Search Results (2,191)

The lotus–fish co-culture (LFC) system leverages plant–fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal–fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC’s ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation. Full article

Mollusks are among the most ecologically and economically significant invertebrates; yet, their associated microbiomes remain understudied relative to those of other metazoans. This scoping review synthesizes the current literature on the diversity, composition, functional roles, and ecological implications of molluscan microbiomes, with an emphasis on three major groups: gastropods, bivalves, and cephalopods. Drawing on studies from terrestrial, freshwater, and marine systems, we identified the dominant bacterial phyla, including Proteobacteria, Bacteroidetes, and Firmicutes, and explored how microbiota vary across different habitats, diets, tissue types, and host taxonomies. We examined the contribution of molluscan microbiomes to host functions, including digestion, immune modulation, stress responses, and nutrient cycling. Particular attention was given to the role of microbiota in shell formation, pollutant degradation, and adaptation to environmental stressors. The review also evaluated microbial interactions at different developmental stages and under aquaculture conditions. Factors influencing microbiome assembly, such as the host’s genetics, life history traits, and environmental exposure, were mapped using conceptual and graphical tools. Applications of molluscan microbiome research in aquaculture, conservation biology, and environmental biomonitoring are highlighted. However, inconsistencies in the sampling methods, taxonomic focus, and functional annotations limit the generalizability across taxa. We identify key knowledge gaps and propose future directions, including the use of meta-omics, standardized protocols, and experimental validation to deepen insights. By synthesizing emerging findings, this review contributes to a growing framework for understanding mollusk–microbiome interactions and their relevance to host fitness and ecosystem health. It further establishes the importance of mollusks as model systems for advancing microbiome science. Full article

Date palm (Phoenix dactylifera L.) is a vital crop cultivated primarily in developing regions, playing a strategic role in global food security through its significant contribution to nutrition, economy, and livelihoods. Global and regional production trends revealed increasing demand and expanded cultivation areas, underpinning the fruit’s importance in national food security policies and economic frameworks. The date fruit’s rich nutritional profile, encompassing carbohydrates, dietary fiber, minerals, and bioactive compounds, supports its status as a functional food with health benefits. Postharvest technologies and quality preservation strategies, including temperature-controlled storage, advanced drying, edible coatings, and emerging AI-driven monitoring systems, are critical to reducing losses and maintaining quality across diverse cultivars and maturity stages. Processing techniques such as drying, irradiation, and cold plasma distinctly influence sugar composition, texture, polyphenol retention, and sensory acceptance, with cultivar- and stage-specific responses guiding optimization efforts. The cold chain and innovative packaging solutions, including vacuum and modified atmosphere packaging, along with biopolymer-based edible coatings, enhance storage efficiency and microbial safety, though economic and practical constraints remain, especially for smallholders. Microbial contamination, a major challenge in date fruit storage and export, is addressed through integrated preservation approaches combining thermal, non-thermal, and biopreservative treatment. However, gaps in microbial safety data, mycotoxin evaluation, and regulatory harmonization hinder broader application. Date fruit derivatives such as flesh, syrup, seeds, press cake, pomace, and vinegar offer versatile functional roles across food systems. They improve nutritional value, sensory qualities, and shelf life in bakery, dairy, meat, and beverage products while supporting sustainable waste valorization. Emerging secondary derivatives like powders and extracts further expand the potential for clean-label, health-promoting applications. This comprehensive review underscores the need for multidisciplinary research and development to advance sustainable production, postharvest management, and value-added utilization of date palm fruits, fostering enhanced food security, economic benefits, and consumer health worldwide. Full article

Background/Aims: Inflammatory bowel diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC), are chronic conditions marked by dysregulated inflammation in the gastrointestinal tract. Although the pathophysiology of IBD remains incompletely understood, it involves complex interactions between genetic predisposition and environmental triggers, such as gut microbiota imbalances and immune dysfunction, leading to chronic inflammation and mucosal injury. IBD affects approximately 7 million individuals globally, with prevalence increasing in Europe, North America, and Oceania. This rise parallels the growing consumption of ultra-processed foods (UPFs), which are typically rich in sugars, fats, and additives but low in fiber, vitamins, and other essential nutrients. These associations, this review critically examines the influence of UPF consumption on gut microbiota composition and function and its potential link to IBD. Methods: A bibliographic search was conducted in the SciELO, PubMed, and Cochrane databases. Results and Conclusions: High UPF consumption is associated with intestinal dysbiosis, marked by reduced microbial diversity, decreased short-chain fatty acid production, impaired barrier integrity, and mucus layer disruption. These alterations may promote immune-mediated diseases, including IBD, where dysbiosis is often characterized by an overgrowth of pathogenic bacteria such as Clostridium and Enterococcus, ultimately triggering inflammatory responses in the host. Full article

Dictyophora indusiata cultivation is severely impeded by premature hyphal regression. This study elucidates the spatiotemporal dynamics of mycelial regression and associated microbial succession in both substrate and soil matrices across progressive regression stages (CK: normal growth; S1: initial recession; S2: advanced recession; S3: complete recession). Microscopic analysis revealed preferential mycelial regression in the substrate, preceding soil regression by 1–2 stages. High-throughput sequencing demonstrated significant fungal community restructuring, characterized by a sharp decline in Phallus abundance (substrate: 99.7% → 7.0%; soil: 78.3% → 5.5%) and concomitant explosive proliferation of Trichoderma (substrate: 0% → 45.2%; soil: 0.1% → 55.3%). Soil fungal communities exhibited a higher richness (Chao1, p < 0.05) and stability, attributed to functional redundancy (e.g., Aspergillus, Conocybe) and physical protection by organic–mineral complexes. Conversely, substrate bacterial diversity dominated, driven by organic matter availability (e.g., the Burkholderia–Caballeronia–Paraburkholderia complex surged to 59%) and optimized porosity. Niche analysis confirmed intensified competition in post-regression soil (niche differentiation) versus substrate niche contraction under Trichoderma dominance. Critically, Trichoderma overgrowing was mechanistically linked to (1) nutrient competition via activated hydrolases (e.g., Chit42) and (2) pathogenic activity (e.g., T. koningii causing rot). We propose ecological control strategies: application of antagonistic Bacillus subtilis (reducing Trichoderma by 63%), substrate C/N ratio modulation via soybean meal amendment, and Sphingomonas–biochar soil remediation. This work provides the first integrated microbial niche model for D. indusiata regression, establishing a foundation for sustainable cultivation. Full article

The infant oral microbiome is a complex and dynamic microbial community that undergoes various transformations during human development. From birth, these microorganisms are modulated by factors such as birth type, nutrition, oral hygiene, hormonal changes, and environmental and socioeconomic conditions. These elements interact continuously, shaping the diversity and stability of the oral microbiome and consequently influencing the oral and general health of individuals. The main objective of this study was to review the literature on the evolution of the oral microbiome at different stages of growth, with special emphasis on the maintenance of dental homeostasis and prevention of pathologies such as caries and periodontitis. A bibliographic review of scientific databases was conducted, focusing on the last decade. In general, oral microbiome dysbiosis increases the risk of oral diseases and systemic conditions. Diet, parental practices, and horizontal transmission of bacteria from caregivers have been shown to modulate and influence the composition and functioning of the infant oral microbiome. Despite these advances, gaps remain in our understanding of the impact of the pediatric oral microbiome on long-term comprehensive health. Therefore, longitudinal research is needed to understand the development of the oral microbiome and its potential role in early prediction, prevention, and treatment of oral and systemic diseases. Full article

Background: Obesity and periodontitis are two chronic inflammatory diseases with a bidirectional relationship possibly mediated by microbial and immunologic signaling pathways. This narrative review aims to investigate how microbial dysbiosis and inflammation link these diseases, focusing on the interactions between the oral and gut microbiomes. Materials and methods: Peer-reviewed studies (2015–2024) from PubMed, MEDLINE, Ovid and Google Scholar were selected for their relevance to microbial dysbiosis and inflammation, prioritizing clear methodology. Non-peer-reviewed sources or studies lacking microbial/inflammatory data were excluded. Conflicting results and methodological differences, including sampling and study design, were assessed qualitatively on the basis of coherence and methodological rigor. Results: Obesity has been shown to significantly alter the composition of the oral microbiome, characterized by reduced diversity and an increased Firmicutes/Bacteroidetes ratio. At the same time, periodontal pathogens such as Porphyromonas gingivalis can invade the gut, impair barrier function and promote systemic inflammation. Both diseases share common inflammatory pathways involving adipokines and immune-system dysregulation, creating a feedback loop that exacerbates disease progression in both conditions. Obesity also appears to impair the effectiveness of conventional periodontal treatments. Conclusions: The microbial axis between the oral cavity and the gut represents a central pathway in the complex interactions between obesity and periodontitis. This relationship involves microbial dysbiosis, bacterial translocation and shared inflammatory mechanisms that collectively contribute to disease progression. Clinical relevance: A better understanding of the relationship between obesity and periodontitis supports the development of customized treatment strategies for obese patients with periodontal disease. Future research should focus on developing targeted interventions that address both conditions simultaneously to improve patient outcomes and develop more effective prevention and treatment strategies. Full article

Iron, an essential element for virtually all known organisms, serves not only as a micronutrient but also as an energy source for bacteria. Iron-oxidizing microorganisms mediate Fe(II) oxidation under diverse redox conditions, yielding amorphous iron (hydr)oxides or crystalline iron minerals. This globally significant biogeochemical process drives modern iron cycling across terrestrial and aquatic ecosystems. The resulting biomineralization not only produces secondary minerals but also effectively immobilizes heavy metals, offering a sustainable strategy for environmental remediation. This review systematically examines (1) the biogeochemical mechanisms and mineralogical signatures of Fe(II) oxidation by four distinct iron oxidizers: acidophilic aerobes (e.g., Acidithiobacillus), neutrophilic microaerophiles (e.g., Gallionella), nitrate-reducing anaerobes (e.g., Acidovorax), and anoxygenic phototrophs (e.g., Rhodobacter); (2) research advances in heavy metal immobilization by biogenic iron minerals: adsorption, coprecipitation, and structural incorporation; and (3) the impact of pH, temperature, organic matter, and coexisting ions on Fe(II) oxidation efficiency and iron mineral formation by iron-oxidizing bacteria. By characterizing iron-oxidizing bacterial species and their functional processes under varying pH and redox conditions, this study provides critical insights into microbial behaviors driving the evolution of acid mine drainage (AMD). Full article

Altered precipitation regimes, both in intensity and duration, can profoundly influence the structure and function of soil microbial communities, yet the patterns and drivers of these responses remain unclear across ecosystem types. Here, using data exclusively from 101 field experiments conducted in China (yielding 695 observations), we investigated the impacts of altered precipitation on soil microbial biomass, diversity, and enzymatic activity in forest and grassland ecosystems. Soil microbial biomass carbon (MBC) and nitrogen (MBN) increased in response to precipitation addition, particularly in grasslands, but they decreased under reduced precipitation, with the decline being more pronounced in forests. The magnitude and duration of precipitation manipulation significantly influenced these effects, with moderate and long-term changes producing divergent responses. Bacterial diversity was largely unaffected by all precipitation treatments, whereas fungal diversity decreased significantly under intense and short-term reductions in precipitation. Enzyme activities exhibited the following element-specific patterns: carbon- and phosphorus-cycling enzymes and antioxidant enzymes were suppressed by precipitation reduction, especially in grasslands, while nitrogen-cycling enzymes showed no consistent response. Moreover, microbial responses were significantly shaped by environmental factors, including mean annual temperature (MAT), mean annual precipitation (MAP), and elevation. Our region-specific analysis highlights precipitation-driven microbial dynamics across China’s diverse climatic and ecological conditions. These findings demonstrate that soil microbial communities respond asymmetrically to precipitation changes, with responses shaped by both ecosystem type and climatic context, underscoring the need to account for environmental heterogeneity when predicting belowground feedback to climate change. Full article

Soil microorganisms play an important role in maintaining the functioning of terrestrial ecosystems. Soil microbial communities usually contain both abundant and rare microorganisms. However, in forest ecosystems, the differences in the functions and assembly processes of abundant and rare microbial taxa in soils between planted pure and mixed forests are currently unknown. In this study, four different forest types in the Zhongtiao Mountains were selected, and the diversity and assembly processes of abundant and rare microbial communities in their soils were quantitatively analyzed. The results show that there are differences in the diversity and assembly processes of abundant and rare microorganisms in the four forests. Significant differences in the α-diversity (Shannon index) of abundant bacteria (p = 0.019) and rare fungi (p = 0.049) were obtained in the four forests. The assembly of abundant bacterial and fungal communities in the four forest types was mainly influenced by stochastic processes, the assembly of rare bacterial communities was mainly influenced by deterministic processes, and the assembly of rare fungal communities was influenced by a combination of deterministic and stochastic processes. Planted mixed forests increase the relative contribution of deterministic processes in the assembly of rare fungal communities compared to planted pure forests. This study determined the relative contributions of deterministic and stochastic processes in the assembly of abundant and rare microbial communities among different forest types, providing a theoretical basis for forest management in mixed forests. Full article

In order to precisely improve the quality of major tree species in northern China, near-natural differentiated management has been gradually introduced into forestry practice, aiming to optimize forest structure, enhance forest quality, and promote nutrient cycling and water conservation. As an essential element of forest ecosystems, soil microbes contribute to biodiversity preservation and nutrient turnover in soils. This study selected three typical forest types (Quercus acutissima forest, Pinus tabulaeformis forest, and Pinus tabulaeformis × Quercus mixed forest) that have been managed with target trees on Zhongtiao Mountain. Using 16S/ITS rRNA high-throughput sequencing, this study systematically assessed the influences of forest type and soil depth (0–60 cm) on the soil properties and microbial communities. The results showed that the fungal alpha diversity indices were the highest in Pinus tabulaeformis forest, which decreased with soil depth. Actinobacteriota exhibited the greatest relative abundance in mixed forest, whereas Ascomycota predominated in the Pinus tabulaeformis forest. The microbial co-occurrence network exhibited greater complexity compared to the pure forest. Microbial carbon and nitrogen cycling functions showed strong correlation with soil pH and nutrient levels. Symbiotrophs dominated the fungal community, and ectomycorrhizae were significantly abundant in mixed forests. pH is the dominant factor driving changes in microbial communities. In summary, the mixed forest improved soil nutrients, enhanced the complexity of microbial networks, and supported higher ectomycorrhizal abundance. These findings provide practical guidance for improving soil health and stability of forest ecosystems through near-natural management. Full article

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

Mulching and irrigation are key practices for improving cotton yield and soil conditions, especially in Xinjiang, China. This study investigated the combined effects of mulching width and irrigation depth on cotton growth and rhizosphere microorganisms. Two mulching widths—conventional (M1) and ultra-wide (M2)—and three irrigation depths, 0.8 ETc (W1), 1.0 ETc (W2), and 1.2 ETc (W3), were tested. The impacts on cotton growth, soil environment, and rhizosphere microbial communities were analyzed. Results showed that under the same irrigation depth, M2 significantly increased soil moisture and reduced salt accumulation. Soil temperature under M2 was higher than M1, with increases of 0.55 °C and 1.65 °C during the budding and flowering–boll stages. M2 also increased root length (3.52–10.72%) and root surface area (5.8–7.51%). The beneficial fungus Cladosporium was enriched, while the pathogen Fusarium was suppressed under M2. With the same mulching width, increasing irrigation improved soil moisture, reduced electrical conductivity, and decreased soil temperature. Root diameter and volume increased by 7.67–47% and 9.43–10.36%, respectively. Mulching width and irrigation depth significantly affected bacterial α-diversity. M2W3 showed the highest microbial richness and functional diversity. This study offers guidance for efficient cotton cultivation in southern Xinjiang. Full article

Groundwater, a critical source of drinking water, plays an essential role in global biogeochemical cycles, yet its microbial ecosystems remain insufficiently characterized, particularly in pristine karst aquifers. This study conducted high-resolution profiling of microbial communities and environmental parameters in two representative alpine karst aquifers in Slovenia: Idrijska Bela and Krajcarca. Monthly groundwater samples from the Krajcarca spring and Idrijska Bela borehole over a 14-month period were analyzed using whole-metagenome sequencing (WMS), UV-Vis spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS), and isotopic analysis. The results revealed stable hydrochemical conditions with clear spatial differences driven by bedrock composition and groundwater residence time. Bacterial communities displayed strong correlations with hydrochemical parameters, while archaeal communities exhibited temporal stability. Functional gene profiles mirrored bacterial patterns, emphasizing the influence of environmental gradients on metabolic potential. No significant temporal changes were detected across two sampling campaigns (2016–2023), highlighting the resilience of these aquifers. This work establishes a valuable baseline for understanding pristine groundwater microbiomes and informs future monitoring and water quality management strategies. Full article

Microbial communities, as critical functional components of riverine ecosystems, play a pivotal role in biogeochemical cycles and water quality regulation. The South-to-North Water Diversion Middle Route Project (SNWD-MRP) is a major cross-basin water transfer initiative, and bacteria are essential for the stability of water quality in the project. This study employed environmental DNA (eDNA) metabarcoding targeting the 16S rRNA gene to investigate spatiotemporal variations in water quality and bacterial communities along the SNWD-MRP during summer and winter. Integrated analyses, including redundancy analysis (RDA), Mantel tests, and ecological network modeling, were applied to unravel the driving mechanisms of microbial succession. The water quality along the SNWD-MRP is generally classified as Grade I, with significant seasonal variations in water quality parameters and microbial community composition. In the summer, higher temperatures lead to an increased abundance of cyanobacteria. In contrast, during the winter, lower water temperatures and higher dissolved oxygen levels result in the dominance of Pseudomonas and Bacillota species. RDA identified the permanganate index as the primary driver of microbial composition across seasons, with total phosphorus and total nitrogen having a greater influence in winter. Mantel tests highlighted significant correlations between Cyanobacteria and total phosphorus during winter. Ecological network analysis revealed that the complexity and connectivity of the winter network increased, likely due to suitable nutrient levels rendering the microbial network more complex and stable. These findings underscore the synergistic effects of temperature and nutrient availability on microbial succession, providing actionable insights for optimizing water quality management and ecological stability in large-scale water diversion systems. Full article