Pub Date : 2025-10-28DOI: 10.1016/j.rhisph.2025.101218
Jian Chen , Qingfeng Sun , Ruirui Chen , Zhihao Zhang , Zhen Liu , Gongyou Chen
Bacterial communities play significant roles in desert ecosystems through diverse interactions, including participation in rhizolith formation and establishment of root symbioses, yet related evidence remain limited. Using 16S rRNA amplicon sequencing, diversity metrics and co-occurrence network analyses, this study explored bacterial communities of rhizolith- and root-associated soils in the Tengeri Desert, China, with a focus on their potential role in carbonate precipitation. We identified significant differences in bacterial communities across root/soil types. The co-occurrence network was simpler in root-associated soils compared to bulk soils. Rhizolith-associated soils harbored unique taxa with low alpha diversity but with enriched specialists Propionibacterium, Corynebacterium and Acinetobacter linked to carbonate genesis. Our study provides new insights into plant–microbe–mineral interactions in desert ecosystems.
{"title":"Bacterial communities of rhizolith- and root-associated in the Tengeri Desert, China","authors":"Jian Chen , Qingfeng Sun , Ruirui Chen , Zhihao Zhang , Zhen Liu , Gongyou Chen","doi":"10.1016/j.rhisph.2025.101218","DOIUrl":"10.1016/j.rhisph.2025.101218","url":null,"abstract":"<div><div>Bacterial communities play significant roles in desert ecosystems through diverse interactions, including participation in rhizolith formation and establishment of root symbioses, yet related evidence remain limited. Using 16S rRNA amplicon sequencing, diversity metrics and co-occurrence network analyses, this study explored bacterial communities of rhizolith- and root-associated soils in the Tengeri Desert, China, with a focus on their potential role in carbonate precipitation. We identified significant differences in bacterial communities across root/soil types. The co-occurrence network was simpler in root-associated soils compared to bulk soils. Rhizolith-associated soils harbored unique taxa with low alpha diversity but with enriched specialists <em>Propionibacterium</em>, <em>Corynebacterium</em> and <em>Acinetobacter</em> linked to carbonate genesis. Our study provides new insights into plant–microbe–mineral interactions in desert ecosystems.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101218"},"PeriodicalIF":3.5,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This study modeled root length density of wheat as a nonlinear function of bulk density, penetration resistance, and soil depth. Field experiments on alluvial soils subjected to tractor-induced compaction generated datasets for model development. A conventional log-linear model and a deep neural network were compared, and global sensitivity analysis was performed to assess parameter influence. Results showed that the deep neural network provided superior predictive accuracy over the analytical model, effectively capturing nonlinear and depth-dependent interactions. Sobol sensitivity analysis identified soil depth as the most influential factor affecting root length density, followed by penetration resistance and bulk density. The study concludes that integrating soil depth with machine learning approaches enhances root length density prediction and interpretation, emphasizing the significance of soil compaction parameters in guiding precision agriculture and sustainable soil management practices.
{"title":"Modeling of root length density of wheat crop in field study using machine learning and sensitivity analysis","authors":"Sanjay Kumar Patel , Sanjay Kumar , Sudarshan Prasad , Raghuraj Singh , Tushar Kumar Pandey","doi":"10.1016/j.rhisph.2025.101214","DOIUrl":"10.1016/j.rhisph.2025.101214","url":null,"abstract":"<div><div>This study modeled root length density of wheat as a nonlinear function of bulk density, penetration resistance, and soil depth. Field experiments on alluvial soils subjected to tractor-induced compaction generated datasets for model development. A conventional log-linear model and a deep neural network were compared, and global sensitivity analysis was performed to assess parameter influence. Results showed that the deep neural network provided superior predictive accuracy over the analytical model, effectively capturing nonlinear and depth-dependent interactions. Sobol sensitivity analysis identified soil depth as the most influential factor affecting root length density, followed by penetration resistance and bulk density. The study concludes that integrating soil depth with machine learning approaches enhances root length density prediction and interpretation, emphasizing the significance of soil compaction parameters in guiding precision agriculture and sustainable soil management practices.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101214"},"PeriodicalIF":3.5,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-25DOI: 10.1016/j.rhisph.2025.101207
Zahra Noviana , Widya Kurniawati , Tirta Kumala Dewi , Riki Ruhimat , Agung Adi Nugroho , Entis Sutisna , Ratdiana , Dwi Agustiyani , Dwi Andreas Santosa , Sarjiya Antonius
Rhizosphere bacterial communities are key to plant health, supporting nutrient uptake and limiting pathogen proliferation through the production of phytohormones, volatile organic compounds, and antimicrobial compounds. Banana, particularly the Cavendish cultivar that dominates global exports, is severely threatened by Fusarium wilt caused by Fusarium oxysporum f. sp. cubense TR4. Crop rotation has shown promise in mitigating this threat by reshaping the rhizobiome toward communities associated with improved plant health. Although effects of crop rotation on banana rhizosphere microbiomes have been reported, the influence of rotation across different banana generations remains unclear, despite higher generations being more susceptible to Fusarium wilt. This study profiled bacterial communities in first- and third-generation banana fields and banana monoculture to identify taxa potentially linked to banana resistance. Bacterial communities clustered according to planting history and generation, likely reflecting differences in rotation practices, plant species, and local soil properties. First-generation bananas harbored distinct taxa such as Candidatus Xiphinematobacter, Pseudolabrys, and members of Sandaracinaceae, which were less abundant in later generations, suggesting potential early plant–microbe associations linked to plant health. Healthy plants were additionally enriched with Gemmatimonas, Chthonomonas, Luteolibacter, Lysinibacillus, Mitsuaria, Mucilaginibacter, and Rhodoplanes. While the functional roles of these taxa in Fusarium wilt suppression were not directly tested, their differential presence across plant generations and health status provides novel descriptive insights into microbiome patterns associated with banana resilience. Together, these findings highlight that planting history, plant health, and local environmental conditions jointly shape the banana rhizosphere microbiome.
根际细菌群落是植物健康的关键，通过产生植物激素、挥发性有机化合物和抗菌化合物来支持养分吸收和限制病原体增殖。香蕉，特别是主导全球出口的卡文迪什香蕉品种，受到由古巴镰刀菌（Fusarium oxysporum f. sp. cubense TR4）引起的枯萎病严重威胁。作物轮作已显示出减轻这一威胁的希望，因为它使根瘤菌群向与改善植物健康有关的群落方向改变。虽然轮作对香蕉根际微生物组的影响已经有报道，但轮作对不同世代香蕉的影响尚不清楚，尽管较高世代的香蕉更容易受到枯萎病的影响。本研究分析了第一代和第三代香蕉田和香蕉单作栽培的细菌群落，以确定可能与香蕉抗性相关的分类群。细菌群落根据种植历史和世代聚集，可能反映了轮作方式、植物种类和当地土壤性质的差异。第一代香蕉拥有独特的分类群，如Candidatus Xiphinematobacter， Pseudolabrys和Sandaracinaceae成员，这些分类群在后代中较少，这表明潜在的早期植物-微生物关联与植物健康有关。健康植物还富含双胞单胞菌、Chthonomonas、木犀草杆菌、Lysinibacillus、Mitsuaria、Mucilaginibacter和Rhodoplanes。虽然这些分类群在抑制枯萎病中的功能作用没有直接测试，但它们在植物世代和健康状态中的差异存在为香蕉恢复力相关的微生物组模式提供了新的描述性见解。总之，这些发现强调了种植历史、植物健康和当地环境条件共同塑造了香蕉根际微生物群。
{"title":"Rhizosphere bacterial communities differ across banana generations and health status under Fusarium wilt pressure","authors":"Zahra Noviana , Widya Kurniawati , Tirta Kumala Dewi , Riki Ruhimat , Agung Adi Nugroho , Entis Sutisna , Ratdiana , Dwi Agustiyani , Dwi Andreas Santosa , Sarjiya Antonius","doi":"10.1016/j.rhisph.2025.101207","DOIUrl":"10.1016/j.rhisph.2025.101207","url":null,"abstract":"<div><div>Rhizosphere bacterial communities are key to plant health, supporting nutrient uptake and limiting pathogen proliferation through the production of phytohormones, volatile organic compounds, and antimicrobial compounds. Banana, particularly the Cavendish cultivar that dominates global exports, is severely threatened by Fusarium wilt caused by <em>Fusarium oxysporum</em> f. sp. <em>cubense</em> TR4. Crop rotation has shown promise in mitigating this threat by reshaping the rhizobiome toward communities associated with improved plant health. Although effects of crop rotation on banana rhizosphere microbiomes have been reported, the influence of rotation across different banana generations remains unclear, despite higher generations being more susceptible to Fusarium wilt. This study profiled bacterial communities in first- and third-generation banana fields and banana monoculture to identify taxa potentially linked to banana resistance. Bacterial communities clustered according to planting history and generation, likely reflecting differences in rotation practices, plant species, and local soil properties. First-generation bananas harbored distinct taxa such as <em>Candidatus</em> Xiphinematobacter, <em>Pseudolabrys</em>, and members of Sandaracinaceae, which were less abundant in later generations, suggesting potential early plant–microbe associations linked to plant health. Healthy plants were additionally enriched with <em>Gemmatimonas</em>, <em>Chthonomonas</em>, <em>Luteolibacter</em>, <em>Lysinibacillus</em>, <em>Mitsuaria</em>, <em>Mucilaginibacter</em>, and <em>Rhodoplanes</em>. While the functional roles of these taxa in Fusarium wilt suppression were not directly tested, their differential presence across plant generations and health status provides novel descriptive insights into microbiome patterns associated with banana resilience. Together, these findings highlight that planting history, plant health, and local environmental conditions jointly shape the banana rhizosphere microbiome.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101207"},"PeriodicalIF":3.5,"publicationDate":"2025-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145416537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-24DOI: 10.1016/j.rhisph.2025.101216
Feifan Leng , Xinyi Liu , Lingtong Zhou , Qian Zhang , Shaowei Li , Fang Wu , Wen Luo , Hongshan Yang , Yonggang Wang , Xinqiang Zhu , Xiaoli Wang
Soil salinization poses a serious threat to global agricultural production. Alfalfa (Medicago sativa L.), as a high-quality leguminous forage, shows significant varietal differences in salt tolerance. However, the mechanisms behind these differences, particularly those mediated by rhizosphere microorganisms and root exudates, remain unclear. This study systematically analyzed the phenotypic, physiological, and biochemical responses of three alfalfa varieties (ZT1, ZL1, and ZM1) under salt stress (0, 100, and 200 mM NaCl), ZM1 and ZT1 exhibited enhanced salt tolerance. Combined 16S rRNA sequencing and metabolomic analysis revealed that salt stress reduced alpha diversity and reshaped the structure of the rhizosphere microbial community. Meanwhile, root exudate profiles underwent significant changes, with key metabolites in flavonoid biosynthesis, arginine metabolism, and bacterial chemotaxis pathways being significantly upregulated. Correlation analysis showed close interactions between specific root exudates and rhizosphere bacteria, with the content of important root exudates (flavonoids and saponins) showing positive correlations with the abundance of rhizosphere microorganisms under salt stress. This research elucidates the synergistic role of root exudates and rhizosphere microorganisms in mediating salt tolerance in alfalfa, providing new insights into plant-microbe interactions under abiotic stress and offering potential strategies for improving crop adaptation in saline soils.
土壤盐碱化对全球农业生产构成严重威胁。苜蓿（Medicago sativa L.）是一种优质豆科牧草，其耐盐性存在显著的品种差异。然而，这些差异背后的机制，特别是由根际微生物和根渗出物介导的机制仍不清楚。本研究系统分析了3个紫花苜蓿品种ZT1、ZL1和ZM1在盐胁迫（0、100和200 mM NaCl）下的表型和生理生化反应，ZM1和ZT1表现出更强的耐盐性。16S rRNA测序和代谢组学分析表明，盐胁迫降低了根际微生物群落的α多样性，重塑了根际微生物群落的结构。与此同时，根分泌物谱发生了显著变化，类黄酮生物合成、精氨酸代谢和细菌趋化途径中的关键代谢物显著上调。相关分析表明，特定根分泌物与根际细菌之间存在密切的交互作用，重要根分泌物（黄酮类和皂苷类）含量与盐胁迫下根际微生物丰度呈正相关。本研究阐明了根系分泌物和根际微生物在苜蓿耐盐性中的协同作用，为非生物胁迫下植物与微生物的相互作用提供了新的认识，并为提高作物在盐碱地的适应性提供了潜在的策略。
{"title":"Salt-tolerance of Alfalfa (Medicago sativa L.) are mediated by rhizosphere microbiome and root exudate","authors":"Feifan Leng , Xinyi Liu , Lingtong Zhou , Qian Zhang , Shaowei Li , Fang Wu , Wen Luo , Hongshan Yang , Yonggang Wang , Xinqiang Zhu , Xiaoli Wang","doi":"10.1016/j.rhisph.2025.101216","DOIUrl":"10.1016/j.rhisph.2025.101216","url":null,"abstract":"<div><div>Soil salinization poses a serious threat to global agricultural production. Alfalfa (<em>Medicago sativa</em> L.), as a high-quality leguminous forage, shows significant varietal differences in salt tolerance. However, the mechanisms behind these differences, particularly those mediated by rhizosphere microorganisms and root exudates, remain unclear. This study systematically analyzed the phenotypic, physiological, and biochemical responses of three alfalfa varieties (ZT1, ZL1, and ZM1) under salt stress (0, 100, and 200 mM NaCl), ZM1 and ZT1 exhibited enhanced salt tolerance. Combined 16S rRNA sequencing and metabolomic analysis revealed that salt stress reduced alpha diversity and reshaped the structure of the rhizosphere microbial community. Meanwhile, root exudate profiles underwent significant changes, with key metabolites in flavonoid biosynthesis, arginine metabolism, and bacterial chemotaxis pathways being significantly upregulated. Correlation analysis showed close interactions between specific root exudates and rhizosphere bacteria, with the content of important root exudates (flavonoids and saponins) showing positive correlations with the abundance of rhizosphere microorganisms under salt stress. This research elucidates the synergistic role of root exudates and rhizosphere microorganisms in mediating salt tolerance in alfalfa, providing new insights into plant-microbe interactions under abiotic stress and offering potential strategies for improving crop adaptation in saline soils.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101216"},"PeriodicalIF":3.5,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145416538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-24DOI: 10.1016/j.rhisph.2025.101209
Amir Hossein Khoshgoftarmanesh , Ali Akbar Zare , Azam Hosseinian Moghaddam
Phytosiderophore secretion and zinc (Zn) uptake by roots of wheat in response to uniform and non-uniform distribution of salt in root environment was investigated. Two Zn-efficient (Triticum aestivum L. cvs. Rushan and Pishtaz) and a Zn-inefficient (Kavir) wheat genotypes were exposed to uniform and static and dynamic non-uniform NaCl salinity either in the presence or absence of Zn (Exp. 1) or at a constant Zn2+ activity (pZn2+ = 4.7) in nutrient solution (Exp. 2). Root zone consisted two equal sections filled with nutrient solution. In non-uniform salinity, one side was non-saline and the other side contained 80 mM NaCl. In static non-uniform salinity, the one side received saline solution to the end of experiment while in dynamic treatment, saline solutions was exchanged between two sides after 4 d. In uniform salinity, both sides were saline (40 mM NaCl). The growth response of wheat to salinity treatments was genotype-dependent, in ‘Kavir’, the shoot dry mass was unaffected by non-uniform dynamic salinity while in ‘Rushan’ and ‘Pishtaz’, all salinity treatments caused a significant decline in the shoot biomass in comparison with the control. Regardless of genotype, the greatest damage of salinity on dry mass of shoot was found at the uniform salinity. A greater reduction in the dry mass of all wheat genotypes observed at uniform salinity compared to non-uniform salinities was associated with a further decrease in Zn and more increase in Na concentration. The highest increase in the root-to-shoot transport of Zn and Na was observed at the uniform salinity. In all wheat genotypes, salinity resulted in higher PS secretion from roots of the Zn-supplied plants. The highest increase in PS secretion from the right side (A) root of ‘Rushan’, ‘Kavir’ and ‘Pishtaz’ (2.24, 1.96 and 1.75 times over the control, respectively) was found at the uniform salinity. At the constant activity of Zn2+, the increasing effect of salinity on the root exudation of PS was considerably reduced. In the Zn-free conditions, salinity was ineffective or slightly increased the PS secretion from roots. In Zn-containing solution, the magnitude of changes in Zn2+ activity determines how the uniform and non-uniform salinity affect the root PS exudation. In contrast, at the absence of Zn, the effect of salinity on the root PS secretion seems to be more associated with plant growth status.
The lower phytosiderophore secretion under saline conditions leads to lower ability to Zn uptake which should be compensated by improved zinc nutrition.
研究了小麦根系对盐均匀分布和不均匀分布对植物铁素分泌和锌吸收的响应。两种高效锌小麦。将乳山（Rushan）和Pishtaz （Pishtaz）和一个锌低效小麦（Kavir）基因型分别暴露于均匀、静态和动态非均匀NaCl盐度（有或无Zn (Exp. 1)）和恒定Zn2+活性（pZn2+ = 4.7）的营养液中（Exp. 2）。根区由两等份的营养液填充而成。在非均匀盐度条件下，一侧为无盐，另一侧为80 mM NaCl。在静态不均匀盐度条件下，一侧接受生理盐水溶液直至实验结束；在动态条件下，4 d后两侧交换生理盐水溶液。等盐条件下，两侧均为盐水（40 mM NaCl）。小麦对盐胁迫的生长响应呈基因型依赖性，‘卡维尔’的茎部干质量不受非均匀动态盐胁迫的影响，而‘如山’和‘皮什塔兹’的茎部生物量均显著低于对照。无论基因型如何，盐度对茎干质量的损害均以均匀盐度下最大。与非均匀盐度相比，均匀盐度条件下所有小麦基因型的干质量下降幅度更大，这与锌进一步下降和钠浓度增加有关。均匀盐分处理下，锌和钠的根到梢转运增加幅度最大。在所有小麦基因型中，盐度导致锌供应植株根系分泌更高的PS。‘Rushan’、‘Kavir’和‘Pishtaz’的右侧(A)根PS分泌量在均匀盐度下增加最多（分别是对照的2.24倍、1.96倍和1.75倍）。在Zn2+活性不变的情况下，盐度对PS根系分泌物的增加作用明显减弱。在无锌条件下，盐度对根系PS分泌无效或略有增加。在含锌溶液中，Zn2+活性的变化幅度决定了均匀和非均匀盐度对根系PS渗出的影响。相反，在没有Zn的情况下，盐度对根系PS分泌的影响似乎更多地与植物的生长状态有关。生理盐水条件下植物铁素分泌减少导致锌吸收能力下降，这需要通过改善锌营养来弥补。
{"title":"Root exudation of phytosiderophores from wheat in response to dynamic and static non-uniform distribution of salt in the root medium","authors":"Amir Hossein Khoshgoftarmanesh , Ali Akbar Zare , Azam Hosseinian Moghaddam","doi":"10.1016/j.rhisph.2025.101209","DOIUrl":"10.1016/j.rhisph.2025.101209","url":null,"abstract":"<div><div>Phytosiderophore secretion and zinc (Zn) uptake by roots of wheat in response to uniform and non-uniform distribution of salt in root environment was investigated. Two Zn-efficient (<em>Triticum aestivum</em> L. cvs. Rushan and Pishtaz) and a Zn-inefficient (Kavir) wheat genotypes were exposed to uniform and static and dynamic non-uniform NaCl salinity either in the presence or absence of Zn (Exp. 1) or at a constant Zn<sup>2+</sup> activity (pZn<sup>2+</sup> = 4.7) in nutrient solution (Exp. 2). Root zone consisted two equal sections filled with nutrient solution. In non-uniform salinity, one side was non-saline and the other side contained 80 mM NaCl. In static non-uniform salinity, the one side received saline solution to the end of experiment while in dynamic treatment, saline solutions was exchanged between two sides after 4 d. In uniform salinity, both sides were saline (40 mM NaCl). The growth response of wheat to salinity treatments was genotype-dependent, in ‘Kavir’, the shoot dry mass was unaffected by non-uniform dynamic salinity while in ‘Rushan’ and ‘Pishtaz’, all salinity treatments caused a significant decline in the shoot biomass in comparison with the control. Regardless of genotype, the greatest damage of salinity on dry mass of shoot was found at the uniform salinity. A greater reduction in the dry mass of all wheat genotypes observed at uniform salinity compared to non-uniform salinities was associated with a further decrease in Zn and more increase in Na concentration. The highest increase in the root-to-shoot transport of Zn and Na was observed at the uniform salinity. In all wheat genotypes, salinity resulted in higher PS secretion from roots of the Zn-supplied plants. The highest increase in PS secretion from the right side (A) root of ‘Rushan’, ‘Kavir’ and ‘Pishtaz’ (2.24, 1.96 and 1.75 times over the control, respectively) was found at the uniform salinity. At the constant activity of Zn<sup>2+</sup>, the increasing effect of salinity on the root exudation of PS was considerably reduced. In the Zn-free conditions, salinity was ineffective or slightly increased the PS secretion from roots. In Zn-containing solution, the magnitude of changes in Zn<sup>2+</sup> activity determines how the uniform and non-uniform salinity affect the root PS exudation. In contrast, at the absence of Zn, the effect of salinity on the root PS secretion seems to be more associated with plant growth status.</div><div>The lower phytosiderophore secretion under saline conditions leads to lower ability to Zn uptake which should be compensated by improved zinc nutrition.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101209"},"PeriodicalIF":3.5,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145416540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-24DOI: 10.1016/j.rhisph.2025.101212
Zaryab Shafi , Mohammad Shahid
Root exudates functions as biochemical signals that shape rhizobacterial community structure and activity in the rhizosphere. This review highlights the chemical diversity and molecular regulation of root exudates and their roles in mediating plant–rhizobacteria interactions. We discuss how specific metabolites such as organic acids, flavonoids, and amino acids govern rhizobacteria recruitment, quorum sensing, biofilm formation, and pathogen suppression. Integrating insights from metabolomics, metagenomics, and transcriptomics, we summarize recent advances linking exudate composition with microbial signaling and functional outcomes. This review also emphasizes translational perspectives, including potential exudate-based bioinoculant development and rhizosphere engineering for improved plant growth and stress tolerance. Collectively, these findings position root exudates as key determinants of rhizobacterial community assembly and promising tools for sustainable crop production.
{"title":"Root exudates as molecular architects shaping the rhizobacterial community: A review","authors":"Zaryab Shafi , Mohammad Shahid","doi":"10.1016/j.rhisph.2025.101212","DOIUrl":"10.1016/j.rhisph.2025.101212","url":null,"abstract":"<div><div>Root exudates functions as biochemical signals that shape rhizobacterial community structure and activity in the rhizosphere. This review highlights the chemical diversity and molecular regulation of root exudates and their roles in mediating plant–rhizobacteria interactions. We discuss how specific metabolites such as organic acids, flavonoids, and amino acids govern rhizobacteria recruitment, quorum sensing, biofilm formation, and pathogen suppression. Integrating insights from metabolomics, metagenomics, and transcriptomics, we summarize recent advances linking exudate composition with microbial signaling and functional outcomes. This review also emphasizes translational perspectives, including potential exudate-based bioinoculant development and rhizosphere engineering for improved plant growth and stress tolerance. Collectively, these findings position root exudates as key determinants of rhizobacterial community assembly and promising tools for sustainable crop production.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101212"},"PeriodicalIF":3.5,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-21DOI: 10.1016/j.rhisph.2025.101213
Xiumei Nie , Rui Zhong , Daniel A. Bastías , Chao Xia , Xingxu Zhang , Chunjie Li , Zhibiao Nan
The dynamics of plant-microorganism interactions in belowground environments are crucial for the function of natural and managed ecosystems. We studied the responses of plant belowground microbiota and rhizosphere metabolites to the presence of aboveground Epichloë fungal endophytes in the field. We hypothesized that Epichloë would increase the diversity, complexity, and abundance of soil/root microbiota and enhance the abundance of bioactive rhizosphere metabolites in plant belowground compartments, and that these microbiota-metabolite changes would be mechanistically linked. Soil samples, root tissues, and rhizosphere extracts were collected from Achnatherum inebrians plants with and without Epichloë grown in an experimental field plot. Fungal and bacterial microbiota associated with bulk soil, rhizosphere soil, and root endosphere of plants were characterized and metabolites associated with rhizosphere extracts were identified and quantified. The diversity, composition, and network complexity of both fungal and bacterial microbiota varied among plant belowground compartments. Epichloë increased the bacterial diversity, altered the composition of fungal and bacterial microbiota in the root endosphere, while generally enhanced the complexity of bacterial networks and richness of predicted fungal keystone taxa within plant belowground compartments. Epichloë increased the abundance of various fungal and bacterial taxa associated with belowground compartments (e.g., Blastococcus, Hygrocybe) and altered the composition and increased the abundance of several metabolites with predicted bioactivity including nutrients, signaling molecules, and antimicrobials (e.g., xanthosine 5′-phosphate, 13-hydroxyoctadecadienoic acid, and neomycin B). As expected, increased abundance in rhizosphere metabolites predicted as nutrients and signaling molecules were associated with enhanced abundance of microbial taxa in plant belowground compartments (e.g., Thermomyces), while increased abundance of metabolites predicted as antimicrobials had the opposite effect on the abundance of belowground-derived microbial taxa (e.g., Zymoseptoria). Our study highlights the key role of Epichloë in shaping the plant belowground microbiota and shows that endophyte-mediated changes in microbial abundance were associated with altered abundance of bioactive rhizosphere metabolites.
{"title":"Belowground microbiota and rhizosphere metabolites are modulated by aboveground Epichloë endophytes in plants","authors":"Xiumei Nie , Rui Zhong , Daniel A. Bastías , Chao Xia , Xingxu Zhang , Chunjie Li , Zhibiao Nan","doi":"10.1016/j.rhisph.2025.101213","DOIUrl":"10.1016/j.rhisph.2025.101213","url":null,"abstract":"<div><div>The dynamics of plant-microorganism interactions in belowground environments are crucial for the function of natural and managed ecosystems. We studied the responses of plant belowground microbiota and rhizosphere metabolites to the presence of aboveground <em>Epichloë</em> fungal endophytes in the field. We hypothesized that <em>Epichloë</em> would increase the diversity, complexity, and abundance of soil/root microbiota and enhance the abundance of bioactive rhizosphere metabolites in plant belowground compartments, and that these microbiota-metabolite changes would be mechanistically linked. Soil samples, root tissues, and rhizosphere extracts were collected from <em>Achnatherum inebrians</em> plants with and without <em>Epichloë</em> grown in an experimental field plot. Fungal and bacterial microbiota associated with bulk soil, rhizosphere soil, and root endosphere of plants were characterized and metabolites associated with rhizosphere extracts were identified and quantified. The diversity, composition, and network complexity of both fungal and bacterial microbiota varied among plant belowground compartments. <em>Epichloë</em> increased the bacterial diversity, altered the composition of fungal and bacterial microbiota in the root endosphere, while generally enhanced the complexity of bacterial networks and richness of predicted fungal keystone taxa within plant belowground compartments. <em>Epichloë</em> increased the abundance of various fungal and bacterial taxa associated with belowground compartments (e.g., <em>Blastococcus</em>, <em>Hygrocybe</em>) and altered the composition and increased the abundance of several metabolites with predicted bioactivity including nutrients, signaling molecules, and antimicrobials (e.g., xanthosine 5′-phosphate, 13-hydroxyoctadecadienoic acid, and neomycin B). As expected, increased abundance in rhizosphere metabolites predicted as nutrients and signaling molecules were associated with enhanced abundance of microbial taxa in plant belowground compartments (e.g., <em>Thermomyces</em>), while increased abundance of metabolites predicted as antimicrobials had the opposite effect on the abundance of belowground-derived microbial taxa (e.g., <em>Zymoseptoria</em>). Our study highlights the key role of <em>Epichloë</em> in shaping the plant belowground microbiota and shows that endophyte-mediated changes in microbial abundance were associated with altered abundance of bioactive rhizosphere metabolites.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101213"},"PeriodicalIF":3.5,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145363389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-21DOI: 10.1016/j.rhisph.2025.101215
Yang Chen , Weitao Wang , Zhanfeng Liu , Xianhui Zhu , Shuyin Li , Xiaoju Yang , Ziyue Jing , Wenqi Luo , Youshi Wang , Buhang Li , Yuanzhi Li , Chengjin Chu
Plant-mycorrhizal symbiosis is influenced both by the types of mycorrhizae (qualitatively) and by mycorrhizal colonization rates (quantitatively). However, research on the variation of arbuscular mycorrhiza colonization rates (AMCR) remains limited, particularly at the individual level, which could provide deeper insights into the impact of mycorrhizae on plant performance. We sampled the roots of 1223 individuals from 103 tree species within a 50-ha subtropical forest plot in southern China and measured their individual-level AMCR. Using multivariate beta-regression analyses and piecewise structural equation models, we investigated how various biotic and abiotic factors jointly influence AMCR and quantified the relative importance of these factors. Our investigation revealed substantial individual-level variation in AMCR within the study plot. Among the factors examined, biotic factors, particularly neighboring effects (e.g., conspecific density, phylogenetic diversity), exerting a stronger influence than abiotic factors. Soil nutrient-based resource diversity (RD) had no direct effect on AMCR. It influenced AMCR only indirectly by altering plant community composition. These findings suggest the complexity of AMCR variation within natural forests, highlighting the potential role of interactions between biotic and abiotic factors in mediating individual-level AMCR. Our study provides a solid foundation for further investigation into the relationship between AMCR, key aspects of plant demographic performance, and other ecological processes.
{"title":"Biotic interactions outweigh abiotic factors in driving individual-level variation in arbuscular mycorrhizal colonization in a subtropical forest","authors":"Yang Chen , Weitao Wang , Zhanfeng Liu , Xianhui Zhu , Shuyin Li , Xiaoju Yang , Ziyue Jing , Wenqi Luo , Youshi Wang , Buhang Li , Yuanzhi Li , Chengjin Chu","doi":"10.1016/j.rhisph.2025.101215","DOIUrl":"10.1016/j.rhisph.2025.101215","url":null,"abstract":"<div><div>Plant-mycorrhizal symbiosis is influenced both by the types of mycorrhizae (qualitatively) and by mycorrhizal colonization rates (quantitatively). However, research on the variation of arbuscular mycorrhiza colonization rates (AMCR) remains limited, particularly at the individual level, which could provide deeper insights into the impact of mycorrhizae on plant performance. We sampled the roots of 1223 individuals from 103 tree species within a 50-ha subtropical forest plot in southern China and measured their individual-level AMCR. Using multivariate beta-regression analyses and piecewise structural equation models, we investigated how various biotic and abiotic factors jointly influence AMCR and quantified the relative importance of these factors. Our investigation revealed substantial individual-level variation in AMCR within the study plot. Among the factors examined, biotic factors, particularly neighboring effects (e.g., conspecific density, phylogenetic diversity), exerting a stronger influence than abiotic factors. Soil nutrient-based resource diversity (RD) had no direct effect on AMCR. It influenced AMCR only indirectly by altering plant community composition. These findings suggest the complexity of AMCR variation within natural forests, highlighting the potential role of interactions between biotic and abiotic factors in mediating individual-level AMCR. Our study provides a solid foundation for further investigation into the relationship between AMCR, key aspects of plant demographic performance, and other ecological processes.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101215"},"PeriodicalIF":3.5,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145416536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-18DOI: 10.1016/j.rhisph.2025.101190
Tamara Valenzuela , Jacquelinne J. Acuña , Haroldo Salvo , Roland Bol , Angela Sessitsch , Milko A. Jorquera
Plant growth–promoting bacteria (PGPB) are widely investigated as tools to mitigate the effects of abiotic stresses in crops; however, their effectiveness under field conditions is still highly variable and sometimes controversial. Consequently, systematic reviews represent a valuable tool for addressing scientific and biotechnological questions. Here, we used the PRISMA guidelines and Scopus database to formulate and answer four relevant questions concerning methodologies and modes of action of PGPB on plants under abiotic stresses. Based on a set of 212 PGPB articles published between 2017 and 2023, our results revealed that PGPB are mostly applied single strain liquid inoculants on seeds (particularly cereals) and typically tested under controlled conditions (growth chamber and greenhouse). Our results also revealed that plant parameters (e.g., physiology and photosynthetic pigments) were typically measured as indicators of the effectiveness of PGPB. In contrast, few studies have investigated the application of PGPB in planta (e.g., germination or flowering stage) under field conditions. The most representative genera of PGPB studied are Bacillus, Pseudomonas and Enterobacter; however, a wide diversity of PGPB taxa (∼60) were also identified as potential PGPB. The main stress conditions to be alleviated by PGPB include drought, salinity and metal toxicity, using diverse action mechanisms, including 1–aminocyclopropane–1–carboxylic acid deaminase activity, tryptophane-induced auxin production, and phosphorus solubilization. In general, our review points to gaps in the adoption of standardized protocols for testing PGPB, universal indicators of efficiency, and the validation of application of a high diversity of PGPB taxa particularly at field level.
{"title":"Systematic review reveals gaps in standardized protocol to determine efficacy of PGPB use in plants grown under abiotic stress conditions at the field level","authors":"Tamara Valenzuela , Jacquelinne J. Acuña , Haroldo Salvo , Roland Bol , Angela Sessitsch , Milko A. Jorquera","doi":"10.1016/j.rhisph.2025.101190","DOIUrl":"10.1016/j.rhisph.2025.101190","url":null,"abstract":"<div><div>Plant growth–promoting bacteria (PGPB) are widely investigated as tools to mitigate the effects of abiotic stresses in crops; however, their effectiveness under field conditions is still highly variable and sometimes controversial. Consequently, systematic reviews represent a valuable tool for addressing scientific and biotechnological questions. Here, we used the PRISMA guidelines and Scopus database to formulate and answer four relevant questions concerning methodologies and modes of action of PGPB on plants under abiotic stresses. Based on a set of 212 PGPB articles published between 2017 and 2023, our results revealed that PGPB are mostly applied single strain liquid inoculants on seeds (particularly cereals) and typically tested under controlled conditions (growth chamber and greenhouse). Our results also revealed that plant parameters (<em>e.g.</em>, physiology and photosynthetic pigments) were typically measured as indicators of the effectiveness of PGPB. In contrast, few studies have investigated the application of PGPB <em>in planta</em> (<em>e.g.</em>, germination or flowering stage) under field conditions. The most representative genera of PGPB studied are <em>Bacillus</em>, <em>Pseudomonas</em> and <em>Enterobacter</em>; however, a wide diversity of PGPB taxa (∼60) were also identified as potential PGPB. The main stress conditions to be alleviated by PGPB include drought, salinity and metal toxicity, using diverse action mechanisms, including 1–aminocyclopropane–1–carboxylic acid deaminase activity, tryptophane-induced auxin production, and phosphorus solubilization. In general, our review points to gaps in the adoption of standardized protocols for testing PGPB, universal indicators of efficiency, and the validation of application of a high diversity of PGPB taxa particularly at field level.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101190"},"PeriodicalIF":3.5,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145363392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-15DOI: 10.1016/j.rhisph.2025.101211
Yuxuan Huang , Fei Wu , Xingping Liu , Linping Zhang , Bo Chen , Shaohua Huang , Jia Cao , Xin You
Camellia oleifera is a widely cultivated woody oil crop in southern China, where low phosphorus (P) availability in soils constrains its productivity. In this study, we investigated how genotype-specific differences in root-associated microbial communities and metabolites influence rhizosphere P availability. Using two contrasting cultivars, P-efficient CL40 and P-inefficient CL3, we integrated untargeted metabolomics and amplicon sequencing to characterize root and rhizosphere microbial and metabolic profiles under field conditions. CL40 enriched beneficial microbial taxa, including Actinobacteriota, Glomeromycota, and Acidothermus, and accumulated metabolites related to lipid metabolism, organic acids, and antioxidants (e.g., neodiosmin, nicotinic acid, triacetic acid), which were positively correlated with microbial abundance and increased soil available phosphorus (AP). In contrast, CL3 exhibited a higher microbial α-diversity and upregulated stress-associated flavonoids and chalcones, suggesting a defensive rather than nutrient-acquisitive strategy. Soil pH was significantly correlated with microbial community structure, metabolite profiles, and AP levels, underscoring its role as a key environmental driver. These findings highlight the importance of genotype-driven metabolite–microbiome interactions in shaping rhizosphere P dynamics and provide a basis for microbiome-informed soil management and cultivar selection in C. oleifera production.
{"title":"Genotypic differences in root-associated microbiomes and metabolites regulate soil available phosphorus in Camellia oleifera","authors":"Yuxuan Huang , Fei Wu , Xingping Liu , Linping Zhang , Bo Chen , Shaohua Huang , Jia Cao , Xin You","doi":"10.1016/j.rhisph.2025.101211","DOIUrl":"10.1016/j.rhisph.2025.101211","url":null,"abstract":"<div><div><em>Camellia oleifera</em> is a widely cultivated woody oil crop in southern China, where low phosphorus (P) availability in soils constrains its productivity. In this study, we investigated how genotype-specific differences in root-associated microbial communities and metabolites influence rhizosphere P availability. Using two contrasting cultivars, P-efficient CL40 and P-inefficient CL3, we integrated untargeted metabolomics and amplicon sequencing to characterize root and rhizosphere microbial and metabolic profiles under field conditions. CL40 enriched beneficial microbial taxa, including Actinobacteriota, Glomeromycota, and Acidothermus, and accumulated metabolites related to lipid metabolism, organic acids, and antioxidants (e.g., neodiosmin, nicotinic acid, triacetic acid), which were positively correlated with microbial abundance and increased soil available phosphorus (AP). In contrast, CL3 exhibited a higher microbial α-diversity and upregulated stress-associated flavonoids and chalcones, suggesting a defensive rather than nutrient-acquisitive strategy. Soil pH was significantly correlated with microbial community structure, metabolite profiles, and AP levels, underscoring its role as a key environmental driver. These findings highlight the importance of genotype-driven metabolite–microbiome interactions in shaping rhizosphere P dynamics and provide a basis for microbiome-informed soil management and cultivar selection in <em>C. oleifera</em> production.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101211"},"PeriodicalIF":3.5,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145578875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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