Pub Date : 2026-03-01Epub Date: 2025-12-05DOI: 10.1016/j.soilbio.2025.110057
C. Pelosi , E. Michel , P. Beltrame , S. Cazaurang , A. Bérard , N. Beudez , F. Cajot , C. Caurel , C. Serbource , P. Renault , C. Doussan
Numerous and diverse edaphic organisms have the capacity to modify several physical and chemical soil characteristics that influence water transfers. Considering these modifications in modeling approaches would make for more accurate descriptions and modeling of water fluxes in soils. Some impacts of biological activity on soil physical aspects (e.g. modification of the pore space) have been described for 5–10 years now, and are being increasingly accounted for in water transfer models. However, the situation is not the same for biologically-driven chemical modifications linked to the secretion of organic molecules by soil organisms: modeling their consequences on pore space chemical properties and water transfers has just started. We here shortly survey prominent effects of biological activity on water-transfer related soil properties, and describe their coupling with existing water transfer models. We then propose possible ways for a better integration of biological soil modifications into such models. Among these, we point out that an energy-based theoretical framework would not only be consistent with the basic principles of thermodynamics, but would also foster synergies between ecologists, physicists and chemists, to better describe and predict water dynamics in soils and interactions with the soil biota. This would pave the way to model the evolution, on the scale of a few decades, of the water flow regulation services provided by soils.
{"title":"How to integrate biology, physics and chemistry for a better description of soil water dynamics?","authors":"C. Pelosi , E. Michel , P. Beltrame , S. Cazaurang , A. Bérard , N. Beudez , F. Cajot , C. Caurel , C. Serbource , P. Renault , C. Doussan","doi":"10.1016/j.soilbio.2025.110057","DOIUrl":"10.1016/j.soilbio.2025.110057","url":null,"abstract":"<div><div>Numerous and diverse edaphic organisms have the capacity to modify several physical and chemical soil characteristics that influence water transfers. Considering these modifications in modeling approaches would make for more accurate descriptions and modeling of water fluxes in soils. Some impacts of biological activity on soil physical aspects (e.g. modification of the pore space) have been described for 5–10 years now, and are being increasingly accounted for in water transfer models. However, the situation is not the same for biologically-driven chemical modifications linked to the secretion of organic molecules by soil organisms: modeling their consequences on pore space chemical properties and water transfers has just started. We here shortly survey prominent effects of biological activity on water-transfer related soil properties, and describe their coupling with existing water transfer models. We then propose possible ways for a better integration of biological soil modifications into such models. Among these, we point out that an energy-based theoretical framework would not only be consistent with the basic principles of thermodynamics, but would also foster synergies between ecologists, physicists and chemists, to better describe and predict water dynamics in soils and interactions with the soil biota. This would pave the way to model the evolution, on the scale of a few decades, of the water flow regulation services provided by soils.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110057"},"PeriodicalIF":10.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145689062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-12-02DOI: 10.1016/j.soilbio.2025.110050
Jana Šerá , Václav Pecina , Vendula Mašláňová , Martin Brtnický , Adéla Baťová , Jiří Holátko , Tereza Hammerschmiedt , Veronika Kučabová , Ondrej Malíček , Markéta Kadlečková , Jiří Kučerík , Marek Koutný
Biodegradable plastics (BPs) are increasingly presented as sustainable alternatives to conventional plastics; however, their ecological effects on soils are poorly understood. BPs can alter soil microbiomes and nutrient cycling; yet, the extent, dynamics, and effects of the plastisphere on soil organic matter (SOM) after biodegradation remain underexplored. This study characterized the microbial plastisphere of three BPs, poly-3-hydroxybutyrate (PHB), poly(butylene succinate-co-adipate) (PBSA), and polybutylene adipate terephthalate (PBAT), and measured polymer biodegradation to link microbial dynamics with material breakdown. Metagenomics, scanning electron microscopy, and thermogravimetric analysis showed that these polymers formed structured plastispheres that significantly altered microbial communities and SOM. Each polymer hosted a distinct plastisphere; bacterial communities diverged more strongly between polymers than fungal ones. Functional profiling revealed shifts in nitrogen metabolism and ecological strategies at BP surfaces, including a decrease in nitrifiers and an increase in parasitic/pathogenic fungi. The plastisphere extended up to 1.25 mm for bacteria and 2.75 mm for fungi. PHB plastispheres were enriched in Comamonadaceae, Oxalobacteriaceae, and Rhodocyclaceae; PBAT favored Xanthobacteraceae and Burkholderiaceae; Xanthomonadaceae colonized all BPs. Fungal communities were dominated by Nectriaceae, Herpotrichiellaceae, and Aspergillaceae, and their composition changed over time. BP exposure reduced SOM, most strongly for PHB and PBSA, and to a lesser extent for PBAT, suggesting a positive priming effect. Overall, BP degradation promoted nitrogen-limited conditions and host-dependent microbial strategies. Although plastisphere communities showed signs of stabilization after 350 days, full recovery of microbial composition and SOM may require longer, indicating potential long-term impacts of BPs on soil ecosystems. These results underscore that BPs can alter soil microbial ecology and organic matter turnover, highlighting the need for further long-term studies.
{"title":"Unveiling the spatial architecture of biodegradable polyester plastisphere in soil and its implications for organic matter composition","authors":"Jana Šerá , Václav Pecina , Vendula Mašláňová , Martin Brtnický , Adéla Baťová , Jiří Holátko , Tereza Hammerschmiedt , Veronika Kučabová , Ondrej Malíček , Markéta Kadlečková , Jiří Kučerík , Marek Koutný","doi":"10.1016/j.soilbio.2025.110050","DOIUrl":"10.1016/j.soilbio.2025.110050","url":null,"abstract":"<div><div>Biodegradable plastics (BPs) are increasingly presented as sustainable alternatives to conventional plastics; however, their ecological effects on soils are poorly understood. BPs can alter soil microbiomes and nutrient cycling; yet, the extent, dynamics, and effects of the plastisphere on soil organic matter (SOM) after biodegradation remain underexplored. This study characterized the microbial plastisphere of three BPs, poly-3-hydroxybutyrate (PHB), poly(butylene succinate-co-adipate) (PBSA), and polybutylene adipate terephthalate (PBAT), and measured polymer biodegradation to link microbial dynamics with material breakdown. Metagenomics, scanning electron microscopy, and thermogravimetric analysis showed that these polymers formed structured plastispheres that significantly altered microbial communities and SOM. Each polymer hosted a distinct plastisphere; bacterial communities diverged more strongly between polymers than fungal ones. Functional profiling revealed shifts in nitrogen metabolism and ecological strategies at BP surfaces, including a decrease in nitrifiers and an increase in parasitic/pathogenic fungi. The plastisphere extended up to 1.25 mm for bacteria and 2.75 mm for fungi. PHB plastispheres were enriched in <em>Comamonadaceae</em>, <em>Oxalobacteriaceae</em>, and <em>Rhodocyclaceae</em>; PBAT favored <em>Xanthobacteraceae</em> and <em>Burkholderiaceae</em>; <em>Xanthomonadaceae</em> colonized all BPs. Fungal communities were dominated by <em>Nectriaceae</em>, <em>Herpotrichiellaceae</em>, and <em>Aspergillaceae</em>, and their composition changed over time. BP exposure reduced SOM, most strongly for PHB and PBSA, and to a lesser extent for PBAT, suggesting a positive priming effect. Overall, BP degradation promoted nitrogen-limited conditions and host-dependent microbial strategies. Although plastisphere communities showed signs of stabilization after 350 days, full recovery of microbial composition and SOM may require longer, indicating potential long-term impacts of BPs on soil ecosystems. These results underscore that BPs can alter soil microbial ecology and organic matter turnover, highlighting the need for further long-term studies.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110050"},"PeriodicalIF":10.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145657199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-12-22DOI: 10.1016/j.soilbio.2025.110076
Viktor Nagy , Roman Sándor , Karel Klem , Otmar Urban
This review critically examines the chemical nature of Glomalin-related soil proteins (GRSP), the biases introduced by non-mycorrhizal sources, and emphasizes the need to avoid misinterpreting GRSP as an arbuscular mycorrhizal fungi (AMF) marker. GRSP have been widely used in agricultural science as indicators of soil health and as a quantitative indicator of the accumulation of decomposed biomass of AMF in soil. GRSP is typically extracted by repeated autoclaving of soil in a citrate buffer, followed by protein quantification using the Bradford assay. However, recent discussions on the composition, structure, and interpretation of GRSP raise concerns about its specificity as an AMF marker, and we have serious doubts about the protein dominance of this mixture. A key limitation is that conventionally measured GRSP concentrations also correlate with plant litter decomposition and organic matter inputs, indicating that GRSP reflects general organic accumulation rather than AMF-specific processes. This underscores the need for more direct and representative measurements of mycorrhizal interactions. To address this issue, we propose renaming GRSP as Bradford-reactive soil compounds (BRSC), a term that more accurately reflects the chemical heterogeneity of the fraction and avoids implying any specific association with AMF.
{"title":"Functional limitations of glomalin-related soil protein as an indicator of arbuscular mycorrhizal fungi while remaining relevant to soil health","authors":"Viktor Nagy , Roman Sándor , Karel Klem , Otmar Urban","doi":"10.1016/j.soilbio.2025.110076","DOIUrl":"10.1016/j.soilbio.2025.110076","url":null,"abstract":"<div><div>This review critically examines the chemical nature of Glomalin-related soil proteins (GRSP), the biases introduced by non-mycorrhizal sources, and emphasizes the need to avoid misinterpreting GRSP as an arbuscular mycorrhizal fungi (AMF) marker. GRSP have been widely used in agricultural science as indicators of soil health and as a quantitative indicator of the accumulation of decomposed biomass of AMF in soil. GRSP is typically extracted by repeated autoclaving of soil in a citrate buffer, followed by protein quantification using the Bradford assay. However, recent discussions on the composition, structure, and interpretation of GRSP raise concerns about its specificity as an AMF marker, and we have serious doubts about the protein dominance of this mixture. A key limitation is that conventionally measured GRSP concentrations also correlate with plant litter decomposition and organic matter inputs, indicating that GRSP reflects general organic accumulation rather than AMF-specific processes. This underscores the need for more direct and representative measurements of mycorrhizal interactions. To address this issue, we propose renaming GRSP as Bradford-reactive soil compounds (BRSC), a term that more accurately reflects the chemical heterogeneity of the fraction and avoids implying any specific association with AMF.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110076"},"PeriodicalIF":10.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145801471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-12-05DOI: 10.1016/j.soilbio.2025.110047
Siddharth Uppal , Jamie Woolet , Muthusubramanian Venkateshwaran , Christopher Baxer , Yari Johnson , Ashley Tung , Charlie Siwei Yu , Thea Whitman , Jason C. Kwan
Prescribed fires are a critical tool for ecosystem restoration and for reducing the risk of wildfires, which have grown in frequency and severity in many regions of the globe. Fires typically cause transient reduction of soil bacterial diversity, and we are beginning to identify certain taxa that seem to be common fire-responders. However, a genetic basis for understanding the mechanisms behind post-fire bacterial community recovery is not well-established. Prescribed burns in particular offer an opportunity to study this process through the use of unburned control plots at the same location and the ease of sampling at early timepoints after the fire. Here, we conducted prescribed burns with paired unburned controls at two prairie locations. We analyzed 16S rRNA data at four timepoints over 5 months, then used these data to select a subset of samples to target for deeply sequenced shotgun metagenomics. Although the bacterial community remained distinct during the study timescale, the functional composition appears to return to the baseline levels at five months post-burn. On a species level, however, we determined that post-fire survival is more nuanced than possession of previously hypothesized pyrophilous traits. For example, we found that spore-related genes are associated with burning only in some spore-forming taxa, and our results suggest that predicted doubling time was not a critical determinant of success post-fire in this system. Our study therefore advances the understanding of how both function and composition contribute to soil bacterial community dynamics, post-disturbance.
{"title":"Complex effects of a prescribed burn on a prairie soil bacterial community","authors":"Siddharth Uppal , Jamie Woolet , Muthusubramanian Venkateshwaran , Christopher Baxer , Yari Johnson , Ashley Tung , Charlie Siwei Yu , Thea Whitman , Jason C. Kwan","doi":"10.1016/j.soilbio.2025.110047","DOIUrl":"10.1016/j.soilbio.2025.110047","url":null,"abstract":"<div><div>Prescribed fires are a critical tool for ecosystem restoration and for reducing the risk of wildfires, which have grown in frequency and severity in many regions of the globe. Fires typically cause transient reduction of soil bacterial diversity, and we are beginning to identify certain taxa that seem to be common fire-responders. However, a genetic basis for understanding the mechanisms behind post-fire bacterial community recovery is not well-established. Prescribed burns in particular offer an opportunity to study this process through the use of unburned control plots at the same location and the ease of sampling at early timepoints after the fire. Here, we conducted prescribed burns with paired unburned controls at two prairie locations. We analyzed 16S rRNA data at four timepoints over 5 months, then used these data to select a subset of samples to target for deeply sequenced shotgun metagenomics. Although the bacterial community remained distinct during the study timescale, the functional composition appears to return to the baseline levels at five months post-burn. On a species level, however, we determined that post-fire survival is more nuanced than possession of previously hypothesized pyrophilous traits. For example, we found that spore-related genes are associated with burning only in some spore-forming taxa, and our results suggest that predicted doubling time was not a critical determinant of success post-fire in this system. Our study therefore advances the understanding of how both function and composition contribute to soil bacterial community dynamics, post-disturbance.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110047"},"PeriodicalIF":10.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145673703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-12-09DOI: 10.1016/j.soilbio.2025.110066
Zhijian Mou , Xuefeng Zhu , Mengqiang Zhu , Hongfei Liu , Chao Liang , Zhanfeng Liu
Amino sugars are key tracers of microbial necromass in soil organic carbon, yet the lack of direct methodological comparison between gas chromatography (GC) and high-performance liquid chromatography (HPLC) limits cross-study integration. Here, we provide the first systematic evaluation of both methods using 395 field samples and 1900 published observations across global ecosystems. GC and HPLC showed strong analytical agreement (R2 > 0.92; RSD <5 %), but GC yielded more accurate measurements in C- and N-rich soils due to superior cleanup and purification, whereas HPLC offered higher throughput and operational simplicity. These results establish a quantitative benchmark for harmonizing amino-sugar datasets and highlight that method choice should align with soil matrix complexity and analytical goals.
{"title":"Benchmarking GC and HPLC for amino sugar analyses across soils: A comprehensive evaluation","authors":"Zhijian Mou , Xuefeng Zhu , Mengqiang Zhu , Hongfei Liu , Chao Liang , Zhanfeng Liu","doi":"10.1016/j.soilbio.2025.110066","DOIUrl":"10.1016/j.soilbio.2025.110066","url":null,"abstract":"<div><div>Amino sugars are key tracers of microbial necromass in soil organic carbon, yet the lack of direct methodological comparison between gas chromatography (GC) and high-performance liquid chromatography (HPLC) limits cross-study integration. Here, we provide the first systematic evaluation of both methods using 395 field samples and 1900 published observations across global ecosystems. GC and HPLC showed strong analytical agreement (R<sup>2</sup> > 0.92; RSD <5 %), but GC yielded more accurate measurements in C- and N-rich soils due to superior cleanup and purification, whereas HPLC offered higher throughput and operational simplicity. These results establish a quantitative benchmark for harmonizing amino-sugar datasets and highlight that method choice should align with soil matrix complexity and analytical goals.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110066"},"PeriodicalIF":10.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145730836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-12-27DOI: 10.1016/j.soilbio.2025.110078
Rike Schwarz , Pia M. Bradler , Anne Chao , Po-Yen Chuang , Marcel Ciobanu , Orsi Decker , Benjamin M. Delory , Peter Dietrich , Sebastian Dittrich , Andreas Fichtner , Ludwig Lettenmaier , Michael Junginger , Oliver Mitesser , Akira S. Mori , Jörg Müller , Goddert von Oheimb , Kerstin Pierick , Nico Eisenhauer , Simone Cesarz
Most production forests are managed primarily for timber production, leading to homogenous forests at landscape scale and reduced biodiversity. To explore whether silviculturally enhanced forest structural heterogeneity can promote biodiversity at landscape scale, we conducted a large-scale experiment in eight German forests. We manipulated structural β complexity, i.e., the heterogeneity of structural elements between forest patches, by experimentally introducing variation in canopy cover and different types of deadwood across 156 patches of 50 × 50 m each, to investigate its effects on biodiversity. Here we analyzed the response of soil nematode communities to heterogenization by assessing taxonomic and functional diversity across patch (α-diversity), site (γ-diversity), and between-patch (β-diversity) scales using Hill–Chao numbers as diversity indices. Additionally, we tested whether environmental variables correlate with nematode diversity responses. Our results show that functional diversity is more responsive than taxonomic diversity. Increases in β-diversity of common and dominant functional groups occurred simultaneously with declines in α- and γ-diversity. This pattern indicates that local community dissimilarity can rise without an increase in overall landscape-level richness and suggests a shift toward more specialized nematode communities in response to the interventions. Moreover, we found that certain site-specific conditions, such as soil texture and understory plant biomass, correlated with these effects. Overall, our findings reveal complex, scale-dependent responses of nematode diversity to changes in aboveground forest structure and highlight the need to further investigate the context dependence of forest biodiversity management to provide informed recommendations. This study represents an important first step toward understanding how to increase soil β-diversity through enhanced forest structural heterogeneity at management-relevant (i.e., landscape level) spatial scales.
{"title":"Enhanced forest structural heterogeneity increases functional β-diversity but reduces α- and γ-diversity in soil nematodes","authors":"Rike Schwarz , Pia M. Bradler , Anne Chao , Po-Yen Chuang , Marcel Ciobanu , Orsi Decker , Benjamin M. Delory , Peter Dietrich , Sebastian Dittrich , Andreas Fichtner , Ludwig Lettenmaier , Michael Junginger , Oliver Mitesser , Akira S. Mori , Jörg Müller , Goddert von Oheimb , Kerstin Pierick , Nico Eisenhauer , Simone Cesarz","doi":"10.1016/j.soilbio.2025.110078","DOIUrl":"10.1016/j.soilbio.2025.110078","url":null,"abstract":"<div><div>Most production forests are managed primarily for timber production, leading to homogenous forests at landscape scale and reduced biodiversity. To explore whether silviculturally enhanced forest structural heterogeneity can promote biodiversity at landscape scale, we conducted a large-scale experiment in eight German forests. We manipulated structural β complexity, i.e., the heterogeneity of structural elements between forest patches, by experimentally introducing variation in canopy cover and different types of deadwood across 156 patches of 50 × 50 m each, to investigate its effects on biodiversity. Here we analyzed the response of soil nematode communities to heterogenization by assessing taxonomic and functional diversity across patch (α-diversity), site (γ-diversity), and between-patch (β-diversity) scales using Hill–Chao numbers as diversity indices. Additionally, we tested whether environmental variables correlate with nematode diversity responses. Our results show that functional diversity is more responsive than taxonomic diversity. Increases in β-diversity of common and dominant functional groups occurred simultaneously with declines in α- and γ-diversity. This pattern indicates that local community dissimilarity can rise without an increase in overall landscape-level richness and suggests a shift toward more specialized nematode communities in response to the interventions. Moreover, we found that certain site-specific conditions, such as soil texture and understory plant biomass, correlated with these effects. Overall, our findings reveal complex, scale-dependent responses of nematode diversity to changes in aboveground forest structure and highlight the need to further investigate the context dependence of forest biodiversity management to provide informed recommendations. This study represents an important first step toward understanding how to increase soil β-diversity through enhanced forest structural heterogeneity at management-relevant (i.e., landscape level) spatial scales.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110078"},"PeriodicalIF":10.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145845097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-12-11DOI: 10.1016/j.soilbio.2025.110065
Taicong Liu , Shuting Tang , Yingpeng Sun , Zhongtao Lao , Daijie Chen , Ming Ao , Haojie Qu , Chao Jin , Liying Lan , Roland Bol , Miaoyue Zhang , Yingjie Cao , Jean Louis Morel , Yuanqing Chao , Yetao Tang , Rongliang Qiu , Shizhong Wang
Reduction of As(V) to As(III) under anaerobic conditions significantly increases arsenic (As) toxicity and bioavailability, making it a crucial process that drives As contamination. Simultaneously, co-occurring microbial nitrogen (N) transformations may accelerate As(V/III) conversion through complex interactions and competition, yet their competing effects remain insufficiently resolved. To address this, we applied six N-addition treatments with varying total N input and form to anaerobic microcosms established with As-contaminated soil. N treatments receiving NH4+ only (MN(NH4+)) and NO3− only (MN(NO3−)) were included to examine how specific N forms and their associated transformations affect As(V/III) speciation. Additionally, low (LN), medium (MN), and high (HN) N levels were applied as NH4NO3 to increase N availability and intensify competition among N transformations. Results showed that MN(NH4+) increased As(III) in soil (1.4–36.0 mg kg−1) and porewater (0.1–138.7 μg L−1) by enhancing anammox (∼40 %) and promoting DOC and Fe(II) accumulation. Conversely, MN(NO3−) lowered As(III) by stimulating denitrification and restricting DOC and Fe(II) accumulation. Increasing N input from LN to HN decreased denitrification rates by 19.9–51.5 % while enhancing anammox rates by 51.9–199.2 % and the transcriptional activity of the anammox gene hzs (up to 1.5). It also increased the abundance of the As-reducing gene arrB, DOC accumulation, and Fe(III) reduction, ultimately elevating As(III) by 22.3–31.4 mg kg−1 and 35.0–130.8 μg L−1 in soil and porewater, respectively. Structural equation modeling (SEM) and linear mixed-effects models (LMM) identified the largest standardized effect (0.79) and importance (19.1 %) for anammox, highlighting anammox as the dominant driver of As(V/III) speciation. This study provides novel insights into N–As interactions.
{"title":"Anammox dominated As(V/III) speciation during long-term anaerobic conditions","authors":"Taicong Liu , Shuting Tang , Yingpeng Sun , Zhongtao Lao , Daijie Chen , Ming Ao , Haojie Qu , Chao Jin , Liying Lan , Roland Bol , Miaoyue Zhang , Yingjie Cao , Jean Louis Morel , Yuanqing Chao , Yetao Tang , Rongliang Qiu , Shizhong Wang","doi":"10.1016/j.soilbio.2025.110065","DOIUrl":"10.1016/j.soilbio.2025.110065","url":null,"abstract":"<div><div>Reduction of As(V) to As(III) under anaerobic conditions significantly increases arsenic (As) toxicity and bioavailability, making it a crucial process that drives As contamination. Simultaneously, co-occurring microbial nitrogen (N) transformations may accelerate As(V/III) conversion through complex interactions and competition, yet their competing effects remain insufficiently resolved. To address this, we applied six N-addition treatments with varying total N input and form to anaerobic microcosms established with As-contaminated soil. N treatments receiving NH<sub>4</sub><sup>+</sup> only (MN(NH<sub>4</sub><sup>+</sup>)) and NO<sub>3</sub><sup>−</sup> only (MN(NO<sub>3</sub><sup>−</sup>)) were included to examine how specific N forms and their associated transformations affect As(V/III) speciation. Additionally, low (LN), medium (MN), and high (HN) N levels were applied as NH<sub>4</sub>NO<sub>3</sub> to increase N availability and intensify competition among N transformations. Results showed that MN(NH<sub>4</sub><sup>+</sup>) increased As(III) in soil (1.4–36.0 mg kg<sup>−1</sup>) and porewater (0.1–138.7 μg L<sup>−1</sup>) by enhancing anammox (∼40 %) and promoting DOC and Fe(II) accumulation. Conversely, MN(NO<sub>3</sub><sup>−</sup>) lowered As(III) by stimulating denitrification and restricting DOC and Fe(II) accumulation. Increasing N input from LN to HN decreased denitrification rates by 19.9–51.5 % while enhancing anammox rates by 51.9–199.2 % and the transcriptional activity of the anammox gene <em>hzs</em> (up to 1.5). It also increased the abundance of the As-reducing gene <em>arrB</em>, DOC accumulation, and Fe(III) reduction, ultimately elevating As(III) by 22.3–31.4 mg kg<sup>−1</sup> and 35.0–130.8 μg L<sup>−1</sup> in soil and porewater, respectively. Structural equation modeling (SEM) and linear mixed-effects models (LMM) identified the largest standardized effect (0.79) and importance (19.1 %) for anammox, highlighting anammox as the dominant driver of As(V/III) speciation. This study provides novel insights into N–As interactions.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110065"},"PeriodicalIF":10.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145731632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-12-24DOI: 10.1016/j.soilbio.2025.110077
Jing Yuan , Zhuyue Yan , Yuanhao Wang , Shaolin Fan , Jiaxu Chen , Kejiang Ye , Guixian Zheng , Shanping Wan , Yi Zheng , Fuqiang Yu , Yanliang Wang , Hans Lambers , Ellen Kandeler
Ectomycorrhiza (EM)-associated bacteria play a pivotal role in hydrolyzing soil organic phosphorus (P), but which taxa of bacteria are enriched by EM fungi remains largely unexplored. Here, we hypothesized that EM hyphae release oxalate, which enriches oxalotrophic bacteria (OxB) that mobilize less-available soil P through enzyme activities. Using frc (formyl-coenzyme A transferase) as a biomarker gene of OxB, we first identified OxB strains from the National Center for Biotechnology Information (NCBI) database and found that soil OxB mainly belong to genera of Bradyrhizobium, Streptomyces, Paraburkholderia, Cupriavidus and Variovorax, and OxB genomes harbored significantly more genes coding for acid and alkaline phosphatases than non-OxB strains did. Subsequently, the abundance of frc genes in the ectomycorrhizosphere and non-mycorrhizosphere were determined using qPCR, amplicon and metagenomic sequencing, and we found that the relative abundance of OxB in the ectomycorrhizosphere was significantly increased under both laboratory and field conditions. Metagenomic sequencing analysis also showed that more than 52 % P-mobilizing bacteria in the ectomycorrhizosphere were OxB, and the abundance of the frc gene was positively correlated with that of genes encoding P-mobilizing enzymes, like ppa, phoA, phoD, phoN and ugpQ. Additionally, a total of 79 OxB strains were isolated, and exogenous oxalate was used as a carbon (C) source to support OxB and affect the bacterial extracellular phosphatase and phytase activities. Finally, since Streptomyces is a widely studied group that plays important roles in P mobilization, we selected five OxB strains rather than Streptomyces to test their ability to mobilize P: three ‘generalist’ OxB that use oxalate as an additional C source, Cupriavidus pinatubonensis, Sphingomonas sp. MY-CA111, and Variovorax paradoxus; and two ‘specialist’ OxB that use oxalate as a sole C source, Cupriavidus sp. UR 7–04, and Ancylobacter rudongensis. The results show that all five tested OxB mobilized and utilized various organic P forms, particularly DNA, thereby promoting EM fungal total P acquisition and growth, and/or OxB proliferation. Our findings indicate that EM-associated OxB play an essential role in soil P mobilization. This study reveals a previously unrecognized eco-physiological role of OxB, elucidating the mechanism of biotic interactions between bacteria, fungi and plants in P mobilization.
外生菌根（EM）相关细菌在水解土壤有机磷(P)中起着关键作用，但EM真菌富集的细菌类群仍未被广泛探索。在这里，我们假设EM菌丝释放草酸，从而丰富草酸营养细菌（OxB），通过酶活性动员较少可利用的土壤P。利用frc（甲酰基辅酶A转移酶）作为OxB的生物标记基因，首先从国家生物技术信息中心（National Center for Biotechnology Information， NCBI）数据库中对OxB菌株进行鉴定，发现土壤OxB主要归属于bryyrhizobium、Streptomyces、Paraburkholderia、Cupriavidus和Variovorax属，并且OxB基因组中含有的酸性和碱性磷酸酶编码基因明显多于非OxB菌株。随后，我们利用qPCR、扩增子和宏基因组测序对外菌根圈和非菌根圈中frc基因的丰度进行了测定，我们发现在实验室和田间条件下，外菌根圈中OxB的相对丰度都显著增加。宏基因组测序分析也表明，外菌根圈中超过52%的p动员菌为OxB， frc基因的丰度与编码p动员酶的基因如ppa、phoA、phoD、phoN和ugpQ的丰度呈正相关。此外，共分离到79株OxB菌株，并以外源草酸作为碳(C)源支持OxB并影响细菌胞外磷酸酶和植酸酶活性。最后，由于链霉菌是一个被广泛研究的在P动员中起重要作用的组，我们选择了5种OxB菌株而不是链霉菌来测试它们动员P的能力：3种使用草酸盐作为额外C源的“多能型”OxB, Cupriavidus pinatubonensis, Sphingomonas sp. MY-CA111和Variovorax paradoxus；以及两种以草酸盐为唯一碳源的“专家”OxB, Cupriavidus sp. ur7 - 04和rudongensis双环杆菌。结果表明，五种OxB均能调动和利用多种有机磷，尤其是DNA，从而促进EM真菌总磷的获取和生长，以及OxB的增殖。我们的研究结果表明，em相关的OxB在土壤P动员中起重要作用。本研究揭示了一个以前未被认识到的OxB的生态生理作用，阐明了细菌、真菌和植物在磷动员中的生物相互作用机制。
{"title":"Oxalotrophic bacteria in the ectomycorrhizosphere play an essential role in phosphorus mobilization","authors":"Jing Yuan , Zhuyue Yan , Yuanhao Wang , Shaolin Fan , Jiaxu Chen , Kejiang Ye , Guixian Zheng , Shanping Wan , Yi Zheng , Fuqiang Yu , Yanliang Wang , Hans Lambers , Ellen Kandeler","doi":"10.1016/j.soilbio.2025.110077","DOIUrl":"10.1016/j.soilbio.2025.110077","url":null,"abstract":"<div><div>Ectomycorrhiza (EM)-associated bacteria play a pivotal role in hydrolyzing soil organic phosphorus (P), but which taxa of bacteria are enriched by EM fungi remains largely unexplored. Here, we hypothesized that EM hyphae release oxalate, which enriches oxalotrophic bacteria (OxB) that mobilize less-available soil P through enzyme activities. Using <em>frc</em> (formyl-coenzyme A transferase) as a biomarker gene of OxB, we first identified OxB strains from the National Center for Biotechnology Information (NCBI) database and found that soil OxB mainly belong to genera of <em>Bradyrhizobium</em>, <em>Streptomyces</em>, <em>Paraburkholderia, Cupriavidus</em> and <em>Variovorax</em>, and OxB genomes harbored significantly more genes coding for acid and alkaline phosphatases than non-OxB strains did. Subsequently, the abundance of <em>frc</em> genes in the ectomycorrhizosphere and non-mycorrhizosphere were determined using qPCR, amplicon and metagenomic sequencing, and we found that the relative abundance of OxB in the ectomycorrhizosphere was significantly increased under both laboratory and field conditions. Metagenomic sequencing analysis also showed that more than 52 % P-mobilizing bacteria in the ectomycorrhizosphere were OxB, and the abundance of the <em>frc</em> gene was positively correlated with that of genes encoding P-mobilizing enzymes, like <em>ppa, phoA, phoD, phoN</em> and <em>ugpQ</em>. Additionally, a total of 79 OxB strains were isolated, and exogenous oxalate was used as a carbon (C) source to support OxB and affect the bacterial extracellular phosphatase and phytase activities. Finally, since <em>Streptomyces</em> is a widely studied group that plays important roles in P mobilization, we selected five OxB strains rather than <em>Streptomyces</em> to test their ability to mobilize P: three ‘generalist’ OxB that use oxalate as an additional C source, <em>Cupriavidus pinatubonensis, Sphingomonas</em> sp. MY-CA111<em>,</em> and <em>Variovorax paradoxus</em>; and two ‘specialist’ OxB that use oxalate as a sole C source, <em>Cupriavidus</em> sp. UR 7–04, and <em>Ancylobacter rudongensis</em>. The results show that all five tested OxB mobilized and utilized various organic P forms, particularly DNA, thereby promoting EM fungal total P acquisition and growth, and/or OxB proliferation. Our findings indicate that EM-associated OxB play an essential role in soil P mobilization. This study reveals a previously unrecognized eco-physiological role of OxB, elucidating the mechanism of biotic interactions between bacteria, fungi and plants in P mobilization.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110077"},"PeriodicalIF":10.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145823020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-12-22DOI: 10.1016/j.soilbio.2025.110074
Haibo Pan , Yingyi Fu , Hairong Tu , Yongxing Cui , Beibei Chen , Jiejun Qi , Ziheng Peng , Shi Chen , Chunling Liang , Jiai Liu , Xiaomeng Li , Min Gao , Yu Luo , Gehong Wei , Shuo Jiao
Soil microbes play a crucial role in the global carbon cycle. However, a comprehensive understanding of how soil carbon emissions (i.e., soil respiration) respond to the loss of soil microbial diversity and the underlying mechanisms remains lacking. In this study, we conducted a microcosm experiment using filter membranes with varying pore sizes (unfiltered, 10 μm, 3 μm, and 0.8 μm) to investigate how the loss of soil prokaryotic and eukaryotic diversity affects soil carbon emissions. We demonstrated that the loss of microbiome diversity, which increases with filtration intensity, significantly stimulated soil respiration. Using enzyme stoichiometry, microbial carbon use efficiency estimated from 18O-labeled water, and metagenomics, we provided robust evidence that microbial diversity loss increased microbial resource demand, reduced microbial carbon use efficiency and growth (e.g., growth rate and biomass), and triggered a shift in metabolic strategies, resulting in elevated carbon emissions. Our study represents a significant advancement in understanding the mechanisms linking soil biodiversity loss and soil carbon emissions, highlighting the importance of protecting soil microbiome diversity for ecosystem carbon sequestration and climate change mitigation.
{"title":"Diversity loss of soil microbiome stimulates soil carbon emissions","authors":"Haibo Pan , Yingyi Fu , Hairong Tu , Yongxing Cui , Beibei Chen , Jiejun Qi , Ziheng Peng , Shi Chen , Chunling Liang , Jiai Liu , Xiaomeng Li , Min Gao , Yu Luo , Gehong Wei , Shuo Jiao","doi":"10.1016/j.soilbio.2025.110074","DOIUrl":"10.1016/j.soilbio.2025.110074","url":null,"abstract":"<div><div>Soil microbes play a crucial role in the global carbon cycle. However, a comprehensive understanding of how soil carbon emissions (i.e., soil respiration) respond to the loss of soil microbial diversity and the underlying mechanisms remains lacking. In this study, we conducted a microcosm experiment using filter membranes with varying pore sizes (unfiltered, 10 μm, 3 μm, and 0.8 μm) to investigate how the loss of soil prokaryotic and eukaryotic diversity affects soil carbon emissions. We demonstrated that the loss of microbiome diversity, which increases with filtration intensity, significantly stimulated soil respiration. Using enzyme stoichiometry, microbial carbon use efficiency estimated from <sup>18</sup>O-labeled water, and metagenomics, we provided robust evidence that microbial diversity loss increased microbial resource demand, reduced microbial carbon use efficiency and growth (e.g., growth rate and biomass), and triggered a shift in metabolic strategies, resulting in elevated carbon emissions. Our study represents a significant advancement in understanding the mechanisms linking soil biodiversity loss and soil carbon emissions, highlighting the importance of protecting soil microbiome diversity for ecosystem carbon sequestration and climate change mitigation.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110074"},"PeriodicalIF":10.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145823030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-12-11DOI: 10.1016/j.soilbio.2025.110068
Hong-Yan Wang , Xin-Yi Hu , Feng-Wu Zhou , Julio-Castillo Hernandez , Zhi-Guo Yu , Maxim Dorodnikov , Klaus-Holger Knorr , Andreas Kappler
Interactions between Fe(III) reduction and methanogenesis in regulating CH4 emissions remain controversial, particularly in peatlands. To address this, we investigated the effects of ferrihydrite amendments on net CH4 formation in four moderately acidic fen soils from the Great Khingan Mountains, the Changbai Mountains, the Tibetan Plateau, and Dajiuhu. Anaerobic microcosms were established to monitor gas formation and porewater chemistry, while detailed geochemical and microbiome profiling was conducted for the soils from the Changbai Mountains. Ferrihydrite additions increased net CH4 formation rates by 1.4–6.2 times, with stronger effects observed in soils with more available carbon. As expected, secondary crystalline magnetite did not form. Ferrihydrite reduction mainly occurred during the pre-methanogenic stage and was mediated by fermentative Fe(III)-reducing bacteria, such as Clostridium and OPB41. These microbes lowered H2 levels, reducing the relative abundance of Methanobacterium from 86% to 56%. However, fermentative Fe(III) reduction mitigated limitations on organic matter decomposition by elevating pH and improving the thermodynamic feasibility of organic carbon fermentation in the pre-methanogenic stage. Beyond enhanced substrate supply, the legacy of elevated pH further promoted activities of acetoclastic methanogens, as indicated by faster net acetate consumption in ferrihydrite treatments. Enriched metagenome-assembled genomes (MAGs) affiliated with Sumerlaeaceae, Clostridium, OPB41, and Prolixibacteraceae revealed the potential for polysaccharide hydrolysis and acetogenesis. Most of the enriched acetogens engaged in syntrophic interactions with methanogens. Collectively, our findings suggest that fermentative Fe(III) reduction can stimulate organic matter decomposition, while its legacy of elevated pH further accelerates organic matter decomposition and methanogenesis in acidic peatland soils.
{"title":"Enhanced methanogenesis in acidic fen peatlands via ferrihydrite reduction-driven microbial metabolisms","authors":"Hong-Yan Wang , Xin-Yi Hu , Feng-Wu Zhou , Julio-Castillo Hernandez , Zhi-Guo Yu , Maxim Dorodnikov , Klaus-Holger Knorr , Andreas Kappler","doi":"10.1016/j.soilbio.2025.110068","DOIUrl":"10.1016/j.soilbio.2025.110068","url":null,"abstract":"<div><div>Interactions between Fe(III) reduction and methanogenesis in regulating CH<sub>4</sub> emissions remain controversial, particularly in peatlands. To address this, we investigated the effects of ferrihydrite amendments on net CH<sub>4</sub> formation in four moderately acidic fen soils from the Great Khingan Mountains, the Changbai Mountains, the Tibetan Plateau, and Dajiuhu. Anaerobic microcosms were established to monitor gas formation and porewater chemistry, while detailed geochemical and microbiome profiling was conducted for the soils from the Changbai Mountains. Ferrihydrite additions increased net CH<sub>4</sub> formation rates by 1.4–6.2 times, with stronger effects observed in soils with more available carbon. As expected, secondary crystalline magnetite did not form. Ferrihydrite reduction mainly occurred during the pre-methanogenic stage and was mediated by fermentative Fe(III)-reducing bacteria, such as <em>Clostridium</em> and <em>OPB41</em>. These microbes lowered H<sub>2</sub> levels, reducing the relative abundance of <em>Methanobacterium</em> from 86% to 56%. However, fermentative Fe(III) reduction mitigated limitations on organic matter decomposition by elevating pH and improving the thermodynamic feasibility of organic carbon fermentation in the pre-methanogenic stage. Beyond enhanced substrate supply, the legacy of elevated pH further promoted activities of acetoclastic methanogens, as indicated by faster net acetate consumption in ferrihydrite treatments. Enriched metagenome-assembled genomes (MAGs) affiliated with <em>Sumerlaeaceae</em>, <em>Clostridium</em>, <em>OPB41</em>, and <em>Prolixibacteraceae</em> revealed the potential for polysaccharide hydrolysis and acetogenesis. Most of the enriched acetogens engaged in syntrophic interactions with methanogens. Collectively, our findings suggest that fermentative Fe(III) reduction can stimulate organic matter decomposition, while its legacy of elevated pH further accelerates organic matter decomposition and methanogenesis in acidic peatland soils.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110068"},"PeriodicalIF":10.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145728777","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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