Microbiological research最新文献_第6页

Microbial strategies for soda saline-alkali soil remediation: The role of haloalkaliphilic bacteria 钠盐碱土壤修复的微生物策略：嗜盐嗜碱菌的作用。

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-03-01 Epub Date: 2025-11-28 DOI: 10.1016/j.micres.2025.128410

Bonaventure Chidi Ezenwanne , Charles Obinwanne Okoye , Huifang Jiang , Lu Gao , Xunfeng Chen , Yanfang Wu , Jianxiong Jiang

Global agriculture is increasingly constrained by soil degradation, with salinization and alkalization reducing crop productivity, soil function, and long-term ecosystem stability. Among salt-affected soils, soda saline-alkali soils represent a particularly challenging subtype, characterized by excessive accumulation of soluble salts, elevated pH, and high sodium content, all of which exacerbate soil structural decline. Haloalkaliphilic bacteria, adapted to high salinity and alkalinity, offer a sustainable bioremediation strategy. This review presents a conceptual framework elucidating the mechanisms by which haloalkaliphilic bacteria mitigate soda saline-alkali stress through osmoprotectant synthesis, ion homeostasis regulation, pH neutralization, extracellular polymeric substance (EPS) formation, and extremozyme activity, thereby enhancing nutrient mobilization and organic-matter turnover. These microbial processes facilitate contaminant degradation and stimulate plant growth by improving nutrient availability and promoting phytohormone production. The resulting plant-microbe synergy translates microbial activity into enhanced soil function by reducing bulk salinity and pH, improving structure and water retention, and promoting overall soil fertility. This review further identifies critical challenges to translating mechanistic insights into field practice, including ecological variability, inoculant efficacy and resilience, regulatory frameworks, scalable inoculant manufacturing, a paucity of multi-season field trials, and socioeconomic constraints. Prospects include integrative multi-omics to link gene expression with ecosystem outcomes; systematic exploration of extremozymes; incorporation of nutrient-rich biomass for consortium support; AI-guided consortia design and predictive modeling for site-specific optimization, and long-term monitoring. These strategies enhance our understanding of tolerance to high salinity and alkalinity, paving the way for innovative microbial interventions to restore soda saline-alkali soils and support more resilient, sustainable agricultural systems.

全球农业日益受到土壤退化的制约，盐碱化和碱化降低了作物生产力、土壤功能和长期生态系统的稳定性。在受盐影响的土壤中，钠盐碱土壤是一种特别具有挑战性的土壤类型，其特征是可溶性盐的过度积累，pH值升高，钠含量高，所有这些都加剧了土壤的结构衰退。嗜盐嗜碱菌，适应高盐度和高碱度，提供了一个可持续的生物修复策略。本文综述了嗜盐嗜碱菌通过渗透保护剂合成、离子稳态调节、pH中和、细胞外聚合物质（EPS）形成和极端酶活性来缓解钠盐碱胁迫的机制，从而增强营养物质的动员和有机物的转化。这些微生物过程通过改善养分利用率和促进植物激素的产生来促进污染物降解和刺激植物生长。由此产生的植物-微生物协同作用将微生物活性转化为增强土壤功能，通过降低总体盐度和pH值，改善结构和保水性，促进土壤整体肥力。这篇综述进一步确定了将机理见解转化为现场实践的关键挑战，包括生态变变性、接种剂的有效性和弹性、监管框架、可扩展的接种剂制造、缺乏多季节的现场试验以及社会经济限制。前景包括整合多组学，将基因表达与生态系统结果联系起来；极端酶的系统探索；将营养丰富的生物质纳入财团支持；人工智能引导的联盟设计和预测建模，用于特定站点的优化和长期监测。这些策略增强了我们对高盐度和高碱度耐受性的理解，为创新微生物干预措施铺平了道路，以恢复苏打盐碱土壤，并支持更具弹性、可持续的农业系统。

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引用次数: 0

Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis 综合多组学研究了微藻对当归生长、品质、植物激素和根际微生物群的影响

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-03-01 Epub Date: 2025-12-11 DOI: 10.1016/j.micres.2025.128418

Tao Yang , Yulong Zhan , Jie Sha , Jiang Zhao , Chengniu Wang , Tong Peng , Lei Zhang

Microalgae have recently been recognized as sustainable biofertilizers that improve soil fertility while enhancing crop performance. However, their roles in regulating medicinal plant growth and quality, as well as the underlying ecological mechanisms, remain poorly understood. In this study, we systematically assessed the effects of three representative microalgae—Anabaena cylindrica (AC), Phormidium tenue (PT), and Chlorella vulgaris (CV)—on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of Angelica sinensis. Field inoculation trials demonstrated that all three microalgae significantly promoted biomass accumulation and increased antioxidant capacity. AC and CV further enhanced the accumulation of ferulic acid and flavonoids, which are two key quality determinants. Microalgal inoculation significantly altered rhizosphere soil properties by increasing total organic carbon and alkali-hydrolyzable nitrogen, with AC uniquely elevating available phosphorus and iron. Metagenomic analysis revealed that AC and PT stimulated nitrification while suppressing denitrification, thereby reducing nitrogen loss and stabilizing the soil nitrogen pools. Distinct microbial taxa, including Rhodanobacter, Streptomyces, and Pseudomonas, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed A. sinensis phytohormone profiles in a species-specific manner. Partial least squares path modeling suggested that AC and CV promote ferulic acid biosynthesis through distinct mechanisms, with AC associated with reduced investment in C-mineralization processes and CV associated with lower salicylic acid levels, whereas PT enhances biomass accumulation mainly by stimulating N-cycle processes. Collectively, this study provides integrated evidence linking microalgae-mediated nutrient cycling, rhizosphere microbiome shifts and hormonal regulation to enhanced quality formation in A. sinensis.

微藻最近被认为是一种可持续的生物肥料，可以提高土壤肥力，同时提高作物性能。然而，它们在调节药用植物生长和质量中的作用以及潜在的生态机制仍然知之甚少。本研究系统评价了3种具有代表性的微藻——白茅水藻（anabaena ica， AC）、黄颡鱼（Phormidium tenue， PT）和小球藻（Chlorella vulgaris， CV）对当归生长、品质、激素调节、土壤养分动态和根际微生物群的影响。田间接种试验表明，三种微藻均能显著促进生物量积累，提高抗氧化能力。AC和CV进一步促进了阿魏酸和黄酮类化合物的积累，这是两个关键的品质决定因素。接种微藻显著改变了根际土壤性质，增加了总有机碳和碱解氮，其中AC显著提高了有效磷和有效铁。宏基因组分析表明，AC和PT在促进硝化作用的同时抑制反硝化作用，从而减少氮的损失，稳定土壤氮库。不同的微生物类群，包括罗丹诺杆菌、链霉菌和假单胞菌，被确定为碳和氮循环的主要贡献者。激素代谢组学研究表明，微藻接种以一种特定的方式重新编程了中华黄芪的植物激素谱。偏最小二乘路径模型表明，AC和CV通过不同的机制促进阿魏酸的生物合成，AC与减少c矿化过程的投资有关，CV与降低水杨酸水平有关，而PT主要通过刺激n循环过程来促进生物量积累。总的来说，本研究提供了微藻介导的营养循环、根际微生物群变化和激素调节与中华沙棘品质形成增强有关的综合证据。

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引用次数: 0

Understanding the dynamics of Pseudomonas syringae tailocin targeting allows for predictive protective microbial inoculation of Actinidia chinensis 了解丁香假单胞菌的靶向动力学，可以预测中华猕猴桃的保护性微生物接种

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-03-01 Epub Date: 2025-11-28 DOI: 10.1016/j.micres.2025.128401

Banyon H. Carnell , Jay Jayaraman , Jose Benjamin P. Dar Juan , Matthew D. Templeton , Iain D. Hay

The Pseudomonas syringae complex is an important group within the Gammaproteobacteria and comprises several pathovars of agricultural significance. Genome mining of the P. syringae species complex has uncovered high-molecular-weight phage tail complexes termed tailocins. Tailocins exert specific bactericidal action against both closely and more distantly related bacteria and significantly shape the ecology of the microbiome. Tailocin targeting specificity is currently understood to be dependent on tail-fibers (TFs) binding to specific molecular epitopes, including lipopolysaccharide (LPS) as a bacterial cell surface receptor for tailocin TF-targeting domains. Recent work in P. syringae has strongly correlated variation at the common polysaccharide antigen of LPS with tailocin sensitivity. Here we provide biochemical evidence for LPS as the major receptor for P. syringae tailocins; examine the mechanisms and genetic basis of tailocin TF targeting; and predict strains that can provide protective colonization of plants. We then use the understanding of these mechanisms that determine the tailocin targeting spectrum and genetic knockouts and complementation to modify the bacterial canker pathogen of kiwifruit plants to predict LPS-mediated tailocin targeting by naturally occurring host microbiota, and then demonstrate the efficacy of these applied microbiome-derived tailocin-carrying commensal strains as biocontrol agents.

丁香假单胞菌复合体是γ -变形菌门中一个重要的类群，由几种具有农业意义的病原菌组成。基因组挖掘的紫丁香属物种复合体已经发现了高分子量的噬菌体尾部复合体称为tailocins。Tailocins对亲缘关系较近和较远的细菌都具有特定的杀菌作用，并显著地塑造了微生物群的生态。目前认为，Tailocin靶向特异性依赖于尾巴纤维（tail-fibers, TFs）与特定分子表位的结合，包括脂多糖（LPS）作为Tailocin tf靶向结构域的细菌细胞表面受体。近年来对丁香属植物的研究表明，多糖抗原的变化与丁香素的敏感性密切相关。本研究为LPS为丁香假单胞菌的主要受体提供了生物化学证据；研究tailocin TF靶向的机制和遗传基础；并预测可以为植物提供保护性定植的菌株。然后，我们利用对这些机制的理解，确定tailocin靶向谱和基因敲除和互补来修饰猕猴桃植物的细菌溃疡病病原体，预测自然存在的宿主微生物群通过lps介导的tailocin靶向，然后证明这些应用微生物组衍生的携带tailocin的共生菌株作为生物防治剂的有效性。

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引用次数: 0

Characterization of novel Vibrio phages as potential biocontrol agents against Vibrio alginolyticus and insights into its phage-resistant mutant 新型噬菌体作为溶藻弧菌潜在生物防治剂的特性及其噬菌体抗性突变体的研究

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-03-01 Epub Date: 2025-12-08 DOI: 10.1016/j.micres.2025.128412

Roshan Nepal , Tony Charles , George Bouras , Richard S. Taylor , James W. Wynne

Pathogenic bacteria are an ongoing threat to intensive agriculture, including aquaculture. With the emergence of antimicrobial resistance (AMR), novel non-traditional antimicrobials are urgently needed to minimize the dependence on antibiotics. Bacteriophage (phage) therapy, which uses naturally occurring viruses to kill specific bacterium, is gaining interest and offers huge potential for targeted pathogen control in aquaculture. However, many challenges regarding stability and emergence of phage-resistance must be overcome. Here, we isolated and characterized eight Vibrio phages against an emerging aquaculture pathogen Vibrio alginolyticus and studied their bactericidal and antibiofilm potency. We then used next-generation sequencing to understand how the Vibrio species may gain phage resistance. Our results indicated that most of the isolated Vibrio phages (seven out of eight) shared < 40 % genomic similarity with phages isolated elsewhere, possibly suggesting novel strains. The phages were stable in different temperatures (4–40 °C), pHs (3−10) and salinities (0–50 ppt) up to 6 h without significant loss in viability. Although individual phages had variable bactericidal efficiency and bacteria rapidly developed phage-resistance, phage cocktail formulations were highly efficient and significantly suppressed bacterial growth up to 15 h, inhibited biofilm formation (p < 0.05) and eradicated established biofilms (p < 0.05). Sequencing confirmed absence of lysogeny modules, known toxins and AMR genes in seven of the phages. Further, tRNAs and a putative anti-CRISPR (Acr) protein was found in two of the most efficient phages. Though bacteria rapidly developed phage-resistance, we observed increased antibiotic sensitivity as a trade-off which possibly resulted from defective efflux pump. Our findings support potential applications of Vibrio phages in aquaculture systems for minimizing the burden of Vibriosis. However, further research is required to elucidate the role of efflux pump system in phage-resistance and antimicrobial resistance.

致病菌对包括水产养殖在内的集约化农业构成持续威胁。随着抗菌素耐药性（AMR）的出现，迫切需要新的非传统抗菌素以尽量减少对抗生素的依赖。噬菌体疗法是一种利用自然产生的病毒杀死特定细菌的疗法，它正在引起人们的兴趣，并为水产养殖中的靶向病原体控制提供了巨大的潜力。然而，关于噬菌体耐药性的稳定性和出现的许多挑战必须克服。在这里，我们分离并鉴定了8种抗新兴水产养殖病原体溶藻弧菌的噬菌体，并研究了它们的杀菌和抗膜效力。然后，我们使用下一代测序来了解弧菌物种如何获得噬菌体抗性。我们的结果表明，大多数分离的弧菌噬菌体（8个中有7个）与其他地方分离的噬菌体具有<； 40 %的基因组相似性，可能表明是新的菌株。噬菌体在温度（4-40 °C）、ph（3−10）和盐度（0-50 ppt） 6 h内均保持稳定，没有明显的活力损失。虽然单个噬菌体具有不同的杀菌效率，细菌迅速产生噬菌体抗性，但噬菌体鸡尾酒配方效率高，可显著抑制细菌生长至15 h，抑制生物膜的形成（p <； 0.05）并根除已建立的生物膜（p <； 0.05）。测序证实，其中7个噬菌体中缺乏溶原模块、已知毒素和抗菌素耐药性基因。此外，在两个最有效的噬菌体中发现了trna和一种推定的抗crispr （Acr）蛋白。虽然细菌迅速发展出噬菌体耐药性，但我们观察到抗生素敏感性的增加可能是由于外排泵缺陷造成的。我们的研究结果支持弧菌噬菌体在水产养殖系统中的潜在应用，以尽量减少弧菌病的负担。然而，外排泵系统在噬菌体耐药和抗菌药物耐药中的作用还有待进一步研究。

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引用次数: 0

Microbial acetyl-CoA synthesis as an emerging metabolic and regulatory hub in plant-microbe interactions 微生物乙酰辅酶a合成是植物与微生物相互作用中一个新兴的代谢和调控中心。

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-03-01 Epub Date: 2025-12-05 DOI: 10.1016/j.micres.2025.128413

Yanan Zhou , Xue-Xian Zhang , Dandan Wang , Mengguang Zhao , Li Sun , Weiwei Huang , Zhihong Xie

Acetyl-CoA synthetase (ACS) is a well-characterized enzyme that catalyzes the ATP-dependent ligation of acetate and coenzyme A to produce acetyl-CoA, a central metabolite coordinating energy metabolism, carbon flux distribution, and post-translational protein modification. Recently, ACS has emerged as a metabolic nexus with broad implications for plant–microbe interactions in agriculture. Beyond its canonical role in primary metabolism, ACS governs diverse physiological processes in beneficial plant-associated microorganisms, including rhizosphere colonization, stress adaptation, secondary metabolite biosynthesis, and morphological development—all of which enhance plant growth and resilience. In contrast, in phytopathogens, ACS is closely related to the expression of virulence factors. Thus, ACS exerts a dual influence, shaping both mutualistic and antagonistic microbial lifestyles in planta. This review synthesizes recent advances in the structural and catalytic diversity of ACS, delineates its ecological and functional roles in agriculturally relevant microorganisms, and explores the environmental and host-derived signals that regulates its expression and activity. Particular attention is given to the interplay between ACS-mediated carbon metabolism and protein acetylation, which together modulate microbial physiology and plant-associated behaviors. ACS is thereby positioned as a strategic metabolic hub, providing a framework for future research at the interface of microbial metabolism, environmental adaptation, and plant health.

乙酰辅酶a合成酶（Acetyl-CoA synthetase， ACS）是一种具有良好特征的酶，它催化乙酸酯和辅酶a的atp依赖性连接产生乙酰辅酶a，这是一种协调能量代谢、碳通量分布和翻译后蛋白质修饰的中心代谢产物。最近，ACS已成为一种代谢联系，在农业中植物与微生物的相互作用具有广泛的意义。除了在初级代谢中的典型作用外，ACS还控制着有益植物相关微生物的多种生理过程，包括根际定植、逆境适应、次生代谢物生物合成和形态发育，所有这些都能增强植物的生长和恢复力。相反，在植物病原体中，ACS与毒力因子的表达密切相关。因此，ACS发挥了双重影响，塑造了植物中共生和拮抗的微生物生活方式。本文综述了ACS的结构和催化多样性的最新进展，描述了其在农业相关微生物中的生态和功能作用，并探讨了调节其表达和活性的环境和宿主来源信号。特别关注acs介导的碳代谢和蛋白质乙酰化之间的相互作用，它们共同调节微生物生理和植物相关行为。因此，ACS被定位为一个战略性的代谢中心，为未来微生物代谢、环境适应和植物健康的研究提供了一个框架。

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引用次数: 0

Surface-layer proteins of Enterococcus faecium WEFA23 inhibit Listeria monocytogenes-induced inflammation via TLR2-mediated NF-κB and MAPK signalling in RAW 264.7 cells 在RAW 264.7细胞中，屎肠球菌表层蛋白WEFA23通过tlr2介导的NF-κB和MAPK信号传导抑制单核细胞增生李斯特菌诱导的炎症

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-02-01 Epub Date: 2025-10-16 DOI: 10.1016/j.micres.2025.128373

Yao He , Xingyi Long , Bing Dong , Yina Huang , Xueying Tao , Hua Wei

Listeria monocytogenes infection, which has a higher mortality rate than other foodborne pathogens, is a major concern in global food safety. Among various interventions, lactic acid bacteria and their metabolites have gained significant attention. Our previous study showed that the surface layer proteins (SLPs) of Enterococcus faecium WEFA23, isolated from the gastrointestinal tract of newborn infants, exhibited strong inhibitory activity against L. monocytogenes CMCC57007; however, the underlying mechanism remained unclear. In this study, the immunomodulatory effects of E. faecium WEFA23 SLPs against L. monocytogenes infection were investigated in RAW 264.7 macrophage cells, focusing on phagocytic and bactericidal activity, as well as cytokine production. Furthermore, LC-MS/MS analysis indicated that ornithine carbamoyltransferase (OTC) could be a functional component of the SLPs. Consequently, otc gene knockout and heterologous expression strains were constructed. The results showed that deletion of the otc gene eliminated the inhibitory activity, while recombinant OTC maintained a satisfactory inhibitory effect. Mechanistically, both SLPs and purified OTC suppressed the activation of the NF-κB/MAPK signalling pathways, which were likely mediated through TLR2. Overall, our findings provide a scientific basis for the application of SLPs and E. faecium in food systems to prevent pathogenic infections.

单核细胞增生李斯特菌感染的死亡率高于其他食源性病原体，是全球食品安全的一个主要问题。在各种干预措施中，乳酸菌及其代谢物受到了极大的关注。我们前期的研究表明，从新生儿胃肠道分离的屎肠球菌WEFA23的表层蛋白（SLPs）对单核增生乳杆菌CMCC57007具有较强的抑制活性；然而，潜在的机制仍不清楚。本研究在RAW 264.7巨噬细胞中研究了屎肠杆菌WEFA23 SLPs对单核增生乳杆菌感染的免疫调节作用，重点研究了其吞噬和杀菌活性以及细胞因子的产生。此外，LC-MS/MS分析表明鸟氨酸氨基甲酰转移酶（OTC）可能是SLPs的一个功能成分。构建了otc基因敲除株和异源表达株。结果表明，otc基因的缺失消除了抑制活性，而重组otc保持了令人满意的抑制效果。在机制上，SLPs和纯化OTC均抑制NF-κB/MAPK信号通路的激活，这可能是通过TLR2介导的。总之，我们的研究结果为SLPs和E. faecium在食品系统中的应用预防致病性感染提供了科学依据。

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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 : 2026-02-01 Epub 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。

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引用次数: 0

Endofungal bacteria: Emerging paradigms and future directions 内生真菌细菌：新出现的范例和未来的方向

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-02-01 Epub Date: 2025-10-10 DOI: 10.1016/j.micres.2025.128361

Adrian Wallner , Utkarsh Talukdar , Aurélie Deveau , Julia Buchner , Deepak Kumar , Pooja Shukla , Stéphane Compant , Satish K. Verma

The colonization of fungal hyphae and spores by bacteria represents a widespread phenomenon with significant ecological and biotechnological implications across all surveyed fungal phyla. First thought to be restricted to Mollicutes and Burkholderiaceae-Related Endobacteria, these endofungal associations exhibit remarkable diversity, from simple uniform populations to complex communities, contradicting earlier assumptions of uniform populations. Acquisition dynamics demonstrate both ancient co-evolutionary relationships and recent horizontal transfer events, with environmental factors driving strain-level variation in symbiont presence even within the same fungal species. Fungi can harbor either uniform or diverse bacterial communities, sometimes within specialized structures, and exhibit varying degrees of dependence on their symbionts. These interactions can be mutualistic, commensal, or parasitic, influencing fungal physiology, metabolism, and ecological function. Yet the underlying mechanisms have been thoroughly characterized in only a few model systems in which endofungal bacteria have been shown to affect nutrient acquisition, stress tolerance, secondary metabolite production, and even fungal pathogenicity. In return, fungi offer a protective niche and promote dispersion. These concepts collectively illustrate the evolutionary flexibility and ecological importance of fungi-bacteria partnerships across terrestrial ecosystems.

This review synthesizes emerging paradigms in endofungal bacteria research, integrating recent discoveries that challenge traditional assumptions about these symbioses. We examine host specificity patterns, acquisition mechanisms, and functional impacts while identifying critical knowledge gaps requiring investigation. A deeper understanding of these associations is essential to establish standardized frameworks for their applications in agriculture, medicine, and environmental sustainability.

细菌对真菌菌丝和孢子的定植代表了一种广泛的现象，在所有被调查的真菌门类中具有重要的生态和生物技术意义。最初被认为仅限于Mollicutes和burkholderacae相关的内细菌，这些内真菌关联表现出显著的多样性，从简单的均匀种群到复杂的群落，与早期的均匀种群假设相矛盾。获取动力学证明了古老的共同进化关系和最近的水平转移事件，即使在同一真菌物种中，环境因素也驱动了共生存在的菌株水平变化。真菌可以容纳统一或多样的细菌群落，有时在专门的结构中，并表现出不同程度的依赖于它们的共生体。这些相互作用可以是互惠的、共生的或寄生的，影响真菌的生理、代谢和生态功能。然而，其潜在机制仅在少数模型系统中得到了彻底的表征，在这些模型系统中，内真菌细菌已被证明影响营养获取、应激耐受性、次生代谢物产生，甚至真菌致病性。作为回报，真菌提供了一个保护性的生态位并促进了扩散。这些概念共同说明了陆地生态系统中真菌-细菌伙伴关系的进化灵活性和生态重要性。这篇综述综合了内真菌细菌研究的新范式，整合了最近的发现，挑战了关于这些共生关系的传统假设。我们研究了宿主特异性模式、获取机制和功能影响，同时确定了需要调查的关键知识空白。深入了解这些关联对于建立标准化框架以将其应用于农业、医学和环境可持续性至关重要。

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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 : 2026-02-01 Epub 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。

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引用次数: 0

Dynamic drivers of PAHs transformation in the spatial and temporal continuum of the rhizosphere: An analysis of plant-microbe synergistic mechanism 多环芳烃在根际时空连续体转化的动态驱动因素：植物-微生物协同机制分析。

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-02-01 Epub Date: 2025-10-29 DOI: 10.1016/j.micres.2025.128380

Jieting Wu , Haoran Yin , Yuxin Li , Lei Zhao , Haijuan Guo , Chengbin Xu , Jing Shang , Xiaofan Fu , Fang Ma , Ruoning Song

The migration and transformation of polycyclic aromatic hydrocarbons (PAHs) in soil systems are inherently constrained by their low solubility, strong sorption affinity to soil particles, and limited bioavailability for biological uptake and degradation. As a critical ecological interface mediating plant-microbe interactions, the rhizosphere plays a pivotal role in facilitating PAHs mobilization and transformation processes. This review systematically examines the spatiotemporal dynamics of PAHs migration and transformation within rhizosphere systems under plant-microbe collaborative regulation, characterized by sequential temporal phases (initial desorption-solubilization, intermediate absorption-accumulation, and terminal degradation-transformation) and spatial stratification (rhizosphere soil-liquid interface, root surface microenvironment, and internal root tissues). We particularly emphasize the synergistic plant-microbe interactions that drive PAHs desorption, solubilization, phytoaccumulation, and biodegradation. Furthermore, we elucidate four potential mechanistic pathways: AHL analogs in root exudates activate bacterial quorum sensing systems to stimulate surfactant production and PAHs-degrading enzyme synthesis; Microbial-derived IAA enhances H⁺ -ATPase activity in plants, facilitating PAHs/H⁺ co-transport mechanisms; Coordinated AHL-IAA signaling promotes Ca²⁺ uptake and upregulates root nodule symbiosis-related gene expression; ROS in root exudates activate bacterial c-di-GMP signaling pathways to enhance microbial colonization and PAHs-degrading enzyme production. We also analyze the practical limitations affecting rhizoremediation efficacy, including climatic conditions, soil heterogeneity, and variations in pollutant types, and propose corresponding future research directions toward the end of the article. This comprehensive analysis establishes a theoretical framework for understanding the mechanistic basis of plant-microbe synergism in rhizospheric PAHs remediation, offering a foundation for advancing rhizosphere engineering and phytoremediation strategies.

多环芳烃（PAHs）在土壤系统中的迁移和转化受到其溶解度低、对土壤颗粒的强吸附亲和力以及生物吸收和降解的生物有效性的限制。根际作为介导植物与微生物相互作用的重要生态界面，在促进多环芳烃的动员和转化过程中起着关键作用。本文系统地研究了植物-微生物协同调控下多环芳烃在根际系统内迁移和转化的时空动态，其特征是时序时间阶段（初始解吸-增溶、中间吸收-积累和最终降解-转化）和空间分层（根际土-液界面、根表面微环境和根内部组织）。我们特别强调协同植物-微生物的相互作用，驱动多环芳烃解吸，增溶，植物积累和生物降解。此外，我们阐明了四种潜在的机制途径：根分泌物中的AHL类似物激活细菌群体感应系统，刺激表面活性剂的产生和多环芳烃降解酶的合成；微生物源IAA增强植物H+ - atp酶活性，促进多环芳烃/H+共转运机制；AHL-IAA信号协调促进Ca2+摄取，上调根瘤共生相关基因表达；根分泌物中的ROS激活细菌c-di-GMP信号通路，促进微生物定植和多环芳烃降解酶的产生。文章最后还分析了影响根茎修复效果的实际限制因素，包括气候条件、土壤异质性和污染物类型的变化，并提出了相应的未来研究方向。这一综合分析为理解根际多环芳烃修复中植物-微生物协同作用的机制基础奠定了理论框架，为推进根际工程和植物修复策略提供了基础。

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引用次数: 0