Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics


Archaea are widespread and abundant in soils, oceans, or human and animal gastrointestinal (GI) tracts. However, very little is known about the presence of Archaea in indoor environments and factors that can regulate their abundances. Using a quantitative PCR approach, and targeting the archaeal and bacterial 16S rRNA genes in floor dust samples, we found that Archaea are a common part of the indoor microbiota, 5.01 ± 0.14 (log 16S rRNA gene copies/g dust, mean ± SE) in bedrooms and 5.58 ± 0.13 in common rooms, such as living rooms. Their abundance, however, was lower than bacteria: 9.20 ± 0.32 and 9.17 ± 0.32 in bedrooms and common rooms, respectively. In addition, by measuring a broad array of environmental factors, we obtained preliminary insights into how the abundance of total archaeal 16S rRNA gene copies in indoor environment would be associated with building characteristics and occupants’ activities. Based on the results, Archaea are not equally distributed within houses, and the areas with greater input of outdoor microbiome and higher traffic and material heterogeneity tend to have a higher abundance of Archaea. Nevertheless, more research is needed to better understand causes and consequences of this microbial group in indoor environments.

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  1. 1.

    Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms—proposal for the domains archaea, bacteria, and eucarya. Proc Natl Acad Sci U S A 87:4576–4579. doi:10.1073/pnas.87.12.4576

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. 2.

    Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3:479–488. doi:10.1038/nrmicro1159

    CAS  Article  PubMed  Google Scholar 

  3. 3.

    Delong EF, Wu KY, Prezelin BB, Jovine RVM (1994) High abundance of archaea in antarctic marine picoplankton. Nature 371:695–697. doi:10.1038/371695a0

    CAS  Article  PubMed  Google Scholar 

  4. 4.

    Timonen S, Bomberg M (2009) Archaea in dry soil environments. Phytochem Rev 8:505–518. doi:10.1007/s11101-009-9137-5

    CAS  Article  Google Scholar 

  5. 5.

    Bengtson P, Sterngren AE, Rousk J (2012) Archaeal abundance across a pH gradient in an arable soil and its relationship to bacterial and fungal growth rates. Appl Environ Microbiol 78:5906–5911. doi:10.1128/aem.01476-12

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Lecours PB, Veillette M, Marsolais D, Duchaine C (2012) Characterization of bioaerosols from dairy barns: reconstructing the puzzle of occupational respiratory diseases by using molecular approaches. Appl Environ Microbiol 78:3242–3248. doi:10.1128/aem.07661-11

    CAS  Article  Google Scholar 

  7. 7.

    Just N, Lecours PB, Marcoux-Voiselle M, Kirychuk S, Veillette M, Singh B, Duchaine C (2013) Archaeal characterization of bioaerosols from cage-housed and floor-housed poultry operations. Can J Microbiol 59:46–50. doi:10.1139/cjm-2012-0305

    CAS  Article  PubMed  Google Scholar 

  8. 8.

    Nehme B, Gilbert Y, Letourneau V, Forster RJ, Veillette M, Villemur R, Duchaine C (2009) Culture-independent characterization of archaeal biodiversity in swine confinement building bioaerosols. Appl Environ Microbiol 75:5445–5450. doi:10.1128/aem.00726-09

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Rolleke S, Witte A, Wanner G, Lubitz W (1998) Medieval wall paintings - a habitat for archaea: identification of archaea by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified gene fragments coding for 16S rRNA in a medieval wall painting. Int Biodeterioration Biodegradation 41:85–92. doi:10.1016/s0964-8305(98)80011-5

    CAS  Article  Google Scholar 

  10. 10.

    Rea S, Bowman JP, Popovski S, Pimm C, Wright ADG (2007) Methanobrevibacter millerae sp nov and Methanobrevibacter olleyae sp nov., methanogens from the ovine and bovine rumen that can utilize formate for growth. Int J Syst Evol Microbiol 57:450–456. doi:10.1099/ijs.0.63984-0

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    Miller TL, Lin CZ (2002) Description of Methanobrevibacter gottschalkii sp nov., Methanobrevibacter thaueri sp nov., Methanobrevibacter woesei sp nov and Methanobrevibacter wolinii sp nov. Int J Syst Evol Microbiol 52:819–822. doi:10.1099/ijs.0.02022-0

    CAS  PubMed  Google Scholar 

  12. 12.

    Sprenger WW, van Belzen MC, Rosenberg J, Hackstein JHP, Keltjens JT (2000) Methanomicrococcus blatticola gen. nov., sp nov., a methanol- and methylamine-reducing methanogen from the hindgut of the cockroach Periplaneta americana. Int J Syst Evol Microbiol 50:1989–1999

    CAS  Article  PubMed  Google Scholar 

  13. 13.

    Jarvis GN, Strompl C, Burgess DM, Skillman LC, Moore ERB, Joblin KN (2000) Isolation and identification of ruminal methanogens from grazing cattle. Curr Microbiol 40:327–332. doi:10.1007/s002849910065

    CAS  Article  PubMed  Google Scholar 

  14. 14.

    Dridi B, Fardeau ML, Ollivier B, Raoult D, Drancourt M (2012) Methanomassiliicoccus luminyensis gen. nov., sp nov., a methanogenic archaeon isolated from human faeces. Int J Syst Evol Microbiol 62:1902–1907. doi:10.1099/ijs.0.033712-0

    CAS  Article  PubMed  Google Scholar 

  15. 15.

    Kulik EM, Sandmeier H, Hinni K, Meyer J (2001) Identification of archaeal rDNA from subgingival dental plaque by PCR amplification and sequence analysis. FEMS Microbiol Lett 196:129–133. doi:10.1016/s0378-1097(01)00051-9

    CAS  Article  PubMed  Google Scholar 

  16. 16.

    Kembel SW, Jones E, Kline J, Northcutt D, Stenson J, Womack AM, Bohannan BJM, Brown GZ, Green JL (2012) Architectural design influences the diversity and structure of the built environment microbiome. ISME 6:1469–1479. doi:10.1038/ismej.2011.211

    CAS  Article  Google Scholar 

  17. 17.

    Rintala H, Pitkaeranta M, Toivola M, Paulin L, Nevalainen A (2008) Diversity and seasonal dynamics of bacterial community in indoor environment. BMC Microbiol 8:1–13, doi:10.1186/1471-2180-8-56

  18. 18.

    Rintala H, Pitkaranta M, Taubel M (2012) Microbial communities associated with house dust. In: Laskin AI, Sariaslani S, Gadd GM (eds) Advances in Applied Microbiology, vol 78., pp 75–120

    Google Scholar 

  19. 19.

    Pitkaranta M, Meklin T, Hyvarinen A, Paulin L, Auvinen P, Nevalainen A, Rintala H (2008) Analysis of fungal flora in indoor dust by ribosomal DNA sequence analysis, quantitative PCR, and culture. Appl Environ Microbiol 74:233–244. doi:10.1128/aem.00692-07

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Amend AS, Seifert KA, Samson R, Bruns TD (2010) Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Acad Sci U S A 107:13748–13753. doi:10.1073/pnas.1000454107

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Flannigan B (2011) Microorganisms in indoor environment. In: Flannigan B, Samson RA, Miller D (eds) Microorganisms in home and indoor work environments: diversity, health impacts, investigation and control. CRC Press, Boca Raton

    Google Scholar 

  22. 22.

    Kuhn DM, Ghannoum MA (2003) Indoor mold, toxigenic fungi, and Stachybotrys chartarum: Infectious disease perspective. Clin Microbiol Rev 16:144–172. doi:10.1128/cmr.16.1.144-172.2003

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Li DW, Kendrick B (1995) Indoor aeromycota in relation to residential characteristics and allergic symptoms. Mycopathologia 131:149–157. doi:10.1007/bf01102894

    CAS  Article  PubMed  Google Scholar 

  24. 24.

    Li DW, Kendrick B (1996) Functional and causal relationships between indoor and outdoor airborne fungi. Can J Bot-Revue Canadienne De Botanique 74:194–209

    Google Scholar 

  25. 25.

    Mentese S, Arisoy M, Rad AY, Gullu G (2009) Bacteria and fungi levels in various indoor and outdoor environments in Ankara, Turkey. Clean-Soil Air Water 37:487–493. doi:10.1002/clen.200800220

    CAS  Article  Google Scholar 

  26. 26.

    Samson RA (2011) Ecology and general characteristics of indoor fungi. In: Olaf C, Adan G, Samson RA (eds) Fundamentals of mold growth in indoor environments and strategies for healthy living. Wageningen Academic Publishers, Netherland, pp 101–107

    Google Scholar 

  27. 27.

    Pakarinen J, Hyvarinen A, Salkinoja-Salonen M, Laitinen S, Nevalainen A, Makela MJ, Haahtela T, von Hertzen L (2008) Predominance of Gram-positive bacteria in house dust in the low-allergy risk Russian Karelia. Environ Microbiol 10:3317–3325. doi:10.1111/j.1462-2920.2008.01723.x

    CAS  Article  PubMed  Google Scholar 

  28. 28.

    Yuan I, Xu JR, Millar BC, Dooley JSG, Rooney PJ, Alexander HD, Moore JE (2007) Molecular identification of environmental bacteria in indoor air in the domestic home: description of a new species of Exiguobactetium. Int J Environ Health Res 17:75–82. doi:10.1080/09603120601124199

    CAS  Article  PubMed  Google Scholar 

  29. 29.

    Kembel SW, Meadow JF, O’Connor TK, Mhuireach G, Northcutt D, Kline J, Moriyama M, Brown GZ, Bohannan BJM, Green JL (2014) Architectural design drives the biogeography of indoor bacterial communities. PLoS One 9:1–10. doi:10.1371/journal.pone.0087093

    Article  Google Scholar 

  30. 30.

    Meadow JF, Altrichter AE, Kembel SW, Kline J, Mhuireach G, Moriyama M, Northcutt D, O’Connor TK, Womack AM, Brown GZ, Green JL, Bohannan BJM (2014) Indoor airborne bacterial communities are influenced by ventilation, occupancy, and outdoor air source. Indoor Air 24:41–48. doi:10.1111/ina.12047

    CAS  Article  PubMed  Google Scholar 

  31. 31.

    Adams RI, Miletto M, Taylor JW, Bruns TD (2013) Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME 7:1262–1273. doi:10.1038/ismej.2013.28

    CAS  Article  Google Scholar 

  32. 32.

    Sousa ACA, Almeida J, Pereira CC, Pastorinho MR, Pereira AMC, Nogueira AJA, Taborda-Barata L, Teixeira JP, Correia ACM, Alves A (2014) Characterization of fungal communities in house dust samples collected from central Portugal—a preliminary survey. J Toxicol Environ Health A 77:972–982. doi:10.1080/15287394.2014.911137

    CAS  Article  PubMed  Google Scholar 

  33. 33.

    Subbarao P, Anand SS, Becker AB, Befus AD, Brauer M, Brook JR, Denburg JA, HayGlass KT, Kobor MS, Kollmann TR, Kozyrskyj AL, Lou WY, Mandhane PJ, Miller GE, Moraes TJ, Pare PD, Scott JA, Takaro TK, Turvey SE, Duncan JM, Lefebvre DL, Sears MR, CHILD Study Investigators (2015) The Canadian Healthy Infant Longitudinal Development (CHILD) Study: examining developmental origins of allergy and asthma. Thorax 70:998–1000. doi:10.1136/thoraxjnl-2015-207246

    Article  PubMed  Google Scholar 

  34. 34.

    Takaro TK, Scott JA, Allen RW, Anand SS, Becker AB, Befus AD, Brauer M, Duncan J, Lefebvre DL, Lou W, Mandhane PJ, McLean KE, Miller G, Sbihi H, Shu H, Subbarao P, Turvey SE, Wheeler AJ, Zeng L, Sears MR, Brook JR, CHILD Study investigators (2015) The Canadian Healthy Infant Longitudinal Development (CHILD) birth cohort study: assessment of environmental exposures. J Expo Sci Environ Epidemiol 25:580–592. doi:10.1038/jes.2015.7

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  35. 35.

    Pakpour S, Olishevska SV, Prasher SO, Milani AS, Chénier MR (2013) DNA extraction method selection for agricultural soil using TOPSIS multiple criteria decision-making model. Am J Mol Biol 3:215–228

    Article  Google Scholar 

  36. 36.

    Kemnitz D, Kolb S, Conrad R (2005) Phenotypic characterization of Rice Cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture. Environ Microbiol 7:553–565. doi:10.1111/j.1462-2920.2005.00723.x

    CAS  Article  PubMed  Google Scholar 

  37. 37.

    Suzuki MT, Taylor LT, DeLong EF (2000) Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5 ′-nuclease assays. Appl Environ Microbiol 66:4605–4614. doi:10.1128/aem.66.11.4605-4614.2000

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Clarke KR, Gorley RN (2015) PRIMER v7: User Manual/Tutorial. PRIMER-E, Plymouth

    Google Scholar 

  39. 39.

    StatSoft Inc. (2013) Electronic Statistics Textbook. StatSoft. WEB:, Tulsa, OK.

  40. 40.

    Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM (1997) Molecular phylogeny of archaea from soil. Proc Natl Acad Sci U S A 94:277–282. doi:10.1073/pnas.94.1.277

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Buckley DH, Graber JR, Schmidt TM (1998) Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils. Appl Environ Microbiol 64:4333–4339

    CAS  PubMed  PubMed Central  Google Scholar 

  42. 42.

    Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol 5:787–797. doi:10.1046/j.1462-2920.2003.00476.x

    CAS  Article  PubMed  Google Scholar 

  43. 43.

    Simon HM, Dodsworth JA, Goodman RM (2000) Crenarchaeota colonize terrestrial plant roots. Environ Microbiol 2:495–505. doi:10.1046/j.1462-2920.2000.00131.x

    CAS  Article  PubMed  Google Scholar 

  44. 44.

    Saengkerdsub S, Ricke SC (2014) Ecology and characteristics of methanogenic Archaea in animals and humans. Crit Rev Microbiol 40:97–116. doi:10.3109/1040841x.2013.763220

    CAS  Article  PubMed  Google Scholar 

  45. 45.

    Auguet JC, Barberan A, Casamayor EO (2010) Global ecological patterns in uncultured Archaea. ISME 4:182–190. doi:10.1038/ismej.2009.109

    Article  Google Scholar 

  46. 46.

    Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME 5:908–917. doi:10.1038/ismej.2010.171

    CAS  Article  Google Scholar 

  47. 47.

    Yin Q, Fu BB, Li BY, Shi XC, Inagaki F, Zhang XH (2013) Spatial variations in microbial community composition in surface seawater from the Ultra-Oligotrophic Center to rim of the South Pacific Gyre. PLoS One 8:1–12. doi:10.1371/journal.pone.0055148

    Google Scholar 

  48. 48.

    Frohlich-Nowoisky J, Nespoli CR, Pickersgill DA, Galand PE, Muller-Germann I, Nunes T, Cardoso JG, Almeida SM, Pio C, Andreae MO, Conrad R, Poschl U, Despres VR (2014) Diversity and seasonal dynamics of airborne archaea. Biogeosciences 11:6067–6079. doi:10.5194/bg-11-6067-2014

    Article  Google Scholar 

  49. 49.

    Orell A, Frols S, Albers SV (2013) Archaeal biofilms: The great unexplored. Annu Rev Microbiol 67:337–354. doi:10.1146/annurev-micro-092412-155616

    CAS  Article  PubMed  Google Scholar 

  50. 50.

    Frols S (2013) Archaeal biofilms: widespread and complex. Biochem Soc Trans 41:393–398. doi:10.1042/bst20120304

    Article  PubMed  Google Scholar 

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The authors are very grateful to all the families who participated in this study, and the whole miniCHILD study team, which included interviewers, laboratory technicians, research scientists, and volunteers. Useful discussions and valuable insight of Dr. Louise Nelson and Ms. Geet Hans from the University of British Columbia are greatly acknowledged. We also acknowledge the financial assistance from the Natural Sciences and Engineering Research Council of Canada (Discovery Grants) and the CHILD Study.

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Correspondence to Sepideh Pakpour.

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Pakpour, S., Scott, J.A., Turvey, S.E. et al. Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics. Microb Ecol 72, 305–312 (2016).

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  • Archaea
  • Bacteria
  • Indoor environment
  • qPCR
  • Building characteristics
  • Human activities