Pub Date : 2025-04-22DOI: 10.1016/j.apsoil.2025.106112
Yanhong Yuan , María Belén Barquero , Yu Li , Shuiqing Zhang , Hongzhu Fan , Huimin Zhang , Qiang Li , Shutang Liu , Linlin Shi , Andong Cai , Chengjie Ren , Minggang Xu , Felipe Bastida , Hu Xu
Conventional and mineral phosphorus (P) fertilizers face depletion risks, but organo-mineral fertilization strategies can reduce P demand in crops. This study examines the long-term effects of applying manure (e.g., sludge, compost) alongside mineral fertilizers (NPKM) on P availability and microbial P cycling in maize and rice agroecosystems across diverse regions of China. We assessed how different fertilization strategies affect soil P availability, phosphatase activity, and the abundance of genes linked to P mineralization, solubilization, transport, and regulation. NPKM treatments significantly increased plant-available P and phosphatase activity, especially in maize, compared to inorganic (NPK) and control (CK) treatments. Enhanced P availability stemmed mainly from microbial-driven P mineralization, indicated by higher phosphatase activity and more abundant P mineralization genes, with no notable impact on P solubilization genes across treatments. Soil pH correlated positively with P solubilization and regulatory processes, highlighting environmental factors' role in P availability and associated microbial processes. Our long-term study demonstrates that combining mineral fertilizers with manure enhances P bioavailability by stimulating microbial mineralization, thereby supporting sustainable P management in agroecosystems.
{"title":"Fertilization type affects the genetic potential for phosphorus mineralization but not for phosphorus solubilization at the continental scale","authors":"Yanhong Yuan , María Belén Barquero , Yu Li , Shuiqing Zhang , Hongzhu Fan , Huimin Zhang , Qiang Li , Shutang Liu , Linlin Shi , Andong Cai , Chengjie Ren , Minggang Xu , Felipe Bastida , Hu Xu","doi":"10.1016/j.apsoil.2025.106112","DOIUrl":"10.1016/j.apsoil.2025.106112","url":null,"abstract":"<div><div>Conventional and mineral phosphorus (P) fertilizers face depletion risks, but organo-mineral fertilization strategies can reduce P demand in crops. This study examines the long-term effects of applying manure (e.g., sludge, compost) alongside mineral fertilizers (NPKM) on P availability and microbial P cycling in maize and rice agroecosystems across diverse regions of China. We assessed how different fertilization strategies affect soil P availability, phosphatase activity, and the abundance of genes linked to P mineralization, solubilization, transport, and regulation. NPKM treatments significantly increased plant-available P and phosphatase activity, especially in maize, compared to inorganic (NPK) and control (CK) treatments. Enhanced P availability stemmed mainly from microbial-driven P mineralization, indicated by higher phosphatase activity and more abundant P mineralization genes, with no notable impact on P solubilization genes across treatments. Soil pH correlated positively with P solubilization and regulatory processes, highlighting environmental factors' role in P availability and associated microbial processes. Our long-term study demonstrates that combining mineral fertilizers with manure enhances P bioavailability by stimulating microbial mineralization, thereby supporting sustainable P management in agroecosystems.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"211 ","pages":"Article 106112"},"PeriodicalIF":4.8,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143855938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-19DOI: 10.1016/j.apsoil.2025.106128
Xincheng Hong , Yudi Song , Dongdong Cao , Shengwen Xu , Feng Gao , Haoxin Fan , Huaiying Yao
Silver nanoparticles (AgNPs) are popular for their antimicrobial properties but their effects on soil carbon cycles remain unclear. This study explored AgNPs' impact on soil carbon dynamics and related microbial structures. Topsoil samples were treated with varying AgNPs concentrations (1, 10, 100, 500, and 1000 mg kg-1) over 56 days. Soil sampling was conducted at five time points (days 7, 14, 28, 42 and 56) to capture temporal changes. We assessed carbon mineralization, dissolved organic carbon (DOC), microbial biomass carbon (MBC), and enzymatic activities, along with 13C-labeled DOC and 13C-phospholipid fatty acid assays for tracing microbial carbon assimilation and evaluating carbon use efficiency (CUE). Following exposure to AgNPs in Ag100, Ag500, and Ag1000 treatments, cumulative CO2 emissions and DOC content increased by 40.3 %–170.0 % and 46.9 %–74.9 %, respectively. However, MBC decreased in Ag500 (63.8 %) and Ag1000 (63.0 %) treatments. Enzyme activities declined: β-glucosidase (43.7 %–48.4 %), β-xylosidase (48.9 %–79.7 %), and Cellobiohydrolase (50.8 %–97.6 %). Additionally, microbial CUE increased 49.7 % in Ag1000 treatment. Soil microbial communities exhibited significant alterations in response to AgNPs in Ag100, Ag500, and Ag1000 treatments as well. By day 56, the relative abundance of Gram-positive bacteria and Actinomycetes decreased by 5.7 %–15.9 % and 9.7 %–25.8 %, respectively, while Gram-negative bacteria increased significantly by 12.9 %–25.6 %. Meanwhile, the proportion of 13C-DOC derived C attributed to Gram-negative bacteria increased by 56.8 %–184.1 %, whereas Gram-positive bacteria (70.8 %–99.5 %) and Actinomycetes (64.2 %–82.3 %) decreased. These findings reveal the substantial role of AgNPs in altering soil carbon processes and microbial communities.
{"title":"Silver nanoparticles altered soil respiration, enzyme activity, carbon use efficiency and microbial community in an upland soil","authors":"Xincheng Hong , Yudi Song , Dongdong Cao , Shengwen Xu , Feng Gao , Haoxin Fan , Huaiying Yao","doi":"10.1016/j.apsoil.2025.106128","DOIUrl":"10.1016/j.apsoil.2025.106128","url":null,"abstract":"<div><div>Silver nanoparticles (AgNPs) are popular for their antimicrobial properties but their effects on soil carbon cycles remain unclear. This study explored AgNPs' impact on soil carbon dynamics and related microbial structures. Topsoil samples were treated with varying AgNPs concentrations (1, 10, 100, 500, and 1000 mg kg-1) over 56 days. Soil sampling was conducted at five time points (days 7, 14, 28, 42 and 56) to capture temporal changes. We assessed carbon mineralization, dissolved organic carbon (DOC), microbial biomass carbon (MBC), and enzymatic activities, along with <sup>13</sup>C-labeled DOC and <sup>13</sup>C-phospholipid fatty acid assays for tracing microbial carbon assimilation and evaluating carbon use efficiency (CUE). Following exposure to AgNPs in Ag100, Ag500, and Ag1000 treatments, cumulative CO<sub>2</sub> emissions and DOC content increased by 40.3 %–170.0 % and 46.9 %–74.9 %, respectively. However, MBC decreased in Ag500 (63.8 %) and Ag1000 (63.0 %) treatments. Enzyme activities declined: β-glucosidase (43.7 %–48.4 %), β-xylosidase (48.9 %–79.7 %), and Cellobiohydrolase (50.8 %–97.6 %). Additionally, microbial CUE increased 49.7 % in Ag1000 treatment. Soil microbial communities exhibited significant alterations in response to AgNPs in Ag100, Ag500, and Ag1000 treatments as well. By day 56, the relative abundance of Gram-positive bacteria and Actinomycetes decreased by 5.7 %–15.9 % and 9.7 %–25.8 %, respectively, while Gram-negative bacteria increased significantly by 12.9 %–25.6 %. Meanwhile, the proportion of <sup>13</sup>C-DOC derived C attributed to Gram-negative bacteria increased by 56.8 %–184.1 %, whereas Gram-positive bacteria (70.8 %–99.5 %) and Actinomycetes (64.2 %–82.3 %) decreased. These findings reveal the substantial role of AgNPs in altering soil carbon processes and microbial communities.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"211 ","pages":"Article 106128"},"PeriodicalIF":4.8,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143850148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-19DOI: 10.1016/j.apsoil.2025.106105
Yufan Yang , Yanhan Ji , Shuying Wang , Congrui Liu , Ping Zhang , Guifeng Gao , Yu Shi , Jiandong Jiang , Xu Liu , Baozhan Wang
Agricultural expansion induces the homogenization of soil bacterial communities on a global scale; however, the extent to which this phenomenon affects different microbial taxa and the consistency of the underlying mechanisms remain largely unexplored. Here, we conducted a comprehensive survey at the Yangtze River estuary, comparing coastal wetlands with adjacent croplands converted from these wetlands. By integrating 16S rRNA gene amplicon sequencing with null model approaches, we characterized soil bacterial and archaeal communities and identified key ecological drivers. Our results reveal that land conversion leads to biotic homogenization across both bacterial and archaeal domains, particularly in archaea. While microbial communities in wetlands are primarily influenced by hydrological factors (e.g., soil moisture and electrical conductivity), total carbon and nitrogen content emerge as the dominant determinants in croplands. Network analysis indicated a significant reduction in the complexity and stability of microbial networks in croplands compared to wetlands. Null model analysis further suggested that homogenizing dispersal, rather than selection, predominantly shapes community structure for both bacteria and archaea. Interestingly, heterogeneous filtering mitigated this homogenization in soil bacteria, accounting for the differences in community similarity observed following agricultural expansion. Specifically, agricultural management induced the dominance of ammonia-oxidizing Thaumarchaeota in archaea, with a significant 86.65 % increase in Nitrososphaerales in croplands, driven by homogenization, while sulfate-reducing bacteria Desulfocapsa showed the strongest response to homogeneous dispersal in bacteria. Overall, our study elucidates the widespread impact of microbial homogenization due to agricultural expansion and clarifies the mechanisms responsible for the observed disparities among microbial taxa.
{"title":"Microbial community assembly elucidates differential biotic homogenization in soils caused by agricultural expansion in the Yangtze River estuary","authors":"Yufan Yang , Yanhan Ji , Shuying Wang , Congrui Liu , Ping Zhang , Guifeng Gao , Yu Shi , Jiandong Jiang , Xu Liu , Baozhan Wang","doi":"10.1016/j.apsoil.2025.106105","DOIUrl":"10.1016/j.apsoil.2025.106105","url":null,"abstract":"<div><div>Agricultural expansion induces the homogenization of soil bacterial communities on a global scale; however, the extent to which this phenomenon affects different microbial taxa and the consistency of the underlying mechanisms remain largely unexplored. Here, we conducted a comprehensive survey at the Yangtze River estuary, comparing coastal wetlands with adjacent croplands converted from these wetlands. By integrating 16S rRNA gene amplicon sequencing with null model approaches, we characterized soil bacterial and archaeal communities and identified key ecological drivers. Our results reveal that land conversion leads to biotic homogenization across both bacterial and archaeal domains, particularly in archaea. While microbial communities in wetlands are primarily influenced by hydrological factors (e.g., soil moisture and electrical conductivity), total carbon and nitrogen content emerge as the dominant determinants in croplands. Network analysis indicated a significant reduction in the complexity and stability of microbial networks in croplands compared to wetlands. Null model analysis further suggested that homogenizing dispersal, rather than selection, predominantly shapes community structure for both bacteria and archaea. Interestingly, heterogeneous filtering mitigated this homogenization in soil bacteria, accounting for the differences in community similarity observed following agricultural expansion. Specifically, agricultural management induced the dominance of ammonia-oxidizing <em>Thaumarchaeota</em> in archaea, with a significant 86.65 % increase in <em>Nitrososphaerales</em> in croplands, driven by homogenization, while sulfate-reducing bacteria <em>Desulfocapsa</em> showed the strongest response to homogeneous dispersal in bacteria. Overall, our study elucidates the widespread impact of microbial homogenization due to agricultural expansion and clarifies the mechanisms responsible for the observed disparities among microbial taxa.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"211 ","pages":"Article 106105"},"PeriodicalIF":4.8,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143850248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-19DOI: 10.1016/j.apsoil.2025.106119
Sicheng Hang , Chen Wu , Guanwei Peng , Feng Li , Fei Ge , Jie Gan , Ling Li , Jie Li
Soil degradation caused by heavy metals and organic pollutants poses a critical global threat to environmental health and agricultural sustainability. Rhizosphere endophytes have garnered significant attention in their roles in enhancing agricultural productivity, promoting ecological sustainability, and serving as effective tools to support host plants in resisting or remediating soil contaminants. This review synthesizes current knowledge of the diversity, sources, and colonization mechanisms of rhizosphere endophytes. It highlights their dual roles in directly mitigating pollutant stress and indirectly enhancing plant resilience, while exploring their potential applications in environmental remediation. Rhizosphere endophytes are valuable sources of bioactive compounds and functional enzymes, secreting extracellular polymers and degradative enzymes to degrade organic pollutants or reduce the bioavailability of heavy metals. These microorganisms engage in co-metabolic processes with their hosts, enhancing plant antioxidant systems and mitigating the accumulation of organic pollutants and heavy metals in plant tissues. Furthermore, rhizosphere endophytes support host plants through indirect mechanisms by promoting plant growth, enhancing defenses against pathogens and pests, and modulating rhizosphere niches to recruit beneficial microbial communities, thereby enhancing plant resilience to environmental stress. Further research is necessary to improve the remediation efficiency of rhizosphere endophyte–plant systems, refine the selection of effective endophytes, and expand their ecological applications. This review underscores their ecological and biotechnological potential and outlines key research priorities to advance their use in sustainable soil remediation.
{"title":"Rhizosphere endophytes as allies in plant defense against heavy metals and organic pollutants in soil: Advances and applications","authors":"Sicheng Hang , Chen Wu , Guanwei Peng , Feng Li , Fei Ge , Jie Gan , Ling Li , Jie Li","doi":"10.1016/j.apsoil.2025.106119","DOIUrl":"10.1016/j.apsoil.2025.106119","url":null,"abstract":"<div><div>Soil degradation caused by heavy metals and organic pollutants poses a critical global threat to environmental health and agricultural sustainability. Rhizosphere endophytes have garnered significant attention in their roles in enhancing agricultural productivity, promoting ecological sustainability, and serving as effective tools to support host plants in resisting or remediating soil contaminants. This review synthesizes current knowledge of the diversity, sources, and colonization mechanisms of rhizosphere endophytes. It highlights their dual roles in directly mitigating pollutant stress and indirectly enhancing plant resilience, while exploring their potential applications in environmental remediation. Rhizosphere endophytes are valuable sources of bioactive compounds and functional enzymes, secreting extracellular polymers and degradative enzymes to degrade organic pollutants or reduce the bioavailability of heavy metals. These microorganisms engage in co-metabolic processes with their hosts, enhancing plant antioxidant systems and mitigating the accumulation of organic pollutants and heavy metals in plant tissues. Furthermore, rhizosphere endophytes support host plants through indirect mechanisms by promoting plant growth, enhancing defenses against pathogens and pests, and modulating rhizosphere niches to recruit beneficial microbial communities, thereby enhancing plant resilience to environmental stress. Further research is necessary to improve the remediation efficiency of rhizosphere endophyte–plant systems, refine the selection of effective endophytes, and expand their ecological applications. This review underscores their ecological and biotechnological potential and outlines key research priorities to advance their use in sustainable soil remediation.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"211 ","pages":"Article 106119"},"PeriodicalIF":4.8,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143850149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-19DOI: 10.1016/j.apsoil.2025.106114
Lijun Ren , Lili Dong , Guopeng Liang , Yanyu Han , Jiaqi Li , Qingfeng Fan , Dan Wei , Hongtao Zou , Yulong Zhang
Bio-organic fertilizer substitution for chemical fertilizer is an important action for nature-based solutions to identify optimal management practices at reducing soil N2O emissions. However, the current understanding of the underlying microbial mechanisms in response to bio-organic fertilizer substitution for chemical fertilizer is primitive, particularly in greenhouse vegetable production system. Herein, we present the field experiment that spans five years and encompasses four treatments, including no fertilizer (CK), chemical fertilizer (CF), bio-organic fertilizer (OF), and chemical fertilizer combined with bio-organic fertilizer (COF) in the greenhouse vegetable production system. We aimed to investigate the effects of replacing chemical fertilizer with bio-organic fertilizer on soil N2O emissions and nitrogen-cycling microbial communities. The OF and COF treatments reduced soil N2O emissions by 70.2 % and 32.3 %, respectively, compared with the CF treatment. The substitution of chemical fertilizer with bio-organic fertilizer led to a reduction in residual nitrate and dissolved organic nitrogen levels in the soil. Additionally, it enhanced the abundance of functional genes associated with both soil assimilatory nitrate reduction and dissimilatory nitrate reduction processes. These changes likely facilitated the conversion of nitrate nitrogen to ammonium nitrogen and mitigated soil denitrification. Additionally, bio-organic fertilizer significantly (P < 0.05) decreased the activity of soil-denitrifying microorganisms and increased the abundance of soil nitrogen-fixing genes to reduce N2O emissions. These results indicate the potential of using bio-organic fertilizer instead of chemical fertilizer to reduce reactive nitrogen emissions in greenhouse vegetable production system, which can contribute to the development of environmentally friendly fertilization strategies.
{"title":"Microbially mediated mechanisms underlie N2O mitigation by bio-organic fertilizer in greenhouse vegetable production system","authors":"Lijun Ren , Lili Dong , Guopeng Liang , Yanyu Han , Jiaqi Li , Qingfeng Fan , Dan Wei , Hongtao Zou , Yulong Zhang","doi":"10.1016/j.apsoil.2025.106114","DOIUrl":"10.1016/j.apsoil.2025.106114","url":null,"abstract":"<div><div>Bio-organic fertilizer substitution for chemical fertilizer is an important action for nature-based solutions to identify optimal management practices at reducing soil N<sub>2</sub>O emissions. However, the current understanding of the underlying microbial mechanisms in response to bio-organic fertilizer substitution for chemical fertilizer is primitive, particularly in greenhouse vegetable production system. Herein, we present the field experiment that spans five years and encompasses four treatments, including no fertilizer (CK), chemical fertilizer (CF), bio-organic fertilizer (OF), and chemical fertilizer combined with bio-organic fertilizer (COF) in the greenhouse vegetable production system. We aimed to investigate the effects of replacing chemical fertilizer with bio-organic fertilizer on soil N<sub>2</sub>O emissions and nitrogen-cycling microbial communities. The OF and COF treatments reduced soil N<sub>2</sub>O emissions by 70.2 % and 32.3 %, respectively, compared with the CF treatment. The substitution of chemical fertilizer with bio-organic fertilizer led to a reduction in residual nitrate and dissolved organic nitrogen levels in the soil. Additionally, it enhanced the abundance of functional genes associated with both soil assimilatory nitrate reduction and dissimilatory nitrate reduction processes. These changes likely facilitated the conversion of nitrate nitrogen to ammonium nitrogen and mitigated soil denitrification. Additionally, bio-organic fertilizer significantly (<em>P</em> < 0.05) decreased the activity of soil-denitrifying microorganisms and increased the abundance of soil nitrogen-fixing genes to reduce N<sub>2</sub>O emissions. These results indicate the potential of using bio-organic fertilizer instead of chemical fertilizer to reduce reactive nitrogen emissions in greenhouse vegetable production system, which can contribute to the development of environmentally friendly fertilization strategies.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"211 ","pages":"Article 106114"},"PeriodicalIF":4.8,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143850150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-18DOI: 10.1016/j.apsoil.2025.106094
Gaoyuan Liu , Ailing He , Zhanping Yang , Jinling Lv , Xiuyan Pan , Nian Zheng , Jun Du
Although diversified crop rotation systems can enhance crop productivity, the impact of such practices on soil microorganisms remains unclear. Therefore, we conducted a 4 - year field experiment in the North China Plain, involving 3 crop rotation systems: wheat - maize (WM), wheat - soybean (WS), and wheat - maize / soybean (‘/’ means intercropping, WMS), to analyze the structure, function and network complexity of soil microbial communities. The results indicated that compared to WM, the microbial abundance and diversity significantly increased in WMS, as evidenced by the rise in chao and shannon indices and the decrease in simpson index, which were not observed in WS. The microbial community structure also varied among different treatments, with significant increases observed in the total number of differential eutrophic bacteria in WMS and the total number of differential pathogenic fungi and archaea linked to Fe(II) oxidation and methane emission in WS. The abundance of microbial genes, encoding Glycoside hydrolases, Glycosyltransferases, Garbohydrate esterases, and Auxiliary activities, as well as those involved in Metabolism, Cellular processes and Genetic information processing, were clearly higher than those in WM or WS. Microbial co - occurrence network in WMS exhibited a greater number of nodes and edges, more positive edges, and higher average degrees and clustering coefficients when compared to WM or WS. For Hub nodes of these networks, they belonged to p_Proteobacteria in WM and WS, while in WMS they belonged to p_Actinobacteria. Organic carbon, alkaline hydrolysis nitrogen, and available phosphorus emerged as the predominant factors regulating the community composition of soil microorganisms. Consequently, we conclude the wheat - maize / soybean rotation system improves the abundance and diversity of soil microbial communities, strengthens microbial degradation and metabolism, and synthesis capabilities, thereby facilitating the establishment of favorable soil environment for crop growth.
{"title":"Introducing intercropping into rotation system altered the structure, function and network complexity of soil microbial communities in farmlands of the North China Plain","authors":"Gaoyuan Liu , Ailing He , Zhanping Yang , Jinling Lv , Xiuyan Pan , Nian Zheng , Jun Du","doi":"10.1016/j.apsoil.2025.106094","DOIUrl":"10.1016/j.apsoil.2025.106094","url":null,"abstract":"<div><div>Although diversified crop rotation systems can enhance crop productivity, the impact of such practices on soil microorganisms remains unclear. Therefore, we conducted a 4 - year field experiment in the North China Plain, involving 3 crop rotation systems: wheat - maize (WM), wheat - soybean (WS), and wheat - maize / soybean (‘/’ means intercropping, WMS), to analyze the structure, function and network complexity of soil microbial communities. The results indicated that compared to WM, the microbial abundance and diversity significantly increased in WMS, as evidenced by the rise in chao and shannon indices and the decrease in simpson index, which were not observed in WS. The microbial community structure also varied among different treatments, with significant increases observed in the total number of differential eutrophic bacteria in WMS and the total number of differential pathogenic fungi and archaea linked to Fe(II) oxidation and methane emission in WS. The abundance of microbial genes, encoding Glycoside hydrolases, Glycosyltransferases, Garbohydrate esterases, and Auxiliary activities, as well as those involved in Metabolism, Cellular processes and Genetic information processing, were clearly higher than those in WM or WS. Microbial co - occurrence network in WMS exhibited a greater number of nodes and edges, more positive edges, and higher average degrees and clustering coefficients when compared to WM or WS. For Hub nodes of these networks, they belonged to p_Proteobacteria in WM and WS, while in WMS they belonged to p_Actinobacteria. Organic carbon, alkaline hydrolysis nitrogen, and available phosphorus emerged as the predominant factors regulating the community composition of soil microorganisms. Consequently, we conclude the wheat - maize / soybean rotation system improves the abundance and diversity of soil microbial communities, strengthens microbial degradation and metabolism, and synthesis capabilities, thereby facilitating the establishment of favorable soil environment for crop growth.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"211 ","pages":"Article 106094"},"PeriodicalIF":4.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143844027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-18DOI: 10.1016/j.apsoil.2025.106108
Huaxiang Wang , Shuoxing Wei , Zhihui Wang , Dian Tian , Zhifeng Lu , Hanbiao Ou , Feng Gao , Shiqi Ren , Lijun Chen
Soil multifunctionality plays a crucial role in ecosystems, not only supporting nutrient cycling and plant productivity but also preserving biodiversity, thus ensuring the health and stability of the ecosystem. Forest soils harbor highly diverse microbial communities which fundamentally regulate the global elemental cycle and ecosystem multifunctionality. Keystone taxa act as “goalkeeper” in microbial community, which deeply portray community composition and functions. However, the mechanisms through which keystone taxa of soil microbes influence the dynamics of soil multifunctionality remain insufficiently elucidated within forest ecosystems. Our study analyzed the soil microbial community structures, soil properties and multifunctionalities of three typic forest stands in subtropic areas in south China, and identified the keystone taxa of bacteria and fungi by constructing co-occurrence networks, respectively. Further, partial least squares path modeling (PLS-PM) was conducted to explore the impact of different microbial taxa on soil multifunctionality. Our findings revealed considerable changes in soil multifunctionality across various forest types, with broad-leaved forest being the highest, then the mixed forest, and then followed by the coniferous forest. Compared with bacterial communities, soil fungal microbial networks in forest ecosystems had higher network nodes and higher module aggregation. Comparative analyses revealed that fungi exhibited greater type heterogeneity relative to bacteria inter-forest, with fungal keystone taxa demonstrating a pronounced influence on the multifaceted functional capacities of soil ecosystems. PLS-PM analysis further confirmed that soil properties (SOC, TN, and MBC) and fungal keystone taxa diversity (r = 0.319, p < 0.05) exert significant direct effects on soil multifunctionality. Furthermore, the total effects analysis highlighted fungal keystone taxa diversity and soil properties were critical determinants of soil multifunctionality. Additionally, this study emphasizes the significance of keystone fungal species in controlling soil multifunctionality in forest ecosystems. Promoting the diversity and abundance of fungal keystone taxa is essential for maintaining and enhancing soil multifunctionality, thereby supporting forest ecosystem health and productivity.
土壤多功能性在生态系统中起着至关重要的作用，不仅支持养分循环和植物生产力，而且还保护生物多样性，从而确保生态系统的健康和稳定。森林土壤具有高度多样化的微生物群落，它们从根本上调节着全球元素循环和生态系统的多功能性。关键类群在微生物群落中扮演着“守门员”的角色，深刻地刻画了群落的组成和功能。然而，在森林生态系统中，土壤微生物的关键分类群影响土壤多功能性动态的机制尚未得到充分阐明。本研究分析了中国南方亚热带地区3个典型林分的土壤微生物群落结构、土壤性质和多功能，并通过构建共生网络分别确定了细菌和真菌的重点类群。利用偏最小二乘路径模型（PLS-PM）探讨不同微生物类群对土壤多功能性的影响。结果表明，土壤多功能性在不同森林类型间存在显著变化，阔叶林土壤多功能性最高，其次是混交林，其次是针叶林。与细菌群落相比，森林生态系统土壤真菌微生物网络具有更高的网络节点和更高的模块聚集性。对比分析表明，真菌在林间表现出更大的类型异质性，真菌的关键分类群对土壤生态系统的多方面功能能力有显著影响。PLS-PM分析进一步证实了土壤性质（SOC、TN和MBC）和真菌关键分类群多样性(r = 0.319, p <；0.05)对土壤多功能性有显著的直接影响。此外，总效应分析表明，真菌关键分类群多样性和土壤性质是土壤多功能性的关键决定因素。此外，本研究还强调了关键真菌物种在森林生态系统土壤多功能性控制中的重要意义。促进真菌关键分类群的多样性和丰度对于维持和增强土壤的多功能性，从而支持森林生态系统的健康和生产力至关重要。
{"title":"The role of fungal keystone taxa in soil multifunctionality across subtropical forests","authors":"Huaxiang Wang , Shuoxing Wei , Zhihui Wang , Dian Tian , Zhifeng Lu , Hanbiao Ou , Feng Gao , Shiqi Ren , Lijun Chen","doi":"10.1016/j.apsoil.2025.106108","DOIUrl":"10.1016/j.apsoil.2025.106108","url":null,"abstract":"<div><div>Soil multifunctionality plays a crucial role in ecosystems, not only supporting nutrient cycling and plant productivity but also preserving biodiversity, thus ensuring the health and stability of the ecosystem. Forest soils harbor highly diverse microbial communities which fundamentally regulate the global elemental cycle and ecosystem multifunctionality. Keystone taxa act as “goalkeeper” in microbial community, which deeply portray community composition and functions. However, the mechanisms through which keystone taxa of soil microbes influence the dynamics of soil multifunctionality remain insufficiently elucidated within forest ecosystems. Our study analyzed the soil microbial community structures, soil properties and multifunctionalities of three typic forest stands in subtropic areas in south China, and identified the keystone taxa of bacteria and fungi by constructing co-occurrence networks, respectively. Further, partial least squares path modeling (PLS-PM) was conducted to explore the impact of different microbial taxa on soil multifunctionality. Our findings revealed considerable changes in soil multifunctionality across various forest types, with broad-leaved forest being the highest, then the mixed forest, and then followed by the coniferous forest. Compared with bacterial communities, soil fungal microbial networks in forest ecosystems had higher network nodes and higher module aggregation. Comparative analyses revealed that fungi exhibited greater type heterogeneity relative to bacteria inter-forest, with fungal keystone taxa demonstrating a pronounced influence on the multifaceted functional capacities of soil ecosystems. PLS-PM analysis further confirmed that soil properties (SOC, TN, and MBC) and fungal keystone taxa diversity (<em>r</em> = 0.319, <em>p</em> < 0.05) exert significant direct effects on soil multifunctionality. Furthermore, the total effects analysis highlighted fungal keystone taxa diversity and soil properties were critical determinants of soil multifunctionality. Additionally, this study emphasizes the significance of keystone fungal species in controlling soil multifunctionality in forest ecosystems. Promoting the diversity and abundance of fungal keystone taxa is essential for maintaining and enhancing soil multifunctionality, thereby supporting forest ecosystem health and productivity.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"211 ","pages":"Article 106108"},"PeriodicalIF":4.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143844028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-18DOI: 10.1016/j.apsoil.2025.106113
Chao Guan , Xinyang Song , Shiyan Zhou , Yifan Jiang , Linjie Qiao , Xiaojun Ma , Ning Chen , Changming Zhao
Biocrusts, which are distinctive elements in arid and semiarid ecosystems, stand out as pivotal regulators of soil respiration. However, the intricate seasonal variability in the response of soil respiration to diverse biocrust types has not been determined. Using three years of continuous field measurements taken at hourly intervals, we explored the seasonal (nongrowing and growing seasons) responses of soil respiration to cyanobacteria-, lichen- and moss-dominated biocrusts in a shrubland on the Loess Plateau in China. Our results revealed that the effects of cyanobacteria-dominated biocrusts on total soil respiration varied between the nongrowing and growing seasons, whereas the effects of moss- and lichen-dominated biocrusts on total soil respiration showed no significant seasonal differences. Notably, the effect of biocrusts on seasonal soil respiration fluctuations was associated with the biocrust type, with biocrust layer respiration increasing mostly in the following order: cyanobacteria < lichen < moss. The magnitude of this effect was influenced not only by the biocrust type but also by the nongrowing and growing seasons. Soil temperature emerged as a primary driver of total soil respiration during the nongrowing season, whereas soil moisture predominated during the growing season. Moreover, annual precipitation dynamics may have shifted the roles of biocrusts and the key determinants of soil respiration. Collectively, our findings emphasize the importance of considering the nongrowing and growing seasons independently, as well as the specific biocrust type, when assessing the responses of soil respiration in arid and semiarid ecosystems.
{"title":"Divergent responses of soil respiration to biocrusts during the nongrowing and growing seasons in a dryland shrubland ecosystem","authors":"Chao Guan , Xinyang Song , Shiyan Zhou , Yifan Jiang , Linjie Qiao , Xiaojun Ma , Ning Chen , Changming Zhao","doi":"10.1016/j.apsoil.2025.106113","DOIUrl":"10.1016/j.apsoil.2025.106113","url":null,"abstract":"<div><div>Biocrusts, which are distinctive elements in arid and semiarid ecosystems, stand out as pivotal regulators of soil respiration. However, the intricate seasonal variability in the response of soil respiration to diverse biocrust types has not been determined. Using three years of continuous field measurements taken at hourly intervals, we explored the seasonal (nongrowing and growing seasons) responses of soil respiration to cyanobacteria-, lichen- and moss-dominated biocrusts in a shrubland on the Loess Plateau in China. Our results revealed that the effects of cyanobacteria-dominated biocrusts on total soil respiration varied between the nongrowing and growing seasons, whereas the effects of moss- and lichen-dominated biocrusts on total soil respiration showed no significant seasonal differences. Notably, the effect of biocrusts on seasonal soil respiration fluctuations was associated with the biocrust type, with biocrust layer respiration increasing mostly in the following order: cyanobacteria < lichen < moss. The magnitude of this effect was influenced not only by the biocrust type but also by the nongrowing and growing seasons. Soil temperature emerged as a primary driver of total soil respiration during the nongrowing season, whereas soil moisture predominated during the growing season. Moreover, annual precipitation dynamics may have shifted the roles of biocrusts and the key determinants of soil respiration. Collectively, our findings emphasize the importance of considering the nongrowing and growing seasons independently, as well as the specific biocrust type, when assessing the responses of soil respiration in arid and semiarid ecosystems.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"211 ","pages":"Article 106113"},"PeriodicalIF":4.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143844025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-18DOI: 10.1016/j.apsoil.2025.106117
Zi Yang , Jingwei Chen , Jiajia Wang , Ziyang Liu , Lihua Meng , Hanwen Cui , Sa Xiao , Anning Zhang , Kun Liu , Lizhe An , Shuyan Chen , Uffe N. Nielsen
Climate warming is a key driver of changes in ecosystem structure and function, with well-documented effects on the vegetation aboveground. Warming can also influence soil organisms both directly and indirectly through impacts on vegetation composition and edaphic properties. The predicted increase in shrub encroachment in grassy alpine ecosystems on the Tibetan plateau due to warming is therefore likely to cause significant impacts belowground. We explored how a dominant shrub moderates the effect of warming on soil nematode richness and abundance in a grassy ecosystem on the Qinghai-Tibet Plateau. We used structural equation modelling (SEM) to examine effects on nematode assemblages through shifts in understory composition, edaphic properties, and soil microbial communities. We found that warming increased nematode richness and abundance, but only when shrubs were present. Similarly, warming changed nematode community composition, mainly due to increased abundance of fungivores and omnivores, only when shrubs were present. In addition, warming impacted nematode-based indices indicative of changes in ecosystem structure and function. The SEM revealed that warming and shrub removal interactively reduced nematode richness and the enrichment index directly. Shrub removal thus suppresses the positive effects of warming on nematode richness, abundance, and nematode-based indices in alpine grassy ecosystems. By inference, our results indicate that the effect of warming on soil fauna community diversity and structure in grassy alpine ecosystems will be exacerbated by shrub encroachment.
{"title":"Shrub removal suppresses the effects of warming on nematode communities in an alpine grassy ecosystem","authors":"Zi Yang , Jingwei Chen , Jiajia Wang , Ziyang Liu , Lihua Meng , Hanwen Cui , Sa Xiao , Anning Zhang , Kun Liu , Lizhe An , Shuyan Chen , Uffe N. Nielsen","doi":"10.1016/j.apsoil.2025.106117","DOIUrl":"10.1016/j.apsoil.2025.106117","url":null,"abstract":"<div><div>Climate warming is a key driver of changes in ecosystem structure and function, with well-documented effects on the vegetation aboveground. Warming can also influence soil organisms both directly and indirectly through impacts on vegetation composition and edaphic properties. The predicted increase in shrub encroachment in grassy alpine ecosystems on the Tibetan plateau due to warming is therefore likely to cause significant impacts belowground. We explored how a dominant shrub moderates the effect of warming on soil nematode richness and abundance in a grassy ecosystem on the Qinghai-Tibet Plateau. We used structural equation modelling (SEM) to examine effects on nematode assemblages through shifts in understory composition, edaphic properties, and soil microbial communities. We found that warming increased nematode richness and abundance, but only when shrubs were present. Similarly, warming changed nematode community composition, mainly due to increased abundance of fungivores and omnivores, only when shrubs were present. In addition, warming impacted nematode-based indices indicative of changes in ecosystem structure and function. The SEM revealed that warming and shrub removal interactively reduced nematode richness and the enrichment index directly. Shrub removal thus suppresses the positive effects of warming on nematode richness, abundance, and nematode-based indices in alpine grassy ecosystems. By inference, our results indicate that the effect of warming on soil fauna community diversity and structure in grassy alpine ecosystems will be exacerbated by shrub encroachment.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"211 ","pages":"Article 106117"},"PeriodicalIF":4.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143844130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-18DOI: 10.1016/j.apsoil.2025.106116
Courtney Horn Herms , Rosanna Catherine Hennessy , Frederik Bak , Ying Guan , Patrick Denis Browne , Tue Kjærgaard Nielsen , Lars Hestbjerg Hansen , Dorte Bodin Dresbøll , Mette Haubjerg Nicolaisen
Diversity within lower taxonomic units in microbial communities is a key trait, giving rise to important ecological functions. In the rhizosphere, these functions include disease suppression and pathogen inhibition. However, limited effort has been given to defining the importance of rhizosphere intragenus microdiversity, despite the increasing homogeneity of agricultural systems. Through an integrative approach combining culture-dependent and -independent methods, we generated a strain library of 373 pseudomonads, benchmarked to long-read 16S rRNA amplicon sequencing, from two modern winter wheat cultivars. Representative isolates were genome sequenced to provide a Pseudomonas pangenome of 112 genomes. The isolates were used to demonstrate cultivar-dependent taxonomic and functional microdiversity between two closely related winter wheat cultivars. A Fusarium-resistant cultivar demonstrated increased Pseudomonas taxonomic diversity but not biosynthetic diversity when compared to the susceptible cultivar, coinciding with a thinner root diameter of the resistant cultivar. We found enrichment of Pseudomonas isolates capable of antagonizing Fusarium as well as chitinase-encoding genes and pyoverdine gene clusters in the resistant cultivar. Across closely related Pseudomonas isolates from the two cultivars, there were differences in genomic content and biosynthetic gene clusters. Ultimately, we highlight the need for fine-scale analysis to uncover the hidden microdiversity within rhizosphere Pseudomonas.
{"title":"Pseudomonas taxonomic and functional microdiversity in the wheat rhizosphere is cultivar-dependent and links to disease resistance profile and root diameter","authors":"Courtney Horn Herms , Rosanna Catherine Hennessy , Frederik Bak , Ying Guan , Patrick Denis Browne , Tue Kjærgaard Nielsen , Lars Hestbjerg Hansen , Dorte Bodin Dresbøll , Mette Haubjerg Nicolaisen","doi":"10.1016/j.apsoil.2025.106116","DOIUrl":"10.1016/j.apsoil.2025.106116","url":null,"abstract":"<div><div>Diversity within lower taxonomic units in microbial communities is a key trait, giving rise to important ecological functions. In the rhizosphere, these functions include disease suppression and pathogen inhibition. However, limited effort has been given to defining the importance of rhizosphere intragenus microdiversity, despite the increasing homogeneity of agricultural systems. Through an integrative approach combining culture-dependent and -independent methods, we generated a strain library of 373 pseudomonads, benchmarked to long-read 16S rRNA amplicon sequencing, from two modern winter wheat cultivars. Representative isolates were genome sequenced to provide a <em>Pseudomonas</em> pangenome of 112 genomes. The isolates were used to demonstrate cultivar-dependent taxonomic and functional microdiversity between two closely related winter wheat cultivars. A <em>Fusarium-</em>resistant cultivar demonstrated increased <em>Pseudomonas</em> taxonomic diversity but not biosynthetic diversity when compared to the susceptible cultivar, coinciding with a thinner root diameter of the resistant cultivar. We found enrichment of <em>Pseudomonas</em> isolates capable of antagonizing <em>Fusarium</em> as well as chitinase-encoding genes and pyoverdine gene clusters in the resistant cultivar. Across closely related <em>Pseudomonas</em> isolates from the two cultivars, there were differences in genomic content and biosynthetic gene clusters. Ultimately, we highlight the need for fine-scale analysis to uncover the hidden microdiversity within rhizosphere <em>Pseudomonas</em>.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"211 ","pages":"Article 106116"},"PeriodicalIF":4.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143844129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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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