Pub Date : 2025-12-11DOI: 10.1016/j.micres.2025.128418
Tao Yang , Yulong Zhan , Jie Sha , Jiang Zhao , Chengniu Wang , Tong Peng , Lei Zhang
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—Anabaena cylindrica (AC), Phormidium tenue (PT), and Chlorella vulgaris (CV)—on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of Angelica sinensis. 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 Rhodanobacter, Streptomyces, and Pseudomonas, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed A. sinensis 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 A. sinensis.
{"title":"Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis","authors":"Tao Yang , Yulong Zhan , Jie Sha , Jiang Zhao , Chengniu Wang , Tong Peng , 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":"2025-12-11","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}
The “flavescence dorée” (FD) phytoplasma is transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. In experimental conditions, this phytoplasma is also transmitted by the leafhopper Euscelidius variegatus to broad bean in which it multiplies and induces symptoms. To be transmitted to plants, phytoplasmas must invade different cell types of their insect vectors. The process of cellular endocytosis involves both bacterial and eucaryotic factors such as adhesins and receptors. In the present study, it is shown that entry of fluorescent beads coated with the adhesin VmpA of the FD phytoplasma into cultured E. variegatus cells depends on the putative receptor Uk1_LRR and clathrin of the insect. In vivo experiments have shown that silencing of uk1_LRR gene increased the colonization of E. variegatus by the FD phytoplasmas without effect on the plant transmission. On the contrary, silencing of clathrin gene significantly reduced the colonization of E. variegatus and the transmission to broad bean.
{"title":"Gene silencing targeting uk1_LRR or clathrin in the experimental vector Euscelidius variegatus modifies insect colonization by \"flavescence dorée\" phytoplasma","authors":"Nathalie Arricau-Bouvery, Marie-Pierre Dubrana, Sybille Duret, Xavier Foissac, Sylvie Malembic-Maher","doi":"10.1016/j.micres.2025.128416","DOIUrl":"10.1016/j.micres.2025.128416","url":null,"abstract":"<div><div>The “flavescence dorée” (FD) phytoplasma is transmitted from grapevine to grapevine by the leafhopper <em>Scaphoideus titanus</em>. In experimental conditions, this phytoplasma is also transmitted by the leafhopper <em>Euscelidius variegatus</em> to broad bean in which it multiplies and induces symptoms. To be transmitted to plants, phytoplasmas must invade different cell types of their insect vectors. The process of cellular endocytosis involves both bacterial and eucaryotic factors such as adhesins and receptors. In the present study, it is shown that entry of fluorescent beads coated with the adhesin VmpA of the FD phytoplasma into cultured <em>E. variegatus</em> cells depends on the putative receptor Uk1_LRR and clathrin of the insect. <em>In vivo</em> experiments have shown that silencing of uk1_LRR gene increased the colonization of <em>E</em>. <em>variegatus</em> by the FD phytoplasmas without effect on the plant transmission. On the contrary, silencing of clathrin gene significantly reduced the colonization of <em>E</em>. <em>variegatus</em> and the transmission to broad bean.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"305 ","pages":"Article 128416"},"PeriodicalIF":6.9,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145753637","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}
Pub Date : 2025-12-08DOI: 10.1016/j.micres.2025.128412
Roshan Nepal , Tony Charles , George Bouras , Richard S. Taylor , James W. Wynne
Pathogenic bacteria are an ongoing threat to intensive agriculture, including aquaculture. With the emergence of antimicrobial resistance (AMR), novel non-traditional antimicrobials are urgently needed to minimize the dependence on antibiotics. Bacteriophage (phage) therapy, which uses naturally occurring viruses to kill specific bacterium, is gaining interest and offers huge potential for targeted pathogen control in aquaculture. However, many challenges regarding stability and emergence of phage-resistance must be overcome. Here, we isolated and characterized eight Vibrio phages against an emerging aquaculture pathogen Vibrio alginolyticus and studied their bactericidal and antibiofilm potency. We then used next-generation sequencing to understand how the Vibrio species may gain phage resistance. Our results indicated that most of the isolated Vibrio phages (seven out of eight) shared < 40 % genomic similarity with phages isolated elsewhere, possibly suggesting novel strains. The phages were stable in different temperatures (4–40 °C), pHs (3−10) and salinities (0–50 ppt) up to 6 h without significant loss in viability. Although individual phages had variable bactericidal efficiency and bacteria rapidly developed phage-resistance, phage cocktail formulations were highly efficient and significantly suppressed bacterial growth up to 15 h, inhibited biofilm formation (p < 0.05) and eradicated established biofilms (p < 0.05). Sequencing confirmed absence of lysogeny modules, known toxins and AMR genes in seven of the phages. Further, tRNAs and a putative anti-CRISPR (Acr) protein was found in two of the most efficient phages. Though bacteria rapidly developed phage-resistance, we observed increased antibiotic sensitivity as a trade-off which possibly resulted from defective efflux pump. Our findings support potential applications of Vibrio phages in aquaculture systems for minimizing the burden of Vibriosis. However, further research is required to elucidate the role of efflux pump system in phage-resistance and antimicrobial resistance.
{"title":"Characterization of novel Vibrio phages as potential biocontrol agents against Vibrio alginolyticus and insights into its phage-resistant mutant","authors":"Roshan Nepal , Tony Charles , George Bouras , Richard S. Taylor , James W. Wynne","doi":"10.1016/j.micres.2025.128412","DOIUrl":"10.1016/j.micres.2025.128412","url":null,"abstract":"<div><div>Pathogenic bacteria are an ongoing threat to intensive agriculture, including aquaculture. With the emergence of antimicrobial resistance (AMR), novel non-traditional antimicrobials are urgently needed to minimize the dependence on antibiotics. Bacteriophage (phage) therapy, which uses naturally occurring viruses to kill specific bacterium, is gaining interest and offers huge potential for targeted pathogen control in aquaculture. However, many challenges regarding stability and emergence of phage-resistance must be overcome. Here, we isolated and characterized eight Vibrio phages against an emerging aquaculture pathogen <em>Vibrio alginolyticus</em> and studied their bactericidal and antibiofilm potency. We then used next-generation sequencing to understand how the <em>Vibrio</em> species may gain phage resistance. Our results indicated that most of the isolated Vibrio phages (seven out of eight) shared < 40 % genomic similarity with phages isolated elsewhere, possibly suggesting novel strains. The phages were stable in different temperatures (4–40 °C), pHs (3−10) and salinities (0–50 ppt) up to 6 h without significant loss in viability. Although individual phages had variable bactericidal efficiency and bacteria rapidly developed phage-resistance, phage cocktail formulations were highly efficient and significantly suppressed bacterial growth up to 15 h, inhibited biofilm formation (p < 0.05) and eradicated established biofilms (p < 0.05). Sequencing confirmed absence of lysogeny modules, known toxins and AMR genes in seven of the phages. Further, tRNAs and a putative anti-CRISPR (Acr) protein was found in two of the most efficient phages. Though bacteria rapidly developed phage-resistance, we observed increased antibiotic sensitivity as a trade-off which possibly resulted from defective efflux pump. Our findings support potential applications of Vibrio phages in aquaculture systems for minimizing the burden of Vibriosis. However, further research is required to elucidate the role of efflux pump system in phage-resistance and antimicrobial resistance.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128412"},"PeriodicalIF":6.9,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733986","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}
Pub Date : 2025-12-06DOI: 10.1016/j.micres.2025.128415
Xinya Pan , Somayah S. Elsayed , Gilles P. van Wezel , Jos M. Raaijmakers , Víctor J. Carrión
Endophytic microorganisms colonize internal plant tissues and enhance host resistance to pathogens. We previously showed that endophytic Flavobacterium sp. 98 (Fl98) protects sugar beet against the fungal root pathogen Rhizoctonia solani via biosynthetic gene cluster 298 (BGC298). 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 bluB abolished DMB production by Fl98, and both ΔBGC298 and ΔbluB mutants were compromised in protecting sugar beet seedlings in greenhouse bioassays. Bioinformatic analyses further indicated that bluB is widespread across Flavobacterium, 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 Flavobacterium sp. 98.
{"title":"Disentangling the molecular mechanisms of disease suppression by endophytic Flavobacterium sp. 98","authors":"Xinya Pan , Somayah S. Elsayed , Gilles P. van Wezel , Jos M. Raaijmakers , 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":"2025-12-06","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}
Bacterial infections pose a significant threat to host cells by inducing DNA damage, potentially leading to chromosomal instability, cell cycle arrest, apoptosis, or even cancer. Pseudomonas aeruginosa (P. aeruginosa) infection-induced DNA double-strand breaks (DSBs) activates DNA damage response (DDR) to facilitate repair. However, the mechanisms linking P. aeruginosa infection and host DNA repair remain unclear. Here, we demonstrate that DSBs-induced by P. aeruginosa in lung epithelial cells promote Tip60 activation and stabilization, which help counteract DNA damage. However, diminished Tip60 activation and reduced protein levels during the post-infection recovery phase exacerbate DNA damage. Mechanistically, elevated Tip60 levels during infection are associated with suppressed K33- and K48-linked ubiquitination, whereas the decline of Tip60 during recovery coincides with enhanced K33- and K48-linked ubiquitination. These specific ubiquitination modifications promote proteasomal degradation of Tip60, thereby reducing its stability. Supporting this, we observed that wild-type Tip60 undergoes markedly less K33- and K48-linked ubiquitination than its histone acetyltransferase (HAT) activity-deficient mutant. Notably, we identify the E3 ubiquitin ligase TRIM37 as a positive regulator of Tip60 stability, largely independent of its E3 ligase activity. Silencing TRIM37 enhances K33- and K48-linked ubiquitination and accelerates Tip60 degradation, thereby exacerbating DNA damage during both infection and recovery. TRIM37 binds to the C-terminal MYST domain of Tip60, with this interaction strengthened during infection but weakened upon recovery. This dynamic regulation arises because TRIM37 preferentially associates with the activated form of Tip60. Collectively, our findings identify the TRIM37-Tip60 axis as a critical regulator of host DDR in response to P. aeruginosa infection, offering new insights into infection-associated DDR and therapeutic strategies.
{"title":"Dynamic regulation of K33- and K48-linked ubiquitination of Tip60 by TRIM37 orchestrates host DNA damage response during Pseudomonas aeruginosa infection and recovery","authors":"Hua Yu , Xingmin Wang , Junzhi Xiong, Xiaomei He, Caifeng Ma, Qilin Wang, Rongrong Chen, Yuanyuan Li, Qian Dai, Qian Min, Jianyun Zhou, Kebin Zhang","doi":"10.1016/j.micres.2025.128414","DOIUrl":"10.1016/j.micres.2025.128414","url":null,"abstract":"<div><div>Bacterial infections pose a significant threat to host cells by inducing DNA damage, potentially leading to chromosomal instability, cell cycle arrest, apoptosis, or even cancer. <em>Pseudomonas aeruginosa</em> (<em>P. aeruginosa</em>) infection-induced DNA double-strand breaks (DSBs) activates DNA damage response (DDR) to facilitate repair. However, the mechanisms linking <em>P. aeruginosa</em> infection and host DNA repair remain unclear. Here, we demonstrate that DSBs-induced by <em>P. aeruginosa</em> in lung epithelial cells promote Tip60 activation and stabilization, which help counteract DNA damage. However, diminished Tip60 activation and reduced protein levels during the post-infection recovery phase exacerbate DNA damage. Mechanistically, elevated Tip60 levels during infection are associated with suppressed K33- and K48-linked ubiquitination, whereas the decline of Tip60 during recovery coincides with enhanced K33- and K48-linked ubiquitination. These specific ubiquitination modifications promote proteasomal degradation of Tip60, thereby reducing its stability. Supporting this, we observed that wild-type Tip60 undergoes markedly less K33- and K48-linked ubiquitination than its histone acetyltransferase (HAT) activity-deficient mutant. Notably, we identify the E3 ubiquitin ligase TRIM37 as a positive regulator of Tip60 stability, largely independent of its E3 ligase activity. Silencing TRIM37 enhances K33- and K48-linked ubiquitination and accelerates Tip60 degradation, thereby exacerbating DNA damage during both infection and recovery. TRIM37 binds to the C-terminal MYST domain of Tip60, with this interaction strengthened during infection but weakened upon recovery. This dynamic regulation arises because TRIM37 preferentially associates with the activated form of Tip60. Collectively, our findings identify the TRIM37-Tip60 axis as a critical regulator of host DDR in response to <em>P. aeruginosa</em> infection, offering new insights into infection-associated DDR and therapeutic strategies.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"305 ","pages":"Article 128414"},"PeriodicalIF":6.9,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145828015","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}
Pub Date : 2025-12-05DOI: 10.1016/j.micres.2025.128413
Yanan Zhou , Xue-Xian Zhang , Dandan Wang , Mengguang Zhao , Li Sun , Weiwei Huang , Zhihong Xie
Acetyl-CoA synthetase (ACS) is a well-characterized enzyme that catalyzes the ATP-dependent ligation of acetate and coenzyme A to produce acetyl-CoA, a central metabolite coordinating energy metabolism, carbon flux distribution, and post-translational protein modification. Recently, ACS has emerged as a metabolic nexus with broad implications for plant–microbe interactions in agriculture. Beyond its canonical role in primary metabolism, ACS governs diverse physiological processes in beneficial plant-associated microorganisms, including rhizosphere colonization, stress adaptation, secondary metabolite biosynthesis, and morphological development—all of which enhance plant growth and resilience. In contrast, in phytopathogens, ACS is closely related to the expression of virulence factors. Thus, ACS exerts a dual influence, shaping both mutualistic and antagonistic microbial lifestyles in planta. This review synthesizes recent advances in the structural and catalytic diversity of ACS, delineates its ecological and functional roles in agriculturally relevant microorganisms, and explores the environmental and host-derived signals that regulates its expression and activity. Particular attention is given to the interplay between ACS-mediated carbon metabolism and protein acetylation, which together modulate microbial physiology and plant-associated behaviors. ACS is thereby positioned as a strategic metabolic hub, providing a framework for future research at the interface of microbial metabolism, environmental adaptation, and plant health.
{"title":"Microbial acetyl-CoA synthesis as an emerging metabolic and regulatory hub in plant-microbe interactions","authors":"Yanan Zhou , Xue-Xian Zhang , Dandan Wang , Mengguang Zhao , Li Sun , Weiwei Huang , Zhihong Xie","doi":"10.1016/j.micres.2025.128413","DOIUrl":"10.1016/j.micres.2025.128413","url":null,"abstract":"<div><div>Acetyl-CoA synthetase (ACS) is a well-characterized enzyme that catalyzes the ATP-dependent ligation of acetate and coenzyme A to produce acetyl-CoA, a central metabolite coordinating energy metabolism, carbon flux distribution, and post-translational protein modification. Recently, ACS has emerged as a metabolic nexus with broad implications for plant–microbe interactions in agriculture. Beyond its canonical role in primary metabolism, ACS governs diverse physiological processes in beneficial plant-associated microorganisms, including rhizosphere colonization, stress adaptation, secondary metabolite biosynthesis, and morphological development—all of which enhance plant growth and resilience. In contrast, in phytopathogens, ACS is closely related to the expression of virulence factors. Thus, ACS exerts a dual influence, shaping both mutualistic and antagonistic microbial lifestyles <em>in planta</em>. This review synthesizes recent advances in the structural and catalytic diversity of ACS, delineates its ecological and functional roles in agriculturally relevant microorganisms, and explores the environmental and host-derived signals that regulates its expression and activity. Particular attention is given to the interplay between ACS-mediated carbon metabolism and protein acetylation, which together modulate microbial physiology and plant-associated behaviors. ACS is thereby positioned as a strategic metabolic hub, providing a framework for future research at the interface of microbial metabolism, environmental adaptation, and plant health.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128413"},"PeriodicalIF":6.9,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145714781","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}
Crop domestication has long been known to reshape rhizosphere microbial communities, yet research has focused disproprotionately on bacteria and fungal responses to crop domestication while neglecting protist communities. Protists, as key microbial predators regulating bacterial populations and thereby their functionalities, remain understudied in this context. Here, we investigate the influence of soybean domestication on both bacterial and protist communities, with a focus on the reorganization of ecological strategies, specifically generalists and specialists, within these microbiomes. We analyzed 270 rhizosphere samples from 27 domesticated and 63 wild soybean varieties. Domestication significantly altered community compositions of bacterial communities, with wild soybeans harboring higher proprotions of Pseudomonadota (71.4 %) and Bacillota (4.8 %), while domesticated soybeans exhibited an enrichment of Bacteroidota (11.0 %). Protist communities also diverged: wild soybeans were dominated by Cercozoa (58.2 %) and Gyrista (23.5 %), while domesticated plants had more Ciliophora (7.1 %) and Evosea (5.7 %). Domesticated soybeans hosted fewer generalist and specialist bacteria but more generalist protists, suggesting divergent microbial responses to domestication. Correlation analyses revealed that bacterial and protist generalists exhibited strong positive correlations with each other. At the same time, bacterial and protist specialists also showed positive correlations in wild soybeans-patterns that were largely absent in their domesticated counterparts. Functionally, wild soybeans supported more ureolytic and methylotrophic bacteria, while domesticated soybeans favored nitrate-respiration taxa. Notably, predatory protists in wild soybeans were significantly correlated with bacteria involved in carbon and nitrogen cycling, a key ecological relationship lost with domestication. These findings suggest that domestication exerts different selection pressures on bacteria and protists, disrupting potential relationships between bacterial and protist functional groups.
{"title":"Soybean domestication alters rhizosphere microbial assembly and disrupts the potential bacteria-protist relationships.","authors":"Shaoguan Zhao, Chen Liu, Ying Yuan, Qingyun Zhao, Zhiyang Zhang, Xiangyu Ren, Yang Yue, Shuo Sun, Shiqi Sun, Qi Zhang, Guangnan Xing, Ming Wang, Wu Xiong, Qirong Shen","doi":"10.1016/j.micres.2025.128295","DOIUrl":"10.1016/j.micres.2025.128295","url":null,"abstract":"<p><p>Crop domestication has long been known to reshape rhizosphere microbial communities, yet research has focused disproprotionately on bacteria and fungal responses to crop domestication while neglecting protist communities. Protists, as key microbial predators regulating bacterial populations and thereby their functionalities, remain understudied in this context. Here, we investigate the influence of soybean domestication on both bacterial and protist communities, with a focus on the reorganization of ecological strategies, specifically generalists and specialists, within these microbiomes. We analyzed 270 rhizosphere samples from 27 domesticated and 63 wild soybean varieties. Domestication significantly altered community compositions of bacterial communities, with wild soybeans harboring higher proprotions of Pseudomonadota (71.4 %) and Bacillota (4.8 %), while domesticated soybeans exhibited an enrichment of Bacteroidota (11.0 %). Protist communities also diverged: wild soybeans were dominated by Cercozoa (58.2 %) and Gyrista (23.5 %), while domesticated plants had more Ciliophora (7.1 %) and Evosea (5.7 %). Domesticated soybeans hosted fewer generalist and specialist bacteria but more generalist protists, suggesting divergent microbial responses to domestication. Correlation analyses revealed that bacterial and protist generalists exhibited strong positive correlations with each other. At the same time, bacterial and protist specialists also showed positive correlations in wild soybeans-patterns that were largely absent in their domesticated counterparts. Functionally, wild soybeans supported more ureolytic and methylotrophic bacteria, while domesticated soybeans favored nitrate-respiration taxa. Notably, predatory protists in wild soybeans were significantly correlated with bacteria involved in carbon and nitrogen cycling, a key ecological relationship lost with domestication. These findings suggest that domestication exerts different selection pressures on bacteria and protists, disrupting potential relationships between bacterial and protist functional groups.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"301 ","pages":"128295"},"PeriodicalIF":6.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812125","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}
Plant growth-promoting rhizobacteria (PGPR) can stimulate crop growth and performance through multiple mechanisms, making them promising bioinoculants for sustainable agriculture. Among known PGPR species, Pseudomonas fluorescens has attracted considerable attention because of its superior growth-promoting mechanisms and broad adaptability. Although P. fluorescens P34 has excellent colonization and growth-promoting abilities, the molecular and ecological mechanisms underlying its growth-promoting effects remain poorly understood. Here, we conducted a 25-day pot experiment utilizing an integrated approach combining transcriptomics and microbial amplicon sequencing to investigate how P. fluorescens P34 influences wheat gene expression profiles and the response of the indigenous rhizosphere microbial community to P34 colonization. P34 application increased the seedling fresh weight, seedling dry weight, root fresh weight, root dry weight, phosphorus content, nitrogen content in wheat leaves and available phosphorus content in rhizosphere soil by 39.61 %, 29.67 %, 84.07 %, 64.71 %, 43.05 %, 17.79 % and 14.45 %, respectively, while it increased the length, projected area and number of forks of the wheat root system by 17.35 %, 35.87 % and 23.57 %, respectively. RNA sequencing revealed 3166 differentially expressed genes that were predominantly involved in nitrogen and phosphorus transport, carbohydrate metabolism, phytohormone biosynthesis and transport, and plantmicrobe signaling recognition. Moreover, microbial community dynamic modulation demonstrated that strain P34 induced shifts in the indigenous rhizosphere microbiome by enriching beneficial microorganisms (e.g., Massilia and Pseudomonas) while reducing potential pathogens. These findings revealed the molecular and ecological mechanisms underlying PGPR-mediated plant growth promotion, providing new insights for optimizing PGPR applications in sustainable agriculture and demonstrating its potential to reduce chemical fertilizer dependency while enhancing soil health in agroecosystems.
{"title":"Pseudomonas fluorescens P34 colonization impacts expression changes in wheat roots, reshapes rhizosphere microbial communities and promotes wheat plant growth.","authors":"Wenfeng Ai, Yanping Qiu, Jiajia Hua, Zixuan Chen, Wei Cheng, Yiping Chen, Shengxian Zhang, Yuanyuan Xue, Sha Li, Run Hong, Ruijie Dong, Yuanyuan Cao","doi":"10.1016/j.micres.2025.128306","DOIUrl":"10.1016/j.micres.2025.128306","url":null,"abstract":"<p><p>Plant growth-promoting rhizobacteria (PGPR) can stimulate crop growth and performance through multiple mechanisms, making them promising bioinoculants for sustainable agriculture. Among known PGPR species, Pseudomonas fluorescens has attracted considerable attention because of its superior growth-promoting mechanisms and broad adaptability. Although P. fluorescens P34 has excellent colonization and growth-promoting abilities, the molecular and ecological mechanisms underlying its growth-promoting effects remain poorly understood. Here, we conducted a 25-day pot experiment utilizing an integrated approach combining transcriptomics and microbial amplicon sequencing to investigate how P. fluorescens P34 influences wheat gene expression profiles and the response of the indigenous rhizosphere microbial community to P34 colonization. P34 application increased the seedling fresh weight, seedling dry weight, root fresh weight, root dry weight, phosphorus content, nitrogen content in wheat leaves and available phosphorus content in rhizosphere soil by 39.61 %, 29.67 %, 84.07 %, 64.71 %, 43.05 %, 17.79 % and 14.45 %, respectively, while it increased the length, projected area and number of forks of the wheat root system by 17.35 %, 35.87 % and 23.57 %, respectively. RNA sequencing revealed 3166 differentially expressed genes that were predominantly involved in nitrogen and phosphorus transport, carbohydrate metabolism, phytohormone biosynthesis and transport, and plantmicrobe signaling recognition. Moreover, microbial community dynamic modulation demonstrated that strain P34 induced shifts in the indigenous rhizosphere microbiome by enriching beneficial microorganisms (e.g., Massilia and Pseudomonas) while reducing potential pathogens. These findings revealed the molecular and ecological mechanisms underlying PGPR-mediated plant growth promotion, providing new insights for optimizing PGPR applications in sustainable agriculture and demonstrating its potential to reduce chemical fertilizer dependency while enhancing soil health in agroecosystems.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"301 ","pages":"128306"},"PeriodicalIF":6.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812124","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}
Pub Date : 2025-11-29DOI: 10.1016/j.micres.2025.128411
Shuai Li , Xin-Ran Wang , Jia-Rui Han , Wen-Hui Lian , Mukhtiar Ali , Yong-Hong Liu , Jun Liu , Jie Huang , Huan-Huan He , Rajivgandhi Govindan , Osama Abdalla Abdelshafy Mohamad , Bao-Zhu Fang , Lei Dong , Wen-Jun Li
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 Actinomycetota, Pseudomonadota, and Bacillota 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.
{"title":"Genome-centric culture-enriched metagenomics reveals temperature-driven reassembly and functional stratification in culturable desert soil bacteria","authors":"Shuai Li , Xin-Ran Wang , Jia-Rui Han , Wen-Hui Lian , Mukhtiar Ali , Yong-Hong Liu , Jun Liu , Jie Huang , Huan-Huan He , Rajivgandhi Govindan , Osama Abdalla Abdelshafy Mohamad , Bao-Zhu Fang , Lei Dong , 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":"2025-11-29","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}
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.
{"title":"Microbial strategies for soda saline-alkali soil remediation: The role of haloalkaliphilic bacteria","authors":"Bonaventure Chidi Ezenwanne , Charles Obinwanne Okoye , Huifang Jiang , Lu Gao , Xunfeng Chen , Yanfang Wu , 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":"2025-11-28","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}
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