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}
Pub Date : 2025-10-15DOI: 10.1016/j.rhisph.2025.101210
Julia Sacharow , David Rosado-Porto , Santiago Quiroga , Stefan Ratering , Rita Geißler-Plaum , Bellinda Schneider , Sylvia Schnell
The application of plant growth-promoting rhizobacteria (PGPR) for inoculation of seeds, soils, and plants is becoming increasingly important due to the environmental impact of extensive use of chemical treatments in plant production. In this study, we investigated the effects of seed inoculation with Hartmannibacter diazotrophicus E19 on the bacterial, fungal and protist (Cercozoa) microbiome of winter wheat. The results showed that the inoculation of H. diazotrophicus E19 had no significant effect on the microbiome of roots, rhizosphere and in the bulk soil of winter wheat. Instead, the composition of the winter wheat microbiome appears to be more influenced by plant developmental stage and sampling material. Inoculation resulted only in minor effects, reflected by a limited number of ASVs showing positive or negative differential abundance compared to the controls like Chryseolinea, Symbiobacterium, Malbranchea, Hormiactis and Sandonidae. These findings confirm that the microbiome composition of winter wheat undergoes only minimal changes upon inoculation with H. diazotrophicus E19.
{"title":"Plant developmental stage, rather than inoculation with Hartmannibacter diazotrophicus, determines the composition of the bacterial, fungal, and protist microbiome in winter wheat","authors":"Julia Sacharow , David Rosado-Porto , Santiago Quiroga , Stefan Ratering , Rita Geißler-Plaum , Bellinda Schneider , Sylvia Schnell","doi":"10.1016/j.rhisph.2025.101210","DOIUrl":"10.1016/j.rhisph.2025.101210","url":null,"abstract":"<div><div>The application of plant growth-promoting rhizobacteria (PGPR) for inoculation of seeds, soils, and plants is becoming increasingly important due to the environmental impact of extensive use of chemical treatments in plant production. In this study, we investigated the effects of seed inoculation with <em>Hartmannibacter diazotrophicus</em> E19 on the bacterial, fungal and protist (Cercozoa) microbiome of winter wheat. The results showed that the inoculation of <em>H. diazotrophicus</em> E19 had no significant effect on the microbiome of roots, rhizosphere and in the bulk soil of winter wheat. Instead, the composition of the winter wheat microbiome appears to be more influenced by plant developmental stage and sampling material. Inoculation resulted only in minor effects, reflected by a limited number of ASVs showing positive or negative differential abundance compared to the controls like <em>Chryseolinea</em>, <em>Symbiobacterium</em>, <em>Malbranchea</em>, <em>Hormiactis</em> and Sandonidae. These findings confirm that the microbiome composition of winter wheat undergoes only minimal changes upon inoculation with <em>H. diazotrophicus</em> E19.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101210"},"PeriodicalIF":3.5,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145363391","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 : 2025-10-12DOI: 10.1016/j.rhisph.2025.101208
Lisa Petzoldt , Miriam Athmann , Timo Kautz
As biochemical ‘hotspot’ in subsoil of arable fields with high total carbon and nitrogen (Ct, Nt) contents, the biopore sheath is an attractive soil compartment for root growth. However, little is known about the modulating effects of either taprooted cover crops or anecic earthworms on the biopore sheath and root growth of following crops. A pot experiment was performed to measure Ct and Nt contents and homorhizous root growth of spring barley (Hordeum vulgare L.) in the sheaths (up to 8 mm distance from macropore) compared to the bulk soil (20–36 mm distance) in 2.5 year old biopores. The biopore types are artificial macropores formerly colonized by either a taprooted perennial crop (Cichorium intybus L.) (‘root type’) or an anecic earthworm (Lumbricus terrestris L.) fed with chicory leaves (‘worm type’). Additionally, δ13C and δ15N were analyzed in the sheaths and bulk soil as an indicator for the organic matter degradation. Indicating the accumulation of organic matter, fewer heavier isotopes were found towards macropore. That coincided with a tendentially (root type) or significantly (worm type) increasing Ct and Nt content, and an increasing root length density (log RLD) of spring barley in worm type. Both pore types facilitate root growth in comparison to the bulk soil, but with stronger gradient in worm type.
{"title":"Earthworm linings induce stronger lateral gradients of Ct, Nt, and cereal root growth from macropore towards bulk soil than root debris","authors":"Lisa Petzoldt , Miriam Athmann , Timo Kautz","doi":"10.1016/j.rhisph.2025.101208","DOIUrl":"10.1016/j.rhisph.2025.101208","url":null,"abstract":"<div><div>As biochemical ‘<em>hotspot</em>’ in subsoil of arable fields with high total carbon and nitrogen (C<sub>t</sub>, N<sub>t</sub>) contents, the biopore sheath is an attractive soil compartment for root growth. However, little is known about the modulating effects of either taprooted cover crops or anecic earthworms on the biopore sheath and root growth of following crops. A pot experiment was performed to measure C<sub>t</sub> and N<sub>t</sub> contents and homorhizous root growth of spring barley (<em>Hordeum vulgare</em> L.) in the sheaths (up to 8 mm distance from macropore) compared to the bulk soil (20–36 mm distance) in 2.5 year old biopores. The biopore types are artificial macropores formerly colonized by either a taprooted perennial crop (<em>Cichorium intybus</em> L.) (‘root type’) or an anecic earthworm (<em>Lumbricus terrestris</em> L.) fed with chicory leaves (‘worm type’). Additionally, δ<sup>13</sup>C and δ<sup>15</sup>N were analyzed in the sheaths and bulk soil as an indicator for the organic matter degradation. Indicating the accumulation of organic matter, fewer heavier isotopes were found towards macropore. That coincided with a tendentially (root type) or significantly (worm type) increasing C<sub>t</sub> and N<sub>t</sub> content, and an increasing root length density (log RLD) of spring barley in worm type. Both pore types facilitate root growth in comparison to the bulk soil, but with stronger gradient in worm type.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101208"},"PeriodicalIF":3.5,"publicationDate":"2025-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145363390","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 : 2025-10-10DOI: 10.1016/j.rhisph.2025.101205
Muhammad Ahtesham Aslam , Azra Seerat , Muhammad Younas , Linxin Li , Yachao Li , Pengfei Wu
Mycorrhizal fungi establishes primitive and indispensable symbiotic relationships with plant roots, significantly enhancing nutrient uptake, water absorption, and resistance to environmental stress resistance. In the forest ecosystem, especially in plantations of Chinese fir (Cunninghamia lanceolata), soil health can be effectively improved by such fungi, which has an advantageous effect on the growth of the trees and the resilience of the ecosystem. The large scale of monoculture Chinese fir plantations has prompted ecological issues such as biodiversity reduction, soil erosion, and multiple pest and disease risks. Improving mycorrhizal associations and introducing broad-leaved tree species in these plantations can alleviate such problems through the establishment of more ecologically diverse and resilient forests. This review aims to highlight the synergistic mechanism underlying the mycorrhizal fungus community and broad-leaved species in the sustainable management of Chinese fir plantations. This article also unveils the functioning of ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi in soil structuring, carbon storage, and microbial diversity. It uncovers the genetic studies of fungal genomics, including evolutionary factors intertwined with the functioning of mycorrhizal symbioses, such as the role of common mycorrhizal networks (CMNs) in interplant communication and resource allocation. Furthermore, the potential of AMF in increasing plants’ tolerance to abiotic stresses, such as drought and salinity, is discussed. The addition of mycorrhizal fungi and broad-leaved species is effective in combining with Chinese fir to construct sustainable forestry features. Future work should address the optimal management of those symbiotic interactions depending on the environment to meet ecological constraints and economic objectives.
{"title":"Lessons from mycorrhizal Synergies: Broad-Leaved trees Boost Chinese fir resilience","authors":"Muhammad Ahtesham Aslam , Azra Seerat , Muhammad Younas , Linxin Li , Yachao Li , Pengfei Wu","doi":"10.1016/j.rhisph.2025.101205","DOIUrl":"10.1016/j.rhisph.2025.101205","url":null,"abstract":"<div><div>Mycorrhizal fungi establishes primitive and indispensable symbiotic relationships with plant roots, significantly enhancing nutrient uptake, water absorption, and resistance to environmental stress resistance. In the forest ecosystem, especially in plantations of Chinese fir (<em>Cunninghamia lanceolata</em>), soil health can be effectively improved by such fungi, which has an advantageous effect on the growth of the trees and the resilience of the ecosystem. The large scale of monoculture Chinese fir plantations has prompted ecological issues such as biodiversity reduction, soil erosion, and multiple pest and disease risks. Improving mycorrhizal associations and introducing broad-leaved tree species in these plantations can alleviate such problems through the establishment of more ecologically diverse and resilient forests. This review aims to highlight the synergistic mechanism underlying the mycorrhizal fungus community and broad-leaved species in the sustainable management of Chinese fir plantations. This article also unveils the functioning of ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi in soil structuring, carbon storage, and microbial diversity. It uncovers the genetic studies of fungal genomics, including evolutionary factors intertwined with the functioning of mycorrhizal symbioses, such as the role of common mycorrhizal networks (CMNs) in interplant communication and resource allocation. Furthermore, the potential of AMF in increasing plants’ tolerance to abiotic stresses, such as drought and salinity, is discussed. The addition of mycorrhizal fungi and broad-leaved species is effective in combining with Chinese fir to construct sustainable forestry features. Future work should address the optimal management of those symbiotic interactions depending on the environment to meet ecological constraints and economic objectives.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101205"},"PeriodicalIF":3.5,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145363388","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 : 2025-10-09DOI: 10.1016/j.rhisph.2025.101199
Maria Clara Zerbinatti , Élida Moreira L. Santana , Marcela Fernanda S. Martins , Fábio Fernando Araújo , Lucas W. Mendes , Romário M. Costa , Ademir Sergio F. Araujo
Agricultural management systems, such as crop-livestock integration and fallow, affect differently soil properties, mainly biological parameters. This can drive the rhizosphere microbiome. In addition, methods of microbial inoculation can affect the rhizosphere. This study aims to investigate the effects of inoculating Bacillus subtilis under different methods (furrow, soil surface, and via organic compost), comparing soybean grown under crop-livestock integration and fallow and their effect on the prokaryotic communities in the rhizosphere. Soybean was grown under these agricultural systems and the prokaryotic communities in the rhizosphere was assessed by 16S rRNA sequencing. The prokaryotic communities in the rhizosphere of soybean differed significantly between crop-livestock and fallow (PERMANOVA p < 0.001), while inoculation methods with B. subtilis had minimal influence. Both systems shaped distinctly the structure of prokaryotic communities, with lower richness and diversity in fallow without inoculation. Actinobacteriota (∼50 %), Proteobacteria (∼15 %), and Firmicutes (∼10 %) dominated, with Proteobacteria more abundant in uninoculated soybean under fallow, and Firmicutes more prevalent in uninoculated soybean under crop-livestock. Soybean grown under crop-livestock enriched specific taxa, such as Bacillus and Bradyrhizobium, while soybean under fallow enriched Streptomyces and Gaiella. Niche analysis showed similar specialists comparing fallow and crop-livestock. In conclusion, crop-livestock shaped a more diverse soybean rhizosphere microbiome than fallow, with minimal influence from inoculation methods.
农牧结合和休耕等农业管理系统会影响不同的土壤性质，主要是生物参数。这可以驱动根际微生物群。此外，微生物接种的方法可以影响根际。本研究旨在研究不同接种方式（垄沟、土壤表面和有机堆肥）接种枯草芽孢杆菌的效果，比较农牧结合和休耕方式对大豆根际原核生物群落的影响。采用16S rRNA测序技术对大豆根际原核生物群落进行了分析。大豆根际原核生物群落在农牧和休耕地之间存在显著差异（PERMANOVA p < 0.001），而接种枯草芽孢杆菌的方式对其影响最小。两个系统的原核生物群落结构明显，未接种休耕区丰富度和多样性较低。放线菌门（~ 50%）、变形菌门（~ 15%）和厚壁菌门（~ 10%）占主导地位，在休耕条件下未接种大豆中变形菌门更为丰富，而在农牧条件下未接种大豆中厚壁菌门更为普遍。在作物-牲畜条件下种植的大豆富含芽孢杆菌和慢生根瘤菌等特定分类群，而在休耕条件下种植的大豆富含链霉菌和盖氏菌。生态位分析显示，类似的专家比较了休耕和作物-牲畜。综上所述，与休耕相比，作物-牲畜形成了更多样化的大豆根际微生物群，接种方法的影响最小。
{"title":"Soybean rhizosphere communities are shaped more by cropping systems than by Bacillus subtilis delivery methods","authors":"Maria Clara Zerbinatti , Élida Moreira L. Santana , Marcela Fernanda S. Martins , Fábio Fernando Araújo , Lucas W. Mendes , Romário M. Costa , Ademir Sergio F. Araujo","doi":"10.1016/j.rhisph.2025.101199","DOIUrl":"10.1016/j.rhisph.2025.101199","url":null,"abstract":"<div><div>Agricultural management systems, such as crop-livestock integration and fallow, affect differently soil properties, mainly biological parameters. This can drive the rhizosphere microbiome. In addition, methods of microbial inoculation can affect the rhizosphere. This study aims to investigate the effects of inoculating <em>Bacillus subtilis</em> under different methods (furrow, soil surface, and via organic compost), comparing soybean grown under crop-livestock integration and fallow and their effect on the prokaryotic communities in the rhizosphere. Soybean was grown under these agricultural systems and the prokaryotic communities in the rhizosphere was assessed by 16S rRNA sequencing. The prokaryotic communities in the rhizosphere of soybean differed significantly between crop-livestock and fallow (PERMANOVA <em>p</em> < 0.001), while inoculation methods with <em>B. subtilis</em> had minimal influence. Both systems shaped distinctly the structure of prokaryotic communities, with lower richness and diversity in fallow without inoculation. Actinobacteriota (∼50 %), Proteobacteria (∼15 %), and Firmicutes (∼10 %) dominated, with Proteobacteria more abundant in uninoculated soybean under fallow, and Firmicutes more prevalent in uninoculated soybean under crop-livestock. Soybean grown under crop-livestock enriched specific taxa, such as <em>Bacillus</em> and <em>Bradyrhizobium</em>, while soybean under fallow enriched <em>Streptomyces</em> and <em>Gaiella</em>. Niche analysis showed similar specialists comparing fallow and crop-livestock. In conclusion, crop-livestock shaped a more diverse soybean rhizosphere microbiome than fallow, with minimal influence from inoculation methods.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101199"},"PeriodicalIF":3.5,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145268073","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 : 2025-10-08DOI: 10.1016/j.rhisph.2025.101206
Luiz Eduardo Souza da Silva Irineu , Cleiton de Paula Soares , Priscila Pires Bittencourt , Leticia Cespom Passos , Sávio Bastos de Souza , Luiz Fernando Wurdig Roesch , Arnoldo Rocha Façanha , Fabio Lopes Olivares
Herbaspirillum seropedicae is a plant growth-promoting bacterium that senses root exudates, colonizes the rhizosphere, attaches to the root surface and establishes endophytically in cereals. However, how these events reshape host physiological responses of maize roots and early microbiome assembly remains unclear. We investigated the metabolic and physiological responses of maize roots to inoculation with H. seropedicae HRC54 and assessed the consequences for the seed-resident/root-associated bacteriome. Gene expression of tricarboxylic acid (TCA) cycle enzymes was quantified by RT-qPCR. Rhizospheric H+ fluxes and surface pH were mapped using the non-invasive scanning ion-selective electrode technique (SIET). Root-zone attachment was visualized using scanning electron microscopy (SEM), and the bacterial community composition was profiled through 16S rRNA sequencing. Inoculation upregulated transcripts for aconitase, citrate synthase, isocitrate dehydrogenase, and succinate-CoA ligase, while downregulating fumarase and malate dehydrogenase. H+ efflux increased in the elongation zone and decreased in the root cap and root-hair zones, corresponding to localized pH shifts. SEM revealed preferential colonization of the elongation zone, matching localized pH shifts. SEM showed preferential colonization of the elongation zone, progressing from aggregates to biofilm within 24 h. Microbiome analysis revealed distinct beta-diversity and enrichment of genera such as Aurantimonas, Mesorhizobium, Novosphingobium, Serratia, and Stenotrophomonas, as well as a reduced abundance of several genera, including Bradyrhizobium, Burkholderia, and Gluconacetobacter. These results link TCA reprogramming to pH modulation and early microbiome reshaping, supporting seed-treatment strategies that enhance nutrient uptake, bolster resilience against root pathogens, and improve crop performance.
{"title":"Herbaspirillum seropedicae inoculation alters maize root metabolism, rhizosphere pH, and seed-resident bacteriome composition","authors":"Luiz Eduardo Souza da Silva Irineu , Cleiton de Paula Soares , Priscila Pires Bittencourt , Leticia Cespom Passos , Sávio Bastos de Souza , Luiz Fernando Wurdig Roesch , Arnoldo Rocha Façanha , Fabio Lopes Olivares","doi":"10.1016/j.rhisph.2025.101206","DOIUrl":"10.1016/j.rhisph.2025.101206","url":null,"abstract":"<div><div><em>Herbaspirillum seropedicae</em> is a plant growth-promoting bacterium that senses root exudates, colonizes the rhizosphere, attaches to the root surface and establishes endophytically in cereals. However, how these events reshape host physiological responses of maize roots and early microbiome assembly remains unclear. We investigated the metabolic and physiological responses of maize roots to inoculation with <em>H. seropedicae</em> HRC54 and assessed the consequences for the seed-resident/root-associated bacteriome. Gene expression of tricarboxylic acid (TCA) cycle enzymes was quantified by RT-qPCR. Rhizospheric H<sup>+</sup> fluxes and surface pH were mapped using the non-invasive scanning ion-selective electrode technique (SIET). Root-zone attachment was visualized using scanning electron microscopy (SEM), and the bacterial community composition was profiled through 16S rRNA sequencing. Inoculation upregulated transcripts for aconitase, citrate synthase, isocitrate dehydrogenase, and succinate-CoA ligase, while downregulating fumarase and malate dehydrogenase. H<sup>+</sup> efflux increased in the elongation zone and decreased in the root cap and root-hair zones, corresponding to localized pH shifts. SEM revealed preferential colonization of the elongation zone, matching localized pH shifts. SEM showed preferential colonization of the elongation zone, progressing from aggregates to biofilm within 24 h. Microbiome analysis revealed distinct beta-diversity and enrichment of genera such as <em>Aurantimonas</em>, <em>Mesorhizobium</em>, <em>Novosphingobium</em>, <em>Serratia</em>, and <em>Stenotrophomonas</em>, as well as a reduced abundance of several genera, including <em>Bradyrhizobium</em>, <em>Burkholderia</em>, and <em>Gluconacetobacter</em>. These results link TCA reprogramming to pH modulation and early microbiome reshaping, supporting seed-treatment strategies that enhance nutrient uptake, bolster resilience against root pathogens, and improve crop performance.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101206"},"PeriodicalIF":3.5,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145267535","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 : 2025-10-08DOI: 10.1016/j.rhisph.2025.101204
Hassan Etesami , Amir Hosein Yadegari , Umarov Otabek , Bafayeva Zahro , Yuldoshov Laziz , Shoniyozov Bobur
Environmental stresses such as salinity, drought, extreme temperatures, nutrient imbalance, and heavy metals disrupt the legume-rhizobia symbiosis, a critical source of sustainable nitrogen, reducing nitrogen fixation by up to 80 %. While silicon (Si) supplementation can ameliorate these stresses, conventional Si fertilizers are inefficient and environmentally costly. Silicate-solubilizing bacteria (SSB) offer a sustainable alternative by dissolving insoluble soil silicates, yet they function as separate entities from the nitrogen-fixing rhizobia. This review proposes a transformative solution: the deliberate development of rhizobia with innate silicate-solubilizing capacity. We first synthesize evidence that SSB enhance symbiosis not only by releasing silicon but by acidifying the rhizosphere to unlock phosphorus and potentially priming early symbiotic signaling. This creates a compelling rationale for consolidating these functions. We then argue that equipping rhizobia themselves with this ability represents a superior strategy. Such “Si-rhizobia' would act as self-sufficient, dual-purpose microbes, directly providing their host plant with both nitrogen and the protective benefits of Si from a single inoculation. This paradigm shift addresses key limitations of current biofertilizers, including microbial competition and application complexity. We detail the mechanistic pathways involved and highlight that natural SSB activity has already been documented in a handful of Rhizobium strains, proving the concept's feasibility. The review concludes by outlining a clear roadmap for future research, prioritizing the systematic screening of rhizobial collections for this trait and the use of genetic engineering to create a new generation of multifunctional inoculants. By engineering silicate-solubilizing rhizobia, we can unlock a new level of resilience in legume crops, moving beyond additive partnerships towards integrated, synthetic symbiosis for a sustainable agricultural future.
{"title":"Engineering silicate-solubilizing rhizobia: A new paradigm for legume symbiosis under stress","authors":"Hassan Etesami , Amir Hosein Yadegari , Umarov Otabek , Bafayeva Zahro , Yuldoshov Laziz , Shoniyozov Bobur","doi":"10.1016/j.rhisph.2025.101204","DOIUrl":"10.1016/j.rhisph.2025.101204","url":null,"abstract":"<div><div>Environmental stresses such as salinity, drought, extreme temperatures, nutrient imbalance, and heavy metals disrupt the legume-rhizobia symbiosis, a critical source of sustainable nitrogen, reducing nitrogen fixation by up to 80 %. While silicon (Si) supplementation can ameliorate these stresses, conventional Si fertilizers are inefficient and environmentally costly. Silicate-solubilizing bacteria (SSB) offer a sustainable alternative by dissolving insoluble soil silicates, yet they function as separate entities from the nitrogen-fixing rhizobia. This review proposes a transformative solution: the deliberate development of rhizobia with innate silicate-solubilizing capacity. We first synthesize evidence that SSB enhance symbiosis not only by releasing silicon but by acidifying the rhizosphere to unlock phosphorus and potentially priming early symbiotic signaling. This creates a compelling rationale for consolidating these functions. We then argue that equipping rhizobia themselves with this ability represents a superior strategy. Such “Si-rhizobia' would act as self-sufficient, dual-purpose microbes, directly providing their host plant with both nitrogen and the protective benefits of Si from a single inoculation. This paradigm shift addresses key limitations of current biofertilizers, including microbial competition and application complexity. We detail the mechanistic pathways involved and highlight that natural SSB activity has already been documented in a handful of <em>Rhizobium</em> strains, proving the concept's feasibility. The review concludes by outlining a clear roadmap for future research, prioritizing the systematic screening of rhizobial collections for this trait and the use of genetic engineering to create a new generation of multifunctional inoculants. By engineering silicate-solubilizing rhizobia, we can unlock a new level of resilience in legume crops, moving beyond additive partnerships towards integrated, synthetic symbiosis for a sustainable agricultural future.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101204"},"PeriodicalIF":3.5,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145325808","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}
Climate change is intensifying water scarcity, posing major challenges to global crop productivity. Improving tolerance to limited water availability is therefore a key agricultural priority. While elite genotypes are widely used in breeding, maize landraces represent an underexploited reservoir of adaptive traits. Their interaction with soil microbial communities may play an important role in stress resilience that needs further investigation to have its extent fully understood. In this study, we investigated the rhizosphere microbiota of four maize landraces from Lombardy (Northern Italy) to assess how soil origin, plant genotype, and water availability interact in shaping bacterial communities. Plants were cultivated in soils collected from four locations, first under well-watered conditions and then exposed to water deficit. Growth and photosynthetic traits were monitored in parallel to link microbial composition with plant performance. Under well-watered conditions, rhizosphere communities were strongly shaped by the soil–genotype combination, with consistent enrichment of Bacillota taxa. Under water deficit, however, most landraces/soil combinations exhibited a reduced rhizosphere effect that brought rhizosphere bacterial communities to become indistinguishable from bulk soil. Strikingly, landraces displaying the best tolerance to water deficit showed an increase of biodiversity in the rhizosphere bacterial community, suggesting a recruitment strategy opposing that shown in well-watered conditions. These results highlight the importance of integrating landrace diversity and microbiome interactions into strategies for improving maize resilience. The study demonstrates that not only soil and genotype, but also the capacity to sustain distinctive and diverse microbial associations under stress, may contribute to plant performance in water-limited environments.
{"title":"Maize landraces under water deficit favor diverse rhizosphere communities associated with improved stress response","authors":"Giulia Castorina , Alessia Follador , Martina Ghidoli , Patrizia Zaccheo , Laura Crippa , Fulvia Tambone , Alessandro Passera , Carlotta Balconi , Gabriella Consonni , Paola Casati","doi":"10.1016/j.rhisph.2025.101200","DOIUrl":"10.1016/j.rhisph.2025.101200","url":null,"abstract":"<div><div>Climate change is intensifying water scarcity, posing major challenges to global crop productivity. Improving tolerance to limited water availability is therefore a key agricultural priority. While elite genotypes are widely used in breeding, maize landraces represent an underexploited reservoir of adaptive traits. Their interaction with soil microbial communities may play an important role in stress resilience that needs further investigation to have its extent fully understood. In this study, we investigated the rhizosphere microbiota of four maize landraces from Lombardy (Northern Italy) to assess how soil origin, plant genotype, and water availability interact in shaping bacterial communities. Plants were cultivated in soils collected from four locations, first under well-watered conditions and then exposed to water deficit. Growth and photosynthetic traits were monitored in parallel to link microbial composition with plant performance. Under well-watered conditions, rhizosphere communities were strongly shaped by the soil–genotype combination, with consistent enrichment of <em>Bacillota</em> taxa. Under water deficit, however, most landraces/soil combinations exhibited a reduced rhizosphere effect that brought rhizosphere bacterial communities to become indistinguishable from bulk soil. Strikingly, landraces displaying the best tolerance to water deficit showed an increase of biodiversity in the rhizosphere bacterial community, suggesting a recruitment strategy opposing that shown in well-watered conditions. These results highlight the importance of integrating landrace diversity and microbiome interactions into strategies for improving maize resilience. The study demonstrates that not only soil and genotype, but also the capacity to sustain distinctive and diverse microbial associations under stress, may contribute to plant performance in water-limited environments.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101200"},"PeriodicalIF":3.5,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145267531","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 : 2025-10-04DOI: 10.1016/j.rhisph.2025.101196
Shouji Gong , Xiaokui Xie , Riming Wang , Xiujian Li
The structure of soil bacterial communities within mangrove forests has received widespread attention, which can promote the growth of mangroves and material transformation. Despite the recognized significance of mangrove ecosystems, the bacterial composition within artificially restored mangroves remains poorly understood. This study investigates the bacterial diversity in the rhizosphere soil of both naturally and artificially restored Kandelia obovata seedlings, utilizing Illumina NovaSeq high-throughput sequencing technologies. The results revealed that only a small fraction of bacteria were identified in the mangrove rhizosphere soil, with the majority of them remaining uncharacterized. The dominant bacterial taxa identified included Sulfurovum, Actibacter, Woeseia, Desulfatiglans, Halioglobus, Ignavibacterium, Spirochaeta, Sulfurimonas, Prolixibacter, Robiginitalea, and Algoriphagus. Furthermore, marked differences were noted in the abundance of Sulfurovum, Actibacter, Woeseia, Desulfatiglans, Halioglobus, Methanosaeta and Robiginitalea between natural and artificially restored Kandelia obovata seedlings. Spatial network analysis suggested that Sulfurovum, Actibacter, Ignavibacterium, and Desulfatiglans may play important roles in the growth process of Kandelia obovata and are potentially important bacteria for its development. These findlings enhance our understanding of bacterial community structure in mangroves and underscore the potential application of bacteria in mangrove restoration.
{"title":"Key bacterial players in the growth of Kandelia obovata: Insights from rhizosphere soil composition","authors":"Shouji Gong , Xiaokui Xie , Riming Wang , Xiujian Li","doi":"10.1016/j.rhisph.2025.101196","DOIUrl":"10.1016/j.rhisph.2025.101196","url":null,"abstract":"<div><div>The structure of soil bacterial communities within mangrove forests has received widespread attention, which can promote the growth of mangroves and material transformation. Despite the recognized significance of mangrove ecosystems, the bacterial composition within artificially restored mangroves remains poorly understood. This study investigates the bacterial diversity in the rhizosphere soil of both naturally and artificially restored <em>Kandelia obovata</em> seedlings, utilizing Illumina NovaSeq high-throughput sequencing technologies. The results revealed that only a small fraction of bacteria were identified in the mangrove rhizosphere soil, with the majority of them remaining uncharacterized. The dominant bacterial taxa identified included <em>Sulfurovum</em>, <em>Actibacter</em>, <em>Woeseia</em>, <em>Desulfatiglans</em>, <em>Halioglobus</em>, <em>Ignavibacterium</em>, <em>Spirochaeta</em>, <em>Sulfurimonas, Prolixibacter</em>, <em>Robiginitalea</em>, and <em>Algoriphagus</em>. Furthermore, marked differences were noted in the abundance of <em>Sulfurovum</em>, <em>Actibacter</em>, <em>Woeseia</em>, <em>Desulfatiglans</em>, <em>Halioglobus</em>, <em>Methanosaeta</em> and <em>Robiginitalea</em> between natural and artificially restored <em>Kandelia obovata</em> seedlings. Spatial network analysis suggested that <em>Sulfurovum</em>, <em>Actibacter</em>, <em>Ignavibacterium</em>, and <em>Desulfatiglans</em> may play important roles in the growth process of <em>Kandelia obovata</em> and are potentially important bacteria for its development. These findlings enhance our understanding of bacterial community structure in mangroves and underscore the potential application of bacteria in mangrove restoration.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101196"},"PeriodicalIF":3.5,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145267533","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 : 2025-10-02DOI: 10.1016/j.rhisph.2025.101203
Youn Hwa Son , Suejin Park , Chung Ho Ko , Mengmeng Gu , Seung Youn Lee
Amsonia elliptica is valued for its medicinal and ornamental potential. However, it is listed as an endangered species in South Korea due to overharvesting and habitat destruction. This study aimed to develop an efficient protocol for mass vegetative propagation of A. elliptica using stem cuttings. We tested Rootone (0.4 % 1-naphthylacetic acid) and potassium salts of indole-3-butyric acid (K-IBA) and 1-naphthaleneacetic acid (K-NAA) applied via basal dip or foliar spray. After six weeks, cuttings treated with 2000 mg L−1 K-NAA showed the best rooting traits, with 93.3 % rooting, 17.5 roots per cutting, and 55.4 mm root length, along with the highest fresh (92.9 mg) and dry root mass (8.8 mg). Dipping cuttings in 2000 mg L−1 K-NAA for 1 min is recommended as the most effective treatment for large-scale propagation of A. elliptica. This optimized propagation method will facilitate the conservation and ornamental use of A. elliptica.
{"title":"Potassium salt of 1-naphthaleneacetic acid promotes rhizogenesis in Amsonia elliptica stem cuttings","authors":"Youn Hwa Son , Suejin Park , Chung Ho Ko , Mengmeng Gu , Seung Youn Lee","doi":"10.1016/j.rhisph.2025.101203","DOIUrl":"10.1016/j.rhisph.2025.101203","url":null,"abstract":"<div><div><em>Amsonia elliptica</em> is valued for its medicinal and ornamental potential. However, it is listed as an endangered species in South Korea due to overharvesting and habitat destruction. This study aimed to develop an efficient protocol for mass vegetative propagation of <em>A. elliptica</em> using stem cuttings. We tested Rootone (0.4 % 1-naphthylacetic acid) and potassium salts of indole-3-butyric acid (K-IBA) and 1-naphthaleneacetic acid (K-NAA) applied via basal dip or foliar spray. After six weeks, cuttings treated with 2000 mg L<sup>−1</sup> K-NAA showed the best rooting traits, with 93.3 % rooting, 17.5 roots per cutting, and 55.4 mm root length, along with the highest fresh (92.9 mg) and dry root mass (8.8 mg). Dipping cuttings in 2000 mg L<sup>−1</sup> K-NAA for 1 min is recommended as the most effective treatment for large-scale propagation of <em>A. elliptica</em>. This optimized propagation method will facilitate the conservation and ornamental use of <em>A. elliptica</em>.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"36 ","pages":"Article 101203"},"PeriodicalIF":3.5,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145221128","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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