Microorganisms, abundant in nature, are prolific producers of a diverse array of natural products (NPs) that are fundamental in the development of innovative therapeutics. Despite their significant potential, the field faces considerable challenges, including the continuous emergence of potential health threats, as well as novel pathogen strains and viruses. The advent and implementation of advanced technologies, such as culture strategies, genomics mining, and artificial intelligence (AI), are facilitating a paradigm shift in pharmaceutical research, introducing innovative methodologies and perspectives. The development and maturation of these technologies have enhanced the exploration of microbial-derived NPs, thereby advancing pharmaceutical research and development. This review synthesizes recent developments in this context, emphasizing their applications in pharmaceutical discovery and development. Through systematic analysis and synthesis, it provides objective insights into the promising prospects and future direction of this essential field.
Biological Products/chemistry* ; Drug Discovery ; Humans ; Artificial Intelligence ; Bacteria/metabolism*

Petroleum hydrocarbon pollution has become one of the global environmental problems, posing a serious threat to the environment and human health. Microbial remediation plays an important role in the remediation of petroleum hydrocarbon-contaminated environment. Nevertheless, the stress factors present in the environment polluted by petroleum hydrocarbons limit the effectiveness of microbial remediation. This paper reviews the common stress factors in petroleum hydrocarbon-polluted environment and the response mechanisms of microorganisms to these factors. Furthermore, we introduce the methods to improve microbial tolerance, such as irrational modification, rational modification based on systems biology tools or tolerance mechanisms, and the construction of microbial consortia. The application of these methods is expected to improve the viability and remediation efficiency of microorganisms in petroleum hydrocarbon-contaminated environment and provide new perspectives and technical support for environmental remediation.
Biodegradation, Environmental ; Petroleum/metabolism* ; Hydrocarbons/isolation & purification* ; Bacteria/genetics* ; Environmental Pollutants/isolation & purification* ; Petroleum Pollution

Membrane vesicles (MVs) are non-replicating spherical nanoparticles produced by bacteria. The MVs actively released from Gram-negative bacteria are termed outer membrane vesicles (OMVs). OMVs carry various biomolecules, such as lipopolysaccharides, peptidoglycans, proteins, and nucleic acids for material exchange between cells and perform component-dependent physiological functions. In recent years, OMVs have been developed into various biological products, such as vaccines, adjuvants, drug delivery carriers, and cancer immunotherapy agents because of their unique structures and functions. This review describes the biogenesis, composition, and physiological functions of OMVs of Gram-negative bacteria, summarizes the recent research progress of OMVs in product development and cell modifications or engineering, highlights new methods for OMV preparation and characterization, and provides an outlook on the future research directions, with the aim to provide a good reference for study and development of the application of OMVs in the biomedical field.
Gram-Negative Bacteria/metabolism* ; Bacterial Outer Membrane/metabolism* ; Bacterial Outer Membrane Proteins/metabolism* ; Lipopolysaccharides/metabolism*

Mercury (Hg)-contaminated soil poses a significant threat to the environment and human health. Hg-resistant microorganisms have the ability to survive under the stress of inorganic and organic Hg and effectively reduce Hg levels and toxicity. Compared to physical and chemical remediation methods, microbial remediation technologies have garnered increasing attention in recent years due to their lower cost, remarkable efficacy, and minimal environmental impact. This paper systematically elucidates the molecular mechanisms of Hg resistance in microbes, with a focus on their potential applications in phytoremediation of Hg-contaminated soils through plant-microbe interactions. Furthermore, it highlights the critical role of microbes in enhancing the effectiveness of transgenic plants for Hg remediation, aiming to provide a theoretical foundation and scientific basis for the bioremediation of Hg-contaminated soils.
Mercury/toxicity* ; Biodegradation, Environmental ; Soil Pollutants/isolation & purification* ; Soil Microbiology ; Plants, Genetically Modified/metabolism* ; Bacteria/genetics*

Microbial denitrification is a major pathway for nitrogen removal from water bodies. However, denitrification is often difficult to continue when there is a lack of microbially available organic matter in the water body to serve as electron donors. In recent years, studies have shown that some denitrifying bacteria can directly utilize photoelectrons generated by sunlight-excited semiconductor minerals or natural organic matter for denitrification without the need for bioavailable organic matter as electron donors. This process is defined as microbial photoelectrotrophic denitrification. The discovery of microbial photoelectrotrophic denitrification phenomenon reshapes the previous knowledge about the chemoheterotrophic mode of denitrifying bacteria and broadens the pathway of nitrogen removal by the new photoelectrotrophic metabolism, which is of great significance to our understanding and exploration of sunlight-driven nitrogen cycling process. In this paper, we comprehensively sort out the existing research reports in the field of microbial photoelectrotrophic denitrification, systematically summarize the principle and the current research progress of microbial photoelectrotrophic denitrification, deeply analyze the problems and challenges faced by this technology, and make an outlook on the future research directions and application prospects of this technology, providing a reference for the further research and application of this technology.
Denitrification/physiology* ; Nitrogen/isolation & purification* ; Bacteria/metabolism* ; Sunlight ; Phototrophic Processes

The regulation of rhizosphere bacterial community structure and metabolism by plants in municipal solid waste landfills is a key to enhancing the biodegradation of chlorobenzene (CB). In this study, we employed biodiversity and metabolomics methods to systematically analyze the mechanisms of different plant species in regulating the rhizosphere bacterial community structure and metabolic features and then improved the methane (CH₄) oxidation and CB degradation capacity. The results showed that the rhizosphere soil of Rumex acetosa exhibited the highest CH₄ oxidation and CB degradation capacity of 0.08 g/(kg·h) and 1.72×10^-6 g/(L·h), respectively, followed by the rhizosphere soil of Amaranthus spinosus L., with the rhizosphere soil of Broussonetia papyrifera showing the weakest activity. Rumex acetosa promoted the colonization of Methylocaldum in the rhizosphere, and the small-molecule organic amine, such as triethylamine and N-methyl-aniline, secreted from the roots of this plant enhanced the tricarboxylic acid cycle and nicotinamide metabolism, thereby increasing microbial activity and improving CH₄ and CB degradation efficiency. Conversely, cinnamic acid and its derivatives secreted by Broussonetia papyrifera acted as autotoxins, inhibiting microbial activity and exacerbating the negative effects of salt stress on key microbes such as methanotrophs. This study probed into the mechanisms of typical plants growing in landfill cover soil in regulating bacterial ecological functions, offering theoretical support and practical guidance for the plant-microbe joint control of landfill gas pollution.
Biodegradation, Environmental ; Rhizosphere ; Soil Microbiology ; Waste Disposal Facilities ; Chlorobenzenes/metabolism* ; Bacteria/metabolism* ; Soil Pollutants/metabolism* ; Methane/metabolism* ; Plant Roots/microbiology* ; Amaranthus/microbiology* ; Soil

The rapid growth of electronic waste has led to the accumulation of large amounts of valuable metal elements in the environment, causing serious environmental pollution and resource wastage. Compared with pyrometallurgical and hydrometallurgical processes which often result in severe environmental pollution and carbon footprints, microbial synthesis of metal nanoparticles has emerged as a green and environmentally friendly metallurgical technology for recovering valuable metals from electronic waste. This paper first reviews the mechanisms of metal nanoparticle synthesis within different structural compartments of microbial cells. It then introduces the applications of microbially synthesized metal nanoparticles in fields such as environmental remediation, energy production, biocatalysis, and biomedicine. Finally, it discusses the development prospects of microbial synthesis of metal nanoparticles, including exploration of diverse microbial resources and synthesis pathways, yield enhancement, integration of new technologies, and industrialization, aiming to promote further research and application of microbial synthesis of metal nanoparticles.
Metal Nanoparticles/chemistry* ; Bacteria/metabolism*

The escalating pressure from global population growth, climate change, and resource consumption is intensifying the burden on traditional agricultural production. Against this backdrop, soil degradation and pollution present increasingly severe challenges, creating a vicious cycle with rising food demands. Maintaining soil health and its ecosystem services has thus become a critical prerequisite for achieving sustainable agriculture in the future. This review explores the impacts of soil carbon (C) and nitrogen (N) dynamics on soil microbial communities and their interactions. Soil C and N are key determinants of microbial diversity and community structure, intrinsically linked to soil C/N cycling, crop productivity, and ecological balance. Environmental factors such as nitrogen fertilizer application, organic matter amendment application, litter decomposition, elevated CO₂ concentrations, and nitrogen deposition significantly influence soil C and N dynamics. Changes in soil C and N content regulate microbial community dynamics and the synergistic, competitive, and antagonistic interactions among microorganisms. Meanwhile, microbial communities actively respond to alterations in soil C and N availability. The resulting shifts in microbial communities and their interactions subsequently regulate soil C/N cycling and ecosystem stability, ultimately influencing ecosystem functions. By elucidating the mechanisms underlying soil carbon-nitrogen-microbial interactions, this review significantly advances our understanding of soil ecosystem responses and feedback mechanisms in the context of global change, while also providing crucial practical guidance for enhancing soil fertility and promoting sustainable agricultural development through microbial regulation.
Soil Microbiology ; Nitrogen/metabolism* ; Carbon/metabolism* ; Soil/chemistry* ; Bacteria/growth & development* ; Fungi/metabolism* ; Ecosystem ; Fertilizers ; Agriculture

The interactions between microorganisms and medicinal plants are crucial to the quality improvement of medicinal plants. Medicinal plants attract microorganisms to colonize by secreting specific compounds and provide niche and nutrient support for these microorganisms, with a symbiotic network formed. These microorganisms grow in the rhizosphere, phyllosphere, and endophytic tissues of plants and significantly improve the growth performance and medicinal component accumulation of medicinal plants by promoting nutrient uptake, enhancing disease resistance, and regulating the synthesis of secondary metabolites. Microorganisms are also widely used in the ecological planting of medicinal plants, and the growth conditions of medicinal plants are optimized by simulating the microbial effects in the natural environment. The interactions between microorganisms and medicinal plants not only significantly improve the yield and quality of medicinal plants but also enhance their geoherbalism, which is in line with the concept of green agriculture and eco-friendly development. This study reviewed the research results on the interactions between medicinal plants and microorganisms in recent years and focused on the analysis of the great potential of microorganisms in optimizing the growth environment of medicinal plants, regulating the accumulation of secondary metabolites, inducing systemic resistance, and promoting the ecological planting of medicinal plants. It provides a scientific basis for the research on the interactions between medicinal plants and microorganisms, the research and development of microbial agents, and the application of microorganisms in the ecological planting of medicinal plants and is of great significance for the quality improvement of medicinal plants and the green and sustainable development of TCM resources.
Plants, Medicinal/metabolism* ; Bacteria/genetics* ; Symbiosis

To investigate the effects of phosphorus fertilizer on the morphological traits, active ingredients and rhizosphere soil microbial community of Polygala tenuifolia. The phosphorus fertilizer was calculated in terms of P_2O_5. Five treatments were set up: 0(CK), 17(P1), 34(P2), 51(P3), and 68(P4) kg per Mu(1 Mu≈667 m~2). A randomized block design was adopted. Samples of P. tenuifolia and its rhizosphere soil were collected under different superphosphate fertilizer treatments. Illumina high-throughput sequencing was used to analyze the rhizosphere soil microbial community, 9 morphological traits were measured and the content of 11 active ingredients were determined. The results showed that the whole plant weight, shoot fresh weight, root weight, and root peel thickness were the highest under P1 treatment, increasing by 34.41%, 38.80%, 39.21%, and 3.17% respectively compared to CK. Under P2 treatment, the plant height, stem diameter, root thickness, and core thickness were significantly higher than CK. Phosphorus fertilizer had a significant impact on the content of tenuifolin, sibiricose A5, sibiricose A6, arillanin A, 3,6'-disinapoyl sucrose, and polygalaxanthone Ⅲ. Correlation analysis results showed that the relative abundance of Arthrobacter, Bacillus, norank＿f＿Vicinamibacteraceae, norank＿o＿Vicinamibacterales, MND1 and other bacteria, as well as the relative abundance of Neocosmospora, Paraphoma and other fungi were positively correlated with root diameter, wood core diameter, the whole plant weight, root weight, shoot fresh weight of P. tenuifolia. Bacillus, Neocosmospora, Subulicystidium were significantly positively correlated with oligosaccharides such as 3,6'-disinapoyl sucrose, sibiricose A5、sibiricose A6、glomeratose A、arillanin A and tenuifoliside C. Arthrobacter, Humicola, Aspergillus, Paraphoma were positively correlated with tenuifolin and norank＿f＿Vicinamibacteraceae, norank＿o＿Vicinamibacterales, Fusarium were positively correlated with polygalaxanthone Ⅲ. Evidently, appropriate phosphorus application is conducive to the growth and quality improvement of P. tenuifolia, and can increase the abundance of beneficial microorganisms in the soil.
Rhizosphere ; Phosphorus/pharmacology* ; Soil Microbiology ; Polygala/anatomy & histology* ; Fertilizers/analysis* ; Bacteria/metabolism* ; Soil/chemistry* ; Microbiota/drug effects* ; Plant Roots/metabolism*