Global Meta-analysis of Airborne Bacterial Communities and Associations with Anthropogenic Activities

Characteristics of airborne bacteria over inland and coastal atmosphere influenced by systemic air mass in northern China

Regional aerosol pollution frequently occurs in winter and spring in northern China. Here, we surveyed four air pollution, categorized as episodes influenced by northerly or southerly air mass, and discussed the bacterial communities in inland and coastal cities. Influenced by northerly airmass, the predominant bacterial phyla were Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria both in the inland and coastal cities. The opportunistic pathogen in the genus Staphylococcus was predominant, and the relative proportion increased with the intensification of air pollution. Gut bacteria of the genus Lactobacillus and aquatic bacteria of the family Flavobacteriaceae were enriched in the coastal city. Influenced by southerly air mass, combined with the transmission of dust air masses in the northwest, air pollution in spring showed obvious sand dust characteristics. The prevalence of the members from the phylum Cyanobacteria was markedly greater in inland city compared to the coastal city, especially in dust samples. This indicated the possibility of soil Cyanobacteria members, subsequently being transported from terrestrial to coastal areas via dust movements. The bacterial community dynamics was intimately linked to meteorological factors and air pollutants. In both cities, pathogenic bacteria predominate in haze pollution influenced by northernly air masses, while a higher proportion of soil bacteria originating from natural sources predominate in southern air mass samples. The impact of varying air masses was particularly pronounced in inland city. Meteorological factors instigated by seasonal changes-especially the transition of wind direction from winter to spring, accompanied by elevated wind speeds and rising temperatures-play a pivotal role in shaping bacterial community structure. This study examined the sea-land variations in bacterial communities transported by systemic air masses during typical air pollution events. These insights lay the groundwork for future research into the distribution, sources, and health risks of bioaerosols during air pollution.

Identifying groundwater anthropogenic disturbances and their predominant impact on microbial nitrogen cycling at a former contamination site adjacent to Baiyangdian Lake

Groundwater ecosystems face increasing threat from declining water quality due to intensified urbanization, agricultural, and industrial activities. Accurately identifying anthropogenic disturbances remains challenging, and their effects on microbial nitrogen cycling are still largely unknown. Here, by collecting 64 groundwater samples from an aquifer beneath the Tanghe sewage reservoir in the North China Plain, we conducted a full-spectrum screening of 228 physiochemical indices, 47 nitrogen cycling genes (NCGs) and 2182 metagenome-assembled genomes (MAGs) harboring NCGs. Unmix model identified antibiotic usage, industrial manufacturing, and agricultural practices as the predominant pollution sources, explaining 49.6-92.2 % (averaged 81.0 %) of the variations in aquifer attributes. These activities were primary drivers governing distributions of groundwater NCGs and NCG-hosts, with fragmented denitrification processes being prevalent. Antibiotic usage and industrial activities were probably associated with suppressed nitrogen cycling, while agriculture had a positive effect. Notably, we observed enhanced mutualistic interactions within NCG-hosts and increased enrichment of NCG-antibiotic resistance gene (ARG), NCG-mental resistance gene (MRG), and NCG-ARG-MRG co-hosts under high anthropogenic stresses, suggesting microbial adaptation to optimize nutrient and energy metabolism. This study provided new insight into how groundwater nitrogen cycling responds to anthropogenic disturbances, offering valuable information for developing groundwater management and pollution control strategies.

Underrated risk of antibiotic resistance genes dissemination mediated by bioaerosols released from anaerobic biological wastewater treatment system

Antibiotic resistance has been recognized as one of the most prevalent public health problems. The bioaerosol-mediated spread of antibiotic resistance genes (ARGs) is an important but underrated pathway. Therefore, this work investigated the comprehensive resistome and pathogen-induced risk in bioaerosols released from anaerobic ammonium oxidation (anammox) process under antibiotic stress. The results showed that the bioaerosol oxidation potential increased by 2.7 times after the addition of sulfamethoxazole (SMX) into the anammox system. Based on the metagenomic analyses, abundant ARGs were enriched in bioaerosols, especially novA, olec, msbA and patA. There were many antibiotic resistance contigs carrying at least two mobile genetic elements (MGEs) in bioaerosols. Compared to the control, SMX caused the significant increase in ARGs proportion in plasmids from 11.4 % to 19.4 %. Similarly, the abundance of the type IV secretion system protein encoding genes (mtrA and mtrB) increased by 30.2 % and 31.5 %, respectively, which was conducive to gene transfer between bacteria. In addition, SMX stress induced the reactive oxygen species (ROS) production and the upregulation of genes related to membrane protein and DNA replication, further facilitating ARGs transfer. The co-occurrence networks showed that Aquamicrobium and Microbacterium probably were the hosts of most ARGs. Notably, four abundant human pathogens were detected in bioaerosols from the anammox system, which raised concerns on the health risk of resistant bioaerosol diffusion. These findings reveal the potential of horizontal gene transfer through bioaerosols and provide a guidance for systematically assessing the risk of environmental antibiotic resistance and relevant pathogens.

Insights into the effects of haze pollution on airborne bacterial communities and antibiotic resistance genes in fine particulate matter

Fine particulate matter (PM2.5) is a key component of haze pollution and poses a substantial threat to human health. However, airborne bacteria and antibiotic-resistance genes (ARGs), which are important biological components of PM2.5, have received less attention. In this study, we investigated the combined effects of haze on airborne bacteria and ARGs in PM2.5. Overall, during haze days, high concentrations of airborne bacteria (haze: 4782.24 ± 2689.85 cells/m3; non-haze: 2866.00 ± 1753.95 cells/m3) were observed with unique bacterial community structures. At the genus level, Microvirga, Arthrobacter, and JG30-KF-CM45 were identified as the bacterial biomarkers of haze days. Neutral processes contributed more to the establishment of airborne bacterial communities on haze days (R2 = 0.724) than that on non-hazy days (R2 = 0.338). The pathogenicity of bacterial communities per unit volume of air was significantly higher during haze days (169.36 ± 8.36 cell/m3) than that during non-haze days (112.66 ± 5.92 cell/m3) (p < 0.05). Redundancy analysis indicated that relatively stable atmospheric conditions and high concentrations of water-soluble ions (Na+, Mg2+, Ca2+, and F-), metals (Cd, As, Mn, and Cr), and carbonaceous fractions (elemental carbon) in PM2.5 play critical roles in shaping the bacterial community during haze days. On haze days, airborne ARGs exhibited unique distribution characteristics and network structures with dominant bacteria. This study highlighted the impact of haze days on airborne bacteria and ARGs on PM2.5 and provides a reference for managing the risks of bioaerosols.

From air to insight: the evolution of airborne DNA sequencing technologies

Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.

Emission Dynamics and Public Health Implications of Airborne Pathogens and Antimicrobial Resistance from Urban Waste Collection Facilities

Airborne pathogens and antimicrobial resistance (AMR) present significant global health threats. Household waste collection facilities (WCFs), crucial initial nodes in urban waste management systems, have been understudied in regards to their role in emitting these hazards. This study investigated the abundance, composition, sources, driving mechanisms, and health risks associated with pathogens and AMR originating from WCFs in a major city, using culture-based analysis, high-throughput sequencing, and health risk modeling, respectively. The atmospheric escape rates of culturable bacteria (43.4%), fungi (71.7%), and antibiotic-resistant bacteria (ARB) (43.7%) were estimated based on the concentration differences between the interior and exterior of the WCFs by using SourceTracker2 analysis. Health risk assessments showed that annual infection risks for waste-handling workers ranged from 0.194 to 0.489, far exceeding the World Health Organization's acceptable limit of 10-4. Community exposure risks were notable up to 220 m downwind from WCFs, marking the maximum extent of pathogen dispersion. Our analysis suggests that approximately 6.3% of the megacity's area (equivalent to 400 km2) is within potential risk zones influenced by WCF emissions. These results underscore the critical need to evaluate and mitigate the public health risks posed by airborne pathogens and AMR emitted from WCFs in megacities globally.

Airborne fungal communities are more susceptible to anthropogenic activities than bacteria

Airborne microorganisms (AM) have significant environmental and health implications. Extensive studies have been conducted to investigate the factors influencing the composition and diversity of AM. However, the knowledge of AM with anthropogenic activities has not reach a consensus. In this study, we took advantage of the dramatic decline of outdoor anthropogenic activities resulting from COVID-19 lockdown to reveal their associations. We collected airborne particulate matter before and during the lockdown period in two cities. The results showed that it was fungal diversity and communities but not bacteria obviously different between pre-lockdown and lockdown samples, suggesting that airborne fungi were more susceptible to anthropogenic activities than bacteria. However, after the implementation of lockdown, the co-occurrence networks of both bacterial and fungal community became more complex, which might be due to the variation of microbial sources. Furthermore, Mantel test and correlation analysis showed that air pollutants also partly contributed to microbial alterations. Airborne fungal community was more affected by air pollutants than bacterial community. Notably, some human pathogens like Nigrospora and Arthrinium were negatively correlated with air pollutants. Overall, our study highlighted the more impacts of anthropogenic activities on airborne fungal community than bacterial community and advanced the understanding of associations between anthropogenic activities and AM.

The dynamics and assembly patterns of airborne pathogen communities in the municipal food waste treatment system and its risk implications

While municipal solid waste (MSW) provides an ideal habitat for pathogen propagation, the dynamics and assembly of airborne pathogen communities in these environments remain largely unknown. Here, we combined amplicon and metagenomics with spatiotemporal sampling to study inhalable particulate matter-carried potential pathogenic bacteria at full-scale food waste treatment plants (FWTPs), alongside comparisons to urban air in the area. The results showed that pathogenic bacteria constituted a notable portion (64.5 % ± 20.6 %, n = 75) of the total bacterial communities in FWTPs-impacted air, with species and relative abundance 2-4 times higher than that of urban air, and contributed over 50 % of pathogens to the outdoor air. Airborne pathogen community structures were highly shaped by sampling sites (i.e. treatment units), but conserved across seasons (summer vs. winter) and particle sizes (PM2.5vs. PM10). Notably, Acinetobacter johnsonii-dominated pathogens (i.e. biofilm-related species) presented high levels of aerosolization and consistently occupied the upper-representative niches in all neutral models, highlighting their persistent exposure risk. Furthermore, pathogen community assembly was strongly driven by stochastic processes (58.8 %-96.8 %), while environmental variables explained only limited variations (3.4 %-28.7 %). In particular, the relative importance of stochastic processes clearly increased along an outdoor-to-indoor gradient (84.9 %-96.5 % vs. 71.3 %-76 %), which might be related to indoor anthropogenic activities that weaken microbial network stability and environmental filtering effects. This work enhances our knowledge of the dynamic behaviors and risk of airborne pathogen communities in MSW disposal and underscores the role of FWTPs in disseminating airborne pathogens.

A potential bioaerosol source from kitchen chimneys in restaurants

Bioaerosols are ubiquitous and have a substantial impact on the atmosphere and human health. Despite the identification of numerous bioaerosol emission sources, the contribution of anthropogenic sources remains inadequately understood. In kitchens, oil stains accumulated at the vent may discharge microorganisms into the environment with airflow, potentially discharging bioaerosol pollution. This putative anthropogenic source of bioaerosols has been long ignored. To investigated whether kitchen chimneys can be a potential source for bioaerosols, air samples, oil stains from in/out chimneys, and surface sand samples were collected near several commercial restaurants. PCoA showed that sampling sites significantly impacted microbiomes, whereas SourceTracker analysis led to the finding that waste grease significantly contributed to bioaerosol composition. Both findings agree with the kitchen chimney as a source of microbes in bioaerosols in the surrounding environment. Furthermore, despite the low biodiversity, a high proportion of stress-tolerant and potential pathogenic bacteria and fungi were found in residual culinary grease, which may escape into the air causing potential risks to human beings. These results led to the proposal that airborne microbiota can originate from cooking waste grease. Immediate actions should be taken into account to enhance disinfection and sterilization aimed at fume vents.

Beyond water and soil: Air emerges as a major reservoir of human pathogens

Assessing the risk of human pathogens in the environment is crucial for controlling the spread of diseases and safeguarding human health. However, conducting a thorough assessment of low-abundance pathogens in highly complex environmental microbial communities remains challenging. This study compiled a comprehensive catalog of 247 human-pathogenic bacterial taxa from global biosafety agencies and identified more than 78 million genome-specific markers (GSMs) from their 17,470 sequenced genomes. Subsequently, we analyzed these pathogens' types, abundance, and diversity within 474 shotgun metagenomic sequences obtained from diverse environmental sources. The results revealed that among the four habitats studied (air, water, soil, and sediment), the detection rate, diversity, and abundance of detectable pathogens in the air all exceeded those in the other three habitats. Air, sediment, and water environments exhibited identical dominant taxa, indicating that these human pathogens may have unique environmental vectors for their transmission or survival. Furthermore, we observed the impact of human activities on the environmental risk posed by these pathogens, where greater amounts of human activities significantly increased the abundance of human pathogenic bacteria, especially in water and air. These findings have remarkable implications for the environmental risk assessment of human pathogens, providing valuable insights into their presence and distribution across different habitats.

Seasonal distribution of human-to-human pathogens in airborne PM2.5 and their potential high-risk ARGs

Airborne microorganisms, an emerging global health threat, have attracted extensive studies. However, few attentions have been paid to the seasonal distribution of airborne pathogens, in particular their associations with antibiotic resistance genes (ARGs). To this end, two-week daily PM2.5 samples were consecutively collected from Nanchang in four seasons, and the human-to-human pathogens were screened based on high-throughput sequencing. The results showed that there were 20 pathogenic taxa in PM2.5 in Nanchang, and the highest relative abundance of pathogens was observed in winter (5.84%), followed by summer (3.51%), autumn (2.66%), and spring (1.80%). Although more than half of pathogenic taxa were shared by the four seasons, the analysis of similarities showed that pathogenic community was shaped by season (r = 0.16, p < 0.01). Co-occurrence network analysis disclosed significant interactions among pathogens in each season. Moreover, some dominant pathogens such as Plesiomonas shigelloides, Bacteroides fragilis, and Escherichia-Shigella were hub pathogens. In addition, PICRUSt2 predicted that there were 35 high-risk ARG subtypes in PM2.5, and the pathogens had strongly positive correlations with these ARGs. Even some pathogens like Plesiomonas shigelloides, Bacteroides fragilis, Aeromonas, Citrobacter, may be multi-drug resistant pathogens, including beta-lactam, aminoglycosides, chloramphenicol and multi-drug resistances, etc. Both air pollutants and meteorological conditions contributed to the seasonal variation of airborne pathogenic bacteria (r = 0.15, p < 0.01), especially CO, O3, PM2.5, temperature and relative humidity. This study furthers our understanding of airborne pathogens and highlights their associations with ARGs.

Diel variations of airborne microbes and antibiotic resistance genes in Response to urban PM2.5 chemical properties during the heating season

Among the components of fine particulate matter (PM2.5), the contributions of airborne microorganisms and antibiotic resistance genes (ARGs) to health risks have been overlooked. Airborne microbial dynamics exhibit a unique diurnal cycle due to environmental influences. However, the specific roles of PM2.5 chemical properties resulting from fossil fuel combustion in driving circadian fluctuations in microbial populations and ARGs remain unclear. This study explored the interactions between toxic components and microbial communities during the heating period to understand the variations in ARGs. Bacterial and fungal communities showed a higher susceptibility to diel variations in PM2.5 compared to their chemical properties. Mantel tests revealed that chemical properties and microbial community interactions contribute differently to ARG variations, both directly and indirectly, during circadian fluctuations. Our findings highlight that, during the daytime, the enrichment of pathogenic microorganisms and ARGs increases the risk of PM2.5 toxicity. Conversely, during the nighttime, the utilization of water-soluble ions by the fungal community increased, leading to a significant increase in fungal biomass. Notably, Aspergillus exhibited a significant correlation with mobile genetic elements and ARGs, implying that this genus is a crucial driver of airborne ARGs. This study provides novel insights into the interplay between the chemical composition, microbial communities, and ARGs in PM, underscoring the urgent need for a comprehensive understanding of effective air pollution control strategies.

Global diversity of airborne pathogenic bacteria and fungi from wastewater treatment plants

Wastewater treatment plants (WWTPs) have been recognized as one of the major potential sources of the spread of airborne pathogenic microorganisms under the global pandemic of COVID-19. The differences in research regions, wastewater treatment processes, environmental conditions, and other aspects in the existing case studies have caused some confusion in the understanding of bioaerosol pollution characteristics. In this study, we integrated and analyzed data from field sampling and performed a systematic literature search to determine the abundance of airborne microorganisms in 13 countries and 37 cities across four continents (Asia, Europe, North America, and Africa). We analyzed the concentrations of bioaerosols, the core composition, global diversity, determinants, and potential risks of airborne pathogen communities in WWTPs. Our findings showed that the culturable bioaerosol concentrations of global WWTPs are 102-105 CFU/m3. Three core bacterial pathogens, namely Bacillus, Acinetobacter, and Pseudomonas, as well as two core fungal pathogens, Cladosporium and Aspergillus, were identified in the air across global WWTPs. WWTPs have unique core pathogenic communities and distinct continental divergence. The sources of airborne microorganisms (wastewater) and environmental variables (relative humidity and air contaminants) have impacts on the distribution of airborne pathogens. Potential health risks are associated with the core airborne pathogens in WWTPs. Our study showed the specificity, multifactorial influences, and potential pathogenicity of airborne pathogenic communities in WWTPs. Our findings can improve the understanding of the global diversity and biogeography of airborne pathogens in WWTPs, guiding risk assessment and control strategies for such pathogens. Furthermore, they provide a theoretical basis for safeguarding the health of WWTP workers and ensuring regional ecological security.

The impact of bioaerosol trajectories on microbial community assembly and physicochemical dynamics in the atmosphere

This study explored the assembly mechanisms and physicochemical dynamics of microbial communities within atmospheric bioaerosols, focusing on the influence of different aerial trajectories. Over two years, samples near Seoul were classified into 'North', 'Southwest', and 'Others' categories based on their aerial trajectories. Physicochemical analysis of the PM2.5 particles revealed distinct ion compositions for each cluster, reflecting diverse environmental influences. Microbial community analysis revealed that shared dominant bacterial phyla were present in all clusters. However, distinct taxonomic profiles and biomarkers were also evident, such as coastal bacteria in the 'Southwest' cluster correlating with wind speed, and arid soil-originated bacteria in the 'North' cluster correlating with cations. These findings demonstrate that biomarkers in each cluster are representative of the distinct environments associated with their aerial trajectories. Notably, cluster 'Southwest' the highest microbial diversity and a strong alignment with the neutral community model, suggesting a large influence of passive dispersal from marine environments. Contrarily, 'North' and 'Others' were more influenced by niche-dependent factors. This study highlights the complex interplay between environmental factors and microbial dynamics in bioaerosols and provides important insights for environmental monitoring and public health risk assessment.

Antipathogenic Applications of Copper Nanoparticles in Air Filtration Systems

The COVID-19 pandemic has underscored the critical need for effective air filtration systems in healthcare environments to mitigate the spread of viral and bacterial pathogens. This study explores the utilization of copper nanoparticle-coated materials for air filtration, offering both antiviral and antimicrobial properties. Highly uniform spherical copper oxide nanoparticles (~10 nm) were synthesized via a spinning disc reactor and subsequently functionalized with carboxylated ligands to ensure colloidal stability in aqueous solutions. The functionalized copper oxide nanoparticles were applied as antipathogenic coatings on extruded polyethylene and melt-blown polypropylene fibers to assess their efficacy in air filtration applications. Notably, Type IIR medical facemasks incorporating the copper nanoparticle-coated polyethylene fibers demonstrated a >90% reduction in influenza virus and SARS-CoV-2 within 2 h of exposure. Similarly, heating, ventilation, and air conditioning (HVAC) filtration pre- (polyester) and post (polypropylene)-filtration media were functionalised with the copper nanoparticles and exhibited a 99% reduction in various viral and bacterial strains, including SARS-CoV-2, Pseudomonas aeruginosa, Acinetobacter baumannii, Salmonella enterica, and Escherichia coli. In both cases, this mitigates not only the immediate threat from these pathogens but also the risk of biofouling and secondary risk factors. The assessment of leaching properties confirmed that the copper nanoparticle coatings remained intact on the polymeric fiber surfaces without releasing nanoparticles into the solution or airflow. These findings highlight the potential of nanoparticle-coated materials in developing biocompatible and environmentally friendly air filtration systems for healthcare settings, crucial in combating current and future pandemic threats.

Polysaccharide preferred minority-dominant community assembly and exoenzyme enrichment in transparent exopolymer particles: Implication for global carbon cycle in water

The ubiquitous transparent exopolymer particles (TEPs) are an important organic carbon pool and an ideal microhabitat for bacteria in aquatic environments. They play a crucial role in the global carbon cycle. Organic matter transformation and carbon turnover in TEPs strongly depend on the assembly of their associated bacterial communities and enzyme activity. However, the mechanisms of bacterial community assembly and their potential effects on the organic carbon cycle in TEPs are still unclear. In this study, we comparatively explored the community assembly of TEP-associated bacteria and bacterioplankton from surface freshwater using metagenomics. It was found that the bacterial community assembly in TEPs followed a minority-dominant rule and was governed by homogeneous selection. Pseudomonadota and Actinomycetota, which are responsible for polysaccharide degradation, serve as taxon-specific biomarkers among the abundant and diverse bacteria in TEPs. The network of TEP-associated bacteria displayed stronger robustness than that of bacterioplankton. Bin 76 (majorly Acinetobacter) was the overwhelmingly dominant taxa in TEPs, whereas there was no clearly dominant taxa in TEP-free water. Exoenzyme analysis showed that 64 out of 71 identified polysaccharide hydrolases were markedly linked with the dominant bin 76 in TEPs, while no such linkage was observed for bacterioplankton. Generally, Acinetobacter, which is capable of utilizing polysaccharides, is preferred to be assembled in TEPs together with high polysaccharide hydrolase activity. This may significantly accelerate the turnover of organic carbon in the giant global TEP pool. These findings are important for a deep understanding of the carbon cycle in water.

Alternations of antibiotic resistance genes and microbial community dynamics on shared bicycles before and after pandemic lockdown

The prevalence of shared bicycles has raised concerns over their potential to transmit pathogens and microbes harboring antibiotic resistance genes (ARGs), which pose significant human health risks. This study investigated the impact of anthropogenic activities on the composition of ARGs and microbial communities on shared bicycles during the COVID-19 pandemic and subsequent lockdown when shared bicycle usage was altered. A total of 600 swab samples from shared bicycle surfaces were collected in Shanghai before and during COVID-19 lockdown periods. Even during lockdown, 12 out of 14 initially detected ARG subtypes persisted, indicating their tenacity in the face of reduced anthropogenic activities. These ARGs displayed significantly higher absolute and relative abundance levels before the lockdown. In addition, the percentage of potential pathogens in the total microbial abundance remained at 0.029 % during the lockdown, which was lower than the pre-lockdown percentage of 0.035 % and suggested that these risks persist within shared bicycle systems. Interestingly, although microbial abundance decreased without the consecutive use of shared bicycles during lockdown, the microbial diversity increased under the impact of restricted anthropogenic activities (p < 0.001). This emphasizes the need for continuous monitoring and research to comprehend microbial community behaviors in various environments. This study uncovered the underlying impacts of the COVID-19 lockdown on the microbial and ARG communities of shared bicycles, providing comprehensive insights into the health management of shared transportation. Although lockdown can decrease the abundance of ARGs and potential pathogens, additional interventions are needed to prevent their continued spread.

Anthropogenic impact on airborne bacteria of the Tibetan Plateau

The Tibetan Plateau is a pristine environment with limited human disturbance, with its aerosol microbiome being primarily influenced by the monsoon and westerly circulations. Additionally, the diversity and abundance of airborne microorganisms are also affected by anthropogenic activities, such as animal farming, agriculture, and tourism, which can lead to increased risks to the ecosystem and human health. However, the impact of anthropogenic activities on airborne microbes on the Tibetan Plateau has been rarely studied. In this work, we investigated the airborne bacteria of areas with weak (rural glacier) and strong human disturbance (urban building), and found that anthropogenic activities increased the diversity of airborne bacteria, and the concentration of potential airborne pathogens. Moreover, airborne bacteria in rural aerosols demonstrated significant differences in their community structure during monsoon- and westerly-affected seasons, while this pattern was weakened in urban aerosols. Additionally, urban aerosols enriched Lactobacillus sp. (member of genus Lactobacillus), which are potential pathogens from anthropogenic sources, whereas rural aerosols enriched A. calcoaceticus (member of genus Acinetobacter) and E. thailandicus (member of genus Enterococcus), which are both speculated to be sourced from surrounding animal farming. This study evaluated the impact of human activities on airborne bacteria in the Tibetan Plateau and contributed to understanding the enrichment of airborne pathogens in natural and anthropogenic background.

Dynamic human exposure to airborne bacteria-associated antibiotic resistomes revealed by longitudinal personal monitoring data

Airborne antibiotic-resistant bacteria (ARB) can critically impact human health. We performed resistome profiling of 283 personal airborne exposure samples from 15 participants spanning 890 days and 66 locations. We found a greater diversity and abundance of airborne bacteria community and antibiotic resistomes in spring than in winter, and temperature contributed largely to the difference. A total of 1123 bacterial genera were detected, with 16 genera dominating. Of which, 7/16 were annotated as major antibiotic resistance gene (ARG) hosts. The participants were exposed to a highly dynamic collection of ARGs, including 322 subtypes conferring resistance to 18 antibiotic classes dominated by multidrug, macrolide-lincosamide-streptogramin, β-lactam, and fosfomycin. Unlike the overall community-level bacteria exposure, an extremely high abundance of specific ARG subtypes, including lunA and qacG, were found in some samples. Staphylococcus was the predominant genus in the bacterial community, serving as a primary bacterial host for the ARGs. The annotation of ARG-carrying contigs indicated that humans and companion animals were major reservoirs for ARG-carrying Staphylococcus. This study contextualized airborne antibiotic resistomes in the precision medicine framework through longitudinal personal monitoring, which can have broad implications for human health.

Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity

Urban microbiome plays crucial roles in human health and are related to various diseases. The MetaSUB Consortium has conducted the most comprehensive global survey of urban microbiomes to date, profiling microbial taxa/functional genes across 60 cities worldwide. However, the influence of environmental/demographic factors on urban microbiome remains to be elucidated. We collected 35 environmental and demographic characteristics to examine their effects on global urban microbiome diversity/composition by PERMANOVA and regression models. PM10 concentration was the primary determinant factor positively associated with microbial α-diversity (observed species: p = 0.004, β = 1.66, R2 = 0.46; Fisher's alpha: p = 0.005, β = 0.68, R2 = 0.43), whereas GDP per capita was negatively associated (observed species: p = 0.046, β = -0.70, R2 = 0.10; Fisher's alpha: p = 0.004, β = -0.34, R2 = 0.22). The β-diversity of urban microbiome was shaped by seven environmental characteristics, including Köppen climate type, vegetation type, greenness fraction, soil type, PM2.5 concentration, annual average precipitation and temperature (PERMANOVA, p < 0.001, R2 = 0.01-0.06), cumulatively accounted for 20.3% of the microbial community variance. Canonical correspondence analysis (CCA) identified microbial species most strongly associated with environmental characteristic variation. Cities in East Asia with higher precipitation showed an increased abundance of Corynebacterium metruchotii, and cities in America with a higher greenness fraction exhibited a higher abundance of Corynebacterium casei. The prevalence of antimicrobial resistance (AMR) genes were negatively associated with GDP per capita and positively associated with solar radiation (p < 0.005). Total pathogens prevalence was positively associated with urban population and negatively associated with average temperature in June (p < 0.05). Our study presents the first comprehensive analysis of the influence of environmental/demographic characteristics on global urban microbiome. Our findings indicate that managing air quality and urban greenness is essential for regulating urban microbial diversity and composition. Meanwhile, socio-economic considerations, particularly reducing antibiotic usage in regions with lower GDP, are paramount in curbing the spread of antimicrobial resistance in urban environments.

Respirable Metals, Bacteria, and Fungi during a Saharan-Sahelian Dust Event in Houston, Texas

Although airborne bacteria and fungi can impact human, animal, plant, and ecosystem health, very few studies have investigated the possible impact of their long-range transport in the context of more commonly measured aerosol species, especially those present in an urban environment. We report first-of-kind simultaneous measurements of the elemental and microbial composition of North American respirable airborne particulate matter concurrent with a Saharan-Sahelian dust episode. Comprehensive taxonomic and phylogenetic profiles of microbial communities obtained by 16S/18S/ITS rDNA sequencing identified hundreds of bacteria and fungi, including several cataloged in the World Health Organization's lists of global priority human pathogens along with numerous other animal and plant pathogens and (poly)extremophiles. While elemental analysis sensitively tracked long-range transported Saharan dust and its mixing with locally emitted aerosols, microbial diversity, phylogeny, composition, and abundance did not well correlate with the apportioned African dust mass. Bacterial/fungal diversity, phylogenetic signal, and community turnover were strongly correlated to apportioned sources (especially vehicular emissions and construction activities) and elemental composition (especially calcium). Bacterial communities were substantially more dissimilar from each other across sampling days than were fungal communities. Generalized dissimilarity modeling revealed that daily compositional turnover in both communities was linked to calcium concentrations and aerosols from local vehicles and Saharan dust. Because African dust is known to impact large areas in northern South America, the Caribbean Basin, and the southern United States, the microbiological impacts of such long-range transport should be assessed in these regions.

Fungal endophyte promotes plant growth and disease resistance of Arachis hypogaea L. by reshaping the core root microbiome under monocropping conditions

Fungal endophytes play critical roles in helping plants adapt to adverse environmental conditions. The root endophyte Phomopsis liquidambaris can promote the growth and disease control of peanut plants grown under monocropping systems; however, how such beneficial traits are produced is largely unknown. Since the plant endophytic microbiome is directly linked to plant growth and health, and the composition of which has been found to be potentially influenced by microbial inoculants, this study aims to clarify the roles of root endophytic bacterial communities in P. liquidambaris-mediated plant fitness enhancement under monocropping conditions. Here, we found that P. liquidambaris inoculation induced significant changes in the root bacterial community: enriching some beneficial bacteria such as Bradyrhizobium sp. and Streptomyces sp. in the roots, and improving the core microbial-based interaction network. Next, we assembled and simplified a synthetic community (SynII) based on P. liquidambaris-derived key taxa, including Bacillus sp. HB1, Bacillus sp. HB9, Burkholderia sp. MB7, Pseudomonas sp. MB2, Streptomyces sp. MB6, and Bradyrhizobium sp. MB15. Furthermore, the application of the simplified synthetic community suppressed root rot caused by Fusarium oxysporum, promoted plant growth, and increased peanut yields under continuous monocropping conditions. The resistance of synII to F. oxysporum is related to the increased activity of defense enzymes. In addition, synII application significantly increased shoot and root biomass, and yield by 35.56%, 81.19%, and 34.31%, respectively. Collectively, our results suggest that the reshaping of root core microbiota plays an important role in the probiotic-mediated adaptability of plants under adverse environments.

Complex temperature dependence of vehicular emissions: Evidence from a global meta-analysis

The significant impact of low ambient temperature, which was less regulated, on vehicle exhaust emissions had garnered considerable attention. This study investigated the impact of ambient temperature on exhaust emissions based on the global meta-analysis. The estimated sizes (mean difference, MDt) of 11 exhaust pollutants were quantified with 1795 observations at low ambient temperatures (LATs, -18 °C to -7 °C) versus warm ambient temperatures (WATs, 20 °C-30 °C). The results indicated a strong and positive effect of LATs on vehicular emissions, with the average ratio of vehicular emission factors at LATs to those at WATs (EFLAT/EFWAT) ranging from 1.14 to 3.84. Oil-based subgroup analysis indicated a quite large MDt [NOx] of diesel engines (12.42-15.10 mg km-1·k-1). Particulate emissions were 0.22-1.41 mg km-1·k-1 enhanced during cold-start tests at LATs. The application of particulate filters on motor vehicles greatly reduced the impact of ambient temperature on tailpipe particulate emissions, at the expense of induced NOx emissions. During the Federal Test Procedure (FTP-75), exhaust emissions showed higher temperature dependence compared to the averaged levels (1.31-39.31 times). Locally weighted regression was used to determine exhaust temperature profiles, revealing that gasoline vehicles emitted more particulates at LATs, while diesel vehicles showed the opposite trend. Given the widespread use of motor vehicles worldwide, future motor vehicle emission standards should include tighter limits on exhaust emissions at LATs.

Metagenomic and Machine Learning Meta-Analyses Characterize Airborne Resistome Features and Their Hosts in China Megacities

Urban ambient air contains a cocktail of antibiotic resistance genes (ARGs) emitted from various anthropogenic sites. However, what is largely unknown is whether the airborne ARGs exhibit site-specificity or their pathogenic hosts persistently exist in the air. Here, by retrieving 1.2 Tb metagenomic sequences (n = 136), we examined the airborne ARGs from hospitals, municipal wastewater treatment plants (WWTPs) and landfills, public transit centers, and urban sites located in seven of China's megacities. As validated by the multiple machine learning-based classification and optimization, ARGs' site-specificity was found to be the most apparent in hospital air, with featured resistances to clinical-used rifamycin and (glyco)peptides, whereas the more environmentally prevalent ARGs (e.g., resistance to sulfonamide and tetracycline) were identified being more specific to the nonclinical ambient air settings. Nearly all metagenome-assembled genomes (MAGs) that possessed the site-featured resistances were identified as pathogenic taxa, which occupied the upper-representative niches in all the neutrally distributed airborne microbial community (P < 0.01, m = 0.22-0.50, R2 = 0.41-0.86). These niche-favored putative resistant pathogens highlighted the enduring antibiotic resistance hazards in the studied urban air. These findings are critical, albeit the least appreciated until our study, to gauge the airborne dimension of resistomes' features and fates in urban atmospheric environments.

From air to airway: Dynamics and risk of inhalable bacteria in municipal solid waste treatment systems

Municipal solid waste treatment (MSWT) system emits a cocktail of microorganisms that jeopardize environmental and public health. However, the dynamics and risks of airborne microbiota associated with MSWT are poorly understood. Here, we analyzed the bacterial community of inhalable air particulates (PM10, n = 71) and the potentially exposed on-site workers' throat swabs (n = 30) along with waste treatment chain in Shanghai, the largest city of China. Overall, the airborne bacteria varied largely in composition and abundance during the treatment (P < 0.05), especially in winter. Compared to the air conditions, MSWT-sources that contributed to 15 ∼ 70% of airborne bacteria more heavily influenced the PM10-laden bacterial communities (PLS-SEM, β = 0.40, P < 0.05). Moreover, our year-span analysis found PM10 as an important media spreading pathogens (104 ∼ 108 copies/day) into on-site workers. The machine-learning identified Lactobacillus and Streptococcus as pharynx-niched featured biomarker in summer and Rhodococcus and Capnocytophaga in winter (RandomForest, ntree = 500, mtry = 10, cross = 10, OOB = 0%), which closely related to their airborne counterparts (Procrustes test, P < 0.05), suggesting that MSWT a dynamic hotspot of airborne bacteria with the pronounced inhalable risks to the neighboring communities.

Augmented dissemination of antibiotic resistance elicited by non-antibiotic factors

The emergence and rapid spread of antibiotic resistance seriously compromise the clinical efficacy of current antibiotic therapies, representing a serious public health threat worldwide. Generally, drug-susceptible bacteria can acquire antibiotic resistance through genetic mutation or gene transfer, among which horizontal gene transfer (HGT) plays a dominant role. It is widely acknowledged that the sub-inhibitory concentrations of antibiotics are the key drivers in promoting the transmission of antibiotic resistance. However, accumulating evidence in recent years has shown that in addition to antibiotics, non-antibiotics can also accelerate the horizontal transfer of antibiotic resistance genes (ARGs). Nevertheless, the roles and potential mechanisms of non-antibiotic factors in the transmission of ARGs remain largely underestimated. In this review, we depict the four pathways of HGT and their differences, including conjugation, transformation, transduction and vesiduction. We summarize non-antibiotic factors accounting for the enhanced horizontal transfer of ARGs and their underlying molecular mechanisms. Finally, we discuss the limitations and implications of current studies.

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.

Perspectives on Sampling and New Generation Sequencing Methods for Low-Biomass Bioaerosols in Atmospheric Environments

Bioaerosols play essential roles in the atmospheric environment and can affect human health. With a few exceptions (e.g., farm or rainforest environments), bioaerosol samples from wide-ranging environments typically have a low biomass, including bioaerosols from indoor environments (e.g., residential homes, offices, or hospitals), outdoor environments (e.g., urban or rural air). Some specialized environments (e.g., clean rooms, the Earth's upper atmosphere, or the international space station) have an ultra-low-biomass. This review discusses the primary sources of bioaerosols and influencing factors, the recent advances in air sampling techniques and the new generation sequencing (NGS) methods used for the characterization of low-biomass bioaerosol communities, and challenges in terms of the bias introduced by different air samplers when samples are subjected to NGS analysis with a focus on ultra-low biomass. High-volume filter-based or liquid-based air samplers compatible with NGS analysis are required to improve the bioaerosol detection limits for microorganisms. A thorough understanding of the performance and outcomes of bioaerosol sampling using NGS methods and a robust protocol for aerosol sample treatment for NGS analysis are needed. Advances in NGS techniques and bioinformatic tools will contribute toward the precise high-throughput identification of the taxonomic profiles of bioaerosol communities and the determination of their functional and ecological attributes in the atmospheric environment. In particular, long-read amplicon sequencing, viability PCR, and meta-transcriptomics are promising techniques for discriminating and detecting pathogenic microorganisms that may be active and infectious in bioaerosols and, therefore, pose a threat to human health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s41745-023-00380-x.

About the Biodiversity of the Air Microbiome

This brief review focuses on the properties of bioaerosols, presenting some recent results of metagenomic studies of the air microbiome performed using next-generation sequencing. The taxonomic composition and structure of the bioaerosol microbiome may display diurnal and seasonal dynamics and be dependent on meteorological events such as dust storms, showers, fogs, etc., as well as air pollution. The Proteobacteria and Ascomycota members are common dominants in bioaerosols in different troposphere layers. The microbiological composition of the lower troposphere air affects the composition and diversity of the indoor bioaerosol microbiome, and information about the latter is very important, especially during exacerbated epidemiological situations. Few studies focusing on the bioaerosol microbiome of the air above Russia urge intensification of such research.