Virus-induced changes in root volatiles attract soil nematode vectors to infected plants.

Plant-derived volatiles mediate interactions among plants, pathogenic viruses, and viral vectors. These volatile-dependent mechanisms have not been previously demonstrated belowground, despite their likely significant role in soil ecology and agricultural pest impacts. We investigated how the plant virus, tobacco rattle virus (TRV), attracts soil nematode vectors to infected plants. We infected Nicotiana benthamiana with TRV and compared root growth relative to that of uninfected plants. We tested whether TRV-infected N. benthamiana was more attractive to nematodes 7 d post infection and identified a compound critical to attraction. We also infected N. benthamiana with mutated TRV strains to identify virus genes involved in vector nematode attraction. Virus titre and associated impacts on root morphology were greatest 7 d post infection. Tobacco rattle virus infection enhanced 2-ethyl-1-hexanol production. Nematode chemotaxis and 2-ethyl-1-hexanol production correlated strongly with viral load. Uninfected plants were more attractive to nematodes after the addition of 2-ethyl-1-hexanol than were untreated plants. Mutation of TRV RNA2-encoded genes reduced the production of 2-ethyl-1-hexanol and nematode attraction. For the first time, this demonstrates that virus-driven alterations in root volatile emissions lead to increased chemotaxis of the virus's nematode vector, a finding with implications for sustainable management of both nematodes and viral pathogens in agricultural systems.

Long-term seawall barriers lead to the formation of an urban coastal lagoon with increased antibiotic resistome.

Urbanization has increased the spread of antibiotic resistance genes (ARGs) impacting urban aquatic ecosystems and threatening human health. However, an overview of the antibiotic resistome in artificial coastal lagoons formed by coastal seawall construction is unclear. This study investigated the resistome of sediment in a coastal lagoon, established for over 60 years and found that the composition of the resistome in the lagoon sediments associated with the seawall significantly differed from that of marine sediment external to the seawall. Moreover, the diversity, number, relative abundance, and absolute abundance of the antibiotic resistome in the lagoon sediments were significantly higher compared to marine sediment. Network analyses revealed that more co-occurrences were found in lagoon sediment between bacterial communities, ARGs and mobile genetic elements (MGEs) than in marine sediments, suggesting that bacteria in lagoon sediments may be associated with multiple antibiotic resistances. Random forest and structural equation models showed that an increase in the absolute abundance of MGEs had a concomitant effect on the absolute abundance and diversity of ARGs, whereas increasing salinity decreased the absolute abundance of ARGs. This study provides a basis to assess the risk of resistome diffusion and persistence in an artificial coastal lagoon.

Phagotrophic protists preserve antibiotic-resistant opportunistic human pathogens in the vegetable phyllosphere.

Food safety of leafy greens is an emerging public health issue as they can harbor opportunistic human pathogens (OHPs) and expose OHPs to consumers. Protists are an integral part of phyllosphere microbial ecosystems. However, our understanding of protist-pathogen associations in the phyllosphere and their consequences on public health remains poor. Here, we examined phyllosphere protists, human pathogen marker genes (HPMGs), and protist endosymbionts from four species of leafy greens from major supermarkets in Xiamen, China. Our results showed that Staphylococcus aureus and Klebsiella pneumoniae were the dominant human pathogens in the vegetable phyllosphere. The distribution of HPMGs and protistan communities differed between vegetable species, of which Chinese chive possessed the most diverse protists and highest abundance of HPMGs. HPMGs abundance positively correlated with the diversity and relative abundance of phagotrophic protists. Whole genome sequencing further uncovered that most isolated phyllosphere protists harbored multiple OHPs which carried antibiotic resistance genes, virulence factors, and metal resistance genes and had the potential to HGT. Colpoda were identified as key phagotrophic protists which positively linked to OHPs and carried diverse resistance and virulence potential endosymbiont OHPs including Pseudomonas nitroreducens, Achromobacter xylosoxidans, and Stenotrophomonas maltophilia. We highlight that phyllosphere protists contribute to the transmission of resistant OHPs through internalization and thus pose risks to the food safety of leafy greens and human health. Our study provides insights into the protist-OHP interactions in the phyllosphere, which will help in food safety surveillance and human health.

Movement of protistan trophic groups in soil-plant continuums.

Protists, functionally divided into consumers, phototrophs, and parasites act as integral components and vital regulators of microbiomes in soil-plant continuums. However, the drivers of community structure, assembly mechanisms, co-occurrence patterns, and the associations with human pathogens and different protistan trophic groups remain unknown. Here, we characterized the phyllosphere and soil protistan communities associated with three vegetables under different fertilization treatments (none and organic fertilization) at five growth stages. In this study, consumers were the most diverse soil protist group, had the role of inter-kingdom connector, and were the primary biomarker for rhizosphere soils which were subjected to decreasing deterministic processes during plant growth. In contrast, phototrophs had the greatest niche breadth and formed soil protistan hubs, and were the primary biomarkers for both bulk soils and the phyllosphere. Parasites had minimal input to microbial co-occurrence networks. Organic fertilization increased the relative abundance (RA) of pathogenic protists and the number of pathogen-consumer connections in rhizosphere soils but decreased protistan richness and the number of internal protistan links. This study advances our understanding of the ecological roles and potential links between human pathogens and protistan trophic groups associated with soil-plant continuums, which is fundamental to the regulation of soil-plant microbiomes and maintenance of environmental and human health.

Acidity of Soil and Water Decreases in Acid-Sensitive Forests of Tropical China.

Acid deposition in China has been declining since the 2000s. While this may help mitigate acidification in forest soils and water, little is known about the recovery of soils and water from previous severe acidification in tropical China. Here, we assessed the chemistry of mineral soils, water, and acid gases (SO2 and NOx) from three successional forest types in tropical China from 2000 to 2022. Our results showed that soil pH increased synchronously from 3.9 (2000-2015) to 4.2 (2016-2022) across all three forest types, with exchangeable acid initially decreasing and thereafter stabilizing. Surface and ground water pH also gradually increased throughout the monitoring period. Soil pH recovery was stronger in the primary than in the planted forest. However, soil pH recovery lagged behind the increase in rainfall pH by approximately a decade. The recovery of soil pH was likely related to the positive effects of the dissolution of Al/Fe-hydroxysulfate mineral and subsequent sulfur desorption on soil acid-neutralizing capacity, increased soil organic matter, and climate warming, but was likely moderated by increased exchangeable aluminum and potentially proton-producing hydroxysulfate mineral dissolution that caused the lagged soil pH recovery. Surface and ground water pH recovery was attributed to increased water acid-neutralizing capacity. Our study reports the potential for the recovery of acidified soil and water following decreased acid deposition and provides new insights into the functional recovery of acid-sensitive forests.

Distinct patterns of the soil and phyllosphere antibiotic resistome in natural forest ecosystems under an altitudinal gradient.

Warming affects microbial functioning of soil and the phyllosphere across global ecosystems. However, little is known about the impact of increasing temperature on antibiotic resistome profiles in natural forests. To address this issue, we investigated antibiotic resistance genes (ARGs) in both soil and the plant phyllosphere using an experimental platform established in a forest ecosystem that delivers a temperature difference of 2.1 °C along an altitudinal gradient. Principal Coordinate Analysis (PCoA) showed that there were significant differences in the composition of soil and plant phyllosphere ARGs at different altitudes (P = 0.001). The relative abundance of phyllosphere ARGs and mobile genetic elements (MGEs) and soil MGEs increased with temperature. More resistance gene classes increased in abundance in the phyllosphere (10 classes) than soil (2 classes), and a Random Forest model analysis suggested that phyllosphere ARGs were more sensitive to temperature change than soil. Increasing temperature as a direct consequence of an altitudinal gradient, and the relative abundance of MGEs were the main drivers that shaped the profiles of ARGs in the phyllosphere and soil. Biotic and abiotic factors affected phyllosphere ARGs indirectly via MGEs. This study enhances our understanding of the influence of altitude gradients on resistance genes in natural environments.

Urban greenspace types influence the microbial community assembly and antibiotic resistome more in the phyllosphere than in the soil.

Urban greenspace (UGS) is recognized to confer significant societal benefits, but few studies explored the microbial communities and antibiotic resistance genes (ARGs) from different urban greenspace types. Here, we collected leaf and soil samples from forest, greenbelt, and parkland to analyze microbial community assembly and ARG profile. For phyllosphere fungal community, the α-diversity was higher in forest, compared to those in greenbelt and parkland. Moreover, urban greenspace types altered the community assembly. Stochastic processes had a greater effect on phyllosphere fungal community in greenbelt and parkland, while in forest they were dominated by deterministic processes. In contrast, no significant differences in bacterial community diversity, community assembly were observed between the samples collected from different urban greenspace types. A total of 153 ARGs and mobile genetic elements (MGEs) were detected in phyllosphere and soil with resistance to the majority classes of antibiotics commonly applied to humans and animals. Structural equation model further revealed that a direct association between greenspace type and ARGs in the phyllosphere even after considering the effects of all other factors simultaneously. Our findings provide new insights into the microbial communities and antibiotic resistome of urban greenspaces and the potential risk linked with human health.

Antibiotic resistome in groundwater and its association with mountain springs and river.

The distribution of antibiotic resistance genes (ARGs) in water sources potentially threatens drinking water safety. However, the sources of antibiotic resistome in groundwater are still under-investigated. Here, we evaluated the profiles of antibiotic resistome in peri-urban groundwater and its associated water sources (river and mountain spring) to characterize the antibiotic resistome from natural water sources on groundwater resistome. A total of 261 antibiotic resistome were detected in groundwater, mountain spring, and river samples. The relative abundances of ARGs and mobile genetic elements (MGEs) were significantly higher in the river samples than in spring water and groundwater samples. The resistome profiles were similar between groundwater and spring water but differed from the river samples. According to source tracking results, the groundwater resistome was likely to be derived from springs (28.0%-50.0%) and rivers (28.6%-48.6%), which share the same trend for the source tracking of bacterial communities. Bacterial α-diversity, bacterial ß-diversity, and MGEs directly or indirectly affected the ARGs in groundwater samples. Although the abundance of groundwater resistome was not elevated by river and spring water, groundwater resistomes were diverse and may be derived from both river and spring water. We highlight the importance of groundwater resistome and its association with potential water sources, providing a better understanding and basis for the effective control of the ARG proliferation and dissemination in groundwater from exogenous water bodies in the future.

Characterization of microbial community, ecological functions and antibiotic resistance in estuarine plastisphere.

The plastisphere is a new ecological niche. Compared to the surrounding water, microbial community composition associated with the plastisphere is known to differ with functional consequences. Here, this study characterized the bacterial and fungal communities associated with four types of plastisphere (polyethylene, polystyrene, polypropylene and polyvinyl chloride) in an estuarine habitat; assessed ecological functions including carbon, nitrogen, phosphorus and sulfur cycling, and determined the presence of antibiotic resistance genes (ARGs) and human pathogens. Stochastic processes dominated the community assembly of microorganisms on the plastisphere. Several functional genera related to nutrient cycling were enriched in the plastisphere. Compared to surrounding water and other plastisphere, the abundances of carbon, nitrogen and phosphorus cycling genes (cdaR, nosZ and chpy etc.) and ARGs (aadA2-1, cfa and catB8 etc.) were significantly increased in polyvinyl chloride plastisphere. In contrast, the polystyrene plastisphere was the preferred substrate for several pathogens being enriched with for example, Giardia lamblia 18S rRNA, Klebsiella pneumoniae phoE and Legionella spp. 23S rRNA. Overall, this study showed that different plastisphere had different effects on ecological functions and health risk in estuaries and emphasizes the importance of controlling plastic pollution in estuaries. Data from this study support global policy drivers that seek to reduce plastic pollution and offer insights into ecological functions in a new ecological niche of the Anthropocene.

Plant identity shapes phyllosphere microbiome structure and abundance of genes involved in nutrient cycling.

The phyllosphere is a fluctuant micro-environment habitat that harbors diverse microbial communities that have the potential to influence plant growth through their effect on host fitness. However, we know little about the driving factors of phyllosphere microbial functional traits, e.g., genes related to nutrient cycling and microbial community structure under anthropic disturbance. Here, we characterized phyllosphere microbial communities and the abundance of genes related to nutrient cycling from diverse plant species between urban and natural habitats. We measured leaf functional traits to investigate the potential drivers of the phyllosphere microbial profile. Results indicated that phyllosphere microbial communities differed significantly between urban and natural habitats, and that this variation was dependent upon plant species. Host plant species had a greater influence on the abundance of genes involved in nutrient cycling in the phyllosphere than habitat. In addition, phyllosphere microbial diversity and functional gene abundance were significantly correlated. Furthermore, host leaf functional traits (e.g., specific leaf area and nutrient content) were potential driving factors of both phyllosphere microbial community structure and the abundance of genes involved in nutrient cycling. These findings contribute to a better understanding of the phyllosphere microbiome and its biotic and abiotic controlling factors, which improves our understanding of plant-microbe interactions and their ecosystem functions under anthropic disturbance.

Distinct patterns of soil bacterial and fungal community assemblages in subtropical forest ecosystems under warming.

Climate change globally affects soil microbial community assembly across ecosystems. However, little is known about the impact of warming on the structure of soil microbial communities or underlying mechanisms that shape microbial community composition in subtropical forest ecosystems. To address this gap, we utilized natural variation in temperature via an altitudinal gradient to simulate ecosystem warming. After 6 years, microbial co-occurrence network complexity increased with warming, and changes in their taxonomic composition were asynchronous, likely due to contrasting community assembly processes. We found that while stochastic processes were drivers of bacterial community composition, warming led to a shift from stochastic to deterministic drivers in dry season. Structural equation modelling highlighted that soil temperature and water content positively influenced soil microbial communities during dry season and negatively during wet season. These results facilitate our understanding of the response of soil microbial communities to climate warming and may improve predictions of ecosystem function of soil microbes in subtropical forests.

Skin microbiota interact with microbes on office surfaces.

The indoor environment is recognized as a potential contributor to human health impacts through resident microbiomes. Indoor surface microbial communities are formed from several sources, environmental and anthropogenic. In this study, we characterized the bacterial and fungal communities from various sources typical of a working office environment including dust, fingers, and computer keyboards and mice. The composition of the dust bacterial community was significantly different from the other tested surfaces (P < 0.05), whereas the dust fungal community was only significantly different from fingers (P < 0.05). Bacterial and fungal communities were both shaped by deterministic processes, and bacterial communities had a higher migration rate. Results of a network analysis showed that the microbial community interactions of keyboards and mice were mainly competitive. Fast expectation-maximization microbial source tracking (FEAST) identified the sources of > 70 % of the keyboard and mouse microbial communities. Biomarkers for each sample types were identified by LDA Effect Size (LEfSE) analysis, some of which were soil-derived and potential anthropogenic pathogens, indicating the potential for exchange of microbes among outdoor, human and indoor surfaces. The current study shows that the source of microorganisms at the office interface is highly traceable and that their migration is linked to human activity. The migration of potentially pathogenic microbes were identified, emphasising the importance of personal hygiene.

Does Plant Identity Affect the Dispersal of Resistomes Above and Below Ground?

Resistomes are ubiquitous in natural environments. Previous studies have shown that both the plant phyllosphere and soil-borne nematodes were reservoirs of above- and below-ground resistomes, respectively. However, the influence of plant identity on soil, nematode, and phyllosphere resistomes remains unclear. Here, a microcosm experiment was used to explore the characteristics of bacterial communities and resistomes in soil, nematode, and phyllosphere associated with six different plant identities (Lactuca sativa, Cichorium endivia, Allium fistulosum, Coriandrum sativum, Raphanus sativus, and Mesembryanthemum crystallinum). A total of 222 antibiotic resistance genes (ARGs) and 7 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR from all samples. Plant identity not only significantly affected the diversity of resistomes in soil, nematode, and phyllosphere but also influenced the abundance of resistomes in nematodes. Shared bacteria and resistomes indicated a possible pathway of resistomes transfer through the soil-nematode-phyllosphere system. Structural equation models revealed that plant identity had no direct effect on phyllosphere ARGs, but altered indirectly through complex above- and below-ground interactions (soil-plant-nematode trophic transfer). Results also showed that bacteria and MGEs were key factors driving the above- and below-ground flow of resistomes. The study extends our knowledge about the top-down and bottom-up dispersal patterns of resistomes.

Pollen season trends as markers of climate change impact: Betula, Quercus and Poaceae.

The incidences of respiratory allergies are at an all-time high. Pollen aeroallergens can reflect changing climate, with recent studies in Europe showing some, but not all, pollen types are increasing in severity, season duration and experiencing an earlier onset. This study aimed to identify pollen trends in the UK over the last twenty-six years for a range of pollen sites, with a focus on the key pollen types of Poaceae (grass), Betula (birch) and Quercus (oak) and to examine the relationship of these trends with meteorological factors. Betula pollen seasons show no significant trends for onset, first high day or duration but increasing pollen production in the Midlands region of the UK is being driven by warmer temperatures in the previous June and July. Quercus pollen seasons are starting earlier, due to increasing temperature and sunshine totals in April, but are not becoming more severe. The seasons are lasting longer, although no significant climate drivers for this were identified. The first high day of the Poaceae pollen season is occurring earlier in central UK regions due to an increasing trend for all temperature variables in the previous December, January, April, May and June. Severity and duration of the season show no significant trends and are spatially and temporally variable. Important changes are occurring in the UK pollen seasons that will impact on the health of respiratory allergy sufferers, with more severe Betula pollen seasons and longer Quercus pollen seasons. Most of the changes identified were caused by climate drivers of increasing temperature and sunshine total. However, Poaceae pollen seasons are neither becoming more severe nor longer. The reasons for this included a lack of change in some monthly meteorological variables, or land-use change, such as grassland being replaced by urban areas or woodland.

Conurbation size drives antibiotic resistance along the river.

With growing concerns about antibiotic resistance, the tracking of antibiotic resistance genes (ARGs) in urban waterways will facilitate our increased understanding of the impact of urbanization on ARGs dissemination. In the current study, we assessed the ARGs profiles and antibiotic resistome in water samples along the Jiulong River basin, a distance of 250 km, to better understand the impact of anthropogenic activities. A total of 244 ARGs and 12 MGEs were detected from 21 sampling sites. Both relative and absolute abundance of the observed resistome decreased with increasing distance from urban areas. Ordinary least-squares (OLS) regression revealed that both the relative and absolute resistome abundance were positively correlated with city size. The resistome had several inputs and outputs and Fast Expectation Maximization Microbial Source Tracking (FEAST), suggested that the majority of the antibiotic resistome originated from anthropogenic activities. A total of 8 ARGs and 20 microbial OTUs were considered as biomarkers that differentiated the location of sampling sites. Bacterial communities were significantly correlated with ARGs according to Procrustes analysis and Mantel test, which was also supported by a co-occurrence network. Variation partitioning analysis revealed that ARG profiles were driven by multiple factors. Although antibiotic resistome abundance significantly increased near urban conurbations, overall resistome abundance decreased as the river flowed downstream. Our study highlights the effect of conurbation size on antibiotic resistance profiles within the river basin and the potential resilience of rivers to recover from ARGs contamination.

Effects of biofertilizer on soil microbial diversity and antibiotic resistance genes.

Spread of antibiotic resistance or the presence of antibiotic resistance genes (ARGs) in pathogens is a globally recognized threat to human health. Numerous studies have shown that application of organic fertilizers may increase the risk of ARGs, however, the risk of resistance genes associated with biofertilizers is largely unknown. To investigate whether biofertilizer application introduces ARGs to the soil, we used high-throughput quantitative polymerization chain reaction (HT-qPCR) to explore the effect of biofertilizer application over three years on soil ARGs in three orchards with different locations in China. Redundancy analysis showed specific and significant differences in the beta diversity of soil bacteria and fungi between treatments (fertilizer vs. no fertilizer). One-way ANOVA analysis revealed findings of the main driver of the significant difference in microbial community structure between fertilizer and control treatment was the change in soil properties following the application of biofertilizer. A total of 139 ARGs and 27 MGEs (mobile genetic elements), and 46 ARGs and 6 MGEs from 11 major taxa were detected in biofertilizer and soil samples, respectively. Only the samples from Guangxi had significant differences in the detected number of ARGs and MGEs between fertilization and control. Through structural equation modeling (SEM), we found that soil properties indirectly affected ARGs by shaping bacterial diversity, while bacterial abundance directly affected ARGs. Biofertilizer application did not significantly alter the relative abundance of ARGs in soil due to the complexity of the soil environment and competition between exogenous and native microorganisms. This study provided new insights into the spread of the antibiotic resistome of the soil through biofertilizer applications.

Mite gut microbiome and resistome exhibited species-specific and dose-dependent effect in response to oxytetracycline exposure.

The importance of the gut microbiome to host health is well recognized, but the effects of environmental pressures on the gut microbiome of soil fauna are poorly understood. Here, Illumina sequencing and high-throughput qPCR were applied to characterize the gut microbiomes and resistomes of two mites, Nenteria moseri and Chiropturopoda sp. AL5866, exposed to different concentrations of oxytetracycline (0, 0.01, 0.1 and 1 µg mg-1). Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant phyla in the gut microbiomes of both studied mite species, but the relative abundance of them was different between mites. After exposure to oxytetracycline, there was no variation in the gut microbiome and resistome of C. sp. AL5866, whereas the gut microbiome and resistome of N. moseri were altered significantly. The relative abundance of Proteobacteria significantly decreased, and those of Bacteroidetes and Firmicutes significantly increased at the high-concentration antibiotic treatments. Excepting the 0.01 µg mg-1 treatment, gut microbial diversity increased with ascending concentrations. A significant resistome enrichment of relative abundance in N. moseri gut microbiome at low-dose antibiotic treatment was noted. These results indicated that the gut microbiome in N. moseri was potentially more sensitive to antibiotics than C. sp. AL5866, which was supported by the greater relative abundance of key tetracycline-resistant genes in the gut microbiome of C. sp. AL5866 compared to N. moseri. Mite gut microbiomes were correlated with their associated resistomes, demonstrating the consistent changes between microbiome and resistome. Thus, this study showed that oxytetracycline amendment resulted in a dose-dependent and species-specific effect on the gut microbiomes and resistomes of two mite species. It will contribute to understanding the relationship between the soil mite gut microbiome and resistome under antibiotic exposure, and extend our knowledge regarding the emergence and transfer of resistomes in soil food webs.

Discarded masks as hotspots of antibiotic resistance genes during COVID-19 pandemic.

The demand for facial masks remains high. However, little is known about discarded masks as a potential refuge for contaminants and to facilitate enrichment and spread of antibiotic resistance genes (ARG) in the environment. We address this issue by conducting an in-situ time-series experiment to investigate the dynamic changes of ARGs, bacteria and protozoa associated with discarded masks. Masks were incubated in an estuary for 30 days. The relative abundance of ARGs in masks increased after day 7 but levelled off after 14 days. The absolute abundance of ARGs at 30 days was 1.29 × 1012 and 1.07 × 1012 copies for carbon and surgical masks, respectively. According to normalized stochasticity ratio analysis, the assembly of bacterial and protistan communities was determined by stochastic (NST = 62%) and deterministic (NST = 40%) processes respectively. A network analysis highlighted potential interactions between bacteria and protozoa, which was further confirmed by culture-dependent assays, that showed masks shelter and enrich microbial communities. An antibiotic susceptibility test suggested that antibiotic resistant pathogens co-exist within protozoa. This study provides an insight into the spread of ARGs through discarded masks and highlights the importance of managing discarded masks with the potential ecological risk of mask contamination.

Dynamics of antibiotic resistance and its association with bacterial community in a drinking water treatment plant and the residential area.

Drinking water treatment techniques are used globally in the context of water security and public health, yet they are not applicable to antibiotic resistance gene (ARG) contamination. Using high-throughput quantitative PCR, we analyzed the prevalence and diversity of ARGs and mobile genetic elements (MGEs) in water supplies. A total of 224 ARGs and MGEs were detected in all sampling sites. Absolute abundance and detected number of ARGs decreased significantly (P < 0.05) in sand filter water after drinking water treatment and increased thereafter at point-of-use (household tap water). Changes in the composition and diversity of the bacterial community were observed in water samples at different steps. A significant correlation (P < 0.001) between microbial communities and ARG profiles was observed, and variance in ARG profiles could be primarily attributed to community composition (11.9%), and interaction between community composition, environmental factors and MGEs (30.7%). A network analysis was performed, and the results showed eight bacterial phyla were significantly correlated with nine different classes of ARGs, suggesting the potential bacterial host for ARGs. This study suggested that although the absolute abundance of ARGs decreased after treatment of drinking water treatment plants (DWTPs), the rebounded of ARGs in the water distribution system should not be neglected.

Vertical distribution of antibiotic resistance genes in an urban green facade.

The phyllosphere is considered a key site for the transfer of both naturally and anthropogenically selected antimicrobial resistance genes (ARGs) to humans. Consequently, the development of green building systems may pose an, as yet, unexplored pathway for ARGs and pathogens to transfer from the environment to outdoor plants. We collected leaves from plants climbing up buildings at 1, 2, 4 and 15 m above ground level and collected associated dust samples from adjacent windowsills to determine the diversity and relative abundance of microbiota and ARGs. Overall, a total of 143 ARGs from 11 major classes and 18 mobile genetic elements (MGEs) were detected. The relative abundance of ARGs within the phyllosphere decreased with increasing height above ground level. Fast expectation-maximization microbial source tracking (FEAST) suggested that the contribution of soil and aerosols to the phyllosphere microbiome was limited. A culture-dependent method to isolate bacteria from plant tissues identified a total of 91 genera from root, stem, and leaf samples as well as endophytes isolated from leaves. Of those bacteria, 20 isolates representing 9 genera were known human pathogenic members to humans. Shared bacterial from culture-dependent and culture-independent methods suggest microorganisms may move from soil to plant, potentially through an endophytic mechanism and thus, there is a clear potential for movement of ARGs and human pathogens from the outdoor environment.