A Metagenomic Framework for the Study of Airborne Microbial Communities

Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria.

[1]  R. A. Leibler,et al.  On Information and Sufficiency , 1951 .

[2]  John M. Hancock,et al.  SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences , 1994, Comput. Appl. Biosci..

[3]  Ross A. Overbeek,et al.  The RDP (Ribosomal Database Project) , 1997, Nucleic Acids Res..

[4]  K. Prather,et al.  Detection and phylogenetic analysis of coastal bioaerosols using culture dependent and independent techniques , 2010 .

[5]  Rob Knight,et al.  Short-Term Temporal Variability in Airborne Bacterial and Fungal Populations , 2007, Applied and Environmental Microbiology.

[6]  Timothy B. Stockwell,et al.  Mechanism of chimera formation during the Multiple Displacement Amplification reaction , 2007, BMC biotechnology.

[7]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[8]  E. Delong,et al.  Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior , 2006, Science.

[9]  G. Vali,et al.  Microbiology and atmospheric processes: the role of biological particles in cloud physics , 2007 .

[10]  C. Hutchison,et al.  Cell-free cloning using φ29 DNA polymerase , 2005 .

[11]  A. Halpern,et al.  The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific , 2007, PLoS biology.

[12]  Michael Y. Galperin,et al.  The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..

[13]  Martin Täubel,et al.  The occupant as a source of house dust bacteria. , 2009, The Journal of allergy and clinical immunology.

[14]  Evidence for metabolic activity of airborne bacteria , 1975 .

[15]  Eoin L. Brodie,et al.  Urban aerosols harbor diverse and dynamic bacterial populations , 2007, Proceedings of the National Academy of Sciences.

[16]  S. Kravitz,et al.  The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data , 2010, Standards in genomic sciences.

[17]  J. Neufeld,et al.  Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology , 2008, The ISME Journal.

[18]  M. Pop,et al.  Metagenomic Analysis of the Human Distal Gut Microbiome , 2006, Science.

[19]  R. Knight,et al.  Sources of Bacteria in Outdoor Air across Cities in the Midwestern United States , 2011, Applied and Environmental Microbiology.

[20]  D. Dockery,et al.  Fungus spores, air pollutants, and other determinants of peak expiratory flow rate in children. , 1996, American journal of epidemiology.

[21]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[22]  D. Nilsson,et al.  Annual Variations in the Diversity, Viability, and Origin of Airborne Bacteria , 2010, Applied and Environmental Microbiology.

[23]  P. Borm,et al.  Temporal variation of hydroxyl radical generation and 8-hydroxy-2′-deoxyguanosine formation by coarse and fine particulate matter , 2003, Occupational and environmental medicine.

[24]  Jeff Kline,et al.  Architectural design influences the diversity and structure of the built environment microbiome , 2012, The ISME Journal.

[25]  Hideaki Sugawara,et al.  The Sequence Read Archive , 2010, Nucleic Acids Res..

[26]  J. Venter,et al.  Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic , 2012, The ISME Journal.

[27]  B. Haas,et al.  Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. , 2011, Genome research.

[28]  G. Church,et al.  Sequencing genomes from single cells by polymerase cloning , 2006, Nature Biotechnology.

[29]  Mihai Pop,et al.  ARDB—Antibiotic Resistance Genes Database , 2008, Nucleic Acids Res..

[30]  L R Maki,et al.  Ice Nucleation Induced by Pseudomonas syringae , 1974, Applied microbiology.

[31]  C. Andrews-Pfannkoch,et al.  Hydroxyapatite-Mediated Separation of Double-Stranded DNA, Single-Stranded DNA, and RNA Genomes from Natural Viral Assemblages , 2010, Applied and Environmental Microbiology.

[32]  William W. Nazaroff,et al.  Human Occupancy as a Source of Indoor Airborne Bacteria , 2012, PloS one.

[33]  Shawn W. Polson,et al.  Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA , 2011, Applied and Environmental Microbiology.

[34]  Gary L Andersen,et al.  Development of a high‐volume aerosol collection system for the identification of air‐borne micro‐organisms , 2002, Letters in applied microbiology.

[35]  M. V. D. van der Heijden,et al.  The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. , 2008, Ecology letters.

[36]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[37]  Lisa Zeigler Allen,et al.  Single Virus Genomics: A New Tool for Virus Discovery , 2011, PloS one.

[38]  Peter B. McGarvey,et al.  UniRef: comprehensive and non-redundant UniProt reference clusters , 2007, Bioinform..

[39]  Tao Zhang,et al.  The Airborne Metagenome in an Indoor Urban Environment , 2008, PloS one.

[40]  Ron Y. Pinter,et al.  A Statistical Framework for the Functional Analysis of Metagenomes , 2008, RECOMB.

[41]  J. Prospero,et al.  Interhemispheric transport of viable fungi and bacteria from Africa to the Caribbean with soil dust , 2005 .

[42]  P. Amato,et al.  Microorganisms isolated from the water phase of tropospheric clouds at the Puy de Dôme: major groups and growth abilities at low temperatures. , 2007, FEMS microbiology ecology.

[43]  M. Lawrence,et al.  Bacteria in the global atmosphere – Part 1: Review and synthesis of literature data for different ecosystems , 2009 .

[44]  W. H. Engelmann,et al.  The National Human Activity Pattern Survey (NHAPS): a resource for assessing exposure to environmental pollutants , 2001, Journal of Exposure Analysis and Environmental Epidemiology.

[45]  G. Blomquist,et al.  18S rRNA Gene Variation among Common Airborne Fungi, and Development of Specific Oligonucleotide Probes for the Detection of Fungal Isolates , 2003, Applied and Environmental Microbiology.

[46]  Shibu Yooseph,et al.  From bacterial to microbial ecosystems (metagenomics). , 2012, Methods in molecular biology.

[47]  S. Aust,et al.  Iron autoxidation and free radical generation: effects of buffers, ligands, and chelators. , 2002, Archives of biochemistry and biophysics.

[48]  T. Wassenaar,et al.  Bacterial virulence: can we draw the line? , 2001, FEMS microbiology letters.

[49]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[50]  Tracy K. Teal,et al.  Identifying and removing artificial replicates from 454 pyrosequencing data. , 2010, Cold Spring Harbor protocols.

[51]  Birgit Sattler,et al.  Bacterial growth in supercooled cloud droplets , 2001 .

[52]  B. Bohannan,et al.  Biodiversity and biogeography of the atmosphere , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[53]  Patrick Minnis,et al.  Dust and Biological Aerosols from the Sahara and Asia Influence Precipitation in the Western U.S. , 2013, Science.

[54]  J. Handelsman.  Metagenomics: Application of Genomics to Uncultured Microorganisms , 2004, Microbiology and Molecular Biology Reviews.

[55]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[56]  P. Hugenholtz,et al.  From deep sequencing to viral tagging: Recent advances in viral metagenomics , 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.

[57]  R. Lockey,et al.  Typical levels of airborne fungal spores in houses without obvious moisture problems during a rainy season in Florida, USA. , 2008, Journal of investigational allergology & clinical immunology.

[58]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[59]  Jian Yang,et al.  VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors , 2011, Nucleic Acids Res..

[60]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.