Search Results (107)

During the industrial restructuring in China, numerous outdated coking enterprises were phased out. Despite the cessation of production for several years, the soil in the production area of the retired coking plant remains heavily contaminated with polycyclic aromatic hydrocarbons (PAHs), which continue to adversely affect soil health. However, research on the pollution characteristics of soil PAHs under prolonged PAH exposure and the associated changes in functional genes related to soil carbon cycling is still inadequate. This study aims to identify the pollution characteristics and ecological risks of PAHs in the coking plant and to investigate the effects of long-term PAH contamination from abandoned coking plants on the functional genes involved in soil carbon cycling. It was found that PAHs in the soil were predominantly composed of high-molecular-weight PAHs (HMW-PAHs), which constituted 65.7% to 83.4% of the total PAH content. The total concentration of PAHs in the surface soil ranged from 3.79 to 554 mg·kg⁻¹, with an average concentration of 147.6 mg·kg⁻¹. Source analysis based on isomer ratios indicated that PAHs primarily originated from the combustion of coal and biomass. Utilizing the toxicity equivalent factor (TEF) method, we found that the PAH levels in the CA group exceeded the Serious Risk Concentration, indicating that PAH pollution poses a potential threat to the ecological environment. Metagenomic analysis revealed that the gene abundance of alpha-amylase in the CA group was significantly higher than that in the OLA group (p < 0.05), suggesting that prolonged exposure to PAHs has enhanced the starch hydrolysis capabilities of soil microorganisms. The findings of this study refine methods for assessing the risks associated with soil PAH contamination and provide a theoretical foundation for the risk management and reuse of retired coking plant sites. Full article

Natural attenuation is a potential way to reduce total petroleum hydrocarbons (TPH) contamination, but the microbial mechanisms that explain differences in attenuation performance between soil and groundwater remain unclear. In this study, field investigation and metagenomic analysis were conducted at a decommissioned refinery site with more than 20 years of operation. Over a four-year period, the average TPH degradation rate in the soil attenuation zone reached 307.7 ± 135.2 mg kg⁻¹ year⁻¹, whereas the groundwater attenuation group showed an average degradation rate of 5.2 ± 3.6 mg L⁻¹ year⁻¹. Metagenomic results showed that TPH attenuation in soil and groundwater was associated with two different microbial consortia adapted to local conditions. In soil, the attenuation zone was characterized by a possibly sessile and cooperative consortium dominated by Pseudomonadota and Actinomycetota, with Sphingomonas and Nocardioides as representative genera. The consortium showed broader amino acid metabolic potential (e.g., ko00250, ko00260, and ko00310) and a higher abundance of functions related to biofilm formation and quorum sensing, which may promote stable and surface-attached growth. In groundwater, the attenuation zone was characterized by a possibly motile and more specialized consortium dominated by Pseudomonadota, including Novosphingobium, Sphingorhabdus, and Tabrizicola. The consortium possessed a less complex catabolic network for TPHs and intermediates (e.g., ko01220/ko00621/ko00624; nahAc/catE/fadA/pcaD/atoB), coupled with stronger potential for motility and secretion. In both soil and groundwater, attenuation was associated with lower eukaryotic activity and enrichment of prokaryotic functions related to oxidative stress defenses and high-yield respiration. These results showed that natural attenuation of TPHs in soil and groundwater involved different microbial features, which could improve the evaluation of natural attenuation in heterogeneous environments. Full article

Heavy metal resistance represents a critical microbial trait shaped by lineage-specific evolutionary pressures, yet its genomic foundations and diversification across major bacterial taxa remain poorly resolved. This study presented a comparative pangenomic analysis of Aeromonas (n = 32), Bacillus (n = 123), and Pseudomonas (n = 350)—three phylogenetically and ecologically distinct genera frequently enriched in metal-contaminated environments and exhibiting notable differences in resistance architectures. All three genera exhibited open pangenomes, with fitted expansion indices of 0.003 (Aeromonas), 0.03 (Bacillus), and 0.04 (Pseudomonas), each showing strong model fit (R² > 0.98). Pseudomonas harbored a significantly greater number of resistance genes, with copper and zinc resistance genes exceeding 25 per strain in some cases. Most heavy metal resistance genes across the three genera were subject to purifying selection (dN/dS < 1), and no significant expansion or contraction of these gene families was observed (p > 0.05). The presence of these genera and their lineage-specific resistance determinants may serve as bioindicators of heavy metal exposure, offering valuable references for assessing contamination levels through environmental metagenomics. Full article

Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal gene transfer (HGT) across human, animal, food, and environmental sources. Despite growing evidence for antibiotic resistance genes (ARGs), Africa lacks a one-health-focused synthesis of mobile genetic element-mediated AMR. Objective: This systematic review and meta-analysis aimed to consolidate information on MGEs and ARGs in AMR dissemination throughout Africa’s one health interface. Methods: The literature was searched using PubMed, Scopus, and ScienceDirect. Observational. molecular epidemiology, whole genome sequencing (WGS), and metagenomic investigations of MGE-associated AMR in Africa were eligible. The study selection, data extraction, and quality assessment were performed by two independent reviewer and quality was graded using ROBVIS 2 utilizing Rayyan software. Narrative synthesis, random-effect meta-analysis, subgroup analysis, and meta-regression were utilized. Results: A total of 109 studies were included, with 91 studies contributing to the meta-analysis. MGEs reported were plasmids (71.7%) and integrons (54.8%). ARGs carried by MGEs were blaCTMX-M-15 (78.6%), Sul2 (69.6%), blaTEM (59.1%), and tetA (49.9%). Horizontal gene transfer was seen in 259 instances; however, transmission was unclear. In 442 observations, transmission pathways across human, animal, and environmental interfaces showed AMR prevalence of 75.1% in human, 98.0% in human–animal, and 61.3% in one health interface. Whole-genome sequencing was the most frequently used method for detecting MGEsThe pooled pathogen and AMR prevalence rates were 73.3% (95% CI: 60.5–83.7%) and 94% (95% CI: 85–98%), with significant heterogeneity (I² = 97.8% and 97.4%, respectively). The prevalence of Escherichia coli was 93% and Salmonella enterica 85% in subgroup analysis. Fluoroquinolones, aminoglycosides, and beta-lactams were prevalent in humans (89.7%) and human–animal interactions (98.0%) according to AMR Class. Conclusions: Horizontal gene transfer has propagated MGE-mediated antimicrobial resistance across human, animal, and environmental interfaces in Africa. To combat AMR in Africa, coordinated, genomics-informed One Health surveillance and antibiotic stewardship are needed. Due to variability and publication bias, these data should be considered cautiously. Pooled data may only show descriptive patterns, and not necessarily precise continent-wide prevalence estimates. Full article

Wastewater is a complex and dynamic issue, particularly at the human–animal–environment interface, bearing biological and chemical hazards that may serve as a resource for transmission pathways for pathogens, antimicrobial resistance (AMR) determinants, heavy metals, pharmaceutical residues, per- and polyfluoroalkyl substances (PFAS), and microplastics. Rising global health issues necessitate effective wastewater treatment and advanced research to support risk-informed circular management within a one health framework, incorporating wastewater-based epidemiology (WBE), multi-omics approaches, nanobiotechnology, and green technologies. Inadequate wastewater treatment and uncontrolled discharge result in the generation of more than 380 billion cubic meters of wastewater annually worldwide, contributing to ecological degradation, the spread of AMR, and long-term toxicological risks. Despite significant advances in wastewater treatment, several challenges remain, including complex contaminant mixtures, limited detection and monitoring technologies, variable treatment efficiency, and weak regulatory and governance frameworks. This review highlights key wastewater treatment issues and presents recent advances in WBE and multi-omics approaches, such as metagenomics, resistome profiling, virome analysis, and chemical fingerprinting for contaminant monitoring and public health risk assessment. This review also examines circular reuse strategies focused on water reclamation, nutrient recovery, bioenergy production, and resource recovery, with particular emphasis on nature-based systems, hybrid biological–physicochemical treatment platforms, and green nanobiotechnology as promising approaches to improve treatment performance while minimizing environmental impacts. In conclusion, this review highlights the importance of integrated and sustainable wastewater management approaches within the One Health framework to address emerging challenges and promote environmental resilience, public health protection, and circular resource recovery. Full article

Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and in a contaminated sample of chicken manure wastewater (CMW). Whole DNA was extracted from CM and CMW, followed by whole-genome shotgun sequencing; data analysis was done using online Galaxy software (ver. 26.0.1.dev1). Metagenomic analysis reveals a complex One Health challenge. Data showed that CM and CMW are different in their microbiota, as indicated by a distinct separation of beta diversity values and limited overlapping of species between sample types. In the current study, we found a greatly significant common functional set of adapted bacterial masses, including major pathogenic bacterial groups as well as opportunistic and environmental bacterial species, indicative of a direct contamination from CM and CMW. Notably, in both CM and CMW, a plethora of opportunistic, enteric, and environmental pathogens like Escherichia coli, Salmonella enterica, and Acinetobacter baumannii were found, coupled with an indication of a direct functional flow between both ecosystems as tangled reservoirs. Chicken manure samples showed differences in taxonomic composition and inferred functional profiles at the time of sampling: CM1 was pathogen-enriched, CM2 exhibited strong nitrogen-supportive metabolism, CM3 was dominated by fiber-degrading decomposers, and CM4 showed high methane-producing potential with environmental risk. Such findings underscore the raising of chickens as a potential source of harmful bacteria for the environment. It is important to note that this study represents a preliminary investigation with certain limitations, including the absence of biological replicates, lack of temporal sampling, and limited capacity to infer dynamic ecological interactions. Yet this metagenomic report is more about describing the taxonomy and functional potential of the bacteria, rather than discussing the actual ecological processes of these microorganisms in the environment. Future studies will be required to explore these aspects. Full article

Coral reefs are biodiversity hotspots increasingly threatened by climate-induced bleaching, yet profiling the coral holobiont—the host and its associated microbiota—remains technically challenging due to high host-DNA contamination (often >95%) and the lack of comprehensive reference databases. Here, we present holo-2bRAD, a type IIB restriction site-associated DNA sequencing approach. This method, strategically integrated with a meticulously curated hologenome database (comprising 404,946 microbial genomes and 56 coral-derived metagenome-assembled genomes), effectively overcomes overwhelming host contamination (~99%). We demonstrate its exceptional species specificity (99.92%) in profiling Galaxea fascicularis (Linnaeus, 1767; Order Scleractinia, Family Euphylliidae) holobionts across bleaching severities, thereby validating its technical feasibility. Leveraging this high-resolution tool, our hologenome analysis revealed significant restructuring of coral-associated microbiota during bleaching, where microbial shifts (e.g., depletion of beneficial Thermoanaerobacterium thermosaccharolyticum and enrichment of stress-responsive bacteria) correlated more strongly with bleaching phenotypes than host genetic variation. By providing cost-effective, multi-domain hologenome profiling at unprecedented resolution, holo-2bRAD offers a practical tool for investigating holobiont dynamics and developing microbiome-informed coral conservation strategies. Full article

Antibiotic resistance genes (ARGs) are increasingly recognized as emerging contaminants in wastewater treatment systems; however, their responses to dissolved oxygen (DO)-limited conditions caused by insufficient aeration, particularly in the presence of microplastics, remain poorly understood. In this study, three sequencing batch reactors (SBRs) were operated for 31 days under progressively oxygen-limited conditions with different concentrations of polyethylene terephthalate (PET) microplastics to investigate their combined effects on treatment performance, microbial communities, ARGs, mobile genetic elements (MGEs), and PET degradation-related genes using metagenomic analysis. Prolonged oxygen limitation maintained relatively stable organic matter removal but progressively deteriorated ammonium removal and sludge settleability, while PET addition significantly aggravated these effects. PET exposure markedly increased the absolute abundance of ARGs without substantially altering resistome composition or dominant resistance mechanisms, suggesting an amplification rather than restructuring of the resistome. Correlation analyses indicated that ARGs enrichment was primarily host-associated and driven by the proliferation of a limited number of microbial taxa. Several potential ARG hosts were also strongly associated with PET degradation-related genes, indicating shared microbial populations linking PET-associated functions and antibiotic resistance. In addition, strong positive correlations between ARGs and MGEs suggested an important role of gene mobility in resistome dynamics under oxygen-limited conditions. Overall, these results demonstrate that oxygen limitation combined with PET microplastics promotes host-associated ARG enrichment in wastewater systems, highlighting potential environmental and public health risks and emphasizing the importance of maintaining operational stability to mitigate antibiotic resistance dissemination. Full article

Spontaneous fermentation processes can promote uncontrolled microbial growth and increase the risk of foodborne contamination, making the characterization of artisanal beverages essential for consumer safety. This study investigated the microbial composition of quinoa-based rejuvelac, a homemade fermented drink often perceived as a functional food, with the objective of identifying potential microbiological hazards associated with its preparation. High-throughput sequencing of the 16S rRNA V3–V4 region was combined with shotgun metagenomics to profile bacterial communities and recover metagenome-assembled genomes. The analysis revealed a strong dominance of Pseudomonadales, mainly Pseudomonas, Acinetobacter, Enterobacter and Burkholderiales, while lactic acid bacteria typically responsible for stable and safe fermentations were not detected. Shotgun metagenomics recovered medium- to high-quality genomes from Burkholderiaceae and Clostridiales, supporting the overrepresentation of non-beneficial taxa and indicating deviations from expected fermentation microbiota. These results show that the spontaneous preparation of rejuvelac may favor bacterial groups associated with environmental contamination rather than fermentative pathways, underscoring the importance of hygiene practices, controlled starter cultures and monitoring strategies to mitigate microbiological risk. The study highlights the need for improved safety standards in artisanal fermented foods to prevent unintended microbial contamination and protect consumers. Full article

Fecal microbiota are shaped by upstream digestive processes and reflect the outcome of host–microbe interactions, including the resistant microbial fraction that survives to be excreted. This is particularly crucial for assessing zoonotic risks and environmental contamination, as feces are the primary source of dissemination, which is considered an emerging One Health threat. Therefore, we conducted a pilot study to obtain the exploratory findings regarding the cattle GIT microbial composition, potential resistome, and their transmission drivers, such as plasmids, using metagenomic analysis from different districts in Khyber Pakhtunkhwa (KP) province, Pakistan. For this purpose, a total of 150 fecal samples (50 from each district) of healthy cattle were collected from various farms in Mardan (FC1), Peshawar (FC2), and Dera Ismail Khan (FC3) districts. Total DNA from each sample was extracted, pooled (FC1, FC2, and FC3), and sequenced via the Illumina platform. Bacteria were the highly abundant kingdom, while Pseudomonadota and Bacillota were dominant phyla in all samples. Caryophanon latum and Escherichia coli were highly abundant at the species level. A large resistome (40–49 genes), including critical genes, such as tet(X), bla_OXA-427, and plasmidomes (16–22), such as IncF, was detected in the samples. The prominence of certain commensal or opportunistic pathogens in the fecal microbiota may indicate the presence of sub-clinical gastrointestinal disruptions or disease that may affect cattle herds. The fecal resistome is extensive, identifying dairy cattle in these regions as important reservoirs for AMR genes capable of spreading via HGT. This pilot study establishes that the fecal microbiota of dairy cattle in this region are not merely a waste product but a complex ecosystem, rich in microbiota of One Health significance. Full article

This study explores the physicochemical properties and microbiological community structure of oil-contaminated soils from Midrand and Roodepoort, South Africa. Due to sample pooling, the analysis provides a composite profile for investigating site-specific microbial adaptations rather than replicated ecological inference. The soils of Midrand exhibited acidity (pH around 5.5–5.9), elevated levels of heavy metals (e.g., Zn exceeding 1000 mg/kg), and the presence of 5–6 ring polycyclic aromatic hydrocarbons (PAHs). The soils in Roodepoort exhibited a near-neutral pH (about 6.2–7.2), characterized by specific metal concentrations (e.g., Cr exceeding 150 mg/kg) and an elevated presence of four-ring polycyclic aromatic hydrocarbons (PAHs). Metagenomic analysis indicated distinct microbial communities: Pseudomonas spp. were prevalent in Midrand, while Bacillus spp. were dominant in Roodepoort. Correlation analysis suggested connections between pollutants and microbial taxa; however, these findings are tentative. Recovered metagenome-assembled genomes (MAGs) indicated genetic potential for polycyclic aromatic hydrocarbon (PAH) degradation in Midrand and for metal resistance in Roodepoort. The findings suggest that localised pollution profiles are associated with unique microbial community structures and genetic potentials, providing a genomic basis for proposing site-specific bioremediation strategies. The research underscores the necessity for measures that take into account pollutant composition, soil pH, and microbial adaptation. Full article

The hypersaline soils of the Odiel Saltmarshes Natural Area in Southwest Spain harbor highly diverse microbial communities adapted to extreme conditions. However, their genomic diversity remains largely unexplored. In addition to high salinity, these soils are contaminated with heavy metals, creating a hostile environment of great interest for studying extremophilic microorganisms and their metabolic adaptations. This study aims to characterize the uncovered prokaryotic taxa as Candidatus species inhabiting the hypersaline soils of the Odiel Saltmarshes, based on their metagenomic assembled genomic sequences. The reconstructed genomes were assessed for quality based on completeness and contamination thresholds and subsequently taxonomically classified. Comparative genomic analysis of six high-quality MAGs revealed key metabolic traits related to survival under extreme salinity and heavy metal conditions. The findings provide new insights about microbial diversity of hypersaline environments and expand the catalog of known prokaryotic genomes. Detailed characterization of six novel Candidatus taxa highlights the unique adaptations of these microorganisms, enhancing our understanding of life in extreme habitats. Full article

In this study, a Nocardia niigatensis strain was isolated from boron-rich mining soils in the Bigadiç region of Türkiye and comprehensively characterized. The primary aim of this study was to isolate boron-tolerant Nocardia species and evaluate their physiological, enzymatic, and biochemical profiles. Selective isolation techniques were employed to obtain Nocardia isolates, and species-level identification was achieved using both 16S rRNA gene sequencing and MALDI-TOF MS analysis, which consistently confirmed the isolate as N. niigatensis. In addition to molecular identification, the morphological, physiological, and biochemical characteristics of the strain were extensively investigated. The strain demonstrated notable boron tolerance, exhibiting robust growth at concentrations up to 50 mM, highlighting its potential applicability in the bioremediation of boron-contaminated environments. Physiological assays further revealed moderate halotolerance and a mesophilic growth profile, with optimal growth observed at 27–37 °C. Enzymatic screening indicated positive L-glutaminase activity, an enzyme of considerable industrial relevance. Moreover, API ZYM profiling revealed a broad enzymatic spectrum, including esterases, arylamidases, phosphatases, and glucosidases, suggesting substantial metabolic versatility. Antibiotic susceptibility testing showed sensitivity to doxycycline, tobramycin, and erythromycin, whereas resistance was observed against imipenem and several β-lactam antibiotics. Metagenomic analysis of boron-rich soils from two distinct mining sites revealed marked differences in microbial community composition, with variations in Actinobacteria abundance associated with mineral type. Overall, these findings emphasize the adaptive capacity and biotechnological potential of environmental Nocardia strains inhabiting chemically stressful ecosystems, warranting further genomic and metabolomic investigations. Full article

Background/Objectives: Postmortem microbiology has traditionally been regarded with caution in forensic practice due to concerns related to contamination, bacterial translocation, and postmortem microbial overgrowth. As a result, microbiological findings obtained after death have often been considered unreliable or of limited diagnostic value. However, growing evidence indicates that, when appropriately interpreted and integrated with autopsy findings, histopathology, and circumstantial information, postmortem microbiology can provide crucial support for cause-of-death determination. This narrative review critically examines the current role of postmortem microbiology in forensic diagnostics, with a focus on its diagnostic applications, interpretative challenges, and future perspectives. Methods/Results: The transition from conventional culture-based techniques to molecular approaches—including polymerase chain reaction, microbiome analysis, and metagenomic methods—is discussed, highlighting both their potential advantages and inherent limitations within the forensic setting. Particular attention is devoted to key interpretative issues such as postmortem interval, sampling strategies, contamination, and bacterial translocation. In addition to cause-of-death attribution, emerging applications—including postmortem interval estimation, trace evidence analysis, and artificial intelligence–based models—are reviewed. Although these approaches show promising research potential, their routine forensic applicability remains limited by methodological heterogeneity, lack of standardization, and interpretative complexity. Conclusions: In conclusion, postmortem microbiology represents a valuable diagnostic tool when applied within a multidisciplinary forensic framework. Its effective use requires cautious interpretation and integration with pathological and contextual evidence, avoiding standalone or automated conclusions. Future progress will depend on standardized methodologies, multidisciplinary collaboration, and a clear distinction between experimental research and routine forensic practice. Full article

Background: Stenotrophomonas maltophilia is an increasingly important multidrug-resistant opportunistic pathogen frequently isolated from clinical, environmental, and plant-associated niches. Despite its medical relevance, the global population structure, species-complex boundaries, and genomic determinants of antimicrobial resistance (AMR) and ecological adaptation remain poorly resolved, partly due to inconsistent annotations and fragmented genomic datasets. Methods: Approximately 2400 genome assemblies annotated as Stenotrophomonas maltophilia were available in the NCBI Assembly database at the time of query. After pre-download filtering to exclude metagenome-assembled genomes and atypical lineages, 1750 isolate genomes were retrieved and subjected to stringent quality control (completeness ≥ 90%, contamination ≤ 5%, ≤500 contigs, N50 ≥ 10 kb, and ≤1% ambiguous bases), yielding a final curated dataset of 1518 high-quality genomes used for downstream analyses. Genomes were assessed using CheckM, annotated with Prokka, and compared using average nucleotide identity (ANI), pan-genome analysis, core-genome phylogenomics, and functional annotation. AMR genes, mobile genetic elements (MGEs), and metadata (source, host, and geographic origin) were integrated to assess lineage-specific genomic features and ecological distributions. Results: ANI-based clustering resolved the S. maltophilia complex into multiple distinct genomospecies and revealed extensive misidentification of publicly deposited genomes. The pan-genome was highly open, reflecting strong genomic plasticity driven by accessory gene acquisition. Core-genome phylogeny resolved well-supported clades associated with clinical, environmental, and plant-related niches. Resistome profiling showed widespread intrinsic MDR determinants, with certain lineages enriched for efflux pumps, β-lactamases, and trimethoprim–sulfamethoxazole resistance markers. MGE analysis identified lineage-specific integrative conjugative elements, prophages, and transposases that correlated with source and geographic distribution. Conclusions: This large-scale analysis provides the most comprehensive genomic overview of the S. maltophilia complex to date. Our findings clarify species boundaries, highlight substantial taxonomic misannotation in public databases, and reveal lineage-specific AMR and mobilome patterns linked to ecological and clinical origins. The curated dataset and evolutionary insights generated here establish a foundation for global genomic surveillance, epidemiological tracking, and future studies on the evolution of antimicrobial resistance in S. maltophilia. Full article