Routine disinfection can reduce microbial burden on hospital surfaces in the short term, but its long-term impacts on surface microbiomes and antimicrobial resistance dynamics remain unclear. We conducted a year-long metagenomic study of 197 in situ hospital surface samples subjected to sustained chlorination to investigate changes in microbiomes, resistomes, and phage-host interactions. Microbial α-diversity increased during the early months, with a decline in dominant Enterobacteriaceae and enrichment of taxa including Propionibacteriaceae and Micrococcaceae, indicating niche replacement. Over time, both diversity and previously suppressed taxa approached baseline levels, suggesting adaptation to sustained disinfection, with evidence of functional shifts. Viral communities exhibited similar temporal dynamics, with composition and relative abundance distinctly shifting. Concurrently, the resistome underwent substantial, largely irreversible restructuring, with decreased total relative abundance and increased diversity of antibiotic resistance genes (ARGs). Chlorination also reduced ARG mobility and pathogenic potential, indicated by weakened co-occurrence with mobile genetic elements and virulence factor genes and lower predicted resistome risks. Phage and host relative abundances remained strongly correlated, although a shift toward lytic viral lifestyles occurred, potentially limiting phage-mediated ARG dissemination. These findings highlight disinfection as both a microbial control measure and ecological pressure, underscoring the need for ecologically informed strategies to manage clinical antimicrobial resistance.

RNA viruses represent an integral component of human-associated environments and human health. However, the ecology of environmental RNA viruses remains largely unexplored. Here, we analyzed 2922 metatranscriptomic samples collected from urban and surrounding environments-including human-dense settings (e.g., transit hubs, hospitals, banks), alongside peri-urban settings - across 102 cities in 31 countries and constructed the Urban & Peri-urban RNA Virus Atlas (UPVAtlas), comprising 54,945 RNA viruses, 77% of which had not been previously observed. Phylogenetic reconstruction based on RNA-dependent RNA polymerases from UPVAtlas greatly expanded the evolutionary diversity of RNA viruses, leading to the identification of two potential candidate phyla, one candidate class, and several unclassified clades. Host association analyses further revealed the ecological complexity of environmental RNA viruses, with the diversity of vertebrate-related and ESKAPE pathogen-related viruses underscoring the importance of continued monitoring of urban environments for tracking RNA viral prevalence and dynamics, with direct relevance to future public health.

Viruses play crucial roles in bacterial ecology and evolution through virus-host interactions; however, their distribution, assembly mechanisms, and temporal turnover remain underexplored in engineered ecosystems. In the present study, we used activated sludge (AS) and anaerobic treatment (AT) reactors from four full-scale industrial textile wastewater treatment plants as model ecosystems, integrating metagenomics, macroecological modeling, and deep learning to characterize viral structure, dynamics, and host interactions. A total of 1046 and 1386 high-quality viral operational taxonomic units were recovered from AS and AT systems, respectively, and most were affiliated with Caudoviricetes. Viral composition and genetic microdiversity were highly plant-specific and shaped by environmental selection and host interactions. Lognormal species abundance distributions and deviations from neutral expectations indicated deterministic assembly. Virulent viruses exhibited faster temporal turnover than temperate viruses. Viral co-occurrence networks showed strong plant-specific modularity and greater temporal stability than bacterial networks, suggesting that they play a stabilizing role in community dynamics. Tight virus-host abundance coupling and gene-level signatures of host-linked selection indicated ongoing coevolutionary interactions. A deep learning model accurately predicted bacterial community dynamics from viral composition at both the taxon and sample levels, highlighting the ecological relevance of viral signatures. Together, these findings reveal dynamic, plant-specific viromes tightly coupled to bacterial communities and highlight viral signatures as potential indicators for monitoring engineered ecosystems. Incorporating viral ecology into microbial management could enhance the stability, resilience, and functional performance of engineered ecosystems.

Aerobiome diversity is extensive; however, species-level community structure remains poorly resolved. Likewise, microbiomes of public transit systems are of public interest due to their importance for health, though few studies have focused on these ecosystems whilst utilising shotgun metagenomics. Aerosol studies have focused predominantly on individual cities, with limited between-city comparisons suggesting specific community structures. Longitudinal studies show aerobiome diversity as dynamic, fluctuating during seasonal and daily cycles, though interannual cycles remains to be considered. Further, a bacterial bias has limited fungal aerobiome studies, with few considering both fractions collectively. As such, the objective of this study was to examine spatial and temporal patterns in the species diversity of public transit aerobiomes, with an emphasis on bacteria and fungi. Air samples taken over a 3-year period (2017–2019) from six global cities were subjected to shotgun metagenomic sequencing. Improved classification databases, notably for fungi, applying stringent parameters for trimming, exogenous contamination removal and classification yielded high species-level resolution. Microbial diversity varied substantially among cities, while human and environmental factors, recorded in parallel, were of secondary significance. Bacteria dominated the public transit aerobiome with increased presence in cities with higher population densities. All aerobiomes had complex compositions, consisting of hundreds to thousands of species. Interannual variation had limited significance on the public transit aerobiome diversity and community structure. Cities were the most important factor contributing to diversity and community structure, demonstrating specific bacterial and fungal signatures. Further, possible correlation between geographical distance and genetic signatures of aerobiomes is suggested. Bacteria are the most abundant constituent of public transit aerobiomes, though no single species is globally dominant, conversely indicating a large inter-city variation in community structure. The presence of a ubiquitous global species core is rejected, though an aerobiome sub-core is confirmed. For the first time, local public transit aerobiome cores are presented for each city and related to ecological niches. Further, the importance of a robust bioinformatics analysis pipeline to identify and remove exogenous contaminants for studying low-biomass samples is highlighted. Lastly, a core and sub-core definition of contaminant aerobiome species with taxon tables, to facilitate future environmental studies, is presented.

The "plastisphere," which comprises microplastics (MPs)-associated microbial communities, is an emerging component of urban river ecosystems. However, its seasonal dynamics remain poorly understood, especially compared with microbiomes on natural particles (NPs). We therefore conducted a year-long metagenomic study at 15 sites across 10 major urban rivers in Hong Kong to compare MP- and NP-associated microbiomes across four seasons. Representative high-quality metagenome-assembled genomes revealed significant seasonal variations in both taxonomic and functional compositions across particle types, with water temperature identified as the primary environmental driver. As temperatures increased, both MP and NP microbiomes exhibited increased taxonomic and functional diversity but reduced functional redundancy and network stability. Compared to NPs, MP microbiomes exhibited higher taxonomic and functional turnover, more complex and connected cooccurrence networks, and distinct taxonomic and functional traits along the temperature gradient. In MP microbiomes, warmer conditions were associated with a higher abundance of pollutant-degrading and putatively virulent taxa (particularly from Firmicutes and Actinobacteria), along with enhanced biosynthetic functions and increased potential microbial sharing and horizontal gene transfer with surrounding aquatic microbiomes. These findings highlight the temperature-dependent ecological impacts of MP microbiomes and underscore the need to consider climatic factors when assessing the long-term ecological risks of MPs in urban riverine ecosystems.

Cigarette butts are common yet overlooked pollutants in urban environments. How this anthropogenic niche shapes microbial life-history strategies and evolutionary mechanisms remains poorly understood, limiting assessments of microbial adaption and urban ecosystem health. However, systematic and multiscale evidence on the ecological effects of cigarette butts on microbial communities remains scarce. Here, we collected cigarette butts, litter, and soil samples from urban parks in 35 Chinese cities and integrated third-generation 16S ribosomal RNA sequencing, metagenomics, and transcriptomics to resolve microbial community composition, functional potential, and evolutionary patterns. The results revealed that microbial communities in cigarette butts were shaped by strong deterministic processes, showed low spatial heterogeneity, and were taxonomically distinct from those in natural niche (i.e., litter) and surrounding soil, with notable enrichment of Proteobacteria, particularly the family Pseudomonadaceae. Functional trait analysis showed that butt-associated communities favored environmental responsiveness and fast-growth strategies, contrasting with metabolism- and resource acquisition-oriented strategies in the litter. Population genomic analysis suggested stronger positive selection in cigarette butt-associated Pseudomonadaceae, while the pure culture experiment provided strain-level evidence that cigarette butt exposure induced the up-regulation of key functional genes in Pseudomonas aeruginosa PAO1. This study demonstrates that cigarette butts, as an emerging ecological niche, reshape microbial community assembly, life-history strategies, and adaptive evolution, offering new insights into microbe-driven evolution on artificial surfaces.

Estuarine and coastal ecosystems are critical interfaces between land and ocean, serving as sinks for anthropogenic pollutants such as ammonium and microplastics. However, the impact of microplastic pollution on nitrification processes in these environments remains largely unexplored. This study investigates the coastal region of the Yangtze River to examine how different microplastic types (polyethylene terephthalate, polypropylene, and polyethylene) affect nitrous oxide (N2O) emissions and the dynamics of nitrifiers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) Nitrospira, and nitrite-oxidizing Nitrospira. Results from incubation experiments show that all microplastic types significantly increase N2O emissions across sediment samples. The reconstructed representative metagenome-assembled genomes revealed that AOA belong to group I.1a, while AOB are classified within the Nitrosomonas genus. Microplastics were found to have a stronger stimulatory effect on AOB, which are linked to higher N2O production, than on AOA, which are associated with low N2O production, thereby enhancing N2O emissions during nitrification. Furthermore, AOB genomes encode a range of putative plastic-degrading enzymes, which may partially explain their enrichment in microplastic-contaminated environments, although other factors such as differential tolerance to ammonium or oxidative stress cannot be ruled out.

Abstract Although fine particulate matter (PM 2.5 ) is linked to cognitive impairment, the mechanistic links between pulmonary exposure and neurodegeneration remain poorly understood. This study investigates the role of the gut–liver–brain axis in mediating PM 2.5 -induced neurotoxicity. We demonstrate that three weeks of intratracheal PM 2.5 instillation in mice causes significant memory deficits, impaired hippocampal adult neurogenesis, and reduced synaptic plasticity in both sexes. Metagenomic analysis revealed that PM 2.5 alters gut microbiota composition, specifically by upregulating pathways involved in trimethylamine (TMA) synthesis. This microbial shift led to a systemic increase in the metabolite trimethylamine N-oxide (TMAO) and its accumulation in the hippocampus. Mechanistic experiments revealed that TMAO drives neurotoxicity by activating the hippocampal PERK-mediated endoplasmic reticulum (ER) stress pathway. Critically, these deficits were reversed by suppressing hepatic TMAO production via either pharmacological inhibitors or genetic knockdown. Additionally, hippocampal-specific PERK silencing or dietary resveratrol intervention attenuated hippocampal ER stress, thereby protecting against PM 2.5 -induced cognitive and hippocampal impairments. These results identify the microbial metabolite TMAO as a key mediator of air pollution-related neurotoxicity and highlight the gut–liver–brain axis as a promising therapeutic strategy to counteract the neurological impacts of air pollution.

Arabian incense (Bakhoor) burning is a widely practiced fragrancing and ceremonial activity, yet how the Bakhoor composition controls particle emissions and oxidative potential remains poorly constrained, especially under repeated use in low-ventilation settings. Here we characterized emissions from Bakhoor burning in a controlled chamber using a charcoal-assisted heating configuration representative of common practice and quantified aerosol oxidative potential using complementary acellular dithiothreitol (DTT) activity and a macrophage-based intracellular oxidative-stress response, with smoldering sidestream cigarette smoke as a protocol-matched indoor combustion reference. Normalized by the initial Bakhoor mass per burn, Bakhoor burning produced particle mass and number emission rates of 670–1690 µg min−1 g−1 and (6–7) × 1011 particles min−1 g−1, respectively. Ultrafine particles contributed 70 %–75 % of the total particle number, and their emission rates substantially exceeded those from sidestream cigarette smoke. Across Bakhoor materials, emission magnitude followed a nonlinear power-law relationship with the loading of the hexane-soluble fraction, indicating that this fraction is an important control on particle production. In the acellular assay, the water-soluble particle mass-normalized DTT consumption rate (OPDTT, mWS) was approximately 32 pmol min−1 µg−1, modestly lower than that of cigarette smoke particles, whereas Bakhoor burning particles elicited stronger intracellular oxidative-stress responses. Ozone aging increased oxidative potential for both sources, and the acellular and cellular responses remained evident after aging equivalent to days of indoor exposure. Overall, Bakhoor burning represents a previously underrecognized source of ultrafine aerosol with substantial oxidative potential.

There is a diverse assemblage of microbes in air in built environments (BEs), but our understanding of viruses and their interactions with hosts in BEs remains incomplete. To address this knowledge gap, this study analyzed 503 metagenomes isolated from air samples from public transit systems in six global cities, namely Denver, Hong Kong, London, New York City, Oslo, and Stockholm. Viral genomes were recovered from samples via metagenomic binning, and viruses’ taxonomy, functional potential, and microbial hosts were determined. The study also investigated correlations between virus and host abundances, the coevolution of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems and anti-CRISPR (Acr) proteins, and the potential impacts of auxiliary metabolic genes (AMGs) on hosts. Airborne viruses in global BEs exhibited biogeographical variations in diversity, composition, function, and virus–host interactions. Nearly half of the vOTUs analyzed were from the Caulimoviridae family, while 31.8

Hot springs, with their well-characterized major abiotic variables and island-like habitats, are ideal systems for studying microbial biogeography. Photosynthetic biofilms are a major biological feature of hot springs but despite this large-scale studies are scarce, leaving critical questions about the drivers of spatial turnover unanswered. Here, we analysed 395 photosynthetic biofilms from neutral-alkaline hot springs (39–66 °C, pH 6.4–9.0) across a 2100 km latitudinal gradient in Southeast Asia. The Cyanobacteria-dominated communities were categorized into six biogeographic regions, each characterized by a distinct core microbiome and biotic interactions. We observed a significant decline in the explanatory power of major abiotic variables with increasing spatial scale, from 62.6

Understanding the types of microbes present and their concentrations over time is essential for deciphering the physical, chemical, and biological processes in the atmospheric environment. In this study, Hong Kong, which experiences four distinct seasons, was selected as the study site. High-throughput amplicon sequencing of the 16S rRNA gene was utilized to analyze the microbiomes present, while a light/laser-induced fluorescence (LIF) instrument was employed to characterize the real-time concentrations of fluorescent aerosol particles (FAPs) or bioaerosols. Seasonal variations in the microbiomes were observed, primarily driven by less abundant taxa that were unique to specific locations. Conversely, spatial variations were minimal, suggesting a homogeneity of microbiomes within the scale of a city. The major taxa of the microbiomes reflected the local environments (e.g., aquatic and soil), with neutral assembly processes dominating each season, indicating a minor role of selection in microbial assembly in the air. FAP concentrations were highest in the fall and winter seasons, deviating from measurements in temperate and tropical regions. Bioaerosol concentrations exhibited diurnal patterns, with higher concentrations during the daytime and lower concentrations at nighttime. Certain atmospheric pollutants were associated with bioaerosol concentrations, and positive matrix factorization analysis identified anthropogenic sources as key drivers of bioaerosol concentrations. In summary, the application of molecular techniques and LIF-based instrumentation has provided insights into the microbial composition of the atmospheric environment in a subtropical location, facilitating further investigations into the interactions involving these biological components.

Indoor sulfur dioxide (SO2) is a common air pollutant that may affect surface-associated bacterial communities. While high concentrations (≥100 ppm) are known to act as disinfectants, the effects of typical indoor concentrations (≤100 ppb) remain unclear. This study investigated SO2 impacts on bacterial viability, biofilm formation, and community composition across nutrient gradients and relative humidity (RH, 20%-97%) using controlled chamber exposures with Escherichia coli to probe mechanistic responses and real-world kitchen surface communities to assess ecological relevance. Bactericidal effects were strongest on loosely adherent E. coli under nutrient-poor, low-RH (20%) conditions and low cell density (106 CFU/cm2), likely due to increased acidification and sulfate adsorption. At this density and nutrient level, ≥30 ppb of SO2 significantly reduced viability across all RH levels, while ≤100 ppb did not affect nutrient-rich surfaces at 97% RH or at higher densities (107 CFU/cm2). Biofilm inhibition required 100 ppb, indicating greater resistance than loosely adherent cells. In kitchen surface communities, bacterial abundance declined at 30 ppb on cooking surfaces and at ≥10 ppb on noncooking surfaces at ≤60% RH, with no effect at 97% RH. At 30 ppb, SO2 reduced bacterial diversity and altered microbial composition, independent of surface type or RH. Ambient SO2 evidently has an underrecognized impact on indoor-surface microbial communities.

Autism spectrum disorder (ASD) is characterized by early-onset challenges in social communication and repetitive behaviors, influenced by both genetic and environmental factors. The global increase in ASD diagnoses has drawn attention to air pollution as a significant environmental risk factor, although the underlying mechanisms remain unclear. This study investigates the impact of maternal exposure to the air pollutant PM2.5 on ASD risk in offspring. In this study, female C57BL/6J mice were exposed to PM2.5 via intratracheal instillation every three days for two weeks prior to mating, with exposure continuing until birth. Both male and female offspring exhibited reduced social novelty and increased repetitive behaviors, only male offspring showed significant impairment in working memory. PM2.5 exposure led to an increased number of proliferating progenitor cells and immature neurons in the hippocampus of male offspring, a change not observed in females. However, PM2.5 exposure resulted in reduced dendritic length exclusively in female offspring, while both sexes experienced decreased long-term potentiation and synaptic GluN2B protein expression. These structural changes were associated with significantly lower cysteine levels in the hippocampi of offspring of both sexes, but not with changes in relative abundance of gut microbiota and neuroinflammatory response in the hippocampus. These findings suggest that maternal PM2.5 exposure may induce autism-like behaviors in offspring, potentially linked to reduced hippocampal cysteine levels and hippocampal dysfunction.

Mercury (Hg) is a global pollutant and its transformation to the highly toxic methylmercury (MeHg) is mediated by anaerobic microbes carrying hgcA gene, which can affect human health risk through fish consumption. The Pearl River Estuary in southern China is productive but suffers from increasing anthropogenic stresses. However, it remains poorly known regarding the environmental response of hgcA+ microorganisms to climatic variations. We demonstrated that saltwater intrusion driven by prolonged drought led to elevated sedimentary MeHg concentrations, particularly in the nearshore zone, compared to a wet year. Drought-induced saltwater intrusion served a dual microbial function: it reinforced a non-random association between oligotrophic Acidobacteriota (putative methylators) and Myxococcota (putative non-methylators), while simultaneously promoting a distinct, copiotrophic microbial module adapted to warmer, saline conditions. The significant correlation of module phyla with MeHg levels, coupled with its genetic capacity for sulfate reduction, points to a potential mechanism for the enhanced Hg methylation. Thus, climate-anthropogenic interactions can regulate MeHg risk by altered microbial community structure and interactions in estuarine ecosystems.

Biological denitrification is a key process for nitrogen removal in wastewater, enabling the conversion of nitrate (NO3-) to nitrogen gas (N2). However, this process can be inhibited in the presence of aromatic substrates. Conventional advanced oxidation protocols involve the mineralization of aromatics, but the widespread adoption of such protocols is limited by high energy and chemical requirements. In this study, we present a novel electrochemical hydrogenation (ECH) protocol to transform bioinhibiting aromatics into bioavailable aliphatic products, thereby promoting biologically driven denitrification. A highly active carbon-supported ruthenium electrode was designed to convert various unsaturated, aromatic, and halogenated aromatic pollutants into aliphatic products, achieving conversion efficiencies of 66.0%-100%. After 5 day incubation, the saturated products enhanced the denitrification rate by up to 614.0%. The relative abundance of denitrifiers in the sequencing batch reactor landfill sludge increased, confirming that the aliphatic products from ECH treatment could enhance bioavailability. This work demonstrates the integration of electrochemical and biological catalysis, valorizing pollutants into biologically useful products that can improve denitrification, especially in existing high-organic-load wastewater treatment networks.

Hydroxyl radicals (•OH), singlet oxygen (1O2*), and organic triplet excited states (3C*) play key roles as oxidants ("reactive intermediates (RIs)") in forming and oxidizing aqueous organic aerosols. Bioaerosols are ubiquitous in the atmosphere, but little is known about their photochemical behavior and contributions to atmospheric photochemistry. We investigated the photochemical behavior of aqueous-phase cellular organic matter (COM) and extracellular polymeric substances (EPS) from cultured bacteria isolated from atmospheric PM2.5, focusing on their photochemical production of 3C*, 1O2*, and •OH. The molecular size and aromaticity of chromophores and fluorophores in COM and EPS increased with molecular weight (MW). Apparent quantum yields (ΦRI) of up to 10% and 5% were measured for 1O2* and 3C*, respectively, which are in the upper range of previously reported values. This indicated that COM and EPS contain photosensitizers that are highly efficient at producing 1O2* and 3C*. ΦRI and concentrations ([RI]ss) decreased with MW due to higher-MW molecules engaging in charge-transfer interactions that disrupt photochemical processes and oxidant production. Machine learning models were used to understand and predict oxidant production based on measurable optical and chemical properties of COM and EPS. This study provides new insights into the roles that bioaerosols can play in atmospheric aqueous photochemistry.

Understanding the factors influencing chemical and biological constituent accumulation on indoor surfaces is crucial, especially as individuals spend approximately 90% of their time indoors and frequently interact with these surfaces. However, the temporal relationships between these constituents remain unclear, as most field studies have relied on single-time snapshots and seldom examined the interplay between chemical and biological dynamics. We conducted a month-long spatiotemporal field study across 20 households in Hong Kong to investigate the factors influencing chemical and biological constituents on common indoor surfaces. Among the 16 household- and occupant-related factors analyzed, routine oil-based cooking was the primary driver of microbial diversity and composition on indoor surfaces. Surfaces in kitchens with frequent cooking exhibited elevated total organic carbon levels, which were linked to an increased bacterial abundance. A focused analysis of six kitchens with well-controlled frequencies of oil-based cooking revealed that cooking-derived organic compounds, particularly alkanes, promoted bacterial abundance while reducing microbial diversity. Network analysis further revealed strong interactions between these organic compounds and bacterial taxa, especially those within the Proteobacteria and Firmicutes phyla. These findings highlight the impact of routine household activities on indoor chemical-biological interactions, enhancing our understanding and informing strategies to improve indoor environments and occupant well-being.

The "plastisphere," comprising microbes associated with microplastics (MPs), may have substantial ecological impacts on riverine ecosystems. However, little is known about how the microbiomes associated with anthropogenic MPs compare with those associated with natural particles (NPs) in urban rivers with varying MP pollution levels. We therefore conducted a comparative analysis of the metagenomes associated with MPs and NPs (100-5000 μm) and river water (RW) across 10 urban river systems. Although we found similarities in taxonomic and functional compositions between the microbiomes associated with MPs and NPs, the plastisphere exhibited distinct associations with specialized taxa and life-history strategies. These unique traits enhanced the potential of the plastisphere for complex carbohydrate and plastic degradation, nitrate and nitric oxide reduction, and antibiotic resistance and virulence compared with the NP or RW microbiomes. Furthermore, MPs supported the sharing of unique microbes with the surrounding RW; these shared microbes possessed enhanced horizontal gene transfer capabilities and potentially could disperse traits of the plastisphere into the broader RW microbiomes. This study highlights the distinct ecological roles and shared microbes of the plastisphere, indicating that MP pollution may substantially and uniquely impact the function and health of riverine ecosystems.