Skip to main content
Log in

Pyrosequencing Analysis of the Bacterial Community in Drinking Water Wells

  • Microbiology of Aquatic Systems
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Figure 1
Figure 2
Figure 3
Figure 4

Similar content being viewed by others

References

  1. Hammes F, Berney M, Wang Y, Vital M, Koster O, Egli T (2008) Flow-cytometric total bacterial cell counts as a descriptive microbiological parameter for drinking water treatment processes. Water Res 42(1–2):269–277. doi:10.1016/j.watres.2007.07.009

    Article  PubMed  CAS  Google Scholar 

  2. Pinto AJ, Xi C, Raskin L (2012) Bacterial community structure in the drinking water microbiome is governed by filtration processes. Environ Sci Technol 46(16):8851–8859. doi:10.1021/es302042t

    Article  PubMed  CAS  Google Scholar 

  3. Brielmann H, Griebler C, Schmidt SI, Michel R, Lueders T (2009) Effects of thermal energy discharge on shallow groundwater ecosystems. FEMS Microbiol Ecol 68(3):273–286. doi:10.1111/j.1574-6941.2009.00674.x

    Article  PubMed  CAS  Google Scholar 

  4. Schoenen D (2002) Role of disinfection in suppressing the spread of pathogens with drinking water: possibilities and limitations. Water Res 36(15):3874–3888

    Article  PubMed  CAS  Google Scholar 

  5. Eichler S, Christen R, Höltje C, Westphal P, Bötel J, Brettar I, Mehling A, Höfle MG (2006) Composition and dynamics of bacterial communities of a drinking water supply system as assessed by RNA- and DNA-based 16S rRNA gene fingerprinting. Appl Environ Microbiol 72(3):1858–1872. doi:10.1128/AEM.72.3.1858-1872.2006

    Article  PubMed  CAS  Google Scholar 

  6. Stelma GN, Wymer LJ (2012) Research considerations for more effective groundwater monitoring. J Water Health 10(4):511–521. doi:10.2166/wh.2012.016

    Article  PubMed  Google Scholar 

  7. Ben-Dov E, Kramarsky-Winter E, Kushmaro A (2009) An in situ method for cultivating microorganisms using a double encapsulation technique. FEMS Microbiol Ecol 68(3):363–371. doi:10.1111/j.1574-6941.2009.00682.x

    Article  PubMed  CAS  Google Scholar 

  8. Shade A, Hogan CS, Klimowicz AK, Linske M, McManus PS, Handelsman J (2012) Culturing captures members of the soil rare biosphere. Environ Microbiol 14(9):2247–2252. doi:10.1111/j.1462-2920.2012.02817.x

    Article  PubMed  Google Scholar 

  9. Armougom F, Raoult D (2009) Exploring microbial diversity using 16S rRNA high-throughput methods. Comput Sci Syst Biol 2(1):074–092, URL: http://www.omicsonline.com/ArchiveJCSB/Ft02/JCSB2.74.php

    Article  CAS  Google Scholar 

  10. Novais RC, Thorstenson YR (2011) The evolution of Pyrosequencing® for microbiology: from genes to genomes. J Microbiol Methods 86(1):1–7. doi:10.1016/j.mimet.2011.04.006

    Article  PubMed  CAS  Google Scholar 

  11. Hoefel D, Monis PT, Grooby WL, Andrews S, Saint CP (2005) Profiling bacterial survival through a water treatment process and subsequent distribution system. J Appl Microbiol 99(1):175–186. doi:10.1111/j.1365-2672.2005.02573.x

    Article  PubMed  CAS  Google Scholar 

  12. Martiny AC, Albrechtsen HJ, Arvin E, Molin S (2005) Identification of bacteria in biofilm and bulk water samples from a nonchlorinated model drinking water distribution system: detection of a large nitrite-oxidizing population associated with Nitrospira sp. Appl Environ Microbiol 71(12):8611–8617. doi:10.1128/AEM.71.12.8611-8617.2005

    Article  PubMed  CAS  Google Scholar 

  13. Aizenberg-Gershtein Y, Vaizel-Ohayon D, Halpern M (2012) Structure of bacterial communities in diverse freshwater habitats. Can J Microbiol 58(3):326–335. doi:10.1139/w11-138

    Article  PubMed  CAS  Google Scholar 

  14. Regan JM, Harrington GW, Noguera DR (2002) Ammonia and nitrite-oxidizing bacterial communities in a pilot-scale chloraminated drinking water distribution system. Appl Environ Microbiol 68(1):73–81. doi:10.1128/AEM.68.1.73-81.2002

    Article  PubMed  CAS  Google Scholar 

  15. Zhou Y, Kellermann C, Griebler C (2012) Spatio-temporal patterns of microbial communities in a hydrologically dynamic pristine aquifer. FEMS Microbiol Ecol 81(1):230–242. doi:10.1111/j.1574-6941.2012.01371

    Article  PubMed  CAS  Google Scholar 

  16. Yagi JM, Madsen EL (2009) Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer. Appl Environ Microbiol 75(20):6478–6487. doi:10.1128/AEM.01091-09

    Article  PubMed  CAS  Google Scholar 

  17. Liao VH, Chu YJ, Su YC, Hsiao SY, Wei CC, Liu CW, Liao CM, Shen WC, Chang FJ (2011) Arsenite-oxidizing and arsenate-reducing bacteria associated with arsenic-rich groundwater in Taiwan. J Contam Hydrol 23(1–2):20–29. doi:10.1016/j.jconhyd.2010

    Article  Google Scholar 

  18. Schulze T, Streck G, Paschke A (2011) Sampling and conservation. In: Wilderer P, Frimmel F (eds) Treatise on water science, vol 3. Elsevier, Amsterdam, pp 131–152

    Chapter  Google Scholar 

  19. APHA (1998) Standard methods for the examination of water and wastewater. American Public Health Association/American Water Works Association/Water Environment Federation, Washington DC

    Google Scholar 

  20. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) b QIIME allows analysis of high–throughput community sequencing data. Nat Methods 7(5):335–336. doi:10.1038/nmeth.f.303

    Article  PubMed  CAS  Google Scholar 

  21. Hamady M, Lozupone C, Knight R (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4(1):17–27. doi:10.1038/ismej.2009.97

    Article  PubMed  CAS  Google Scholar 

  22. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73(16):5261–5267. doi:10.1128/AEM.00062-07

    Article  PubMed  CAS  Google Scholar 

  23. Oksanen J, Blanchet FG, Kindt R, Legendre P, O’Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H (2011) Vegan: community ecology package. http://CRAN.R-project.org/package 0vegan, R package version 1.17-6

  24. Clarke K, Gorley R (2006) PRIMER: User manual/tutorial. PRIMER-E, Plymouth

    Google Scholar 

  25. Lennon JT (2011) Replication, lies and lesser-known truths regarding experimental design in environmental microbiology. Environ Microbiol 13(6):1383–1386. doi:10.1111/j.1462-2920.2011.02445.x

    Article  PubMed  Google Scholar 

  26. Kirchman DL (2002) The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39(2):91–100. doi:10.1111/j.1574-6941.2002.tb00910.x

    PubMed  CAS  Google Scholar 

  27. Sack EL, van der Wielen PW, van der Kooij D (2011) Flavobacterium johnsoniae as a model organism for characterizing biopolymer utilization in oligotrophic freshwater environments. Appl Environ Microbiol 77(19):6931–6938. doi:10.1128/AEM.00372-11

    Article  PubMed  CAS  Google Scholar 

  28. Liu RY, Yu ZS, Guo HG, Liu MM, Zhang HX, Yang M (2012) Pyrosequencing analysis of eukaryotic and bacterial communities in faucet biofilms. Sci Total Environ 1(435–436):124–131. doi:10.1016/j.scitotenv.2012.07.022

    Article  Google Scholar 

  29. Vaz-Moreira I, Nunes OC, Manaia CM (2012) Diversity and antibiotic resistance in Pseudomonas spp. from drinking water. Sci Total Environ 426(1):366–374. doi:10.1016/j.scitotenv.2012.03.046

    Article  PubMed  CAS  Google Scholar 

  30. Griebler C, Mindl B, Slezak D, Geiger-Kaiser M (2002) Distribution patterns of attached and suspended bacteria in pristine and contaminated shallow aquifers studied with an in situ sediment exposure microcosm. Aquat Microb Ecol 28(2):117–129. doi:10.3354/ame028117

    Article  Google Scholar 

  31. Stumm W, Morgan JJ (1995) Aquatic chemistry. Wiley, New York

    Google Scholar 

  32. Wingender J, Flemming HC (2011) Biofilms in drinking water and their role as reservoir for pathogens. Int J Hyg Environ Health 214(6):417–423. doi:10.1016/j.ijheh.2011.05.009

    Article  PubMed  Google Scholar 

  33. Stewart CR, Muthye V, Cianciotto NP (2012) Legionella pneumophila persists within biofilms formed by Klebsiella pneumoniae, Flavobacterium sp., and Pseudomonas fluorescens under dynamic flow conditions. PLoS One 7(11):e50560

    Article  PubMed  CAS  Google Scholar 

  34. Dippon U, Pantke C, Porsch K, Larese-Casanova P, Kappler A (2012) Potential function of added minerals as nucleation sites and effect of humic substances on mineral formation by the nitrate-reducing Fe(II)-oxidizer Acidovorax sp. BoFeN1. Environ Sci Technol 46(12):6556–6565. doi:10.1021/es2046266

    Article  PubMed  CAS  Google Scholar 

  35. Christensen TH, Kjeldsen P, Bjerg PL, Jensen DL, Christensen JB, Baun A, Albrechtsen H-J, Heron G (2001) Biogeochemistry of landfill leachate plumes. Appl Geochem 16(7–8):659–718. doi:10.1016/S0883-2927(00)00082-2

    Article  CAS  Google Scholar 

  36. Yu R, Gan P, Mackay AA, Zhang S, Smets BF (2010) Presence, distribution, and diversity of iron-oxidizing bacteria at a landfill leachate-impacted groundwater surface water interface. FEMS Microbiol Ecol 71(2):260–271. doi:10.1111/j.1574-6941.2009.00797.x

    Article  PubMed  CAS  Google Scholar 

  37. Li D, Li Z, Yu J, Cao N, Liu R, Yang M (2010) Characterization of bacterial community structure in a drinking water distribution system during an occurrence of red water. Appl Environ Microbiol 76(21):7171–7180. doi:10.1128/AEM.00832-10

    Article  PubMed  CAS  Google Scholar 

  38. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461. doi:10.1093/bioinformatics/btq461

    Article  PubMed  CAS  Google Scholar 

  39. Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61(1):1–10. doi:10.1016/0006-3207(92)91201-3

    Article  Google Scholar 

Download references

Acknowledgments

The research was funded by Cinvestav (Saltillo, Coahuila, Mexico) and ‘Consejo Nacional de Ciencia y Tecnología’ (CONACyT) ‘Fondos Mixtos Conacyt-Gobierno del Estado de Coahuila’ Project COAH-2010-C14-149610. Y.E.N.-N. received a postdoctoral grant from ABACUS and CONACyT.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yendi E. Navarro-Noya.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

ESM 1

(DOCX 136 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Navarro-Noya, Y.E., Suárez-Arriaga, M.C., Rojas-Valdes, A. et al. Pyrosequencing Analysis of the Bacterial Community in Drinking Water Wells. Microb Ecol 66, 19–29 (2013). https://doi.org/10.1007/s00248-013-0222-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-013-0222-3

Keywords

Navigation