Pub Date : 2025-11-21DOI: 10.1016/j.micres.2025.128400
Peigen Li , Yujie Shi , Yujie Zhao , Xiaotong Lu , Jingtao Duan , Qingsong Yang , Yangchun Xu , Xiaogang Li , Caixia Dong , Zhonghua Wang , Qirong Shen
Growth of container-grown Pyrus calleryana is often containered in heavy clay soils. Trichoderma-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 Bacillus. The ferment filtrates supported growth of the isolated Bacillus. Across treatments, Bacillus abundance correlated positively with indole-3-acetic acid (IAA) and isopentenyladenine (IP) and negatively with abscisic acid (ABA) (P < 0.05). Consistently, co-inoculation of Trichoderma and Bacillus increased IAA/IP and reduced ABA (P < 0.05), yielding stronger growth responses than single inoculations. These findings outline a BOF-mediated path in which Trichoderma-guided microbiome restructuring, together with a Trichoderma-responsive Bacillus, rebalances IAA/IP/ABA and promotes pear rootstock growth.
{"title":"Trichoderma bio-organic fertilizer modulates the rhizosphere microbiome and Bacillus-assisted plant hormone regulation to promote pear rootstock growth","authors":"Peigen Li , Yujie Shi , Yujie Zhao , Xiaotong Lu , Jingtao Duan , Qingsong Yang , Yangchun Xu , Xiaogang Li , Caixia Dong , Zhonghua Wang , 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 < 0.05). Consistently, co-inoculation of <em>Trichoderma</em> and Bacillus increased IAA/IP and reduced ABA (P < 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":"2025-11-21","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}
Pub Date : 2025-11-19DOI: 10.1016/j.micres.2025.128399
Aida Nabila Rahim , Gwo Rong Wong , Kah Ooi Chua , Kausalyaa Kaliapan , Jennifer Ann Harikrishna , Siah Ying Tang , Bey Hing Goh , Purabi Mazumdar
Sclerotinia sclerotiorum 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 in vitro growth of S. sclerotiorum. 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 Pseudomonas protegens. Whole-genome sequencing revealed gene clusters for key antifungal metabolites, including 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, hydrogen cyanide, and orfamides, widely associated with Pseudomonas spp. Although closely related to P. protegens 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 S. sclerotiorum-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 (PR1, PR2, PR5) and jasmonic acid (PR3, PR4, PDF1.2, VSP2) pathway genes. Collectively, these findings establish P. protegens CS11 as a promising candidate for the development of biopesticides to control fungal pathogens and enhance plant defence.
{"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 , Gwo Rong Wong , Kah Ooi Chua , Kausalyaa Kaliapan , Jennifer Ann Harikrishna , Siah Ying Tang , Bey Hing Goh , 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":"2025-11-19","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}
Pub Date : 2025-11-12DOI: 10.1016/j.micres.2025.128398
Paul Iturbe-Espinoza , Lars Elsgaard , Rumakanta Sapkota , Lea Ellegaard-Jensen , Anne Winding
Biochar improves agricultural soil properties and short-term microbial diversity. However, biochar’s long-term effects on microbiomes and soil health remain poorly understood. This study assessed the effects of 8-year field-aged biochar on microbiomes from two contrasting soils: a sandy clay soil and a coarse sandy soil, under temperate climate conditions. We hypothesize that even after 8 years, biochar amendment persistently alters soil physicochemical properties, stimulates extracellular enzyme activity, increases the abundance of N-cycling genes, and shifts the prokaryotic and fungal community structures. In June 2015, the topsoil in field lysimeters was amended with 2 % w/w straw biochar, and by August 2023, this biochar amendment resulted in a significant increased activity of five key extracellular enzymes (α-glucosidase, β-galactosidase, cellobiosidase, phosphomonoesterase, and arylsulfatase) involved in C, P, and S cycling in both soils. In the coarse sandy soil, biochar boosted the abundance of prokaryotes (16S rRNA gene), key nitrification genes (AOA-amoA and AOB-amoA), and the denitrification gene nosZ Clade I. In both soils, biochar caused an increase in the abundance of the nitrite reductase (nirS) gene, indicating a sustained impact on the N cycle, and an enrichment of an ammonia-oxidizing archaeon of the family Nitrosophaeraceae. Finally, a persistent shift in prokaryotic community structure was observed in both soils. The study clearly demonstrates that the effects of biochar persist after eight years, providing insights into the long-term impact of biochar on soil health.
{"title":"Eight-year effect of biochar amendment on soil properties, extracellular enzyme activity, N-cycling genes and microbiome structure in two Danish fallow soils","authors":"Paul Iturbe-Espinoza , Lars Elsgaard , Rumakanta Sapkota , Lea Ellegaard-Jensen , Anne Winding","doi":"10.1016/j.micres.2025.128398","DOIUrl":"10.1016/j.micres.2025.128398","url":null,"abstract":"<div><div>Biochar improves agricultural soil properties and short-term microbial diversity. However, biochar’s long-term effects on microbiomes and soil health remain poorly understood. This study assessed the effects of 8-year field-aged biochar on microbiomes from two contrasting soils: a sandy clay soil and a coarse sandy soil, under temperate climate conditions. We hypothesize that even after 8 years, biochar amendment persistently alters soil physicochemical properties, stimulates extracellular enzyme activity, increases the abundance of N-cycling genes, and shifts the prokaryotic and fungal community structures. In June 2015, the topsoil in field lysimeters was amended with 2 % w/w straw biochar, and by August 2023, this biochar amendment resulted in a significant increased activity of five key extracellular enzymes (α-glucosidase, β-galactosidase, cellobiosidase, phosphomonoesterase, and arylsulfatase) involved in C, P, and S cycling in both soils. In the coarse sandy soil, biochar boosted the abundance of prokaryotes (16S rRNA gene), key nitrification genes (AOA-<em>amoA</em> and AOB-<em>amoA</em>), and the denitrification gene <em>nosZ</em> Clade I. In both soils, biochar caused an increase in the abundance of the nitrite reductase (<em>nirS</em>) gene, indicating a sustained impact on the N cycle, and an enrichment of an ammonia-oxidizing archaeon of the family <em>Nitrosophaeraceae.</em> Finally, a persistent shift in prokaryotic community structure was observed in both soils. The study clearly demonstrates that the effects of biochar persist after eight years, providing insights into the long-term impact of biochar on soil health.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128398"},"PeriodicalIF":6.9,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145517482","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 : 2025-11-11DOI: 10.1016/j.micres.2025.128397
Xixi Li , Xiaojing Gao , Shuyao Yu , Fengfeng Du , Jixiang Liu , Xuhui Kan , Xiaojing Liu , Dongrui Yao
Saline–alkali land significantly threatens global food security and ecological safety, and root-associated microorganisms help plants survive salt–alkali stress. However, the ecological functions and factors that influence the rhizosphere microbiomes of salt-tolerant plants remain poorly understood. In this study, we used high-throughput sequencing and metagenomics to reveal the microbial communities and functional traits of bulk and rhizosphere soil from salt-tolerant species (Suaeda glauca, Phragmites australis, and Spartina alterniflora) growing in saline soil. Bacterial and fungal taxa were significantly enriched in the rhizosphere soil compared to the non-rhizosphere soil. Metagenomic analyses revealed that metabolic pathways, including glycolysis and ABC transporters, were highly enriched in the rhizosphere. Functional profiling indicated that salt stress-related pathways were more abundant in the core genera Pseudomonas and Woeseia. The abundance of functional genes related to plant growth–promoting traits, including phosphate solubilization and salt adaptation pathways, was higher in the rhizosphere soil than in the non-rhizosphere soil, which was mainly driven by soil salinity, total nitrogen content, and total carbon content. Additionally, P. aeruginosa obtained from the rhizosphere of S. alterniflora exhibited high phosphorus solubilization efficiency (908.38 μg/mL), nitrogen fixation activity (2.84 μg/mL) and salt tolerance (≦ 5 % NaCl). These findings demonstrate that salt-tolerant plants shape microbial activities by controlling the rhizosphere microenvironment, mitigating salt stress, providing a scientific and practical foundation for the development of targeted microbial inoculants for saline–alkali land reclamation.
{"title":"Rhizosphere microbiota diversity and salt stress–alleviating functional genes in coastal wild salt-tolerant plants","authors":"Xixi Li , Xiaojing Gao , Shuyao Yu , Fengfeng Du , Jixiang Liu , Xuhui Kan , Xiaojing Liu , Dongrui Yao","doi":"10.1016/j.micres.2025.128397","DOIUrl":"10.1016/j.micres.2025.128397","url":null,"abstract":"<div><div>Saline–alkali land significantly threatens global food security and ecological safety, and root-associated microorganisms help plants survive salt–alkali stress. However, the ecological functions and factors that influence the rhizosphere microbiomes of salt-tolerant plants remain poorly understood. In this study, we used high-throughput sequencing and metagenomics to reveal the microbial communities and functional traits of bulk and rhizosphere soil from salt-tolerant species (<em>Suaeda glauca</em>, <em>Phragmites australis</em>, and <em>Spartina alterniflora</em>) growing in saline soil. Bacterial and fungal taxa were significantly enriched in the rhizosphere soil compared to the non-rhizosphere soil. Metagenomic analyses revealed that metabolic pathways, including glycolysis and ABC transporters, were highly enriched in the rhizosphere. Functional profiling indicated that salt stress-related pathways were more abundant in the core genera <em>Pseudomonas</em> and <em>Woeseia</em>. The abundance of functional genes related to plant growth–promoting traits, including phosphate solubilization and salt adaptation pathways, was higher in the rhizosphere soil than in the non-rhizosphere soil, which was mainly driven by soil salinity, total nitrogen content, and total carbon content. Additionally, <em>P. aeruginosa</em> obtained from the rhizosphere of <em>S. alterniflora</em> exhibited high phosphorus solubilization efficiency (908.38 μg/mL), nitrogen fixation activity (2.84 μg/mL) and salt tolerance (≦ 5 % NaCl). These findings demonstrate that salt-tolerant plants shape microbial activities by controlling the rhizosphere microenvironment, mitigating salt stress, providing a scientific and practical foundation for the development of targeted microbial inoculants for saline–alkali land reclamation.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128397"},"PeriodicalIF":6.9,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145534496","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 : 2025-11-11DOI: 10.1016/j.micres.2025.128395
María Emilia Cuervo , Diego Del Balzo , María Natalia Zanetti , Mariela Beatriz Nolly , Hugo Lachuer , Rostislav Petkov , Nour Ismail , John Manzi , Rubén Walter Caron , Christophe Le Clainche , Maria Teresa Damiani , Julien Pernier , Kristine Schauer , Anahi Capmany
Chlamydia trachomatis (Ct), a Gram-negative obligate intracellular pathogen, manipulates host actin dynamics to facilitate its entry, development, and exit. It assembles a dynamic actin cage around its intracellular niche, known as the ‘inclusion’, which provides structural stability for bacterial growth, and is crucial for exit via the non-cell-lytic extrusion process. We found that Ct recruits Myosin 1 C (MYO1C), a ubiquitous actin dependent motor protein, to the inclusion throughout its life cycle. Consequently, loss of MYO1C activity reduced Ct infection and the production of bacterial progenies. Mechanistically, MYO1C functions as a dynamic tether that assembles an actin cage around the inclusion membrane, as depletion of MYO1C or its inhibition by pentachloropseudilin (PClP) leads to the loss of the actin network surrounding the inclusion. In vitro reconstitution assays revealed that the presence of purified MYO1C was necessary and sufficient to build an actin cage around giant membranous vesicles. In summary, our findings identified MYO1C as a novel host target of Ct and provided mechanistic evidence for its role as a dynamic tether to recruit the essential actin cage around the bacterial inclusion.
沙眼衣原体（Ct）是一种革兰氏阴性专性细胞内病原体，操纵宿主肌动蛋白动力学以促进其进入、发展和退出。它在其细胞内生态位周围组装了一个动态肌动蛋白笼，称为“内含物”，它为细菌生长提供了结构稳定性，并且对于通过非细胞裂解挤出过程退出至关重要。我们发现Ct在其整个生命周期中招募肌动蛋白1 C (MYO1C)，这是一种普遍存在的肌动蛋白依赖的运动蛋白。因此，MYO1C活性的丧失减少了Ct感染和细菌后代的产生。在机制上，MYO1C作为一个动态系绳，在包涵膜周围组装一个肌动蛋白笼，因为MYO1C的耗尽或其被五氯代戊二醇（PClP）抑制导致包涵周围的肌动蛋白网络的丢失。体外重建分析显示，纯化的MYO1C的存在是必要的，足以在巨大的膜囊泡周围建立肌动蛋白笼。总之，我们的研究结果确定了MYO1C是Ct的一个新的宿主靶点，并为其作为一种动态系绳在细菌包涵体周围招募必需肌动蛋白笼的作用提供了机制证据。
{"title":"Chlamydia trachomatis highjacks host MYO1C for actin cage recruitment at the bacterial inclusion","authors":"María Emilia Cuervo , Diego Del Balzo , María Natalia Zanetti , Mariela Beatriz Nolly , Hugo Lachuer , Rostislav Petkov , Nour Ismail , John Manzi , Rubén Walter Caron , Christophe Le Clainche , Maria Teresa Damiani , Julien Pernier , Kristine Schauer , Anahi Capmany","doi":"10.1016/j.micres.2025.128395","DOIUrl":"10.1016/j.micres.2025.128395","url":null,"abstract":"<div><div><em>Chlamydia trachomatis</em> (Ct), a Gram-negative obligate intracellular pathogen, manipulates host actin dynamics to facilitate its entry, development, and exit. It assembles a dynamic actin cage around its intracellular niche, known as the ‘inclusion’, which provides structural stability for bacterial growth, and is crucial for exit via the non-cell-lytic extrusion process. We found that Ct recruits Myosin 1 C (MYO1C), a ubiquitous actin dependent motor protein, to the inclusion throughout its life cycle. Consequently, loss of MYO1C activity reduced Ct infection and the production of bacterial progenies. Mechanistically, MYO1C functions as a dynamic tether that assembles an actin cage around the inclusion membrane, as depletion of MYO1C or its inhibition by pentachloropseudilin (PClP) leads to the loss of the actin network surrounding the inclusion. In vitro reconstitution assays revealed that the presence of purified MYO1C was necessary and sufficient to build an actin cage around giant membranous vesicles. In summary, our findings identified MYO1C as a novel host target of Ct and provided mechanistic evidence for its role as a dynamic tether to recruit the essential actin cage around the bacterial inclusion.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128395"},"PeriodicalIF":6.9,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145517483","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 : 2025-11-10DOI: 10.1016/j.micres.2025.128390
Deborah González-Abradelo , Lyselle Ruíz de León , Reinier Gesto-Borroto , Tonatiuh Moreno-Perlín , Nilda del C. Sánchez-Castellanos , Yordanis Pérez-Llano , Juán Cabral-Miramontes , Elva Aréchiga-Carbajal , María del Rayo Sánchez-Carbente , Cene Gostinčar , Nina Gunde-Cimerman , Ramón Alberto Batista-García
Studies on microbial adaptations to salt stress, particularly in fungi, have focused mainly on high concentrations of NaCl. The effects of other inorganic salts on biological systems are much less well known. This study investigates the effects of MgCl2 (0–2.0 M), a chaotropic salt, on the halophilic fungus Aspergillus sydowii (EXF-12860) and compares these results with those obtained with the kosmotropic NaCl. While A. sydowii thrived at MgCl2 concentrations previously considered lethal (up to 2.0 M), differences in morphological, physiological, metabolic, and molecular responses were observed. At 0.5–1.0 M, growth rates were similar under both salts, but higher MgCl2 concentrations (1.5–2.0 M) significantly inhibited growth, reduced hyphal elongation, and decreased cell density. During growth in the presence of NaCl, a wide range of carbon sources was utilized, but high MgCl2 interfered with substrate metabolism and uncoupled growth from metabolic activity. Both salts induced the production of compatible solutes (glycerol, erythritol), with higher accumulation under MgCl2. Oxidative stress responses were also stronger under MgCl2, including increased catalase and glutathione peroxidase activity. Transcriptomic analyses revealed significant changes in gene expression under MgCl2 stress, with upregulation of ion transport, cell wall remodelling, glycerol biosynthesis, and oxidative defense pathways. In contrast, NaCl triggered responses focused on osmotic balance and maintenance of cell integrity. These findings emphasize the need for a deeper investigation of microbial tolerance mechanisms in chaotropic environments.
{"title":"Cellular responses of Aspergillus sydowii to growth at extreme chaotropic concentrations of MgCl2","authors":"Deborah González-Abradelo , Lyselle Ruíz de León , Reinier Gesto-Borroto , Tonatiuh Moreno-Perlín , Nilda del C. Sánchez-Castellanos , Yordanis Pérez-Llano , Juán Cabral-Miramontes , Elva Aréchiga-Carbajal , María del Rayo Sánchez-Carbente , Cene Gostinčar , Nina Gunde-Cimerman , Ramón Alberto Batista-García","doi":"10.1016/j.micres.2025.128390","DOIUrl":"10.1016/j.micres.2025.128390","url":null,"abstract":"<div><div>Studies on microbial adaptations to salt stress, particularly in fungi, have focused mainly on high concentrations of NaCl. The effects of other inorganic salts on biological systems are much less well known. This study investigates the effects of MgCl<sub>2</sub> (0–2.0 M), a chaotropic salt, on the halophilic fungus <em>Aspergillus sydowii</em> (EXF-12860) and compares these results with those obtained with the kosmotropic NaCl. While <em>A. sydowii</em> thrived at MgCl<sub>2</sub> concentrations previously considered lethal (up to 2.0 M), differences in morphological, physiological, metabolic, and molecular responses were observed. At 0.5–1.0 M, growth rates were similar under both salts, but higher MgCl<sub>2</sub> concentrations (1.5–2.0 M) significantly inhibited growth, reduced hyphal elongation, and decreased cell density. During growth in the presence of NaCl, a wide range of carbon sources was utilized, but high MgCl<sub>2</sub> interfered with substrate metabolism and uncoupled growth from metabolic activity. Both salts induced the production of compatible solutes (glycerol, erythritol), with higher accumulation under MgCl<sub>2</sub>. Oxidative stress responses were also stronger under MgCl<sub>2</sub>, including increased catalase and glutathione peroxidase activity. Transcriptomic analyses revealed significant changes in gene expression under MgCl<sub>2</sub> stress, with upregulation of ion transport, cell wall remodelling, glycerol biosynthesis, and oxidative defense pathways. In contrast, NaCl triggered responses focused on osmotic balance and maintenance of cell integrity. These findings emphasize the need for a deeper investigation of microbial tolerance mechanisms in chaotropic environments.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128390"},"PeriodicalIF":6.9,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145557450","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 : 2025-11-10DOI: 10.1016/j.micres.2025.128396
Jinwoo Kim , Haejoon Park , Young Hyun Jung , Ho Jae Han , Doyeon Kim , Sangryeol Ryu , Minsik Kim
As the development of new antibiotics struggles with the continuous emergence of drug-resistant bacteria, targeting bacterial virulence factors instead of viability has been proposed as one of the alternative approaches to combat the pathogens. Here, we genetically engineered the temperate phage SPC32H to serve as a delivery vehicle for key negative regulators of Salmonella virulence to inhibit Salmonella infection. Negative regulator genes associated with Salmonella pathogenicity island 1 (SPI1), hilE, csrA, and lrp, were inserted into the phage SPC32H genome and expressed under a strong constitutive promoter. When Salmonella cells lysogenized by the engineered phages were exposed to the virulence-inducing condition, the expression of key positive regulators and major virulence factors associated with SPI1 was significantly reduced. Furthermore, in a murine early-intervention model, oral administration of the engineered phage 32H-hilE shortly after a lethal Salmonella challenge led to a significant increase in survival. No noticeable side effects were observed in mice treated with the engineered phage alone. These results suggest the relevance of the engineered phages that suppress the Salmonella virulence network as alternative anti-Salmonella agents without resistance concerns. This proof-of-concept study of anti-virulence phages could open a new avenue for controlling pathogenic bacteria using engineered temperate phages as vectors of anti-virulence factors.
{"title":"Disarming Salmonella virulence with 32H-hilE anti-virulence bacteriophage","authors":"Jinwoo Kim , Haejoon Park , Young Hyun Jung , Ho Jae Han , Doyeon Kim , Sangryeol Ryu , Minsik Kim","doi":"10.1016/j.micres.2025.128396","DOIUrl":"10.1016/j.micres.2025.128396","url":null,"abstract":"<div><div>As the development of new antibiotics struggles with the continuous emergence of drug-resistant bacteria, targeting bacterial virulence factors instead of viability has been proposed as one of the alternative approaches to combat the pathogens. Here, we genetically engineered the temperate phage SPC32H to serve as a delivery vehicle for key negative regulators of <em>Salmonella</em> virulence to inhibit <em>Salmonella</em> infection. Negative regulator genes associated with <em>Salmonella</em> pathogenicity island 1 (SPI1), <em>hilE</em>, <em>csrA</em>, and <em>lrp</em>, were inserted into the phage SPC32H genome and expressed under a strong constitutive promoter. When <em>Salmonella</em> cells lysogenized by the engineered phages were exposed to the virulence-inducing condition, the expression of key positive regulators and major virulence factors associated with SPI1 was significantly reduced. Furthermore, in a murine early-intervention model, oral administration of the engineered phage 32H-<em>hilE</em> shortly after a lethal <em>Salmonella</em> challenge led to a significant increase in survival. No noticeable side effects were observed in mice treated with the engineered phage alone. These results suggest the relevance of the engineered phages that suppress the <em>Salmonella</em> virulence network as alternative anti-<em>Salmonella</em> agents without resistance concerns. This proof-of-concept study of anti-virulence phages could open a new avenue for controlling pathogenic bacteria using engineered temperate phages as vectors of anti-virulence factors.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128396"},"PeriodicalIF":6.9,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145517481","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 : 2025-11-07DOI: 10.1016/j.micres.2025.128387
Hokuto Ohtsuka, Takafumi Shimasaki, Hirofumi Aiba
In nature, nutrient-poor environments are more common than exposure to nutrient-rich environments, and living organisms have developed countermeasures to survive nutrient starvation. Increasing research has revealed beneficial aspects of starvation for an individual’s life, including lifespan extension. The fission yeast Schizosaccharomyces pombe is a model unicellular eukaryotic organism and has greatly contributed to the understanding of various cellular processes, including the cell cycle, cell morphology, sexual development, cell lifespan, and nutritional responses. Traditionally, research on starvation in fission yeast has focused on glucose starvation and nitrogen starvation. Recently, studies on cellular responses to the starvation of various nutrients, such as phosphorus, sulfur, iron, zinc, copper, and amino acids have been reported, revealing similarities and differences among the various types of nutrient starvation. In fission yeast, Ecl proteins, which are conserved among fungi, can sense the starvation of multiple nutrients. These proteins also repress the target of rapamycin complex 1 (TORC1), which is conserved across eukaryotes. They channel a variety of starvation signals into common cellular responses, such as growth arrest, sexual differentiation, autophagy, and lifespan extension. This review summarizes and discusses the signaling mechanisms involved in the initial cellular responses of fission yeast to the starvation of various nutrients.
{"title":"Responses to nutrient starvation in the fission yeast Schizosaccharomyces pombe","authors":"Hokuto Ohtsuka, Takafumi Shimasaki, Hirofumi Aiba","doi":"10.1016/j.micres.2025.128387","DOIUrl":"10.1016/j.micres.2025.128387","url":null,"abstract":"<div><div>In nature, nutrient-poor environments are more common than exposure to nutrient-rich environments, and living organisms have developed countermeasures to survive nutrient starvation. Increasing research has revealed beneficial aspects of starvation for an individual’s life, including lifespan extension. The fission yeast <em>Schizosaccharomyces pombe</em> is a model unicellular eukaryotic organism and has greatly contributed to the understanding of various cellular processes, including the cell cycle, cell morphology, sexual development, cell lifespan, and nutritional responses. Traditionally, research on starvation in fission yeast has focused on glucose starvation and nitrogen starvation. Recently, studies on cellular responses to the starvation of various nutrients, such as phosphorus, sulfur, iron, zinc, copper, and amino acids have been reported, revealing similarities and differences among the various types of nutrient starvation. In fission yeast, Ecl proteins, which are conserved among fungi, can sense the starvation of multiple nutrients. These proteins also repress the target of rapamycin complex 1 (TORC1), which is conserved across eukaryotes. They channel a variety of starvation signals into common cellular responses, such as growth arrest, sexual differentiation, autophagy, and lifespan extension. This review summarizes and discusses the signaling mechanisms involved in the initial cellular responses of fission yeast to the starvation of various nutrients.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128387"},"PeriodicalIF":6.9,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145495840","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 : 2025-11-07DOI: 10.1016/j.micres.2025.128394
Lizhen Li , Shaocong Huang , Zhiyi Bai , Hao Xu , Qun Ji , Wei Song
The development of the digestive system and its interaction with microbiota are critical for fish growth and health. Transcriptomic and 16S rRNA sequencing analyses were conducted to investigate the gene expression profiles of the digestive system and microbial community dynamics in Larimichthys crocea from the embryonic stage to day 28 to elucidate their potential roles in larval and juvenile development and their associations with immune and metabolic functions. The results revealed stage-specific changes in gene expression and microbial composition during development, and two critical transitional phases were identified: day 1 vs embryonic stage (C1 vs CE) and day 15 vs day 9 (C15 vs C9). Microbial succession demonstrated clear temporal characteristics: Pseudoalteromonas were dominant during the embryonic stage (CE), which was succeeded by Stenotrophomonas after hatching (C1, C3, C4, and C9), by Cohaesibacter on day 15 (C15), and by Psychrobacter as the core genus after formulated feed introduction on day 19. Functional enrichment analyses revealed predominant enrichment of differentially expressed genes in immune- and metabolic-related pathways, such as calcium signaling, steroid biosynthesis, and amino acid metabolism. Weighted gene co-expression network and correlation analyses revealed significant associations between specific genera (e.g., Rhodococcus and Psychrobacter) and immune- and metabolism-related genes. This study analyzed the developmental patterns of the digestive system of L. crocea and revealed significant correlations between shifts in the microbiota and host metabolism and immunity, highlighting the close association between the microbiota and metabolic and immune responses.
消化系统的发育及其与微生物群的相互作用对鱼类的生长和健康至关重要。通过转录组学和16S rRNA测序分析，研究了胭脂鱼（Larimichthys crocea）从胚胎期到第28天消化系统和微生物群落动态的基因表达谱，以阐明其在幼虫和幼鱼发育中的潜在作用及其与免疫和代谢功能的关联。结果揭示了发育过程中基因表达和微生物组成的阶段性变化，并确定了两个关键过渡阶段：第1天与胚胎期（C1 vs CE）和第15天与第9天（C15 vs C9）。微生物演替表现出明显的时间特征：假互变单胞菌在胚胎期（CE）占主导地位，孵化后为窄养单胞菌（C1、C3、C4和C9），第15天为Cohaesibacter (C15)，第19天引入配方饲料后为Psychrobacter成为核心属。功能富集分析显示，差异表达基因主要富集于免疫和代谢相关途径，如钙信号、类固醇生物合成和氨基酸代谢。加权基因共表达网络和相关分析显示，特定属（如红球菌和冷杆菌）与免疫和代谢相关基因之间存在显著关联。本研究分析了羊草消化系统的发育模式，揭示了微生物群的变化与宿主代谢和免疫之间的显著相关性，强调了微生物群与代谢和免疫应答之间的密切联系。
{"title":"Combined transcriptome and microbiome characterization highlights digestive system development involved in the metabolism and immunity of the large yellow croaker (Larimichthys crocea)","authors":"Lizhen Li , Shaocong Huang , Zhiyi Bai , Hao Xu , Qun Ji , Wei Song","doi":"10.1016/j.micres.2025.128394","DOIUrl":"10.1016/j.micres.2025.128394","url":null,"abstract":"<div><div>The development of the digestive system and its interaction with microbiota are critical for fish growth and health. Transcriptomic and 16S rRNA sequencing analyses were conducted to investigate the gene expression profiles of the digestive system and microbial community dynamics in <em>Larimichthys crocea</em> from the embryonic stage to day 28 to elucidate their potential roles in larval and juvenile development and their associations with immune and metabolic functions. The results revealed stage-specific changes in gene expression and microbial composition during development, and two critical transitional phases were identified: day 1 vs embryonic stage (C1 vs CE) and day 15 vs day 9 (C15 vs C9). Microbial succession demonstrated clear temporal characteristics: <em>Pseudoalteromonas</em> were dominant during the embryonic stage (CE), which was succeeded by <em>Stenotrophomonas</em> after hatching (C1, C3, C4, and C9), by <em>Cohaesibacter</em> on day 15 (C15), and by <em>Psychrobacter</em> as the core genus after formulated feed introduction on day 19. Functional enrichment analyses revealed predominant enrichment of differentially expressed genes in immune- and metabolic-related pathways, such as calcium signaling, steroid biosynthesis, and amino acid metabolism. Weighted gene co-expression network and correlation analyses revealed significant associations between specific genera (e.g., <em>Rhodococcus</em> and <em>Psychrobacter</em>) and immune- and metabolism-related genes. This study analyzed the developmental patterns of the digestive system of <em>L. crocea</em> and revealed significant correlations between shifts in the microbiota and host metabolism and immunity, highlighting the close association between the microbiota and metabolic and immune responses.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128394"},"PeriodicalIF":6.9,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145568959","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}
Post-stroke depression (PSD), a frequent and debilitating complication after stroke, severely hinders rehabilitation. Emerging evidence underscores the role of neuroinflammation and the gut microbiota in PSD pathogenesis. This review systematically elaborates the mechanisms by which gut dysbiosis contributes to PSD-related neuroinflammation via immune cell regulation (e.g., Treg/Th17 balance), microbial metabolites (e.g., SCFAs, tryptophan derivatives), and neural pathways (vagus nerve, HPA axis). A key focus is the comparative analysis of the gut microbiota in PSD against major depressive disorder (MDD) and Alzheimer's disease (AD), revealing a unique, stroke-induced microbial signature characterized by a loss of protective symbionts and a bloom of pro-inflammatory taxa. We further discuss the translational potential of microbiota-targeted interventions (e.g., probiotics, prebiotics) for PSD. By integrating clinical microbial ecology with mechanistic insights, this review synthesizes evidence suggesting that the gut microbiome may represent a promising diagnostic and therapeutic target for PSD, offering a distinct perspective from previous literature.
{"title":"The gut microbiota in post-stroke depression: A systematic review of microbial mechanisms and therapeutic targeting of neuroinflammation","authors":"Qianwen Zhang , Shiqing Zhang , Xingqin Cao , Yinghao Zhi , Ying Guo","doi":"10.1016/j.micres.2025.128391","DOIUrl":"10.1016/j.micres.2025.128391","url":null,"abstract":"<div><div>Post-stroke depression (PSD), a frequent and debilitating complication after stroke, severely hinders rehabilitation. Emerging evidence underscores the role of neuroinflammation and the gut microbiota in PSD pathogenesis. This review systematically elaborates the mechanisms by which gut dysbiosis contributes to PSD-related neuroinflammation via immune cell regulation (e.g., Treg/Th17 balance), microbial metabolites (e.g., SCFAs, tryptophan derivatives), and neural pathways (vagus nerve, HPA axis). A key focus is the comparative analysis of the gut microbiota in PSD against major depressive disorder (MDD) and Alzheimer's disease (AD), revealing a unique, stroke-induced microbial signature characterized by a loss of protective symbionts and a bloom of pro-inflammatory taxa. We further discuss the translational potential of microbiota-targeted interventions (e.g., probiotics, prebiotics) for PSD. By integrating clinical microbial ecology with mechanistic insights, this review synthesizes evidence suggesting that the gut microbiome may represent a promising diagnostic and therapeutic target for PSD, offering a distinct perspective from previous literature.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128391"},"PeriodicalIF":6.9,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145557409","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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