Pub Date : 2026-01-14DOI: 10.1016/j.soilbio.2026.110083
Timothy J. Fahey, Joseph B. Yavitt
{"title":"Rhizosphere carbon flux of eight temperate tree species growing on a common site","authors":"Timothy J. Fahey, Joseph B. Yavitt","doi":"10.1016/j.soilbio.2026.110083","DOIUrl":"https://doi.org/10.1016/j.soilbio.2026.110083","url":null,"abstract":"","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"30 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145962528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-14DOI: 10.1016/j.soilbio.2026.110093
Axelle Tortosa, Grégoire T. Freschet, Jean Trap, Alain Brauman, Yvan Capowiez, Sylvain Coq, Jim Félix-Faure, Nathalie Fromin, Laure Gandois, Maritxu Guiresse, Raoul Huys, Antoine Lecerf, Jean-Marc Limousin, Alexandru Milcu, Johanne Nahmani, Agnès Robin, José-Miguel Sánchez-Pérez, Sabine Sauvage, Tiphaine Tallec, Claire Wittling, Stephan Hattenschwiler
Soil biodiversity as a critical component of terrestrial ecosystems and their functioning varies across spatial scales and environmental conditions. However, it remains unclear whether and how biodiversity patterns co-vary among different soil taxa across ecosystems.In this study, we compared diversity patterns of plants, earthworms, nematodes, bacteria, and fungi, as five major groups of soil organisms, across six strongly contrasting ecosystems ranging from mountain peatland to crop fields, including within-ecosystem variation in soil moisture. We hypothesized co-variation in taxonomic richness (alpha diversity) and composition (beta diversity) of multiple groups of soil organisms across ecosystems, moisture conditions and spatial scales.In partial contrast to our initial hypothesis, co-variation in the taxonomic richness among these groups was limited, though significant positive associations were found among bacteria, fungi, and earthworms across all sites. Plant diversity showed distinct associations with soil organism diversity, particularly with earthworms and bacteria, highlighting above–belowground biodiversity linkages. Beta diversity showed substantial co-variation among all soil organism groups, reflecting a spatial coupling of their communities that was influenced by differences in soil moisture conditions. These patterns were more pronounced in near-natural and no-till agroecosystems compared to conventional agricultural systems. Our results highlight that ecosystem type shapes broad-scale taxonomic richness, while local soil moisture critically influences soil biodiversity and spatial community composition, emphasizing the multi-scale drivers of soil biodiversity.
{"title":"Biodiversity co-variation patterns in a range of soil organism taxa across highly contrasting ecosystems","authors":"Axelle Tortosa, Grégoire T. Freschet, Jean Trap, Alain Brauman, Yvan Capowiez, Sylvain Coq, Jim Félix-Faure, Nathalie Fromin, Laure Gandois, Maritxu Guiresse, Raoul Huys, Antoine Lecerf, Jean-Marc Limousin, Alexandru Milcu, Johanne Nahmani, Agnès Robin, José-Miguel Sánchez-Pérez, Sabine Sauvage, Tiphaine Tallec, Claire Wittling, Stephan Hattenschwiler","doi":"10.1016/j.soilbio.2026.110093","DOIUrl":"https://doi.org/10.1016/j.soilbio.2026.110093","url":null,"abstract":"Soil biodiversity as a critical component of terrestrial ecosystems and their functioning varies across spatial scales and environmental conditions. However, it remains unclear whether and how biodiversity patterns co-vary among different soil taxa across ecosystems.In this study, we compared diversity patterns of plants, earthworms, nematodes, bacteria, and fungi, as five major groups of soil organisms, across six strongly contrasting ecosystems ranging from mountain peatland to crop fields, including within-ecosystem variation in soil moisture. We hypothesized co-variation in taxonomic richness (alpha diversity) and composition (beta diversity) of multiple groups of soil organisms across ecosystems, moisture conditions and spatial scales.In partial contrast to our initial hypothesis, co-variation in the taxonomic richness among these groups was limited, though significant positive associations were found among bacteria, fungi, and earthworms across all sites. Plant diversity showed distinct associations with soil organism diversity, particularly with earthworms and bacteria, highlighting above–belowground biodiversity linkages. Beta diversity showed substantial co-variation among all soil organism groups, reflecting a spatial coupling of their communities that was influenced by differences in soil moisture conditions. These patterns were more pronounced in near-natural and no-till agroecosystems compared to conventional agricultural systems. Our results highlight that ecosystem type shapes broad-scale taxonomic richness, while local soil moisture critically influences soil biodiversity and spatial community composition, emphasizing the multi-scale drivers of soil biodiversity.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"38 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145972563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-12DOI: 10.1016/j.soilbio.2026.110086
Ziliang Yin , Xin Sun , Tijiu Cai , Xiaoxin Sun
Shrub encroachment disrupts the dynamic balance between soil organic carbon (SOC) input and output in marsh ecosystems, and directly influences SOC accumulation. Traditional paradigms primarily attribute SOC dynamics to plant traits and soil physicochemical properties, whereas emerging evidence indicates underestimated roles of microbial communities in this process. This study used laboratory incubation, 13C NMR spectroscopy, and metagenomic sequencing to explore the key factors regulating marsh SOC stock and stability across four shrub encroachment stages in the largest temperate marsh in Northeast China. The results demonstrate that, although shrub encroachment significantly increased potential sources (e.g., marsh plant biomass and carbon stock) of SOC, low carbon quality prevented a substantial increase in SOC stocks and stability. Notably, soil microbial communities were pivotal drivers in regulating SOC dynamics in plant-soil-microbe interactions. Six carbon fixation pathways dominated by abundant and transitional taxa explained only 0.07 % of SOC stock variation, whereas the synergistic interactions between microorganisms and plants or soil had the most significant effect on SOC stocks. In contrast, the variation in SOC stability was primarily attributed to changes in carbohydrate-active enzyme (CAZyme) gene profiles dominated by rare taxa (61.26 %), surpassing the explanatory power of plant traits and soil physicochemical properties. Additionally, rare taxa substantially influenced synergistic interactions among nitrogen cycling, phosphorus cycling, carbon fixation, and CAZyme genes via the quorum sensing (QS) pathway. This study provides novel insights into the effects of plant-soil-microbial interactions on marsh SOC transformation during shrub encroachment, highlighting the potential of rare taxa to release available nutrients and accelerating carbon, nitrogen, and phosphorus cycling.
{"title":"Rare and abundant soil microbes coordinate C, N, P, and quorum sensing pathways to destabilize SOC in shrub-encroached marshes","authors":"Ziliang Yin , Xin Sun , Tijiu Cai , Xiaoxin Sun","doi":"10.1016/j.soilbio.2026.110086","DOIUrl":"10.1016/j.soilbio.2026.110086","url":null,"abstract":"<div><div>Shrub encroachment disrupts the dynamic balance between soil organic carbon (SOC) input and output in marsh ecosystems, and directly influences SOC accumulation. Traditional paradigms primarily attribute SOC dynamics to plant traits and soil physicochemical properties, whereas emerging evidence indicates underestimated roles of microbial communities in this process. This study used laboratory incubation, <sup>13</sup>C NMR spectroscopy, and metagenomic sequencing to explore the key factors regulating marsh SOC stock and stability across four shrub encroachment stages in the largest temperate marsh in Northeast China. The results demonstrate that, although shrub encroachment significantly increased potential sources (e.g., marsh plant biomass and carbon stock) of SOC, low carbon quality prevented a substantial increase in SOC stocks and stability. Notably, soil microbial communities were pivotal drivers in regulating SOC dynamics in plant-soil-microbe interactions. Six carbon fixation pathways dominated by abundant and transitional taxa explained only 0.07 % of SOC stock variation, whereas the synergistic interactions between microorganisms and plants or soil had the most significant effect on SOC stocks. In contrast, the variation in SOC stability was primarily attributed to changes in carbohydrate-active enzyme (CAZyme) gene profiles dominated by rare taxa (61.26 %), surpassing the explanatory power of plant traits and soil physicochemical properties. Additionally, rare taxa substantially influenced synergistic interactions among nitrogen cycling, phosphorus cycling, carbon fixation, and CAZyme genes via the quorum sensing (QS) pathway. This study provides novel insights into the effects of plant-soil-microbial interactions on marsh SOC transformation during shrub encroachment, highlighting the potential of rare taxa to release available nutrients and accelerating carbon, nitrogen, and phosphorus cycling.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"215 ","pages":"Article 110086"},"PeriodicalIF":10.3,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145957375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-12DOI: 10.1016/j.soilbio.2026.110085
Shunyin Huang, Chen Huang, Yan Xiao
Global soil microplastics (MPs) pollution has become increasingly severe and is exerting persistent impacts on soil bacterial communities. Thus, a thorough investigation is imperative to elucidate the integrated impacts of MPs on soil microbial diversity, community composition, network patterns, and potential metabolic functions. In this study, we conducted a data synthesis of 182 publications and demonstrated that MPs exert pronounced adverse impacts on soil bacterial communities. Firstly, MPs significantly reduced soil bacterial alpha diversity (−1.1 % ∼ −3.2 %), with stronger inhibitory effects observed for conventional MPs, small size particles, and high dose MPs exposure. Further, biodegradable MPs significantly decreased the heterogeneity of soil bacterial communities, whereas conventional MPs increased it. Furthermore, the presence of MPs induced substantial changes in both the composition and structure of bacterial communities. Briefly, MPs significantly decreased the relative abundance of phylum Firmicutes, Campilobacterota, and WPS2 while increased the relative abundance of class Alphaproteobacteria and Blastocatellia. Meanwhile, MPs diminished the complexity and stability of bacterial co-occurrence networks, suggesting the soil microbial community exhibits higher vulnerability to environmental disturbances. The bacterial network exhibited a keystone transition favoring organic-degrading taxa. Finally, functional profiling showed significant upregulation of genes associated with human pathogenesis, organic degradation, and nitrogen fixation, while downregulation of nitrification. Collectively, our results highlight the pervasive negative impacts of MPs on soil bacterial communities, providing critical insights for assessing the ecological consequences of soil MPs pollution.
{"title":"Microplastics reduce soil bacterial alpha diversity and network stability","authors":"Shunyin Huang, Chen Huang, Yan Xiao","doi":"10.1016/j.soilbio.2026.110085","DOIUrl":"10.1016/j.soilbio.2026.110085","url":null,"abstract":"<div><div>Global soil microplastics (MPs) pollution has become increasingly severe and is exerting persistent impacts on soil bacterial communities. Thus, a thorough investigation is imperative to elucidate the integrated impacts of MPs on soil microbial diversity, community composition, network patterns, and potential metabolic functions. In this study, we conducted a data synthesis of 182 publications and demonstrated that MPs exert pronounced adverse impacts on soil bacterial communities. Firstly, MPs significantly reduced soil bacterial alpha diversity (−1.1 % ∼ −3.2 %), with stronger inhibitory effects observed for conventional MPs, small size particles, and high dose MPs exposure. Further, biodegradable MPs significantly decreased the heterogeneity of soil bacterial communities, whereas conventional MPs increased it. Furthermore, the presence of MPs induced substantial changes in both the composition and structure of bacterial communities. Briefly, MPs significantly decreased the relative abundance of phylum <em>Firmicutes</em>, <em>Campilobacterota</em>, and <em>WPS2</em> while increased the relative abundance of class <em>Alphaproteobacteria</em> and <em>Blastocatellia</em>. Meanwhile, MPs diminished the complexity and stability of bacterial co-occurrence networks, suggesting the soil microbial community exhibits higher vulnerability to environmental disturbances. The bacterial network exhibited a keystone transition favoring organic-degrading taxa. Finally, functional profiling showed significant upregulation of genes associated with human pathogenesis, organic degradation, and nitrogen fixation, while downregulation of nitrification. Collectively, our results highlight the pervasive negative impacts of MPs on soil bacterial communities, providing critical insights for assessing the ecological consequences of soil MPs pollution.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"215 ","pages":"Article 110085"},"PeriodicalIF":10.3,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145957376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-10DOI: 10.1016/j.soilbio.2026.110084
Boyu Jia , Siyu Zhang , Ningning Wu , Liqi Cai , Zhongdan Li , Shanquan Wang
The integration of biotic- and abiotic-dehalogenation strategies offers a transformative approach to remediating organohalide-contaminated soils, harnessing the synergistic benefits of biological selectivity and abiotic efficiency. However, challenges in modulating electron flux partitioning at biotic-abiotic interfaces and in reconstructing adaptive microbial metabolic networks continue to impede practical implementation.
This review comprehensively synthesizes recent advances in synergistic biotic-abiotic strategies for removing organohalide pollutants from contaminated sites, with a particular emphasis on iron-sulfur mineral species (FemSn)-mediated electron transfer mechanisms and the regulation of microbial metabolic networks. In this framework, electrons are transferred via surface Fe–S active sites on mineral phases, enabling electron tunneling at interfaces to microbial extracellular carriers and soluble redox mediators that coordinate flux in soil dechlorination system. This review begins with respiratory electron transport chains in organohalide-respiring bacteria (OHRB), while highlighting evolutionary trade-offs in electron carrier utilization and energy conservation. It then explores microbial interactions, showing how crystallographic defect engineering enhances enzymatic activation via electron tunneling and mitigates nanomaterial toxicity. Extending to ecosystem dynamics, it maps electron flux routing across microbial consortia, showing in which manner nanowire topologies and redox mediators orchestrate dehalogenation pathways amid metabolic competition. Finally, it bridges scales through machine learning-driven multi-omics integration, translating atomic-scale Fe–S coordination patterns into predictive models for optimizing electron flux. Overall, this review provides critical insights for designing next-generation dehalogenation remediation strategies that maximize biotic-abiotic synergies by precisely controlling electron flux.
{"title":"Advances in synergistic biotic-abiotic dehalogenation in soil: FemSn-mediated electron transfer and microbial metabolic network regulation","authors":"Boyu Jia , Siyu Zhang , Ningning Wu , Liqi Cai , Zhongdan Li , Shanquan Wang","doi":"10.1016/j.soilbio.2026.110084","DOIUrl":"10.1016/j.soilbio.2026.110084","url":null,"abstract":"<div><div>The integration of biotic- and abiotic-dehalogenation strategies offers a transformative approach to remediating organohalide-contaminated soils, harnessing the synergistic benefits of biological selectivity and abiotic efficiency. However, challenges in modulating electron flux partitioning at biotic-abiotic interfaces and in reconstructing adaptive microbial metabolic networks continue to impede practical implementation.</div><div>This review comprehensively synthesizes recent advances in synergistic biotic-abiotic strategies for removing organohalide pollutants from contaminated sites, with a particular emphasis on iron-sulfur mineral species (Fe<sub>m</sub>S<sub>n</sub>)-mediated electron transfer mechanisms and the regulation of microbial metabolic networks. In this framework, electrons are transferred <em>via</em> surface Fe–S active sites on mineral phases, enabling electron tunneling at interfaces to microbial extracellular carriers and soluble redox mediators that coordinate flux in soil dechlorination system. This review begins with respiratory electron transport chains in organohalide-respiring bacteria (OHRB), while highlighting evolutionary trade-offs in electron carrier utilization and energy conservation. It then explores microbial interactions, showing how crystallographic defect engineering enhances enzymatic activation <em>via</em> electron tunneling and mitigates nanomaterial toxicity. Extending to ecosystem dynamics, it maps electron flux routing across microbial consortia, showing in which manner nanowire topologies and redox mediators orchestrate dehalogenation pathways amid metabolic competition. Finally, it bridges scales through machine learning-driven multi-omics integration, translating atomic-scale Fe–S coordination patterns into predictive models for optimizing electron flux. Overall, this review provides critical insights for designing next-generation dehalogenation remediation strategies that maximize biotic-abiotic synergies by precisely controlling electron flux.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"215 ","pages":"Article 110084"},"PeriodicalIF":10.3,"publicationDate":"2026-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145947708","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}
Soil biodiversity monitoring requires standardized and practical sample storage methods, particularly for large-scale surveys. Yet, the influence of the soil storage conditions on eDNA-based assessments of microbial and faunal communities remains a key concern. Here, we assessed whether air-drying of soils at room temperature alters microbial (prokaryotes, fungi, micro-eukaryotes) and faunal (nematodes, annelids, micro-arthropods) abundance and diversity compared to freezing at −20 °C across different land-use types and management intensities through quantitative polymerase chain reaction (qPCR) and multi-marker DNA metabarcoding. We sampled topsoil (0–10 cm) from 42 sites of the Swiss Central Plateau spanning forests, grasslands, arable lands, orchards, wetlands, and urban areas. Forests, grasslands and arable lands were sampled in sites varying in management intensities. Across land-use types and management intensities, air-drying of soil followed by four to eight weeks of storage at room temperature or at −20 °C and freezing soil directly yielded comparable gene abundances, alpha-diversity, and community structure for all microbial and faunal groups. Moreover, microbial and faunal community structure were consistently shaped by land-use types and soil physicochemical variables regardless of the soil storage method used. These findings demonstrate that air-drying is a cost-effective and reliable method for short-term storing soil samples in large-scale biodiversity monitoring without compromising data quality.
{"title":"Air-drying of soil preserves microbial and faunal eDNA abundance and diversity regardless of land-use type or management intensity","authors":"Xingguo Han , Jessica Cuartero , Verena Koppe , Seraina Nohl , Astrid Sneyders , Karen Vancampenhout , Beat Frey , Aline Frossard","doi":"10.1016/j.soilbio.2026.110082","DOIUrl":"10.1016/j.soilbio.2026.110082","url":null,"abstract":"<div><div>Soil biodiversity monitoring requires standardized and practical sample storage methods, particularly for large-scale surveys. Yet, the influence of the soil storage conditions on eDNA-based assessments of microbial and faunal communities remains a key concern. Here, we assessed whether air-drying of soils at room temperature alters microbial (prokaryotes, fungi, micro-eukaryotes) and faunal (nematodes, annelids, micro-arthropods) abundance and diversity compared to freezing at −20 °C across different land-use types and management intensities through quantitative polymerase chain reaction (qPCR) and multi-marker DNA metabarcoding. We sampled topsoil (0–10 cm) from 42 sites of the Swiss Central Plateau spanning forests, grasslands, arable lands, orchards, wetlands, and urban areas. Forests, grasslands and arable lands were sampled in sites varying in management intensities. Across land-use types and management intensities, air-drying of soil followed by four to eight weeks of storage at room temperature or at −20 °C and freezing soil directly yielded comparable gene abundances, alpha-diversity, and community structure for all microbial and faunal groups. Moreover, microbial and faunal community structure were consistently shaped by land-use types and soil physicochemical variables regardless of the soil storage method used. These findings demonstrate that air-drying is a cost-effective and reliable method for short-term storing soil samples in large-scale biodiversity monitoring without compromising data quality.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"215 ","pages":"Article 110082"},"PeriodicalIF":10.3,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145902311","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 : 2025-12-30DOI: 10.1016/j.soilbio.2025.110081
Shengwei Yi , Zan Tian , Lanlan Wei , Feng Li , Lizhong Zhu , Fangbai Li , Songxiong Zhong , Fei Ge , Na Liu , Xionghui Ji , Jiang Tian , Yujun Wu
Microbial metabolites and root exudates significantly influence the fate of cadmium (Cd) in rhizosphere microdomains, but its interactions and regulatory mechanisms during the rice and microbiome dialogue remain poorly understood. Therefore, pyocyanin (PYO), a phenazine compound with redox properties secreted by Pseudomonas aeruginosa, was added to the rice rhizosphere microdomains. Subsequently, the response mechanisms of rice root exudates, rhizosphere microbiome, and Cd transformation were investigated using rice transcriptomics, metabolomics, and high-throughput 16S rRNA gene sequencing. The results indicated that PYO enhanced the biosynthesis of benzoxazinoids (BXs) and their intermediates by 1.2–2.0-fold in rice roots, thereby increasing the total accumulation of Cd in the roots through chelation. In turn, PYO and BXs reshaped functional rhizobacterial communities centered around Nitrospira, Kaistobacter, and Rubrivivax, which have potential Cd tolerance and adsorption capabilities. Consequently, the overall Cd adsorption by the rhizosphere microbial community increased significantly by 56.2 %–66.1 %. Pot experiments demonstrated that after the addition of PYO, the Cd bioavailability in the rhizosphere soil decreased by 5.6 %–27.5 %, and the translocation capacity of Cd from roots to shoot tissues was reduced by 15.4 %–46.0 %. Moreover, the application of PYO improved the catalase activity and the availability of major nutrients (nitrogen, phosphorus, and potassium) in the lightly contaminated soil during the jointing stage. The findings enhance the understanding of how microbial metabolites regulate rice root exudates to co-alleviate heavy metal toxicity and accumulation, thereby providing a theoretical basis for the development of biological prevention and control technologies for Cd in paddy soils.
{"title":"Pyocyanin induces rice benzoxazinoid synthesis to co-drive cadmium immobilization in rhizosphere microdomain: Microbial metabolite-mediated spatiotemporal communication mechanisms","authors":"Shengwei Yi , Zan Tian , Lanlan Wei , Feng Li , Lizhong Zhu , Fangbai Li , Songxiong Zhong , Fei Ge , Na Liu , Xionghui Ji , Jiang Tian , Yujun Wu","doi":"10.1016/j.soilbio.2025.110081","DOIUrl":"10.1016/j.soilbio.2025.110081","url":null,"abstract":"<div><div>Microbial metabolites and root exudates significantly influence the fate of cadmium (Cd) in rhizosphere microdomains, but its interactions and regulatory mechanisms during the rice and microbiome dialogue remain poorly understood. Therefore, pyocyanin (PYO), a phenazine compound with redox properties secreted by <em>Pseudomonas aeruginosa</em>, was added to the rice rhizosphere microdomains. Subsequently, the response mechanisms of rice root exudates, rhizosphere microbiome, and Cd transformation were investigated using rice transcriptomics, metabolomics, and high-throughput 16S rRNA gene sequencing. The results indicated that PYO enhanced the biosynthesis of benzoxazinoids (BXs) and their intermediates by 1.2–2.0-fold in rice roots, thereby increasing the total accumulation of Cd in the roots through chelation. In turn, PYO and BXs reshaped functional rhizobacterial communities centered around <em>Nitrospira</em>, <em>Kaistobacter</em>, and <em>Rubrivivax</em>, which have potential Cd tolerance and adsorption capabilities. Consequently, the overall Cd adsorption by the rhizosphere microbial community increased significantly by 56.2 %–66.1 %. Pot experiments demonstrated that after the addition of PYO, the Cd bioavailability in the rhizosphere soil decreased by 5.6 %–27.5 %, and the translocation capacity of Cd from roots to shoot tissues was reduced by 15.4 %–46.0 %. Moreover, the application of PYO improved the catalase activity and the availability of major nutrients (nitrogen, phosphorus, and potassium) in the lightly contaminated soil during the jointing stage. The findings enhance the understanding of how microbial metabolites regulate rice root exudates to co-alleviate heavy metal toxicity and accumulation, thereby providing a theoretical basis for the development of biological prevention and control technologies for Cd in paddy soils.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110081"},"PeriodicalIF":10.3,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884105","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 : 2025-12-29DOI: 10.1016/j.soilbio.2025.110080
Zi-Kai Liu , Weidong Chen , Ju-Pei Shen , Zi-Yang He , Hang-Wei Hu , Dan-Ting Yu , Ji-Zheng He
Manual isolation of tardigrades for molecular analysis is time-consuming and limits large-scale biodiversity studies. To enhance the efficiency of soil tardigrade molecular research, we developed a membrane filtration method to enrich soil tardigrades and other microfauna (nematodes and rotifers) for DNA extraction and the subsequent sequencing analyses. Filtration accelerated the workflow and detected more tardigrade species than manual isolation, although all membrane extraction methods underestimate their relative abundance. Filtration with a 15 μm membrane yielded the highest richness, while community differences were mainly driven by soil type rather than extraction method. Our results highlight the potential of filtration approaches in saving sample processing time and improving the detection of tardigrade species richness.
{"title":"Membrane filtration as an effective alternative to manual isolation for soil tardigrade DNA extraction","authors":"Zi-Kai Liu , Weidong Chen , Ju-Pei Shen , Zi-Yang He , Hang-Wei Hu , Dan-Ting Yu , Ji-Zheng He","doi":"10.1016/j.soilbio.2025.110080","DOIUrl":"10.1016/j.soilbio.2025.110080","url":null,"abstract":"<div><div>Manual isolation of tardigrades for molecular analysis is time-consuming and limits large-scale biodiversity studies. To enhance the efficiency of soil tardigrade molecular research, we developed a membrane filtration method to enrich soil tardigrades and other microfauna (nematodes and rotifers) for DNA extraction and the subsequent sequencing analyses. Filtration accelerated the workflow and detected more tardigrade species than manual isolation, although all membrane extraction methods underestimate their relative abundance. Filtration with a 15 μm membrane yielded the highest richness, while community differences were mainly driven by soil type rather than extraction method. Our results highlight the potential of filtration approaches in saving sample processing time and improving the detection of tardigrade species richness.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110080"},"PeriodicalIF":10.3,"publicationDate":"2025-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884106","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 : 2025-12-27DOI: 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":"2025-12-27","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 : 2025-12-25DOI: 10.1016/j.soilbio.2025.110079
François Maillard , Danny Lopes Ramos , Bowen Zhang , Ashish Ahlawat , Allison L. Gill , Carl Troein , Mattias Hedenström , Tobias Sparrman , Per Persson , Anders Tunlid
Fungal necromass is increasingly recognized as a major component of soil organic matter, and identifying the factors that govern its formation is critical for understanding and predicting the global carbon cycle. Among these factors, the biochemical composition of mycelial residues at senescence, particularly melanin content, has been consistently identified as a key determinant of the fraction of fungal necromass that persists in soils. However, even non-melanized mycelial residues exhibit a recalcitrant fraction that resists microbial decomposition, and the reasons for this persistence are not well understood. To address this gap, we asked whether the growth stage at which a single non-melanized fungal species dies governs the decay of its necromass in soil. Using Neurospora crassa, we produced seven necromass types that ranged from early exponential growth to prolonged starvation and decomposed them in forest soil. Necromass derived from biomass experiencing net growth at the time of harvest decomposed up to ten times faster than necromass from starved cultures, which were undergoing biomass loss. By the end of decomposition, only about 10 % of necromass from early-growth-stage biomass remained, while nearly 65 % of necromass from starved biomass persisted. Differences in mycelial biochemical traits, particularly C:N ratio and the degree of branching of glucans, which varied with fungal growth stage at death, explained variation in both decay rates and the size of the persistent fractions. Our findings suggest that the growth stage of fungi at death is a key factor driving fungal necromass decay profiles, with potentially large consequences for the contribution of fungal necromass to soil organic matter stocks.
{"title":"Mycelial biomass growth stage at death determines fungal necromass decay dynamics","authors":"François Maillard , Danny Lopes Ramos , Bowen Zhang , Ashish Ahlawat , Allison L. Gill , Carl Troein , Mattias Hedenström , Tobias Sparrman , Per Persson , Anders Tunlid","doi":"10.1016/j.soilbio.2025.110079","DOIUrl":"10.1016/j.soilbio.2025.110079","url":null,"abstract":"<div><div>Fungal necromass is increasingly recognized as a major component of soil organic matter, and identifying the factors that govern its formation is critical for understanding and predicting the global carbon cycle. Among these factors, the biochemical composition of mycelial residues at senescence, particularly melanin content, has been consistently identified as a key determinant of the fraction of fungal necromass that persists in soils. However, even non-melanized mycelial residues exhibit a recalcitrant fraction that resists microbial decomposition, and the reasons for this persistence are not well understood. To address this gap, we asked whether the growth stage at which a single non-melanized fungal species dies governs the decay of its necromass in soil. Using <em>Neurospora crassa</em>, we produced seven necromass types that ranged from early exponential growth to prolonged starvation and decomposed them in forest soil. Necromass derived from biomass experiencing net growth at the time of harvest decomposed up to ten times faster than necromass from starved cultures, which were undergoing biomass loss. By the end of decomposition, only about 10 % of necromass from early-growth-stage biomass remained, while nearly 65 % of necromass from starved biomass persisted. Differences in mycelial biochemical traits, particularly C:N ratio and the degree of branching of glucans, which varied with fungal growth stage at death, explained variation in both decay rates and the size of the persistent fractions. Our findings suggest that the growth stage of fungi at death is a key factor driving fungal necromass decay profiles, with potentially large consequences for the contribution of fungal necromass to soil organic matter stocks.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110079"},"PeriodicalIF":10.3,"publicationDate":"2025-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145830498","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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