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Differential Habitat Use and Niche Partitioning by Pseudomonas Species in Human Homes

  • Environmental Microbiology
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Abstract

Many species of Pseudomonas have the ability to use a variety of resources and habitats, and as a result Pseudomonas are often characterized as having broad fundamental niches. We questioned whether actual habitat use by Pseudomonas species is equally broad. To do this, we sampled extensively to describe the biogeography of Pseudomonas within the human home, which presents a wide variety of habitats for microbes that live in close proximity to humans but are not part of the human flora, and for microbes that are opportunistic pathogens, such as Pseudomonas aeruginosa. From 960 samples taken in 20 homes, we obtained 163 Pseudomonas isolates. The most prevalent based on identification using the SepsiTest BLAST analysis of 16S rRNA (http://www.sepsitest-blast.de) were Pseudomonas monteilii (42 isolates), Pseudomonas plecoglossicida, Pseudomonas fulva, and P. aeruginosa (approximately 25 each). Of these, all but P. fulva differed in recovery rates among evaluated habitat types (drains, soils, water, internal vertebrate sites, vertebrate skin, inanimate surfaces, and garbage/compost) and all four species also differed in recovery rates among subcategories of habitat types (e.g., types of soils or drains). We also found that at both levels of habitat resolution, each of these six most common species (the four above plus Pseudomonas putida and Pseudomonas oryzihabitans) were over- or under-represented in some habitats relative to their contributions to the total Pseudomonas collected across all habitats. This pattern is consistent with niche partitioning. These results suggest that, whereas Pseudomonas are often characterized as generalists with broad fundamental niches, these species in fact have more restricted realized niches. Furthermore, niche partitioning driven by competition among Pseudomonas species may be contributing to the observed variability in habitat use by Pseudomonas in this system.

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References

  1. Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H (2000) Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50:1563–1589

    Article  PubMed  CAS  Google Scholar 

  2. Aumeran C, Paillard C, Robin F, Kanold J, Baud O, Bonnet R, Souweine B, Traore O (2007) Pseudomonas aeruginosa and Pseudomonas putida outbreak associated with contaminated water outlets in an oncohaematology paediatric unit. J Hosp Infect 65:47–53

    Article  PubMed  CAS  Google Scholar 

  3. Bass-Becking LGM (1934) Geobiologie of inleiding tot de milieukunde. Van Stockum & Zoon, The Hague, the Netherlands

    Google Scholar 

  4. Belyea LR, Lancaster J (1999) Assembly rules within a contingent ecology. Oikos 86:402–416

    Article  Google Scholar 

  5. Berg G, Eberl L, Hartmann A (2005) The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environ Microbiol 7:1673–1685

    Article  PubMed  CAS  Google Scholar 

  6. Booth BD, Swanton CJ (2002) Assembly theory applied to seed communities. Weed Science 50:2–13

    Article  CAS  Google Scholar 

  7. Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ, Green JL (2008) Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proc Natl Acad Sci USA 105:11505–11511

    Article  PubMed  CAS  Google Scholar 

  8. Cho JJ, Schroth MN, Kiminos SD, Green SK (1975) Ornamental plants as carriers of Pseudomonas aeruginosa. Phytopathology 65:425–431

    Article  Google Scholar 

  9. Cho JC, Tiedje JM (2000) Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl Environ Microbiol 66:5448–5456

    Article  PubMed  CAS  Google Scholar 

  10. Cycoń M, Wójcik M, Piotrowska-Seget Z (2009) Biodegradation of the organophosphorus insecticide diazinon by Serratia sp and Pseudomonas sp and their use in bioremediation of contaminated soil. Chemosphere 76:494–501

    Article  PubMed  Google Scholar 

  11. Goldberg JB (2000) Pseudomonas: global bacteria. Trends Microbiol 8:55–57

    Article  PubMed  CAS  Google Scholar 

  12. Green J, Bohannan BJM (2006) Spatial scaling of microbial biodiversity. Trends Ecol Evol 21:501–507

    Article  PubMed  Google Scholar 

  13. Green SK, Schroth MN, Cho JJ, Kominos SD, Vitanza-Jack VB (1974) Agricultural plants and soil as a reservoir for Pseudomonas aeruginosa. Appl Microbiol 28:987–991

    PubMed  CAS  Google Scholar 

  14. Gupta S, Prakash R, Prakash NT, Pearce C, Pattrick R, Hery M, Lloyd J (2010) Selenium mobilization by Pseudomonas aeruginosa (SNT-SG1) isolated from seleniferous soils from India. Geomicrobiol J 27:35–42

    Article  CAS  Google Scholar 

  15. Heuer H, Krögerrecklenfort E, Wellington EMH, Egan S, van Elsas JD, van Overbeek L, Collard JM, Guillaume G, Karagouni AD, Nikolakopoulou TL, Smalla K (2002) Gentamicin resistance genes in environmental bacteria: prevalence and transfer. FEMS Microbiol Ecol 42:289–302

    Article  PubMed  CAS  Google Scholar 

  16. Hutchinson GE (1959) Homage to Santa Rosalia or why are there so many kinds of animals? Am Nat 93:145–159

    Article  Google Scholar 

  17. Jackson ST, Overpeck JT (2000) Responses of plant populations and communities to environmental changes of the late Quaternary. Paleobiology 26:194–220

    Article  Google Scholar 

  18. Kaarakainen P, Rintala H, Vepsäläinen A, Hyvärinen A, Nevalainen A, Meklin T (2009) Microbial content of house dust samples determined with qPCR. Sci Total Environ 407:4673–4680

    Article  PubMed  CAS  Google Scholar 

  19. Kapatral V, Zago A, Kamath S, Chugani S (2000) Pseudomonas. In: Lederberg J (ed) Encyclopedia of microbiology, vol 3. Academic Press, San Diego, pp 876–892

    Google Scholar 

  20. Khan N, Ahsan M, Yoshizawa S, Hosoya S, Yokota A, Kogure K (2008) Multilocus sequence typing and phylogenetic analyses of Pseudomonas aeruginosa isolates from the ocean. Appl Environ Microbiol 74:6194–6205

    Article  PubMed  CAS  Google Scholar 

  21. Kiska DL, Gilligan PH (2003) Pseudomonas. In: Murray PR, Baron EJ, Jorgensen JH, Pfaller MA, Yolken RH (eds) Manual of clinical microbiology, vol 1. ASM Press, Washington DC, pp 719–726

    Google Scholar 

  22. Kneitel JM, Chase JM (2004) Trade-offs in community ecology: linking spatial scales and species coexistence. Ecol Lett 7:69–80

    Article  Google Scholar 

  23. Madigan MT, Martinko JM, Parker J (2000) Brock biology of microorganisms. Pearson Higher Education, New York

    Google Scholar 

  24. Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, Morin PJ, Naeem S, Øvreås L, Reysenbach AL, Smith VH, Staley JT (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102–112

    Article  PubMed  CAS  Google Scholar 

  25. Mortensen JE, Fisher MC, LiPuma JJ (1995) Recovery of Pseudomonas cepacia and other Pseudomonas species from the environment. Infect Control Hosp Epidemiol 16:30–32

    Article  PubMed  CAS  Google Scholar 

  26. Nwachukwu SCU, James P, Gurney TR (2001) Inorganic nutrient utilisation by “adapted” Pseudomonas putida strain used in the bioremediation of agricultural soil polluted with crude petroleum. J Environ Biol 22:153–162

    PubMed  CAS  Google Scholar 

  27. Ojima M, Toshima Y, Koya E, Ara K, Tokuda H, Kawai S, Kasuga F (2002) Hygiene measures considering actual distributions of microorganisms in Japanese households. J Appl Microbiol 93:800–809

    Article  PubMed  CAS  Google Scholar 

  28. Parret AHA, De Mot R (2002) Bacteria killing their own kind: novel bacteriocins of Pseudomonas and other gamma-proteobacteria. Trends Microbiol 10:107–112

    Article  PubMed  CAS  Google Scholar 

  29. Pulliam HR (2000) On the relationship between niche and distribution. Ecol Lett 3:349–361

    Article  Google Scholar 

  30. Regnath T, Kreutzberger M, Illing S, Oehme R, Liesenfeld O (2004) Prevalence of Pseudomonas aeruginosa in households of patients with cystic fibrosis. Int J Hyg Environ Health 207:585–588

    Article  PubMed  Google Scholar 

  31. Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225

    Google Scholar 

  32. Saitou K, Furuhata K, Kawakami Y, Fukuyama M (2009) Isolation of Pseudomonas aeruginosa from cockroaches captured in hospitals in Japan, and their antibiotic susceptibility. Biocontrol Sci 14:155–159

    Article  PubMed  CAS  Google Scholar 

  33. SAS Institute I (2009) SAS/STAT 9.2 user’s guide. SAS Institute Inc, Cary

    Google Scholar 

  34. Schelstraete P, Van Daele S, De Boeck KMB, Proesmans M, Lebecque P, Leclercq-Foucart J, Malfroot A, Vaneechoutte M, De Baets F (2008) Pseudomonas aeruginosa in the home environment of newly infected cystic fibrosis patients. Eur Respir J 31:822–829

    Article  PubMed  CAS  Google Scholar 

  35. Shourian M, Noghabi K, Zahiri H, Bagheri T, Karballaei G, Mollaei M, Rad I, Ahadi S, Raheb J, Abbasi H (2009) Efficient phenol degradation by a newly characterized Pseudomonas sp SA01 isolated from pharmaceutical wastewaters. Desalination 246:577–594

    Article  CAS  Google Scholar 

  36. Speert D, Campbell M, Henry D, Milner R, Taha F, Gravelle A, Davidson A, Wong L, Mahenthiralingam E (2002) Epidemiology of Pseudomonas aeruginosa in cystic fibrosis in British Columbia, Canada. Am J Respir Crit Care Med 166:988–993

    Article  PubMed  Google Scholar 

  37. Vos M, Velicer GJ (2008) Isolation by distance in the spore-forming soil bacterium Myxococcus xanthus. Curr Biol 18:386–391

    Article  PubMed  CAS  Google Scholar 

  38. Weisburg W, Barns S, Pelletier D, Lane D (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bact 173:697–703

    PubMed  CAS  Google Scholar 

  39. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R (2008) The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250

    Article  PubMed  CAS  Google Scholar 

  40. Young VM (ed) (1977) Pseudomonas aeruginosa: ecological aspects and patient colonization. Raven Press, New York

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Acknowledgments

We thank Amber Carrier, Jay Nelson, and Justin Wells for their assistance in sample collection and identification. Dan Dykhuizen, Margaret Carreiro, Karen Golemboski, and Nemr Eid provided helpful discussions, and Eileen Remold-O’Donnell, Paul Turner, and two anonymous reviewers gave valuable comments on the manuscript. This work was supported through start-up funding to SR from the University of Louisville Department of Biology and College of Arts and Sciences.

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Author notes

  1. Christopher K. Brown

    Present address: Department of Public and International Affairs, Program in Biodefense, George Mason University, Fairfax, VA, 22030, USA

Authors and Affiliations

  1. Department of Biology, University of Louisville, 137 Life Sciences Building, Louisville, KY, 40292, USA

    Susanna K. Remold, Thomas C. Hundley & Megan E. Purdy

  2. College of Veterinary Medicine, Auburn University, Auburn, AL, 36830, USA

    Justin E. Farris

  3. College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48823, USA

    Jessica A. Perpich

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  1. Susanna K. Remold
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  2. Christopher K. Brown
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Correspondence to Susanna K. Remold.

Appendix

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Table 3

Table 3 Details of sites of isolation for all 163 Pseudomonas isolates collected from human households
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Remold, S.K., Brown, C.K., Farris, J.E. et al. Differential Habitat Use and Niche Partitioning by Pseudomonas Species in Human Homes. Microb Ecol 62, 505–517 (2011). https://doi.org/10.1007/s00248-011-9844-5

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