Metagenomic analysis of the airborne environment in urban spaces.
Ontology highlight
ABSTRACT:
SUBMITTER: Be NA
PROVIDER: S-EPMC4312561 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The indoor atmosphere is an ecological unit that impacts on public health. To investigate the composition of organisms in this space, we applied culture-independent approaches to microbes harvested from the air of two densely populated urban buildings, from which we analyzed 80 megabases genomic DNA sequence and 6000 16S rDNA clones. The air microbiota is primarily bacteria, including potential opportunistic pathogens commonly isolated from human-inhabited environments such as hospitals, but none of the data contain matches to virulent pathogens or bioterror agents. Comparison of air samples with each other and nearby environments suggested that the indoor air microbes are not random transients from surrounding outdoor environments, but rather originate from indoor niches. Sequence annotation by gene function revealed specific adaptive capabilities enriched in the air environment, including genes potentially involved in resistance to desiccation and oxidative damage. This baseline index of air microbiota will be valuable for improving designs of surveillance for natural or man-made release of virulent pathogens.
| S-EPMC2270337 | biostudies-literature
Project description:The urbanization of the Las Vegas Valley has transformed this part of the Mohave Desert into a green oasis by introducing many non-native plant species, some of which are allergenic. Typically, one monitoring station is established per city to obtain pollen counts for an entire metropolitan area. However, variations in pollen concentrations could occur among different microenvironments. The objective of this study is to measure and compare pollen concentrations in five locations in Las Vegas to determine if there are significant differences between microenvironments within the city. Air samples were collected from five sites across the Las Vegas Valley over a 1-year period. Prepared slides were analyzed with a light microscope for pollen grains and converted into airborne pollen concentrations. Mixed model methods were used to determine mean differences. Tree pollen was the greatest contributor to the annual average airborne pollen concentrations (130 grains/m3) compared to weeds (6 grains/m3) and grass (3 grains/m3). The highest peak occurred in March 2016 (9589 total grains/m3). There were several differences among sites with respect to concentrations of individual tree species and for total weed and grass concentrations. We observed significant variations in concentration and composition among the five pollen collection stations that were established across the Las Vegas Valley. This study presented new outdoor pollen data for the southwest region of the USA, focused in Las Vegas. The results indicate that more sites and comprehensive monitoring of outdoor allergens are needed to provide accurate information to the community about outdoor air quality conditions.
| S-EPMC6018573 | biostudies-literature
Project description:The Phl p 5 allergen of the plant species Phleum pratense is considered one of the most crucial grass pollen allergenic molecules inducing respiratory allergies. In this study, we evaluated seasonal variation in the concentration of both grass pollen and Phl p 5 allergens as well as the ratio allergen/pollen (pollen potency) in the air of Bratislava during two consecutive years, 2019-2020. These 2 years differed in terms of air pollution, as COVID-19 lockdown in spring 2020 considerably improved air quality in the study area. Air samples were collected using a Hirst-type sampler for pollen detection and the cyclone sampler for aeroallergen detection. In 2020, we observed 80.3% higher seasonal pollen integral, probably associated with the longer pollen season duration, however, 43.6% lower mean daily pollen potency than in 2019. The mean daily pollen value was 37.5% higher in 2020 than in the previous year, while the mean daily allergen value was 14.9% lower in 2020. To evaluate the relationship between the amount of pollen or allergen in the air and selected meteorological factors and air pollution parameters, we used multiple regression analysis. Regarding weather factors, precipitation and relative humidity were significantly associated with pollen and/or allergen concentration, though these associations were negative. Atmospheric pollutants, especially CO, NO2 and O3 were significantly associated with pollen and/or allergen levels. The associations with CO and O3 were positive, while the association with NO2 was negative. Our results indicate that for grasses, an air pollutant that has a significant positive relationship to the ratio of allergen/pollen is nitrogen dioxide.
| S-EPMC8248954 | biostudies-literature
Project description:Analyzing temporal and spatial distributions of airborne particles of biological origins is vital for the assessment and monitoring of air quality, especially with regard to public health, environmental ecology, and atmospheric chemistry. However, the analysis is frequently impeded by the low levels of biomass in the air, especially with metagenomic DNA analysis to explore diversity and composition of living organisms and their components in the air. To obtain sufficient amounts of metagenomic DNA from bioaerosols, researchers usually need a long sampling time with an expensive high-volume air sampler. This work shows the utilization of an air sampling device containing an economical, high-volume portable ventilation fan in combination with customized multi-sheet filter holders to effectively obtain high yields of genomic DNA in a relatively short time. The device, named 'AirDNA' sampler, performed better than other commercial air samplers, including MD8 Airport and Coriolis compact air samplers. Using the AirDNA sampler, an average DNA yield of 40.49 ng (12.47-23.24 ng at 95% CI) was obtained in only 1 hour of air sampling with a 0.85 probability of obtaining ≥10 ng of genomic DNA. The genomic DNA obtained by the AirDNA system is of suitable quantity and quality to be further used for amplicon metabarcoding sequencing of 16S, 18S, and cytochrome c oxidase I (COI) regions, indicating that it can be used to detect various prokaryotes and eukaryotes. Our results showed the effectiveness of our AirDNA sampling apparatus with a simple setup and affordable devices to obtain metagenomic DNA for short-term or long-term spatiotemporal analysis. The technique is well suited for monitoring air in built environments, especially monitoring bioaerosols for health purposes and for fine-scale spatiotemporal environmental studies.
| S-EPMC10309600 | biostudies-literature
Project description:SPATIO-TEMPORAL VARIABILITY AND COMMUNITY-ASSEMBLY PROCESSES OF AIRBORNE BACTERIA ACROSS TWO URBAN AREAS
| PRJEB7001 | ENA
Project description:Metagenomic analysis of wild urban Rats (Rattus spp.) highlights the sympatric nature of rat and human microbial ecology
| PRJEB9661 | ENA
Project description:Airborne fungal spores constitute an important type of bioaerosol and are responsible for a number of negative effects on human health, including respiratory diseases and allergies. We investigated the diversity and concentration of culturable airborne fungi on pedestrian bridges in Tianjin, China, using an HAS-100B air sampler. We compared the airborne fungal communities at the top central area of the selected pedestrian bridges and along the corresponding sidewalk, at ground level. A total of 228 fungal strains belonging to 96 species and 58 genera of Ascomycota (68.86%), Basidiomycota (30.26%), and Mucoromycota (0.88%) were isolated and identified using morphological and molecular analysis. Alternaria was the dominant genus (20.61%), followed by Cladosporium (11.48%), Schizophyllum (6.14%), Sporobolomyces (5.70%), and Sporidiobolus (4.82%). Alternaria alternata was the most frequently occurring fungal species (6.58%), followed by Schizophyllum commune (5.26%), Alternaria sp. (4.82%), Sporobolomyces carnicolor (4.39%), and Cladosporium cladosporioides (3.95%). The recorded fungal concentration ranged from 10 to 180 CFU/m3. Although there was no significant difference in the distribution and abundance of the dominant airborne fungal taxa between the two investigated bridges' sites, numerous species detected with a low percentage of abundance belonging to well-known pathogenic fungal genera, including Alternaria, Aspergillus, Aureobasidium, Cladosporium, Penicillium, and Trichoderma, were exclusively present in one of the two sites. The relative humidity showed a stronger influence compared to the temperature on the diversity and concentration of airborne fungi in the investigated sites. Our results may provide valuable information for air quality monitoring and for assessing human health risks associated with microbial pollution.
| S-EPMC10458245 | biostudies-literature
Project description:Risk events frequently occur in "complex urban public spaces" (CUPSs) and cause serious economic losses and casualties. To reduce the risks and enhance the system resilience, this paper formulates a theoretical framework to assess the resilience of CUPSs. Resilience is defined as the ratio of preparedness to vulnerability, according to the implication of the concept. Three-level practical indicator systems were established for these two dimensions, respectively. Furthermore, a hybrid approach combining the Analytic Network Process (ANP) and the Decision-Making Trial and Evaluation Laboratory (DEMATEL) was adopted. The Chongqing West Railway Station (the Station (W)) and the Lianglukou Rail Transit Station (the Station (L)) were used for a case study. The results showed that the Chongqing West Railway Station was more resilient to risks than the Lianglukou Rail Transit Station. Therefore, the proposed theoretical framework could be applied in assessing the resilience level of CUPSs. Resilience improvement strategies can be formulated according to the assessment results. Furthermore, the practical indicators could also provide references for urban disaster management.
| S-EPMC7014252 | biostudies-literature
Project description:Urbanization is among the largest threats to wildlife populations through factors such as fragmentation, isolation, and habitat destruction. Urban open spaces, such as parks and golf courses, have the potential to provide wildlife with suitable habitat within an urbanized matrix. These refugia may be particularly important for amphibians, which represent one of the most endangered and least vagile vertebrate groups on earth. During the spring and summer of 2018, we conducted surveys to determine the presence of anurans at 51 wetland sites within the Piedmont ecoregion of South Carolina. Nearly one-third of these wetlands were located within urban open spaces, one-third in low development areas, and one-third in highly developed areas. Impervious surface and total road length surrounding the wetlands were measured at two scales, a core habitat scale (300 m) and average maximum migration scale (750 m), and we measured several within-wetland habitat variables. Urban Open Space wetlands had levels of surrounding impervious surface similar to High Urbanization wetlands at the larger scale and were intermediate between Low and High Urbanization wetlands at the smaller scale. The total length of road segments occurring within buffers (at both scales) surrounding our study wetlands was higher for Urban Open Space compared to Low and High Urbanization sites. Among the within-wetland variables measured, Low Urbanization sites had higher canopy cover and were more likely to have a terrestrial buffer zone relative to the other categories. Species richness decreased significantly as total road length increased among all wetlands. Wetland category was not a significant driver explaining species richness, but β-diversity was more variable among Urban Open Space wetlands than either Low or High Urbanization wetlands. Urban Open Space wetlands did not appear to increase suitability for anurans relative to High Urbanization wetlands. Urban Open Space wetlands had higher variability in species composition, which was perhaps attributable to the diversity among sites represented in the Urban Open Space category.
| S-EPMC7822500 | biostudies-literature
Project description:Although the benefits from exposure to urban green spaces (UGS) are increasingly reported, there are important knowledge gaps in the nature of UGS-health relationships. One such unknown area is the dependence of UGS-health associations on the types of UGS studied, the way they are quantified, and the spatial scale used in the analysis. These knowledge gaps have important ramifications on our ability to develop generalizations to promote implementation and facilitate comparative studies across different socio-cultural and socio-economic contexts. We conducted a study in Singapore to examine the dependence of UGS-health associations on the metrics for quantifying UGS (vegetation cover, canopy cover and park area) in different types of buffer area (circular, nested and network) at different spatial scales. A population-based household survey (n = 1000) was used to collect information on self-reported health and perception and usage pattern of UGS. The results showed that although all three UGS metrics were positively related to mental health at certain scales, overall, canopy cover showed the strongest associations with mental health at most scales. There also appears to be minimum and maximum threshold levels of spatial scale at which UGS and health have significant associations, with the strongest associations consistently shown between 400 m to 1600 m in different buffer types. We discuss the significance of these results for UGS-health studies and applications in UGS planning for improved health of urban dwellers.
| S-EPMC6406785 | biostudies-literature