Microbiological research最新文献_第6页

Regulatory effect of fadR on the inhibition of Aspergillus flavus infection of walnut kernels by Enterobacter ludwigii AA4 fadR对路德维希肠杆菌AA4对核桃仁黄曲霉侵染的抑制作用

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2025-11-25 DOI: 10.1016/j.micres.2025.128402

Zhibo Yuan , Yibo Zan , Xu Li , Bin Lu , Yanjie Chao , Xinwu Xiong , Yanpo Yao , Di Wu , Ben Niu , Dong Pei

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 Aspergillus flavus 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 Enterobacter ludwigii AA4 against the growth of A. flavus colonizing walnut kernels and aflatoxin B₁ production. Mutant E. ludwigii AA4 strains, generated by genetically modifying five biofilm-related genes, notably fadR (which encodes a transcriptional regulator), exhibited significantly impaired biofilm development and reduced efficacy in suppressing A. flavus. These results indicated that biofilm establishment is indispensable for the inhibitory effect of E. ludwigii AA4 against A. flavus. We further investigated the kernel colonization of fadR knockout mutant, which exhibited the most pronounced reduction in biofilm formation, via colony counting and laser scanning confocal microscopy. We found that fadR contributed to the suppression of A. flavus by influencing bacterial biofilm production and kernel settlement. Gene expression analysis and site-directed mutagenesis revealed that fadR modulated biofilm development by negatively regulating the transcription of rcsA, 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 A. flavus contamination in walnut kernels.

坚果的霉菌毒素污染通常归因于储存不当，在全球造成重大经济损失和健康问题。利用有益微生物进行生物防治已成为一种有效减轻食品中黄曲霉污染和随之消除霉菌毒素的环境友好型方法。然而，这些生物防治微生物保护坚果免受这种产毒真菌侵害的确切机制在很大程度上仍然未知。通过真菌感染实验，我们观察到路德维希肠杆菌AA4对黄曲霉定殖核桃仁的生长和黄曲霉毒素B1的产生有显著的抑制作用。通过基因修饰5个生物膜相关基因（尤其是编码转录调控因子的fadR）而产生的突变株ludwigii AA4，其生物膜发育明显受损，抑制黄曲霉的效果降低。这些结果表明，生物膜的建立是路德维希菌AA4对黄曲霉产生抑制作用的必要条件。我们通过菌落计数和激光扫描共聚焦显微镜进一步研究了fadR敲除突变体的内核定植，该突变体表现出最明显的生物膜形成减少。我们发现，fadR通过影响细菌生物膜的生成和果仁沉降来抑制黄曲霉的生长。基因表达分析和位点定向诱变表明，fadR通过负调控Rcs磷酸化接力系统中的辅助蛋白基因rcsA的转录，可能通过影响乙酰磷酸介导的RcsB磷酸化来调节生物膜的发育。这些发现突出了AA4在生物防治黄曲霉污染核桃仁中的潜力。

{"title":"Regulatory effect of fadR on the inhibition of Aspergillus flavus infection of walnut kernels by Enterobacter ludwigii AA4","authors":"Zhibo Yuan , Yibo Zan , Xu Li , Bin Lu , Yanjie Chao , Xinwu Xiong , Yanpo Yao , Di Wu , Ben Niu , 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 B<sub>1</sub> 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":"2025-11-25","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}

引用次数: 0

Trichoderma bio-organic fertilizer modulates the rhizosphere microbiome and Bacillus-assisted plant hormone regulation to promote pear rootstock growth 木霉生物有机肥调节根际微生物群和芽孢杆菌辅助植物激素调节促进梨砧木生长

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2025-11-21 DOI: 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.

容器生长的梨在重质粘土中生长。基于木霉的生物有机肥（BOF）可以提高幼苗性能，但BOF如何在这种条件下调动微生物-激素相互作用尚不清楚。本研究采用盆栽试验方法，在控制条件下，采用水分控制（CK）、10 % (v/v) BOF和20 % (v/v) BOF三种处理，对植物生长、根激素分布和根际群落进行了评价。当BOF为20 %时，幼苗高、根长和根生物量增加（分别为+131 %、+160 %和+165 %），细菌多样性增加，其中厚壁菌门/放线菌门数量增加8.3倍。发酵滤液支持分离的芽孢杆菌生长。芽孢杆菌丰度与吲哚-3-乙酸（IAA）和异戊烯腺嘌呤（IP）呈正相关，与脱落酸（ABA）呈负相关（P <； 0.05）。同样，木霉和芽孢杆菌共接种提高了IAA/IP，降低了ABA (P <； 0.05)，比单独接种产生更强的生长反应。这些发现概述了一种由bof介导的途径，其中木霉引导的微生物组重组与木霉响应芽孢杆菌一起，重新平衡IAA/IP/ABA并促进梨砧木生长。

{"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}

引用次数: 0

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 假单胞菌蛋白CS11的基因组和功能分析揭示了番茄菌核病的多重生物防治机制，包括抗真菌代谢产物、根定植和植物防御诱导

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2025-11-19 DOI: 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.

菌核菌是威胁全球作物生产的众多真菌病原体之一。拮抗根瘤菌已成为合成农药的有前途的环保替代品，可用于有效和可持续的真菌疾病管理。从本研究分离的60株根瘤菌中，有8株能够抑制菌核葡萄球菌的体外生长。其中，菌株CS11表现出完全抑制作用（100% %），并表现出多种促进植物生长的性状，包括铁载体产生、氮同化、磷酸盐溶解和裂解酶活性。运动性和根定植试验证实CS11具有高运动性和有效的根际建立。通过16S rRNA测序和多位点序列分析，鉴定CS11为假单胞菌蛋白。全基因组测序揭示了关键抗真菌代谢物的基因簇，包括2,4-二乙酰间苯三酚、pyoluteorin、pyrrolnitrin、氰化氢和orfamides，它们与假单胞菌广泛相关。尽管与P. protegens CHA0密切相关，CS11还具有与蛋白酶产生（耐热碱性蛋白酶）、根定植（环二gmp磷酸二酯酶）和根际适应性（群体感知相关基因）相关的额外编码序列。突出其新颖性和强大的生物防治潜力。在温室试验中，用CS11处理菌核葡萄球菌感染的番茄植株，可以完全抑制疾病进展，显著提高植株高度和叶绿素含量。与未处理的植物相比，cs11处理的植物GLU、Chi、PAL和PPO活性升高，RT-qPCR分析显示水杨酸（PR1、PR2、PR5）和茉莉酸（PR3、PR4、PDF1.2、VSP2）途径基因上调。总之，这些发现确定了P. protegens CS11是开发生物农药的一个有希望的候选者，以控制真菌病原体和增强植物防御。

{"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}

引用次数: 0

Eight-year effect of biochar amendment on soil properties, extracellular enzyme activity, N-cycling genes and microbiome structure in two Danish fallow soils 8年生物炭对两种丹麦休耕土壤性状、胞外酶活性、氮循环基因和微生物组结构的影响

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2025-11-12 DOI: 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.

生物炭改善农业土壤性质和短期微生物多样性。然而，生物炭对微生物群和土壤健康的长期影响仍然知之甚少。本研究评估了在温带气候条件下，8年野外陈化的生物炭对两种对比土壤（砂质粘土和粗砂质土壤）微生物组的影响。我们假设，即使在8年后，生物炭的添加也会持续改变土壤的理化性质，刺激细胞外酶活性，增加n循环基因的丰度，并改变原核生物和真菌的群落结构。2015年6月，在田间溶渗器的表层土壤中添加2 % w/w的秸秆生物炭，到2023年8月，这种生物炭的添加导致两种土壤中参与C、P和S循环的5种关键细胞外酶（α-葡萄糖苷酶、β-半乳糖苷酶、纤维生物苷酶、磷酸单酯酶和芳香硫酸酯酶）的活性显著增加。在粗砂质土壤中，生物炭提高了原核生物（16S rRNA基因）、关键硝化基因（AOA-amoA和AOB-amoA）和反硝化基因nosZ Clade i的丰度，增加了亚硝酸盐还原酶（nirS）基因的丰度，表明对N循环有持续的影响，并增加了亚硝化菌科氨氧化古菌的富集。最后，在两种土壤中观察到原核生物群落结构的持续变化。这项研究清楚地表明，生物炭的影响在8年后仍会持续，这为生物炭对土壤健康的长期影响提供了见解。

{"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}

引用次数: 0

Rhizosphere microbiota diversity and salt stress–alleviating functional genes in coastal wild salt-tolerant plants 沿海野生耐盐植物根际微生物群多样性与盐胁迫缓解功能基因

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2025-11-11 DOI: 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.

盐碱地严重威胁着全球粮食安全和生态安全，根系相关微生物帮助植物在盐碱胁迫下生存。然而，影响耐盐植物根际微生物群的生态功能和因素仍然知之甚少。本研究利用高通量测序和宏基因组学技术，揭示了盐碱地中耐盐植物（Suaeda glauca, Phragmites australis，和互花米草）块状土壤和根际土壤的微生物群落和功能特征。与非根际土壤相比，根际土壤中细菌和真菌分类群明显丰富。宏基因组分析显示，代谢途径，包括糖酵解和ABC转运蛋白，在根际高度富集。功能分析表明，盐胁迫相关途径在假单胞菌属和假单胞菌属中更为丰富。与植物促生长性状相关的功能基因丰度在根际土壤中高于非根际土壤，主要受土壤盐分、全氮含量和全碳含量的驱动。此外，从互花荆芥根际获得的铜绿假单胞菌具有较高的增磷效率（908.38 μg/mL）、固氮活性（2.84 μg/mL）和耐盐性（≦5 % NaCl）。研究结果表明，耐盐植物通过控制根际微环境，减轻盐胁迫影响微生物活性，为盐碱地垦殖微生物靶向接种剂的开发提供了科学和实践依据。

{"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}

引用次数: 0

Chlamydia trachomatis highjacks host MYO1C for actin cage recruitment at the bacterial inclusion 沙眼衣原体劫持宿主MYO1C，在细菌包涵体处进行肌动蛋白笼募集

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2025-11-11 DOI: 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}

引用次数: 0

Cellular responses of Aspergillus sydowii to growth at extreme chaotropic concentrations of MgCl2 西多曲霉对MgCl2极端混沌浓度下生长的细胞反应。

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2025-11-10 DOI: 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.

微生物对盐胁迫的适应性研究，特别是真菌的适应性研究，主要集中在高浓度NaCl环境下。其他无机盐对生物系统的影响鲜为人知。本文研究了朝向盐MgCl2（0-2.0 M）对嗜盐真菌西多曲霉（EXF-12860）的影响，并将其与朝向盐NaCl的影响进行了比较。虽然以前认为致命的MgCl2浓度（高达2.0 M）会使A. sydowii繁殖，但观察到形态学、生理、代谢和分子反应的差异。在0.5-1.0 M浓度下，两种盐的生长速率相似，但较高的MgCl2浓度（1.5-2.0 M）显著抑制了生长，减少了菌丝伸长，降低了细胞密度。在NaCl存在下的生长过程中，利用了广泛的碳源，但高浓度的MgCl2干扰了底物代谢和代谢活性的不耦合生长。两种盐均诱导相容溶质（甘油、赤藓糖醇）的产生，且在MgCl2下积累量更高。MgCl2处理下的氧化应激反应也更强，包括过氧化氢酶和谷胱甘肽过氧化物酶活性增加。转录组学分析显示，MgCl2胁迫下基因表达发生显著变化，离子转运、细胞壁重塑、甘油生物合成和氧化防御途径上调。相比之下，NaCl引发的反应主要集中在渗透平衡和维持细胞完整性上。这些发现强调了对混沌环境中微生物耐受机制进行更深入研究的必要性。

{"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}

引用次数: 0

Disarming Salmonella virulence with 32H-hilE anti-virulence bacteriophage 用32h -hil抗毒噬菌体解除沙门氏菌的毒力

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2025-11-10 DOI: 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.

随着新抗生素的开发与耐药细菌的不断出现作斗争，针对细菌毒力因子而不是生存力已被提出作为对抗病原体的替代方法之一。在这里，我们对温带噬菌体SPC32H进行基因工程改造，使其成为沙门氏菌毒力关键负调节因子的递送载体，以抑制沙门氏菌感染。将与沙门氏菌致病性岛1 （SPI1）相关的负调控基因hil、csrA和lrp插入噬菌体SPC32H基因组，并在强组成启动子下表达。当经工程噬菌体溶原的沙门氏菌细胞暴露于毒力诱导条件下时，SPI1相关的关键阳性调节因子和主要毒力因子的表达显著降低。此外，在小鼠早期干预模型中，在致命沙门氏菌攻击后不久口服工程噬菌体32H-hilE可显著提高存活率。在单独使用工程噬菌体治疗的小鼠中未观察到明显的副作用。这些结果表明，抑制沙门氏菌毒力网络的工程噬菌体作为无耐药性问题的替代抗沙门氏菌剂的相关性。这一抗毒力噬菌体的概念验证研究为利用工程温带噬菌体作为抗毒因子载体控制致病菌开辟了新的途径。

{"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}

引用次数: 0

Responses to nutrient starvation in the fission yeast Schizosaccharomyces pombe 分裂酵母对营养饥饿的反应。

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2025-11-07 DOI: 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.

在自然界中，营养贫乏的环境比营养丰富的环境更常见，生物已经发展出应对营养饥饿的对策。越来越多的研究揭示了饥饿对人的生命有益的方面，包括延长寿命。裂糖酵母（Schizosaccharomyces pombe）是一种典型的单细胞真核生物，对了解细胞周期、细胞形态、性发育、细胞寿命和营养反应等细胞过程做出了重要贡献。传统上对裂变酵母饥饿的研究主要集中在葡萄糖饥饿和氮饥饿两方面。近年来，关于细胞对磷、硫、铁、锌、铜和氨基酸等多种营养物质饥饿反应的研究已被报道，揭示了各种营养物质饥饿的异同。在裂变酵母中，在真菌中保守的Ecl蛋白可以感知多种营养物质的饥饿。这些蛋白也抑制雷帕霉素复合体1 （TORC1）的靶标，这在真核生物中是保守的。它们将各种饥饿信号转化为常见的细胞反应，如生长停滞、性别分化、自噬和寿命延长。本文综述并讨论了裂变酵母对各种营养物质饥饿的初始细胞反应的信号机制。

{"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}

引用次数: 0

Combined transcriptome and microbiome characterization highlights digestive system development involved in the metabolism and immunity of the large yellow croaker (Larimichthys crocea) 转录组学和微生物组学的结合研究揭示了大黄鱼代谢和免疫过程中消化系统的发育

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2025-11-07 DOI: 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}

引用次数: 0