Search Results (3,123)

Microorganisms can aggregate and organise into structured communities embedded within an exopolysaccharide-based matrsix, which serves as a protective barrier and a functional environment around microbial cells. The formation of biofilms is widely recognised as a pivotal factor in bacterial virulence, impeding the efficacy of antimicrobial agents and hindering immune responses, whilst concomitantly contributing to the development of antimicrobial resistance and the onset of persistent infections. Biofilm formation is a tightly regulated and dynamic process, controlled by quorum-sensing mechanisms and profoundly influenced by environmental factors and nutrient availability. The objective of this review is to elucidate the significance of biofilms in clinical settings, with a particular focus on their role in the pathogenesis of infectious diseases. Particular attention is devoted to biofilm-associated infections and infections related to invasive medical devices, with a particular emphasis on the most prevalent microbial pathogens, which include S. aureus, S. epidermidis, P. aeruginosa, E. coli, K. pneumoniae, A. baumannii and various species of Candida. Furthermore, the present review encompasses biofilm-associated chronic infections, conditions manifesting in predisposed patients, including individuals affected by cystic fibrosis. This review further examines the most recent strategies for combating antibiotic resistance in bacterial biofilms. This review focuses on recent biofilm pathogenesis advancements, with a focus on diagnosis challenges and the need for new ways to disrupt biofilm integrity. Full article

Healthcare-associated infections (HAIs) remain a significant global challenge, affecting approximately 7% of patients in developed countries and over 10% in developing regions, according to the World Health Organization. Medical textiles, particularly hospital bed linens and pillowcases, play a critical role in the transmission of pathogenic microorganisms due to their porous structure and moisture-retaining properties, which support microbial survival and proliferation, including bacteria such as Staphylococcus aureus and Escherichia coli. Conventional disinfection methods, including laundering and thermal treatments, provide only temporary protection, leading to rapid recontamination during use. In recent years, various antimicrobial agents and functionalization techniques have been developed to impart long-lasting antiseptic properties to textile materials. However, these approaches differ significantly in terms of antimicrobial efficiency, durability, cost-effectiveness, and environmental impact, making the selection of optimal strategies challenging for practical healthcare applications. This review provides a comprehensive comparative analysis of antimicrobial agents used in healthcare textile functionalization, including metal-based nanoparticles, organic compounds, and bio-based materials. In addition, it evaluates key modification methods such as coating, padding, and in situ synthesis, with particular emphasis on their influence on antimicrobial performance, wash durability, and practical applicability. Furthermore, this review discusses major challenges associated with the use of antiseptic coatings, including toxicity, environmental concerns, and economic limitations. Based on the analysis, promising directions for the development of safer, cost-effective, and durable antimicrobial textile systems are highlighted, offering valuable insights for future research and real-world healthcare applications. Full article

Abiotic stress factors, including drought and salinity, severely limit crop productivity worldwide. Furthermore, the extensive use of herbicides, such as glyphosate, disrupts beneficial soil microbiota, further impairing crop growth. Plant growth-promoting bacteria (PGPB) represent a sustainable and efficient strategy to enhance crop yields, particularly under unfavorable environmental and soil conditions. In this study, we characterized Paenibacillus sp. JSM-10, newly isolated from glyphosate-exposed agricultural soil, for its stress tolerance and plant growth-promoting potential, including its morphology examined using complementary microscopy techniques. The strain tolerated up to 0.5 g/L glyphosate, 15 g/L NaCl, and 100 g/L polyethylene glycol (PEG-6000) without significant growth inhibition (p > 0.05), demonstrating robust resilience to such multiple abiotic stresses. Beyond its tolerance, the strain exhibited several beneficial characteristics, including indole-3-acetic acid (IAA) synthesis, siderophore production, and inorganic phosphate solubilization. Furthermore, both living cells and culture filtrates of JSM-10 exhibited a positive trend toward enhancing buckwheat growth under normal and saline conditions, with effect sizes ranging from Hedges’ g = 0.56−0.92. In addition, JSM-10 exhibited antagonistic activity against a range of pathogenic microorganisms, including Nigrospora oryzae, Bipolaris sorokiniana, Alternaria spp., and Escherichia coli. Altogether, these characteristics highlight the Paenibacillus sp. JSM-10 strain and its culture filtrates as promising candidates for application in organic farming aimed at promoting plant growth and improving stress tolerance via plant–microbe interactions. Full article

Cover crops in woody crops as a sustainable land management alternative to conventional tillage induce changes in soil properties that improve ecosystem functioning. Soil is highly dynamic, and disturbances in environmental conditions affect soil microorganisms, particularly in gypsiferous soils, where microbiological activity remains poorly understood. This study evaluated the effects of three cover crop systems: spontaneous permanent vegetation cover (SVE), annual legume cover (VIC), and permanent grass cover (BRA), compared with conventional tillage (TIL), on soil physicochemical and biological properties in an olive grove over two crop seasons. Overall, cover crops promoted higher microbial activity and carbon storage than tillage, with responses being more pronounced during the wetter year. Conventional tillage consistently exhibited the lowest levels of enzyme activities and carbon stocks, whereas permanent covers showed stronger positive effects on soil functioning. These findings indicate that the benefits of cover crops on soil processes are reinforced under favorable moisture conditions but also remain under drier years, highlighting their stabilizing role. The improvement of soil health induced by cover crops contributes to enhancing soil ecosystem services, including soil fertility, in olive groves, supporting their adoption as a sustainable management strategy in Mediterranean agroecosystems, even under lower rainfall conditions. Full article

Reactive oxygen species (ROS) are a class of molecules or free radicals with strong oxidizing properties. They have attracted increasing attention in soil research in recent years because of their perceived importance in many soil biochemical processes. Previous reviews of ROS in soil mainly focused on their impacts on carbon emissions and organic pollutant remediation, with few descriptions of the mechanisms responsible for ROS generation, and a comprehensive understanding of their environmental effects is still lacking. Therefore, the present review provides details on the sources and underlying generation mechanisms of ROS in soil. These mechanisms include inputs via atmospheric deposition, metal–mineral reactions, root exudation, microbial metabolism, enzymatic reactions and various organic matter transformations. In contrast to previous reviews, we also discuss mutual conversion between different types of ROS in soil. The impacts of ROS on the soil environment are further explored, such as element cycling, pollutant degradation, and the growth and reproduction of plants and microorganisms, in order to provide a systematic understanding of the various processes involving ROS in soil, thereby guiding better soil management decisions. Finally, we highlight future research trends, suggesting that the advancement of in situ detection methods is crucial for establishing the precise contribution of abiotic ROS processes to global soil carbon and nutrient models. Full article

Hydrogen (H₂) is a promising clean energy carrier with the potential to partially replace fossil fuels. Biological H₂ production using microorganisms offers an environmentally friendly alternative. The halotolerant cyanobacterium Aphanothece halophytica can produce H₂ under nitrogen-deprived and dark anaerobic conditions. In this study, a co-culture strategy was investigated to enhance H₂ production. Five bacterial strains were screened for their ability to improve H₂ production when co-cultivated with A. halophytica. Among them, Staphylococcus aureus significantly enhanced H₂ production, achieving a maximum rate of 11.11 ± 0.18 µmol H₂ g⁻¹ dry weight h⁻¹. Optimization of the bacterial partner revealed that S. aureus cells harvested at 12 h in the mid-logarithmic phase with an OD₆₀₀ of 4.0 were the most effective. An inoculum ratio of A. halophytica to S. aureus of 4:1 further enhanced H₂ production, increased bidirectional hydrogenase activity, and reduced O₂ accumulation. Under optimal conditions (0.945 mmol C-atom L⁻¹ glucose, 0.25 M NaCl, pH 7.4, and 35 °C), the maximum H₂ production rate reached 132.49 ± 4.45 µmol H₂ g⁻¹ dry weight h⁻¹, approximately 5.5-fold higher than that under normal conditions. The co-culture achieved a cumulative H₂ yield of 3248.51 ± 88.11 µmol H₂ g⁻¹ dry weight after 48 h. Full article

Growing municipal solid wastes, environmental deterioration, and the world’s increasing energy demand highlight the urgent need for effective, sustainable energy recovery solutions. Uncontrolled municipal solid wastes contribute explicitly to the global crises of climate change, pollution, and biodiversity loss. Food and organic waste are converted into value-added products using biochemical and thermochemical techniques. Anaerobic digestion (AD) is a versatile, multi-phase waste-to-energy technology that transforms organic waste into renewable energy in an oxygen-free environment. AD uses microorganisms to break down waste, yielding biogas (mostly methane and carbon dioxide) and digestate, a nutrient-fortified by-product. Compared with traditional Single-Stage Anaerobic Digesters (SSAD), Two-Stage Anaerobic Digesters (TSAD) offer notable benefits by separating hydrolysis–acidogenesis from acetogenesis–methanogenesis. These include increased methane yield, improved process control, increased microbial stability, and resistance to inhibitory substances. According to the literature, TSAD systems have been shown to increase methane yield by about 10–30% compared to SSAD. This article covers the dynamics of the microbial population at various stages, the impact of operational factors (HRT, OLR, pH, and temperature), and novel reactor designs with modular and multi-state functions. In line with Oman’s Vision 2040, this study discusses the continuous operation of a two-phase AD co-digestion process and the in-depth techno-economic feasibility of decentralized waste management through optimized biogas production. Optimizing the carbon-to-nitrogen (C/N) ratio within the range of 20–30 in co-digestion systems significantly enhances microbial activity and methane production. The potential of recent developments, such as microbial immobilization, biogas generation techniques, and hybrid integration with photobioreactors or electrochemical systems, to enhance the scalability and efficiency of bioconversion is addressed in a TSAD system. In addition to encouraging circular economy principles through efficient organic waste valorization, this review identifies TSAD as a promising approach to achieving the SDGs related to sustainable cities, clean energy, and responsible consumption. Full article

Returning spent mushroom substrate (SMS) to the field is an effective way to dispose of it. However, given the substantial nutrient consumption associated with Volvariella volvacea SMS, their effects on soil properties and crop performance warrant further investigation. By analyzing the effects of three different application rates of SMS on soil nutrients and lettuce (Lactuca sativa L.) quality, the results showed that the group with 1.5 kg m⁻² SMS addition improved the total nitrogen (+21.2%), and organic content (+27.9%) in soil, and it demonstrated particularly outstanding performance in enhancing the survival rate (+21.9%), average weight (+71.7%), chlorophyll content (+45.6%), and total phenolic content (+25.2%) of lettuce. By comparing the soil microbial communities in the control group, the SMS (1.5 kg m⁻²) treatment group, and the organic fertilizer treatment group, it was found that they were mainly composed of Group S1, S2, and S3 microorganisms, respectively. The microbial community evenness in the treatment groups was greater than that in the control group. Furthermore, the results also revealed that the microbial conversion efficiency of nitrogen and phosphorus in the SMS treatment group was higher than the control group, which promoted nutrient cycling and improved the quality of lettuce. Our analysis provides an environmentally friendly way for Volvariella volvacea SMS disposal. Full article

River sediment microbial communities are an integral part of fluvial ecosystems, where they play a central role in nutrient cycling. Although these communities share a core group of microorganisms, their overall composition can be influenced by natural environmental conditions and anthropogenic factors. While anthropogenic influences on river microbial communities have been extensively studied, natural drivers have received comparatively less attention. In this study, we evaluated the impact of tributary inflow on the microbial assemblages of a main river stem. Sediment samples were collected from both the main channel and some of its tributaries, and bacterial community composition was characterized using 16S rRNA gene amplicon sequencing. Taxonomic profiling revealed a largely shared core community typical of riverine sediments across all sites. While alpha diversity did not differ significantly between main river and tributary samples, beta diversity analyses demonstrated clear segregation between the two environments, indicating distinct community structures. Correlation analyses further showed that microbial assemblages in the main river downstream of tributary confluences were significantly associated with tributary community composition, highlighting the influence of tributary inflow on bacterial communities in the main river. Full article

Fungal endophytes are symbiotic microorganisms that establish strong relationships inside plant tissues, providing potential advantages, especially in grasses, by enhancing tolerance to both abiotic and biotic stresses. This review investigates the molecular mechanisms through which fungal endophytes mediate stress tolerance, targeting host–pathogen interactions. By modulating pathogen-associated molecular patterns (PAMPs), damage-associated molecular patterns (DAMPs), and effector proteins, fungal endophytes may contribute to priming the plant’s immune system, enhancing its resistance to pathogen invasion. Moreover, endophyte colonization regulates core processes such as osmotic regulation, reactive oxygen species (ROS) detoxification, and secondary metabolite biosynthesis that enable plants to tolerate environmental stresses like drought, heat, and salinity. The review highlights the impact of endophytes on immune priming, systemic acquired resistance (SAR), and the regulation of non-coding RNAs that regulate host gene networks associated with stress tolerance. Furthermore, the integration of advanced multi-omics techniques genomics, transcriptomics, proteomics, metabolomics, and fluxomics has revealed emerging insights into the genetic and metabolic pathways driving these symbiotic associations. However, grass-specific molecular datasets remain limited, and the consistency of endophyte-mediated tolerance across host species and environmental conditions is not yet fully resolved. Fungal endophytes increase grass stress resilience through coordinated pathogen recognition, RNA regulation, and metabolic reprogramming while AI-assisted multi-omics approaches are emerging as tools for identifying candidate regulatory networks, although empirical validation in grass–endophyte systems remains limited. Together, these advances highlight the potential for climate-smart and sustainable crop improvement. Future research integrating functional genomics, field validation, and biosafety assessment will be essential for translating endophyte-based strategies into reliable agricultural applications. Full article

Quorum Quenching (QQ) is a mechanism that disrupts Quorum Sensing (QS) signaling systems, which regulate gene expression based on bacterial population density. Many fish pathogens, such as Aeromonas, utilize QS systems to regulate the expression of their virulence factors. Disrupting these systems using QQ is a promising approach for infection control in aquaculture and may provide a safe alternative to antibiotics. Therefore, identifying microorganisms with QQ activity is a relevant task in agricultural microbiology and veterinary medicine. This study examines the identification of isolates with QQ activity in the microbial community of perch and assesses their probiotic potential for the prevention of aeromonosis. In this study, we isolated 32 strains of microorganisms capable of degrading N-acylhomoserine lactone (AHL), six of which exhibited stable QQ activity. Five strains were found to belong to the genus Rhodococcus, and one strain to the genus Exiguobacterium. The selected strains were tested for the enzymatic/non-enzymatic and intra-/extracellular QQ activity, pathogen growth inhibition, biofilm formation, and hemolytic activity, as well as growth ability under various environmental conditions (salinity, pH, bile acids, and temperature). Based on the results of these tests, the R. erythropolis PFS1.20 strain was selected as the most promising probiotic. The genomic analysis revealed that the studied strain contains genes encoding QQ enzymes, siderophore biosynthesis clusters, osmoprotectors, and compounds with antimicrobial properties. These results indicate the high probiotic potential of the R. erythropolis PFS1.20. Full article

Macrobrachium nipponense is one of the major economic species in freshwater aquaculture in China. As an important component of aquaculture ecosystem, microorganisms participate in key processes such as material cycling and water quality regulation, exerting significant impacts on the cultured organisms. In this study, high-throughput sequencing of the 16S rRNA, 18S rRNA, and ITS regions was employed to comparatively analyze the characteristics of microbial communities before and during the cultivation period, combined with correlation analysis of environmental factors. The results showed that the dominant microbial groups in the prawn pond water were Proteobacteria, Cyanobacteria, Ascomycota, Basidiomycota, Chlorophyta, and Arthropoda. The microbial community structure differed significantly between the pond water during the culture period and the pre-culture external river baseline: manifested as an increase in the relative abundances of Cyanobacteria, Chytridiomycota, and zooplankton, and a decrease in the abundances of Ascomycota, Basidiomycota, and Chlorophyta. Analysis of LEfSe revealed that the low-nitrogen pond was enriched with taxa such as Muribaculaceae; the high-nitrogen pond was enriched with taxa such as Cyanobium_PCC-6307; and the control pond was enriched with taxa such as CL500-29_marine_group. Functional prediction indicated that heterotrophic metabolism-related functions dominated the microbial communities. The abundance of fungal pathogens was significantly higher in the low-nitrogen group, while potential pathogenic bacteria were enriched in the high-nitrogen group. Ammonia nitrogen is a core environmental factor associated with differences in microbial community structure. The findings of this study can provide theoretical references and data support for water quality optimization and the construction of healthy aquaculture models in freshwater shrimp and crab farming waters. Full article

In situ coagulation is regarded as the most effective measure in response to the frequent metal spills in China. Excessive coagulant is often used in pursuit of extremely high removal rates of contaminants. Yet the secondary ecological impact of the iron-containing coagulation flocs left on the river sediments after emergency response is still unclear. In the current study, we investigated the impact of flocs derived from three different iron-based coagulants, polymeric ferric sulfate (PFS), polymeric ferric chloride (PFC), and ferric chloride (FeCl₃), on microbial communities in sediment based on microcosm experiments. Metagenomics, quantitative PCR, and determination of ammonia oxidation potential were adopted to elucidate community shifts. The results indicate that the community structure and function of microorganisms in sediments have been affected, especially processes and species related to nitrogen cycling, and the effect was coagulant-specific. Flocs retrieved from FeCl₃ caused a more pronounced decline in diversity, shifts in community composition, and decreased potential ammonia oxidation. Ammonia-oxidizing archaea (AOA) was more sensitive to iron-containing flocs than ammonia-oxidizing bacteria (AOB), while PFS-flocs tended to reduce multiple genes involved in nitrate reduction. This indicates that the pre-polymerization of inorganic coagulants may be the primary factor leading to different microbial ecological effects. Sulfate, on the other hand, may affect specific biogeochemical processes due to its competition for electron donors. Our results confirmed that even without heavy metals as contaminants, coagulant flocs alone could present an effect on nitrogen cycling in sediments. The results will provide a scientific basis for environmental emergency decision-making: in emergency response to metal pollution incidents, the use of coagulants should be limited to only the necessary level. Full article

Petroleum contamination of soils remains a significant environmental problem in boreal regions, where low temperatures constrain natural attenuation processes and complicate bioremediation. Nitrogen biostimulation is widely used to enhance petroleum hydrocarbon degradation; however, the combined effects of temperature regime, nitrogen form, contamination level, and nitrogen dosage remain insufficiently resolved for sandy podzolic soils of northern regions. This study investigated nitrogen-assisted biostimulation of petroleum-contaminated sandy podzolic soil collected in the Khanty–Mansi Autonomous Okrug (Western Siberia, Russia) using a factorial experimental design. Soil samples were artificially contaminated with crude oil at concentrations of 25, 50, and 100 g kg⁻¹ and incubated under warm and cold temperature regimes. Two nitrogen sources, urea and ammonium nitrate, were applied at several dosages. Changes in residual petroleum hydrocarbon content were monitored together with the abundance of culturable microorganisms under the applied cultivation conditions at the intermediate contamination level on day 60. Nitrogen supplementation enhanced petroleum hydrocarbon removal relative to the untreated control, but the magnitude of the effect depended substantially on temperature, nitrogen form, and contamination level. Under the tested conditions, ammonium nitrate was generally associated with stronger hydrocarbon removal than urea, particularly at the intermediate contamination level (50 g kg⁻¹). The results indicate that the response to nitrogen biostimulation in sandy boreal soils is controlled by interacting experimental factors rather than by nitrogen addition alone. These findings improve the positioning of nutrient-assisted remediation in cold-region soils and provide a basis for future mechanistic and field-scale studies. Full article