, Volume 33, Issue 1, pp 71–86 | Cite as

Molecular analysis of environmental plant DNA in house dust across the United States

  • Joseph M. Craine
  • Albert Barberán
  • Ryan C. Lynch
  • Holly L. Menninger
  • Robert R. Dunn
  • Noah Fierer


Despite the prevalence and costs of allergic diseases caused by pollen, we know little about the distributions of allergenic and non-allergenic pollen inside and outside homes at the continental scale. To better understand patterns in potential pollen diversity across the United States, we used DNA sequencing of a chloroplast marker gene to identify the plant DNA found in settled dust collected on indoor and outdoor surfaces across 459 homes. House location was the best predictor of the relative abundance of plant taxa found in outdoor dust samples. Urban, southern houses in hotter climates that were further from the coast were more likely to have more DNA from grass and moss species, while rural houses in northern, cooler climates closer to the coast were more likely to have higher relative abundances of DNA from Pinus and Cedrus species. In general, those plant taxa that were more abundant outdoors were also more abundant indoors, but indoor dust had uniquely high abundances of DNA from food plants and plants associated with lawns. Approximately 14 % of the plant DNA sequences found outside were from plant taxa that are known to have allergenic pollen compared to just 8 % inside. There was little geographic pattern in the total relative abundance of these allergens highlighting the difficulties associated with trying to predict allergen exposures based on geographic location alone. Together, this work demonstrates the utility of using environmental DNA sequencing to reconstruct the distributions of plant DNA inside and outside buildings, an approach that could prove useful for better understanding and predicting plant allergen exposures.


Environmental DNA Plant allergens Geography Next-generation sequencing 



We thank the volunteers who participated in the Wild Life of Our Homes project for collecting dust samples. Funding for the sample collection was provided by a grant from the A. P. Sloan Microbiology of the Built Environment Program (to NF and RRD).


  1. Anderson, M. J. (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecology, 26(1), 32–46.Google Scholar
  2. Barberán, A., Dunn, R. R., Reich, B. J., Pacifici, K., Laber, E. B., Menninger, H. L., et al. (2015a). The ecology of microscopic life in household dust. Proceedings of the Royal Society B-Biological Sciences,. doi: 10.1098/rspb.2015.1139.Google Scholar
  3. Barberán, A., Ladau, J., Leff, J. W., Pollard, K. S., Menninger, H. L., Dunn, R. R., et al. (2015b). Continental-scale distributions of dust-associated bacteria and fungi. Proceedings of the National Academy of Science of the United States of America, 112(18), 5756–5761. doi: 10.1073/pnas.1420815112.CrossRefGoogle Scholar
  4. Bruni, I., Galimberti, A., Caridi, L., Scaccabarozzi, D., De Mattia, F., Casiraghi, M., et al. (2015). A DNA barcoding approach to identify plant species in multiflower honey. Food Chemistry, 170, 308–315. doi: 10.1016/j.foodchem.2014.08.060.CrossRefGoogle Scholar
  5. Burge, H. A. (2002). An update on pollen and fungal spore aerobiology. Journal of Allergy and Clinical Immunology, 110(4), 544–552. doi: 10.1067/mai.2002.128674.CrossRefGoogle Scholar
  6. Campbell, I. D., McDonald, K., Flannigan, M. D., & Kringayark, J. (1999). Long-distance transport of pollen into the Arctic. Nature, 399(6731), 29–30.CrossRefGoogle Scholar
  7. Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., et al. (2012). Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal, 6(8), 1621–1624.CrossRefGoogle Scholar
  8. Cecchi, L., Morabito, M., Domeneghetti, P., Crisci, A., Onorari, M., & Orlandini, S. (2006). Long distance transport of ragweed pollen as a potential cause of allergy in central Italy. Annals of Allergy, Asthma & Immunology, 96(1), 86–91.CrossRefGoogle Scholar
  9. D’Amato, G., Cecchi, L., Bonini, S., Nunes, C., Annesi-Maesano, I., Behrendt, H., et al. (2007). Allergenic pollen and pollen allergy in Europe. Allergy, 62(9), 976–990. doi: 10.1111/j.1398-9995.2007.01393.x.CrossRefGoogle Scholar
  10. Denning, D., O’Driscoll, B., Hogaboam, C., Bowyer, P., & Niven, R. (2006). The link between fungi and severe asthma: A summary of the evidence. European Respiratory Journal, 27(3), 615–626.CrossRefGoogle Scholar
  11. Dufrêne, M., & Legendre, P. (1997). Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecological Monographs, 67(3), 345–366.Google Scholar
  12. Dunwiddie, P. W. (1987). Macrofossil and pollen representation of coniferous trees in modern sediments from Washington. Ecology, 68(1), 1–11.CrossRefGoogle Scholar
  13. Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26(19), 2460–2461.CrossRefGoogle Scholar
  14. Edgar, R. C. (2013). UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10(10), 996–998.CrossRefGoogle Scholar
  15. Esch, R. E., Hartsell, C. J., Crenshaw, R., & Jacobson, R. S. (2001). Common allergenic pollens, fungi, animals, and arthropods. Clinical Reviews in Allergy and Immunology, 21(2), 261–292.CrossRefGoogle Scholar
  16. Fahlbusch, B., Hornung, D., Heinrich, J., Dahse, H. M., & Jäger, L. (2000). Quantification of group 5 grass pollen allergens in house dust. Clinical and Experimental Allergy, 30(11), 1646–1652.CrossRefGoogle Scholar
  17. Fahlbusch, B., Hornung, D., Heinrich, J., & Jäger, L. (2001). Predictors of group 5 grass-pollen allergens in settled house dust: Comparison between pollination and nonpollination seasons. Allergy, 56(11), 1081–1086. doi: 10.1034/j.1398-9995.2001.00106.x.CrossRefGoogle Scholar
  18. Gavin, D. G., Brubaker, L. B., McLachlan, J. S., & Oswald, W. W. (2005). Correspondence of pollen assemblages with forest zones across steep environmental gradients, Olympic Peninsula, Washington, USA. The Holocene, 15(5), 648–662.CrossRefGoogle Scholar
  19. Grantham, N. S., Reich, B. J., Pacifici, K., Laber, E. B., Menninger, H. L., Henley, J. B., et al. (2015). Fungi identify the geographic origin of dust samples. PLoS One, 10(4), e0122605. doi: 10.1371/journal.pone.0122605.CrossRefGoogle Scholar
  20. Heusser, C. J. (1978). Modern pollen rain of Washington. Canadian Journal of Botany, 56(13), 1510–1517.CrossRefGoogle Scholar
  21. Hjelmroos, M. (1991). Evidence of long-distance transport of Betula pollen. Grana, 30(1), 215–228.CrossRefGoogle Scholar
  22. Hugg, T., & Rantio-Lehtimäki, A. (2007). Indoor and outdoor pollen concentrations in private and public spaces during the Betula pollen season. Aerobiologia, 23(2), 119–129. doi: 10.1007/s10453-007-9057-z.CrossRefGoogle Scholar
  23. Klepeis, N. E., Nelson, W. C., Ott, W. R., Robinson, J. P., Tsang, A. M., Switzer, P., et al. (2001). The National Human Activity Pattern Survey (NHAPS): A resource for assessing exposure to environmental pollutants. Journal of Exposure Analysis and Environmental Epidemiology, 11(3), 231–252.CrossRefGoogle Scholar
  24. Kress, W. J., Garcia-Robledo, C., Uriarte, M., & Erickson, D. L. (2015). DNA barcodes for ecology, evolution, and conservation. Trends in Ecology & Evolution, 30(1), 25–35. doi: 10.1016/j.tree.2014.10.008.CrossRefGoogle Scholar
  25. Legendre, P., & Gallagher, E. D. (2001). Ecologically meaningful transformations for ordination of species data. Oecologia, 129(2), 271–280.CrossRefGoogle Scholar
  26. McLauchlan, K. K., Commerford, J. L., & Morris, C. J. (2013). Tallgrass prairie pollen assemblages in mid-continental North America. Vegetation History and Archaeobotany, 22(3), 171–183.CrossRefGoogle Scholar
  27. O’Rourke, M. K., & Lebowitz, M. D. (1984). A comparison of regional atmospheric pollen with pollen collected at and near homes. Grana, 23(1), 55–64.CrossRefGoogle Scholar
  28. Pawankar, R., Canonica, G. W., Holgate, S. T., & Lockey, R. F. (2012). Allergic diseases and asthma: A major global health concern. Current Opinion in Allergy and Clinical Immunology, 12(1), 39–41. doi: 10.1097/ACI.0b013e32834ec13b.CrossRefGoogle Scholar
  29. Pichot, C., Calleja, M., Penel, V., Bues-Charbit, M., & Charpin, D. (2015). Inference of the pollen penetration and remanence into dwellings using seasonal variation of indoor/outdoor pollen counts. Aerobiologia, 31(3), 315–322. doi: 10.1007/s10453-015-9366-6.CrossRefGoogle Scholar
  30. Richardson, R. T., Lin, C. H., Sponsler, D. B., Quijia, J. O., Goodell, K., & Johnson, R. M. (2015). Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in an agroecosystem. Applications in plant Sciences,. doi: 10.3732/apps.1400066.Google Scholar
  31. Rogers, C. A., & Levetin, E. (1998). Evidence of long-distance transport of mountain cedar pollen into Tulsa, Oklahoma. International Journal of Biometeorology, 42(2), 65–72.CrossRefGoogle Scholar
  32. Salvatori, N., Reccardini, F., Convento, M., Purinan, A., Colle, R., De Carli, S., et al. (2008). Asthma induced by inhalation of flour in adults with food allergy to wheat. Clinical and Experimental Allergy, 38(8), 1349–1356.CrossRefGoogle Scholar
  33. Sicherer, S. H., Furlong, T. J., DeSimone, J., & Sampson, H. A. (1999). Self-reported allergic reactions to peanut on commercial airliners. Journal of Allergy and Clinical Immunology, 104(1), 186–189.CrossRefGoogle Scholar
  34. Sterling, D. A., & Lewis, R. D. (1998). Pollen and fungal spores indoor and outdoor of mobile homes. Annals of Allergy, Asthma & Immunology, 80(3), 279–285.CrossRefGoogle Scholar
  35. Sugita, S. (1993). A model of pollen source area for an entire lake surface. Quaternary Research, 39(2), 239–244.CrossRefGoogle Scholar
  36. Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., et al. (2007). Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research, 35(3), e14. doi: 10.1093/nar/gkl938.CrossRefGoogle Scholar
  37. Takahashi, Y., Takano, K., Suzuki, M., Nagai, S., Yokosuka, M., Takeshita, T., et al. (2008). Two routes for pollen entering indoors: Ventilation and clothes. Journal of Investigational Allergology and Clinical Immunology, 18, 382–388.Google Scholar
  38. Taylor, P. E., Flagan, R. C., Valenta, R., & Glovsky, M. M. (2002). Release of allergens as respirable aerosols: A link between grass pollen and asthma. Journal of Allergy and Clinical Immunology, 109(1), 51–56.CrossRefGoogle Scholar
  39. WAO. (2011). World allergy organization white book on allergy. Milwaukee: World Allergy Organization.Google Scholar
  40. Yoshimura, Y. (2011). Wind tunnel and field assessment of pollen dispersal in Soybean [Glycine max (L.) Merr.]. Journal of Plant Research, 124(1), 109–114.CrossRefGoogle Scholar
  41. Zavada, M. S., McGraw, S. M., & Miller, M. A. (2007). The role of clothing fabrics as passive pollen collectors in the north-eastern United States. Grana, 46(4), 285–291. doi: 10.1080/00173130701780104.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Joseph M. Craine
    • 1
  • Albert Barberán
    • 2
  • Ryan C. Lynch
    • 3
  • Holly L. Menninger
    • 4
  • Robert R. Dunn
    • 5
  • Noah Fierer
    • 2
    • 6
  1. 1.Jonah VenturesManhattanUSA
  2. 2.Cooperative Institute for Research in Environmental SciencesUniversity of ColoradoBoulderUSA
  3. 3.Medicinal GenomicsWoburnUSA
  4. 4.Department of Biological SciencesNorth Carolina State UniversityRaleighUSA
  5. 5.Department of Applied EcologyNorth Carolina State UniversityRaleighUSA
  6. 6.Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderUSA

Personalised recommendations