Search Results (1,246)

The circadian rhythm is an internal timing system formed by the body’s adaptation to the Earth’s rotation, which helps maintain homeostasis by regulating physiological, metabolic, and behavioral activities. The gut microbiota (GM), the largest microbial ecosystem in the human body, exhibits a bidirectional regulatory relationship with the host circadian clock. Emerging evidence indicates that circadian rhythm disruption (CRD) is linked to disturbances in the diurnal oscillations and compositional balance of the GM, accompanied by reduced short-chain fatty acid levels, increased lipopolysaccharide leakage, and altered tryptophan metabolism. These microbial abnormalities may be involved in anxiety-like behaviors through three major pathways: neuroendocrine (hyperactivation of the HPA axis), immune (microglia-mediated neuroinflammation), and neurotransmitter (imbalance of the serotonergic and dopaminergic systems). Conversely, microbial metabolites such as butyrate and secondary bile acids may reciprocally regulate peripheral clock gene expression, forming a complex “circadian rhythm–GM–anxiety” interaction network. This review summarizes the molecular basis of circadian–GM interactions, potential GM-mediated mechanisms linking CRD with anxiety, and emerging intervention strategies including chrononutrition (time-restricted feeding, sequential nutrient intake), microbiota-targeted therapies (probiotics/prebiotics, fecal microbiota transplantation), and light therapy and melatonin supplementation. Future directions should focus on cell-specific mechanisms using single-cell and spatial transcriptomics, developing personalized interventions that integrate chronotype and microbiome profiling, and conducting large-scale randomized controlled trials to facilitate clinical translation. This review provides a framework for understanding the integrative role of circadian biology and gut microbiota in anxiety and may help develop precision intervention paradigms. Full article

Background/Objectives: Dolphins inhabiting coastlines can be influenced by anthropogenic factors. As biochemical changes accumulate in blubber over weeks to months, blubber metabolites may be informative biomarkers of molecular adaptations to environmental changes. Methods: We investigated the blubber metabolomic signatures of live free-ranging bottlenose dolphins for the first time. This exploratory study analyzed blubber samples from 35 common bottlenose dolphins (Tursiops truncatus) in South Texas waters using untargeted ultra-high-performance liquid chromatography-Orbitrap metabolomics. Results: Blubber samples exhibited distinct temporal and spatial metabolic patterns. Pathway enrichment analyses comparing detected metabolites (n = 2777) revealed that dolphins sampled in the spring had enhanced lipid quality and immune regulation, while dolphins sampled in the summer showed stress-associated metabolic responses. Dolphins inhabiting areas previously reported to experience heavy vessel traffic and contaminant burdens exhibited enriched immune- and inflammation-associated pathways. Dolphins that visually appeared to have poorer body condition exhibited metabolite profiles suggestive of increased protein catabolism. Dolphins in extreme salinity conditions had more abundant membrane maintenance and endocrine pathways. Conclusions: Dolphins from each system exhibited distinct metabolic signatures that may be associated with differing physiological responses, highlighting the potential utility of blubber biomarkers for assessing physiological adaptations in free-ranging marine mammals. Improved understanding of habitat-specific physiological responses offers critical insights into how cumulative impacts may affect the health and adaptive capacity of vulnerable species in dynamic coastal ecosystems. Full article

Planktothrix species are among the most widespread bloom-forming cyanobacteria in freshwater ecosystems and are of particular concern because of their ability to produce cyanotoxins and form persistent harmful algal blooms (HABs). Among them, Planktothrix agardhii and Planktothrix rubescens are the most extensively studied species and are responsible for a large proportion of bloom events reported in European lakes. This review synthesizes current knowledge on the taxonomy, ecophysiology, toxin production, environmental drivers, species interactions, and management of Planktothrix blooms, with a particular focus on European freshwater ecosystems. The available evidence highlights marked ecological differences between the two dominant species. P. agardhii is primarily associated with shallow, eutrophic, and well-mixed lakes, whereas P. rubescens is typically found in deep, stratified, and relatively transparent water bodies, where it forms persistent metalimnetic populations. These contrasting ecological strategies influence bloom development, toxin dynamics, detection, and management. Nutrient availability, light climate, temperature, water column stability, and biological interactions all contribute to bloom establishment and persistence, while climate change is expected to further modify bloom frequency, duration, and geographic distribution. The review also examines current monitoring and mitigation approaches, highlighting the limitations of conventional surface-based surveys for detecting deep P. rubescens populations and emphasizing the need for integrated monitoring strategies combining depth-resolved sampling, molecular tools, and toxin analyses. Overall, understanding the ecological and physiological diversity of Planktothrix species is essential for improving risk assessment, developing effective management measures, and mitigating the impacts of cyanobacterial blooms in European freshwaters. Full article

Haemonchus contortus is one of the most prevalent gastrointestinal nematodes in all ecosystems in Mexico, where sheep are raised on pasture, and it poses a significant threat. This study aimed to examine the surgical isolation of a Mexican H. contortus strain, its morphological and molecular characterization, and the maintenance of this strain for future research. Biological behavior and some phenotypic aspects of the adults were considered. Fecal samples were obtained from naturally infected sheep, larval cultures were performed, and a nematode-free lamb was infected. Once the infection was established, the donor sheep were euthanized, the adults recovered, and H. contortus females and males were selected. A surgical transfer from H. contortus adult to the abomasum of a receptor lamb was performed, and the beginning of the egg excretion was confirmed three days post-transfer; fecal cultures from the receptor lamb were conducted to verify the purity of the strain. After three lambs were infected with 3000, 5000, and 10,000 L3, the pre-patent period, prolificacy, and measurements of the adult stages of the strain were studied. The molecular characteristics were evaluated by qPCR; primers were designed based on NCBI genomic DNA sequences of H. contortus to amplify a 176 bp fragment, and the amplicon was sequenced for taxonomic identification. The results of this study describe biological characteristics and some phenotypic aspects of the adults, as well as eggs and infective larvae, and molecular characteristics of the isolated strain, and establish a successful methodology for isolating and maintaining a pure strain of H. contortus (FESC-strain); it can be used as a reference in experimental infections or anthelmintic resistance studies. Full article

Oil pollution remains a persistent global environmental challenge due to the recalcitrance and toxicity of lipid-rich contaminants in terrestrial and aquatic ecosystems. Bacterial lipases (EC 3.1.1.3) play a pivotal role in the initial stages of bioremediation by catalysing the hydrolysis of complex lipids into more bioavailable intermediates, thereby facilitating downstream microbial degradation and mineralisation. This review critically examines the mechanistic basis of lipase-mediated hydrocarbon degradation, with emphasis on enzyme structure–function relationships, catalytic pathways, and regulation under environmentally relevant conditions. In addition to conventional applications in soil and wastewater bioremediation, emerging strategies involving immobilised enzymes, microbial consortia, and waste-derived substrates are evaluated for their effectiveness and scalability. Attention is given to advances in molecular and omics approaches, including metagenomics, transcriptomics, and proteomics, which have expanded the discovery of novel lipases but remain limited in their ability to predict in situ functionality. The review highlights the growing role of protein engineering and artificial intelligence in tailoring lipase properties; however, it also critically assesses current limitations, including insufficient experimental validation and challenges in translating computational predictions to complex environmental systems. Furthermore, integrating multi-omics data into quantitative and predictive frameworks is identified as a key future direction for improving bioremediation efficiency. Despite significant progress, major gaps persist in linking enzyme activity to real-world degradation performance and in developing standardized, scalable approaches. This review therefore provides a comprehensive and critical synthesis of current knowledge while identifying strategic research priorities required to advance bacterial lipases as robust tools for sustainable bioremediation of lipid-based pollutants. Full article

Honey bees (Apis mellifera) are key pollinators in agricultural ecosystems that face increasing pressure from pathogens and environmental change. However, how these environmental factors interact remains incompletely understood. To assess associations between climate, landscape composition, and pathogen occurrence in real agroecosystems, we monitored honey bee colonies across 30 apiaries in southern Italy over two years, in summer and autumn. Molecular screening revealed widespread multi-pathogen exposure, with two viruses, Black Queen Cell Virus (BQCV) and Deformed Wing Virus (DWV), and gut trypanosomatid parasite (Lotmaria passim) being the most frequently detected. In contrast, Nosema ceranae, along with Bee Macula-like Virus (BeeMLV) and Acute Bee Paralysis Virus (ABPV), occurred at lower but still notable frequencies. Infections were generally more frequent in adult foragers than in in-hive bees and larvae, and overall pathogen occurrence tended to be higher in summer than in autumn. Higher humidity was associated with higher overall pathogen occurrence and coinfection levels, whereas higher temperature showed a weaker association with these outcomes. Associations between landscape composition and pathogen occurrence differed across pathogens: a higher proportion of semi-natural habitats was associated with lower viral occurrence, particularly BQCV and DWV; however, N. ceranae was more frequently detected under the same landscape conditions. In contrast, L. passim showed context-dependent responses, with landscape effects emerging only through interactions with humidity and temperature. Pathogen coinfections were more occurrent under warm, humid conditions, although this pattern was partially buffered in landscapes richer in semi-natural habitats. Together, these results indicate that, within the studied apiaries, honey bee pathogen occurrence was associated with climate, season, and land use. These findings suggest that environmental context should be considered when interpreting honey bee health monitoring data in heterogeneous agricultural landscapes, with potential implications for apiary management. Full article

Carex is among the most species-rich genera of angiosperms and plays important ecological roles in wetlands, alpine regions, and temperate ecosystems worldwide. However, research on this genus has long been challenged by pronounced phenotypic plasticity, reduced floral morphology, frequent hybridization, and complex chromosomal evolution. Although recent advances in molecular phylogenetics, comparative genomics, reproductive biology, and ecophysiology have substantially expanded the knowledge of Carex, these findings remain fragmented across disciplines. Here, we synthesize current evidence on Carex taxonomy and phylogeny, genomic and karyotypic evolution, reproductive and life history strategies, abiotic stress responses, ecosystem functions, and bioresource potential within a cross-scale framework. This review emphasizes how genomic architecture, life history variation, and ecophysiological adaptation jointly shape species diversification and ecosystem functioning, while clarifying their implications for habitat restoration and the sustainable use of Carex resources. Finally, we identify key priorities for future research, including improved phylogenomic resolution, comparative functional studies, climate-resilience assessment, and germplasm conservation and sustainable use. Full article

Dybowski’s frog (Rana dybowskii) supports a multi-billion-dollar aquaculture sector in northern China and plays a critical ecological role in forest ecosystems. Despite its immense economic value, germplasm degradation and the mystery surrounding its homomorphic sex-determination system present major bottlenecks for the industry. Here, we integrated PacBio HiFi long-read sequencing, Illumina short-read sequencing, and High-Throughput Chromosome Conformation Capture (Hi-C) technologies to assemble the first chromosome-level reference genome of R. dybowskii. The final assembled genome size is 3.77 Gb, with a contig N50 of 16.27 Mb and a scaffold N50 of 41.54 Mb. A total of 97.82% of the sequences were successfully anchored onto 12 definitive pseudochromosomes corresponding to haploid chromosome number. Repetitive elements account for 65.61% of the genome, characterized by an unusual dominance of DNA transposons (37.19%) over retrotransposons, suggesting a genomic landscape shaped by extreme cold adaptation. Combining multi-tissue transcriptomic evidence, we structurally predicted 26,862 protein-coding genes, and the predicted gene set showed a BUSCO completeness of 96.1%. Functional annotation successfully categorized 96.55% of the total genes. This genomic resource successfully fills a crucial phylogenetic gap in the Rana genus, driving high-efficiency molecular breeding and sustainable conservation of this economic amphibian. Full article

In the current study, soil samples were collected from regions contaminated with industrial waste containing petroleum and its derivatives, including areas around a tire factory in Kırşehir, a chrome factory in Mersin and Kazanlı, and the Karaduvar refinery regions in Mersin, Türkiye. A total of 40 bacteria were isolated from the soil samples. The isolates were identified using molecular methods as well as morphological, physiological, and biochemical tests. Based on the results of 16S rRNA sequence analysis, it was revealed that the isolates belonged to the genera Bacillus, Diaphorobacter, Cupriavidus, Acinetobacter, Massilia, Staphylococcus, and Azospirillum. The antibiotic and heavy metal resistance of the strains were determined. Furthermore, the Drop Collapse method was employed to evaluate the biosurfactant production abilities of the strains, confirming that certain strains possess biosurfactant-producing capabilities. Consequently, distinct bacterial species capable of degrading polyaromatic hydrocarbons, resisting antibiotics and heavy metals, and producing biosurfactants were successfully isolated from contaminated areas in the current study. It is thought that the utilization of species with these properties in bioremediation studies will contribute to the restoration of ecosystem balance. Full article

This study aims to determine the prevalence of infection by larvae from the Anisakidae family in fish commonly consumed in the north of Chile. Then, 2968 specimens belonging to 22 different fish genera were studied. Anisakis spp. third-stage larvae were collected and used for PCR and proteomics studies. Trachurus murphyi was the most parasitized species (51.6%), whereas Scomber japonicus (21.3%) and Isacia conceptions (9.5%) were also found parasitized. PCR studies showed that the only species detected was Anisakis simplex. By LC-MS/MS, we identified a total of 8119 peptide precursors, which correspond to 1919 proteins. Gene Ontology analysis indicated that, among molecular functions, catalytic and binding activities were the most highly expressed. Among biological processes, cellular and metabolic processes were the most highly expressed, while among cellular components, cellular anatomical entities and complex-containing proteins were the most highly detected. By in silico analyses, novel putative allergens were detected through comparative analyses with related genera. Among them, apolipophorin is proposed as a potential new allergen. These findings are of relevance for advancing the understanding of allergen–host immune system interactions. Proteomics and bioinformatics studies strongly suggest that A. simplex is a mosaic of allergens whose implications for public health must be properly evaluated. Finally, a One Health approach is proposed to mitigate Anisakidae infections by integrating multisectoral prevention across human and animal interfaces while concurrently preserving aquatic ecosystem integrity. Full article

Diffuse large B-cell lymphoma (DLBCL) is a biologically heterogeneous mature B-cell neoplasm whose classification, prognosis, and therapy have been reshaped by advances in genomic, transcriptomic, epigenomic, single-cell, and spatial profiling technologies. This review focuses on how these approaches have refined the molecular landscape of DLBCL, including recurrent chromosomal translocations, tumor-suppressor alterations, oncogenic signaling pathways, and tumor-microenvironment programs. Cell-of-origin (COO) frameworks remain clinically useful. However, contemporary models extend beyond conventional germinal center categories by incorporating probabilistic genetic subtypes, expression-defined high-risk states, and spatially resolved lymphoma-cell and immune-cell ecosystems. These high-resolution methods clarify intratumoral heterogeneity, identify biologically distinct subgroups, and inform prognosis and therapeutic selection. The review also summarizes how tumor-intrinsic biology and the tumor-microenvironment (TME) shape responses to frontline therapy, targeted agents, antibody-drug conjugates, bispecific antibodies, and CD19-directed CAR T-cell therapy. Particular emphasis is placed on product-specific evidence in relapsed/refractory disease, rational sequencing of immunotherapies, and emerging biomarkers such as circulating tumor DNA-based measurable residual disease (ctDNA-MRD). Together, these developments support a shift from COO-centric classification toward dynamic, biology-driven models that incorporate tumor-intrinsic and microenvironmental determinants to guide personalized therapy in DLBCL. Full article

The Qinghai–Tibet Plateau, a globally significant ecological barrier and a core pastoral region, is persistently constrained by cold and arid climatic conditions, nutrient poor soils, and progressive grassland degradation. These challenges necessitate maintaining forage productivity while enhancing ecological stability. Medicago sativa L., valued for its high nutritional quality and capacity for biological nitrogen fixation, has been widely incorporated into regional grassland systems. Rhizobial inoculation, as an environmentally sustainable agronomic practice, is regarded as an effective approach to improving nutrient use efficiency and promoting ecological restoration; however, its underlying mechanisms in cold and arid environments remain insufficiently understood. This study established a field experiment in Delingha, Qaidam Basin, using the cultivar ‘Beilin 201’. Treatments included an uninoculated control (CK) and four rhizobial seed coating rates: E1 (0.75 g·m⁻²), E2 (1.50 g·m⁻²), E3 (2.24 g·m⁻²), and E4 (3.00 g·m⁻²). The effects on yield, rhizosphere soil physicochemical properties, bacterial community structure, and molecular ecological networks were systematically evaluated. The composite microbial inoculant maintained Medicago sativa L. yield, with only modest and non-significant increases in some treatments. In contrast, soil organic matter increased significantly with application rate (p < 0.001), suggesting a stronger short-term effect on soil properties than on yield. Although network vulnerability was lowest in E4, the differences among treatments were not statistically significant. Mixed effects modeling showed that soil factors (74.79%) and microbial factors (25.12%) jointly influenced yield variation. Structural equation modeling further revealed that microbial factors exerted a positive direct effect on yield (0.3), whereas soil factors exhibited a stronger direct effect (0.57), with inoculation rate primarily influencing yield indirectly through soil mediated pathways. This study elucidates the ecological functions and regulatory mechanisms of rhizobial formulations in high elevation dryland ecosystems and provides both theoretical support and practical guidance for the rational application of microbial fertilizers and the sustainable management of forage systems on the Qinghai–Tibet Plateau. Full article

Leaf litter decomposition is a key pathway for carbon transfer from forest ecosystems to soils and surface waters. Dissolved organic matter (DOM) released during early-stage leaching represents a potentially reactive fraction of this carbon pool; however, its molecular composition and short-term reactivity remain insufficiently characterised. This study provides a comparative characterisation of DOM released from composite leaf litter samples representing five common deciduous tree species (Betula pendula, Carpinus betulus, Alnus glutinosa, Populus tremula, and Quercus robur) under controlled laboratory conditions. Leaf material collected from multiple trees per species was pooled to obtain a single composite sample; therefore, replicate leaching experiments represent procedural rather than biological replication. DOM was isolated using solid-phase extraction (SPE) and analysed by gas chromatography–mass spectrometry (GC–MS) following trimethylsilyl (TMS) derivatisation, while chemical oxygen demand (COD) and biochemical oxygen demand (BOD₅) were used as indicators of oxidative reactivity and short-term biodegradability. The applied analytical approach captures a selective and operationally defined fraction of DOM, primarily low-molecular-weight and derivatisable compounds; therefore, the results are interpreted as semi-quantitative compositional fingerprints. Carbohydrates, phenolic compounds, and low-molecular-weight organic acids dominated the detected fraction of DOM, with differences observed among composite samples. The composite samples representing A. glutinosa and P. tremula contained higher relative proportions of carbohydrate-related compounds, whereas the composite samples representing B. pendula and C. betulus showed higher relative contributions of aromatic compounds. Apparent differences in BOD₅ were observed among composite samples; however, these observations likely reflect procedural variability rather than independent biological effects. The results indicate variability in DOM composition and apparent reactivity among composite litter samples under controlled laboratory conditions. Due to the lack of biological replication and the selective nature of the analytical approach, the findings should be interpreted as exploratory and not as evidence of generalised tree-species effects. Full article

Thermophilic cyanobacteria successfully colonize thermal gradients within hot springs, implying evolved mechanisms to cope with temperature-induced oxidative stress. Although polyphosphate (polyP) is known to contribute to oxidative stress resistance, its specific role in thermophilic cyanobacteria remains poorly understood. To address this, this study established a temperature gradient (30–70 °C) and used phloretin (polyP synthesis inhibitor) plus exogenous polyP to investigate polyP metabolism, redox homeostasis, photosynthetic function, and growth of Thermosynechococcus sp. FJSJ-1 from hot spring. The results show that temperature fluctuations specifically induce polyP accumulation, whereas inhibiting polyP synthesis sharply elevates reactive oxygen species (ROS) and overloads intrinsic defenses including superoxide dismutase, catalase, glutathione, and heat shock proteins. Crucially, exogenous polyP rescued phloretin-induced oxidative damage and growth inhibition. PolyP mitigates oxidative damage not by direct ROS scavenging but by integrating and reinforcing endogenous antioxidant network. This protective effect in turn safeguards photosystem II from oxidative attack, thereby preserving photosynthetic pigment stability, phycobiliprotein content, and electron transport efficiency. Taken together, polyP contributes to temperature adaptability in Thermosynechococcus sp. FJSJ-1 by coordinating antioxidant defense. This study elucidates a key molecular strategy for thriving across temperature ranges in geothermal ecosystems, advancing microbial adaptation knowledge and providing a theoretical basis for engineering thermotolerant strains for bioremediation and biofuel production. Full article

Sourdoughs are complex microbial ecosystems fundamental to traditional breadmaking. Despite extensive research, variability among traditional sourdough ecosystems remains a key area of investigation. In this context, 13 type I sourdough starters from Villaurbana (Sardinia, Italy) were characterised combining molecular and biochemical techniques. Bacterial and fungal communities were identified by NGS-based amplicon sequencing, while lactic and acetic acid, and residual sugars were quantified. The bacterial population was dominated by the genus Fructilactobacillus, whereas the fungal community spanned multiple genera. To explore the mycobiota, 130 yeast isolates were identified sequencing D1–D2 domain and through MALDI-TOF mass spectrometry. Six yeast species were detected: Saccharomyces cerevisiae was the dominant species (58.46%), followed by non-Saccharomyces yeasts (41.54%), including Torulaspora delbrueckii, Pichia fermentans, Wickerhamomyces anomalus, Maudiozyma humilis, and Monosporozyma unispora. Strain-level typing via microsatellite analysis revealed high intraspecific diversity among S. cerevisiae and T. delbrueckii isolates. S. cerevisiae strains were distributed across distinct genetic lineages, with some clustering alongside industrial reference strains and others displaying unique evolutionary trajectories. T. delbrueckii strains formed two clonal groups substantially divergent from reference strains. This study supports the restitution of characterized yeast strains to the community as a resource for establishing a new microbial consortium representative of Villaurbana sourdough tradition. Full article