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Microbial Ecology

, Volume 72, Issue 1, pp 70–84 | Cite as

Airborne Bacterial Diversity from the Low Atmosphere of Greater Mexico City

  • Jaime García-MenaEmail author
  • Selvasankar Murugesan
  • Ashael Alfredo Pérez-Muñoz
  • Matilde García-Espitia
  • Otoniel Maya
  • Monserrat Jacinto-Montiel
  • Giselle Monsalvo-Ponce
  • Alberto Piña-Escobedo
  • Lilianha Domínguez-Malfavón
  • Marlenne Gómez-Ramírez
  • Elsa Cervantes-González
  • María Teresa Núñez-Cardona
Environmental Microbiology

Abstract

Greater Mexico City is one of the largest urban centers in the world, with an estimated population by 2010 of more than 20 million inhabitants. In urban areas like this, biological material is present at all atmospheric levels including live bacteria. We sampled the low atmosphere in several surveys at different points by the gravity method on LB and blood agar media during winter, spring, summer, and autumn seasons in the years 2008, 2010, 2011, and 2012. The colonial phenotype on blood agar showed α, β, and γ hemolytic activities among the live collected bacteria. Genomic DNA was extracted and convenient V3 hypervariable region libraries of 16S rDNA gene were high-throughput sequenced. From the data analysis, Firmicutes, Proteobacteria, and Actinobacteria were the more abundant phyla in all surveys, while the genera from the family Enterobacteriaceae, in addition to Bacillus spp., Pseudomonas spp., Acinetobacter spp., Erwinia spp., Gluconacetobacter spp., Proteus spp., Exiguobacterium spp., and Staphylococcus spp. were also abundant. From this study, we conclude that it is possible to detect live airborne nonspore-forming bacteria in the low atmosphere of GMC, associated to the microbial cloud of its inhabitants.

Keywords

Bioaerosols Hemolysis High-throughput sequencing Ion torrent Mass spectrometry MALDI-TOF MS 

Notes

Acknowledgments

This work was financed by Cinvestav, REMAS-CONACyT 0123119, CONACyT AP LIC 104881, ICYTDF/324/2009 FOLIO: 0649, CONACyT 163235 INFR-2011-01, and FONSEC SS/IMSS/ISSSTE-CONACYT-233361 granted to JGM. We thank a Postdoctoral Fellowship from FONSEC SS/IMSS/ISSSTE-CONACYT-233361 granted to SM. We also thank Mrs. Antonia López Salazar for clerical assistance and Mr. José Rodrigo García Gutiérrez for technical assistance.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflicts of interest. The authors alone are responsible for the content and writing of the paper. The authors declared that they have no financial and personal relationships with other people or organizations that can inappropriately influence their work. There is no professional or other personal interest of any nature or kind in any product, service, and/or company.

Supplementary material

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ESM 1 (DOCX 14 kb)
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Fig. S1

LB and Blood Agar plates from gravity sampling. The figure shows digital images of representative sampling plates of the surveys. a) Typical bacterial colony growth on Luria-Bertani (LB) and b) Typical bacterial colony growth on Blood-Agar (BA); hemolysis halos can be observed around some colonies (GIF 158 kb)

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High resolution image (TIF 2644 kb)
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Fig. S2

Escherichia coli 16S rDNA gene and primers. Figure shows a representation of the Brosius 1,541 bp rrnB 16S ribosomal gene of E. coli. Primers used for PCR are shown: First Set, forward FBac 5′-ATC ATG GCT CAG ATT GAA CGC-3′ (complementary positions 16-36), reverse RBAc 5′-ACT CCT ACG GGA GGC AGC AG-3′ (position 337-356); Second Set, CGO Forward 465 5′-CTC CTA CGG GAG GCA GCA G-3′ (positions 338-356), CGO Reverse 465 5′-CAG GAT TAG ATA CCC TGG TAG-3′, (positions 782-802); and Third Set, CGO Forward 605 5′-CAG GAT TAG ATA CCC TGG TAG-3′ (positions 782-802), CGO Reverse 605 5′-CGG TGA ATA CGT TCC CGG G-3′ (1368-1386). The primer V3-341F which indicates the complementary sequence for the seven forward primers used for 16S rDNA based high-throughput sequencing (V3-341F2, V3-341F4, V3-341F7, V3-341F8, V3-341F9, V3-341F18, V3-341F49) (position 334-354), and the reverse V3-518R primer (position 506-529) have described elsewhere [42]. Solid arrows indicate complementary regions for primers; larger gray color filled arrows from V1 to V9, indicate the polymorphic variable sequences in the molecule: GenBank: J01859.1 [31, 32] (GIF 15 kb)

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High resolution image (TIF 818 kb)
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Fig. S3

Mass spectroscopy identification of selected bacteria. The figure shows the spectra of selected isolated bacteria in the 2008 survey in GMC, generated using the Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry, technology AXIMA@SARAMIS from Anagnostec as described in Material and methods [30]. Identified bacteria using this method are: a) Bacillus subtilis; b) Staphylococcus epidermidis; c) Bacillus subtilis; d) Bacillus pumilus; e) Bacillus subtilis; f) Staphylococcus xylosus; g) Bacillus cereus; h) Not analyzed by Anagnostec; i) Bacillus subtilis; j) Staphylococcus epidermidis; k) Bacillus pumilus; l) Bacillus pumilus; m) Bacillus pumilus; n) Staphylococcus saprophyticus; o) Bacillus pumilus; p) Psychrobacter phenylpyruvicus; q) Not identified by the AXIMA@SARAMIS database; r) Psychrobacter phenylpyruvicus; s) Bacillus megaterium; t) Bacillus sp.; u) Bacillus subtilis; v) Bacillus coagulans; w) Psychrobacter phenylpyruvicus; x) Bacillus sp. See bacteria in Table 3 (GIF 224 kb)

248_2016_747_Fig9_ESM.gif (262 kb)
Fig. S3

Mass spectroscopy identification of selected bacteria. The figure shows the spectra of selected isolated bacteria in the 2008 survey in GMC, generated using the Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry, technology AXIMA@SARAMIS from Anagnostec as described in Material and methods [30]. Identified bacteria using this method are: a) Bacillus subtilis; b) Staphylococcus epidermidis; c) Bacillus subtilis; d) Bacillus pumilus; e) Bacillus subtilis; f) Staphylococcus xylosus; g) Bacillus cereus; h) Not analyzed by Anagnostec; i) Bacillus subtilis; j) Staphylococcus epidermidis; k) Bacillus pumilus; l) Bacillus pumilus; m) Bacillus pumilus; n) Staphylococcus saprophyticus; o) Bacillus pumilus; p) Psychrobacter phenylpyruvicus; q) Not identified by the AXIMA@SARAMIS database; r) Psychrobacter phenylpyruvicus; s) Bacillus megaterium; t) Bacillus sp.; u) Bacillus subtilis; v) Bacillus coagulans; w) Psychrobacter phenylpyruvicus; x) Bacillus sp. See bacteria in Table 3 (GIF 224 kb)

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High resolution image (TIF 700 kb)
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High resolution image (TIF 814 kb)
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Fig. S4

Beta diversity. Unweighted UniFrac analyses were used to calculate distances between samples obtained from the seven surveys, determined by massive sequencing of V3-16S rDNA libraries prepared from DNA from bacterial growth on LB plates as described in Materials and methods. Three-dimensional scatter plots were generated by principal coordinates analysis (PCoA). (GIF 33 kb)

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High resolution image (TIF 2190 kb)
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Fig. S5

Alpha diversity Rarefaction curves. Rarefaction curves were generated using massive sequencing data of V3-16S rDNA libraries from the seven surveys, as described in Materials and methods. The vertical axes display the diversity of the community, while the horizontal axes display the number of sequences considered in the diversity calculation. Each color indicates diversity of community for each survey. Panel A, displays rarefaction curves of the number of observed species was calculated at a similarity threshold of 97 %; Panel B, represents the rarefaction curves using the Shannon index; Panel C, shows rarefaction curves using the Chao1. (GIF 61 kb)

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High resolution image (TIF 3992 kb)
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Fig. S6

Jacknifed beta diversity. Unweighted UniFrac analyses were used to calculate distances among sequencing data of the seven surveys, determined by massive sequencing of V3-16S rDNA libraries prepared as described in Materials and methods; tree chart was generated by using Jacknifing method. (GIF 16 kb)

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High resolution image (TIF 1392 kb)

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Jaime García-Mena
    • 1
    Email author
  • Selvasankar Murugesan
    • 1
  • Ashael Alfredo Pérez-Muñoz
    • 1
  • Matilde García-Espitia
    • 2
  • Otoniel Maya
    • 1
  • Monserrat Jacinto-Montiel
    • 1
  • Giselle Monsalvo-Ponce
    • 1
  • Alberto Piña-Escobedo
    • 1
  • Lilianha Domínguez-Malfavón
    • 1
  • Marlenne Gómez-Ramírez
    • 1
    • 3
  • Elsa Cervantes-González
    • 1
    • 4
  • María Teresa Núñez-Cardona
    • 5
  1. 1.Departamento de Genética y Biología MolecularCentro de Investigación y de Estudios Avanzados del IPNCiudad de MéxicoMexico
  2. 2.Escuela Nacional de Medicina y Homeopatía del IPNCiudad de MéxicoMexico
  3. 3.CICATA-QuerétaroSantiago de QuerétaroMexico
  4. 4.Departamento de Ingeniería QuímicaUniversidad Autónoma de San Luis PotosíMatehualaMexico
  5. 5.Departamento El Hombre y su AmbienteUniversidad Autónoma Metropolitana-XochimilcoCiudad de MéxicoMexico

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