Pub Date : 2025-12-12DOI: 10.1016/j.apsoil.2025.106702
Pengpeng Lü , Zhe Zhao , Zexin Jin , Junmin Li
Although increasing nitrogen (N) deposition seriously threatens soil microbial communities and plant-microbe interactions, little research has been conducted on endangered plants. In this study, the impacts of simulated N deposition on root morphology, soil properties, as well as the arbuscular mycorrhizal (AM) fungal and bacterial communities in the rhizosphere of the endangered species Calycanthus chinensis were investigated. Based on the results, N deposition altered root morphology (e.g., root diameter, length, volume, and surface area) of C. chinensis seedlings and soil extracellular enzyme activities (e.g., urease and catalase). Additionally, N deposition increased soil microbial biomass N but not soil microbial biomass carbon, particularly at high N levels. Although N deposition had no significant effect on AM fungal diversity and community composition, it significantly reduced bacterial diversity. Notably, AM fungal co-occurrence networks became more complex with increasing N deposition, suggesting enhanced network stability, whereas bacterial networks exhibited the opposite pattern. The variation of soil properties, particularly soil pH, nitrate and available potassium, contributed to the co-occurrence network structures. These findings provide insights into the differential responses of soil microbial communities to N deposition and their potential implications for the growth and survival of endangered plants in disturbed ecosystems.
{"title":"Simulated nitrogen deposition differentially reshapes AM fungal and bacterial co-occurrence networks in the rhizosphere of endangered Calycanthus chinensis seedlings","authors":"Pengpeng Lü , Zhe Zhao , Zexin Jin , Junmin Li","doi":"10.1016/j.apsoil.2025.106702","DOIUrl":"10.1016/j.apsoil.2025.106702","url":null,"abstract":"<div><div>Although increasing nitrogen (N) deposition seriously threatens soil microbial communities and plant-microbe interactions, little research has been conducted on endangered plants. In this study, the impacts of simulated N deposition on root morphology, soil properties, as well as the arbuscular mycorrhizal (AM) fungal and bacterial communities in the rhizosphere of the endangered species <em>Calycanthus chinensis</em> were investigated. Based on the results, N deposition altered root morphology (e.g., root diameter, length, volume, and surface area) of <em>C. chinensis</em> seedlings and soil extracellular enzyme activities (e.g., urease and catalase). Additionally, N deposition increased soil microbial biomass N but not soil microbial biomass carbon, particularly at high N levels. Although N deposition had no significant effect on AM fungal diversity and community composition, it significantly reduced bacterial diversity. Notably, AM fungal co-occurrence networks became more complex with increasing N deposition, suggesting enhanced network stability, whereas bacterial networks exhibited the opposite pattern. The variation of soil properties, particularly soil pH, nitrate and available potassium, contributed to the co-occurrence network structures. These findings provide insights into the differential responses of soil microbial communities to N deposition and their potential implications for the growth and survival of endangered plants in disturbed ecosystems.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"218 ","pages":"Article 106702"},"PeriodicalIF":5.0,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749279","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 : 2025-12-12DOI: 10.1016/j.apsoil.2025.106705
Nicola M. Reid , Preeti Panda , Sarah L. Addison , Rebecca L. McDougal , Loretta G. Garrett , Thomas S.H. Paul , Steve A. Wakelin
Microorganisms underpin forest soil multifunctionality and delivery of ecosystem services. As climate and land-use change drive shifts in land cover, afforestation of pastoral land is becoming increasingly important. The New Forest Trial Series (NFTS) offers a novel system to assess how local soil microbiomes respond to interactions between site conditions, tree species, and functional traits. We investigated how tree species, their functional traits, and site conditions shape early soil fungal, bacterial, and oomycete communities during afforestation.
In the first experiment, replicated plots of Pinus radiata, Podocarpus totara, and Cupressocyparis ovensii were sampled across three NFTS sites (Mangatoa, Te Apiti, and Rewanui). Fungal communities showed compositional shifts related to both tree species and site, whereas bacterial communities varied by site only. Oomycete communities remained similar across all samples.
In the second experiment, plots planted with seven tree species (the three above plus Leptospermum scoparium, Eucalyptus fastigata, Fraxinus excelsior, and Sequoia sempervirens) were sampled at Rewanui. Tree species again influenced soil fungal microbiomes, but not those of bacteria or oomycetes. Trait-centred analysis revealed that mycorrhizal type (ectomycorrhizal vs. arbuscular) explained more variance in fungal composition than tree species. Whether species were native or introduced to New Zealand had no effect on soil microbial composition.
The influence of tree species and mycorrhizal association on fungal communities appeared to be direct, with no evidence of mediation via modification of soil chemistry. These sites were sampled ∼4.5 years after afforestation. As tree-specific effects on site conditions intensify over time, secondary impacts on soil microbiomes are expected, providing opportunities to observe how both primary and secondary effects of tree selection interact to influence site development, soil microbiology, and ecosystem service delivery. These results establish an early-stage baseline showing that fungi respond rapidly to tree selection, while other microbial groups remain stable. This provides a foundation for forecasting how afforestation choices influence soil development, ecosystem functions, and potential disease dynamics as forests mature.
{"title":"Early afforestation influences on soil fungal communities but bacterial and oomycetes are slower to respond","authors":"Nicola M. Reid , Preeti Panda , Sarah L. Addison , Rebecca L. McDougal , Loretta G. Garrett , Thomas S.H. Paul , Steve A. Wakelin","doi":"10.1016/j.apsoil.2025.106705","DOIUrl":"10.1016/j.apsoil.2025.106705","url":null,"abstract":"<div><div>Microorganisms underpin forest soil multifunctionality and delivery of ecosystem services. As climate and land-use change drive shifts in land cover, afforestation of pastoral land is becoming increasingly important. The New Forest Trial Series (NFTS) offers a novel system to assess how local soil microbiomes respond to interactions between site conditions, tree species, and functional traits. We investigated how tree species, their functional traits, and site conditions shape early soil fungal, bacterial, and oomycete communities during afforestation.</div><div>In the first experiment, replicated plots of <em>Pinus radiata</em>, <em>Podocarpus totara</em>, and <em>Cupressocyparis ovensii</em> were sampled across three NFTS sites (Mangatoa, Te Apiti, and Rewanui). Fungal communities showed compositional shifts related to both tree species and site, whereas bacterial communities varied by site only. Oomycete communities remained similar across all samples.</div><div>In the second experiment, plots planted with seven tree species (the three above plus <em>Leptospermum scoparium</em>, <em>Eucalyptus fastigata</em>, <em>Fraxinus excelsior</em>, and <em>Sequoia sempervirens</em>) were sampled at Rewanui. Tree species again influenced soil fungal microbiomes, but not those of bacteria or oomycetes. Trait-centred analysis revealed that mycorrhizal type (ectomycorrhizal vs. arbuscular) explained more variance in fungal composition than tree species. Whether species were native or introduced to New Zealand had no effect on soil microbial composition.</div><div>The influence of tree species and mycorrhizal association on fungal communities appeared to be direct, with no evidence of mediation via modification of soil chemistry. These sites were sampled ∼4.5 years after afforestation. As tree-specific effects on site conditions intensify over time, secondary impacts on soil microbiomes are expected, providing opportunities to observe how both primary and secondary effects of tree selection interact to influence site development, soil microbiology, and ecosystem service delivery. These results establish an early-stage baseline showing that fungi respond rapidly to tree selection, while other microbial groups remain stable. This provides a foundation for forecasting how afforestation choices influence soil development, ecosystem functions, and potential disease dynamics as forests mature.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"218 ","pages":"Article 106705"},"PeriodicalIF":5.0,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145750175","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 : 2025-12-11DOI: 10.1016/j.apsoil.2025.106697
Tong Wang , Jingwen Zhang , Xue Yang , Yinuo Zhu , Lin Qi , Mingyan Li , Xiao Guo , Hongwei Yu , Haifang Li
As a novel pollutant, microplastics threaten the plant–microbe–soil system. However, the effects of microplastics on aquatic plant–microbe–soil systems have been insufficiently studied. The present study explored the effects of polyamide microplastic (PA), a dominant microplastic pollutant in aquatic ecosystems, on the sediment microbiome in the presence of four common native submerged plants – Stuckenia pectinata (L.) Börner, Potamogeton wrightii Morong, Myriophyllum spicatum L. and Potamogeton maackianus A. Benn. We found that PA had no significant effect on plant performance. However, the sediment fungal structures associated with different plant species shifted under different PA pollution conditions, whereas the sediment enzymatic activity and microbial diversity remained consistent. In particular, PA pollution disrupted beneficial fungi such as arbuscular mycorrhizal fungi, ectomycorrhizal fungi, and plant growth-promoting fungi in the presence of S. pectinata and M. spicatum and promoted the accumulation of harmful plant pathogenic fungi such as Fusarium in the presence of P. maackianus. The loss of beneficial sediment microbes and the aggregation of harmful microbes may be disadvantageous for the colonization and establishment of plant descendants. Therefore, microplastic pollution may threaten macrophyte diversity and interfere with the ecological stability of vegetated aquatic ecosystems via alteration of the sediment microbiome. Species selection for wetland restoration should be conducted prudently in regard to microplastic pollution. Future studies should focus on the effects of microplastics of different types, sizes and residence times on macrophyte communities and the effects of the sediment microbiome on macrophytes with long-term exposure to microplastic pollution.
{"title":"Polyamide microplastic pollution modifies the sediment fungal structures associated with different submerged plant species: An insight from aquatic mesocosm experiment","authors":"Tong Wang , Jingwen Zhang , Xue Yang , Yinuo Zhu , Lin Qi , Mingyan Li , Xiao Guo , Hongwei Yu , Haifang Li","doi":"10.1016/j.apsoil.2025.106697","DOIUrl":"10.1016/j.apsoil.2025.106697","url":null,"abstract":"<div><div>As a novel pollutant, microplastics threaten the plant–microbe–soil system. However, the effects of microplastics on aquatic plant–microbe–soil systems have been insufficiently studied. The present study explored the effects of polyamide microplastic (PA), a dominant microplastic pollutant in aquatic ecosystems, on the sediment microbiome in the presence of four common native submerged plants – <em>Stuckenia pectinata</em> (L.) Börner, <em>Potamogeton wrightii</em> Morong, <em>Myriophyllum spicatum</em> L. and <em>Potamogeton maackianus</em> A. Benn. We found that PA had no significant effect on plant performance. However, the sediment fungal structures associated with different plant species shifted under different PA pollution conditions, whereas the sediment enzymatic activity and microbial diversity remained consistent. In particular, PA pollution disrupted beneficial fungi such as arbuscular mycorrhizal fungi, ectomycorrhizal fungi, and plant growth-promoting fungi in the presence of <em>S. pectinata</em> and <em>M. spicatum</em> and promoted the accumulation of harmful plant pathogenic fungi such as <em>Fusarium</em> in the presence of <em>P. maackianus</em>. The loss of beneficial sediment microbes and the aggregation of harmful microbes may be disadvantageous for the colonization and establishment of plant descendants. Therefore, microplastic pollution may threaten macrophyte diversity and interfere with the ecological stability of vegetated aquatic ecosystems via alteration of the sediment microbiome. Species selection for wetland restoration should be conducted prudently in regard to microplastic pollution. Future studies should focus on the effects of microplastics of different types, sizes and residence times on macrophyte communities and the effects of the sediment microbiome on macrophytes with long-term exposure to microplastic pollution.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"218 ","pages":"Article 106697"},"PeriodicalIF":5.0,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145750238","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 : 2025-12-11DOI: 10.1016/j.apsoil.2025.106708
Artur Sokołowski , Dominika Siegieda , Jacek Panek , Magdalena Frąc , Rafał Kobyłecki , Robert Zarzycki , Tomasz Klepka , Patryk Oleszczuk , Yanzheng Gao , Bożena Czech
Phthalic acid esters (PAEs), as persistent organic pollutants, alter soil microbial communities, with long-term implications for ecosystem function. This study examined microbial responses to PAEs contamination and the role of biochar (BC) amendment in promoting microbial resilience and succession. PAEs' exposure led to modest reductions in dominant bacterial phyla (Firmicutes, Proteobacteria, Actinobacteriota) and increased pollutant-degrading groups such as Bdellovibrionota, Cyanobacteria, and Nitrospirota. Key nutrient-cycling phyla (Acidobacteriota, Chloroflexi) declined, indicating disruption of carbon and nitrogen turnover. Short-term BC application promoted plant growth-promoting and decomposer taxa (e.g., Alicyclobacillaceae, Oxalobacteraceae), suppressed opportunistic pathogens, and partially restored microbial functionality through direct (sorption, habitat) and indirect (pH, enzyme activity) mechanisms. Fungal communities showed higher sensitivity to both PAEs and BC. While BC reduced overall fungal diversity, it increased stress-tolerant taxa such as Gibellulopsis piscis and Solicoccozyma. Long-term BC amendment, especially post-cultivation, triggered microbial succession favoring K-strategists, particularly Actinobacteria, due to their ability to degrade biochar-derived aromatic compounds and thrive in alkaline, carbon-rich soils. Though bacterial diversity recovered partially after lettuce cultivation, some beneficial genera (e.g., Massilia, Sphingomonas) declined, and unclassified taxa expanded significantly, reflecting lasting ecological shifts. Strong β-diversity changes suggested a transition toward a more specialized and resilient microbial community. Overall, biochar demonstrates strong potential as a long-term soil amendment in PAEs-contaminated environments by enhancing detoxification and supporting microbial recovery. However, the observed trade-offs in diversity and community composition highlight the need for careful, long-term monitoring to ensure sustainable bioremediation outcomes.
{"title":"Long-term biochar amendment promotes microbial resilience and detoxification in phthalate-contaminated soil","authors":"Artur Sokołowski , Dominika Siegieda , Jacek Panek , Magdalena Frąc , Rafał Kobyłecki , Robert Zarzycki , Tomasz Klepka , Patryk Oleszczuk , Yanzheng Gao , Bożena Czech","doi":"10.1016/j.apsoil.2025.106708","DOIUrl":"10.1016/j.apsoil.2025.106708","url":null,"abstract":"<div><div>Phthalic acid esters (PAEs), as persistent organic pollutants, alter soil microbial communities, with long-term implications for ecosystem function. This study examined microbial responses to PAEs contamination and the role of biochar (BC) amendment in promoting microbial resilience and succession. PAEs' exposure led to modest reductions in dominant bacterial phyla (Firmicutes, Proteobacteria, Actinobacteriota) and increased pollutant-degrading groups such as Bdellovibrionota, Cyanobacteria, and Nitrospirota. Key nutrient-cycling phyla (Acidobacteriota, Chloroflexi) declined, indicating disruption of carbon and nitrogen turnover. Short-term BC application promoted plant growth-promoting and decomposer taxa (e.g., Alicyclobacillaceae, Oxalobacteraceae), suppressed opportunistic pathogens, and partially restored microbial functionality through direct (sorption, habitat) and indirect (pH, enzyme activity) mechanisms. Fungal communities showed higher sensitivity to both PAEs and BC. While BC reduced overall fungal diversity, it increased stress-tolerant taxa such as <em>Gibellulopsis piscis</em> and Solicoccozyma. Long-term BC amendment, especially post-cultivation, triggered microbial succession favoring K-strategists, particularly Actinobacteria, due to their ability to degrade biochar-derived aromatic compounds and thrive in alkaline, carbon-rich soils. Though bacterial diversity recovered partially after lettuce cultivation, some beneficial genera (e.g., Massilia, Sphingomonas) declined, and unclassified taxa expanded significantly, reflecting lasting ecological shifts. Strong β-diversity changes suggested a transition toward a more specialized and resilient microbial community. Overall, biochar demonstrates strong potential as a long-term soil amendment in PAEs-contaminated environments by enhancing detoxification and supporting microbial recovery. However, the observed trade-offs in diversity and community composition highlight the need for careful, long-term monitoring to ensure sustainable bioremediation outcomes.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"218 ","pages":"Article 106708"},"PeriodicalIF":5.0,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145750239","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}
Climate change, rising atmospheric CO2 and more frequent weather extremes are putting pressure on global food security and increasing the need for climate-resilient and economically realistic farming practices that build soil carbon while maintaining yields. Biochar application to agricultural soils is often proposed as a promising strategy, but it remains unclear whether current research is geographically balanced, thematically comprehensive and well aligned with conditions for large-scale use. Using CiteSpace, this study analysed 2244 peer-reviewed articles (2007–2023) on biochar application in agricultural soils for carbon sequestration and CO2 mitigation to test the hypothesis that global research is concentrated in a limited number of countries and topics, dominated by fundamental studies, and only partly connected to agronomic, economic and policy questions. Publication, citation, collaboration and keyword patterns were used to show where research activity and influence are concentrated and which themes have attracted sustained attention. The results indicate that China, the United States, Australia and Germany form the main knowledge hubs, and that hotspots have shifted from biochar production and basic carbon storage towards soil physicochemical properties, carbon stabilization, microbial regulation, greenhouse gas dynamics and crop yield responses. At the same time, under-representation of certain regions, the scarcity of long-term field studies and limited consideration of cost-effectiveness and carbon market conditions point to clear gaps between scientific progress and practical deployment needs. By mapping global patterns of research activity and collaboration, the study helps to identify where the evidence base is relatively strong or weak and to guide priorities for field trials, integrated environmental–economic assessments and policy design to support realistic scaling of biochar use in agriculture.
{"title":"Biochar for agricultural soil carbon sequestration and CO2 mitigation: a bibliometric analysis of research hotspots, gaps and climate-resilient pathways","authors":"Qi Wei , Qi Wei , Junzeng Xu , Peng Chen , Ziwei Li , Zhiming Qi","doi":"10.1016/j.apsoil.2025.106672","DOIUrl":"10.1016/j.apsoil.2025.106672","url":null,"abstract":"<div><div>Climate change, rising atmospheric CO<sub>2</sub> and more frequent weather extremes are putting pressure on global food security and increasing the need for climate-resilient and economically realistic farming practices that build soil carbon while maintaining yields. Biochar application to agricultural soils is often proposed as a promising strategy, but it remains unclear whether current research is geographically balanced, thematically comprehensive and well aligned with conditions for large-scale use. Using CiteSpace, this study analysed 2244 peer-reviewed articles (2007–2023) on biochar application in agricultural soils for carbon sequestration and CO<sub>2</sub> mitigation to test the hypothesis that global research is concentrated in a limited number of countries and topics, dominated by fundamental studies, and only partly connected to agronomic, economic and policy questions. Publication, citation, collaboration and keyword patterns were used to show where research activity and influence are concentrated and which themes have attracted sustained attention. The results indicate that China, the United States, Australia and Germany form the main knowledge hubs, and that hotspots have shifted from biochar production and basic carbon storage towards soil physicochemical properties, carbon stabilization, microbial regulation, greenhouse gas dynamics and crop yield responses. At the same time, under-representation of certain regions, the scarcity of long-term field studies and limited consideration of cost-effectiveness and carbon market conditions point to clear gaps between scientific progress and practical deployment needs. By mapping global patterns of research activity and collaboration, the study helps to identify where the evidence base is relatively strong or weak and to guide priorities for field trials, integrated environmental–economic assessments and policy design to support realistic scaling of biochar use in agriculture.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"218 ","pages":"Article 106672"},"PeriodicalIF":5.0,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145750237","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 : 2025-12-10DOI: 10.1016/j.apsoil.2025.106690
Thaynara Lorenzoni Entringer , Tomás Gomes Reis Veloso , Eduardo Luís Menezes de Almeida , Gabriel Costa Públio , José Maria Rodrigues da Luz , Lucas Louzada Pereira , Denise Mara Soares Bazzolli , Marliane de Cássia Soares da Silva
Brazil is the world's largest coffee exporter and coffee cultivation has been a key socio-economic driver since the 18th century. However, climate change and intensive agricultural practices pose significant challenges, including reduced productivity and negative environmental impacts. In this context, sustainable alternatives, such as organic fertilization, are promising for reconciling productivity with sustainability. In this study, the microbiota of coffee fruits subjected to two fertilization treatments, chemical (conventional) and organic fertilization were analyzed using amplicon sequencing. The organic fertilization regimen favors the development of plant growth-promoting microorganisms and biocontrol agents (Apiotrichum sp., Papiliotrema sp., Sphingomonas sp., and Vinishiacozyma sp.), while the conventional fertilization is associated with a high relative abundance of phytopathogenic microorganisms (Colletotrichum sp. and Pantoea sp.). Furthermore, coffee fruits from organic fertilization exhibit a more stable microbial community and there is a positive correlation between the yeast community and the sensory attribute (body) of the coffee beverage. Thus, the results demonstrated that organic fertilization fosters the development of beneficial microbial communities and contributes to coffee quality.
{"title":"Conventional and organic fertilization and their implications for microbiota and coffee quality","authors":"Thaynara Lorenzoni Entringer , Tomás Gomes Reis Veloso , Eduardo Luís Menezes de Almeida , Gabriel Costa Públio , José Maria Rodrigues da Luz , Lucas Louzada Pereira , Denise Mara Soares Bazzolli , Marliane de Cássia Soares da Silva","doi":"10.1016/j.apsoil.2025.106690","DOIUrl":"10.1016/j.apsoil.2025.106690","url":null,"abstract":"<div><div>Brazil is the world's largest coffee exporter and coffee cultivation has been a key socio-economic driver since the 18th century. However, climate change and intensive agricultural practices pose significant challenges, including reduced productivity and negative environmental impacts. In this context, sustainable alternatives, such as organic fertilization, are promising for reconciling productivity with sustainability. In this study, the microbiota of coffee fruits subjected to two fertilization treatments, chemical (conventional) and organic fertilization were analyzed using amplicon sequencing. The organic fertilization regimen favors the development of plant growth-promoting microorganisms and biocontrol agents (<em>Apiotrichum</em> sp., <em>Papiliotrema</em> sp., <em>Sphingomonas</em> sp., and <em>Vinishiacozyma</em> sp.), while the conventional fertilization is associated with a high relative abundance of phytopathogenic microorganisms (<em>Colletotrichum</em> sp. and <em>Pantoea</em> sp.). Furthermore, coffee fruits from organic fertilization exhibit a more stable microbial community and there is a positive correlation between the yeast community and the sensory attribute (body) of the coffee beverage. Thus, the results demonstrated that organic fertilization fosters the development of beneficial microbial communities and contributes to coffee quality.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"218 ","pages":"Article 106690"},"PeriodicalIF":5.0,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749278","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 : 2025-12-10DOI: 10.1016/j.apsoil.2025.106691
Sarah Zecchin , Camilla Valli , Alice Melzi , Milena Colombo , Sara Martinengo , Luisella Celi , Lucia Cavalca
Phosphorus (P) and nitrogen (N) cycling in paddy soils is essential for sustaining global rice production. However, mineral fertilization efficiency is limited by substantial N losses and strong soil-driven P fixation. This study explored the potential of winter cover crops incorporated before rice seeding to stimulate microorganisms involved in nutrient cycling. Microbial genomics and cultivation-based approaches were integrated to investigate bacterial, archaeal and fungal communities in the rhizosphere compartments (rhizosphere soil, rhizoplane, root endosphere) of rice cultivated with or without hairy vetch (Vicia villosa) as cover crop in a temperate European rice district.
Microbial diversity and community composition were significantly shaped by plant species (rice, vetch) and compartments. Cover cropping increased the abundance of cultured and uncultured microorganisms able to solubilize and mineralize inorganic and organic P species, and of mycorrhizal fungi, with a corresponding increase of bioavailable P. Moreover, a higher number of bacterial strains with plant growth-promoting traits, including diazotrophy, production of indole acetic acid, extracellular polymeric substances and siderophores, was isolated from cover-cropped rice plants. Network analysis evidenced a 40 % increase in synergistic microbial interactions, with P-solubilizing/mineralizing genera like Cladosporium and Penicillium but also uncharacterized ammonia-oxidizing archaea playing a key role. Rhizoplane hosted a higher percentage of culturable strains with P- and N-cycling potential (>90 %), compared to other rhizosphere compartments (75 %), emerging as a crucial boundary among soil-plant-microbiome ecosystems.
This work gives a microbial perspective to the benefits of winter cover cropping for improving nutrient pools in paddy soils, providing valuable insights to support sustainable agronomic practices.
{"title":"Winter cover cropping increases synergistic species interactions and plant growth-promoting traits involved in phosphorus and nitrogen cycling in rice rhizosphere microbiome","authors":"Sarah Zecchin , Camilla Valli , Alice Melzi , Milena Colombo , Sara Martinengo , Luisella Celi , Lucia Cavalca","doi":"10.1016/j.apsoil.2025.106691","DOIUrl":"10.1016/j.apsoil.2025.106691","url":null,"abstract":"<div><div>Phosphorus (P) and nitrogen (N) cycling in paddy soils is essential for sustaining global rice production. However, mineral fertilization efficiency is limited by substantial N losses and strong soil-driven P fixation. This study explored the potential of winter cover crops incorporated before rice seeding to stimulate microorganisms involved in nutrient cycling. Microbial genomics and cultivation-based approaches were integrated to investigate bacterial, archaeal and fungal communities in the rhizosphere compartments (rhizosphere soil, rhizoplane, root endosphere) of rice cultivated with or without hairy vetch (<em>Vicia villosa</em>) as cover crop in a temperate European rice district.</div><div>Microbial diversity and community composition were significantly shaped by plant species (rice, vetch) and compartments. Cover cropping increased the abundance of cultured and uncultured microorganisms able to solubilize and mineralize inorganic and organic P species, and of mycorrhizal fungi, with a corresponding increase of bioavailable P. Moreover, a higher number of bacterial strains with plant growth-promoting traits, including diazotrophy, production of indole acetic acid, extracellular polymeric substances and siderophores, was isolated from cover-cropped rice plants. Network analysis evidenced a 40 % increase in synergistic microbial interactions, with P-solubilizing/mineralizing genera like <em>Cladosporium</em> and <em>Penicillium</em> but also uncharacterized ammonia-oxidizing archaea playing a key role. Rhizoplane hosted a higher percentage of culturable strains with P- and N-cycling potential (>90 %), compared to other rhizosphere compartments (75 %), emerging as a crucial boundary among soil-plant-microbiome ecosystems.</div><div>This work gives a microbial perspective to the benefits of winter cover cropping for improving nutrient pools in paddy soils, providing valuable insights to support sustainable agronomic practices.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"218 ","pages":"Article 106691"},"PeriodicalIF":5.0,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749277","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 : 2025-12-09DOI: 10.1016/j.apsoil.2025.106687
Camille D'Hervilly , Jan Frouz
Soil macrofauna affects litter decomposition by modifying organic matter availability for microorganisms. Litter-feeders accumulate partially decomposed organic matter at the soil surface, while burrowing earthworms mix the organic matter with mineral particles. Synergistic effects of the combined presence of litter-feeders and burrowing earthworms through facilitation are expected but seldom tested. We performed a three-months microcosm experiment in which we tested the effect of the presence of litter-feeders (an epigeic earthworm and an isopod) on the biomass of the burrowing earthworm Aporrectodea caliginosa and on C incorporation into individual soil organic matter fractions. We used a recent post mining soil, limited in food resources to promote interactions, and alder litter which is suitable food for soil invertebrates. We hypothesized that A. caliginosa would be positively affected by the presence of litter feeders, and that this would impact C addition to the more stable fractions. Contrary to our hypotheses, we found no variation in the biomass of A. caliginosa among treatments, as this species could feed directly on alder leaves. The accumulation of poorly stabilized particulate organic C was negatively affected by the presence of both earthworm species (i.e. less than cumulative), suggesting either that A. caliginosa fed on the particulate organic matter produced by the epigeic earthworm, or that competition for the limiting food resources took place. However, A. caliginosa promoted a similar increase in stable mineral-associated C in all treatments. This confirms the plasticity of A. caliginosa regarding food resources observed in other experiments, and shows that the effect of the burrowing earthworm A. caliginosa on stable C accumulation is not necessarily mediated by litter-feeders in the presence of litter of good quality.
{"title":"Interactions between litter-feeders and the burrowing earthworm A. caliginosa do not affect mineral-associated C addition in recent spoil material","authors":"Camille D'Hervilly , Jan Frouz","doi":"10.1016/j.apsoil.2025.106687","DOIUrl":"10.1016/j.apsoil.2025.106687","url":null,"abstract":"<div><div>Soil macrofauna affects litter decomposition by modifying organic matter availability for microorganisms. Litter-feeders accumulate partially decomposed organic matter at the soil surface, while burrowing earthworms mix the organic matter with mineral particles. Synergistic effects of the combined presence of litter-feeders and burrowing earthworms through facilitation are expected but seldom tested. We performed a three-months microcosm experiment in which we tested the effect of the presence of litter-feeders (an epigeic earthworm and an isopod) on the biomass of the burrowing earthworm <em>Aporrectodea caliginosa</em> and on C incorporation into individual soil organic matter fractions. We used a recent post mining soil, limited in food resources to promote interactions, and alder litter which is suitable food for soil invertebrates. We hypothesized that <em>A. caliginosa</em> would be positively affected by the presence of litter feeders, and that this would impact C addition to the more stable fractions. Contrary to our hypotheses, we found no variation in the biomass of <em>A. caliginosa</em> among treatments, as this species could feed directly on alder leaves. The accumulation of poorly stabilized particulate organic C was negatively affected by the presence of both earthworm species (i.e. less than cumulative), suggesting either that <em>A. caliginosa</em> fed on the particulate organic matter produced by the epigeic earthworm, or that competition for the limiting food resources took place. However, <em>A. caliginosa</em> promoted a similar increase in stable mineral-associated C in all treatments. This confirms the plasticity of <em>A. caliginosa</em> regarding food resources observed in other experiments, and shows that the effect of the burrowing earthworm <em>A. caliginosa</em> on stable C accumulation is not necessarily mediated by litter-feeders in the presence of litter of good quality.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"218 ","pages":"Article 106687"},"PeriodicalIF":5.0,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145750242","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 : 2025-12-09DOI: 10.1016/j.apsoil.2025.106703
Sam van Loon , Lotte de Jeu , Shin Woong Kim , Rachel Hurley , Laura J. Zantis , Salla Selonen , Luca Nizzetto , Tessa Steenhof , Chiara Consolaro , Matty P. Berg , Cornelis A.M. van Gestel
Agricultural mulching films represent a major source of microplastics (MPs; defined as particles 1 μm-5 mm in size) in soils. With a projected exponential increase of the global use of agricultural mulching films, concentrations of MPs in soil are bound to increase. Short-term single species toxicity tests using mulching film-based MPs showed effects on soil invertebrates at high concentrations, up to 5 % (w/w dry soil), as well as on soil physicochemical properties. This study aimed to provide insight into the long-term effects of mulching film-based MPs by simulating an agricultural growing season in a highly controlled mesocosm system called CLIMECS. Eight replicate constructed cores of Lufa 2.2 soil spiked with 0 % (control), 0.025 %, 0.05 %, 0.2 % or 0.8 % starch-polybutadiene adipate terephthalate MPs received a constant springtail community (Heteromurus nitidus, Protaphorura fimata and Sinella curviseta), two species of earthworm (Aporrectodea caliginosa and Lumbricus rubellus), cress (Lepidium sativum) as vegetation cover, and lettuce (Lactuca sativa) as a crop. After 13 weeks incubation, soil pH and smaller soil aggregate fractions were significantly decreased already at the lowest exposure concentration of 0.025 % MPs compared to the control (p < 0.05 and p < 0.001, respectively). Springtail community composition did not show differences between treatments. Earthworm survival was not affected by the MPs, but total earthworm reproduction was lower at 0.2 % and 0.8 % MPs compared to the 0.05 % treatment. This study showed that MPs derived from biodegradable mulching film plastics may affect soil physicochemical properties and earthworm reproduction at environmentally relevant concentrations.
{"title":"Microplastics from biodegradable mulching films affect soil physicochemical properties and earthworm reproduction, but not microarthropod communities","authors":"Sam van Loon , Lotte de Jeu , Shin Woong Kim , Rachel Hurley , Laura J. Zantis , Salla Selonen , Luca Nizzetto , Tessa Steenhof , Chiara Consolaro , Matty P. Berg , Cornelis A.M. van Gestel","doi":"10.1016/j.apsoil.2025.106703","DOIUrl":"10.1016/j.apsoil.2025.106703","url":null,"abstract":"<div><div>Agricultural mulching films represent a major source of microplastics (MPs; defined as particles 1 μm-5 mm in size) in soils. With a projected exponential increase of the global use of agricultural mulching films, concentrations of MPs in soil are bound to increase. Short-term single species toxicity tests using mulching film-based MPs showed effects on soil invertebrates at high concentrations, up to 5 % (<em>w</em>/w dry soil), as well as on soil physicochemical properties. This study aimed to provide insight into the long-term effects of mulching film-based MPs by simulating an agricultural growing season in a highly controlled mesocosm system called CLIMECS. Eight replicate constructed cores of Lufa 2.2 soil spiked with 0 % (control), 0.025 %, 0.05 %, 0.2 % or 0.8 % starch-polybutadiene adipate terephthalate MPs received a constant springtail community (<em>Heteromurus nitidus, Protaphorura fimata</em> and <em>Sinella curviseta</em>), two species of earthworm (<em>Aporrectodea caliginosa</em> and <em>Lumbricus rubellus</em>), cress (<em>Lepidium sativum</em>) as vegetation cover, and lettuce (<em>Lactuca sativa</em>) as a crop. After 13 weeks incubation, soil pH and smaller soil aggregate fractions were significantly decreased already at the lowest exposure concentration of 0.025 % MPs compared to the control (<em>p</em> < 0.05 and <em>p</em> < 0.001, respectively). Springtail community composition did not show differences between treatments. Earthworm survival was not affected by the MPs, but total earthworm reproduction was lower at 0.2 % and 0.8 % MPs compared to the 0.05 % treatment. This study showed that MPs derived from biodegradable mulching film plastics may affect soil physicochemical properties and earthworm reproduction at environmentally relevant concentrations.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"218 ","pages":"Article 106703"},"PeriodicalIF":5.0,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749276","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 : 2025-12-08DOI: 10.1016/j.apsoil.2025.106678
Hao Shi , Wei Wei , Jun-qiang Wang , Fei Xia , Cai-hong Yang , Lin-ling Ran , Yun-yin Xue , Hao-yang Wu , Shuang Yan , Yu Zhang , Shai-kun Zheng , Xiao-qing Qiu
Global warming and grassland restoration profoundly alter soil microbial dynamics on the Qinghai-Tibet Plateau, threatening underground ecological processes of alpine ecosystems. Here, by conducting a field experiment integrating three restoration methods (natural-restoration, no-till-replanting, and till-replanting) with open-top-chamber warming, we aimed to elucidate how warming modulates structural responses of soil microbial communities and nutrient limitations during grassland restoration. Results revealed that warming decreased the inverse-Simpson (InvSimpson) diversity of bacteria by 23 % in 0–5 cm soil depth but increased it by 70 % in 5–20 cm depth, and it decreased the InvSimpson diversity of fungi by 30 % and 45 % for both depths, respectively. Compared to warming, soil depth had a stronger effect on the dominant microbial community species. All systems showed strong phosphorus limitations, with warming amplifying carbon‑phosphorus co-limitation effect, whereas deeper depths alleviated carbon limitation. Warming combined with grassland restoration exacerbated carbon limitations, which in turn significantly suppressed the InvSimpson diversity of the bacterial and fungal communities. To summarize, although deeper soil depths had a buffering effect, warming not only exacerbated soil phosphorus limitation but also interacted with grassland restoration to intensify carbon limitation, which in turn negatively affected the microbial community InvSimpson diversity. These findings reveal the synergistic response mechanisms between the alpine grassland microbial community and nutrient limitation, providing theoretical support for the sustainable restoration of warming-adapted grasslands.
{"title":"Warming-driven and depth-dependent responses of soil microbial communities toward nutrient limitations: Ecological insights into alpine grassland restoration","authors":"Hao Shi , Wei Wei , Jun-qiang Wang , Fei Xia , Cai-hong Yang , Lin-ling Ran , Yun-yin Xue , Hao-yang Wu , Shuang Yan , Yu Zhang , Shai-kun Zheng , Xiao-qing Qiu","doi":"10.1016/j.apsoil.2025.106678","DOIUrl":"10.1016/j.apsoil.2025.106678","url":null,"abstract":"<div><div>Global warming and grassland restoration profoundly alter soil microbial dynamics on the Qinghai-Tibet Plateau, threatening underground ecological processes of alpine ecosystems. Here, by conducting a field experiment integrating three restoration methods (natural-restoration, no-till-replanting, and till-replanting) with open-top-chamber warming, we aimed to elucidate how warming modulates structural responses of soil microbial communities and nutrient limitations during grassland restoration. Results revealed that warming decreased the inverse-Simpson (InvSimpson) diversity of bacteria by 23 % in 0–5 cm soil depth but increased it by 70 % in 5–20 cm depth, and it decreased the InvSimpson diversity of fungi by 30 % and 45 % for both depths, respectively. Compared to warming, soil depth had a stronger effect on the dominant microbial community species. All systems showed strong phosphorus limitations, with warming amplifying carbon‑phosphorus co-limitation effect, whereas deeper depths alleviated carbon limitation. Warming combined with grassland restoration exacerbated carbon limitations, which in turn significantly suppressed the InvSimpson diversity of the bacterial and fungal communities. To summarize, although deeper soil depths had a buffering effect, warming not only exacerbated soil phosphorus limitation but also interacted with grassland restoration to intensify carbon limitation, which in turn negatively affected the microbial community InvSimpson diversity. These findings reveal the synergistic response mechanisms between the alpine grassland microbial community and nutrient limitation, providing theoretical support for the sustainable restoration of warming-adapted grasslands.</div></div>","PeriodicalId":8099,"journal":{"name":"Applied Soil Ecology","volume":"218 ","pages":"Article 106678"},"PeriodicalIF":5.0,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749136","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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