Pub Date : 2025-10-31DOI: 10.1016/j.soilbio.2025.110025
Ziyue Wang , Man Liu , Wenli Ding , Zhihui Chang , Benjamin L. Turner , Hans Lambers
Earthworms are integral to soil processes and influence plant growth and phosphorus (P) nutrition. We investigated the role of earthworms in the P cycle by synthesizing data from 181 studies, of which 22 % were field observations and 78 % were from pot or mesocosm experiments. Earthworms increase the concentration of soil Olsen P and microbial P, phosphatase activity, and plant biomass. Deep-dwelling epi-anecic and anecic earthworms are more effective than other ecological groups at increasing the soil available P, although surface-dwelling earthworms (epigeic and endogeic) contribute more effectively to plant P uptake. The increase of plant biomass by earthworms decreases with increasing organic matter content, but Olsen P concentration and plant P uptake show the opposite trend. Moreover, the impact of endogeic earthworms on P is sensitive to soil organic matter content. The positive effects of earthworms on P cycling are more pronounced under acidic and alkaline conditions than under neutral conditions (6.5–7.5). Finally, the increased available P concentration due to earthworms directly stimulates microbial P uptake, while all three main ecological categories of earthworms indirectly stimulate root growth and increase plant P uptake. Overall, earthworms can effectively promote P cycling in ecosystems, with a more significant effect in nutrient-poor soils.
{"title":"Earthworms enhance soil phosphorus cycling but plant responses differ among earthworm ecological categories: a meta-analysis","authors":"Ziyue Wang , Man Liu , Wenli Ding , Zhihui Chang , Benjamin L. Turner , Hans Lambers","doi":"10.1016/j.soilbio.2025.110025","DOIUrl":"10.1016/j.soilbio.2025.110025","url":null,"abstract":"<div><div>Earthworms are integral to soil processes and influence plant growth and phosphorus (P) nutrition. We investigated the role of earthworms in the P cycle by synthesizing data from 181 studies, of which 22 % were field observations and 78 % were from pot or mesocosm experiments. Earthworms increase the concentration of soil Olsen P and microbial P, phosphatase activity, and plant biomass. Deep-dwelling <em>epi</em>-anecic and anecic earthworms are more effective than other ecological groups at increasing the soil available P, although surface-dwelling earthworms (epigeic and endogeic) contribute more effectively to plant P uptake. The increase of plant biomass by earthworms decreases with increasing organic matter content, but Olsen P concentration and plant P uptake show the opposite trend. Moreover, the impact of endogeic earthworms on P is sensitive to soil organic matter content. The positive effects of earthworms on P cycling are more pronounced under acidic and alkaline conditions than under neutral conditions (6.5–7.5). Finally, the increased available P concentration due to earthworms directly stimulates microbial P uptake, while all three main ecological categories of earthworms indirectly stimulate root growth and increase plant P uptake. Overall, earthworms can effectively promote P cycling in ecosystems, with a more significant effect in nutrient-poor soils.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110025"},"PeriodicalIF":10.3,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145411692","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 : 2025-10-29DOI: 10.1016/j.soilbio.2025.110024
M. Bahram , L. Lehtovirta-Morley , V. Mikryukov , T.R. Sveen , A. Grant , M. Pent , F. Hildebrand , M. Labouyrie , J. Köninger , L. Tedersoo , A. Jones , P. Panagos , A. Orgiazzi
Archaea are an important group of soil organisms that play key roles in carbon and nitrogen cycling, particularly in nitrification (ammonia oxidation) and methanogenesis. However, there are knowledge gaps regarding their importance in ecosystem processes relative to other microbial groups and how they may be impacted by land-use and environmental changes. Here, by carrying out a continental-scale sample collection and utilising archaea-specific primers for metabarcoding and shotgun metagenomics, we aimed to decipher the structure and function of archaeal communities across various land-use types in Europe. Metagenomic data reveal that land-use intensification increases the relative abundance of archaea, whereas bacteria and eukaryotes show no increase. Alongside this, ammonia oxidising archaea (AOA) increase as a proportion of the total metabarcoding reads, from 1 % of archaea in coniferous woodland to >90 % in croplands. Functional gene profiles reveal that land-use intensification shifts archaeal communities from adaptive metabolic pathways in forests to specialised, ammonia-oxidising microbes in fertiliser-enriched cropland soils. Our data suggest that land-use intensification may shift archaeal communities toward greater dependence on external nitrogen inputs, with potential consequences for soil fertility and greenhouse gas emissions.
{"title":"Intensive land use enhances soil ammonia-oxidising archaea at a continental scale","authors":"M. Bahram , L. Lehtovirta-Morley , V. Mikryukov , T.R. Sveen , A. Grant , M. Pent , F. Hildebrand , M. Labouyrie , J. Köninger , L. Tedersoo , A. Jones , P. Panagos , A. Orgiazzi","doi":"10.1016/j.soilbio.2025.110024","DOIUrl":"10.1016/j.soilbio.2025.110024","url":null,"abstract":"<div><div>Archaea are an important group of soil organisms that play key roles in carbon and nitrogen cycling, particularly in nitrification (ammonia oxidation) and methanogenesis. However, there are knowledge gaps regarding their importance in ecosystem processes relative to other microbial groups and how they may be impacted by land-use and environmental changes. Here, by carrying out a continental-scale sample collection and utilising archaea-specific primers for metabarcoding and shotgun metagenomics, we aimed to decipher the structure and function of archaeal communities across various land-use types in Europe. Metagenomic data reveal that land-use intensification increases the relative abundance of archaea, whereas bacteria and eukaryotes show no increase. Alongside this, ammonia oxidising archaea (AOA) increase as a proportion of the total metabarcoding reads, from 1 % of archaea in coniferous woodland to >90 % in croplands. Functional gene profiles reveal that land-use intensification shifts archaeal communities from adaptive metabolic pathways in forests to specialised, ammonia-oxidising microbes in fertiliser-enriched cropland soils. Our data suggest that land-use intensification may shift archaeal communities toward greater dependence on external nitrogen inputs, with potential consequences for soil fertility and greenhouse gas emissions.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110024"},"PeriodicalIF":10.3,"publicationDate":"2025-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145382540","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 : 2025-10-25DOI: 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":"2025-10-25","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}
Pub 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":"2025-10-22","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 : 2025-10-19DOI: 10.1016/j.soilbio.2025.110023
Ling Li , Chao Xue , Yue Wang , Mingtao Liu , Junjie Guo , Manqiang Liu , Qirong Shen , Ning Ling
Microbial life-history strategies determine how microbial communities prioritize resource allocation toward growth, resource acquisition, or stress tolerance. However, how soil microbial communities adjust their life-history strategies in response to distinct soil fertility remains poorly understood. In this study, metatranscriptomic sequencing was performed to investigate shifts in microbial life-history strategies in soils with different fertility, developed by 37 year diverse fertilization regimes: no fertilization, mineral fertilization, manure fertilization, and combined mineral/manure fertilization. Organic amendments increased the transcript abundance of genes (normalized by transcripts per million [TPM]) related to biogeochemical cycles by 13 %–246 % relative to unfertilized soils. We quantified the relative transcript abundance of each functional pathway within individual biogeochemical cycles to compare transcriptional allocation across treatments. Within each cycle, organic amendments increased the relative transcript abundance of genes involved in organic matter degradation by 9 %–12 % and dissimilatory nitrate reduction by 24 %–37 % relative to unfertilized soils. Although TPM-normalized transcript abundance of growth-associated genes increased 1.8- to 2.2-fold in fertilized soils, their relative abundance among all life-history transcripts remained stable at approximately 77 %. Organic inputs altered microbial resource allocation by favoring resource acquisition over stress tolerance. This shift was associated with increased nutrient availability and soil pH neutralization. Taxonomic analysis revealed growth yield as the dominant strategy across most phyla. Within each strategy, Desulfobacterota showed a strong association with growth yield, Verrucomicrobiota with resource acquisition, and Pseudomonadota and Actinomycetota with stress tolerance. Notably, while strategy preferences were broadly conserved across phyla, fertilization modulated the intensity of strategy-specific gene expression, indicating functional plasticity of microbial communities in response to environmental change. Collectively, our findings suggest that differences in soil fertility resulting from long-term fertilization alter microbial resource allocation among life-history strategies by changing the functional expression of transcripts assigned to different taxa, reflecting the functional plasticity of soil microbial communities under intensified agriculture.
{"title":"Microbial lifestyles adapted to distinct soil fertility","authors":"Ling Li , Chao Xue , Yue Wang , Mingtao Liu , Junjie Guo , Manqiang Liu , Qirong Shen , Ning Ling","doi":"10.1016/j.soilbio.2025.110023","DOIUrl":"10.1016/j.soilbio.2025.110023","url":null,"abstract":"<div><div>Microbial life-history strategies determine how microbial communities prioritize resource allocation toward growth, resource acquisition, or stress tolerance. However, how soil microbial communities adjust their life-history strategies in response to distinct soil fertility remains poorly understood. In this study, metatranscriptomic sequencing was performed to investigate shifts in microbial life-history strategies in soils with different fertility, developed by 37 year diverse fertilization regimes: no fertilization, mineral fertilization, manure fertilization, and combined mineral/manure fertilization. Organic amendments increased the transcript abundance of genes (normalized by transcripts per million [TPM]) related to biogeochemical cycles by 13 %–246 % relative to unfertilized soils. We quantified the relative transcript abundance of each functional pathway within individual biogeochemical cycles to compare transcriptional allocation across treatments. Within each cycle, organic amendments increased the relative transcript abundance of genes involved in organic matter degradation by 9 %–12 % and dissimilatory nitrate reduction by 24 %–37 % relative to unfertilized soils. Although TPM-normalized transcript abundance of growth-associated genes increased 1.8- to 2.2-fold in fertilized soils, their relative abundance among all life-history transcripts remained stable at approximately 77 %. Organic inputs altered microbial resource allocation by favoring resource acquisition over stress tolerance. This shift was associated with increased nutrient availability and soil pH neutralization. Taxonomic analysis revealed growth yield as the dominant strategy across most phyla. Within each strategy, Desulfobacterota showed a strong association with growth yield, Verrucomicrobiota with resource acquisition, and Pseudomonadota and Actinomycetota with stress tolerance. Notably, while strategy preferences were broadly conserved across phyla, fertilization modulated the intensity of strategy-specific gene expression, indicating functional plasticity of microbial communities in response to environmental change. Collectively, our findings suggest that differences in soil fertility resulting from long-term fertilization alter microbial resource allocation among life-history strategies by changing the functional expression of transcripts assigned to different taxa, reflecting the functional plasticity of soil microbial communities under intensified agriculture.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 110023"},"PeriodicalIF":10.3,"publicationDate":"2025-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145314683","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 : 2025-10-18DOI: 10.1016/j.soilbio.2025.110019
Jie Zheng , Ziyi Peng , Francisco Dini-Andreote , Andrew D. Barnes , Guangping Shi , Anton M. Potapov , Shungui Zhou , Yuji Jiang
Energy fluxes driven by predation are crucial to the relationships between biodiversity and ecosystem functioning in soils. However, there is little empirical evidence connecting these fluxes within soil micro-food webs to soil multifunctionality. Here, we initially used a long-term field experiment to investigate the extent to which nematode predation influences energy fluxes in soil micro-food webs and, in turn, impacts soil multifunctionality. Based on our analysis of body mass-scaled metabolic rates for 70 organismal groups, we estimated that nematodes require roughly three orders of magnitude more energy per individual than bacteria. In the field, we found nematode addition to increase multitrophic diversity and to strengthen interactions between bacteria-feeding nematodes and bacteria. This resulted in multitrophic energy fluxes that were 5.9–169.4 % greater than in soil lacking nematode additions. Specifically, nematode addition reinforced the bacterial energy channel, resulting in greater energy transfer from basal resources to bacteria and subsequently to protists and bacterivorous or omnivorous-predatory nematodes, which altered energy composition and reduced energy flow uniformity. Moreover, our results revealed that elevated multitrophic diversity and shifts in the energetic structure of soil micro-food webs mediated the enhancement in soil multifunctionality. Lastly, a complementary 13C-tracer microcosm experiment validated selective predation by nematodes on bacterial taxa (e.g., Mesorhizobium and Paenibacillus), as shown by significant positive correlations between 13C-labeled bacteria and 13C-enriched nematodes that explain the trophic transfer observed in nematode addition field treatments. Taken together, this study demonstrates that selective predation by nematodes reorganizes energy flow within soil micro-food webs, offering mechanistic evidence that predator-driven shifts in energy flow underpin biodiversity-function relationships in agricultural soils.
{"title":"Nematode predation modulates the energetic dynamics of soil micro-food webs with consequences for soil multifunctionality","authors":"Jie Zheng , Ziyi Peng , Francisco Dini-Andreote , Andrew D. Barnes , Guangping Shi , Anton M. Potapov , Shungui Zhou , Yuji Jiang","doi":"10.1016/j.soilbio.2025.110019","DOIUrl":"10.1016/j.soilbio.2025.110019","url":null,"abstract":"<div><div>Energy fluxes driven by predation are crucial to the relationships between biodiversity and ecosystem functioning in soils. However, there is little empirical evidence connecting these fluxes within soil micro-food webs to soil multifunctionality. Here, we initially used a long-term field experiment to investigate the extent to which nematode predation influences energy fluxes in soil micro-food webs and, in turn, impacts soil multifunctionality. Based on our analysis of body mass-scaled metabolic rates for 70 organismal groups, we estimated that nematodes require roughly three orders of magnitude more energy per individual than bacteria. In the field, we found nematode addition to increase multitrophic diversity and to strengthen interactions between bacteria-feeding nematodes and bacteria. This resulted in multitrophic energy fluxes that were 5.9–169.4 % greater than in soil lacking nematode additions. Specifically, nematode addition reinforced the bacterial energy channel, resulting in greater energy transfer from basal resources to bacteria and subsequently to protists and bacterivorous or omnivorous-predatory nematodes, which altered energy composition and reduced energy flow uniformity. Moreover, our results revealed that elevated multitrophic diversity and shifts in the energetic structure of soil micro-food webs mediated the enhancement in soil multifunctionality. Lastly, a complementary <sup>13</sup>C-tracer microcosm experiment validated selective predation by nematodes on bacterial taxa (e.g., <em>Mesorhizobium</em> and <em>Paenibacillus</em>), as shown by significant positive correlations between <sup>13</sup>C-labeled bacteria and <sup>13</sup>C-enriched nematodes that explain the trophic transfer observed in nematode addition field treatments. Taken together, this study demonstrates that selective predation by nematodes reorganizes energy flow within soil micro-food webs, offering mechanistic evidence that predator-driven shifts in energy flow underpin biodiversity-function relationships in agricultural soils.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 110019"},"PeriodicalIF":10.3,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145314682","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 : 2025-10-17DOI: 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":"2025-10-17","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 : 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":"2025-10-17","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 : 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":"2025-10-16","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 : 2025-10-15DOI: 10.1016/j.soilbio.2025.110018
Xueru Huang , Zhuo Zhang , Taoyi Ren , Song Li , Ping Zhu , Jingjing Ma , Zhongjun Jia , Jingkuan Wang , Marcela Hernández
Ammonia-oxidizing microorganisms (AOMs) primarily use chemoautotrophic CO2 fixation for growth, while their decay substantially contributes to soil organic carbon (SOC) that may be respired as CO2, leaving their net impact on soil carbon neutrality unclear. This study employed two-phase microcosm incubation to examine how AOM cell proliferation and death affect SOC accumulation in long-term unfertilized CK (continuous maize) and chemically fertilized CC (continuous maize), CS (continuous soybean), and RCS (rotation maize-soybean) treatments. During the 28-day incubation with 13CO2 and urea (Phase I), net production of soil organic 13C (13C–SOC) showed no significant differences (p > 0.05) among treatments: CK (23.6 μg g−1), CC (20.9 μg g−1), CS (22.8 μg g−1), and RCS (25.0 μg g−1). This 13C–SOC originated entirely from active ammonia-oxidizing bacteria (AOB) and archaea (AOA), with fertilized treatments showing significantly higher AOB: AOA protein-C ratios (CC: 4.48; CS: 5.88; RCS: 12.5) than CK (1.56). The mortality of active cells was further assessed (Phase II) by measuring AOM-related 13C–CO2 mineralization, which was approximately twice as high in the CK compared with the fertilized treatments (p < 0.05) within 30 days. This derived mortality rate followed the same trend, which confirmed that the respired portion of the newly generated microbial carbon was lower under chemical fertilizer application. We conclude that long-term chemical fertilizer application increases the AOB: AOA protein-C ratio and promotes the ammonia oxidizer-derived SOC accumulation through their life cycles, ultimately supporting carbon neutrality.
{"title":"Long-term chemical fertilizer application enhances ammonia oxidizers-mediated soil carbon neutrality","authors":"Xueru Huang , Zhuo Zhang , Taoyi Ren , Song Li , Ping Zhu , Jingjing Ma , Zhongjun Jia , Jingkuan Wang , Marcela Hernández","doi":"10.1016/j.soilbio.2025.110018","DOIUrl":"10.1016/j.soilbio.2025.110018","url":null,"abstract":"<div><div>Ammonia-oxidizing microorganisms (AOMs) primarily use chemoautotrophic CO<sub>2</sub> fixation for growth, while their decay substantially contributes to soil organic carbon (SOC) that may be respired as CO<sub>2</sub>, leaving their net impact on soil carbon neutrality unclear. This study employed two-phase microcosm incubation to examine how AOM cell proliferation and death affect SOC accumulation in long-term unfertilized CK (continuous maize) and chemically fertilized CC (continuous maize), CS (continuous soybean), and RCS (rotation maize-soybean) treatments. During the 28-day incubation with <sup>13</sup>CO<sub>2</sub> and urea (Phase I), net production of soil organic <sup>13</sup>C (<sup>13</sup>C–SOC) showed no significant differences (p > 0.05) among treatments: CK (23.6 μg g<sup>−1</sup>), CC (20.9 μg g<sup>−1</sup>), CS (22.8 μg g<sup>−1</sup>), and RCS (25.0 μg g<sup>−1</sup>). This <sup>13</sup>C–SOC originated entirely from active ammonia-oxidizing bacteria (AOB) and archaea (AOA), with fertilized treatments showing significantly higher AOB: AOA protein-C ratios (CC: 4.48; CS: 5.88; RCS: 12.5) than CK (1.56). The mortality of active cells was further assessed (Phase II) by measuring AOM-related <sup>13</sup>C–CO<sub>2</sub> mineralization, which was approximately twice as high in the CK compared with the fertilized treatments (p < 0.05) within 30 days. This derived mortality rate followed the same trend, which confirmed that the respired portion of the newly generated microbial carbon was lower under chemical fertilizer application. We conclude that long-term chemical fertilizer application increases the AOB: AOA protein-C ratio and promotes the ammonia oxidizer-derived SOC accumulation through their life cycles, ultimately supporting carbon neutrality.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"212 ","pages":"Article 110018"},"PeriodicalIF":10.3,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145288998","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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