Microbiological research最新文献

{"title":"Rhizosphere metagenomics and metabolomes provide new insights into the relationship between rhizosphere microecology and early bolting of Angelica dahurica","authors":"Weimeng Feng ,&nbsp;Rui Ma ,&nbsp;Yichen Guo ,&nbsp;Bao Zhang ,&nbsp;Jinxu Lan ,&nbsp;Jun Liu ,&nbsp;Suiqing Chen","doi":"10.1016/j.micres.2025.128435","DOIUrl":"10.1016/j.micres.2025.128435","url":null,"abstract":"<div><div><em>Angelica dahurica</em> is a medicinal and edible plant with a wide range of pharmaceutical and food applications. However, the early bolting, which leads to reduced yield and loss of bioactive constituents, has become a major obstacle to the industrial development of <em>A. dahurica</em>. Rhizosphere microecology affects plant growth and secondary metabolite accumulation, but the association of rhizosphere microecology with the early bolting of <em>A. dahurica</em> is not fully understood. This study integrated metagenomic and metabolomic analyses to systematically characterize the differences in rhizosphere microecology of non-bolting and early bolting <em>A. dahurica</em> plants. Results revealed significant disparities in soil physicochemical properties, root exudate profiles, and microbial community composition between two groups, all of which exhibited correlations with the coumarin compounds content, the primary pharmacologically active constituents of <em>A. dahurica</em>. Integrated analysis suggested that root-derived acyl-homoserine lactone (AHL) quorum-sensing signals, as the primary chemical signals of the prevalent Gram-negative bacteria, may participate in regulating the microbial community structure and soil properties, thereby influencing the bolting and flowering process. This study proposes a potential complex regulatory network of \"rhizosphere microbiome – quorum-sensing signals – soil nitrogen cycle – bolting and flowering\" linking the rhizosphere microecology to early bolting in <em>A. dahurica</em>, thereby addressing a key knowledge gap in this area. The findings offer a scientific foundation and innovative strategy for the simultaneous prevention of early bolting and quality improvement in <em>A. dahurica</em> through soil microecological management, which is of significant importance for promoting the sustainable commercial development of the <em>A. dahurica</em> industry.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"305 ","pages":"Article 128435"},"PeriodicalIF":6.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145863553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial auxin catabolism as a driver of plant growth promotion and rhizosphere colonization fitness","authors":"Amalia Roca ,&nbsp;Juan Gorts ,&nbsp;Miguel A. Matilla","doi":"10.1016/j.micres.2025.128431","DOIUrl":"10.1016/j.micres.2025.128431","url":null,"abstract":"<div><div>Inter-kingdom communication between plants and their associated microbiota is central to plant development and environmental adaptation. Indole-3-acetic acid (IAA) is the primary auxin in plants and regulates plant growth and development, while also modulating bacterial physiology and behavior. The concentration at which IAA exerts its biological effects in plants is critical and maintaining auxin homeostasis is essential. Although IAA production by plant growth-promoting bacteria typically stimulates plant growth, excessive IAA levels can be detrimental to plant physiology. Here, we investigate the <em>in planta</em> functional role of bacterial IAA catabolism using <em>Pseudomonas putida</em> 1290, a model plant-associated bacterium that degrades IAA through the Iac aerobic pathway. By constructing a mutant strain defective in the <em>iac</em> gene cluster, we show that IAA catabolism is essential for reversing auxin-mediated growth inhibition in tomato and maize, both <em>in vitro</em> and in microcosms. In addition, bacterial IAA degradation also prevented the formation of IAA-induced tumor-like structures in maize roots. Moreover, competitive colonization assays revealed that IAA catabolism enhances bacterial fitness in the rhizosphere, particularly under high-auxin conditions. Our findings establish bacterial IAA catabolism as a mechanism of metabolic signal interference that maintains auxin homeostasis <em>in planta</em> and promotes successful rhizosphere colonization. This work highlights the significance of microbial auxin metabolism in shaping plant–microbe interactions and its potential for application in sustainable agriculture strategies.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"305 ","pages":"Article 128431"},"PeriodicalIF":6.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145863544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulatory effect of fadR on the inhibition of Aspergillus flavus infection of walnut kernels by Enterobacter ludwigii AA4","authors":"Zhibo Yuan ,&nbsp;Yibo Zan ,&nbsp;Xu Li ,&nbsp;Bin Lu ,&nbsp;Yanjie Chao ,&nbsp;Xinwu Xiong ,&nbsp;Yanpo Yao ,&nbsp;Di Wu ,&nbsp;Ben Niu ,&nbsp;Dong Pei","doi":"10.1016/j.micres.2025.128402","DOIUrl":"10.1016/j.micres.2025.128402","url":null,"abstract":"<div><div>Mycotoxin contamination of nuts, frequently attributed to inappropriate storage, causes substantial economic losses and health concerns globally. Biological control using beneficial microorganisms has emerged as an environment friendly method for efficient mitigation of <em>Aspergillus flavus</em> pollution and consequent mycotoxin elimination in foodstuffs. Nevertheless, the exact mechanisms by which these biocontrol microbes protect nuts from this toxigenic fungus remain largely unknown. Using a fungal infection assay, we observed a remarkable inhibitory effect of <em>Enterobacter ludwigii</em> AA4 against the growth of <em>A</em>. <em>flavus</em> colonizing walnut kernels and aflatoxin B₁ production. Mutant <em>E. ludwigii</em> AA4 strains, generated by genetically modifying five biofilm-related genes, notably <em>fadR</em> (which encodes a transcriptional regulator), exhibited significantly impaired biofilm development and reduced efficacy in suppressing <em>A</em>. <em>flavus</em>. These results indicated that biofilm establishment is indispensable for the inhibitory effect of <em>E. ludwigii</em> AA4 against <em>A. flavus</em>. We further investigated the kernel colonization of <em>fadR</em> knockout mutant, which exhibited the most pronounced reduction in biofilm formation, via colony counting and laser scanning confocal microscopy. We found that <em>fadR</em> contributed to the suppression of <em>A. flavus</em> by influencing bacterial biofilm production and kernel settlement. Gene expression analysis and site-directed mutagenesis revealed that <em>fadR</em> modulated biofilm development by negatively regulating the transcription of <em>rcsA</em>, an auxiliary protein gene within the Rcs phosphorelay system, potentially by influencing acetyl phosphate-mediated RcsB phosphorylation. These findings highlight the potential of AA4 in the biological control of <em>A. flavus</em> contamination in walnut kernels.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128402"},"PeriodicalIF":6.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145654911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trichoderma bio-organic fertilizer modulates the rhizosphere microbiome and Bacillus-assisted plant hormone regulation to promote pear rootstock growth","authors":"Peigen Li ,&nbsp;Yujie Shi ,&nbsp;Yujie Zhao ,&nbsp;Xiaotong Lu ,&nbsp;Jingtao Duan ,&nbsp;Qingsong Yang ,&nbsp;Yangchun Xu ,&nbsp;Xiaogang Li ,&nbsp;Caixia Dong ,&nbsp;Zhonghua Wang ,&nbsp;Qirong Shen","doi":"10.1016/j.micres.2025.128400","DOIUrl":"10.1016/j.micres.2025.128400","url":null,"abstract":"<div><div>Growth of container-grown <em>Pyrus calleryana</em> is often containered in heavy clay soils. <em>Trichoderma</em>-based bio-organic fertilizer (BOF) can improve seedling performance, yet how BOF mobilizes microbiome-hormone interactions under such conditions remains unclear. Here, we conducted a pot experiment with three treatments— water control (CK), 10 % (v/v) BOF and 20 % (v/v) BOF—under controlled conditions to assess plant growth, root hormone profiles, and rhizosphere communities. With 20 % BOF, seedling height, root length and root biomass increased (up to +131 %, +160 % and +165 %), bacterial diversity rose, and Firmicutes/Actinobacteria were enriched with an 8.3-fold increase of <em>Bacillus</em>. The ferment filtrates supported growth of the isolated <em>Bacillus</em>. Across treatments, <em>Bacillus</em> abundance correlated positively with indole-3-acetic acid (IAA) and isopentenyladenine (IP) and negatively with abscisic acid (ABA) (P &lt; 0.05). Consistently, co-inoculation of <em>Trichoderma</em> and Bacillus increased IAA/IP and reduced ABA (P &lt; 0.05), yielding stronger growth responses than single inoculations. These findings outline a BOF-mediated path in which <em>Trichoderma</em>-guided microbiome restructuring, together with a <em>Trichoderma</em>-responsive Bacillus, rebalances IAA/IP/ABA and promotes pear rootstock growth.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128400"},"PeriodicalIF":6.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and functional analysis of Pseudomonas protegens CS11 reveals multifaceted biocontrol mechanisms against Sclerotinia sclerotiorum via antifungal metabolites, root colonisation and plant defence induction in tomato","authors":"Aida Nabila Rahim ,&nbsp;Gwo Rong Wong ,&nbsp;Kah Ooi Chua ,&nbsp;Kausalyaa Kaliapan ,&nbsp;Jennifer Ann Harikrishna ,&nbsp;Siah Ying Tang ,&nbsp;Bey Hing Goh ,&nbsp;Purabi Mazumdar","doi":"10.1016/j.micres.2025.128399","DOIUrl":"10.1016/j.micres.2025.128399","url":null,"abstract":"<div><div><em>Sclerotinia sclerotiorum</em> is one of many fungal pathogens that threaten global crop production. Antagonistic rhizobacteria have emerged as promising eco-friendly alternatives to synthetic pesticides that can be deployed for effective and sustainable management of the fungal disease. From 60 rhizobacterial strains isolated in this study, eight were able to inhibit the <em>in vitro</em> growth of <em>S. sclerotiorum</em>. Among these, strain CS11 exhibited complete (100 %) inhibition and demonstrated multiple plant growth-promoting traits, including siderophore production, nitrogen assimilation, phosphate solubilisation, and lytic enzyme activity. Motility and root colonisation assays confirmed CS11 to have high motility and efficient rhizosphere establishment. Molecular identification using 16S rRNA sequencing and Multi-locus sequence analysis identified CS11 as <em>Pseudomonas protegens</em>. Whole-genome sequencing revealed gene clusters for key antifungal metabolites, including 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, hydrogen cyanide, and orfamides, widely associated with <em>Pseudomonas</em> spp. Although closely related to <em>P. protegens</em> CHA0, CS11 has additional coding sequences associated with protease production (thermostable alkaline protease), root colonisation (cyclic di-GMP phosphodiesterase), and rhizosphere fitness (quorum-sensing-related genes), highlighting its novelty and strong biocontrol potential. In greenhouse trials, treatment of <em>S. sclerotiorum</em>-infected tomato plants with CS11 led to complete suppression of disease progression and significantly enhanced plant height and chlorophyll content. Compared to untreated infected plants, CS11-treated plants had elevated GLU, Chi, PAL, and PPO activities, and RT-qPCR analysis demonstrated upregulation of salicylic acid (<em>PR1, PR2, PR5</em>) and jasmonic acid (<em>PR3, PR4, PDF1.2, VSP2</em>) pathway genes. Collectively, these findings establish <em>P. protegens</em> CS11 as a promising candidate for the development of biopesticides to control fungal pathogens and enhance plant defence.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128399"},"PeriodicalIF":6.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145570972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Faecalibacterium prausnitzii suppresses ovarian cancer by inducing ferroptosis via phenylalanine metabolism activation","authors":"Kaiyue Ding ,&nbsp;Yuexue Huo ,&nbsp;Kangzhe Fu ,&nbsp;Yingting Chen ,&nbsp;Lunyue Xia ,&nbsp;Junhao Zhan ,&nbsp;Jiahua Liu ,&nbsp;Jiayu Liu ,&nbsp;Yudi Liu ,&nbsp;Mingyang Zhang ,&nbsp;Xingchen Wu ,&nbsp;HyokChol Choe ,&nbsp;Danping Zhao ,&nbsp;Junnan Ma ,&nbsp;Chunmei Dai ,&nbsp;Zhenlong Yu ,&nbsp;Yulin Peng ,&nbsp;Xiaochi Ma ,&nbsp;Lin Zhang","doi":"10.1016/j.micres.2025.128342","DOIUrl":"10.1016/j.micres.2025.128342","url":null,"abstract":"<div><div>Ovarian cancer (OC) is a highly lethal gynecologic malignancy characterized by limited availability of treatment options and frequent recurrence. The gut microbiota has emerged as a key regulator of tumor progression; however, the anticancer potential of individual probiotic species remains insufficiently characterized and warrants further investigation. Ferroptosis is a regulated iron-dependent cell death with therapeutic potential in cancer. In this study, we initially observed that the traditional herbal pair, <em>Scutellaria barbata</em> D. Don (SB) and <em>Scleromitrion diffusum</em> (Wild) R.J. Wang (SD) exerted antitumor effects in a mouse model of OC, which was accompanied by a marked increase in the abundance of <em>Faecalibacterium prausnitzii</em> (<em>F.prausnitzii</em>) — a beneficial commensal bacterium not previously associated with cancer or ferroptosis. This observation prompted us to explore the functional role of <em>F.prausnitzii</em> in OC and revealed that it significantly suppressed ovarian tumor growth both <em>in vitro</em> and <em>in vivo</em>. Mechanistically, <em>F.prausnitzii</em> treatment elevated Fe²⁺ levels, increased lipid peroxidation, and depleted glutathione (GSH), which are hallmarks of ferroptosis. Transcriptomic analysis of tumor tissues from <em>F.prausnitzii</em>-treated mice identified ferroptosis and metal ion homeostasis pathways as major regulatory networks. Furthermore, metabolomic profiling revealed the activation of phenylalanine metabolism and increased production of phenylacetylglutamine (PAGln), suggesting a microbiota-metabolite axis contributing to ferroptosis induction. Our findings reveal that <em>F.prausnitzii</em> represents a novel ferroptosis-inducing probiotic with potent antitumor activity in OC. This study reveals a previously unrecognized role for this gut commensal and provides a mechanistic basis for the development of microbiota-based, ferroptosis-targeted therapeutic strategies in oncology.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128342"},"PeriodicalIF":6.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-centric culture-enriched metagenomics reveals temperature-driven reassembly and functional stratification in culturable desert soil bacteria","authors":"Shuai Li ,&nbsp;Xin-Ran Wang ,&nbsp;Jia-Rui Han ,&nbsp;Wen-Hui Lian ,&nbsp;Mukhtiar Ali ,&nbsp;Yong-Hong Liu ,&nbsp;Jun Liu ,&nbsp;Jie Huang ,&nbsp;Huan-Huan He ,&nbsp;Rajivgandhi Govindan ,&nbsp;Osama Abdalla Abdelshafy Mohamad ,&nbsp;Bao-Zhu Fang ,&nbsp;Lei Dong ,&nbsp;Wen-Jun Li","doi":"10.1016/j.micres.2025.128411","DOIUrl":"10.1016/j.micres.2025.128411","url":null,"abstract":"<div><div>Desert ecosystems cover nearly one-third of Earth’s land surface and face rising temperatures and climatic variability. Soil microbiomes underpin biogeochemical cycling and ecosystem resilience in these arid landscapes, yet the genome-resolved temperature responses of their culturable fraction remain poorly understood. Here, we employed genome-centric culture-enriched metagenomics (CE-MGS) to rhizosphere and bulk desert soils from the Gurbantunggut Desert incubated at 15°C, 30°C, and 45°C. From 90 culture-enriched metagenomes, we reconstructed 1184 cultivated metagenome-assembled genomes (cMAGs), including 218 putative novel genomospecies across 73 bacterial genera, substantially expanding the genomic representation of desert bacteria. Temperature influenced both community composition and interactions, with <em>Actinomycetota</em>, <em>Pseudomonadota</em>, and <em>Bacillota</em> dominating at 15°C, 30°C, and 45°C, respectively. Co-occurrence networks showed that lower temperatures and rhizosphere soils supported more interconnected consortia of culturable bacteria and that key hub taxa shifted across thermal regimes, reflecting temperature-driven reorganization of interactions within the culturable microbial community. Functional profiling revealed that temperature selected for specialized taxa, with elevated temperatures favoring redox-efficient pathways and more energy-efficient resource use. While representing only the culturable fraction of desert soil microbiomes, CE-MGS enables genome reconstruction of experimentally tractable microbes, linking identity, function, and thermal adaptation. These results provide a genome-resolved view of temperature responses, extend understanding of desert microbial adaptation beyond previous culture-independent studies, and establish CE-MGS as a practical approach to access ecologically relevant microbes for conservation and biotechnological applications under a warming climate.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128411"},"PeriodicalIF":6.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145661404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disentangling the molecular mechanisms of disease suppression by endophytic Flavobacterium sp. 98","authors":"Xinya Pan ,&nbsp;Somayah S. Elsayed ,&nbsp;Gilles P. van Wezel ,&nbsp;Jos M. Raaijmakers ,&nbsp;Víctor J. Carrión","doi":"10.1016/j.micres.2025.128415","DOIUrl":"10.1016/j.micres.2025.128415","url":null,"abstract":"<div><div>Endophytic microorganisms colonize internal plant tissues and enhance host resistance to pathogens. We previously showed that endophytic <em>Flavobacterium</em> sp. 98 (Fl98) protects sugar beet against the fungal root pathogen <em>Rhizoctonia solani</em> via biosynthetic gene cluster 298 (BGC298)<em>.</em> However, the molecular mechanisms underlying this protection remained poorly understood. Here, comparative metabolomic analyses revealed that knockout of BGC298 led to reduced production of the antifungal compound 5,6-dimethylbenzimidazole (DMB) in Fl98. We hypothesized that BGC298 is involved in regulating DMB biosynthesis and therefore contributes to Fl98’s disease suppression as a novel protective mechanism. Subsequent site-directed mutagenesis of the DMB-synthase gene <em>bluB</em> abolished DMB production by Fl98, and both ΔBGC298 and Δ<em>bluB</em> mutants were compromised in protecting sugar beet seedlings in greenhouse bioassays. Bioinformatic analyses further indicated that <em>bluB</em> is widespread across <em>Flavobacterium</em>, while BGC298 is limited to a small subset of plant-associated strains. Together, our findings highlight the pivotal role of BGC298 and DMB biosynthesis in plant protection by endophytic <em>Flavobacterium</em> sp. 98.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128415"},"PeriodicalIF":6.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial strategies for soda saline-alkali soil remediation: The role of haloalkaliphilic bacteria","authors":"Bonaventure Chidi Ezenwanne ,&nbsp;Charles Obinwanne Okoye ,&nbsp;Huifang Jiang ,&nbsp;Lu Gao ,&nbsp;Xunfeng Chen ,&nbsp;Yanfang Wu ,&nbsp;Jianxiong Jiang","doi":"10.1016/j.micres.2025.128410","DOIUrl":"10.1016/j.micres.2025.128410","url":null,"abstract":"<div><div>Global agriculture is increasingly constrained by soil degradation, with salinization and alkalization reducing crop productivity, soil function, and long-term ecosystem stability. Among salt-affected soils, soda saline-alkali soils represent a particularly challenging subtype, characterized by excessive accumulation of soluble salts, elevated pH, and high sodium content, all of which exacerbate soil structural decline. Haloalkaliphilic bacteria, adapted to high salinity and alkalinity, offer a sustainable bioremediation strategy. This review presents a conceptual framework elucidating the mechanisms by which haloalkaliphilic bacteria mitigate soda saline-alkali stress through osmoprotectant synthesis, ion homeostasis regulation, pH neutralization, extracellular polymeric substance (EPS) formation, and extremozyme activity, thereby enhancing nutrient mobilization and organic-matter turnover. These microbial processes facilitate contaminant degradation and stimulate plant growth by improving nutrient availability and promoting phytohormone production. The resulting plant-microbe synergy translates microbial activity into enhanced soil function by reducing bulk salinity and pH, improving structure and water retention, and promoting overall soil fertility. This review further identifies critical challenges to translating mechanistic insights into field practice, including ecological variability, inoculant efficacy and resilience, regulatory frameworks, scalable inoculant manufacturing, a paucity of multi-season field trials, and socioeconomic constraints. Prospects include integrative multi-omics to link gene expression with ecosystem outcomes; systematic exploration of extremozymes; incorporation of nutrient-rich biomass for consortium support; AI-guided consortia design and predictive modeling for site-specific optimization, and long-term monitoring. These strategies enhance our understanding of tolerance to high salinity and alkalinity, paving the way for innovative microbial interventions to restore soda saline-alkali soils and support more resilient, sustainable agricultural systems.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128410"},"PeriodicalIF":6.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145668962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis","authors":"Tao Yang ,&nbsp;Yulong Zhan ,&nbsp;Jie Sha ,&nbsp;Jiang Zhao ,&nbsp;Chengniu Wang ,&nbsp;Tong Peng ,&nbsp;Lei Zhang","doi":"10.1016/j.micres.2025.128418","DOIUrl":"10.1016/j.micres.2025.128418","url":null,"abstract":"<div><div>Microalgae have recently been recognized as sustainable biofertilizers that improve soil fertility while enhancing crop performance. However, their roles in regulating medicinal plant growth and quality, as well as the underlying ecological mechanisms, remain poorly understood. In this study, we systematically assessed the effects of three representative microalgae—<em>Anabaena cylindrica</em> (AC), <em>Phormidium tenue</em> (PT), and <em>Chlorella vulgaris</em> (CV)—on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of <em>Angelica sinensis</em>. Field inoculation trials demonstrated that all three microalgae significantly promoted biomass accumulation and increased antioxidant capacity. AC and CV further enhanced the accumulation of ferulic acid and flavonoids, which are two key quality determinants. Microalgal inoculation significantly altered rhizosphere soil properties by increasing total organic carbon and alkali-hydrolyzable nitrogen, with AC uniquely elevating available phosphorus and iron. Metagenomic analysis revealed that AC and PT stimulated nitrification while suppressing denitrification, thereby reducing nitrogen loss and stabilizing the soil nitrogen pools. Distinct microbial taxa, including <em>Rhodanobacter</em>, <em>Streptomyces</em>, and <em>Pseudomonas</em>, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed <em>A</em>. <em>sinensis</em> phytohormone profiles in a species-specific manner. Partial least squares path modeling suggested that AC and CV promote ferulic acid biosynthesis through distinct mechanisms, with AC associated with reduced investment in C-mineralization processes and CV associated with lower salicylic acid levels, whereas PT enhances biomass accumulation mainly by stimulating N-cycle processes. Collectively, this study provides integrated evidence linking microalgae-mediated nutrient cycling, rhizosphere microbiome shifts and hormonal regulation to enhanced quality formation in <em>A</em>. <em>sinensis</em>.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128418"},"PeriodicalIF":6.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}