Contribution of Vegetation to the Microbial Composition of Nearby Outdoor Air

A review of pathogenic airborne fungi and bacteria: unveiling occurrence, sources, and profound human health implication

Airborne fungi and bacteria have been extensively studied by researchers due to their significant effects on human health. We provided an overview of the distribution and sources of airborne pathogenic microbes, and a detailed description of the detrimental effects that these microorganisms cause to human health in both outdoor and indoor environments. By analyzing the large body of literature published in this field, we offered valuable insights into how airborne microbes influence our well-being. The findings highlight the harmful consequences associated with the exposure to airborne fungi and bacteria in a variety of natural and human-mediated environments. Certain demographic groups, including children and the elderly, immunocompromised individuals, and various categories of workers are particularly exposed and vulnerable to the detrimental effect on health of air microbial pollution. A number of studies performed up to date consistently identified Alternaria, Cladosporium, Penicillium, Aspergillus, and Fusarium as the predominant fungal genera in various indoor and outdoor environments. Among bacteria, Bacillus, Streptococcus, Micrococcus, Enterococcus, and Pseudomonas emerged as the dominant genera in air samples collected from numerous environments. All these findings contributed to expanding our knowledge on airborne microbe distribution, emphasizing the crucial need for further research and increased public awareness. Collectively, these efforts may play a vital role in safeguarding human health in the face of risks posed by airborne microbial contaminants.

Health by design; optimising our urban environmental microbiomes for human health

Humans have evolved in direct and intimate contact with their environment and the microbes that it contains, over a period of 2 million years. As a result, human physiology has become intrinsically linked to environmental microbiota. Urbanisation has reduced our exposure to harmful pathogens, however there is now increasing evidence that these same health-protective improvements in our environment may also be contributing to a hidden disease burden: immune dysregulation. Thoughtful and purposeful design has the potential to ameliorate these health concerns by providing sources of microbial diversity for human exposure. In this narrative review, we highlight the role of environmental microbiota in human health and provide insights into how we can optimise human health through well-designed cities, urban landscapes and buildings. The World Health Organization recommends there should be at least one public green space of least 0.5 ha in size within 300m of a place of residence. We argue that these larger green spaces are more likely to permit functioning ecosystems that deliver ecosystem services, including the provision of diverse aerobiomes. Urban planning must consider the conservation and addition of large public green spaces, while landscape design needs to consider how to maximise environmental, social and public health outcomes, which may include rewilding. Landscape designers need to consider how people use these spaces, and how to optimise utilisation, including for those who may experience challenges in access (e.g. those living with disabilities, people in residential care). There are also opportunities to improve health via building design that improves access to diverse environmental microbiota. Considerations include having windows that open, indoor plants, and the relationship between function, form and organization. We emphasise possibilities for re-introducing potentially health-giving microbial exposures into urban environments, particularly where the benefits of exposure to biodiverse environments may have been lost.

Airborne antibiotic and metal resistance genes - A neglected potential risk at e-waste recycling facilities

Heavy metal-rich environments can promote the selection of metal-resistance genes (MRGs) in bacteria, often leading to the simultaneous selection of antibiotic-resistance genes (ARGs) through a process known as co-selection. To comprehensively evaluate the biological pollutants at electronic-waste (e-waste) recycling facilities, air, soil, and river samples were collected at four distinct Swiss e-waste recycling facilities and analyzed for ARGs, MRGs, mobile genetic elements (MGEs), endotoxins, and bacterial species, with correlations drawn to heavy metal occurrence. To our knowledge, the present work marks the first attempt to quantify these bio-pollutants in the air of e-waste recycling facilities, that might pose a significant health risk to workers. Although ARG and MRG's profiles varied among the different sample types, intl1 consistently exhibited high relative abundance rates, identifying it as the predominant MGE across all sample types and facilities. These findings underscore its pivol role in driving diverse bacterial adaptations to extreme heavy metal exposure by selection and dissemination of ARGs and MRGs. All air samples exhibited consistent profiles of ARGs and MRGs, with blaTEM emerging as the predominant ARG, alongside pbrT and nccA as the most prevalent MRGs. However, one facility, engaged in batteries recycling and characterized by exceptionally high concentrations of heavy metals, showcased a more diverse resistance gene profile, suggesting that bacteria in this environment required more complex resistance mechanisms to cope with extreme metal exposure. Furthermore, this study unveiled a strong association between gram-negative bacteria and ARGs and less with MRGs. Overall, this research emphasizes the critical importance of studying biological pollutants in the air of e-waste recycling facilities to inform robust safety measures and mitigate the risk of resistance gene dissemination among workers. These findings establish a solid foundation for further investigations into the complex interplay among heavy metal exposure, bacterial adaptation, and resistance patterns in such distinctive ecosystems.

Aboveground plants determine the exchange of pathogens within air-phyllosphere-soil continuum in urban greenspaces

The microbiome in the air-phyllosphere-soil continuum of urban greenspaces plays a crucial role in re-connecting urban populations with biodiverse environmental microbiomes. However, little is known about whether plant type affects the airborne microbiomes, as well as the extent to which soil and phyllosphere microbiomes contribute to airborne microbiomes. Here we collected soil, phyllosphere and airborne microbes with different plant types (broadleaf tree, conifer tree, and grass) in urban parks. Despite the significant impacts of plant type on soil and phyllosphere microbiomes, plant type had no obvious effects on the diversity of airborne microbes but shaped airborne bacterial composition in urban greenspaces. Soil and phyllosphere microbiomes had a higher contribution to airborne bacteria in broadleaf trees (37.56%) compared to conifer trees (9.51%) and grasses (14.29%). Grass areas in urban greenspaces exhibited a greater proportion of potential pathogens compared to the tree areas. The abundance of bacterial pathogens in phyllosphere was significantly higher in grasses compared to broadleaf and conifer trees. Together, our study provides novel insights into the microbiome patterns in air-phyllosphere-soil continuum, highlighting the potential significance of reducing the proportion of extensively human-intervened grass areas in future urban environment designs to enhance the provision of ecosystem services in urban greenspaces.

Focus on studying the effects of different exposure durations on the microbial structures and characteristics of three types of body fluids

BACKGROUND

Body fluid traceability inferences can provide important clues to the investigation of forensic cases. Microbiome has been proven to be well applied in forensic body fluid traceability studies. Most of the specimens at crime scenes are often exposed to the external environment when collected, so it is extremely important to exploring the structure characteristics of microbial communities of body fluid samples under different exposure durations for tracing the origin of body fluids based on microorganisms.

METHODS

Full-length 16S rRNA sequencing technology and multiple data analysis methods were used to explore the microbial changes in three types of body fluid samples at five different exposure time points.

RESULTS

With increasing exposure time, the Proteobacteria abundance gradually increased in the negative control and body fluid samples, and the Bacteroidetes and Firmicutes abundance decreased gradually, but the relative abundance of dominant genera in each body fluid remained dynamically stable. The microbial community structures of those samples from the same individual at different exposure durations were similar, and there were no significant differences in the microbial community structures among the different exposure time points. LEfSe and random forest analyses were applied to screen stable and differential microbial markers among body fluids, such as Streptococcus thermophilus, Streptococcus pneumoniae and Haemophilus parainfluenzae in saliva; Lactobacillus iners and Streptococcus agalactiae in vaginal fluid.

CONCLUSIONS

There were no significant differences in microbial community structures of the three types of body fluid samples exposed to the environment for various time periods, although the relative abundance of some microbes in these samples would change. The exposed samples could still be traced back to their source of the body fluid samples using the microbial community structures.

Bioaerosols in the atmosphere: A comprehensive review on detection methods, concentration and influencing factors

In the past few decades, especially since the outbreak of the coronavirus disease (COVID-19), the effects of atmospheric bioaerosols on human health, the environment, and climate have received great attention. To evaluate the impacts of bioaerosols quantitatively, it is crucial to determine the types of bioaerosols in the atmosphere and their spatial-temporal distribution. We provide a concise summary of the online and offline observation strategies employed by the global research community to sample and analyze atmospheric bioaerosols. In addition, the quantitative distribution of bioaerosols is described by considering the atmospheric bioaerosols concentrations at various time scales (daily and seasonal changes, for example), under various weather, and different underlying surfaces. Finally, a comprehensive summary of the reasons for the spatiotemporal distribution of bioaerosols is discussed, including differences in emission sources, the impact process of meteorological factors and environmental factors. This review of information on the latest research progress contributes to the emergence of further observation strategies that determine the quantitative dynamics of public health and ecological effects of bioaerosols.

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.

Relationships between Phyllosphere Bacterial Communities and Leaf Functional Traits in a Temperate Forest

As a vital component of biodiversity, phyllosphere bacteria in forest canopy play a critical role in maintaining plant health and influencing the global biogeochemical cycle. There is limited research on the community structure of phyllosphere bacteria in natural forests, which creates a gap in our understanding of whether and/or how phyllosphere bacteria are connected to leaf traits of their host. In this study, we investigated the bacterial diversity and composition of the canopy leaves of six dominant tree species in deciduous broad-leaved forests in northeastern China, using high-throughput sequencing. We then compare the differences in phyllosphere bacterial community structure and functional genes of dominant tree species. Fourteen key leaf functional traits of their host trees were also measured according to standard protocols to investigate the relationships between bacterial community composition and leaf functional traits. Our result suggested that tree species with closer evolutionary distances had similar phyllosphere microbial alpha diversity. The dominant phyla of phyllosphere bacteria were Proteobacteria, Actinobacteria, and Firmicutes. For these six tree species, the functional genes of phyllosphere bacteria were mainly involved in amino acid metabolism and carbohydrate metabolism processes. The redundancy and envfit analysis results showed that the functional traits relating to plant nutrient acquisition and resistance to diseases and pests (such as leaf area, isotope carbon content, and copper content) were the main factors influencing the community structure of phyllosphere bacteria. This study highlights the key role of plant interspecific genetic relationships and plant attributes in shaping phyllosphere bacterial diversity.

Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet

Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.

Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome

Leaves harbor distinct microbial communities that can have an important impact on plant health and microbial ecosystems worldwide. Nevertheless, the ecological processes that shape the composition of leaf microbial communities remain unclear, with previous studies reporting contradictory results regarding the importance of bacterial dispersal versus host selection. This discrepancy could be driven in part because leaf microbiome studies typically consider the upper and lower leaf surfaces as a single entity despite these habitats possessing considerable anatomical differences. We characterized the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces across 24 plant species. Leaf surface pH and stomatal density were found to shape phyllosphere community composition, and the underside of leaves had lower richness and higher abundances of core community members than upper leaf surfaces. We found fewer endemic bacteria on the upper leaf surfaces, suggesting that dispersal is more important in shaping these communities, with host selection being a more important force in microbiome assembly on lower leaf surfaces. Our study illustrates how changing the scale in which we observe microbial communities can impact our ability to resolve and predict microbial community assembly patterns on leaf surfaces. IMPORTANCE Leaves can harbor hundreds of different bacterial species that form unique communities for every plant species. Bacterial communities on leaves are really important because they can, for example, protect their host against plant diseases. Usually, bacteria from the whole leaf are considered when trying to understand these communities; however, this study shows that the upper and lower sides of a leaf have a very different impact on how these communities are shaped. It seems that the bacteria on the lower leaf side are more closely associated with the plant host, and communities on the upper leaf side are more impacted by immigrating bacteria. This can be really important when we want to treat, for example, crops in the field with beneficial bacteria or when trying to understand host-microbe interactions on the leaves.

The aerobiome-health axis: a paradigm shift in bioaerosol thinking

Historically, a primary aim of bioaerosol research has been to understand and prevent 'unhealthy' human exposures to pathogens and allergens. However, there has been a recent paradigm shift in thinking about bioaerosols. Exposure to a diverse aerobiome - the microbiome of the air - is now considered necessary to be healthy.

Greener residential environment is associated with increased bacterial diversity in outdoor ambient air

In urban areas, exposure to greenspace has been found to be beneficial to human health. The biodiversity hypothesis proposed that exposure to diverse ambient microbes in greener areas may be one pathway leading to health benefits such as improved immune system functioning, reduced systemic inflammation, and ultimately reduced morbidity and mortality. Previous studies observed differences in ambient outdoor bacterial diversity between areas of high and low vegetated land cover but didn't focus on residential environments which are important to human health. This research examined the relationship between vegetated land and tree cover near residence and outdoor ambient air bacterial diversity and composition. We used a filter and pump system to collect ambient bacteria samples outside residences in the Raleigh-Durham-Chapel Hill metropolitan area and identified bacteria by 16S rRNA amplicon sequencing. Geospatial quantification of total vegetated land or tree cover was conducted within 500 m of each residence. Shannon's diversity index and weighted UniFrac distances were calculated to measure α (within-sample) and β (between-sample) diversity, respectively. Linear regression for α-diversity and permutational analysis of variance (PERMANOVA) for β-diversity were used to model relationships between vegetated land and tree cover and bacterial diversity. Data analysis included 73 ambient air samples collected near 69 residences. Analysis of β-diversity demonstrated differences in ambient air microbiome composition between areas of high and low vegetated land (p = 0.03) and tree cover (p = 0.07). These relationships remained consistent among quintiles of vegetated land (p = 0.03) and tree cover (p = 0.008) and continuous measures of vegetated land (p = 0.03) and tree cover (p = 0.03). Increased vegetated land and tree cover were also associated with increased ambient microbiome α-diversity (p = 0.06 and p = 0.03, respectively). To our knowledge, this is the first study to demonstrate associations between vegetated land and tree cover and the ambient air microbiome's diversity and composition in the residential ecosystem.

Contribution of soil bacteria to the atmosphere across biomes

The dispersion of microorganisms through the atmosphere is a continual and essential process that underpins biogeography and ecosystem development and function. Despite the ubiquity of atmospheric microorganisms globally, specific knowledge of the determinants of atmospheric microbial diversity at any given location remains unresolved. Here we describe bacterial diversity in the atmospheric boundary layer and underlying soil at twelve globally distributed locations encompassing all major biomes, and characterise the contribution of local and distant soils to the observed atmospheric community. Across biomes the diversity of bacteria in the atmosphere was negatively correlated with mean annual precipitation but positively correlated to mean annual temperature. We identified distinct non-randomly assembled atmosphere and soil communities from each location, and some broad trends persisted across biomes including the enrichment of desiccation and UV tolerant taxa in the atmospheric community. Source tracking revealed that local soils were more influential than distant soil sources in determining observed diversity in the atmosphere, with more emissive semi-arid and arid biomes contributing most to signatures from distant soil. Our findings highlight complexities in the atmospheric microbiota that are relevant to understanding regional and global ecosystem connectivity.

History of Discovery and Environmental Role of Ice Nucleating Bacteria

The phenomenon of biological ice nucleation that is exhibited by a variety of bacteria is a fascinating phenotype, which has been shown to incite frost damage to frost-sensitive plants and has been proposed to contribute to atmospheric processes that affect the water cycle and earth's radiation balance. This review explores the several possible drivers for the evolutionary origin of the ice nucleation phenotype. These bacteria and the gene required for this phenotype have also been exploited in processes as diverse as reporter gene assays to assess environmentally responsive gene expression in various plant pathogenic and environmental bacteria and in the detection of foodborne human pathogens when coupled with host-specific bacteriophage, whereas ice nucleating bacteria themselves have been exploited in the production of artificial snow for recreation and oil exploration and in the process of freezing of various food products. This review also examines the historical development of our understanding of ice nucleating bacteria, details of the genetic determinants of ice nucleation, and features of the aggregates of membrane-bound ice nucleation protein necessary for catalyzing ice. Lastly, this review also explores the role of these bacteria in limiting the supercooling ability of plants and the strategies and limitations of avoiding plant frost damage by managing these bacterial populations by bactericides, antagonistic bacteria, or cultural control strategies.

Abundant bacteria and fungi attached to airborne particulates in vegetable plastic greenhouses

The proliferation of modern vegetable plastic greenhouses (VPGS) supplies more and more vegetables for food all over the world. The airborne bacteria and fungi induce more exposure opportunities for workers toiling in confined plastic greenhouses. Culture-independent approaches by qPCR and high-throughput sequencing technology were used to study the airborne particulates microbiota in typic VPGS in Shandong, a large base of vegetables in China. The result revealed the mean airborne bacteria concentrations reached 1.67 × 10³ cells/m³ (PM_2.5) and 2.38 × 10³ cells/m³ (PM₁₀), and the mean airborne fungal concentrations achieved 1.49 × 10² cells/m³ (PM_2.5) and 3.19 × 10² cells/m³ (PM₁₀) in VPGS. The predominant bacteria in VPGS included Ralstonia, Alcanivorax, Pseudomonas, Bacillus, and Acinetobacter. Botrytis, Alternaria, Fusarium, Sporobolomyces, and Cladosporium were frequently detected fungal genera in VPGS. A higher Chao1 of bacteria in PM₁₀ was significantly different from PM_2.5 in VPGS. The potential pathogens in VPGS include Raltonia picketti, Acinetobacter lwoffii, Bacillus anthracis, Botrytis cinerea, and Cladosporium sphaerospermum. The network analysis indicated that airborne microbiota was associated with soil microbiota which was affected by anthropologic activities. The predicted gene functions revealed that bacterial function mainly involved metabolism, neurodegenerative diseases, and fungal trophic mode dominated by Pathotroph-Saprotroph in VPGS. These findings unveiled airborne microbiomes in VPGS so that a strategy for improving air quality can be applied to safeguard health and vegetation.

Comparison of bacterial community structure in PM2.5 during hazy and non-hazy periods in Guilin, South China

In recent years, significant efforts have been made to study changes in the levels of air pollutants at regional and urban scales, and changes in bioaerosols during air pollution events have attracted increasing attention. In this study, the bacterial structure of PM_2.5 was analysed under different environmental conditions during hazy and non-hazy periods in Guilin. A total of 32 PM_2.5 samples were collected in December 2020 and July 2021, and the microbial community structures were analysed using high-throughput sequencing methods. The results show that air pollution and climate change alter the species distribution and community diversity of bacteria in PM_2.5, particularly Sphingomonas and Pseudomonas. The structure of the bacterial community composition is related to diurnal variation, vertical height, and urban area and their interactions with various environmental factors. This is a comprehensive study that characterises the variability of bacteria associated with PM_2.5 in a variety of environments, highlighting the impacts of environmental effects on the atmospheric microbial community. The results will contribute to our understanding of haze trends in China, particularly the relationship between bioaerosol communities and the urban environment.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10453-022-09777-0.

The bacteriome of the halophyte Atriplex nummularia (old man saltbush) in salt-affected soils - an ecological model

Halophytes, plants capable of growing under saline conditions, are an important source of bacteria with biotechnological potential for plant growth under extreme conditions. In this study, we evaluated the halophyte Atriplex nummularia bacteriome assemblage from three different salinized sites in northeastern Brazil with different edaphoclimatic characteristics, understanding the participation of the plant in the assembly of its microbiome. We sampled 30 specimens, from which the leaves, roots, and rhizospheric soil were subjected to 16S rRNA gene sequencing, bringing forth patterns of alpha and beta diversity, taxonomical composition, co-occurrence network, and the core microbiome of each compartment. Overall, this species harbors a very restricted set of endophytic microbes, and communities showed an increasing gradient of complexity (soil > root > leaf), reflecting a change in the main selective pressure being active over the microbial community. Although the leaf bacteriome was influenced basically by host factors, the soil community was modulated by the environment, and the root bacteriome was structured by both factors. These results help us understand how plant-microbe interactions occur in saline environments. As these plants shelter microbes that potentially alleviate abiotic stresses, we discuss how culture-independent methods could contribute to the prospection of plant growth promoting bacteria in plants.

Fungal exposome, human health, and unmet needs: A 2022 update with special focus on allergy

Humans inhale, ingest, and touch thousands of fungi each day. The ubiquity and diversity of the fungal kingdom, reflected by its complex taxonomy, are in sharp contrast with our scarce knowledge about its distribution, pathogenic effects, and effective interventions at the environmental and individual levels. Here, we present an overview of salient features of fungi as permanent players of the human exposome and key determinants of human health, through the lens of fungal allergy and other fungal hypersensitivity reactions. Improved understanding of the fungal exposome sheds new light on the epidemiology of fungal-related hypersensitivity diseases, their immunological substratum, the currently available methods, and biomarkers for environmental and medical fungi. Unmet needs are described and potential approaches are highlighted as perspectives.

The Relationship Between Dust Sources and Airborne Bacteria in the Southwest of Iran

The biological agents are carried from deserts and dried lands to long distances by high dust volumes. Their adverse effects can be reduced by specifying and controlling dust sources and their related biological agents. Thus, the current work examined the relationship between the bacteria in air and soil samples by taking samples from the soil surface of two dust sources, as well as from air samples during spring from Khorramshahr and Abadan cities. The dust event is the most influential factor on airborne bacteria. There is an insignificant negative (-0.06), insignificant positive (0.14), and weak positive (0.24) correlation between airborne bacteria and UV radiation, relative humidity, and temperature, respectively. After preparing a 16S ribosomal DNA (rDNA) clone library from the soil and air samples, operational taxonomic unit picking and taxonomic assignment were conducted using QIIME Virtual Box. In the present work, Bacillus was the dominant species. The relationship between dust sources and air samples was determined by principal component analysis. Bacteria in the Hoor-Al-Azim dust source and airborne bacteria on dusty and non-dusty days showed a more significant correlation compared to bacteria in the Shadegan dust source. Source Tracker software was used to estimate the contribution of dust sources. The primary source of dust was associated with the dried areas of Hoor-Al-Azim on the non-dusty and dusty days. Finally, the long transport of airborne bacteria was assessed by moderate resolution imaging spectroradiometer (MODIS) and the back trajectory model of Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) data. The research findings can help decision-makers prioritize dust sources to control the adverse effects of dust.

Season, Vegetation Proximity and Building Age Shape the Indoor Fungal Communities' Composition at City-Scale

Exposure to particular microbiome compositions in the built environment can affect human health and well-being. Identifying the drivers of these indoor microbial assemblages is key to controlling the microbiota of the built environment. In the present study, we used culture and metabarcoding of the fungal Internal Transcribed Spacer ribosomal RNA region to assess whether small-scale variation in the built environment influences the diversity, composition and structure of indoor air fungal communities between a heating and an unheated season. Passive dust collectors were used to collect airborne fungi from 259 dwellings representative of three major building periods and five building environments in one city-Lausanne (Vaud, Switzerland)-over a heating and an unheated period. A homogenous population (one or two people with an average age of 75 years) inhabited the households. Geographic information systems were used to assess detailed site characteristics (altitude, proximity to forest, fields and parks, proximity to the lake, and density of buildings and roads) for each building. Our analysis indicated that season was the factor that explained most of the variation in colonies forming unit (CFU) concentration and indoor mycobiome composition, followed by the period of building construction. Fungal assemblages were more diverse during the heating season than during the unheated season. Buildings with effective insulation had distinct mycobiome compositions from those built before 1975 - regardless of whether they were constructed with pre-1945 technology and materials or 1945 - 1974 ones. The urban landscape-as a whole-was a significant predictor of cultivable Penicillium load-the closer the building was to the lake, the higher the Penicillium load-but not of fungal community composition. Nevertheless, the relative abundance of eleven fungal taxa detected by metabarcoding decreased significantly with the urbanization gradient. When urban landscape descriptors were analyzed separately, the explanatory power of proximity to vegetation in shaping fungal assemblages become significant, indicating that land cover type had an influence on fungal community structure that was obscured by the effects of building age and sampling season. In conclusion, indoor mycobiomes are strongly modulated by season, and their assemblages are shaped by the effectiveness of building insulation, but are weakly influenced by the urban landscape.

Seed Imbibition and Metabolism Contribute Differentially to Initial Assembly of the Soybean Holobiont

Seed germination critically determines successful plant establishment and agricultural productivity. In the plant holobiont's life cycle, seeds are hubs for microbial communities' assembly, but what exactly shapes the holobiont during germination remains unknown. Here, 16S rRNA gene amplicon sequencing characterized the bacterial communities in embryonic compartments (cotyledons and axes) and on seed coats pre- and post-germination of four soybean (Glycine max) cultivars, in the presence or absence of exogenous abscisic acid (ABA), which prevented germination and associated metabolism of seeds that had imbibed. Embryonic compartments were metabolically profiled during germination to design minimal media mimicking the seed endosphere for bacterial growth assays. The distinction between embryonic and seed coat bacterial microbiomes of dry seeds weakened during germination, resulting in the plumule, radicle, cotyledon, and seed coat all hosting the same most abundant and structurally influential genera in germinated seeds of every cultivar. Treatment with ABA prevented the increase of bacterial microbiomes' richness, but not taxonomic homogenization across seed compartments. Growth assays on minimal media containing the most abundant metabolites that accumulated in germinated seeds revealed that seed reserve mobilization promoted enrichment of copiotrophic bacteria. Our data show that seed imbibition enabled distribution of seed-coat-derived epiphytes into embryos irrespective of germination, while germinative metabolism promoted proliferation of copiotrophic taxa, which predominated in germinated seeds.

Schoolyard Biodiversity Determines Short-Term Recovery of Disturbed Skin Microbiota in Children

Creating biodiverse urban habitat has been proposed, with growing empirical support, as an intervention for increasing human microbial diversity and reducing associated diseases. However, ecological understanding of urban biodiversity interventions on human skin microbiota remains limited. Here, we experimentally test the hypotheses that disturbed skin microbiota recover better in outdoor schoolyard environments and that greater biodiversity provides a greater response. Repeating the experiment three times, we disturbed skin microbiota of fifty-seven healthy 10-to-11-year-old students with a skin swab (i.e., cleaning), then exposed them to one school environment-either a 'classroom' (n = 20), 'sports field' (n = 14), or biodiverse 'forest' (n = 23)-for 45 min. Another skin swab followed the exposure to compare 'before' and 'after' microbial communities. After 45 min, the disturbance immediately followed by outdoor exposure, especially the 'forest', had an enriching and diversifying effect on skin microbiota, while 'classroom' exposure homogenised inter-personal variability. Each effect compounded over consecutive days indicating longer-term exposure outcomes. The experimental disturbance also reduced the core skin microbiota, and only outdoor environments were able to replenish lost species richness to core membership (n species > 50% prevalent). Overall, we find that environmental setting, especially including biodiversity, is important in human microbiota recovery periods and that the outdoors provide resilience to skin communities. This work also has implications for the inclusion of short periods of outside or forest exposure in school scheduling. Future investigations of the health impacts of permanent urban biodiversity interventions are needed.

Phyllosphere Microorganisms: Sources, Drivers, and Their Interactions with Plant Hosts

The leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms. Phyllosphere microorganisms mainly originate from soil, air, and seeds. The composition of phyllosphere microorganisms is mainly affected by ecological and abiotic factors. Phyllosphere microorganisms execute multiple ecological functions by influencing leaf functions and longevity, seed mass, fruit development, and homeostasis of host growth. A plant can respond to phyllosphere microorganisms by secondary metabolite secretion and its immune system. Meanwhile, phyllosphere microorganisms play an important role in ecological stability and environmental safety assessment. However, as a result of the instability of the phyllosphere environment and the poor cultivability of phyllosphere microorganisms in the current research, there are still many limitations, such as the lack of insight into the mechanisms of plant-microorganism interactions, the roles of phyllosphere microorganisms in plant growth processes, the responses of phyllosphere microorganisms to plant metabolites, etc. This review summarizes the latest progress made in the research of the phyllosphere in recent years. This is beneficial for deepening our understanding of phyllosphere microorganisms and promoting the research of plant-atmosphere interactions, plant pathogens, and plant biological control.

Microbial Activity and Community Structure in PM2 .5 at Different Heights in Ground Boundary Layer of Beijing Atmosphere under Various Air Quality Levels

The outbreak of the COVID-19 epidemic is a reminder that aerosols have important health effects as a potential route for disease transmission. Biological components in aerosols (especially PM_2.5 ) may pose potential threats to humans as pathogens and allergens. Research on PM_2.5 and biological components currently focuses mainly on polluted conditions, with less emphasis on clean environments. Sampling has also been primarily based on a single point with a lack of data at different positions. In this study, a modified fluorescein diacetate hydrolysis method was used to measure microbial activity in PM_2.5 at different altitudes over a year in Beijing, China. A high-throughput sequencing method was used to study the microbial community. Results showed that microbial activity 1.5 m (0.0465 ng m^-3 ) above the ground was higher than 31.5 m (0.0348 ng m^-3 ). There was higher microbial activity at both heights during spring. Furthermore, a positive correlation was observed between microbial activity and relative abundance of dominant species. Microbial activity increased during autumn and winter increased alongside the pollution level, but in spring higher levels of microbial activity were observed in excellent or good weather conditions. The results from this study are valuable for further research regarding the biological components of atmospheric PM, the prevention of biological pollution, and establishing a comprehensive air quality evaluation system. This article is protected by copyright. All rights reserved.

Assessing the relationship between airborne fungi and potential dust sources using a combined approach

Dust events impose negative socio-economic, health, and environmental impacts on vulnerable areas and reflect their sources' physiochemical and biological characteristics. This study aimed to assess the impact of two dust sources on the concentration and diversity of airborne fungi in one of the dustiest areas in the world. This study is the first attempt to investigate the relationship between dust sources fungal community and those in airborne dust. Also, the contribution of dust sources to airborne fungi was estimated. Air masses arriving at the study area were assessed using local wind rose and the HYSPLIT model. Sampling was carried out from airborne dust at the Arvand Free Zone as target areas and soil in the dried parts of the Hor al-Azim and Shadegan wetlands as source areas to explore the relationship between fungi in the dust sources and the downwind area. The samples were analyzed in the lab to extract DNA. The internal transcribed spacer (ITS) regions of the rDNA gene were amplified using the primers ITS1F and ITS4, and then PCR products were sent to the lab for sequencing. The raw DNA data were processed using the QIIME virtual box to pick operational taxonomic units and taxonomy assignments. The most common fungi at the genus level were in the order of Penicillium > Aspergillus > Alternaria > Fusarium > Paradendryphiella > Talaromyces. The similarity between air and soil fungal genera was investigated using richness and diversity indices, the phylogenetic tree, and principal component analysis. The results showed that the community structures of ambient fungi in the Hor al-Azim and Shadegan dust sources were more similar to those on dusty days than non-dusty days. The source tracker model was used to quantify the contributions of known dust sources to airborne fungi. The results showed that the main source of airborne fungi was Hor al-Azim on dusty and non-dusty days. This study's results can help managers identify and prioritize dust sources regarding fungal species.

Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene

Global change is a defining feature of the Anthropocene, the current human-dominated epoch, and poses imminent threats to ecosystem dynamics and services such as plant productivity, biodiversity, and environmental regulation. In this era, terrestrial ecosystems are experiencing perturbations linked to direct habitat modifications as well as indirect effects of global change on species distribution and extreme abiotic conditions. Microorganisms represent an important reservoir of biodiversity that can influence macro-organisms as they face habitat loss, rising atmospheric CO₂ concentration, pollution, global warming, and increased frequency of drought. Plant-microbe interactions in the phyllosphere have been shown to support plant growth and increase host resistance to biotic and abiotic stresses. Here, we review how plant-microbe interactions in the phyllosphere can influence host survival and fitness in the context of global change. We highlight evidence that plant-microbe interactions (1) improve urban pollution remediation through the degradation of pollutants such as ultrafine particulate matter, black carbon, and atmospheric hydrocarbons, (2) have contrasting impacts on plant species range shifts through the loss of symbionts or pathogens, and (3) drive plant host adaptation to drought and warming. Finally, we discuss how key community ecology processes could drive plant-microbe interactions facing challenges of the Anthropocene.

Diversity and Source of Airborne Microbial Communities at Differential Polluted Sites of Rome

Biogenic fraction of airborne PM10 which includes bacteria, viruses, fungi and pollens, has been proposed as one of the potential causes of the PM10 toxicity. The present study aimed to provide a comprehensive understanding of the microbial community variations associated to PM10, and their main local sources in the surrounding environment in three urban sites of Rome, characterized by differential pollution rate: green area, residential area and polluted area close to the traffic roads. We combined high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer (ITS) region, with detailed chemical analysis of particulate matter sampled from air, paved road surfaces and leaf surfaces of Quercus ilex. Our results demonstrated that bacterial and fungal airborne communities were characterized by the highest alpha-diversity and grouped separately from epiphytic and road dust communities. The reconstruction of source-sink relationships revealed that the resuspension/deposition of road dust from traffic might contribute to the maximum magnitude of microbial exchanges. The relative abundance of extremotolerant microbes was found to be enhanced in epiphytic communities and was associated to a progressively increase of pollution levels as well as opportunistic human pathogenicity in fungal communities.

Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome

Microbial communities associated with plant leaf surfaces (i.e., the phyllosphere) are increasingly recognized for their role in plant health. While accumulating evidence suggests a role for host filtering of its microbiota, far less is known about how community composition is shaped by dispersal, including from neighboring plants. We experimentally manipulated the local plant neighborhood within which tomato, pepper, or bean plants were grown in a 3-month field trial. Focal plants were grown in the presence of con- or hetero-specific neighbors (or no neighbors) in a fully factorial combination. At 30-day intervals, focal plants were harvested and replaced with a new age- and species-matched cohort while allowing neighborhood plants to continue growing. Bacterial community profiling revealed that the strength of host filtering effects (i.e., interspecific differences in composition) decreased over time. In contrast, the strength of neighborhood effects increased over time, suggesting dispersal from neighboring plants becomes more important as neighboring plant biomass increases. We next implemented a cross-inoculation study in the greenhouse using inoculum generated from the field plants to directly test host filtering of microbiomes while controlling for directionality and source of dispersal. This experiment further demonstrated that focal host species, the host from which the microbiome came, and in one case the donor hosts' neighbors, contribute to variation in phyllosphere bacterial composition. Overall, our results suggest that local dispersal is a key factor in phyllosphere assembly, and that demographic factors such as nearby neighbor identity and biomass or age are important determinants of phyllosphere microbiome diversity.

OUP accepted manuscript

The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.

Spread of airborne antibiotic resistance from animal farms to the environment: Dispersal pattern and exposure risk

Animal farms have been considered as the critical reservoir of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). Spread of antibiotic resistance from animal farms to the surrounding environments via aerosols has become a growing concern. Here we investigated the dispersal pattern and exposure risk of airborne ARGs (especially in zoonotic pathogens) in the environment of chicken and dairy farms. Aerosol, dust and animal feces samples were collected from the livestock houses and surrounding environments (upwind and downwind areas) for assessing ARG profiles. Antibiotic resistance phenotype and genotype of airborne Staphylococcus spp. was especially analyzed to reveal the exposure risk of airborne ARGs. Results showed that airborne ARGs were detected from upwind (50 m/100 m) and downwind (50 m/100 m/150 m) air environment, wherein at least 30% of bacterial taxa dispersed from the animal houses. Moreover, atmospheric dispersion modeling showed that airborne ARGs can disperse from the animal houses to a distance of 10 km along the wind direction. Clinically important pathogens were identified in airborne culturable bacteria. Genus of Staphylococcus, Sphingomonas and Acinetobacter were potential bacterial host of airborne ARGs. Airborne Staphylococcus spp. were isolated from the environment of chicken farm (n = 148) and dairy farm (n = 87). It is notable that all isolates from chicken-related environment were multidrug-resistance (>3 clinical-relevant antibiotics), with more than 80% of them carrying methicillin resistance gene (mecA) and associated ARGs and MGEs. Presence of numerous ARGs and diverse pathogens in dust from animal houses and the downwind residential areas indicated the accumulation of animal feces origin ARGs in bioaerosols. Employees and local residents in the chick farming environment are exposed to chicken originated ARGs and multidrug resistant Staphylococcus spp. via inhalation. This study highlights the potential exposure risks of airborne ARGs and antibiotic resistant pathogens to human health.

Fungal Community Composition and Enzyme Activity in Different Type Bark of Pinus koraiensis

Pinus koraiensis Sieb. et Zucc. is an endemic and dominant tree in temperate zone needle broad-leaf mixed forest and has great economic and ecological value. As the barrier, pine bark has many important functions. However, the ecological functions and forming mechanism of bark fungal community are poorly understood. The aim of this study was to reveal the fungal community of Korean pine bark from Changbai Nature Reserve of Northeast China. Based on Illumina Hiseq2000 platform with five different types from three sites, the results showed that the bark types and collecting sites have strong influence on the fungal community structure. CCA demonstrates the physico-chemical properties of barks and sample collecting height are important factors. Spearman’s correlation coefficients between dominant ASVs and these factors showed the impact in detail. Dominant ASVs in living and dead tree bark are animal or plant pathogens mainly, and they are negative with the total N and P. Meanwhile, wood saprotroph and other undefined saprotroph fungi occur in the bark near the ground and they prefer the substrate with higher total N and P content. Furthermore, enzymes activities including lignin-related oxidoreductases, cellulose and hydrolytic enzyme are affected significantly by the bark’s physico-chemical properties.

Abundance and diversity of antibiotic resistance genes possibly released to ambient air by experiments in biology laboratories

Antibiotic resistance genes (ARG) have been considered as a global emerging threat to public health systems. As special locations where both antibiotics and ARGs are directly used, biology laboratories are poorly studied but potential important emission sources where not only the environmental stress is strong but also obtaining resistance is much easier comparing to other well studied hot spots including farms, hospitals, wastewater treatment plants and landfills where antibiotics but not ARGs are used or discharged. Therefore, in this study, 11 Swiss biology laboratories working on different fields and located in the city center, suburb and rural area were studied to reveal the abundance and diversity of airborne ARGs in them and their surrounding areas with Colony-forming units (CFU) cultivation and quantitative Polymerase Chain Reaction (qPCR). Most biology laboratories did not discharge significant amounts or varieties of ARGs and cultivable bacteria via air. No correlation was found between the number of CFUs and the abundance of 16S rRNA, but two clusters of correlated airborne ARGs, the animal husbandry related cluster, and city and hospital related cluster were identified in this study. Although most biology laboratories may not be the emission sources of a wide variety of airborne ARGs, the ARGs in the animal husbandry related cluster which are abundant in the animal laboratories and aadA1 which is abundant in the laboratories working on other eukaryocytes need to be furtherly studied to make sure if they are potential health risks for the researchers.

Global Patterns and Climatic Controls of Dust-Associated Microbial Communities

The ubiquity and long-range transport of the microorganisms inhabiting dust can pose a serious risk to human, animal, and plant health. The well-recognized importance of dust-associated microorganisms contrasts starkly with our limited understanding of the factors determining the variation in the composition of these communities at the global scale. Here, we provide the first insight into the global determinants of dust-associated microorganisms by quantifying the environmental factors shaping bacterial and fungal community composition in 467 outdoor settled dust samples collected from 33 countries and 6 continents. Our results show that the global variation in dust-associated bacterial and fungal community composition was, to some degree, predictable from mean annual precipitation and temperature. Notably, our results show that the fungal genera Alternaria and Aspergillus, which contain many species that can serve as triggers of allergenic disease in humans and as plant pathogens, were more abundant in drier regions. Collectively, these results highlight the key influence of climate on the global distribution of dust-associated microorganisms and provide the baseline information needed to build a more comprehensive understanding of how microbial exposures vary across the globe and in response to climate change. IMPORTANCE A broad diversity of microorganisms can be found in dust, with some of these microorganisms capable of causing allergenic disease in human via inhalation or affecting plant health by acting as plant pathogens. However, the spatial variation in dust microbiomes and the environmental factors associated with this variation have not been comprehensively assessed at the global scale. Here, we investigated the bacteria and fungi found in outdoor settled dust samples spanning 33 countries and 6 continents. Our results show that dust-associated bacteria and fungi exhibit climate-driven variability in community composition at the global scale. Our results call for the development of strategies to predict the geographic distribution of dust-associated microorganisms and to identify the potential associations between microbial exposures and the health of humans, animals, and plants.

Residential airborne culturable fungi under general living scenario: On-site investigation in 12 typical cities, China

BACKGROUND

Residential airborne fungi may present obvious risk to human health. However, many countries do not recognize the necessarily need to control residential airborne culturable fungi (RAF). In China, few systemic investigations have been conducted to illustrate the distribution of residential airborne fungi and identify the association between indoor influencing variables and RAF under general living scenario in China.

OBJECTIVE

This study aimed to investigate RAF with the on-site research of 12 typical cities in China, and provided the latest characteristics and potential influencing factors of RAF under general living scenario.

METHODS

We measured RAF and investigated residential characteristics in 12 typical cities in China, 2018. At least 50 resident families were randomly selected both from downwind and upwind districts in each city with pre-proposed requirements. The RAF were sampled by the six-stage Anderson impactor. PM_2.5 and PM₁₀ were monitored by calibrated light-scattering dust meters. CO and CO₂ were monitored by non-dispersive infrared analyzer method. NO₂ was determined by Saltzman method. General linear model was used to evaluate the association between RAF exposure and residential characteristics with adjustment for potential confounders.

RESULTS

The RAF concentrations ranged from 0 to 9371 CFU/m³ with a median concentration of 396 CFU/m³. The median concentrations of RAF in the warm season were statistically higher than the cold season in Panjin, Qingdao, Lanzhou and Luoyang, but lower than the cold season in Shijiazhuang, Ningbo and Nanning. RAF in the bedrooms were more than the living rooms in all cities except Xi'an. Temperature and humidity had an interactive effect on the RAF (OR = 1.0006, 95% CI: 1.0005, 1.0006). Some residential environmental pollutants, including PM_2.5 (OR = 0.9989, 95% CI: 0.9988, 0.9989), PM₁₀ (OR = 0.9993, 95% CI: 0.9993, 0.9993), and CO₂ (OR = 0.0236, 95% CI: 0.0230, 0.0243), were negatively correlated with RAF. CO (OR = 1.1450, 95% CI: 1.1433, 1.1467) and NO₂ (OR = 1.0026, 95% CI: 1.0024, 1.0028) were positively correlated with RAF. Architectural characteristics (sunlight exposure, building history, longitude, latitude, total living area, living floor, distance from the road, house type, the layers of window glass and decoration), family-related information (income) and lifestyle behaviors (keeping pets, growing plants, cooking, using insecticide, burning incense, heating, using air conditioner and cleaning frequencies) were also significantly related with RAF.

CONCLUSIONS

This study reported nation-wide baseline condition of RAF and related influencing factors under general living scenario with quantitative details, which are exceedingly promising for evidence-driven standard and reasonable control strategy of residential airborne culturable in China.

Urban Aerobiomes are Influenced by Season, Vegetation, and Individual Site Characteristics

Exposure to biodiverse environments such as forests can benefit human well-being, and evidence suggests exposure to high microbial diversity may improve mental and immune health. However, the factors that drive microbial community assembly are poorly understood, as is the relationship between exposure to these communities and human health. We characterized airborne bacterial communities in two disparate types of urban greenspace (forest and grass) in late-spring 2017 at sites previously sampled in late-summer 2015 in Eugene-Springfield, Oregon, using high-throughput metabarcode sequencing. While all sites shared a core aerobiome in late-spring consisting of plant- and soil-associated genera, forests had significantly higher diversity than grass sites (F = 12, P = 0.004). Vegetation type explained 14% of the difference between forest and grass aerobiomes, yet individual site location explained 41% of the variation. These results were similar to but amplified over those from late summer, suggesting that both aerobiome diversity and vegetation-driven effects are higher when deciduous foliage is fresher and more active, temperatures cooler, and humidity higher. Continued exploration and hypothesis-driven research will enable development of mechanistic theory describing key drivers of urban aerobiome assembly and its relationship to human health, which, in turn, will help urban designers and planners create evidence-based salutogenic cities for future generations.

Urban greenness and plant species are key factors in shaping air microbiomes and reducing airborne pathogens

Urban green space has been implicated in shaping airborne microbes, but there is an only rudimentary understanding of the key factors of urban green space affecting the composition and structures of airborne microbes. Here, we selected 40 urban sites based on stratified random sampling design and investigated the effects of multiple factors including landscapes, plant, soil, and anthropogenic factors on airborne microbial communities, especially bacterial and fungal pathogens. Bacterial and fungal communities in the control area with lower greenness were significantly (P < 0.05) different from those in other areas with a gradient of green space. The relative abundance of bacterial and fungal pathogens significantly (P < 0.05) decreased with increasing greenness. Other than soil thickness, soil type, slope position, and population density, plant species considerably contributed to the shift in the composition and abundance of potential bacterial and fungal pathogens. A significantly (P < 0.05) reduced abundance of bacterial and fungal pathogens was observed in areas with >30% masson pine. Together, these results provide insights into the importance of green space for providing health benefits for city dwellers by reducing pathogens in air, as well as providing support for the inclusion of plant species in the management of urban green space to reduce exposure risk of airborne pathogens.

Orchard Management and Landscape Context Mediate the Pear Floral Microbiome

Crop-associated microbiota are a key factor affecting host health and productivity. Most crops are grown within heterogeneous landscapes, and interactions between management practices and landscape context often affect plant and animal biodiversity in agroecosystems. However, whether these same factors typically affect crop-associated microbiota is less clear. Here, we assessed whether orchard management strategies and landscape context affected bacterial and fungal communities in pear (Pyrus communis) flowers. We found that bacteria and fungi responded differently to management schemes. Organically certified orchards had higher fungal diversity in flowers than conventional or bio-based integrated pest management (IPM) orchards, but organic orchards had the lowest bacterial diversity. Orchard management scheme also best predicted the distribution of several important bacterial and fungal genera that either cause or suppress disease; organic and bio-based IPM best explained the distributions of bacterial and fungal genera, respectively. Moreover, patterns of bacterial and fungal diversity were affected by interactions between management, landscape context, and climate. When examining the similarity of bacterial and fungal communities across sites, both abundance- and taxon-related turnovers were mediated primarily by orchard management scheme and landscape context and, specifically, the amount of land in cultivation. Our study reveals local- and landscape-level drivers of floral microbiome structure in a major fruit crop, providing insights that can inform microbiome management to promote host health and high-yielding quality fruit. IMPORTANCE Proper crop management during bloom is essential for producing disease-free tree fruit. Tree fruits are often grown in heterogeneous landscapes; however, few studies have assessed whether landscape context and crop management affect the floral microbiome, which plays a critical role in shaping plant health and disease tolerance. Such work is key for identification of tactics and/or contexts where beneficial microbes proliferate and pathogenic microbes are limited. Here, we characterize the floral microbiome of pear crops in Washington State, where major production occurs in intermountain valleys and basins with variable elevation and microclimates. Our results show that both local-level (crop management) and landscape-level (habitat types and climate) factors affect floral microbiota but in disparate ways for each kingdom. More broadly, these findings can potentially inform microbiome management in orchards for promotion of host health and high-quality yields.

Combining culturing and 16S rDNA sequencing to reveal seasonal and room variations of household airborne bacteria and correlative environmental factors in nanjing, southeast china

Exposure to bioaerosols poses important health effects on occupants. To elucidate seasonal and room variations of household airborne bacteria, this study investigated 30 residential homes during summer and winter throughout Nanjing, Southeast China, with a humid subtropical climate. Culturing and 16S rDNA sequencing methods were combined in this study. Results showed that the community structure and composition in the same season but different homes show similarity, however, they in the same home but in different seasons show a huge difference, with Sphingomonas (25.3%), Clostridium (14.8%), and Pseudomonas (7.6%) being the dominant bacteria in summer, and Pseudomonas (57.1%) was dominant bacteria in winter. Culturable concentrations of bacteria were also significantly higher in summer (854 ± 425 CFU/m³ ) than in winter (231 ± 175 CFU/m³ ), but difference by home or room was relatively minor. More than 80% of culturable bacteria (<4.7 μm) could penetrate into lower respiratory tract. The seasonal variations of bacterial community and concentrations were closely associated with seasonal variations of temperature, humidity, and PM_2.5 . Higher concentrations and larger sizes were observed in the bathroom and kitchen, typically with higher humidity than other rooms.

Aerobiological study of bacterial and fungal community composition in the atmosphere of Mexico City throughout an annual cycle

The atmosphere as a temporary habitat for airborne microbial communities is a valuable topic to explore, and it is through aerobiological studies that the diversity of biological particles and their release, emission, transport, deposition, and impact are assessed. Specific microorganisms are involved in meteorological processes, and phytosanitary and public health concerns. Airborne microbial composition is related to factors such as geographic region and weather conditions. In this study a metagenomic approach was used to determine the composition of bacterial and fungal communities in the air of two different land-use areas (urban area and semi-rural area), during dry and rainy seasons in Mexico City. Air sampling was carried out with a Hirst-type spore trap, collecting the samples simultaneously in both study areas. Forty-two bioaerosol samples were collected, and the DNA obtained was sequenced using Next-Generation Sequencing. The results indicated that the bacterial communities were represented mainly by the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria, and the fungal communities by the phyla Ascomycota followed by Basidiomycota. The evident changes in microbial composition were related more to seasonality than to locality, since both UA and SRA showed a high degree of urbanization, despite some differences in land use. Continuous monitoring of atmospheric bioaerosols is essential to determine the influence of meteorological factors on the composition of the aerial microbiota.

Exposure to airborne bacteria depends upon vertical stratification and vegetation complexity

Exposure to biodiverse aerobiomes supports human health, but it is unclear which ecological factors influence exposure. Few studies have investigated near-surface green space aerobiome dynamics, and no studies have reported aerobiome vertical stratification in different urban green spaces. We used columnar sampling and next generation sequencing of the bacterial 16S rRNA gene, combined with geospatial and network analyses to investigate urban green space aerobiome spatio-compositional dynamics. We show a strong effect of habitat on bacterial diversity and network complexity. We observed aerobiome vertical stratification and network complexity that was contingent on habitat type. Tree density, closer proximity, and canopy coverage associated with greater aerobiome alpha diversity. Grassland aerobiomes exhibited greater proportions of putative pathogens compared to scrub, and also stratified vertically. We provide novel insights into the urban ecosystem with potential importance for public health, whereby the possibility of differential aerobiome exposures appears to depend on habitat type and height in the airspace. This has important implications for managing urban landscapes for the regulation of aerobiome exposure.

The association of fractional cover, foliage projective cover and biodiversity with birthweight

INTRODUCTION

Environmental exposures can contribute both benefits and risks to human health. Maternal exposure to green space has been associated with improvements in birthweight, among other birth outcomes. Newer measures of green space have been developed, which allows for an exploration of the effect of different ground covers (green, dry and bare earth), as well as measures of biodiversity. This study explores the association of these novel green space measures with birthweight in a large birth cohort in Queensland, Australia.

METHODS

Birthweight was acquired from the routine health records. Records were allocated green space values for fractional cover, biodiversity and foliage projective cover. Directed acyclic graphs were developed to guide variable selection. Mixed-effects linear regression and generalised linear mixed-effects models were developed, with random intercepts for maternal residential locality and year of birth. Results are presented as standardised beta coefficients or odds ratios, with 95% confidence intervals.

RESULTS

An IQR increase of green cover (29.6 g, 95% CI 13.8-45.5) and foliage projective cover (26.0 g, 95% CI 10.8-41.3) are associated with birthweight in urban areas. An IQR increase in dry cover -34.4 g, 95% CI -60.4 to -8.4) and bare earth (-17.7 g, 95% CI -32.8 to -2.6) are associated with lower birthweight. Mothers living in rural areas had similar results, with an IQR increase in green cover (17.8 g, 95% CI 2.9-32.7) associated with higher birthweight, and bare earth (-27.7 g, 95% CI -45.7 to -9.7) was associated with lower birthweight. The biodiversity measure used in this study was not associated with any birthweight outcomes.

CONCLUSION

This study finds that the types of ground cover within the maternal residential locality are associated with small, but significant, changes in estimated birthweight, and these effects are not limited to urban areas.

Land Use Effects on Airborne Bacterial Communities Are Evident in Both Near-Surface and Higher-Altitude Air

Land use influences the composition of near-surface airborne bacterial communities, and bacteria can be transported through the atmosphere at global scales. The atmosphere mixes vertically, but rigorously assessing whether the effects of land use on atmospheric communities extends to higher altitudes requires examining communities from multiple altitudes collected at a stable location and timeframe. In this study, we collected near-surface (<2 m) and higher-altitude (150 m) air samples from three sites in an agricultural/developed location and a forested/undeveloped location. We used bacterial 16S rRNA amplicon sequencing to compare communities and predict functionality by altitude. Higher-altitude and near-surface communities did not differ in composition within each location. Communities collected above the undeveloped location were equally variable at both altitudes; higher-altitude samples from the developed location predominantly contained Firmicutes and were less variable than near-surface samples. We also compared airborne taxa to those present in soil and snow. Communities from higher-altitude samples above the developed location contained fewer overlapping taxa with soil and snow sources, and overlapping Operational Taxonomic Units (OTUs) among the three sources differed by location. Our results suggest that land use affects the composition of both near-surface and higher-altitude airborne bacterial communities and, therefore, may influence broad bacterial dispersal patterns. This small-scale pilot study provides a framework for simultaneously examining local and regional airborne microbial communities that can be applied to larger studies or studies using different types of samplers.

Outdoor Atmospheric Microbial Diversity Is Associated With Urban Landscape Structure and Differs From Indoor-Transit Systems as Revealed by Mobile Monitoring and Three-Dimensional Spatial Analysis

Microbes are abundant inhabitants of the near-surface atmosphere in urban areas. The distribution of microbial communities may benefit or hinder human wellbeing and ecosystem function. Surveys of airborne microbial diversity are uncommon in both natural and built environments and those that investigate diversity are stationary in the city, thus missing continuous exposure to microbes that covary with three-dimensional urban structure. Individuals in cities are generally mobile and would be exposed to diverse urban structures outdoors and within indoor-transit systems in a day. We used mobile monitoring of microbial diversity and geographic information system spatial analysis, across Philadelphia, Pennsylvania, USA in outdoor and indoor-transit (subways and train cars) environments. This study identifies to the role of the three-dimensional urban landscape in structuring atmospheric microbiomes and employs mobile monitoring over ~1,920 kilometers to measure continuous biodiversity. We found more diverse communities outdoors that significantly differ from indoor-transit air in microbial community structure, function, likely source environment, and potentially pathogenic fraction of the community. Variation in the structure of the urban landscape was associated with diversity and function of the near-surface atmospheric microbiome in outdoor samples.

Microbial Flow Within an Air-Phyllosphere-Soil Continuum

The phyllosphere is populated by numerous microorganisms. Microbes from the wider environment, i.e., air and soil, are considered key contributors to phyllosphere microbial communities, but their contribution is unclear. This study seeks to address this knowledge gap by controlling the movement of microbes along the air-phyllosphere-soil continuum. Customized equipment with dual chambers was constructed that permitted airflow to enter the first chamber while the second chamber recruited filtered microbe-free air from the initial chamber. Allium schoenoprasum (chive) and Sonchus oleraceus (sow thistle) were cultivated in both chambers, and the microbial communities from air, phyllosphere, and soil samples were characterized. Shares of microbial OTUs in the equipment suggested a potential interconnection between the air, phyllosphere, and soil system. Fast expectation-maximization microbial source tracking (FEAST) suggested that soil was the major source of airborne microbial communities. In contrast, the contribution of airborne and soil microbes to phyllosphere microbial communities of either A. schoenoprasum or S. oleraceus was limited. Notably, the soilborne microbes were the only environmental sources to phyllosphere in the second chamber and could affect the composition of phyllosphere microbiota indirectly by air flow. The current study demonstrated the possible sources of phyllosphere microbes by controlling external airborne microbes in a designed microcosm system and provided a potential strategy for recruitment for phyllosphere recruitment.

Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems

Grafting connects root and shoot systems of distinct individuals, bringing microbial communities of different genotypes together in a single plant. How do root system and shoot system genotypes influence plant microbiota in grafted grapevines? To address this, we utilized clonal replicates of the grapevine ‘Chambourcin’, growing ungrafted and grafted to three different rootstocks in three irrigation treatments. Our objectives were to (1) characterize the microbiota (bacteria and fungi) of below-ground compartments (roots, adjacent soil) and above-ground compartments (leaves, berries), (2) determine how rootstock genotype, irrigation, and their interaction influences grapevine microbiota in different compartments, and (3) investigate abundance of microorganisms implicated in the late-season grapevine disease sour rot (Acetobacterales and Saccharomycetes). We found that plant compartment had the largest influence on microbial diversity. Neither rootstock genotype nor irrigation significantly influenced microbial diversity or composition. However, differential abundance of bacterial and fungal taxa varied as a function of rootstock and irrigation treatment; in particular, Acetobacterales and Saccharomycetes displayed higher relative abundance in berries of grapevines grafted to ‘1103P’ and ‘SO4’ rootstocks and varied across irrigation treatments. This study demonstrates that grapevine compartments retain distinct microbiota and identifies associations between rootstock genotypes, irrigation treatment, and the relative abundance of agriculturally relevant microorganisms in the berries.

The source and transport of bioaerosols in the air: A review

Recent pandemic outbreak of the corona-virus disease 2019 (COVID-19) has raised widespread concerns about the importance of the bioaerosols. They are atmospheric aerosol particles of biological origins, mainly including bacteria, fungi, viruses, pollen, and cell debris. Bioaerosols can exert a substantial impact on ecosystems, climate change, air quality, and public health. Here, we review several relevant topics on bioaerosols, including sampling and detection techniques, characterization, effects on health and air quality, and control methods. However, very few studies have focused on the source apportionment and transport of bioaerosols. The knowledge of the sources and transport pathways of bioaerosols is essential for a comprehensive understanding of the role microorganisms play in the atmosphere and control the spread of epidemic diseases associated with them. Therefore, this review comprehensively summarizes the up to date progress on the source characteristics, source identification, and diffusion and transport process of bioaerosols. We intercompare three types of diffusion and transport models, with a special emphasis on a widely used mathematical model. This review also highlights the main factors affecting the source emission and transport process, such as biogeographic regions, land-use types, and environmental factors. Finally, this review outlines future perspectives on bioaerosols.

Impact of air, water and dock microbial communities on boat microbial community composition

AIMS

This study explores the microbial diversity of sources which may influence boat microbial communities. We investigated the impact of dock, air and water microbial communities on the hull, transom and bilge microbial communities over the span of 11 days.

METHODS AND RESULTS

Using source tracking software, we investigated the extent to which each of our potential sources (air, water and dock) influenced the overall microbial community. This study concluded that the dock impacted 14-64% of the hull and transom microbial community. Micro-organisms from the water were shown to impact 5·6% the bilge microbial community but had minimal impact on hull and transom microbial communities. Micro-organisms from the air had minimal impact in all areas of the boat.

CONCLUSIONS

Our results demonstrate that micro-organisms from sources other than water can influence the microbial community of a boat, suggesting that terrestrial micro-organisms can impact the boat microbial community.

SIGNIFICANCE AND IMPACT OF THE STUDY

Outside of ballast tanks, microbial diversity on boats is largely unexplored. While ballast water is widely recognized as a route for dispersal of allochthonous micro-organisms, comparatively little is known about the microbial diversity on other areas of the boat. If the organisms on a boat originate from sources other than water, there is potential that terrestrial micro-organisms could be dispersed by shipping activity.

Urbanisation reduces the abundance and diversity of airborne microbes - but what does that mean for our health? A systematic review

Over half of people live in cities and while urban environments offer myriad social, cultural and economic benefits, they alter the microbial communities to which people are exposed: with potentially important but underexplored health impacts. In particular, higher rates of asthma and allergies in urban areas have been linked to urban-altered microbial communities - including aerial microbial communities. To date, however, there has been no synthesis of the disparate literature on the impacts of urbanisation on aerial microbial communities, making it difficult to ascertain potential health impacts. We fill this knowledge gap by systematically examining studies that compare the characteristics (e.g. microbial abundance/diversity) and/or health effects of airborne fungal and bacterial communities (hereafter referred to as 'aerobiomes') across urban and rural locations. We included 19 studies, with 31 distinct urban-rural comparisons, in our analysis. We found that rural aerobiomes more often have a greater abundance of microbes (57% of studies). Aerobiome diversity was under-reported but when comparisons were made, rural aerobiome diversity was often higher (67%). Only two studies experimentally examined the impact of urban and rural aerobiomes on human health outcomes; both found rural aerobiomes shifted immune function away from allergic (Th2-type) responses. Overall, we conclude that significant gaps remain in our understanding of how urbanisation impacts aerobiomes and the health implications of those changes. We highlight the need to standardise methods and make aerobiome data open access to facilitate cross-study comparisons. Further mechanistic studies are urgently needed to examine the impact of aerobiome composition on immune function to demonstrate how urban-driven changes to the aerobiome impact human health - ultimately facilitating the development of healthier cities.