Pub Date : 2026-02-16DOI: 10.1007/s00374-026-01988-8
Mateo Córdoba-Agudelo, Maximilian Schmidt, Maria Serwetnicka, Carolyn-Monika Görres, Jana Zinkernagel, Davide Francioli
Organic amendments, such as compost, are widely used to improve soil organic matter content, nutrient retention, and microbial activity; however, their effectiveness depends on multiple factors, including compost type, application rate, soil and crop characteristics, and mode of application. The spatial placement of compost can profoundly influence soil nutrient dynamics and the assembly of plant-beneficial microbial communities, such as microorganisms involved in nutrient cycling, organic matter decomposition, and plant growth promotion. Here, we investigated how two compost application strategies—surface broadcasting and deep banding of green-waste compost—affect soil physicochemical properties and the rhizosphere bacterial community of red bell pepper ( Capsicum annuum var. Fritz G740 ) across two developmental stages (maturation and ripening). To resolve microbial responses at high taxonomic resolution, we applied Oxford Nanopore long-read sequencing of the full-length 16S rRNA gene, enabling improved taxonomic assignments and more reliable functional predictions compared to short-read approaches. Deep banding resulted in significantly higher organic C, total N, and nitrate concentrations than surface broadcasting, particularly at the ripening stage. These changes were closely associated with pronounced shifts in rhizosphere bacterial community composition, with deep banding selectively enriching N-associated genera, including Azoarcus , Alcaligenes , and Ochrobactrum . Functional predictions further indicated an enhanced potential for N cycle-related pathways, such as nitrate reduction and nitrogen respiration. Overall, our results demonstrate that deep compost banding may enhances soil fertility while promoting a functionally enriched rhizosphere microbiome. By integrating temporal sampling with long-read amplicon sequencing, this study provides a comprehensive framework to evaluate how compost placement modulates soil–plant–microbe interactions in horticultural production systems.
有机改良剂，如堆肥，被广泛用于提高土壤有机质含量、养分保留和微生物活性；然而，它们的有效性取决于多种因素，包括堆肥类型、施用量、土壤和作物特性以及施用方式。堆肥的空间放置可以深刻影响土壤养分动态和植物有益微生物群落的聚集，如参与养分循环、有机物分解和促进植物生长的微生物。本研究研究了两种堆肥施用策略——地表撒施和绿色垃圾堆肥深施——对红甜椒（Capsicum annuum var. Fritz G740）成熟期和成熟期土壤理化性质和根际细菌群落的影响。为了在高分类学分辨率下解决微生物反应，我们应用了Oxford Nanopore全长16S rRNA基因的长读测序，与短读方法相比，可以改进分类分配和更可靠的功能预测。深条带处理导致有机碳、全氮和硝酸盐浓度显著高于地表撒播，尤其是在成熟期。这些变化与根际细菌群落组成的显著变化密切相关，深条带选择性地富集了氮相关属，包括偶氮菌属（Azoarcus）、Alcaligenes和Ochrobactrum。功能预测进一步表明，氮循环相关途径的潜力增强，如硝酸盐还原和氮呼吸。总的来说，我们的研究结果表明，深层堆肥带可以提高土壤肥力，同时促进根际微生物群的功能丰富。通过将时间采样与长读扩增子测序相结合，本研究提供了一个全面的框架来评估堆肥放置如何调节园艺生产系统中土壤-植物-微生物的相互作用。
{"title":"Compost-driven modulation of rhizosphere bacterial communities during red bell pepper development revealed by long-read 16S metabarcoding","authors":"Mateo Córdoba-Agudelo, Maximilian Schmidt, Maria Serwetnicka, Carolyn-Monika Görres, Jana Zinkernagel, Davide Francioli","doi":"10.1007/s00374-026-01988-8","DOIUrl":"https://doi.org/10.1007/s00374-026-01988-8","url":null,"abstract":"Organic amendments, such as compost, are widely used to improve soil organic matter content, nutrient retention, and microbial activity; however, their effectiveness depends on multiple factors, including compost type, application rate, soil and crop characteristics, and mode of application. The spatial placement of compost can profoundly influence soil nutrient dynamics and the assembly of plant-beneficial microbial communities, such as microorganisms involved in nutrient cycling, organic matter decomposition, and plant growth promotion. Here, we investigated how two compost application strategies—surface broadcasting and deep banding of green-waste compost—affect soil physicochemical properties and the rhizosphere bacterial community of red bell pepper ( <jats:italic>Capsicum annuum</jats:italic> var. <jats:italic>Fritz G740</jats:italic> ) across two developmental stages (maturation and ripening). To resolve microbial responses at high taxonomic resolution, we applied Oxford Nanopore long-read sequencing of the full-length 16S rRNA gene, enabling improved taxonomic assignments and more reliable functional predictions compared to short-read approaches. Deep banding resulted in significantly higher organic C, total N, and nitrate concentrations than surface broadcasting, particularly at the ripening stage. These changes were closely associated with pronounced shifts in rhizosphere bacterial community composition, with deep banding selectively enriching N-associated genera, including <jats:italic>Azoarcus</jats:italic> , <jats:italic>Alcaligenes</jats:italic> , and <jats:italic>Ochrobactrum</jats:italic> . Functional predictions further indicated an enhanced potential for N cycle-related pathways, such as nitrate reduction and nitrogen respiration. Overall, our results demonstrate that deep compost banding may enhances soil fertility while promoting a functionally enriched rhizosphere microbiome. By integrating temporal sampling with long-read amplicon sequencing, this study provides a comprehensive framework to evaluate how compost placement modulates soil–plant–microbe interactions in horticultural production systems.","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":"506 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146205073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-13DOI: 10.1007/s00374-026-01991-z
Yu Xie, Siyuan Deng, Chong Wang, Congju Zhao, Lei Meng, Xingliang Xu, Erdeng Ma, Tongbin Zhu, Christoph Müller
{"title":"Contrasting effects of glyphosate on soil nitrogen turnover and N2O emissions in greenhouse vegetable soils under short- and long-term cultivation","authors":"Yu Xie, Siyuan Deng, Chong Wang, Congju Zhao, Lei Meng, Xingliang Xu, Erdeng Ma, Tongbin Zhu, Christoph Müller","doi":"10.1007/s00374-026-01991-z","DOIUrl":"https://doi.org/10.1007/s00374-026-01991-z","url":null,"abstract":"","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":"16 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146196630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-10DOI: 10.1007/s00374-026-01990-0
Shenliang Zhao, Hua Chai, Mingxu Li, Chaolian Jiao, Cheng Liu, Li Xu, Jie Li, Nianpeng He
{"title":"Low substrate concentration intensifies the earthworm-driven increase in temperature sensitivity of SOM decomposition","authors":"Shenliang Zhao, Hua Chai, Mingxu Li, Chaolian Jiao, Cheng Liu, Li Xu, Jie Li, Nianpeng He","doi":"10.1007/s00374-026-01990-0","DOIUrl":"https://doi.org/10.1007/s00374-026-01990-0","url":null,"abstract":"","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":"86 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146153636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-07DOI: 10.1007/s00374-026-01981-1
Upulika Jayaneththi, Paramsothy Jeyakumar, Nicholas W. Sneddon, Lucy L. Burkitt, Christopher W. N. Anderson, Lisanne M. Fermin, Daniel J. Donaghy
Pasture systems strongly influence microbiome diversity in both soils and grazing ruminants, and their interactions through interconnected microbial exchange pathways. In temperate regions, grazed pasture systems are predominantly composed of perennial ryegrass-white clover, representing standard systems under contemporary management. However, sustainable alternatives such as regenerative agriculture, which emphasise diverse pasture species, are gaining attention. Diverse pastures, due to their varied root structures and nutritional composition, exert more pronounced effects on soil and ruminant microbiomes than standard swards. This review synthesises current knowledge on soil and ruminant gut microbiome responses to diverse pasture systems. Diverse swards enhance soil organic carbon and microbial abundance, while their varied nutrient profiles and bioactive compounds, together with ingested soil microbes during grazing, contribute to a more diverse and stable gut microbiome, potentially strengthening soil–gut microbial interactions. However, few omics-based studies have explored microbiome responses to pasture management, and none have simultaneously investigated soil and ruminant gut microbiomes under regenerative management. This review highlights these gaps and proposes future research directions, including integrated multi-omics approaches, to advance understanding of soil–gut microbiome dynamics, interactions, and functional roles within pasture-based agroecosystems.
{"title":"Soil and ruminant gut microbiomes in diverse pasture systems and regenerative agriculture: a review","authors":"Upulika Jayaneththi, Paramsothy Jeyakumar, Nicholas W. Sneddon, Lucy L. Burkitt, Christopher W. N. Anderson, Lisanne M. Fermin, Daniel J. Donaghy","doi":"10.1007/s00374-026-01981-1","DOIUrl":"https://doi.org/10.1007/s00374-026-01981-1","url":null,"abstract":"Pasture systems strongly influence microbiome diversity in both soils and grazing ruminants, and their interactions through interconnected microbial exchange pathways. In temperate regions, grazed pasture systems are predominantly composed of perennial ryegrass-white clover, representing standard systems under contemporary management. However, sustainable alternatives such as regenerative agriculture, which emphasise diverse pasture species, are gaining attention. Diverse pastures, due to their varied root structures and nutritional composition, exert more pronounced effects on soil and ruminant microbiomes than standard swards. This review synthesises current knowledge on soil and ruminant gut microbiome responses to diverse pasture systems. Diverse swards enhance soil organic carbon and microbial abundance, while their varied nutrient profiles and bioactive compounds, together with ingested soil microbes during grazing, contribute to a more diverse and stable gut microbiome, potentially strengthening soil–gut microbial interactions. However, few omics-based studies have explored microbiome responses to pasture management, and none have simultaneously investigated soil and ruminant gut microbiomes under regenerative management. This review highlights these gaps and proposes future research directions, including integrated multi-omics approaches, to advance understanding of soil–gut microbiome dynamics, interactions, and functional roles within pasture-based agroecosystems.","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":"211 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Significant role of microbial nitrogen use efficiency in regulating long-term soil carbon and nitrogen stoichiometry","authors":"Wanyu Li, Gangsheng Wang, Daifeng Xiang, Shanshan Qi, Jing Tian, Zehao Lv","doi":"10.1007/s00374-026-01985-x","DOIUrl":"https://doi.org/10.1007/s00374-026-01985-x","url":null,"abstract":"","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":"9 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Climate warming enhances the accumulation of microbial necromass carbon in the soils of an invasive species via regulating microbial traits","authors":"Xiaohu Wang, Wenqiang Zhao, Jipeng Wang, Xiaohui Zhou, Weiming He, Jingji Li, Huajun Yin","doi":"10.1007/s00374-026-01982-0","DOIUrl":"https://doi.org/10.1007/s00374-026-01982-0","url":null,"abstract":"","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":"3 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-04DOI: 10.1007/s00374-026-01986-w
Jordan M. Sayre, Daoyuan Wang, Christian Erikson, Júlia Brandão Gontijo, Kate Scow, Jorge L. Mazza Rodrigues
{"title":"Increased microbial carbon use efficiency and metabolic capacity in manure amended soils: A 665-day field experiment","authors":"Jordan M. Sayre, Daoyuan Wang, Christian Erikson, Júlia Brandão Gontijo, Kate Scow, Jorge L. Mazza Rodrigues","doi":"10.1007/s00374-026-01986-w","DOIUrl":"https://doi.org/10.1007/s00374-026-01986-w","url":null,"abstract":"","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":"15 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-29DOI: 10.1007/s00374-026-01979-9
Yan Wang, Mary Beth Adams, Yanjiang Cai, Paolo Nannipieri
{"title":"Responses of soil carbon and nutrient cycling to global change and human disturbances in forest ecosystems","authors":"Yan Wang, Mary Beth Adams, Yanjiang Cai, Paolo Nannipieri","doi":"10.1007/s00374-026-01979-9","DOIUrl":"https://doi.org/10.1007/s00374-026-01979-9","url":null,"abstract":"","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":"218 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146095797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-27DOI: 10.1007/s00374-026-01980-2
Yang Xuefang, Du Dan, Yang Xueping, Xue Ruiqing, Hu Chunyan, Sun Dasheng, Yuan Xiangyang, Ma Chunsen
{"title":"Dual-functional Bacillus amyloliquefaciens mediates autotoxin degradation and pathogen suppression in monocropped foxtail millet","authors":"Yang Xuefang, Du Dan, Yang Xueping, Xue Ruiqing, Hu Chunyan, Sun Dasheng, Yuan Xiangyang, Ma Chunsen","doi":"10.1007/s00374-026-01980-2","DOIUrl":"https://doi.org/10.1007/s00374-026-01980-2","url":null,"abstract":"","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":"44 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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