Search Results (838)

Climate variability is a major driver of belowground microbial assembly, yet its effects on rhizosphere microbiomes in perennial crops remain insufficiently resolved. We investigated how macroclimatic oscillations associated with the El Niño–Southern Oscillation (ENSO) influence bacterial communities in the rhizosphere of Coffea arabica. Using 16S rRNA amplicon sequencing across five sampling campaigns covering El Niño, La Niña, and Neutral phases in the Colombian Andes, together with multivariate and variance-partitioning analyses, we quantified the relative contributions of climatic and edaphic factors to rhizosphere community structure. PERMANOVA across three dissimilarity metrics showed that the ENSO explained 11–17% of β-diversity, exceeding the contribution of intra-annual seasonality (6–12%). Ordination analyses indicated moderate compositional differentiation with considerable overlap among ENSO groups, consistent with gradual community turnover under contrasting hydroclimatic conditions. Rainfall and soil pH emerged as the main edaphic correlates of community composition, although their independent effects were no longer significant after accounting for the ENSO phase and season. Despite these shifts, the rhizosphere remained dominated by Acidobacteriota, Actinobacteriota, and Proteobacteria, and a prevalence-defined core microbiome (genera detected in ≥85% of samples) was maintained across climatic phases and seasons. These results indicate that, within the explained fraction of variation, macroclimatic variability contributed more to rhizosphere bacterial turnover than local edaphic heterogeneity, while a conserved prevalence-defined bacterial core may contribute to taxonomic stability in climate-sensitive coffee systems. Full article

Aquatic–terrestrial ecotones are highly dynamic biogeochemical hotspots where hydrological fluctuations profoundly influence microbial community structure and ecosystem functioning. However, the mechanisms underlying microbial community responses across hydrological gradients remain insufficiently understood. In this study, 16S rRNA gene sequencing was used to comparatively analyze bacterial communities in the waterward and landward zones of the drawdown area of the Danjiangkou Reservoir. The results showed that bacterial community composition differed significantly between the two zones, and waterlogging markedly increased bacterial α-diversity. Community variation was primarily associated with key environmental factors, including total phosphorus (TP), soil moisture content (SMC), and nitrate nitrogen (NO₃⁻-N). Compared with the landward zone, stochastic processes contributed more to community assembly in the waterward zone, which also exhibited higher network complexity and topological stability. In addition, several keystone taxa were identified, suggesting their potential roles in maintaining network structure and ecological stability. Functional prediction further revealed distinct metabolic potentials between zones, with enhanced anaerobic and redox-related functions in the waterward zone and predominantly aerobic metabolism in the landward zone. These findings suggest that hydrological fluctuations reshape bacterial community structure and potential ecological functions by jointly regulating water availability and nutrient dynamics. This study provides new insights into microbial ecological processes in reservoir riparian zones and offers a scientific basis for the management of aquatic–terrestrial ecotone ecosystems. Full article

Rumen microbial fermentation plays a central role in nutrient utilization and milk production in dairy cows. This study evaluated the effects of supplementation with exogenous fibrolytic enzymes, alone or in combination with live yeast on rumen microbiota, fermentation characteristics, nitrogen-related metabolites, and production performance during the transition from outdoor grazing to indoor housing. Thirty Lithuanian Red dairy cows were assigned to control (CTR), enzyme (E), or enzyme plus yeast (YE) treatments across outdoor (OD) and transit (T) periods, while nine cows (three per group) were selected for rumen and microbiota analysis. Rumen bacterial communities were characterized using 16S rRNA gene sequencing, and functional parameters were evaluated using linear mixed-effects models. Supplementation resulted in selective changes in several bacterial genera, including Blautia spp., WPS-2, Ruminococcus spp., Erysipelotrichaceae UCG-009, Sharpea spp., uncultured Bacteroidales, and Prevotellaceae UCG-003, and was associated with alterations in fermentation patterns, particularly propionate concentration, and in nitrogen metabolism, including putrescine dynamics. The transition period significantly influenced microbial diversity and total bacterial abundance across treatments. Cows in the YE group maintained higher milk yield during the transition period. Overall, dietary supplementation modulated specific rumen metabolic responses and contributed to production stability without causing large-scale changes in overall microbial structure. Full article

Euonymus bungeanus is a highly valued ornamental tree/shrub species widely utilized in landscaping and afforestation in Northeast Asia, yet molecular studies on this species remain limited due to the lack of validated reference genes for reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). In this study, 16 candidate reference genes were selected based on classical plant reference genes and our previous transcriptome data. Their expression stability was comprehensively evaluated using 64 samples collected from diverse tissues and plants subjected to various abiotic stress/hormone treatments across multiple time points. Across all samples analyzed, PBG1 (20S proteasome beta subunit G1) exhibited the highest overall expression stability, followed by VAPD (vacuolar ATP synthase subunit D) and EIF4A (eukaryotic translation initiation factor 4A). For tissue-specific analysis, TSR2 (pre-rRNA-processing protein), VAPD, and PBG1 demonstrated the greatest stability. Under specific stress conditions, PBG1 and EIF4A were identified as the most stable genes under low- and high-temperature conditions. PP2A (protein phosphatase 2A) and TUB6 (beta-6 tubulin) were optimal for drought stress, while TSR2, SRP (nuclear speckle splicing regulatory-like protein), and PBG1 exhibited superior stability under salt stress. These findings establish a validated panel of reference genes enabling accurate and reliable gene expression normalization in E. bungeanus, thereby facilitating future functional genomics studies in this economically and ecologically important species. Full article

Lipid nanoparticles (LNPs) have emerged as a groundbreaking delivery platform, revolutionizing the development of nucleic acid-based medicines for gene delivery and gene therapy. This review provides an insightful industrial perspective on the production process of LNPs, focusing on cutting-edge manufacturing equipment, downstream processing and the crucial transition from laboratory to large scale. While LNP production in the discovery phase relies on a small scale (µL to mL) for screening various LNP formulation candidates, transferring to preclinical (up to hundreds of mL) and clinical/commercial scales (up to liters) requires a robust and reproducible manufacturing process. Thus, mixing technologies throughout these scales must be carefully selected and require precision, scalability and high reproducibility to meet the target quality of the LNP drug product. Key mixing technologies in mRNA-LNP production primarily include microfluidic systems and impinging jet mixers (IJMs). In this review, we discuss key critical process parameters (CPPs) in LNP preparation, including flow rate ratio (FRR) or total flow rate (TFR), in relation to associated critical quality attributes (CQAs) across multiple manufacturing scales. We further assess the impact of downstream processing, specifically tangential flow filtration (TFF), on the formulation’s CQAs. In particular, the review highlights the importance of maintaining CQAs along each step of the process and emphasizes the role of robust analytical methods in ensuring product quality and safety. Additionally, we touch on current challenges associated with these advanced delivery vehicles, such as their long-term stability, and introduce the readership to innovative stabilization strategies aimed to extent LNP shelf-life. Full article

Plant fungal diseases, such as apple tree canker caused by Valsa mali, have caused severe losses in agricultural production. Traditional chemical fungicides induce drug resistance in pathogens and cause environmental pollution. Therefore, it is of substantial importance to screen efficient and environmentally friendly bacterial strains as potential biocontrol agents. The tea rhizosphere harbors abundant microbial resources, and previous research has identified microorganisms with antifungal activity existing in this environment. Therefore, in this study, we isolated antagonistic bacteria with broad-spectrum biocontrol potential from tea rhizosphere soil. In this study, a strain with strong antagonistic activity against V. mali was isolated from tea rhizosphere soil. Based on morphological characteristics, 16S rRNA gene sequencing, and whole-genome analysis, the isolated strain was identified as Bacillus velezensis and designated as LW-66. This strain demonstrated broad-spectrum antifungal activity against various plant pathogenic fungi, including Valsa mali, Fusarium graminearum, Bipolaris sorokinianum, Alternaria solani, and Exserohilum turcicum. The active extract of B. velezensis maintained strong stability across a wide range of temperatures (25–90 °C) and pH values (2–8), with stability decreasing only when the temperature reached 100 °C or pH ≥ 10. In a preventive assay using detached apple branches inoculated with V. mali, the control efficacy of LW-66 against apple tree canker reached more than 90%. Additionally, in a therapeutic assay using V. mali-infected potted apple seedlings, the LW-66 bone-glue bacterial agent achieved a survival rate of up to 90%. Whole-genome analysis revealed that the genome of LW-66 contains 13 predicted secondary metabolite biosynthetic gene clusters, seven of which showed high homology (≥92% similarity) with known antimicrobial gene clusters, including surfactin, bacillaene, macrolactin H, fengycin, difficidin, bacillibactin, and bacilysin. These gene clusters may be connected to the broad-spectrum antifungal activity of B. velezensis, as well as its ability to disrupt hyphal morphology. The volatile organic compounds produced by LW-66 inhibited V. mali growth by 91.70%. Collectively, these findings demonstrate that B. velezensis LW-66 has a wide antimicrobial range and strong antagonistic effects against multiple plant pathogenic fungi. Therefore, B. velezensis shows promise as a biocontrol agent for managing fungal diseases in plants, providing a basis for developing LW-66-derived biocontrol products aimed at controlling diseases such as apple tree canker. Full article

Given livestock’s crucial role in global food security and economic stability, the alarming threat of climate change calls for the implementation of effective mitigation strategies for climate-resilient livestock production. Management and nutritional strategies offer temporary relief, whereas genetic approaches represent a permanent solution. The role of genetic tools in enabling the development of climate-resilient livestock breeds is widely recognized. Genetic tools like microarrays, RNA-seq, omics, and GWAS can improve the understanding of livestock’s climate adaptability at a molecular level. These tools facilitate the identification of biomarkers for thermo-tolerance, bordering on climate-resilient livestock breeding. Among them, studies employing genome-wide association studies (GWAS) have increased in recent years. GWAS have the potential to improve the genetic basis of thermo-tolerance in heat-stressed livestock populations. GWAS have been used to identify candidate genes for complex and economically important traits in livestock. These include growth, reproduction, disease resistance, milk, meat, and wool production traits under heat stress conditions. This makes GWAS a useful tool for identifying biomarkers that can be incorporated in breeding programs through marker-assisted selection (MAS). The integration of these potential biomarkers into selection and breeding programs would allow GWAS to substantially refine breeding strategies, thereby advancing the climate-resilient potential and sustainability of the livestock sector. Furthermore, GWAS, when utilized along with emerging technologies like Artificial Intelligence (AI), machine learning (ML), and deep learning (DL) for genomic prediction, can predict genetic aspects of livestock adaptation more efficiently and precisely. Thus, future studies should focus on integrated modeling approaches for improving the climate resilience of livestock without jeopardizing their production potential. Such an effort will contribute to sustainable livestock production as well as ensure food security for the growing human population amid changing climate conditions. Full article

Background/Objective: RNA modifications, including N⁶-methyladenosine (m⁶A), 5-methylcytosine (m⁵C), 7-methylguanosine (m⁷G), N¹-methyladenosine (m¹A), pseudouridine (Ψ), N⁴-acetylcytidine (ac⁴C), 5-methoxycarbonylmethyl-2-thiouridine (mcm⁵s²U) and adenosine-to-inosine (A-to-I) editing, constitute a critical layer of post-transcriptional regulation that influences RNA stability, splicing, translation and degradation. This review aims to systematically summarise the current understanding of the molecular mechanisms and regulatory networks of RNA modifications in the female reproductive physiology and to evaluate their pathological implications in obstetric and gynaecologic disorders. Methods: We conducted a comprehensive literature review, synthesising findings from high-throughput sequencing studies, functional experiments and clinical investigations. The review integrates evidence across multiple RNA modification types, their regulatory enzymes (writers, erasers and readers) and their roles in physiological processes (germ cell development, oocyte maturation, embryogenesis and endometrial function) and pathological conditions (gynaecologic cancers, preeclampsia, endometriosis, polycystic ovary syndrome and premature ovarian insufficiency). Results: RNA modifications function as dynamic and reversible regulators that orchestrate key reproductive events, including primordial germ cell differentiation, oocyte meiosis, the maternal-to-zygotic transition, the establishment of uterine receptivity, and placental development. These modifications operate through coordinated writer–eraser–reader networks that fine tune transcripts’ stability, translation efficiency and RNA decay. The dysregulation of these epitranscriptomic networks is strongly implicated in the pathogenesis of gynaecologic malignancies (cervical, ovarian, endometrial cancers and choriocarcinoma), pregnancy-related disorders (preeclampsia, gestational diabetes mellitus and recurrent miscarriage), reproductive endocrine disorders (polycystic ovary syndrome and premature ovarian insufficiency) and benign gynaecological conditions (endometriosis and adenomyosis). Emerging evidence also reveals complex crosstalk among RNA modifications, such as cooperative interactions between m⁶A and m⁵C in translation regulation and antagonistic relationships between m⁶A and A-to-I editing. Conclusions: RNA modifications represent an essential and multifaceted regulatory layer in female reproduction, with broad implications for disease pathogenesis. Their unique reversibility and context-dependent functions offer promising opportunities for the development of diagnostic biomarkers and targeted therapeutic interventions. Future researchers should prioritise integrated multi-omics approaches, enhanced human-relevant models and clinical translation to fully realise the potential of epitranscriptomic medicine in reproductive health. Full article

Owing to topographical constraints, rural domestic sewage management in karst areas faces unique challenges (scattered pollution sources, fragile hydrogeology, and inadequate infrastructure), but research on decentralized treatment technologies and their microbial mechanisms in this area remains scarce. This study aimed to evaluate the efficiency of a physicobiological process (pre-treatment + BAF) for decentralized rural sewage treatment in karst areas and clarify the relationship between microbial community composition and treatment efficiency under different scales. Annual analyses of influent/effluent pollutants and 16S rRNA gene sequencing were conducted for BAF systems of varying scales. The average removal rates of COD, TN, NH₃-N, and TP were 65.35–79.25%, 32.09–66.66%, 49.50–75.42%, and 44.92–67.69%, respectively. Treatment efficiency varied significantly with scale, being higher in larger systems (p < 0.001). All scales shared a core microbial community (dominated by Proteobacteria, Bacteroidetes, and Chlorobi), but the relative abundance of core taxa decreased with decreasing scale. Nitrification and denitrification were positively associated with NH₃-N and TN removal, respectively. Smaller treatment units were more prone to miscellaneous bacteria proliferation, potentially reducing treatment stability. This study fills the research gap of decentralized BAF application in rural karst areas and provides a scientific basis for the scale optimization of rural wastewater treatment facilities. Full article

G-quadruplexes (G4s) are noncanonical nucleic acid structures involved in gene regulation and genome stability. Among them, the telomeric repeat-containing RNA (TERRA) forms biologically relevant RNA G4s (rG4s) that participate in telomere maintenance and genome stability. Although many ligands targeting DNA G4s have been reported, the recognition and modulation of RNA G4 topologies remain less explored. In this work, we investigated the interaction between TERRA and the spermine-functionalized Zn(II) porphyrin, ZnTCPPSpm4, using UV–vis absorption, fluorescence, resonance light scattering (RLS), and circular dichroism (CD) spectroscopy. In K⁺, where TERRA adopts a parallel G4 conformation, ZnTCPPSpm4 binds through a stepwise mechanism involving external end-stacking, forming discrete supramolecular complexes without altering the native topology. In contrast, under Na⁺ conditions, ZnTCPPSpm4 induces a gradual conformational rearrangement of TERRA from the antiparallel to a parallel-like G4 topology. A CD melting study showed that ZnTCPPSpm4 stabilizes the parallel RNA G4, while slightly destabilizing the antiparallel topology. Overall, our results demonstrate that ZnTCPPSpm4 is not a simple G4 binder, but a topology-selective ligand capable of remodeling TERRA G4 structures, highlighting the potential of metalloporphyrins as RNA G4-targeting scaffolds. Full article

Dietary supplementation with functional nutrients is a safe strategy to improve bone health. This study aimed to investigate the ameliorative effects of Berberine (BBR) on dexamethasone-induced bone loss in mice and its potential mechanisms. Micro-CT, histological staining, ELISA and Western blot were employed to evaluate BBR’s skeletal benefits; 16S rRNA sequencing, serum metabolomics and correlation analysis were used to explore its regulatory mechanisms. In vivo experiments showed that BBR improved bone mineral density and trabecular microarchitecture, and upregulated osteogenic markers (COL1 and BMP2). Intestinal bacterial sequencing showed that BBR altered gut bacterial composition, increasing the abundance of Desulfovibrio and Bacteroides while decreasing opportunistic pathogens. BBR also modulated bacterial richness, evenness, and community stability. Serum metabolomics identified 107 BBR-reversed differential metabolites; of these, 33.64% were lipids and lipid-like molecules, which were mainly involved in glycerophospholipid metabolism. Further correlation analysis revealed that BBR-enriched Desulfovibrio was linked to pathway R04864, producing a key glycerophospholipid metabolite positively correlated with bone mass parameters. Overall, these findings suggest that the attenuation of bone loss by BBR may be associated with alterations in the gut microbiota–glycerophospholipid metabolic axis, supporting its potential as a functional food ingredient for bone health. Full article

Temperature and nutrient availability are pivotal drivers of coastal phytoplankton dynamics; however, how they regulate the interplay between community assembly and ecological network stability remains less explored. In this study, we integrated 18S rRNA high-throughput sequencing with molecular ecological network analysis and the iCAMP model to investigate the seasonal succession and driving mechanisms of phytoplankton in a coastal region (Qiongdong) of the South China Sea. Our results suggest that water temperature is a key factor influencing community succession. However, rather than following a linear response to temperature rise, the molecular ecological network exhibited a significant network contraction in spring, characterized by minimized complexity and peak vulnerability. This structural shift coincided with a transition in nutrient limitation (from phosphorus to nitrogen) induced by spring upwelling. Assembly process analysis revealed that while stochastic processes dominated overall community construction, a notable increase in dispersal limitation occurred in spring. The intensification of dispersal limitation driven by changes in the nutritional structure may be the main cause of network simplification and reduced stability. In conclusion, our findings highlight that while temperature affects the seasonal replacement of phytoplankton species, nutrient-induced shifts in assembly mechanisms degrade ecological network integrity in coastal environments. Full article

Two mineral-based solid residues, namely coal gangue (CG) and phosphorus tailings (PT), two of the largest solid waste streams in the mining industry, were used as the sole metal feedstocks to fabricate a novel MgCaFeAl layered double hydroxide (LDH-GT) via a 700 °C calcination, acid leaching and hydrothermal coprecipitation route, with simultaneous synthesis of white carbon black from the reaction byproducts. Under optimized conditions (total metal load is 150 mg kg⁻¹, LDH-GT dose is 0.09 g, pH from 6 to 7), the synthesized material achieved concurrent immobilization efficiencies of 76.28%, 99.96%, and 99.95% for Cr (VI), Cd (II) and Ni (II), respectively, within a 24 h reaction period. TCLP leachability decreased by 82 to 91% relative to the untreated soil. After three wetting, drying and freeze–thaw cycles, the leached concentrations of all three metals remained below 0.3 mg L⁻¹, confirming excellent long-term stability. Mechanistic analyses revealed that Cr (VI) was mainly sequestered through interlayer anion exchange and surface complexation, whereas Cd (II) and Ni (II) were immobilized via isomorphic substitution into the LDH lattice, precipitation as carbonates, and incorporation into Fe/Mn oxides. A 7-day mung bean bioassay showed that LDH-GT amendment increased seed germination from 50% to 73%, enhanced root and shoot biomass by 1.1- to 1.6-fold, and decreased plant Cr, Cd, and Ni contents by over 80%. The 16S rRNA sequencing further demonstrated that LDH-GT reversed the decline in microbial α diversity induced by heavy metal stress, restored aerobic chemoheterotrophic and sulfur cycling functional guilds, and reduced pathogenic signatures. This study provides the demonstration of a waste-to-resource LDH that achieves efficient, durable remediation of multi-metal-contaminated soils, offering a scalable route for coupling solid waste valorization with in situ site restoration. Full article

Anaerobic digestion (AD) of animal manures for biogas production faces challenges including nutritional imbalance, foaming, and process instability. This study evaluated bioaugmentation with surfactant-degrading microbial consortia and cell-free extracts derived from well-characterized oil-contaminated soils during cow and pig manure digestion. These previously analyzed soils contained distinct microbial communities dominated by Pseudomonas in acidic, high-PAH soils and Bacillus in neutral-pH soils with genetic potential for hydrocarbon degradation. Over 30 days, six treatments were assessed using the Automatic Methane Potential Test System (AMPTS II), with pH monitoring, foaming analysis, and 16S rRNA sequencing coupled with PICRUSt2 functional prediction. Supplementation with microbial consortia and extract markedly increased cumulative biogas outputs (cow manure: 407.76 to 603.28 mL/gVS and pig manure: 403.82 to 627.5 mL/gVS), biomethane by 30–50%, reduced digestion time by 5–6 days, and improved pH stability. Foaming reduction was substrate-specific: extracts reduced foam by up to 60% in pig manure, while consortia reduced it by up to 65% in cow manure. Microbial analysis revealed enrichment of fermentative and syntrophic taxa (Clostridium sensu stricto and Paludibacter) and upregulation of methanogenesis pathways (tetrahydromethanopterin S-methyltransferase). This study illustrates that tailored bioaugmentation utilizing consortia from hydrocarbon-contaminated soils provides an environmentally sustainable method to enhance methane yields, improve stability, and control foaming in manure AD, with outcomes significantly affected by the type of manure and amendment strategy employed. Full article

The western honey bee (Apis mellifera) represents a key pollinator for both crops and wild plants, and its global decline raises serious concerns for ecosystem stability and agricultural productivity. Several biotic and abiotic factors are responsible for colony losses, including alterations in the bee microbiota, which is essential for host metabolism, development, and immune responses. In this study, we employed both molecular protocols and metagenomic approaches based on Next-Generation Sequencing (NGS) to characterize the microbial composition and identify commensal, symbiotic, and pathogenic microorganisms, both known and emerging, associated with A. mellifera colonies from 20 apiaries across the Italian territory. Molecular screening revealed Vairimorpha ceranae, Lotmaria passim, Crithidia mellificae and several viruses, including Sacbrood virus (SBV), Black Queen Cell virus (BQCV), Deformed Wing virus (DWV), Chronic Bee Paralysis virus (CBPV) and Acute Bee Paralysis virus (ABPV). 16S rRNA gene sequencing highlighted a bacterial community mainly composed of the Lactobacillus, Gilliamella, and Snodgrassella genera. Virome analysis detected members belonging to the families Dicistroviridae and Iflaviridae, as well as previously unreported viruses in Italy, such as Apis rhabdovirus (ARV-1, ARV-2), Bee Macula-like virus (BeeMLV), and Lake Sinai virus (LSV). This research expands current knowledge of the A. mellifera metagenome, offering valuable insights for epidemiological surveillance and diagnostic assay development. Full article