Spatial-temporal survey and occupancy-abundance modeling to predict bacterial community dynamics in the drinking water microbiomez

mBio

Volumn 5, Issue 3, 2014, Pages

  Pinto, Ameet J ^a   Schroeder, Joanna ^a   Lunn, Mary ^a   Sloan, William ^a   Raskin, Lutgarde ^b  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRINKING WATER;

ALPHAPROTEOBACTERIA; ARTICLE; BACTERIUM CONTAMINATION; BETAPROTEOBACTERIA; COMMUNITY DYNAMICS; DELTAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; GAMMAPROTEOBACTERIA; MATHEMATICAL MODEL; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; POPULATION ABUNDANCE; PREDICTION; PRIORITY JOURNAL; REPRODUCIBILITY; RISK BENEFIT ANALYSIS; RISK REDUCTION; SEASONAL VARIATION; SPATIOTEMPORAL ANALYSIS; SPECIES COMPOSITION; TREND STUDY; WATER CONTAMINATION; WATER QUALITY; WATER SAMPLING; WATER SUPPLY; WATER TEMPERATURE; BACTERIA; BACTERIAL LOAD; BIODIVERSITY; CLASSIFICATION; ENVIRONMENT; ISOLATION AND PURIFICATION; MICROBIOLOGY; MICROFLORA; PROTEOBACTERIA; SEASON;

BACTERIA; BACTERIAL LOAD; BIODIVERSITY; ENVIRONMENT; MICROBIOTA; PROTEOBACTERIA; SEASONS; SPATIO-TEMPORAL ANALYSIS; WATER MICROBIOLOGY;

EID: 84903956929     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.01135-14     Document Type: Article

References (60)

1. Hammes F, Berney M, Wang Y, Vital M, Köster O, Egli T. 2008. Flow-cytometric total bacterial cell counts as a descriptive microbiological parameter for drinking water treatment processes. Water Res. 42: 269-277. http://dx. doi. org/10. 1016/j. watres. 2007. 07. 009.
2. Berry D, Xi C, Raskin L. 2006. Microbial ecology of drinking water distribution systems. Curr. Opin. Biotechnol. 17: 297-302. http://dx. doi. org/10. 1016/j. copbio. 2006. 05. 007.
3. Liu G, Verberk JQJC, Dijk JC. 2013. Bacteriology of drinking water distribution systems: an integral and multidimensional review. Appl. Microbiol. Biotechnol. 97: 1-12. http://dx. doi. org/10. 1007/s00253-012-4519-9.
4. Pinto AJ, Xi C, Raskin L. 2012. Bacterial community structure in the drinking water microbiome is governed by filtration processes. Environ. Sci. Technol. 46: 8851-8859. http://dx. doi. org/10. 1021/es302042t.
5. van der Wielen PW, Voost S, van der Kooij D. 2009. Ammoniaoxidizing bacteria and archaea in groundwater treatment and drinking water distribution systems. Appl. Environ. Microbiol. 75: 4687-4695. http://dx. doi. org/10. 1128/AEM. 00387-09.
6. Thomas JM, Ashbolt NJ. 2011. Do free-living amoebae in treated drinking water systems present an emerging health risk? Environ. Sci. Technol. 45: 860-869. http://dx. doi. org/10. 1021/es102876y.
7. Hageskal G, Lima N, Skaar I. 2009. The study of fungi in drinking water. Mycol. Res. 113: 165-172. http://dx. doi. org/10. 1016/j. mycres. 2008. 10. 002.
8. Gomez-Alvarez V, Revetta RP, Santo Domingo JW. 2012. Metagenomic analyses of drinking water receiving different disinfection treatments. Appl. Environ. Microbiol. 78: 6095-6102. http://dx. doi. org/10. 1128/AEM. 01018-12.
9. Szewzyk U, Szewzyk R, Manz W, Schleifer KH. 2000. Microbiological safety of drinking water. Annu. Rev. Microbiol. 54: 81-127. http://dx. doi. org/10. 1146/annurev. micro. 54. 1. 81.
10. Zhang Y, Griffin A, Edwards M. 2008. Nitrification in premise plumbing: role of phosphate, pH and pipe corrosion. Environ. Sci. Technol. 42: 4280-4284. http://dx. doi. org/10. 1021/es702483d.
11. Cerrato JM, Falkinham JO III, Dietrich AM, Knocke WR, McKinney CW, Pruden A. 2010. Manganese-oxidizing and-reducing microorganisms isolated from biofilms in chlorinated drinking water systems. Water Res. 44: 3935-3945. http://dx. doi. org/10. 1016/j. watres. 2010. 04. 037.
12. Bouwer EJ, Crowe PB. 1988. Biological processes in drinking water treatment. J. Am. Water Works Assoc. 80: 82-93.
13. Henne K, Kahlisch L, Brettar I, Höfle MG. 2012. Analysis of structure and composition of bacterial core communities in mature drinking water biofilms and bulk water of a citywide network in Germany. Appl. Environ. Microbiol. 78: 3530-3538. http://dx. doi. org/10. 1128/AEM. 06373-11.
14. Martiny AC, Jørgensen TM, Albrechtsen HJ, Arvin E, Molin S. 2003. Long-term succession of structure and diversity of a biofilm formed in a model drinking water distribution system. Appl. Environ. Microbiol. 69: 6899-6907. http://dx. doi. org/10. 1128/AEM. 69. 11. 6899-6907. 2003.
15. Liu G, Lut MC, Verberk JQ, Van Dijk JC. 2013. A comparison of additional treatment processes to limit particle accumulation and microbial growth during drinking water distribution. Water Res. 47: 2719-2728. http://dx. doi. org/10. 1016/j. watres. 2013. 02. 035.
16. McCoy S, VanBriesen J. 2014. Comparing spatial and temporal diversity of bacteria in a chlorinated drinking water distribution system. Environ. Eng. Sci. 31: 32-41. http://dx. doi. org/10. 1089/ees. 2013. 0174.
17. Lautenschlager K, Hwang C, Liu W-T, Boon N, Köster O, Vrouwenvelder H, Egli T, Hammes F. 2011. A microbiology-based multiparametric approach towards assessing biological stability in drinking water distribution networks. Water Res. 45: 3015-3025. http://dx. doi. org/10. 1016/j. watres. 2011. 02. 017.
18. Berney M, Vital M, Hülshoff I, Weilenmann HU, Egli T, Hammes F. 2008. Rapid, cultivation-independent assessment of microbial viability in drinking water. Water Res. 42: 4010-4018. http://dx. doi. org/10. 1016/j. watres. 2008. 07. 017.
19. Hong PY, Hwang C, Ling F, Andersen GL, LeChevallier MW, Liu WT. 2010. Pyrosequencing analysis of bacterial biofilm communities in water meters of a drinking water distribution system. Appl. Environ. Microbiol. 76: 5631-5635. http://dx. doi. org/10. 1128/AEM. 00281-10.
20. Wang H, Masters S, Hong Y, Stallings J, Falkinham JO, Edwards MA, Pruden A. 2012. Effect of disinfectant, water age, and pipe material on occurrence and persistence of Legionella, Mycobacteria, Pseudomonas aeruginosa, and two amoebas. Environ. Sci. Technol. 46: 11566-11574. http://dx. doi. org/10. 1021/es303212a.
21. Hwang C, Ling F, Andersen GL, LeChevallier MW, Liu WT. 2012. Microbial community dynamics of an urban drinking water distribution system subjected to phases of chloramination and chlorination treatments. Appl. Environ. Microbiol. 78: 7856-7865. http://dx. doi. org/10. 1128/AEM. 01892-12.
22. McCoy S, VanBriesen J. 2012. Temporal variability of bacterial diversity in a chlorinated drinking water distribution system. J. Environ. Eng. 138: 786-795. http://dx. doi. org/10. 1061/(ASCE)EE. 1943-7870. 0000539.
23. Lautenschlager K, Boon N, Wang Y, Egli T, Hammes F. 2010. Overnight stagnation of drinking water in household taps induces microbial growth and changes in community composition. Water Res. 44: 4868-4877. http://dx. doi. org/10. 1016/j. watres. 2010. 07. 032.
24. Wang H, Pryor MA, Edwards MA, Falkinham JO, III, Pruden A. 2013. Effect of GAC pre-treatment and disinfectant on microbial community structure and opportunistic pathogen occurrence. Water Res. 47: 5760-5772. http://dx. doi. org/10. 1016/j. watres. 2013. 06. 052.
25. Wang H, Edwards MA, Falkinham JO, Pruden A. 2013. Probiotic approach to pathogen control in premise plumbing systems? A review. Environ. Sci. Technol. 47: 10117-10128. http://dx. doi. org/10. 1021/es402455r.
26. Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, Turnbaugh PJ, Lander ES, Mitzenmacher M, Sabeti PC. 2011. Detecting novel associations in large data sets. Science 334: 1518-1524. http://dx. doi. org/10. 1126/science. 1205438.
27. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. 2012. A travel guide to cytoscape plugins. Nat. Methods 9: 1069-1076. http://dx. doi. org/10. 1038/nmeth. 2212.
28. Holt AR, Gaston KJ, He F. 2002. Occupancy-abundance relationships and spatial distribution: a review. Basic Appl. Ecol. 3: 1-13. http://dx. doi. org/10. 1078/1439-1791-00083.
29. Gaston KJ, Blackburn TM, Greenwood JJD, Gregory RD, Quinn RM, Lawton JH. 2000. Abundance-occupancy relationships. J. Appl. Ecol. 37: 39-59. http://dx. doi. org/10. 1046/j. 1365-2664. 2000. 00485. x.
30. Wright DH. 1991. Correlations between incidence and abundance are expected by Chance. J. Biogeogr. 18: 463-466. http://dx. doi. org/10. 2307/2845487.
31. Boswell MT, Patil GP. 1970. Chance mechanisms generating the negative binomial distribution. In Patil GP (ed), Random counts in scientific work, vol 1. Pennsylvania State University Press, University Park, PA.
32. Leitner WA, Rosenzweig ML. 1997. Nested species-area curves and stochastic sampling: a new theory. Oikos 79: 503-512. http://dx. doi. org/10. 2307/3546894.
33. Nachman G. 1981. A mathematical model of the functional relationship between density and spatial distribution of a population. J. Anim. Ecol. 50: 453-460. http://dx. doi. org/10. 2307/4066.
34. Hanski I, Gyllenberg M. 1997. Uniting two general patterns in the distribution of species. Science 275: 397-400. http://dx. doi. org/10. 1126/science. 275. 5298. 397.
35. Nocker A, Sossa-Fernandez P, Burr MD, Camper AK. 2007. Use of propidium monoazide for live/dead distinction in microbial ecology. Appl. Environ. Microbiol. 73: 5111-5117. http://dx. doi. org/10. 1128/AEM. 02987-06.
36. Chiao TH, Clancy TM, Pinto A, Xi C, Raskin L. 2014. Differential resistance of drinking water bacterial populations to monochloramine disinfection. Environ. Sci. Technol. 48: 4038-4047. http://dx. doi. org/10. 1021/es4055725.
37. Keinänen-Toivola MM, Revetta RP, Santo Domingo JW. 2006. Identification of active bacterial communities in a model drinking water biofilm system using 16S rRNA-based clone libraries. FEMS Microbiol. Lett. 257: 182-188. http://dx. doi. org/10. 1111/j. 1574-6968. 2006. 00167. x.
38. 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: 175-186. http://dx. doi. org/10. 1111/j. 1365-2672. 2005. 02573. x.
39. McCarty SC, Atlas RM. 1993. Effect of amplicon size on PCR detection of bacteria exposed to chlorine. PCR Methods Appl. 3: 181-185. http://dx. doi. org/10. 1101/gr. 3. 3. 181.
40. Holinger EP, Ross KA, Robertson CE, Stevens MJ, Harris JK, Pace NR. 2014. Molecular analysis of point-of-use municipal drinking water microbiology. Water Res. 49: 225-235. http://dx. doi. org/10. 1016/j. watres. 2013. 11. 027.
41. Williams MM, Santo Domingo JW, Meckes MC. 2005. Population diversity in model potable water biofilms receiving chlorine or chloramine residual. Biofouling 21: 279-288. http://dx. doi. org/10. 1080/08927010500452695.
42. Revetta RP, Pemberton A, Lamendella R, Iker B, Santo Domingo JW. 2010. Identification of bacterial populations in drinking water using 16S rRNA-based sequence analyses. Water Res. 44: 1353-1360. http://dx. doi. org/10. 1016/j. watres. 2009. 11. 008.
43. Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, Naeem S. 2006. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc. Natl. Acad. Sci. U. S. A. 103: 13104-13109. http://dx. doi. org/10. 1073/pnas. 0602399103.
44. Srinivasan S, Harrington GW, Xagoraraki I, Goel R. 2008. Factors affecting bulk to total bacteria ratio in drinking water distribution systems. Water Res. 42: 3393-3404. http://dx. doi. org/10. 1016/j. watres. 2008. 04. 025.
45. Egli T. 2010. How to live at very low substrate concentration. Water Res. 44: 4826-4837. http://dx. doi. org/10. 1016/j. watres. 2010. 07. 023.
46. Berry D, Horn M, Xi C, Raskin L. 2010. Mycobacterium avium infections of Acanthamoeba strains: host strain variability, grazing-acquired infections, and altered dynamics of inactivation with monochloramine. Appl. Environ. Microbiol. 76: 6685-6688. http://dx. doi. org/10. 1128/AEM. 00644-10.
47. Yu J, Kim D, Lee T. 2010. Microbial diversity in biofilms on water distribution pipes of different materials. Water Sci. Technol. 61: 163-171. http://dx. doi. org/10. 2166/wst. 2010. 813.
48. Flowers JJ, Cadkin TA, McMahon KD. 2013. Seasonal bacterial community dynamics in a full-scale enhanced biological phosphorus removal plant. Water Res. 47: 7019-7031. http://dx. doi. org/10. 1016/j. watres. 2013. 07. 054.
49. Gilbert JA, Field D, Swift P, Newbold L, Oliver A, Smyth T, Somerfield PJ, Huse S, Joint I. 2009. The seasonal structure of microbial communities in the Western English Channel. Environ. Microbiol. 11: 3132-3139. http://dx. doi. org/10. 1111/j. 1462-2920. 2009. 02017. x.
50. MacKenzie DI, Nichols JD, Royle JA, Pollock KH, Hines JE, Bailey LL. 2005. Occupancy estimation and modeling: inferring patterns and dynamics of species occurrence. Elsevier, San Diego, CA.
51. Buckley HL, Freckleton RP. 2010. Understanding the role of species dynamics in abundance-occupancy relationships. J. Ecol. 98: 645-658. http://dx. doi. org/10. 1111/j. 1365-2745. 2010. 01650. x.
52. Pinto AJ, Raskin L. 2012. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One 7: e43093. http://dx. doi. org/10. 1371/journal. pone. 0043093.
53. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: open source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75: 7537-7541. http://dx. doi. org/10. 1128/AEM. 01541-09.
54. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. 2007. Silva: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35: 7188-7196. http://dx. doi. org/10. 1093/nar/gkm864.
55. Huse SM, Welch DM, Morrison HG, Sogin ML. 2010. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12: 1889-1898. http://dx. doi. org/10. 1111/j. 1462-2920. 2010. 02193. x.
56. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200. http://dx. doi. org/10. 1093/bioinformatics/btr381.
57. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73: 5261-5267. http://dx. doi. org/10. 1128/AEM. 00062-07.
58. Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. 2011. UniFrac: an effective distance metric for microbial community comparison. ISME J. 5: 169-172. http://dx. doi. org/10. 1038/ismej. 2010. 133.
59. Evans J, Sheneman L, Foster J. 2006. Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method. J. Mol. Evol. 62: 785-792. http://dx. doi. org/10. 1007/s00239-005-0176-2.
60. Oksanen J, Guillame Blanchet F, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos R, Stevens HHS, Wagner H. 2013. vegan: Community Ecology Package. R Package version 2.-0-7. http://CRAN. R-project. org/package_vegan.