Search Results (1,555)

Acid mine drainage (AMD) environments feature extreme acidity (pH ≤ 2) and high heavy metal concentrations. Acidophiles survive these conditions through unique genetic adaptations and secondary metabolite (SM) pathways. Leptospirillum ferriphilum, known for its acid and heavy metal resistance, serves as a model for AMD bioremediation, though systematic multi-omics studies on its key SMs and biosynthesis pathways remain underexplored. In this study, L. ferriphilum YR01 was isolated and identified from the AMD of the Zijinshan copper mine, China. Pangenomic analysis revealed that YR01 possesses the largest number of genes (2623) among the eight sequenced L. ferriphilum strains. Comparative genomics, antiSMASH, BiG-SCAPE, and metabolomic analyses (LC-MS and HPLC-MS) were integrated to comprehensively explore its biosynthetic capacity. A total of 39 biosynthetic gene clusters (BGCs) were identified, of which 60% shared <50% similarity with known clusters, indicating substantial novel biosynthetic potential. The sequence alignment of SM biosynthetic gene clusters (BGCs) demonstrated the potential of L. ferriphilum to synthesize conserved clusters for ectoine, choline, carotenoids, terpenoids, and terpene precursors. YR01 harbors complete BGCs for all five SM types. Notably, key nonribosomal peptide synthetase (NRPS) modules implicated in N-acyl homoserine lactone (AHL) synthesis were identified. Untargeted metabolomics (LC-MS) revealed the production of diverse SMs (18 types) putatively involved in environmental adaptation, including phosphocholine, carotenoids (e.g., anteraxanthin), cholera autoinducer-1 (CAI-1), and multiple AHLs. Targeted detection (HPLC-MS) further confirmed that YR01 could produce ectoine (0.10 ng/mL) and specific AHLs (C₁₄-HSL, C₁₂-HSL, C₁₂-OH-HSL), which were beneficial for the survival of the strain in extremely acidic environments and interspecies communication through SMs. This study represents the first comprehensive multi-omics characterization of BGCs in L. ferriphilum and experimentally validates the production of key SMs. Collectively, this study provides a comprehensive elucidation of the SM biosynthetic repertoire and environmental adaptation strategies in L. ferriphilum, advancing our understanding of microbial adaptation and interspecies communication in AMD systems, and offering potential implications for biomining applications. Full article

The human skin microbiome plays a crucial role in maintaining skin health by acting as a barrier against pathogens and modulating immune regulation. This case study investigates the skin microbiome of two healthy Korean male individuals in their 20s during Antarctic expeditions, focusing on microbial changes, reversion to pre-expedition states, and the influence of environmental and lifestyle factors. Notable microbial alterations were observed, including increases in Pseudomonadota and decreases in Actinomycetota, indicating pronounced microbial shifts in response to harsh environmental factors such as low temperature and humidity. Post-expedition revealed incomplete recovery to pre-expedition states, with Host A showing a higher resilience index, suggesting faster microbial recovery. Correlation analyses revealed associations between microbial changes and environmental factors (e.g., temperature, humidity, atmospheric pressure) as well as lifestyle factors (e.g., sunblock usage, outdoor activities), highlighting complex interactions between host behaviors and microbiome dynamics. Despite the study’s limited sample size, these findings offer insights into the adaptability and resilience of the skin microbiome under extreme environments, with potential implications for health management and skincare strategies during isolated and prolonged expeditions. Full article

Antibodies are produced by cells of the adaptive immune response and recognize epitopes of microbial structures with high affinity and specificity. Antibodies are recognized by Fc fragment receptors (FcRs) found on the surface of phagocytic cells (neutrophils, monocytes, macrophages) and NK cells, among others. Hence, antibodies link the adaptive immune response with the innate immune response. The functions of antibodies are related to the N-glycosylation profile of these proteins. In this review, we describe how N-glycosylation of the Fc fragment of the different antibody classes is carried out, and which oligosaccharides are most commonly found in these antibodies. Subsequently, we summarize the biological effects of N-glycosylation of antibodies: on the binding of antibodies to FcRs (which affects various functions, such as antibody-dependent cellular cytotoxicity, antibody-dependent phagocytosis, and the production of pro- or anti-inflammatory chemokines and cytokines), on the ability of antibodies to activate complement and on the ability of some antibodies to directly neutralize the adhesion of bacteria and viruses to host cells (independently of Fab recognition). We describe how the N-glycosylation profile of antibodies is modified during certain infections (such as tuberculosis, COVID-19, influenza and dengue) and in response to vaccination, and the potential use of this profile to identify the stage and severity of an infection. Finally, we review the importance of N-glycosylation for the pharmacokinetic, pharmacodynamic and safety profiles of therapeutic monoclonal antibodies. Full article

The intricate connections between plants and the microbial populations that surround them are crucial for plant development and resilience, but little is known about the evolutionary processes influencing these partnerships. Less is known about how pathogenic and beneficial microbes coevolve with their plant hosts over ecological and evolutionary timeframes, despite the fact that several studies identify rhizosphere and endophytic microbes that support nutrient acquisition, disease resistance, and stress tolerance. Using molecular, ecological, and evolutionary investigations from soil, rhizosphere, and endosphere habitats, this review summarizes current findings on microbial coevolution in plant–microbe systems. We look at the endosymbiotic processes that underlie the development of organelles, the mechanisms of mutualism and antagonism, and the eco-evolutionary feedbacks that affect plant health and agricultural output. The inadequate comprehension of intraspecific microbial diversity, the application of laboratory coevolution experiments to field settings, and the long-term effects of climate change on the evolutionary dynamics of plants and microbiomes are some of the major knowledge gaps. When pathogenic and beneficial microbes apply selective pressures to one another and their common host, coevolution takes place. This results in mutual genetic and physiological adaptations, such as modifications to host immunity, microbial virulence, or competitive tactics, which influence the way the two types interact over time. We conclude that understanding plants as holobiont-integrated units of hosts and their microbiomes offers fresh chances to develop microbiome-based approaches to sustainable agriculture, such as coevolutionary breeding programs, precision biofertilizers, and resilient cropping systems. Full article

CRISPR-Cas systems are best known as adaptive immune defenses in prokaryotes, but they also function as versatile regulators bridging bacterial immunity with host-related processes. Beyond neutralizing invasive phages and plasmids, these systems influence core aspects of bacterial physiology, such as modulating gene expression, stress responses, biofilm formation, quorum sensing, and virulence. Notably, CRISPR-mediated regulation can facilitate immune evasion at the host-pathogen interface, underscoring these systems as central orchestrators of microbial survival and host interactions. In addition, CRISPR-Cas has rapidly become a cornerstone of synthetic biology and microbiome engineering. Recent strategies repurpose native and engineered CRISPR systems to precisely modulate microbiome composition or deliver sequence-specific antimicrobials, underscoring the expanding translational potential of this system. Collectively, emerging insights highlight both the canonical immune function and non-canonical regulatory roles of CRISPR-Cas, as well as their broad biological and biotechnological relevance. This review provides a critical synthesis of these developments, illustrating how CRISPR-Cas bridges adaptive immunity and microbial physiology, and outlines future directions for harnessing this duality to deepen understanding of microbial physiology and inform new translational applications. Full article

Antimicrobial resistance (AMR) poses an escalating global health crisis, projected to cause up to 10 million deaths annually by 2050. Conventional antibiotics are increasingly ineffective due to microbial adaptation, overuse, and disruption of gut microbiota. Nanotechnology offers promising alternatives, but traditional nanoparticle synthesis often relies on toxic chemicals and energy-intensive processes. This review explores mushroom-derived nanoparticles (myco-NPs) as sustainable, eco-friendly antimicrobials. Edible and medicinal mushrooms contain bioactive compounds, including polysaccharides, flavonoids, and proteins, that act as reducing and stabilizing agents in nanoparticle biosynthesis. Myco-NPs exhibit antimicrobial activity through membrane disruption, oxidative stress, immune modulation, and biofilm inhibition, while also demonstrating synergistic effects with antibiotics and potential roles in regulating the gut microbiota. Recent advances highlight their potential applications in medicine, food safety, and environmental protection. However, challenges remain regarding standardization, safety evaluation, and large-scale production. We emphasize interdisciplinary collaboration as essential to translating mushroom-based nanotechnology into effective clinical and industrial solutions. Full article

Although rhizobacteria are known to improve plant adaptation to abiotic stressors, their possible contribution to the inherent resilience exhibited by crops such as Sorghum bicolor is still poorly quantified. Here, three sorghum pre-release lines and three check varieties were established and evaluated at two low-altitude sites of less than 600 masl. Treatments were laid out in a randomized complete block design, replicated two times. Twenty-four rhizospheric soil samples comprising six sorghum genotypes with two replications across two sites were collected, processed using Zymo Research DNA extraction protocols, and the 16S rRNA amplicon sequences were generated for bacterial diversity quantifications following the Divisive Amplicon Denoising Algorithm 2 (DADA2) workflow. Grain yield data were also recorded and expressed in tonnes per hectare. Rhizobacteria recruitment and GY performance significantly (p < 0.05) varied with sorghum genotypes. Bacterial abundance significantly (p < 0.05) associated with sorghum grain yield performance with Actinobacteriota and Firmicutes being identified to be of economic importance, explaining between 52.23 and 85.64% of the variation in grain yield performance. The modelled relationships between rhizobacteria and grain yield performance revealed R² predicted values of up to 75.25% and a 10-fold R² of 75.54%, implying no model overfitting. Sorghum genotypes did not consistently exhibit direct variation between genetic worth values and grain yield performance. Superior grain yield performers, namely ICSV111IN, CHITICHI, and SV4, consistently associated with high incidences of occurrence of the bacteria phyla Chloroflexi (class = Chloroflexia) and Firmicutes (class = Bacilli), whilst integrating the conventional selection method with microbial diversity data, changed the genotype performance ranking, in which all the three pre-release lines, namely, IESV91070DL, ASARECA12-3-1, and ICSV111IN, exhibited superiority over the check varieties. The results demonstrated that the inherent stress resilience exhibited by some sorghum genotypes under climate change-induced stresses such as CDHS may be influenced by specific bacterial taxa recruited in the rhizosphere environment of the plants. Hence, more effort should be made to further exploit these beneficial plant–microbe interactions for enhanced sorghum productivity under abiotic stress conditions. Full article

Bacterial synthetic microbial communities (SynCom) have exhibited significant effects for enhancing plant growth and delivering ecological benefits. However, persistent challenges, including structural instability, limited environmental adaptability, and transient efficacy, remain critical barriers to their practical application. Herein, we propose Arbuscular Mycorrhizal fungi (AMF) as the keystone component to optimize SynCom’s ecological fitness in sustainable agricultural systems. AMF modulate microbiome assembly through hyphal networks, enhancing community stability via facilitative interactions and augmenting nutrient cycling functionalities. This review systematically evaluates methodologies for AMF-based SynCom design and construction, investigates the dynamics of AMF-microbe interactions, delineates plant growth-promoting mechanisms, identifies candidate microbial taxa, and addresses implementation bottlenecks with corresponding strategies. We posit that AMF-Based SynComs represent a transformative management tool for ensuring global food security amid impending climatic perturbations and declining agricultural productivity. Full article

Smallholder farming plays a crucial role in global food security, contributing more than half of the world’s food supply. However, it is increasingly threatened by climate variability, declining soil fertility, and financial constraints, all of which suppress plant growth, reduce yields, and endanger livelihood stability. Addressing these challenges requires sustainable, eco-friendly alternatives to costly and environmentally damaging agrochemicals. Sorghum, a climate-resilient cereal, harbours a diverse microbiome that contributes significantly to its remarkable adaptability under adverse conditions. Harnessing the sorghum-associated microbiome, therefore, represents a promising, low-cost, and sustainable strategy to enhance sorghum productivity and resilience in smallholder farming systems. However, despite its potential, the adoption of microbiome-based technologies among smallholders remains limited due to a lack of local production units, poor government policies, knowledge gaps, and perceived risks. Although many studies report positive outcomes from microbiome-based interventions, translating this potential from controlled experiments to real-world field applications requires a critical evaluation of the efficacy, practicality, and limitations of microbial interventions. Furthermore, the outcomes of these studies are uneven, highly context-dependent, and often restricted to short-term or small-scale trials. This review, therefore, seeks to highlight current understanding of the sorghum microbiome, including its composition and the procedures for isolating and characterising beneficial microbes. It further evaluates the key challenges hindering adoption and proposes strategies to overcome them. Ultimately, this review advocates for integrating sorghum-associated microbiome technologies within integrated farming systems, underscoring their potential to enhance sustainable crop production, strengthen smallholder resilience, and contribute to the global sustainable development goals. Full article

Qatar’s arid and semi-arid landscapes subject native plants to severe abiotic stresses, including salinity, drought, intense solar radiation, and high temperatures, along with biotic challenges such as herbivory, microbial pathogens, and competition. The ways in which plants coordinate responses to these simultaneous pressures remain insufficiently understood, creating a knowledge gap in desert persistence strategies. This study investigates the integrated defence mechanisms that enable survival under dual stress conditions. We analyse chemical responses such as the synthesis of antimicrobial and phenolic compounds, structural adaptations including thickened cuticles, trichomes, and reinforced cell walls, and physiological trade-offs affecting water-use efficiency and gas exchange. Emphasis is placed on the regulatory role of abscisic acid, which links abiotic stress responses to enhanced pathogen resistance through interconnected biochemical pathways. The study also evaluates the benefits and costs of these structural and biochemical defences. Our findings reveal that native desert species employ adaptive strategies that integrate structural, physiological, and biochemical processes to withstand simultaneous abiotic and biotic pressures. These coordinated mechanisms enhance plant persistence under extreme conditions and play a crucial role in maintaining biodiversity, ecological resilience, and the long-term stability of Qatar’s fragile desert ecosystems. Full article

Background: Land use change fundamentally alters soil microbial communities and biochemical processes, yet the integrated effects on rhizosphere microbiome–metabolome networks remained poorly understood. Objective: This study investigated land uses as forest, grassland and intermediary edge shape the rhizosphere biochemical networks of naturally grown Barbarea vulgaris. Methods: Rhizosphere soils of Barbarea vulgaris were analysed for microbial community structure abundance, and metabolomic profile applying phospholipid fatty acid (PLFA) profiling and mass spectrometric untargeted metabolomics (GC–MS/MS and MALDI–TOF/TOF MS). These were coupled with co–inertia analysis to assess microbiome–metabolome interactions. Results: Microbial community analysis revealed significant effects of land use on bacterial community structure (G+/G−, p < 0.001). Untargeted metabolomics identified 248 metabolites, of which 161 were mapped to KEGG pathways. Amino acids and derivatives (21.1%) followed by organic acids (16.8%) were the most representative among identified metabolites. Pathway enrichment analysis revealed coordinated reprogramming of central carbon and nitrogen metabolism across land use gradients, particularly in the amino acid metabolism, TCA cycle, and glycolysis/gluconeogenesis pathways. Microbiome–metabolome coupling analysis revealed distinct correlation patterns between microbial phenotypes and metabolite classes, with forest environments showing the strongest biochemical network integration (RV = 0.91). Edge habitats presented intermediate signatures, supporting their role as transitional zones with unique biochemical properties. Conclusions: The environmental context fundamentally shapes rhizosphere biochemical network organization through coordinated shifts in bacterial community structure and metabolic pathway activity. These habitat-specific metabolic signatures suggest that land use change triggers adaptive biochemical responses that may influence plant performance and ecosystem functioning across environmental gradients. Full article

Straw return is crucial for sustainable agriculture, but its efficiency is limited by low temperatures in cold regions, especially in saline-alkali soils. This study investigates the degradation process of maize straw and the response of soil properties and microbial communities during the winter low-temperature period in the alkaline farmland of Anda, China. A two-year field experiment with straw return (SR) and no return (NR) treatments was conducted. Straw degradation rates and structural changes (as observed via scanning electron microscope, SEM) were monitored. Soil physicochemical properties and enzyme activities were analyzed. Microbial community composition was characterized using 16S rRNA and ITS sequencing. The cumulative straw degradation rate over two years reached 94.81%, with 18.33% occurring in the first winter freeze–thaw period. Freeze–thaw cycles significantly damaged the straw structure, facilitating microbial colonization. Straw return significantly improved soil properties after winter, increasing field water capacity (3.45%), content of large aggregates (6.57%), available nutrients (P 38.17 mg/kg, K 191.93 mg/kg), and organic carbon fractions compared to NR. Microbial analysis revealed that low temperatures filtered the community, enriching cold-tolerant taxa like Pseudogymnoascus, Penicillium, and Pedobacter, which are crucial for lignocellulose decomposition under cold conditions. The winter period plays a significant role in initiating straw degradation in cold regions. Straw return mitigates the adverse effects of winter freezing on soil quality and promotes the development of a cold-adapted microbial consortium, thereby enhancing the sustainability of alkaline farmland ecosystems in Northeast China. Full article

The gut microbiota plays a crucial role in maintaining swine health and understanding its stage-specific variations provides a scientific basis for health assessment. This study investigated the structural changes in intestinal microbiota during the development of Sichuan–Tibetan black pigs (n = 15) by collecting fecal samples at three growth stages: the nursery period (1 month), growing period (3 months), and finishing period (10 months). Microbial profiling was performed using 16S rRNA sequencing. Results showed no significant difference in the Shannon index between the nursery and growing periods, while the finishing period exhibited distinct ACE and Chao 1 indices compared to other stages. PCoA and NMDS analyses revealed significant structural divergence in the finishing period microbiota, with greater intra-group variability observed in the nursery and growing periods. At the phylum level, Firmicutes abundance increased progressively with growth, becoming the absolute dominant phylum, whereas Bacteroidota showed a declining trend. These characteristics are particularly prominent during the finishing period. At the family level, Lactobacillaceae abundance increased continuously. Oscillospiraceae remained stable during the early stages but decreased significantly in the finishing period. Genus-level analysis shows that Lactobacillus, especially L. amylovorus and L. reuteri, become dominant bacterial species during the finishing period. A total of 84 differentially abundant core microbiota were identified, with the finishing period containing the highest number. Functional annotation revealed 19 significantly different metabolic pathways across the three stages. The most significant is the enhanced activity of microorganisms during the finishing period in pathogen-related metabolism and exogenous degradation, reflecting their adaptability to complex feed. These findings demonstrate stage-dependent variations in the gut microbiota of Sichuan–Tibetan black pigs, providing valuable references for nutritional regulation and feeding management practices. Full article

Snakes are model animals to study energy balance, but studies on the gut microbiota of the animals are rather scarce. To fill the gap, we used metagenome sequencing to investigate the microbial community composition and adaptability in the stomach, small intestine, and large intestine of Big-eyed Bamboo Snake. The results showed that there was no significant differences in α-diversity among different gastrointestinal segments. Pseudomonadota, Bacteroidota, and Bacillota were the most abundant phyla. The dominant genera in the stomach and small intestine were similar, while those in the large intestine were distinct. The abundance of Bacteroides, Citrobacter and Clostridium was significantly higher in the large intestine than in the small intestine. The LEfSe analysis revealed that the small intestine had the most characteristic bacteria, with a total of 20 species, while the stomach and large intestine each had two species. Additionally, in the current study, we also focused on the impact of the microbial community structure on functions through functional annotations in the KEGG and CAZy. There were significant differences in the KEGG level 2 between the stomach and the small intestine. The LEfSe analysis revealed the differences in the CAZy level 2 between the large intestine and the small intestine. Overall, our study provided a comparative and contrastive analysis of the gut microbiota in different gastrointestinal segments of Big-eyed Bamboo Snake, offering valuable insights for the co-evolution mechanism of the host and the gut microbiota. Full article

In response to the issues of increased brittleness and insufficient toughness in microbially solidified saline sandy soils in cold and arid plateau regions, this study investigated saline sandy soils and indigenous microorganisms from the Qaidam Basin, Qinghai. A dual-reinforcement method combining microbial-induced calcium carbonate precipitation (MICP) with alkali-modified reed fiber (ARF) was proposed to enhance both strength and ductility. The study explored the adsorption characteristics and solidification mechanisms of this approach. Key innovations include: (1) alkali modification significantly improved the interfacial bonding between reed fibers and sand particles, with pull-out tests indicating a 1.24-fold increase in adhesion strength; (2) an orthogonal experimental design identified optimal parameters—fiber length of 15 mm, fiber content of 0.5%, and cementation solution concentration of 3 mol/L—leading to the development of a synergistic “microbial cementation–fiber bridging” enhancement model. Experimental results showed that the proposed method increased the unconfined compressive strength (UCS) of the solidified soil to 2082.85 kPa, 2.99 times higher than that of traditional MICP-treated soil, while it significantly enhanced the ductility of the soil. This approach offers a mechanically robust and environmentally adaptive solution within the ambient temperature range of 0–35 °C for the ecological restoration of saline soils in high-altitude regions. Full article