搜索结果：Applied and environmental microbiology

Nontyphoidal Salmonella enterica (NTS) is a major public‑health threat in the United States of America (U.S.). Evaluating associations between serovars, exposure sources, and settings in multistate outbreaks can reveal the drivers of NTS transmission and guide prioritization of targeted prevention and control strategies. We analyzed multistate animal‑contact-related NTS outbreaks reported to the CDC National Outbreak Reporting System during 2009-2022. We calculated incidence rates (IR) per 10 million population-years (MPY) and assessed temporal trends in IRs using Joinpoint regression. We constructed interstate co-occurrence networks linking serovars, exposure sources, settings, and states, and applied a random forest classifier to identify variables most useful for distinguishing outbreak profiles. We identified 177 multistate outbreaks (0.06 per 10 MPY) involving 40 serovars. Incidence significantly declined from 2009 to 2013 and remained stable thereafter. Random forest rankings identified birds and reptiles as the most influential exposure sources and agricultural feed stores and residential homes as the most influential exposure settings in distinguishing outbreak profiles. Co-occurrence network analysis revealed two major communities. The first included outbreaks involving serovars Enteritidis and Infantis, bird exposure source, and agricultural feed stores or farms as exposure settings, with co-occurrence hubs across the Midwest, Northeast, and Southern regions. The second community involved outbreaks linked with reptiles and mammals as exposure sources, residential homes and farms as exposure settings, and serovars Hadar, Typhimurium, and Braenderup, which were co-occurring in the Western and Southern regions. Multistate animal-contact NTS outbreaks clustered into distinct serovar-exposure, source, setting, and region patterns, suggesting different NTS outbreak transmission pathways. The persistence of NTS serovars across states, diverse animal-contact sources, and exposure settings underscores the ongoing zoonotic transmission risk at the human-animal and environmental interfaces. A region-specific One Health approach to prevent and control NTS outbreaks is suggested to reduce the health burden.

Nontuberculous mycobacteria (NTM) are environmental microorganisms for which large, systematic studies of niche diversity are lacking. We performed a semi-longitudinal state-wide sampling campaign (2015-2019) for environmental NTM across Hawai'i. A volunteer network collected 2,334 water biofilms, soil, and dust samples from built (n = 1,946) and natural (n = 388) sites. Of these, 541 contained culturable NTM (23%) and per island hotspots identified. Of 74 NTM species recovered, the most prevalent rapid growing mycobacteria (RGM) were Mycobacterium porcinum, Mycobacterium chelonae, and Mycobacterium abscessus. Mycobacterium intracellulare subsp. chimaera was the most frequently isolated slow growing mycobacteria (SGM). Our longitudinal analyses indicate widespread colonization of diverse niches by species less associated with lung infections such as M. chelonae. In contrast, household water biofilms tended to be reliable niches for M. abscessus and M. avium complex species colonization across the 5-year study. Analysis of 590 deidentified lung samples from Hawai'i and other Pacific Islands revealed M. chimaera as the most frequently isolated species (40%, 238/590). Phylogenetic analysis of environmental and lung M. abscessus suggests most cluster within dominant circulating clone 1 (DCC1). Contrastingly, most Hawai'i and other Pacific Island M. chimaera were distinct from previously studied European isolates, leading to the identification of two novel clusters of phylogenetically related strains we have termed Pacific Island Circulating Cluster 1 and 2 (PCC1, PCC2). PCC1 consists exclusively of Hawai'i/Pacific Island isolates, while PCC2 was enriched by lung samples and was mostly collected from Hawai'i/Pacific Islands. These data reveal the genetic diversity, ecological niches, and potential reservoirs of NTM in varied Hawai'i ecosystems.IMPORTANCENearly one in four environmental Hawai'i samples tested positive for any NTM species, with hotspots often overlapping population centers. Recovery of any NTM species occurred just as often from natural settings as homes and public buildings, highlighting exposures as a normal part of life. Soil was the most common reservoir for NTM colonization, but we distinguish NTM species pertinent to lung disease that were far more likely to be found in water biofilms, such as showerheads and kitchen sinks. No single species dominated the environment; yet, the type of NTM found in water systems closely mirrored those recovered from patients' lung samples. Genetic analyses revealed that Hawai'i harbors distinct, locally circulating strains, including lineages not linked to known hospital outbreaks. Together, these findings improve our understanding of where precarious exposures can occur and inform public health strategies to reduce exposures by highlighting niches that are common hotspots for NTM colonization.

Developing rice varieties that combine high yield, disease resistance, grain quality, and climatic adaptability is critical for sustaining rice production, particularly under current climate change. Mid-altitude rice regions face severe challenges from rice blast, climate variability, lodging, and yield-quality trade-offs. This study integrated accelerated generation advancement with multi-environment selection to develop a high-yielding, adaptable rice variety suitable to a mid-altitude production system. Yunjing-60 is a novel rice variety developed through pedigree selection combined with double-cropping acceleration. The cross was applied between Shengnong-5 and Chujing-44. Shengnong-5 is a blast-resistant, compact architecture with medium maturity. Chujing-44 is high-yielding, lodging-tolerant, and high-quality grain. Double-cropping was applied at Yuanjiang, which is characterized by a hot and dry climate. Moreover, greenhouse cultivation was conducted during cooler months from November to February. This enabled multiple generations per year for accelerating breeding cycles. The variety comparison trial in 2022 demonstrated that Yunjing-60 surpassed the check variety Chujing-38 with superior agronomic performance. It exhibited higher effective panicle density (400.5 per m²), greater sink capacity (135 filled grains per panicle), and 8.62% higher grain yield of 13,290 kg ha⁻¹. Principal component biplot confirmed its association with key yield components. This yield advantage was supported by its ideal plant architecture and favorable growth cycle. Moreover, the variety exceeded the check variety Chujing-38 across various pathogens. It exhibited superior disease resistance with a Grade 1 rating to rice blast (index 0.80). Also, it displayed high resistance to bacterial blight, sheath blight, and rice false smut. Multi-environment selection across different altitudes accelerated trait stabilization. Regional and production trials were applied in eight diverse locations across 2023-2024. It recorded a high average yield of 10,721 kg ha⁻¹ with a yield gain of 9.8% in production trials. AMMI and GGE biplots across tested environments confirmed its superior mean yield and stability, surpassing Chujing-38. Besides, multivariate analysis using clustered heatmap visualization confirmed its consistently high-yield performance across test environments. Consistent yield across diverse ecological zones indicates its environmental adaptability and low genotype-environment interaction. Quality assessments confirmed excellent values of rice-eating compared to the national level standard. It provided a brown rice rate of 83.5%, a milled rice rate of 75.2%, and a head rice rate of 73.7%. It recorded Grade 1 transparency, 17.6% amylose content, and 70-mm gel consistency. These parameters confirm its superior milling, appearance, and eating quality. Consequently, Yunjing-60 integrated adaptive traits, accelerated breeding efficiency, and superior market value. Hence, this approach contributes to sustainable intensification, broad adaptability, and food security in subtropical highland rice systems.

Vibrio parahaemolyticus is a foodborne pathogen that threatens seafood safety globally. Endolysins are promising antibacterial candidates with rapid action and low resistance induction. Through genome mining of 163 Vibrio phages, we identified 168 potential endolysin genes and expressed the first Vibrio-phage-derived L-alanyl-D-glutamate peptidase, LysMD30, in Pichia pastoris. Although LysMD30 exhibited peptidoglycan hydrolytic activity, it lacked an intrinsic bactericidal activity. However, it displayed broad-spectrum synergy with colistin against pathogenic Vibrio species (V. parahaemolyticus, V. harveyi, and V. alginolyticus), yielding fractional inhibitory concentration index values lower than 0.5. This synergism was marked by a fourfold reduction in the minimum inhibitory concentration of colistin, decreasing from 16-32 μg/mL to 4-8 μg/mL across all tested strains. The bactericidal kinetics indicated that the combination triggered rapid lysis within 5 min, and the majority of turbidity reduction occurred within 20 min. Moreover, the combination effectively eradicated biofilms on both polystyrene and stainless steel surfaces within 1 h, reducing the viable bacterial counts by >3  log units. In the Galleria mellonella infection model, the combination provided 100% protection against lethal Vibrio challenge while confirming its excellent in vivo safety. Furthermore, LysMD30 exhibited robust biochemical stability-maintaining 36.96% activity at 85°C, over 90% activity at pH 5.0-8.0, and exceeding 60% activity at 800 mM NaCl-while effectively delaying the emergence of colistin resistance in V. parahaemolyticus during serial passage. In summary, LysMD30 is a newly characterized and stable enzyme that synergizes powerfully with colistin and represents a promising biocontrol agent for Vibrio control in food and aquaculture. Vibrio pathogens pose a severe threat to seafood safety and aquaculture. Conventional intervention strategies often face significant limitations: physical treatments can adversely affect the organoleptic and nutritional quality of seafood, whereas chemical agents carry the risk of toxic residues and environmental pollution. Furthermore, the escalating antimicrobial resistance of Vibrio and its capacity to form biofilms on food-contact surfaces exacerbate these challenges. This study identified LysMD30 as the first Vibrio-phage-derived L-alanyl-D-glutamate peptidase that exerts a potent synergistic bactericidal effect with colistin. This combination significantly reduced the required antibiotic dosage, rapidly eliminated both pathogenic Vibrio planktonic cells and biofilms, and demonstrated excellent in vivo safety. Our findings expand the repertoire of Vibrio-targeting biocontrol agents and provide an eco-friendly and efficient strategy for Vibrio control in food processing and aquaculture, offering robust technical support for safeguarding seafood safety and public health.

Coliform contamination has become a major threat to global water security and public health, particularly in developing regions where dependence on untreated or partially treated surface and groundwater remains high. As indicator organisms, coliform bacteria signal fecal pollution and the potential presence of pathogenic microbes responsible for waterborne diseases such as diarrhea, typhoid, and hepatitis. The Kashmir Valley, which has experienced a rapid population increase and lacks proper sewage treatment facilities, is particularly vulnerable to such dangers. This study assessed the bacteriological quality of drinking water sources in Srinagar (urban) and Ganderbal (semi-urban) districts during autumn and spring. A total of 200 samples were collected from tap water, groundwater, springs, and water treatment plants, and analyzed for total coliforms (TC), fecal coliforms (FC), and fecal streptococci (FS) using the most probable number (MPN) method. Multivariate statistical approaches, including non-metric multidimensional scaling (NMDS) and indicator species analysis (ISA), were applied to examine spatial and seasonal patterns in microbial communities. Results revealed widespread contamination, with 94% of samples in Srinagar and 88% in Ganderbal testing positive for coliforms. Groundwater and spring sources exhibited the highest contamination levels, while even treated water from filtration plants showed significant microbial presence. Coliform levels were consistently higher in autumn than in spring, with greater contamination in Srinagar, reflecting the influence of urbanization on the microbial loading. While environmental parameters such as temperature, pH, and dissolved oxygen affected coliform abundance, overall microbial community structure showed no significant relationship with these variables. The findings highlight the urgent need for improved water treatment practices, routine microbial monitoring, and infrastructure upgrades. Reliance on chlorination alone is insufficient; advanced disinfection technologies and improved sanitation systems are vital to ensure safe drinking water and guard public health in the Kashmir Valley.

Across ecosystems, autotroph growth and susceptibility to disease are strongly constrained by the availability of essential nutrients such as nitrogen and phosphorus. Understanding how nutrient availability influences disease transmission is important for predicting disease persistence, outbreak risk, and long-term ecosystem dynamics under changing environmental conditions. At the same time, infectious diseases in autotrophs can reshape ecosystem processes by altering elemental recycling and the nutrient supply available to hosts. Here, we formulate a five-dimensional deterministic system of nonlinear ordinary differential equations within a disease-mediated nutrient dynamic framework. We incorporate novel nutrient-driven transmission and nonlinear resource uptake kinetics to capture the bidirectional relationships linking elemental cycles with infectious disease in a natural forest ecosystem. Using a combination of qualitative mathematical analysis, including proofs of solutions boundedness and derivations of basic reproductive number, and numerical bifurcation analyses, we evaluate the system's long-term behavior. Our results show that nutrient-disease feedbacks strongly regulate the distribution of host densities and nutrients between autotrophs and the abiotic environment. Incorporating nutrient-driven transmission reveals bifurcation structures distinct from frameworks with constant transmission, highlighting high sensitivity to nutrient availability and stronger nonlinear feedbacks. Bifurcation analyses indicate that nutrient enrichment lowers the transmission threshold for disease persistence and accelerates the onset of oscillatory dynamics with greater amplitude under high nutrient levels. Similarly, higher transmission rates reduce the nutrient threshold for disease persistence and shift oscillatory dynamics to emerge at lower nutrient levels. We further show that even small differences in infected host uptake rates strongly influence dynamics: lower uptake dampens oscillations and weakens feedbacks, whereas higher uptake amplifies bottom-up nutrient effects on disease and reinforces top-down effects on nutrient cycling, producing pronounced limit cycles in hosts, nutrients, and prevalence. Overall, nutrient-driven transmission alters thresholds and oscillatory regimes in ecosystem disease models, leading to dynamics that are not captured under constant transmission assumptions. This work advances applied ecosystem and ecological disease sciences by improving our understanding of disease transmission processes in plant communities.

Although manganese-modified biochar (MBC) effectively immobilizes Cd and As, the effects of low-molecular-weight organic acids (LA) on the performance and efficiency of Cd and As remediation in agricultural soils when co-applied with MBC in different application sequences remain unclear. This study examined the effects of LA on the MBC-mediated remediation of Cd/As-contaminated soil via the immersion of MBC in LA and LA-MBC to facilitate co-applications on contaminated soil using different application sequences. Results revealed that after LA immersion, the pH of MBC decreased by 0.14-2.10 units, accompanied by increases in electrical conductivity and Mn concentration. LA treatment also induced surface alterations characterized by cracks, depressions, reduced Mn oxide particles, and weakened MnO2 diffraction peaks. These changes promoted soil Cd/As mobilization, increasing the TCLP-Cd by 40.2-110.1% and available As by 22.0-70.0%, thereby reducing MBC immobilization efficiency. Application sequence markedly affected the remediation outcomes, in order of decreasing remediation effectiveness: LA pre-addition > MBC pre-addition > simultaneous application. Simultaneous LA-MBC application led to a 12.4-62.6% decrease in the relative abundance of soil Gemmatimonadota. In contrast, the relative abundance of Firmicutes and Myxococcota increased by 47.0-184.9% and 39.5-273.8%, respectively. This study systematically assessed the effects of LA and MBC application sequences at different time intervals on the bioavailability of Cd/As. A "LA-MBC-microorganism" interaction model is proposed, demonstrating that LA structurally reshapes MBC and alters microbial communities, which may modulate Cd/As speciation. Based on pollutant behavior and amendment dynamics, a spatiotemporally optimized strategy is proposed to improve in situ remediation and reduce environmental risks.

Antimicrobial resistance (AMR) in aquatic environments represents a critical global public health threat, yet comprehensive environmental surveillance data remain scarce in low- and middle-income countries. The Kelani River Basin, supplying approximately 80% of Colombo's potable water and Sri Lanka's most industrially impacted waterway, lacks a basin-wide characterization of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) across spatial and seasonal gradients. This study provides the first comprehensive basin-wide assessment of ARB distribution, ARG occurrence, minimum inhibitory concentrations (MICs), and multidrug-resistant (MDR) pathogen diversity across surface water and groundwater during wet and dry seasons. A total of 71 water samples (surface water: 53; groundwater: 18) were screened against ten clinically relevant antibiotics using standard pour-plate and agar dilution methods. ARG profiling was conducted using environmental DNA (eDNA)-based PCR, and MDR isolates were characterized by sequencing of the 16S rRNA gene. The transitional zone was identified as the principal contamination hotspot, with ARB loads significantly elevated during the wet season (p&#x2009;<&#x2009;0.05). Phenotypic resistance was highest against cloxacillin (20.4%), amoxicillin (14.8%), and cefuroxime (14.4%), while ciprofloxacin and tetracycline exhibited the lowest resistance rates. MIC profiling revealed that 41.9% of isolates tolerated concentrations up to 600&#xa0;&#xb5;g/mL, with MDR isolates exhibiting MICs&#x2009;&#x2265;&#x2009;540&#xa0;&#xb5;g/mL. MAR indices ranged from 0.1 to 1.0, with high MAR (&#x2265;&#x2009;0.5) predominant in dry (59.9%) and wet (43.5%) seasons. ARG screening detected sul1 (93%), qnrB (66.2%), mefA (43.7%), and blaCTX-M (23.9%) basin-wide across both water compartments. 16S rRNA sequencing confirmed clinically significant pathogens, including Klebsiella pneumoniae, Pseudomonas fluorescens, and Proteus mirabilis among high-level MDR isolates. Water temperature, total phosphorus, and nitrogen compounds were significantly associated with ARB abundance spatially and seasonally (p&#x2009;<&#x2009;0.05). These findings reveal the Kelani River Basin as a high-risk environmental AMR reservoir, while delivering a low-cost, replicable surveillance framework for resource-limited settings to support evidence-based water quality policy and Sri Lanka's National Action Plan for AMR.

Klebsiella pneumoniae (K. pneumoniae) is recognized as a significant opportunistic pathogen capable of infecting both humans and animals. The emergence of multidrug-resistant strains presents a severe challenge to current antimicrobial therapies, necessitating the development of alternative treatments such as bacteriophages and their encoded enzymes. In this study, a polysaccharide depolymerase, designated DepZ57, was identified, expressed, and characterized from the K57-specific lytic phage vB_Kp_Z57. Bioinformatic analysis indicated that DepZ57 is a hydrophilic protein with a theoretical isoelectric point of 6.27 and adopts a typical &#x3b2;-helix structure. The purified depolymerase exhibited high physicochemical stability across a broad pH range (2.0-11.0) and temperature range (4&#xb0;C-70&#xb0;C). In vitro, the K57 capsule was degraded by DepZ57 at a minimum effective concentration ranging from 0.04 to 0.4 &#x3bc;g/mL, which subsequently sensitized the bacteria to macrophage phagocytosis and complement-mediated serum killing. In a lethal systemic mouse infection model induced by intraperitoneal injection, a 100% survival rate was achieved following the administration of 50 &#x3bc;g of DepZ57, compared with a 60% survival rate observed with the phage treatment. Bacterial burdens were effectively reduced by both treatments. Notably, the bacterial loads in the blood, lungs, and liver were significantly decreased in the DepZ57 treatment group. Specifically, the bacterial load in the blood was completely eliminated, and the bacterial loads in the liver and lungs were reduced by more than 99%. Histopathological analysis confirmed that DepZ57 treatment effectively prevented hepatic necrosis and pulmonary inflammatory infiltration. Collectively, these findings demonstrate the in vivo efficacy and stability of DepZ57, suggesting it may represent a viable candidate for the control of K. pneumoniae infections. The emergence of multidrug-resistant and hypervirulent Klebsiella pneumoniae represents a severe threat to human health and the dairy industry. Capsular polysaccharide (CPS) is the primary virulence factor that shields K. pneumoniae from host immune clearance, and the hypervirulent K57 serotype is frequently linked to severe invasive infections. Phage-derived depolymerases have emerged as promising antivirulence agents capable of specifically dismantling bacterial capsules without inducing bacterial resistance. Here, we characterized a novel, highly stable phage depolymerase, DepZ57, which exhibits robust tolerance to extreme pH and temperature conditions and specifically targets K57-type CPS. Distinct from the parental phage, DepZ57 provides full protection against lethal K57 K. pneumoniae infection in vivo and effectively alleviates infection-induced tissue damage. This work highlights the potential of phage depolymerases as stable, safe, and efficient nonantibiotic therapeutics for the prevention and control of hypervirulent K. pneumoniae infections.

Trichlorobacter lovleyi (formerly Geobacter lovleyi) is a gram-negative bacterium that can couple the oxidation of acetate or other small organic acids with the reduction of soluble and insoluble electron acceptors, such as chlorinated solvents, heavy metals, and nitrate. Evidence has shown that T. lovleyi plays a direct role in nitrogen, iron, and carbon cycling, and its versatile metabolism can be leveraged for environmental biotechnology applications. However, the contributions of T. lovleyi to treatment of contaminants at groundwater sites or electron transfer in bioelectrochemical systems have been largely overlooked. This minireview examines the genetic and metabolic features of T. lovleyi for dissimilatory reduction of nitrate to ammonium, extracellular electron, and organohalide-respiration, highlighting unique and conserved features relative to other genera in Geobacterales. We highlight applications of T. lovleyi in bioremediation of contaminated environments and identify knowledge gaps to fully leverage the metabolic potential of this bacterium. We feature T. lovleyi's ability to produce the important vitamin B12 cofactor and the syntrophic partnership it establishes with cobalamin-scavenging, obligate organohalide-respiring bacteria, particularly in environments where the concentration of chlorinated solvents poses toxicity challenges to the groundwater microbiome. We conclude that T. lovleyi has a meaningful, multi-faceted, but often neglected, contribution to groundwater and soil bioremediation. We hope this minireview will prompt researchers and bioremediation practitioners to more closely monitor T. lovleyi during reductive dechlorination enrichment efforts and bioremediation applications at sites contaminated with organohalogens, uranium, or nitrate.

Fungi play essential roles in human health, agriculture, and ecosystems, yet their diversity has long been underestimated due to reliance on morphology and culture. Molecular innovations-DNA barcoding, multilocus and whole-genome sequencing, NGS, and rapid nucleic acid diagnostics (qPCR, LAMP, CRISPR/Cas)-have revolutionized fungal taxonomy and detection. The ITS region now serves as a universal barcode, often complemented by other loci or genomic data. High-throughput and portable tools enable near real-time identification, supported by AI-driven bioinformatics for species recognition and resistance prediction. Despite progress, challenges remain in database accuracy, primer design, and standardization. Integrating molecular taxonomy, AI, and global collaboration promises scalable, reliable frameworks for fungal surveillance and control across clinical, agricultural, and environmental domains.

Foliar application of nanomaterials (NMs) offers great potential for sustainable crop disease management. However, how the presence of surfactants alters the behavior of NMs on leaf surfaces and their subsequent modulation of disease resistance remains unclear. Here, surfactants were incorporated into NMs suspensions to enhance foliar adhesion and deposition, thereby suppressing early blight (Alternaria solani) in tomato. Nonionic surfactants (Tween-80 and Silwet L-77) significantly improved the foliar deposition and translocation of La10Si6O27 nanorods (NRs). The treatment combining La10Si6O27 NRs with Silwet L-77 (NRs + L77) achieved the highest efficacy, reducing disease severity by 70%, which is 19.99% higher than La10Si6O27 NRs alone treatment. Mechanistically, (1) NRs + L77 activated the antioxidant defense system, increasing superoxide dismutase and peroxidase activities by 21.22% and 140.10%, respectively, while decreasing malondialdehyde content by 28.72%; (2) NRs + L77 optimized the phyllosphere microbiome, enriching beneficial genera such as Bacillus, Pantoea, and Klebsiella and restoring microbial network complexity; and (3) NRs + L77 upregulated defense-related gene expression, activated phenylpropanoid and flavonoid metabolic pathways, and induced systemic acquired resistance. In addition, NRs + L77 exhibited favorable biosafety toward nontarget organisms. This study demonstrates the potential of surfactant-modified NMs in improving disease control efficiency and contributing to sustainable crop protection.

We have retrieved approximately 9,000 protein sequences annotated as fungal acid phosphatase or phytase from the UniProtKB database. Following stringent quality filtering, a curated dataset comprising 3,058 high-confidence sequences was assembled. Phylogenetic analysis resolved these enzymes into eight distinct clades, representing distinct groups of fungal acid phosphatases: purple acid phosphatases, phytases, and groups containing both phytases and acid phosphatases annotations. Based on this classification, we have developed three representative protein profiles referred to as Prf-A-Fungal_phos, Prf-B-Fungal_phos, and Prf-C-Fungal_phos, each designed to capture the phylogenetic and functional diversity of these enzyme families. Heat-map analyses confirmed the breadth and high specificity of these profiles. Application of these profiles to public protein and metagenomic databases enabled the identification of hundreds of previously uncharacterized fungal proteins, with a broad taxonomic distribution and notable prevalence in the Ascomycota and Basidiomycota phyla. Functional validation through heterologous expression of selected candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, supporting the accuracy of the in silico predictions. By integrating large-scale bioinformatics with experimental validation, this study provides robust tools for the discovery of novel fungal phosphatases and for investigation of their ecological roles in nutrient-limited environments.IMPORTANCEFungal acid phosphatases are critical enzymes in global phosphorus cycling, yet no dedicated bioinformatic tools exist to comprehensively identify and classify them across fungal diversity. Here, we present the first PROSITE generalized profiles specific to fungal acid phosphatases, derived from a curated data set of over 3,000 high-confidence sequences spanning eight phylogenetic groups. These profiles exhibit high specificity and sensitivity, enabling the detection of hundreds of previously uncharacterized proteins from public protein databases. Experimental expression of representative candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, validating our in silico predictions. By bridging large-scale bioinformatics with functional validation, this study delivers robust resources to uncover novel fungal phosphatases and to explore their ecological roles in nutrient-limited environments. The developed profiles will advance metagenomic annotation, support soil and environmental microbiology research, and foster biotechnological innovation in sustainable phosphorus management.

Bacteriophages (phages), viral predators of bacteria, are an attractive way to combat the rise of antimicrobial resistance. By infecting and killing bacteria, phages generate selection pressure for the evolution of defense systems. Successfully applying phages in the clinic will, in part, depend on understanding and predicting how bacterial defense systems determine the outcomes of a phage infection. Here, we present morphological, genomic, phylogenetic, and modification-based characterization of 12 new bacteriophage species targeting Escherichia coli, isolated from water sources in Durham, UK, during undergraduate practical classes. These phages, added to our growing "Durham Collection," were all determined to be sensitive to the GmrSD-family Type IV restriction enzyme, BrxU. As such, these phages have modified genomic DNAs. HPLC and MS analysis of the genomic DNAs identified a range of modifications present in the Tequatrovirus, Krischvirus, and Mosigvirus phages, the latter of which contained 5-arabinosyl-2'-deoxycytidine (5-ara-dC) and disaccharide arabinobiose (5-ara-ara-dC) moieties. Curiously, Krischvirus phages were shown to have modification pathways distinct from those of Tequatrovirus phages. Finally, testing the modified genomic DNAs in in vitro cleavage assays with BrxU demonstrated cleavage of all modifications tested. This further extends the broad substrate specificity previously identified for BrxU. Collectively, these data provide a larger standardized Durham Collection to be used for better prediction of phage-host interactions and infection outcomes.IMPORTANCEWidespread antibiotic use has led to rising rates of antibiotic resistance. It is estimated that deaths from antibiotic-resistant bacterial infections will outpace deaths from cancer by 2050. Alternate methods of treatment are required. Bacteriophages (phages), are viruses that specifically target bacteria and are predominantly harmless to humans. There is increased interest in using phage therapy in clinics to treat infections. Studying interactions between bacteria and phages is necessary so that we can understand and better predict the outcomes of phage therapy. This will increase the chances of clinical success. Our presented work provides detailed characterization of a set of phages isolated from the environment that infect Escherichia coli, a common pathogen and model experimental system. Standardized collections of phages are time-consuming to generate and the results from our ongoing characterization of the Durham Collection presented here represent a community resource for the ease of comparison between these and other phages strains, as well as across different experimental systems.

Listeria monocytogenes (LM) is found in various environmental sources, including animal intestinal tracts, soil, and sewage. LM can contaminate various food products, including meat, seafood, cheese, fruits, and vegetables. Individuals with underlying medical conditions, the elderly, pregnant women, and infants, may develop meningitis and sepsis upon consuming LM-contaminated food. A rapid and standardized quantification method for evaluating initial contamination levels of LM in food remains to be established. This study aimed to develop a rapid quantification method to monitor LM contamination in food handling facilities. A regression equation was developed to determine the concentrations of LM cells before and after enrichment. Regression equations developed to estimate LM cell concentrations in food samples (ground poultry and green salad) were evaluated. The concentrations of LM cells in ground poultry and green salad before enrichment were 2.44 and 2.92 log10 CFU/g, respectively, and the concentrations obtained using a rapid qPCR-based detection and quantification method were 2.05 and 3.27 log10 CFU/g, respectively. The proposed method can semi-quantitatively estimate LM contamination at approximately 102 CFU/g of food, which is the maximum allowable level of LM contamination in foods. This study may serve as a basis for establishing and improving hygiene management systems and preventing listeriosis.

Organohalide-respiring bacteria (OHRB) are globally distributed, yet their ecological roles in marine environments remain poorly understood, with few isolates characterized from these systems. Here, we describe a stable anaerobic consortium from estuarine sediments that performs sustained dechlorination of 1,1,2-trichloroethane (1,1,2-TCA) to vinyl chloride (VC) at a rate of 126.3 &#xb1; 0.9 &#xb5;M d-1. This activity was associated with the stable co-enrichment of two key populations, Dehalogenimonas and Desulfitobacterium, which increased to dominate the community at 49.7% and 32.5%, respectively. Metagenome-assembled genomes confirmed both populations represent novel species with distinct genomic adaptations. Dehalogenimonas sp. strain H harbors 24 putative reductive dehalogenase genes and complete ectoine biosynthesis pathways (ectABC) essential for osmotolerance, while Desulfitobacterium sp. strain Y represents the first cultivated marine-associated member of this genus. Proteomic analysis confirmed active expression of multiple reductive dehalogenases from strain H, strongly supporting its role as the primary dechlorinator. Concurrently, physiological and genomic data suggest that strain Y is strongly co-selected under 1,1,2-TCA-amended conditions and likely occupies a crucial supportive niche. Alongside its extensive metabolic versatility that likely buffers the consortium against environmental fluctuations, its complete de novo corrinoid biosynthesis pathway implies a complementary role as a vitamin B12 provider for the extreme corrinoid-auxotrophic strain H. This study provides evidence for a stable co-enrichment consistent with nutritional niche differentiation within native microbial communities and suggests a potential cooperative interaction between novel Dehalogenimonas and Desulfitobacterium species, advancing our understanding of halogen cycling in coastal ecosystems.IMPORTANCEEstuaries serve as critical interfaces between terrestrial and marine ecosystems, yet the microbial processes governing chlorinated pollutant fate in these vulnerable zones remain largely unexplored. Our discovery of a novel partnership between Dehalogenimonas and Desulfitobacterium species challenges the conventional understanding that Desulfitobacterium is restricted to terrestrial habitats. Integrative multi-omic and physiological analyses reveal that Dehalogenimonas strain H serves as the highly specialized primary dechlorinator, while Desulfitobacterium strain Y is stably co-enriched and exhibits genomic potential to sustain the consortium by providing essential corrinoid cofactors. The identification of genomic determinants underlying salt tolerance in Dehalogenimonas, including ectoine and mannosylglycerate biosynthesis pathways, provides mechanistic insights into OHRB adaptation to fluctuating salinity. These findings have direct implications for developing bioremediation strategies for contaminated coastal sites and highlight the importance of characterizing microbial diversity in transitional ecosystems.

Infectious diseases remain a major global health concern, with a growing burden of antimicrobial resistance and consequent higher mortality in the human population. Accurate bacterial identification is fundamental across clinical, veterinary, agricultural, and research settings, supporting effective diagnosis, antimicrobial stewardship, infection control, food safety, and environmental monitoring; however, conventional approaches are limited by time constraints, reduced sensitivity, and challenges in detecting fastidious or uncultivable organisms. This review provides a comprehensive overview of classical and advanced methods, including microscopy, culture, biochemical testing, immunological and serological assays, proteomic and spectroscopy-based techniques, and molecular approaches, such as polymerase chain reaction (PCR), digital PCR, DNA hybridization, 16S rRNA gene sequencing, whole-genome sequencing, and metagenomics. The integration of artificial intelligence has further enhanced analytical performance. Nevertheless, harmonization of bioinformatics frameworks remains essential, as variability in algorithm-defined cut-off values limits standardized implementation of whole-genome sequencing in routine laboratories. Emerging technologies, including CRISPR-based diagnostics and phage- and nanomaterial-based detection systems, offer promising alternatives. Overall, the integration of these approaches is expected to improve the accuracy, speed, and applicability of bacterial identification across diverse settings; however, these advances should be implemented cautiously, with standardization remaining a key priority alongside technological modernization.

Fraxinus xanthoxyloides Wall. ex DC (Family-Oleaceae) is a tiny tree found in arid highlands, often referred to as "Afghan ash". This study aimed to explore F. xanthoxyloides bark extract as a potential anti-diabetic agent by conducting GC-MS analysis along with in vitro and in vivo studies. F. xanthoxyloides bark methanol extract (FXBM) was fractionated with n-hexane (FXBH), followed by chloroform (FXBC), ethyl acetate (FXBE), and residual aqueous fraction (FXBA). GC-MS and HPLC-MS analysis of the total extract were performed. The inhibitory activities against &#x3b1;-amylase, &#x3b1;-glucosidase,&#xa0;and DPP4 were assessed for the extract and its fractions. The in vivo&#xa0;study included five groups: control group, diabetic control, groups pretreated with alloxan (150 mg/kg) + glibenclamide (5 mg/kg), group pretreated with alloxan (150 mg/kg) + FXBH (200 mg/kg), and group pretreated with alloxan (150 mg/kg) + FXBH (400 mg/kg). Further, a histopathological investigation was conducted. GC-MS analysis of FXBM revealed the presence of 17 compounds predominated by esters (17.9%), polyols (16.35%), and O-glycosides (12.24%). Among all extract/fractions, FXBH showed maximum &#x3b1;-amylase, &#x3b1;-glucosidase, and DPP4 inhibition when compared to acarbose and berberine, respectively. It also achieved the highest glucose uptake among all extract/fractions when compared with metformin. HPLC-DAD analysis showed the presence of gallic acid (3.29 &#xb5;g/mg), catechin (4.23 &#xb5;g/mg), caffeic acid (6.05 &#xb5;g/mg), ferulic acid (2.99 &#xb5;g/mg), and quercetin (6.4 &#xb5;g/mg). FXBH-treated rats showed a significant increase in body weight and reduced blood glucose levels (p&#x2009;<&#x2009;0.05) from days 1-30. The biochemical parameters like triglyceride, low-density lipoprotein, cholesterol, lipase, amylase, C-reactive protein, alanine aminotransferase, aspartate aminotransferase, creatinine, HbA1c, and urea were decreased, while high-density lipoprotein was elevated, compared to diabetic control. Histopathological studies demonstrated restoration of pancreatic &#x3b2;-cells. In conclusion, F. xanthoxyloides bark extract exhibited potential antidiabetic effects; meanwhile, further studies are recommended to characterize the pharmacodynamics, pharmacokinetics, and synergistic effects with standard drugs.

Viruses are a vital part of the aquatic food web and hold a profound role in carbon and energy cycling at different trophic levels. Despite the rising interest in aquatic viruses, very few studies were conducted in estuaries, where freshwater and marine communities meet along the salinity gradient. We present a paired analysis of metagenomic and metatranscriptomic data focusing on the viral fraction derived from seasonal sampling between May 2021 and November 2022 in one of Europe's largest estuaries, the temperate mesotidal Elbe River downstream of Hamburg. Our results reveal a sharp delineation of viral communities along specific salinity niches and provide evidence for their adaptation. This implicates viruses as a structural component of microbial and phytoplankton ecology across the estuary. We provide a detailed overview of the spatiotemporal distribution of viruses, including taxonomy and hosts, which emphasizes the role of giant viruses (Megaviricetes) in waters of lower salinity and RNA viruses in marine environments. We identify, besides salinity, total dissolved phosphate and temperature as the main drivers of estuarine viral communities. We find a broad spectrum of metabolic pathways, potentially altered by viruses via auxiliary metabolic genes. Potential metabolisms impacted included the underlying carbon processes like photosynthesis or methane metabolism, but may also extend to some xenobiotics and antibiotics metabolisms in this anthropogenically altered estuary. This is the first detailed molecular study of viruses in the Elbe Estuary, shedding light on viral communities and their ecological roles in controlling microbial populations at the base of the estuarine food web. Estuaries are the interfaces between marine and limnic waters, with their own specific hydrological and biochemical processes due to, e.g., salinity gradients, tides, and terrestrial inflows. In particular, they are sites of intensive carbon cycling. Their often high economic importance causes substantial anthropogenic pressure on the ecosystem. All of these result in extremely complex factors interacting and influencing microbial populations. Our study provides a first comprehensive overview of the viral communities in Europe's largest estuary. We made an attempt to disentangle the numerous environmental parameters, and we highlight salinity as the most important factor, providing evidence of its multidimensional influence on the estuarine virome. Our findings deepen our understanding of viral communities and their interactions with microbes and bring us a step closer to their role in aquatic food webs, particularly in carbon turnover in estuaries.