Search Results (1,223)

Microorganisms exhibit remarkable diversity, making their comprehensive characterization essential for understanding ecosystem functioning and safeguarding human health. However, traditional culture-based methods entail inherent limitations for resolving microbial heterogeneity, isolating slow-growing microorganisms, and accessing uncultivated microbes. Conversely, droplet-based microfluidics enables a high-throughput and precise platform for single-bacterium manipulation by physically isolating individual cells within microdroplets. This technology presents a transformative approach to overcoming the constraints of conventional techniques. This review outlines the fundamental principles, recent research advances, and key application domains of droplet-based microfluidics, with a particular focus on innovations in single-bacterium encapsulation, sorting, cultivation, and functional analysis. Applications such as antibiotic susceptibility testing, enzyme-directed evolution screening, microbial interaction studies, and the cultivation of novel bacterial species are discussed, underscoring the technology’s broad potential in microbiological research and biotechnology. Full article

Global agricultural intensification has exacerbated soil compaction and nitrogen (N) inefficiency, thereby threatening sustainable crop production. Sub-soiling, a tillage technique that fractures subsurface layers while preserving surface structure, offers potential solutions by modifying soil physical properties and enhancing microbial-mediated N cycling. This study investigated the effects of subsoiling depth (0, 20, and 40 cm) on soil microbial communities and N transformations in a semi-arid maize system in China. The results demonstrated that subsoiling to a depth of 40 cm (D2) significantly enhanced the retention of nitrate-N and ammonium-N, which correlated with improved soil porosity and microbial activity. High-throughput 16S rDNA sequencing revealed subsoiling depth-driven reorganization of microbial communities, with D2 increasing the abundance of Proteobacteria (+11%) and ammonia-oxidizing archaea (Nitrososphaeraceae, +19.9%) while suppressing denitrifiers (nosZ gene: −41.4%). Co-occurrence networks indicated greater complexity in microbial interactions under subsoiling, driven by altered aeration and carbon redistribution. Functional gene analysis highlighted a shift from denitrification to nitrification-mineralization coupling, with D2 boosting maize yield by 9.8%. These findings elucidate how subsoiling depth modulates microbiome assembly to enhance N retention, providing a mechanistic basis for optimizing tillage practices in semi-arid agroecosystems. Full article

This review provides a critical summary of the biological remediation of heavy metals by leveraging the potential of microbes in soils and water ecosystems, highlighting major research findings and practical obstacles. Heavy metals (HMs) pose a severe threat to environmental health due to their toxicity and persistence, necessitating effective remediation strategies. Biological remediation, especially through microorganisms and enzymatic actions, offers a promising alternative to conventional methods due to its eco-friendly and cost-effective nature. The review discusses various microbes, including bacteria, fungi, and algae known for their metal-binding capacities and transformation abilities. It delves into the mechanisms of bioremediation, such as biosorption, bioaccumulation, and biotransformation, facilitated by microbial enzymes like oxidoreductases and hydrolases that remove or bind the chemical structure of HMs. This paper also explores genetic engineering approaches to enhance microbial efficacy in HMs’ uptake and resistance. Furthermore, the review addresses the significant challenges in scaling bioremediation from a laboratory to the field, such as the complexity of environmental conditions, the presence of mixed contaminants, and the need for system optimization to improve efficiency and sustainability. It also evaluates the current legislative framework governing bioremediation practices, suggesting a need for clearer policies to support the integration of biological methods into mainstream remediation strategies. Conclusively, while microbial and enzymatic remediation presents considerable potential, extensive research is needed to overcome existing hurdles and develop robust, field-applicable systems. This paper calls for a multidisciplinary approach combining microbiology, engineering, and environmental sciences to advance this promising field. Full article

The accelerating threat of antimicrobial resistance (AMR) demands transformative strategies that go beyond conventional antibiotic therapies. Nanoparticles (NPs) have emerged as versatile antimicrobial agents, offering a combination of physical, chemical, and immunological mechanisms to combat multidrug-resistant (MDR) pathogens. Their small size, surface tunability, and ability to disrupt microbial membranes, generate reactive oxygen species (ROS), and deliver antibiotics directly to infection sites position them as powerful tools for infection control. This narrative review explores the major classes, mechanisms of action, and biomedical applications of antimicrobial NPs—including their roles in wound healing, implant coatings, targeted drug delivery, inhalation-based therapies, and the treatment of intracellular infections. We also highlight the current landscape of clinical trials and evolving regulatory frameworks that govern the translation of these technologies into clinical practice. A distinctive feature of this review is its focus on the interplay between NPs and the human microbiota—an emerging frontier with significant implications for therapeutic efficacy and safety. Addressing this bidirectional interaction is essential for developing microbiota-informed, safe-by-design nanomedicines. Despite promising advances, challenges such as scalability, regulatory standardization, and long-term biosafety remain. With interdisciplinary collaboration and continued innovation, antimicrobial NPs could reshape the future of infectious disease treatment and help curb the growing tide of AMR. Full article

Oxytocin (OT), traditionally associated with reproduction and social bonding, has emerged as a key modulator of gastrointestinal (GI) physiology and appetite regulation behavior through its actions within the gut–brain axis. Central to this regulation are vagal oxytocin receptors (VORs), which are located along vagal afferent and efferent fibers and within brainstem nuclei such as the nucleus tractus solitarius and dorsal motor nucleus of the vagus. This review presents a comprehensive synthesis of current knowledge on the anatomical distribution, molecular signaling, developmental plasticity, and functional roles of VORs in the regulation of GI motility, satiety, and energy homeostasis. We highlight how VORs integrate hormonal, microbial, and stress-related cues and interact with other neuropeptidergic systems including GLP-1, CCK, and nesfatin-1. Recent advances in spatial transcriptomics, single-nucleus RNA sequencing, chemogenetics, and optogenetics are discussed as transformative tools for mapping and manipulating VOR-expressing circuits. Particular attention is given to sex differences, translational challenges, and the limited understanding of VOR function in humans. This article proposes VORs as promising therapeutic targets in dysphagia, obesity, and functional GI disorders. We outline future research priorities, emphasizing the need for integrative, cross-species approaches to clarify VOR signaling and guide the development of targeted, personalized interventions. Full article

Microbial exopolysaccharides from extreme environments are increasingly becoming valuable candidates for drug development. In this study, four fractions named XL-1, XMRS-1, XL-1-D, and XMRS-1-D were isolated and purified from the hadal bacterium Psychrobacter pulmonis by column chromatography. The structural features of these fractions were characterized by molecular weight, monosaccharide composition, Fourier transform infrared (FTIR) spectrum, amino acid analysis and NMR. The results showed that XL-1 and XMRS-1 were mainly composed of mannose, glucose, and glucosamine, while XL-1-D and XMRS-1-D were mainly composed of mannose. In vitro bioactivity assays demonstrated that all four fractions significantly enhanced RAW264.7 macrophage proliferation and phagocytosis, stimulated nitric oxide (NO) and reactive oxygen species (ROS) production, and induced the secretion of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and the expression of inducible nitric oxide synthase (iNOS) mRNA. Moreover, plate cloning tests, cell scratch tests, and apoptosis assays, along with RT-qPCR analysis, demonstrated that the four fractions significantly inhibited A549 cells’ proliferation. Specifically, XMRS-1 and XMRS-1-D upregulated Bax, Caspase-3, Caspase-8, and Caspase-9, while downregulating Bcl-2, suggesting transcriptional activation of apoptosis-related pathways. These results offered a reference for the further development and utilization of this hadal bacterium in the future. Full article

Bacterial endophytes have emerged as critical components of plant microbiomes, offering multifaceted benefits ranging from growth promotion to stress resilience. This review synthesizes two decades of research, from 2004 to 2024, on bacterial endophyte identification and applications, highlighting advances in both traditional culture-based techniques and modern omics approaches. The review also focuses on interactions between these microorganisms and their host plants, emphasizing their roles in biocontrol, phytoremediation, and nanoparticle biosynthesis. While significant progress has been made in characterizing cultivable bacterial endophytes, challenges persist in accessing unculturable species and understanding strain-specific functional mechanisms. The integration of metagenomics, metatranscriptomics, and metabolomics has begun unraveling this hidden diversity, revealing novel metabolic pathways and plant–microbe communication systems. There have been limitations in endophyte isolation protocols and field applications, and therefore a need exists for standardized frameworks to bridge lab-based discoveries with agricultural practices. Cutting-edge multi-omics techniques, such as genomics, transcriptomics, metabolomics, proteomics, and phenomics, should be used more in future research to clarify the mechanistic underpinnings of plant–endophyte interactions to thoroughly profile the microbial communities and unlock their functional potential under diverse environmental conditions. Overall, bacterial endophytes present viable paths toward sustainable farming methods, supporting food security and crop resilience in the face of environmental difficulties by providing a transformative opportunity for next-generation agriculture, mitigating climate-related agricultural stressors, reducing dependence on synthetic agrochemicals, and enhancing crop productivity. Full article

Digestion was once viewed as a host-driven process, dependent on salivary, gastric, pancreatic, and intestinal enzymes to break down macronutrients. However, new insights into the gut microbiota have redefined this view, highlighting digestion as a cooperative effort between host and microbial enzymes. Host enzymes initiate nutrient breakdown, while microbial enzymes, especially in the colon, extend this process by fermenting resistant polysaccharides, modifying bile acids, and transforming phytochemicals and xenobiotics into bioactive compounds. These microbial actions produce metabolites like short-chain fatty acids, which influence gut barrier function, immune regulation, and metabolism. I propose two frameworks to describe this interaction: the “duet,” emphasizing sequential enzymatic cooperation, and the “orchestra,” reflecting a spatially and temporally coordinated system with host–microbiota feedback. Disruption of this symbiosis, through antibiotics, inflammation, diet, or aging, leads to dysbiosis, impaired digestion, and contributes to metabolic, neurologic, cardiovascular, and inflammatory diseases. Recognizing digestion as a dynamic, integrated system opens new paths for therapies and nutrition. These include enzyme-targeted prebiotics, probiotics, postbiotics, and personalized diets. Embracing this systems-level perspective enables innovative diagnostics and treatments, aiming to restore enzymatic balance and improve digestive and systemic health. Full article

This study investigates the composition and transformation of soil organic matter (SOM) across seven sites in Maritime Antarctica, focusing on the impact of bird activity and vegetation cover on SOM dynamics. There is limited knowledge of the stability of Antarctic SOM and the effects of seabird colonies on it. This study aims to address the knowledge gap regarding drivers of soil organic matter transformations in polar ecosystems. Hot water-extractable carbon (HWC) and carbon extracted with phosphoric acid (PHP-C) were chosen as parameters for the labile carbon pool. A stable carbon pool was here characterized as one with alkali-soluble organic compounds opposing microbial decomposition. This carbon pool has long (decades) turnover rates, and therefore is regarded stable. The mentioned carbon pools were used to calculate humification indices. The HWC in studied soils ranged from 1.5 to 4.3% of total carbon, while the PHP-C varied largely and was not correlated with HWC. Soils influenced by current or historical bird colonies (particularly penguins and skuas) exhibited elevated labile carbon fractions, indicating active microbial processing. In contrast, sites without bird influence showed lower biological activity. The stable carbon peaked at 18.9% of total carbon, indicating distinct soil transformation stages. The humification degree (HD) and labile-to-stable carbon (L/S) ratio were used to assess SOM stability, revealing that former bird rookeries had the most stabilized SOM, while recently deglaciated sites were in early stages of organic matter accumulation. Vegetation cover, though secondary to bird impact, was positively correlated with SOM humification, supporting the role of vascular plant-derived organic input in carbon stabilization. The study showed a clear link between bird activity and SOM dynamics, supporting the concept of biological legacies in soil formation in Antarctica. It highlighted the role of vegetation in SOM stabilization, which is crucial for understanding how terrestrial ecosystems may evolve as ice retreats and plant colonization expands. Full article

Lycium barbarum L. (goji berry), a traditional Chinese medicinal plant, depends heavily on nitrogen input to maintain productivity. Nitrogen application also profoundly influences rhizosphere microbial dynamics, which are critical for soil health and plant performance. This study aimed to investigate how the rhizosphere fungal community responds to nitrogen input and explore the potential role of beneficial fungi (e.g., Chaetomium) in goji berry rhizosphere enrichment. A field experiment with four nitrogen levels (0, 53.82, 67.62, and 80.73 g·N m⁻²·year⁻¹, designated as N0, N1, N2, and N3) was conducted to analyze the fungal community structure in the rhizosphere of goji berry using ITS rRNA gene amplicon sequencing. The results showed that nitrogen input significantly altered the rhizosphere fungal community composition and diversity. Redundancy analysis (RDA) and Mantel tests indicated that soil electrical conductivity, total phosphorus, available phosphorus, and nitrate nitrogen were key environmental factors driving the fungal communities’ shifts. Notably, specific fungal genera, including Chaetomium, Cladosporium, Gibberella, Fusarium, Pyxidiophora, Acaulium, and Lophotrichus, exhibited differential enrichment across nitrogen levels. In particular, Chaetomium was significantly enriched under the conventional nitrogen treatment (N2), a strain of Chaetomium sp. LC101 was successfully isolated from the goji berry rhizosphere, and its functional roles were verified via pot experiments. Inoculation with Chaetomium sp. LC101 significantly promoted goji berry growth, with the most pronounced effects observed under N0 treatments, root fresh weight, root vitality, and leaf chlorophyll content increased by up to 55.10%, 15.69%, and 43.27%, respectively, compared to non-inoculated controls. Additionally, Chaetomium sp. LC101 regulated rhizosphere nitrogen transformation by enhancing urease, nitrite reductase, and polyphenol oxidase activities while inhibiting nitrate reductase activity. These findings demonstrate that Chaetomium responds sensitively to nitrogen input, with enrichment under moderate nitrogen levels, and acts as a beneficial rhizosphere fungus by promoting plant growth and regulating nitrogen cycling. This study provides novel insights for nitrogen management in the goji berry industry, where synergistic regulation via “nitrogen reduction combined with microbial inoculation” can reduce nitrogen loss, improve yield and quality through functional fungi, and contribute to ecological sustainability. Full article

Most of the knowledge available on the composition and functionality of microbial communities in different ecosystems comes from short-read sequencing methods. It implies limitations regarding taxonomic resolution, variant detection, and genome assembly contiguity. Long-read sequencing technologies can overcome these limitations, transforming the analysis of microbial community composition and functionality. It is essential to understand the characteristics of each sequencing technology to select the most suitable one for each microbiome study. This review aims to show how long-read sequencing methods have revolutionized microbiome analysis in ecosystems and to provide a practical tool for selecting sequencing methods. To this end, the evolution of sequencing technologies, their advantages and disadvantages for microbiome studies, and the new dimensions enabled by long-read sequencing technologies, such as virome and epigenetic analysis, are described. Moreover, desirable characteristics for microbiome sequencing technologies are proposed, including a visual comparison of available sequencing platforms. Finally, amplicon and metagenomics approaches and the sequencing depth are discussed when using long-read sequencing technologies in microbiome studies. In conclusion, although no single sequencing method currently possesses all the ideal features for microbiome analysis in ecosystems, long-read sequencing technologies represent an advancement in key aspects, including longer read lengths, higher accuracy, shorter runtimes, higher output, more affordable costs, and greater portability. Therefore, more research using long-read sequencing is recommended to strengthen its application in microbiome analysis. Full article

The conversion of wetlands into croplands often leads to significant losses of peat soil salinity and soil organic matter (SOM), though quantifying these changes is challenging due to limited historical data. In this study, we compared current soil physicochemical properties with rare historical data from the Mezzano Lowland (ML) in Northeastern Italy, a former wetland drained over 60 years ago. The transformation, which affected approximately 18,100 hectares, was achieved through the construction of a network of drainage canals and pumping stations capable of removing large volumes of water, enabling intensive agricultural use. Results showed a marked decrease in electrical conductivity (EC) and sulphate concentration, indicating extensive salt leaching from the upper peat soil layers. EC dropped from historical values up to 196 $\mathrm{m}$$\mathrm{S}$/cm (1967–1968) to a current maximum of 4.93 $\mathrm{m}$$\mathrm{S}$/cm, while sulphate levels declined by over 90%. SOM also showed significant depletion, especially in deeper layers (50–100 cm), with losses ranging from 50 to 60 $\mathrm{wt}\%$, due to increased aeration and microbial activity post-drainage. These climatic and environmental changes, including a marked reduction in soil salinity and sulphate concentrations due to prolonged leaching, have likely shifted the Mezzano Lowland from a carbon sink to a net source of CO₂ and CH₄ by promoting microbial processes that enhance methane production under anaerobic conditions. To detect residual peat layers, we used Ground-Penetrating Radar (GPR), which, combined with soil sampling, proved effective for tracking long-term peat soil changes. This approach can inform sustainable land management strategies to prevent further carbon loss and maintain peat soil stability. Full article

Wetlands frequently experience drying and rewetting (DRW) alternation, which intricately influences the physical, chemical, and biological processes within the soil matrix. The conversion of agricultural land into wetland ecosystems has raised significant concerns regarding the release of phosphorus. However, a significant knowledge gap persists in understanding the implications of this phenomenon for phosphorus transformation and release dynamics within soils situated in the freeze–thaw zone of Northeast China. To address this gap, we conducted a series of experiments involving the simulation of varying intensities and frequencies of DRW alternation using soil column samples collected from restored wetlands. This study evaluated phosphorus fractions with different levels of mobility and availability using methods based on standardized chemical extraction. We subsequently analyzed the impacts of these alterations on phosphorus fractions from the perspectives of soil chemical properties and microbial community changes. DRW events were found to facilitate the conversion of labile inorganic phosphorus into organic phosphorus fractions, driving the transformation of mobile phosphorus into potentially mobile fractions. Moderate drought events showed a significant increase in soil bacterial diversity and abundance, while both normal and extreme drought events caused a decrease in bacterial diversity. Moreover, DRW treatment increased the relative abundance of Proteobacteria and decreased the relative abundance of Chloroflexi. Redundancy analysis identified organic carbon and bacterial diversity as key drivers influencing phosphorus fractions. Overall, this study contributes to our understanding of the intricate relationships among soil characteristics, microbial ecosystems, and the complex behavior of phosphorus under various DRW regimes in restored wetlands. Full article

Microorganisms, as abundant biological resources, offer significant potential in the development of selenium-enrichment technologies. Selenium-enriched microorganisms not only absorb, reduce, and accumulate selenium efficiently but also produce various selenium compounds without relying on synthetic chemical processes. In particular, nano-selenium produced by these microorganisms during cultivation has garnered attention due to its unique physicochemical properties and biological activity, making it a promising raw material for functional foods and pharmaceutical products. This paper reviews selenium-enriched microorganisms, focusing on their classification, selenium metabolism, and transformation mechanisms. It explores how selenium is absorbed, reduced, and transformed within microbial cells, analyzing the biochemical processes by which inorganic selenium is converted into organic and nano-selenium forms. Finally, the broad applications of selenium-enriched microbial products in food, medicine, and agriculture are explored, including their roles in selenium-rich foods, nano-selenium materials, and disease prevention and treatment. Full article

Excessive alcohol consumption is associated with systemic health risks due to the production of acetaldehyde, a primary carcinogen that not only pollutes the environment but also endangers human health. In this study, a promising bacterial strain for biodegrading both ethanol and acetaldehyde was successfully isolated from the traditional fermented food Jiaosu and identified as Acetobacter ghanensis JN01 based on average nucleotide identity (ANI) analysis. Initial ethanol of 1 g/L was completely biodegraded within 4 h, while initial acetaldehyde of 1 g/L was also rapidly removed at 2 or 1 h by whole cells or cell-free extracts (CEs) of JN01, respectively, which indicated that JN01 indeed has a strong ability in the biodegradation of both ethanol and acetaldehyde. Whole-genome sequencing revealed a 2.85 Mb draft genome of JN01 with 57.0% guanine–cytosine (GC) content and the key metabolic genes (adh1, adh2, and aldh) encoding involving alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH), co-located with NADH dehydrogenase genes and ethanol-responsive regulatory motifs, supporting the metabolic pathway of transforming ethanol to acetaldehyde, and, subsequently, converting acetaldehyde to acetic acid. Furthermore, selected in vitro safety-related traits of JN01 were also assessed, which is very important in the development of microbial catalysts against both ethanol and acetaldehyde. Full article