Rhizosphere最新文献_第6页

Rhizobacteria of native aquatic macrophytes in coal mining subsidence ponds are shaped by compartment niche differentiation 煤矿沉陷塘原生水生植物的根菌群是由隔间生态位分化形成的

IF 3.5 3区生物学 Q1 PLANT SCIENCES

Rhizosphere

Pub Date : 2026-03-01 Epub Date: 2025-11-19 DOI: 10.1016/j.rhisph.2025.101235

Ting Gao , Songbao Feng , Sanping Yu , Xianyang Shi , Jin Cheng

Aquatic macrophytes have evolved adaptive mechanisms to thrive in the heterogeneous environments of coal mining subsidence areas. While such mechanisms provide practical solutions for ecological restoration in mining areas, general principles driving community assembly and the potential functions of bacterial microbiotas associated with these plants remain poorly characterized. In this study, we employed Illumina-based sequencing approaches to systematically characterize the bacterial microbiota in two root-associated compartments (rhizosphere and root endosphere) of four dominant macrophyte species (common reed, narrow-leaf cattail, short-lived flatsedge, and tuber bulrush) colonizing contrasting substrates (sediment and coal gangue). Our analyses revealed that the characteristics of root-associated bacterial communities were determined primarily by root compartment rather than by macrophyte species or plant habitat. Rhizospheric and root endophytic communities differed significantly in composition, network complexity, and keystone species, confirming a compartmentalized niche-assembly pattern. Functional predictions demonstrated metabolic niche partitioning between compartments, with distinct biogeochemical pathways enriched in each microenvironment. Specifically, rhizosphere communities were enriched in anaerobic respiration, nitrogen cycling, lignin degradation, and anoxygenic photosynthesis; meanwhile, endospheric microbiota were enriched in dark hydrogen oxidation, ureolysis, methylotrophy, and fumarate respiration. This study sheds new light on the assembly and functional roles of root-associated bacterial communities in coal mining subsidence ponds, supporting future ecological restoration efforts by identifying key functional bacteria.

水生植物已经进化出适应机制，在煤矿沉陷区异质环境中茁壮成长。虽然这些机制为矿区的生态恢复提供了切实可行的解决方案，但驱动群落组装的一般原理以及与这些植物相关的细菌微生物群的潜在功能仍不清楚。在这项研究中，我们采用基于illumina的测序方法，系统地表征了四种优势大型植物物种（芦苇、窄叶香蒲、短寿扁草和块茎芦苇）在两个根相关隔间（根际和根内圈）中定殖在不同基质（沉积物和煤矸石）中的细菌微生物群。我们的分析表明，根相关细菌群落的特征主要由根室决定，而不是由大型植物种类或植物栖息地决定。根际和根内生群落在组成、网络复杂性和关键物种方面存在显著差异，证实了分区的生态位组合模式。功能预测表明，在每个微环境中，不同的生物地球化学途径丰富的隔间之间的代谢生态位分配。具体而言，根际群落在厌氧呼吸、氮循环、木质素降解和无氧光合作用中富集；同时，在暗氢氧化、尿素溶解、甲基化和富马酸呼吸过程中，内圈微生物群富集。该研究揭示了煤矿沉陷池中与根相关的细菌群落的组成和功能作用，通过识别关键功能细菌，为未来的生态修复工作提供支持。

{"title":"Rhizobacteria of native aquatic macrophytes in coal mining subsidence ponds are shaped by compartment niche differentiation","authors":"Ting Gao , Songbao Feng , Sanping Yu , Xianyang Shi , Jin Cheng","doi":"10.1016/j.rhisph.2025.101235","DOIUrl":"10.1016/j.rhisph.2025.101235","url":null,"abstract":"<div><div>Aquatic macrophytes have evolved adaptive mechanisms to thrive in the heterogeneous environments of coal mining subsidence areas. While such mechanisms provide practical solutions for ecological restoration in mining areas, general principles driving community assembly and the potential functions of bacterial microbiotas associated with these plants remain poorly characterized. In this study, we employed Illumina-based sequencing approaches to systematically characterize the bacterial microbiota in two root-associated compartments (rhizosphere and root endosphere) of four dominant macrophyte species (common reed, narrow-leaf cattail, short-lived flatsedge, and tuber bulrush) colonizing contrasting substrates (sediment and coal gangue). Our analyses revealed that the characteristics of root-associated bacterial communities were determined primarily by root compartment rather than by macrophyte species or plant habitat. Rhizospheric and root endophytic communities differed significantly in composition, network complexity, and keystone species, confirming a compartmentalized niche-assembly pattern. Functional predictions demonstrated metabolic niche partitioning between compartments, with distinct biogeochemical pathways enriched in each microenvironment. Specifically, rhizosphere communities were enriched in anaerobic respiration, nitrogen cycling, lignin degradation, and anoxygenic photosynthesis; meanwhile, endospheric microbiota were enriched in dark hydrogen oxidation, ureolysis, methylotrophy, and fumarate respiration. This study sheds new light on the assembly and functional roles of root-associated bacterial communities in coal mining subsidence ponds, supporting future ecological restoration efforts by identifying key functional bacteria.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"37 ","pages":"Article 101235"},"PeriodicalIF":3.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749558","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}

引用次数: 0

Root-microbiome signaling networks under climate stress: Mechanistic insights and rhizosphere engineering opportunities 气候胁迫下的根微生物信号网络：机制见解和根际工程机会

IF 3.5 3区生物学 Q1 PLANT SCIENCES

Rhizosphere

Pub Date : 2026-03-01 Epub Date: 2026-01-10 DOI: 10.1016/j.rhisph.2026.101271

Sipra Mohapatra , Vishal Johar , Hina Upadhyay , Anand Kumar , Premdeep , Prayasi Nayak , Mouli Paul , Swagatika Babu , Rahul Pradhan , Pragnyashree Mishra , Himanshu Saini

Climate change is reshaping the structure and function of rhizosphere microbiomes, with profound implications for plant health, nutrient acquisition, and stress tolerance. Emerging evidence reveals that root-microbiome interactions are governed by intricate signaling networks involving root exudates, microbial metabolites, hormonal crosstalk, and redox-mediated pathways. These signals dynamically modulate microbial recruitment, functional assembly, and stress-induced shifts in community stability. This review synthesizes cutting-edge mechanistic insights into how climate stressors including drought, heat, salinity, and elevated CO₂ alter biochemical communication between roots and microbes. We highlight advances in multi-omics, isotope tracing, spatial metabolomics, and high-resolution imaging that are transforming our understanding of rhizosphere signaling landscapes. Finally, we evaluate emerging strategies for rhizosphere engineering, including microbiome-informed breeding, targeted exudate modulation, synthetic communities, and real-time microbiome monitoring tools. By integrating mechanistic and applied perspectives, this review outlines a roadmap for leveraging root-microbiome signaling networks to build climate-resilient, low-input agricultural systems.

气候变化正在重塑根际微生物群的结构和功能，对植物健康、养分获取和抗逆性具有深远的影响。新出现的证据表明，根与微生物的相互作用是由复杂的信号网络控制的，包括根分泌物、微生物代谢物、激素串扰和氧化还原介导的途径。这些信号动态调节微生物招募、功能组装和应激诱导的群落稳定性变化。这篇综述综合了包括干旱、高温、盐度和二氧化碳升高在内的气候压力因素如何改变根和微生物之间的生化通讯的前沿机制见解。我们强调了多组学、同位素示踪、空间代谢组学和高分辨率成像的进展，这些进展正在改变我们对根际信号景观的理解。最后，我们评估了根际工程的新兴策略，包括微生物群信息育种、有针对性的分泌物调节、合成群落和实时微生物群监测工具。通过整合机理和应用观点，本文概述了利用根系微生物信号网络构建气候适应型低投入农业系统的路线图。

{"title":"Root-microbiome signaling networks under climate stress: Mechanistic insights and rhizosphere engineering opportunities","authors":"Sipra Mohapatra , Vishal Johar , Hina Upadhyay , Anand Kumar , Premdeep , Prayasi Nayak , Mouli Paul , Swagatika Babu , Rahul Pradhan , Pragnyashree Mishra , Himanshu Saini","doi":"10.1016/j.rhisph.2026.101271","DOIUrl":"10.1016/j.rhisph.2026.101271","url":null,"abstract":"<div><div>Climate change is reshaping the structure and function of rhizosphere microbiomes, with profound implications for plant health, nutrient acquisition, and stress tolerance. Emerging evidence reveals that root-microbiome interactions are governed by intricate signaling networks involving root exudates, microbial metabolites, hormonal crosstalk, and redox-mediated pathways. These signals dynamically modulate microbial recruitment, functional assembly, and stress-induced shifts in community stability. This review synthesizes cutting-edge mechanistic insights into how climate stressors including drought, heat, salinity, and elevated CO<sub>2</sub> alter biochemical communication between roots and microbes. We highlight advances in multi-omics, isotope tracing, spatial metabolomics, and high-resolution imaging that are transforming our understanding of rhizosphere signaling landscapes. Finally, we evaluate emerging strategies for rhizosphere engineering, including microbiome-informed breeding, targeted exudate modulation, synthetic communities, and real-time microbiome monitoring tools. By integrating mechanistic and applied perspectives, this review outlines a roadmap for leveraging root-microbiome signaling networks to build climate-resilient, low-input agricultural systems.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"37 ","pages":"Article 101271"},"PeriodicalIF":3.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977509","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}

引用次数: 0

Continuous cropping obstacle in Ganoderma lucidum is driven by antagonistic bacterial enrichment and soil bacterial community imbalance 灵芝连作障碍是由拮抗菌富集和土壤细菌群落失衡驱动的

IF 3.5 3区生物学 Q1 PLANT SCIENCES

Rhizosphere

Pub Date : 2026-03-01 Epub Date: 2026-01-17 DOI: 10.1016/j.rhisph.2026.101267

Xiaomeng Lv, Xiaofang He, Yuting Zhuang, Jinxiang Zhang, Jianhui Chen, Ying Zhou, Senxiang Xie, Lixin Liang, Liping Deng, Xiaoping Wu

Ganoderma lucidum is a valuable medicinal mushroom used extensively in traditional medicine and modern health industries. Continuous cropping often alters soil microbial communities, leading to continuous cropping obstacles that limit sustainable production. Although fungal diversity has been extensively studied, bacterial dynamics and their functional roles remain less understood. Here, we combined bacterial isolation and identification, third-generation full-length 16S rDNA amplicon sequencing, and confrontation assays to systematically investigate soil bacterial communities before and after G. lucidum cultivation. Significant changes in microbial richness, diversity, and composition were observed with notable shifts in Proteobacteria, Firmicutes, and Acidobacteria. Importantly, we identified key bacterial species, including Bacillus velezensis, B. subtilis, B. amyloliquefaciens, Streptoverticillium reticulum, and Paenibacillus mucilaginosus, that strongly inhibited G. lucidum mycelial growth, highlighting their potential role in continuous cropping obstacles. This study provides the first integrative framework linking species-level bacterial dynamics to continuous cropping barriers in G. lucidum, offering a theoretical basis for targeted microbial management in sustainable cultivation.

灵芝是一种被广泛应用于传统医药和现代保健产业的珍贵药用蘑菇。连作经常改变土壤微生物群落，导致连作障碍，限制可持续生产。尽管真菌多样性已被广泛研究，但细菌动力学及其功能作用仍然知之甚少。本研究采用细菌分离鉴定、第三代16S rDNA全长扩增子测序和对抗试验相结合的方法，系统研究了绿植前后土壤细菌群落。微生物丰富度、多样性和组成发生了显著变化，变形菌门、厚壁菌门和酸性菌门发生了显著变化。重要的是，我们发现了一些关键的细菌物种，包括velezensis芽孢杆菌、枯草芽孢杆菌、解淀粉芽孢杆菌、网状链杆菌和粘液芽孢杆菌，它们强烈地抑制了G. lucidum菌丝体的生长，突出了它们在连作障碍中的潜在作用。本研究提供了第一个将种属水平的细菌动态与绿豆连作障碍联系起来的综合框架，为可持续栽培中有针对性的微生物管理提供了理论依据。

{"title":"Continuous cropping obstacle in Ganoderma lucidum is driven by antagonistic bacterial enrichment and soil bacterial community imbalance","authors":"Xiaomeng Lv, Xiaofang He, Yuting Zhuang, Jinxiang Zhang, Jianhui Chen, Ying Zhou, Senxiang Xie, Lixin Liang, Liping Deng, Xiaoping Wu","doi":"10.1016/j.rhisph.2026.101267","DOIUrl":"10.1016/j.rhisph.2026.101267","url":null,"abstract":"<div><div><em>Ganoderma lucidum</em> is a valuable medicinal mushroom used extensively in traditional medicine and modern health industries. Continuous cropping often alters soil microbial communities, leading to continuous cropping obstacles that limit sustainable production. Although fungal diversity has been extensively studied, bacterial dynamics and their functional roles remain less understood. Here, we combined bacterial isolation and identification, third-generation full-length 16S rDNA amplicon sequencing, and confrontation assays to systematically investigate soil bacterial communities before and after <em>G. lucidum</em> cultivation. Significant changes in microbial richness, diversity, and composition were observed with notable shifts in Proteobacteria, Firmicutes, and Acidobacteria. Importantly, we identified key bacterial species, including <em>Bacillus velezensis</em>, <em>B. subtilis</em>, <em>B. amyloliquefaciens</em>, <em>Streptoverticillium reticulum</em>, and <em>Paenibacillus mucilaginosus</em>, that strongly inhibited <em>G. lucidum</em> mycelial growth, highlighting their potential role in continuous cropping obstacles. This study provides the first integrative framework linking species-level bacterial dynamics to continuous cropping barriers in <em>G. lucidum</em>, offering a theoretical basis for targeted microbial management in sustainable cultivation.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"37 ","pages":"Article 101267"},"PeriodicalIF":3.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146037896","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}

引用次数: 0

Predictive modeling of soil pathogenic microorganisms in diseased plants: A comparative machine learning approach 患病植物中土壤病原微生物的预测建模：一种比较机器学习方法

IF 3.5 3区生物学 Q1 PLANT SCIENCES

Rhizosphere

Pub Date : 2026-03-01 Epub Date: 2026-01-30 DOI: 10.1016/j.rhisph.2026.101282

Meriem Benbernou , Meriem Kenzi , Hadjer Khelifa , Hadja Fatima Tbahriti

Background

Soil, borne pathogenic microorganisms are major threats to plant health and the whole agricultural system. The need for early and correct identification of the most pathogens cannot be overemphasized as it is the only way for directed disease management strategies.

Objective

This research employs maching learning methods to identify the primary pathogen in one diseased plant based on soil microbiome data gathered from the SciSpace literature platforms.

Methods

We studied 5000 samples collected systematically from the SciSpace literature platforms, including soil physicochemical properties, plant health indicators, and microbiome composition. We experimented with six machine learning models i.e. Light Gradient Boosting Machine (LightGBM), XGBoost, Random Forest, Support Vector Machine, Deep Neural Network, and Logistic Regression to find which one performed better and the performance of the models was measured through AUC, ROC, precision, recall, F1, score, and cross-validation methods.

Results

LightGBM achieved the best performance, with an AUC of 0.94, and outperformed the deep learning method (AUC: 0.87) and the other traditional models. Soil pH, organic matter content, and moisture levels were the most predictive variables, according to feature importance analysis. SHAP value analysis provided clear insights into pathogen-specific risk factors.

Conclusions

When working with medium-sized tabular soil microbiome data, gradient boosting methods, especially LightGBM, are the best performers for prediction and offer better interpretability than deep learning architectures. Such a system is a powerful tool that can be used in precision agriculture and first disease intervention.

土壤源性病原微生物是植物健康和整个农业系统的主要威胁。早期和正确识别大多数病原体的必要性再怎么强调也不为过，因为这是制定定向疾病管理战略的唯一途径。目的利用科学空间文献平台收集的土壤微生物组数据，采用机器学习方法鉴定一株病害植物的主要病原菌。方法系统分析了从中国科学院科学院文献平台收集的5000份样品，包括土壤理化性质、植物健康指标和微生物组组成。我们实验了6种机器学习模型，即光梯度增强机（LightGBM）、XGBoost、随机森林、支持向量机、深度神经网络和逻辑回归，以找出哪一种模型表现更好，并通过AUC、ROC、精度、召回率、F1、分数和交叉验证方法来衡量模型的性能。结果slightgbm获得了最佳性能，AUC为0.94，优于深度学习方法（AUC: 0.87）和其他传统模型。根据特征重要性分析，土壤pH值、有机质含量和水分水平是最具预测性的变量。SHAP值分析提供了对病原体特异性危险因素的清晰见解。当处理中等规模的表格土壤微生物组数据时，梯度增强方法，特别是LightGBM，在预测方面表现最好，并且比深度学习架构提供更好的可解释性。该系统是一种强大的工具，可用于精准农业和首次疾病干预。

{"title":"Predictive modeling of soil pathogenic microorganisms in diseased plants: A comparative machine learning approach","authors":"Meriem Benbernou , Meriem Kenzi , Hadjer Khelifa , Hadja Fatima Tbahriti","doi":"10.1016/j.rhisph.2026.101282","DOIUrl":"10.1016/j.rhisph.2026.101282","url":null,"abstract":"<div><h3>Background</h3><div>Soil, borne pathogenic microorganisms are major threats to plant health and the whole agricultural system. The need for early and correct identification of the most pathogens cannot be overemphasized as it is the only way for directed disease management strategies.</div></div><div><h3>Objective</h3><div>This research employs maching learning methods to identify the primary pathogen in one diseased plant based on soil microbiome data gathered from the SciSpace literature platforms.</div></div><div><h3>Methods</h3><div>We studied 5000 samples collected systematically from the SciSpace literature platforms, including soil physicochemical properties, plant health indicators, and microbiome composition. We experimented with six machine learning models i.e. Light Gradient Boosting Machine (LightGBM), XGBoost, Random Forest, Support Vector Machine, Deep Neural Network, and Logistic Regression to find which one performed better and the performance of the models was measured through AUC, ROC, precision, recall, F1, score, and cross-validation methods.</div></div><div><h3>Results</h3><div>LightGBM achieved the best performance, with an AUC of 0.94, and outperformed the deep learning method (AUC: 0.87) and the other traditional models. Soil pH, organic matter content, and moisture levels were the most predictive variables, according to feature importance analysis. SHAP value analysis provided clear insights into pathogen-specific risk factors.</div></div><div><h3>Conclusions</h3><div>When working with medium-sized tabular soil microbiome data, gradient boosting methods, especially LightGBM, are the best performers for prediction and offer better interpretability than deep learning architectures. Such a system is a powerful tool that can be used in precision agriculture and first disease intervention.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"37 ","pages":"Article 101282"},"PeriodicalIF":3.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146188505","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}

引用次数: 0

Key processes of iron acquisition in strategy I plants: Assessment by mechanistic modelling 战略I工厂铁获取的关键过程：机械模型评估

IF 3.5 3区生物学 Q1 PLANT SCIENCES

Rhizosphere

Pub Date : 2026-03-01 Epub Date: 2026-01-23 DOI: 10.1016/j.rhisph.2026.101279

Thibault Sterckeman

Key mechanisms of iron uptake as highlighted by recent modelling works are reviewed. Calculations indicate that Fe²⁺ is often much more abundant than Fe³⁺ in soil solutions, contrarily to what is generally considered in the literature. However, mechanistic modelling of root Fe uptake shows that the concentrations of these ions are far below the levels required by plants. Furthermore, the acidification hypothetically triggered by iron deficiency is insufficient to increase their levels to the required extent. This confirms that AHA2, FRO2 and IRT1 evolved not only to process free ferric and ferrous ions, but also Fe-complexes with organic ligands. Numerical simulations show that aqueous dissociation of those Fe-complexes close to the root cell membrane is never quick enough to supply the root. Therefore, Fe complexes may dissociate at high speed after forming a transient ternary complex with a biotic ligand at the cell membrane near the AHA2-FRO2-IRT1 system. This catalyses Fe³⁺ reduction and internalisation of Fe²⁺. Moreover, a Fe ligand exuded by roots would be efficient only if it dissolves the soil iron hydroxides through a surface dissolution process much quicker than the aqueous dissolution. Simulations show that the mean concentration of Fe complexed by microbial siderophores in soils is sufficient to meet plant needs for iron, considering a moderate ‘shaping’ of the rhizosphere microflora and supposing that the roots are able to process the various types of complexes. Simulations also show that root absorption of intact Fe-complexes is as efficient as their processing by AHA2-FRO2-IRT1.

铁摄取的关键机制，强调了最近的建模工作进行了审查。计算表明，在土壤溶液中，Fe2+往往比Fe3+丰富得多，这与文献中普遍认为的相反。然而，根系铁吸收的机制模型表明，这些离子的浓度远远低于植物所需的水平。此外，假设由缺铁引发的酸化不足以将它们的水平提高到所需的程度。这证实了AHA2， FRO2和IRT1不仅可以处理游离铁离子和亚铁离子，还可以处理与有机配体的铁配合物。数值模拟表明，靠近根细胞膜的铁络合物的水解离速度永远不足以供应根。因此，Fe配合物在靠近AHA2-FRO2-IRT1体系的细胞膜上与生物配体形成瞬态三元配合物后可能会高速解离。这催化了Fe3+的还原和Fe2+的内化。此外，根渗出的铁配体只有在通过比水溶快得多的表面溶解过程溶解土壤铁氢氧化物时才有效。模拟表明，考虑到根际微生物群的适度“塑造”，并假设根能够处理各种类型的复合物，土壤中微生物铁载体络合的平均铁浓度足以满足植物对铁的需求。模拟还表明，完整铁配合物的根吸收效率与AHA2-FRO2-IRT1处理效率相当。

{"title":"Key processes of iron acquisition in strategy I plants: Assessment by mechanistic modelling","authors":"Thibault Sterckeman","doi":"10.1016/j.rhisph.2026.101279","DOIUrl":"10.1016/j.rhisph.2026.101279","url":null,"abstract":"<div><div>Key mechanisms of iron uptake as highlighted by recent modelling works are reviewed. Calculations indicate that Fe<sup>2+</sup> is often much more abundant than Fe<sup>3+</sup> in soil solutions, contrarily to what is generally considered in the literature. However, mechanistic modelling of root Fe uptake shows that the concentrations of these ions are far below the levels required by plants. Furthermore, the acidification hypothetically triggered by iron deficiency is insufficient to increase their levels to the required extent. This confirms that AHA2, FRO2 and IRT1 evolved not only to process free ferric and ferrous ions, but also Fe-complexes with organic ligands. Numerical simulations show that aqueous dissociation of those Fe-complexes close to the root cell membrane is never quick enough to supply the root. Therefore, Fe complexes may dissociate at high speed after forming a transient ternary complex with a biotic ligand at the cell membrane near the AHA2-FRO2-IRT1 system. This catalyses Fe<sup>3+</sup> reduction and internalisation of Fe<sup>2+</sup>. Moreover, a Fe ligand exuded by roots would be efficient only if it dissolves the soil iron hydroxides through a surface dissolution process much quicker than the aqueous dissolution. Simulations show that the mean concentration of Fe complexed by microbial siderophores in soils is sufficient to meet plant needs for iron, considering a moderate ‘shaping’ of the rhizosphere microflora and supposing that the roots are able to process the various types of complexes. Simulations also show that root absorption of intact Fe-complexes is as efficient as their processing by AHA2-FRO2-IRT1.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"37 ","pages":"Article 101279"},"PeriodicalIF":3.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146188498","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}

引用次数: 0

Shovelomics meets microbiomics: root phenotype-microbiome associations and links with maize yield under nitrogen limitation 土壤组学与微生物组学：氮限制下根系表型与微生物组的关联及其与玉米产量的联系

IF 3.5 3区生物学 Q1 PLANT SCIENCES

Rhizosphere

Pub Date : 2026-03-01 Epub Date: 2025-12-03 DOI: 10.1016/j.rhisph.2025.101241

Elena Giuliano , Jagdeep Singh Sidhu , Ivan Lopez-Valdivia , Rafaela Feola Conz , Cody Depew , Jonathan P. Lynch , Johan Six , Martin Hartmann , Tania Galindo-Castañeda

Improving crop nitrogen (N) uptake is essential for a more sustainable agriculture. Deploying resource-efficient root phenotypes, beneficial soil microbiomes and their interplay is a promising approach. To test the hypothesis that adaptive root phenotypes under N limitation associate to specific microbial taxa, we characterized 11 architectural and 13 anatomical root phenotypes, and associated rhizosphere prokaryotic and fungal communities across 16 field-grown maize (Zea mays L.) inbred lines under optimal and low N availability. While maize genotypes were not significant to the rhizosphere microbial diversity, the number of crown roots significantly affected fungal β-diversity under N limitation. Moreover, the relative abundance of 98 rhizosphere microbial taxa significantly correlated with individual root architectural or anatomical phenotypes in a N- and plant yield-specific way. Interestingly, a greater number of correlations was found under optimal than under low N availability. Our results suggest the importance of investigating root phenotypes as predictors of rhizosphere microbial communities in maize inbred lines. Moreover, maize root architecture and anatomy may associate with microbes more frequently under optimal than under suboptimal N conditions. The relative contribution of root phenotypes and specific microbial taxa to plant performance under N limitation deserves more attention in future research.

提高作物对氮的吸收对于实现更可持续的农业至关重要。利用资源高效的根系表型、有益的土壤微生物群及其相互作用是一种很有前途的方法。为了验证氮素限制下适应性根系表型与特定微生物类群相关的假设，我们对16个大田玉米（Zea mays L.）自交系在最佳和低氮素有效度条件下的11种结构型和13种解剖型根系表型以及相关根际原核生物和真菌群落进行了分析。玉米基因型对根际微生物多样性影响不显著，但在氮素限制下，冠根数量显著影响真菌β多样性。此外，98个根际微生物类群的相对丰度与单个根结构或解剖表型呈氮特异性和植物产量特异性显著相关。有趣的是，与低氮可用性相比，在最优条件下发现了更多的相关性。我们的结果表明，研究根系表型作为玉米自交系根际微生物群落预测因子的重要性。此外，玉米根系结构和解剖结构可能在最优氮条件下比在次优氮条件下更频繁地与微生物相关。氮素限制下根系表型和特定微生物类群对植物生产性能的相对贡献值得进一步研究。

{"title":"Shovelomics meets microbiomics: root phenotype-microbiome associations and links with maize yield under nitrogen limitation","authors":"Elena Giuliano , Jagdeep Singh Sidhu , Ivan Lopez-Valdivia , Rafaela Feola Conz , Cody Depew , Jonathan P. Lynch , Johan Six , Martin Hartmann , Tania Galindo-Castañeda","doi":"10.1016/j.rhisph.2025.101241","DOIUrl":"10.1016/j.rhisph.2025.101241","url":null,"abstract":"<div><div>Improving crop nitrogen (N) uptake is essential for a more sustainable agriculture. Deploying resource-efficient root phenotypes, beneficial soil microbiomes and their interplay is a promising approach. To test the hypothesis that adaptive root phenotypes under N limitation associate to specific microbial taxa, we characterized 11 architectural and 13 anatomical root phenotypes, and associated rhizosphere prokaryotic and fungal communities across 16 field-grown maize (<em>Zea mays</em> L.) inbred lines under optimal and low N availability. While maize genotypes were not significant to the rhizosphere microbial diversity, the number of crown roots significantly affected fungal β-diversity under N limitation. Moreover, the relative abundance of 98 rhizosphere microbial taxa significantly correlated with individual root architectural or anatomical phenotypes in a N- and plant yield-specific way. Interestingly, a greater number of correlations was found under optimal than under low N availability. Our results suggest the importance of investigating root phenotypes as predictors of rhizosphere microbial communities in maize inbred lines. Moreover, maize root architecture and anatomy may associate with microbes more frequently under optimal than under suboptimal N conditions. The relative contribution of root phenotypes and specific microbial taxa to plant performance under N limitation deserves more attention in future research.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"37 ","pages":"Article 101241"},"PeriodicalIF":3.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145798606","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}

引用次数: 0

Changes in rhizospheric bacterial communities of the Andean shrub Fabiana densa in response to salinity 安第斯灌木Fabiana densa根际细菌群落对盐度的响应

IF 3.5 3区生物学 Q1 PLANT SCIENCES

Rhizosphere

Pub Date : 2026-03-01 Epub Date: 2025-12-03 DOI: 10.1016/j.rhisph.2025.101244

Cinthia Copeticona-Callejas, Isabel Morales-Belpaire

The expansion of quinoa cultivation areas in the Bolivian Altiplano has diminished the populations of native plants which play key ecological roles in the harsh environments of the high Andes. The shrub Fabiana densa not only thrives under extreme climatic conditions and nutrient-poor soils, but also shows tolerance to salinity. Among these species, the shrub Fabiana densa not only thrives under extreme climatic conditions and nutrient-poor soils, but it also shows tolerance to salinity. Understanding the adaptation mechanisms of F. densa to salinity could help revegetate salt-affected areas. Rhizobacteria, among other factors, may contribute to salinity tolerance of F. densa. Therefore, we aimed to assess how salinity affects the rhizospheric bacterial communities of F. densa, as a first step toward identifying bacterial families potentially involved in saline stress alleviation. We irrigated F. densa plants with 0, 15, 25, and 40 mM NaCl solutions under controlled conditions. After ten and twenty weeks of exposure to the salinity treatments, DNA was extracted from rhizospheric soil. The bacterial communities were analyzed by high-throughput sequencing of the V4 region of the 16S rRNA gene. Both salinity level and exposure time had a strong effect on the composition of the rhizospheric bacterial communities. After 10 weeks of exposure, differential abundances of Cyclobacteriaceae and Shewanellaceae were positively related to salinity. After 20 weeks of exposure, salinity caused a decrease in the differential abundances of Aeromonaceae and Rhodocyclaceae but an increase for Rhizobiaceae. The changes in community composition with time of sampling suggest that besides exposure to salinity, other environmental factors influenced bacterial communities and should be taken into account in further studies.

玻利维亚高原藜麦种植区的扩大减少了本土植物的数量，而这些植物在安第斯山脉的恶劣环境中起着关键的生态作用。灌木Fabiana densa不仅在极端的气候条件和贫瘠的土壤中茁壮成长，而且具有耐盐性。在这些物种中，灌木Fabiana densa不仅在极端气候条件和营养贫乏的土壤下茁壮成长，而且还表现出对盐度的耐受性。了解密螺旋藻对盐度的适应机制，有助于盐渍化地区的植被恢复。根细菌和其他因素可能有助于F. densa耐盐性。因此，我们旨在评估盐度如何影响F. densa根际细菌群落，作为鉴定可能参与盐胁迫缓解的细菌家族的第一步。在控制条件下，分别用0、15、25和40 mM NaCl溶液灌溉密莲植株。在盐处理10周和20周后，从根际土壤中提取DNA。采用16S rRNA基因V4区高通量测序分析细菌群落。盐度水平和暴露时间对根际细菌群落的组成有较强的影响。暴露10周后，环菌科和雪瓦菌科的差异丰度与盐度呈正相关。暴露20周后，盐度降低了气单菌科和红霉素科的差异丰度，但增加了根瘤菌科的差异丰度。群落组成随采样时间的变化表明，除了暴露于盐度外，其他环境因素也影响细菌群落，应在进一步的研究中加以考虑。

{"title":"Changes in rhizospheric bacterial communities of the Andean shrub Fabiana densa in response to salinity","authors":"Cinthia Copeticona-Callejas, Isabel Morales-Belpaire","doi":"10.1016/j.rhisph.2025.101244","DOIUrl":"10.1016/j.rhisph.2025.101244","url":null,"abstract":"<div><div>The expansion of quinoa cultivation areas in the Bolivian Altiplano has diminished the populations of native plants which play key ecological roles in the harsh environments of the high Andes. The shrub <em>Fabiana densa</em> not only thrives under extreme climatic conditions and nutrient-poor soils, but also shows tolerance to salinity. Among these species, the shrub <em>Fabiana densa</em> not only thrives under extreme climatic conditions and nutrient-poor soils, but it also shows tolerance to salinity. Understanding the adaptation mechanisms of <em>F. densa</em> to salinity could help revegetate salt-affected areas. Rhizobacteria, among other factors, may contribute to salinity tolerance of <em>F. densa</em>. Therefore, we aimed to assess how salinity affects the rhizospheric bacterial communities of <em>F. densa</em>, as a first step toward identifying bacterial families potentially involved in saline stress alleviation. We irrigated <em>F. densa</em> plants with 0, 15, 25, and 40 mM NaCl solutions under controlled conditions. After ten and twenty weeks of exposure to the salinity treatments, DNA was extracted from rhizospheric soil. The bacterial communities were analyzed by high-throughput sequencing of the V4 region of the 16S rRNA gene. Both salinity level and exposure time had a strong effect on the composition of the rhizospheric bacterial communities. After 10 weeks of exposure, differential abundances of Cyclobacteriaceae and Shewanellaceae were positively related to salinity. After 20 weeks of exposure, salinity caused a decrease in the differential abundances of Aeromonaceae and Rhodocyclaceae but an increase for Rhizobiaceae. The changes in community composition with time of sampling suggest that besides exposure to salinity, other environmental factors influenced bacterial communities and should be taken into account in further studies.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"37 ","pages":"Article 101244"},"PeriodicalIF":3.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145939435","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}

引用次数: 0

Lanthanum chloride mitigates root-knot nematode infection on tomato plants through the ethylene pathway and antioxidant activity 氯化镧通过乙烯途径和抗氧化活性减轻番茄根系结线虫感染

IF 3.5 3区生物学 Q1 PLANT SCIENCES

Rhizosphere

Pub Date : 2026-03-01 Epub Date: 2026-02-20 DOI: 10.1016/j.rhisph.2026.101297

Ensieh Sadat Esmaeili, Majid Pedram, Mohammad Reza Atighi

Lanthanum, a rare earth element that is relatively common in the earth's crust. Its role in plant-pathogen interactions, particularly with root-knot nematodes, remains to be investigated. To address this lack of knowledge, tomato plants were treated with different concentrations of LaCl₃ (20 μM, 40 μM, 60 μM, and 100 μM), and the day after, they were inoculated with root-knot nematode. The highest reduction in the number of galls and nematodes was recorded when LaCl₃ was treated at a concentration of 100 μM, and the experiment was repeated twice independently. The time line monitoring of LaCl₃ effect on antioxidant activity at 24, 48 and 72 hours post-inoculation (hpi) (in five replicates) showed a significant rise in antioxidant activity, including catalase, peroxidase, and superoxide dismutase, and a decrease in H₂O₂ accumulation at 72 hpi, which was further investigated by analysis of expression of respective genes. Additionally, expression analysis of phytohormones signaling markers revealed a significant upregulation of ethylene marker upon LaCl₃ treatment. This was further validated by performing a susceptibility assay on plants deficient in ethylene accumulation, specifically ACC deaminase (ACCD) transgenic plants, which did not exhibit LaCl₃-mediated resistance. Finally, expression levels of calmodulin genes were assessed locally in galls formed by the root-knot nematode, and it was found that they were highly modulated. These expression changes highlight the diverse roles and importance of calmodulin genes in the early defense responses of tomato plants to infection by root-knot nematode.

镧，一种在地壳中相对常见的稀土元素。它在植物与病原体相互作用中的作用，特别是与根结线虫的相互作用，仍有待研究。为了解决这一问题，研究人员用不同浓度的LaCl3（20 μM、40 μM、60 μM和100 μM）处理番茄植株，并在第二天接种根结线虫。当LaCl3浓度为100 μM时，记录了虫瘿和线虫数量的最大减少，实验独立重复两次。对接种后24、48和72 h（5个重复）LaCl3对抗氧化活性的影响进行时间线监测，结果显示，接种后24、48和72 h （hpi）时，过氧化氢酶、过氧化物酶和超氧化物歧化酶的抗氧化活性显著升高，72 hpi时H2O2积累显著降低，并通过对相关基因的表达分析进一步研究。此外，植物激素信号标记的表达分析显示，LaCl3处理显著上调乙烯标记。通过对缺乏乙烯积累的植物，特别是ACC脱氨酶（ACCD）转基因植物的敏感性试验，进一步验证了这一点，这些植物没有表现出lacl3介导的抗性。最后，在根结线虫形成的瘿中局部评估了钙调素基因的表达水平，发现它们是高度调节的。这些表达变化凸显了钙调素基因在番茄根系对根结线虫感染的早期防御反应中的不同作用和重要性。

{"title":"Lanthanum chloride mitigates root-knot nematode infection on tomato plants through the ethylene pathway and antioxidant activity","authors":"Ensieh Sadat Esmaeili, Majid Pedram, Mohammad Reza Atighi","doi":"10.1016/j.rhisph.2026.101297","DOIUrl":"10.1016/j.rhisph.2026.101297","url":null,"abstract":"<div><div>Lanthanum, a rare earth element that is relatively common in the earth's crust. Its role in plant-pathogen interactions, particularly with root-knot nematodes, remains to be investigated. To address this lack of knowledge, tomato plants were treated with different concentrations of LaCl<sub>3</sub> (20 μM, 40 μM, 60 μM, and 100 μM), and the day after, they were inoculated with root-knot nematode. The highest reduction in the number of galls and nematodes was recorded when LaCl<sub>3</sub> was treated at a concentration of 100 μM, and the experiment was repeated twice independently. The time line monitoring of LaCl<sub>3</sub> effect on antioxidant activity at 24, 48 and 72 hours post-inoculation (hpi) (in five replicates) showed a significant rise in antioxidant activity, including catalase, peroxidase, and superoxide dismutase, and a decrease in H<sub>2</sub>O<sub>2</sub> accumulation at 72 hpi, which was further investigated by analysis of expression of respective genes. Additionally, expression analysis of phytohormones signaling markers revealed a significant upregulation of ethylene marker upon LaCl<sub>3</sub> treatment. This was further validated by performing a susceptibility assay on plants deficient in ethylene accumulation, specifically ACC deaminase (ACCD) transgenic plants, which did not exhibit LaCl<sub>3</sub>-mediated resistance. Finally, expression levels of calmodulin genes were assessed locally in galls formed by the root-knot nematode, and it was found that they were highly modulated. These expression changes highlight the diverse roles and importance of calmodulin genes in the early defense responses of tomato plants to infection by root-knot nematode.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"37 ","pages":"Article 101297"},"PeriodicalIF":3.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147395911","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}

引用次数: 0

The rhizosphere as a hidden pharmacy: A review of bioactive compounds from plant–soil interfaces 根际作为一种隐藏的药物：植物-土壤界面生物活性化合物的研究进展

IF 3.5 3区生物学 Q1 PLANT SCIENCES

Rhizosphere

Pub Date : 2026-03-01 Epub Date: 2026-02-26 DOI: 10.1016/j.rhisph.2026.101298

Tamer Ali Sweellum , Dia Soltan , Hosam A. El Adawy , Deyala M. Naguib , Hanan Gahin

The rhizosphere is a highly organized and chemically dynamic interface where plant roots, soil chemistry, and dense microbial communities interact to produce extraordinary metabolic diversity. This review critically synthesizes current evidence to show that rhizosphere-associated bacteria, actinomycetes, fungi, and root-derived metabolites are a reliable and mechanistically grounded source of bioactive compounds with antimicrobial, anticancer, immunomodulatory, and anti-inflammatory properties. We demonstrate that secondary metabolite production in the rhizosphere is tightly regulated by ecological drivers such as plant genotype-dependent root exudation, microbe-microbe competition, and abiotic stressors such as nutrient limitation, salinity, pH variation, and metal toxicity, all of which collectively activate cryptic biosynthetic gene clusters and diversify chemical scaffolds. This review describes how advances in targeted sampling, selective enrichment, co-cultivation, genome mining, metagenomics, metabolomics, and molecular networking have transformed the rhizosphere from an underexplored habitat to a rational platform for drug discovery. We conclude that ecological context-driven activation of microbial and plant metabolism is critical for discovering novel natural products, and that future drug discovery efforts should prioritize rhizosphere-informed culture tactics and multi-omics-guided prioritization pipelines. Collectively, the evidence points to the rhizosphere as a strategically significant and mechanistically known reservoir for next-generation treatments targeting antimicrobial resistance, cancer, immunological dysfunction, and emerging infectious illnesses.

根际是一个高度组织化和化学动态的界面，在这里植物根系、土壤化学和密集的微生物群落相互作用，产生非凡的代谢多样性。这篇综述综合了目前的证据，表明根际相关细菌、放线菌、真菌和根源代谢物是具有抗菌、抗癌、免疫调节和抗炎特性的生物活性化合物的可靠和机械基础来源。研究表明，根际次生代谢物的产生受到生态驱动因素的严格调控，如植物基因型依赖的根分泌、微生物-微生物竞争以及营养限制、盐度、pH变化和金属毒性等非生物胁迫因素，所有这些因素共同激活了隐藏的生物合成基因簇，并使化学支架多样化。本文介绍了靶向取样、选择性富集、共同培养、基因组挖掘、宏基因组学、代谢组学和分子网络等方面的进展如何将根际从一个未被开发的栖息地转变为一个合理的药物发现平台。我们得出结论，生态环境驱动的微生物和植物代谢激活对于发现新的天然产物至关重要，未来的药物发现工作应优先考虑根际知情培养策略和多组学指导的优先管道。总的来说，证据表明根际是一个具有战略意义和机制已知的针对抗菌素耐药性、癌症、免疫功能障碍和新发传染病的下一代治疗的储存库。

{"title":"The rhizosphere as a hidden pharmacy: A review of bioactive compounds from plant–soil interfaces","authors":"Tamer Ali Sweellum , Dia Soltan , Hosam A. El Adawy , Deyala M. Naguib , Hanan Gahin","doi":"10.1016/j.rhisph.2026.101298","DOIUrl":"10.1016/j.rhisph.2026.101298","url":null,"abstract":"<div><div>The rhizosphere is a highly organized and chemically dynamic interface where plant roots, soil chemistry, and dense microbial communities interact to produce extraordinary metabolic diversity. This review critically synthesizes current evidence to show that rhizosphere-associated bacteria, actinomycetes, fungi, and root-derived metabolites are a reliable and mechanistically grounded source of bioactive compounds with antimicrobial, anticancer, immunomodulatory, and anti-inflammatory properties. We demonstrate that secondary metabolite production in the rhizosphere is tightly regulated by ecological drivers such as plant genotype-dependent root exudation, microbe-microbe competition, and abiotic stressors such as nutrient limitation, salinity, pH variation, and metal toxicity, all of which collectively activate cryptic biosynthetic gene clusters and diversify chemical scaffolds. This review describes how advances in targeted sampling, selective enrichment, co-cultivation, genome mining, metagenomics, metabolomics, and molecular networking have transformed the rhizosphere from an underexplored habitat to a rational platform for drug discovery. We conclude that ecological context-driven activation of microbial and plant metabolism is critical for discovering novel natural products, and that future drug discovery efforts should prioritize rhizosphere-informed culture tactics and multi-omics-guided prioritization pipelines. Collectively, the evidence points to the rhizosphere as a strategically significant and mechanistically known reservoir for next-generation treatments targeting antimicrobial resistance, cancer, immunological dysfunction, and emerging infectious illnesses.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"37 ","pages":"Article 101298"},"PeriodicalIF":3.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147395912","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}

引用次数: 0

Long-term nutrient management regimes alter root exudation and rhizosphere fungal community structure in turmeric (Curcuma longa L.) 长期营养管理改变姜黄根系分泌物和根际真菌群落结构

IF 3.5 3区生物学 Q1 PLANT SCIENCES

Rhizosphere

Pub Date : 2026-03-01 Epub Date: 2026-01-06 DOI: 10.1016/j.rhisph.2026.101265

Anitta Abraham , C. Sarathambal , V. Srinivasan , C.K. Thankamani

Nutrient management practices profoundly influence rhizosphere microbial dynamics, which are central to soil fertility and sustainable crop production. However, too little consideration has been given to the taxonomic compositions of rhizosphere soil fungi and their interactions with root exudates under different fertilizer regimes in the turmeric cropping system. Here, we investigated the effects of long-term nutrient management regimes, organic (ONM), integrated (INM) and chemical (CNM) on the fungal community structure in turmeric (Curcuma longa L.), rhizosphere, as well as their relationship with soil properties and root exudation patterns. The results showed that nutrient management regimes clearly separated the fungal communities between the treatments. The ONM treatment supported a higher abundance and diversity of beneficial fungal taxa, including Glomeraceae, whereas INM and CNM were dominated by Psathyrellaceae and Spizellomycetaceae. Organic amendments had a significant effect on root exudate composition, the total abundance of sugars, alcohols, alkaloids and derivatives and amino acids and derivatives were high in ONM and INM treatments. NMDS and Mantel analysis revealed significant correlations of fungal diversity with soil pH, OC, P, Ca, Fe, and Zn, while K showed a negative relationship. Redundancy analysis identified soil pH, P, and root-exuded alcohols and amino acids and derivatives as key determinants of fungal community structure. Collectively, these findings demonstrate that biologically driven organic nutrient inputs enhance rhizosphere fungal diversity and improve soil health. Understanding these relationships provides valuable insights for developing nutrient management strategies that promote robust fungal communities and enable sustainable turmeric production systems through ecologically optimized fertilization practices.

养分管理实践深刻影响根际微生物动态，这是土壤肥力和可持续作物生产的核心。然而，对不同施肥制度下姜黄根际土壤真菌的分类组成及其与根系分泌物的相互作用研究甚少。本文研究了有机（ONM）、综合（INM）和化学（CNM）三种长期营养管理方式对姜黄根际真菌群落结构的影响，以及它们与土壤性质和根系渗出模式的关系。结果表明，不同的营养管理制度明显地分离了不同处理之间的真菌群落。ONM处理的有益真菌类群（包括Glomeraceae）的丰度和多样性更高，而INM和CNM处理的有益真菌类群以Psathyrellaceae和Spizellomycetaceae为主。有机改性对根分泌物组成有显著影响，ONM和INM处理的糖、醇类、生物碱及其衍生物、氨基酸及其衍生物的总丰度较高。NMDS和Mantel分析显示，真菌多样性与土壤pH、OC、P、Ca、Fe和Zn呈显著相关，与K呈负相关。冗余分析表明，土壤pH、磷、根部渗出的醇、氨基酸及其衍生物是真菌群落结构的关键决定因素。总的来说，这些发现表明，生物驱动的有机养分投入可以增强根际真菌多样性，改善土壤健康。了解这些关系为制定营养管理策略提供了有价值的见解，这些策略可以促进强健的真菌群落，并通过生态优化的施肥实践实现可持续的姜黄生产系统。

{"title":"Long-term nutrient management regimes alter root exudation and rhizosphere fungal community structure in turmeric (Curcuma longa L.)","authors":"Anitta Abraham , C. Sarathambal , V. Srinivasan , C.K. Thankamani","doi":"10.1016/j.rhisph.2026.101265","DOIUrl":"10.1016/j.rhisph.2026.101265","url":null,"abstract":"<div><div>Nutrient management practices profoundly influence rhizosphere microbial dynamics, which are central to soil fertility and sustainable crop production. However, too little consideration has been given to the taxonomic compositions of rhizosphere soil fungi and their interactions with root exudates under different fertilizer regimes in the turmeric cropping system. Here, we investigated the effects of long-term nutrient management regimes, organic (ONM), integrated (INM) and chemical (CNM) on the fungal community structure in turmeric (<em>Curcuma longa</em> L.), rhizosphere, as well as their relationship with soil properties and root exudation patterns. The results showed that nutrient management regimes clearly separated the fungal communities between the treatments. The ONM treatment supported a higher abundance and diversity of beneficial fungal taxa, including Glomeraceae, whereas INM and CNM were dominated by Psathyrellaceae and Spizellomycetaceae. Organic amendments had a significant effect on root exudate composition, the total abundance of sugars, alcohols, alkaloids and derivatives and amino acids and derivatives were high in ONM and INM treatments. NMDS and Mantel analysis revealed significant correlations of fungal diversity with soil pH, OC, P, Ca, Fe, and Zn, while K showed a negative relationship. Redundancy analysis identified soil pH, P, and root-exuded alcohols and amino acids and derivatives as key determinants of fungal community structure. Collectively, these findings demonstrate that biologically driven organic nutrient inputs enhance rhizosphere fungal diversity and improve soil health. Understanding these relationships provides valuable insights for developing nutrient management strategies that promote robust fungal communities and enable sustainable turmeric production systems through ecologically optimized fertilization practices.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"37 ","pages":"Article 101265"},"PeriodicalIF":3.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977454","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}

引用次数: 0