Seasonal variability in bacterial and fungal diversity of the near-surface atmosphere.
22 Oct 2013-Environmental Science & Technology (Environ Sci Technol)-Vol. 47, Iss: 21, pp 12097-12106
TL;DR: A comprehensive analysis of airborne microbes across two aerosol size fractions at urban and rural sites in the Colorado Front Range over a 14-month period suggests that a complex set of environmental factors act to control the composition of microbial bioaerosols in rural and urban environments.
Abstract: Bacteria and fungi are ubiquitous throughout the Earth's lower atmosphere where they often represent an important component of atmospheric aerosols with the potential to impact human health and atmospheric dynamics. However, the diversity, composition, and spatiotemporal dynamics of these airborne microbes remain poorly understood. We performed a comprehensive analysis of airborne microbes across two aerosol size fractions at urban and rural sites in the Colorado Front Range over a 14-month period. Coarse (PM10-2.5) and fine (PM2.5) particulate matter samples were collected at weekly intervals with both bacterial and fungal diversity assessed via high-throughput sequencing. The diversity and composition of the airborne communities varied across the sites, between the two size fractions, and over time. Bacteria were the dominant type of bioaerosol in the collected air samples, while fungi and plants (pollen) made up the remainder, with the relative abundances of fungi peaking during the spring and summer months. As bacteria made up the majority of bioaerosol particles, we analyzed the bacterial communities in greater detail using a bacterial-specific 16S rRNA gene sequencing approach. Overall, bacterial taxonomic richness and the relative abundances of specific bacterial taxa exhibited significant patterns of seasonality. Likewise, airborne bacterial communities varied significantly between sites and across aerosol size fractions. Source-tracking analyses indicate that soils and leaves represented important sources of bacteria to the near-surface atmosphere across all locations with cow fecal bacteria also representing an important source of bioaerosols at the more rural sites during early fall and early spring. Together, these data suggest that a complex set of environmental factors, including changes in atmospheric conditions and shifts in the relative importance of available microbial sources, act to control the composition of microbial bioaerosols in rural and urban environments.
Citations
More filters
TL;DR: A review of the state of bioaerosol research, highlights recent advances, and outlines future perspectives in terms of identification, characterization, transport and transformation processes, as well as their interactions with climate, health, and ecosystems, focusing on the role bio-aerosols play in the Earth system.
588 citations
Additional excerpts
...Plant pollen, fungal spores, bacteria, algae, and cyanobacteria have been identified in bioaerosol samples (e.g., Bauer et al., 2002a; Bowers et al., 2013; Brown et al., 1964; DeLeon-Rodriguez et al., 2013; Delort et al., 2010; Després et al., 2012; Favero-Longo et al., 2014; Fröhlich-Nowoisky et…...
[...]
...…(RNA analysis), and have been successfully used in several recent bioaerosol related studies (e.g., Be et al., 2013; Bertolini et al., 2013; Bowers et al., 2013, 2012, 2011, 2010, 2009; Cao et al., 2014; DeLeon-Rodriguez et al., 2013; Franzetti et al., 2011; Kraaijeveld et al., 2015;…...
[...]
TL;DR: It is shown that with sufficient sequencing depth, airborne microbes including bacteria, archaea, fungi, and dsDNA viruses can be identified at the species level and suggested that the majority of the inhalable microorganisms were soil-associated and nonpathogenic to human.
Abstract: Particulate matter (PM) air pollution poses a formidable public health threat to the city of Beijing. Among the various hazards of PM pollutants, microorganisms in PM2.5 and PM10 are thought to be responsible for various allergies and for the spread of respiratory diseases. While the physical and chemical properties of PM pollutants have been extensively studied, much less is known about the inhalable microorganisms. Most existing data on airborne microbial communities using 16S or 18S rRNA gene sequencing to categorize bacteria or fungi into the family or genus levels do not provide information on their allergenic and pathogenic potentials. Here we employed metagenomic methods to analyze the microbial composition of Beijing's PM pollutants during a severe January smog event. We show that with sufficient sequencing depth, airborne microbes including bacteria, archaea, fungi, and dsDNA viruses can be identified at the species level. Our results suggested that the majority of the inhalable microorganisms were soil-associated and nonpathogenic to human. Nevertheless, the sequences of several respiratory microbial allergens and pathogens were identified and their relative abundance appeared to have increased with increased concentrations of PM pollution. Our findings may serve as an important reference for environmental scientists, health workers, and city planners.
557 citations
TL;DR: This work addresses air contaminants and their multiphase chemical interactions at the atmosphere−biosphere interface, including human lungs and skin, plant leaves, cryptogamic covers, soil, and aquatic surfaces, and the chemical interactions of reactive oxygen species and reactive nitrogen species, as well as carbonaceous combustion aerosols.
Abstract: This is an open access article published under a Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. Review pubs.acs.org/CR Multiphase Chemistry at the Atmosphere−Biosphere Interface Influencing Climate and Public Health in the Anthropocene Ulrich Po schl* and Manabu Shiraiwa* Multiphase Chemistry Department, Max Planck Institute for Chemistry, 55128 Mainz, Germany air contaminants (SHCC) and their multiphase chemical interactions at the atmosphere−biosphere interface, including human lungs and skin, plant leaves, cryptogamic covers, soil, and aquatic surfaces. After an overview of different groups of SHCC, we address the chemical interactions of reactive oxygen species and reactive nitrogen species (ROS, RNS), primary biological and secondary organic aerosols (PBA, SOA), as well as carbonaceous combustion aerosols (CCA) including soot, black/elemental carbon, polycyclic aromatic hydrocarbons, and related compounds (PAH, PAC). ROS and RNS interact strongly with other SHCC and are central to both atmospheric and physiological processes and their coupling through the atmosphere−biosphere interface, for example, in the formation and aging of biogenic and combustion aerosols as well as in CONTENTS inflammatory and allergic immune responses triggered by air pollution. Deposition of atmospheric ROS/RNS and aerosols 1. Introduction and Motivation can damage biological tissues, modify surface microbiomes, and 2. Health- and Climate-Relevant Air Contaminants induce oxidative stress through Fenton-like reactions and 2.1. Reactive Oxygen and Nitrogen Species immune responses. The chemical mechanisms and kinetics are 2.2. Primary Biological Aerosols not yet fully elucidated, but the available evidence suggests that 2.3. Secondary Organic Aerosols multiphase processes are crucial for the assessment, prediction, 2.4. Carbonaceous Combustion Aerosols and handling of air quality, climate, and public health. Caution 2.5. Other Air Contaminants Linking Atmospher- should be taken to avoid that human activities shaping the ic and Physiological Chemistry Anthropocene create a hazardous or pathogenic atmosphere 3. Multiphase Chemical Reactions at Specific Bio- overloaded with allergenic, corrosive, toxic, or infectious logical Interfaces contaminants. 3.1. Lung Lining Fluid Multiphase chemistry deals with chemical reactions, trans- 3.2. Human Skin port processes, and transformations between gaseous, liquid, 3.3. Plant Surfaces and Cryptogamic Covers and solid matter. These processes are essential for Earth system 3.4. Soil and Aquatic Surfaces science and climate research as well as for life and health 4. Conclusions and Outlook sciences on molecular and global levels, bridging a wide range Author Information of spatial and temporal scales from below nanometers to Corresponding Authors thousands of kilometers and from less than nanoseconds to Notes years and millennia as illustrated in Figure 1. Biographies From a chemical perspective, life and the metabolism of most Acknowledgments living organisms can be regarded as multiphase processes References involving gases like oxygen and carbon dioxide; liquids like water, blood, lymph, and plant sap; and solid or semisolid substances like bone, tissue, skin, wood, and cellular 1. INTRODUCTION AND MOTIVATION membranes. Even primitive forms of life and metabolic activity Multiphase chemistry plays a vital role in the Earth system, under anaerobic conditions generally involve multiple liquid climate, and health. Chemical reactions, mass transport, and and solid or semisolid phases structured by cells, organelles, and phase transitions between gases, liquids, and solids are essential membranes. 2 On global scales, the biogeochemical cycling of for the interaction and coevolution of life and climate. chemical compounds and elements, which can be regarded as Knowledge of the mechanisms and kinetics of these processes the metabolism of planet Earth, also involves chemical is also required to address societally relevant questions of global reactions, mass transport, and phase transitions within and environmental change and public health in the Anthropocene, that is, in the present era of globally pervasive and steeply Special Issue: 2015 Chemistry in Climate increasing human influence on planet Earth. 1 In this work, we review the current scientific understanding and recent advances Received: September 1, 2014 in the investigation of short-lived health- and climate-relevant Published: April 9, 2015 © 2015 American Chemical Society DOI: 10.1021/cr500487s Chem. Rev. 2015, 115, 4440−4475
449 citations
01 Apr 2009
TL;DR: By DNA analysis, pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter are found, with more plant pathogens in the coarse fraction and more human pathogens and allergens in the respirable fine particle fraction.
Abstract: Fungal spores can account for large proportions of air particulate matter, and they may potentially influence the hydrological cycle and climate as nuclei for water droplets and ice crystals in clouds, fog, and precipitation. Moreover, some fungi are major pathogens and allergens. The diversity of airborne fungi is, however, not well-known. By DNA analysis we found pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter, with more plant pathogens in the coarse fraction and more human pathogens and allergens in the respirable fine particle fraction (<3 μm). Moreover, the ratio of Basidiomycota to Ascomycota was found to be much higher than previously assumed, which might also apply to the biosphere.
364 citations
TL;DR: In this article, the authors investigated the correlation between the degree of accelerated diffusion and lethality of COVID-19 and the surface air pollution in Milan metropolitan area, Lombardy region, Italy.
343 citations
References
More filters
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Abstract: Supplementary Figure 1 Overview of the analysis pipeline. Supplementary Table 1 Details of conventionally raised and conventionalized mouse samples. Supplementary Discussion Expanded discussion of QIIME analyses presented in the main text; Sequencing of 16S rRNA gene amplicons; QIIME analysis notes; Expanded Figure 1 legend; Links to raw data and processed output from the runs with and without denoising.
28,911 citations
TL;DR: The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
Abstract: The Ribosomal Database Project (RDP) Classifier, a naive Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (≥95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.
16,048 citations
TL;DR: A new and simple method to find indicator species and species assemblages characterizing groups of sites, and a new way to present species-site tables, accounting for the hierarchical relationships among species, is proposed.
Abstract: This paper presents a new and simple method to find indicator species and species assemblages characterizing groups of sites The novelty of our approach lies in the way we combine a species relative abundance with its relative frequency of occurrence in the various groups of sites This index is maximum when all individuals of a species are found in a single group of sites and when the species occurs in all sites of that group; it is a symmetric indicator The statistical significance of the species indicator values is evaluated using a randomization procedure Contrary to TWINSPAN, our indicator index for a given species is independent of the other species relative abundances, and there is no need to use pseudospecies The new method identifies indicator species for typologies of species releves obtained by any hierarchical or nonhierarchical classification procedure; its use is independent of the classification method Because indicator species give ecological meaning to groups of sites, this method provides criteria to compare typologies, to identify where to stop dividing clusters into subsets, and to point out the main levels in a hierarchical classification of sites Species can be grouped on the basis of their indicator values for each clustering level, the heterogeneous nature of species assemblages observed in any one site being well preserved Such assemblages are usually a mixture of eurytopic (higher level) and stenotopic species (characteristic of lower level clusters) The species assemblage approach demonstrates the importance of the ''sampled patch size,'' ie, the diversity of sampled ecological combinations, when we compare the frequencies of core and satellite species A new way to present species-site tables, accounting for the hierarchical relationships among species, is proposed A large data set of carabid beetle distributions in open habitats of Belgium is used as a case study to illustrate the new method
7,449 citations
TL;DR: This work sequences a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample to demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature.
Abstract: The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
6,767 citations
TL;DR: SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains.
Abstract: Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs.
5,733 citations