms. Such N uptake was predominantly affected by N intrinsic properties, followed by effects of soil properties and microbial N functional genes on soil N availability, while controls by tree root traits were weakest. Mean uptake rates of single amino acids contributed to 39 % of the total root N uptake, with NH<sub>4</sub><sup>+</sup> showing the highest (56 %), and NO<sub>3</sub><sup>−</sup> showing the lowest uptake rates (5.0 %). Uptake rates of positively charged and high N% amino acids such as arginine, histidine, and lysine were fastest, i.e., 0.98, 0.81, and 0.78 μg N g<sup>−1</sup> d. w. root h<sup>−1</sup>, respectively. Nitrogen uptake rates were faster when trees have longer and thinner fine roots, in soils with higher pH and phosphorus (P) availability and faster microbial N turnover. Our findings highlight the important role of organic N and NH<sub>4</sub><sup>+</sup> for tree nutrition and reveal how tree N uptake is influenced (in increasing importance) by tree root morphological traits, soil microbial N functional composition, soil resource availability, and N form intrinsic properties. These findings provide profound quantitative and predictive insights into our understanding of forest N sink processes, offering a scientific foundation for optimizing global forestry N management strategies in the context of environmental change.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110027"},"PeriodicalIF":10.3,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145411688","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}
Anthropogenic nitrogen (N) deposition and phosphorus (P) enrichment are profoundly altering terrestrial ecosystem stoichiometry, with particularly pronounced impacts on the fragile alpine meadow ecosystems. Yet, the effects of N and P inputs on critical metabolic functions of soil microbial communities remain poorly understood. Here, we conducted a 4-year N and P addition experiment in alpine meadows on the Qinghai-Tibetan Plateau. Our results demonstrate that N and P additions increased soil nitrate by 10.3-fold and 2-fold, respectively, but concurrently reduced plant species richness by 44.3 % and 33.6 %, favoring the dominance of grasses. N fertilization markedly increased the abundance of amoA genes (5.7-fold) and microbial alpha-diversity, accelerating nitrification processes. In contrast, low-level P addition (50 kg P Ha−2) enhanced the diversity of phoD (alkaline phosphatase) genes (Richness: +6.8 %, Shannon index: +2.0 %). Metagenomic analysis revealed a shift towards copiotrophic bacteria (e.g., Proteobacteria) by N enrichment, while P addition boosted predatory bacteria (e.g., Myxococcus). Both nutrient additions altered carbon (C) metabolism. This shift favored the metagenomic functions of proteins biosynthesis and ATP synthases for growth-associated synthetic processes, over the synthesis of complex compounds (e.g, aromatic compounds). This led to a depletion of complex lipids and aromatic compounds, which are crucial for stable soil organic matter formation. These findings demonstrate that N and (or) P inputs profoundly reshape microbial community structure and metabolism, with implications for C stability and functioning of these vulnerable ecosystems under ongoing global change and human disturbance.
{"title":"Nitrogen and phosphorus additions reshape soil microbial metabolic functions in Qinghai-Tibetan Plateau alpine meadows","authors":"Jiayi Zhao , Yuying Jiang , Fei Ren , Lanping Li , Huaihai Chen","doi":"10.1016/j.soilbio.2025.110026","DOIUrl":"10.1016/j.soilbio.2025.110026","url":null,"abstract":"<div><div>Anthropogenic nitrogen (N) deposition and phosphorus (P) enrichment are profoundly altering terrestrial ecosystem stoichiometry, with particularly pronounced impacts on the fragile alpine meadow ecosystems. Yet, the effects of N and P inputs on critical metabolic functions of soil microbial communities remain poorly understood. Here, we conducted a 4-year N and P addition experiment in alpine meadows on the Qinghai-Tibetan Plateau. Our results demonstrate that N and P additions increased soil nitrate by 10.3-fold and 2-fold, respectively, but concurrently reduced plant species richness by 44.3 % and 33.6 %, favoring the dominance of grasses. N fertilization markedly increased the abundance of <em>amoA</em> genes (5.7-fold) and microbial alpha-diversity, accelerating nitrification processes. In contrast, low-level P addition (50 kg P Ha<sup>−2</sup>) enhanced the diversity of <em>phoD</em> (alkaline phosphatase) genes (Richness: +6.8 %, Shannon index: +2.0 %). Metagenomic analysis revealed a shift towards copiotrophic bacteria (e.g., Proteobacteria) by N enrichment, while P addition boosted predatory bacteria (e.g., <em>Myxococcus</em>). Both nutrient additions altered carbon (C) metabolism. This shift favored the metagenomic functions of proteins biosynthesis and ATP synthases for growth-associated synthetic processes, over the synthesis of complex compounds (e.g, aromatic compounds). This led to a depletion of complex lipids and aromatic compounds, which are crucial for stable soil organic matter formation. These findings demonstrate that N and (or) P inputs profoundly reshape microbial community structure and metabolism, with implications for C stability and functioning of these vulnerable ecosystems under ongoing global change and human disturbance.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110026"},"PeriodicalIF":10.3,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145411689","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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