Bacterial characterization of Beijing drinking water by flow cytometry and MiSeq sequencing of the 16S rRNA gene

Ecology and Evolution

Volumn 6, Issue 4, 2016, Pages 923-934

  Liu, Tingting ^a   Kong, Weiwen ^a   Chen, Nan ^a   Zhu, Jing ^a   Wang, Jingqi ^a   He, Xiaoqing ^a   Jin, Yi ^a  

^a BEIJING FORESTRY UNIVERSITY   (China)

Author keywords

Drinking water quality monitoring; Flow cytometry; Fluorescence fingerprints; MiSeq sequencing; Opportunistic pathogenic bacteria

Indexed keywords

EID: 84958973550     PISSN: None     EISSN: 20457758     Source Type: Journal    
DOI: 10.1002/ece3.1955     Document Type: Article

References (58)

1. Abecasis, A. B., M. Serrano, R. Alves, L. Quintais, J. B. Pereira-Leal, and A. O. Henriques . 2013. A genomic signature and the identification of new sporulation genes. J. Bacteriol. 195:2101-2115.
2. Besmer, M. D., D. G., Weissbrodt, B. E. Kratochvil, J. A. Sigrist, M. S. Weyland, and F. Hammes . 2014. The feasibility of automated online flow cytometry for in-situ monitoring of microbial dynamics in aquatic ecosystems. Front. Microbiol. 5:1-12.
3. Bombach, P., T. Huebschmann, I. Fetzer, S. Kleinsteuber, R. Geyer, H. Harms, et al. 2011. Resolution of natural microbial community dynamics by community fingerprinting, flow cytometry, and trend interpretation analysis. Vol. 124. Tecan Trading AG, Switzerland. Pp. 151-181.
4. Caporaso, J. G., C. L. Lauber, W. A. Walters, D. Berg-Lyons, J. Huntley, N. Fierer, S. M. Owens, et al. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6:1621-1624.
5. De Roy, K., L. Clement, O. Thas, Y. Y. Wang, and N. Boon . 2012. Flow cytometry for fast microbial community fingerprinting. Water Res. 46:907-919.
6. Degnan, P. H., and H. Ochman . 2012. Illumina-based analysis of microbial community diversity. ISME J. 6:183-194.
7. Edgar, R. C. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10:996-998.
8. Emde, K., D. Smith, and R. Facey . 1992. Initial investigation of microbially influenced corrosion (MIC) in a low temperature water distribution system. Water Res. 26:169-175.
9. Foladori, P., L. Bruni, S. Tamburini, V. Menapace, and G. Ziglio . 2015. Surrogate parameters for the rapid microbial monitoring in a civil protection module used for drinking water production. Chem Eng J. 265:67-74.
10. Gillespie, S., P. Lipphaus, J. Green, S. Parsons, P. Weir, K. Juskowiak, et al. 2014. Assessing microbiological water quality in drinking water distribution systems with disinfectant residual using flow cytometry. Water Res. 65:224-234.
11. Gomez-Alvarez, V., B. W. Humrighouse, R. P. Revetta, and J. W. Santo Domingo . 2015. Bacterial composition in a metropolitan drinking water distribution system utilizing different source waters. J. Water Health 13:140-151.
12. Hammes, F., T. Broger, H. Weilenmann, M. Vital, J. Helbing, U. Bosshart, et al. 2012. Development and laboratory-scale testing of a fully automated online flow cytometer for drinking water analysis. Cytometry Part A 81A:508-516.
13. Hardalo, C., and S. C. Edberg . 1997. Pseudomonas aeruginosa: assessment of risk from drinking water. Crit. Rev. Microbiol. 23:47-75.
14. Hill, V. R., A. L. Polaczyk, D. Hahn, J. Narayanan, T. L. Cromeans, J. M. Roberts, et al. 2005. Development of a rapid method for simultaneous recovery of diverse microbes in drinking water by ultrafiltration with sodium polyphosphate and surfactants. Appl. Environ. Microbiol. 71:6878-6884.
15. Hill, V. R., A. M. Kahler, N. Jothikumar, T. B. Johnson, D. Hahn, and T. L. Cromeans . 2007. Multistate evaluation of an ultrafiltration-based procedure for simultaneous recovery of enteric microbes in 100-liter tap water samples. Appl. Environ. Microbiol. 73:4218-4225.
16. Hoefel, D., W. L. Grooby, P. T. Monis, S. Andrews, and C. P. Saint . 2003. Enumeration of water-borne bacteria using viability assays and flow cytometry: a comparison to culture-based techniques. J. Microbiol. Methods 55:585-597.
17. Hoefel, D., P. T. Monis, W. L. Grooby, S. Andrews, and C. P. Saint . 2005. Profiling bacterial survival through a water treatment process and subsequent distribution system. J. Appl. Microbiol. 99:175-186.
18. Holmfeldt, K., C. Dziallas, J. Titelman, K. Pohlmann, H. Grossart, and L. Riemann . 2009. Diversity and abundance of freshwater Actinobacteria along environmental gradients in the brackish northern Baltic Sea. Environ. Microbiol. 11:2042-2054.
19. Hong, P.-Y., C. Hwang, F. Ling, G. L. Andersen, M. W. LeChevallier, and W.-T. Liu . 2010. Pyrosequencing analysis of bacterial biofilm communities in water meters of a drinking water distribution system. Appl. Environ. Microbiol. 76:5631-5635.
20. Huang, K., X.-X. Zhang, P. Shi, B. Wu, and H.-Q. Ren . 2014. A comprehensive insight into bacterial virulence in drinking water using 454 pyrosequencing and Illumina high-throughput sequencing. Ecotoxicol. Environ. Saf. 109:15-21.
21. Jones, S. E., R. J. Newton, and K. D. McMahon . 2009. Evidence for structuring of bacterial community composition by organic carbon source in temperate lakes. Environ. Microbiol. 11:2463-2472.
22. Koch, C., I. Fetzer, H. Harms, and S. Muller . 2013. CHIC - An automated approach for the detection of dynamic variations in complex microbial communities. Cytometry Part A 83A:561-567.
23. Kostka, J. E., D. D. Dalton, H. Skelton, S. Dollhopf, and J. W. Stucki . 2002. Growth of iron(III)-reducing bacteria on clay minerals as the sole electron acceptor and comparison of growth yields on a variety of oxidized iron forms. Appl. Environ. Microbiol. 68:6256-6262.
24. Kwon, S., E. Moon, T.-S. Kim, S. Hong, and H.-D. Park . 2011. Pyrosequencing demonstrated complex microbial communities in a membrane filtration system for a drinking water treatment plant. Microbes Environ. 26:149-155.
25. Lautenschlager, K., N. Boon, Y. Wang, T. Egli, and F. hammes . 2010. Overnight stagnation of drinking water in household taps induces microbial growth and changes in community composition. Water Res. 44:4868-4877.
26. Lautenschlager, K., C. Hwang, W.-T. Liu, N. Boon, O. Koster, H. Vrouwenvelder, et al. 2013. A microbiology-based multi-parametric approach towards assessing biological stability in drinking water distribution networks. Water Res. 47:3015-3025.
27. Lewis, K. 2001. Riddle of biofilm resistance. Antimicrob. Agents Chemother. 45:999-1007.
28. Li, D., Z. Li, J. Yu, N. Cao, R. Liu, and M. Yang . 2010. Characterization of bacterial community structure in a drinking water distribution system during an occurrence of red water. Appl. Environ. Microbiol. 76:7171-7180.
29. Liu, P., V. R. Hill, D. Hahn, T. B. Johnson, Y. Pan, and N. Jothikumar, et al. 2012a. Hollow-fiber ultrafiltration for simultaneous recovery of viruses, bacteria and parasites from reclaimed water. J. Microbiol. Methods 88:155-161.
30. Liu, R., Z. Yu, H. Zhang, M. Yang, B. Shi, and X. Liu . 2012b. Diversity of bacteria and mycobacteria in biofilms of two urban drinking water distribution systems. Can. J. Microbiol. 58:261-270.
31. Luo, C., D. Tsementzi, N. Kyrpides, T. Read, and K. T. Konstantinidis . 2012. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7:e30087.
32. Magoč, T., and S. L. Salzberg . 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957-2963.
33. Moritz, M. M., H.-C. Flemming, and J. Wingender . 2010. Integration of Pseudomonas aeruginosa and Legionella pneumophila in drinking water biofilms grown on domestic plumbing materials. Int. J. Hyg. Environ. Health 213:190-197.
34. Mull, B., and V. R. Hill . 2012. Recovery of diverse microbes in high turbidity surface water samples using dead-end ultrafiltration. J. Microbiol. Methods 91:429-433.
35. Newton, R. J., S. E. Jones, M. R. Helmus, and K. D. McMahon . 2007. Phylogenetic ecology of the freshwater Actinobacteria acI lineage. Appl. Environ. Microbiol. 73:7169-7176.
36. Newton, R. J., S. E. Jones, A. Eiler, K. D. McMahon, and S. Bertilsson . 2011. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75:14-49.
37. Ng, T. W., G. Huang, and P. K. Wong . 2015. Investigation of drinking water bacterial community through high-throughput sequencing. J. Environ. Sci. 37:154-156.
38. Organization, W. H.. 2004. Guidelines for drinking-water quality: recommendations. World Health Organization, Geneva, Switzerland.
39. Phe, M. H., M. Dossot, H. Guilloteau, and J.-C. Block . 2005. Nucleic acid fluorochromes and flow cytometry prove useful in assessing the effect of chlorination on drinking water bacteria. Water Res. 39:3618-3628.
40. Pinto, A. J., C. Xi, and L. Raskin . 2012. Bacterial community structure in the drinking water microbiome is governed by filtration processes. Environ. Sci. Technol. 46:8851-8859.
41. Polaczyk, A. L., J. Narayanan, T. L. Cromeans, D. Hahn, J. M. Roberts, J. E. Amburgey, et al. 2008. Ultrafiltration-based techniques for rapid and simultaneous concentration of multiple microbe classes from 100-L tap water samples. J. Microbiol. Methods 73:92-99.
42. Prest, E. I., F. Hammes, S. kotzsch, M. Van Loosdrecht, and J. Vrouwenvelder . 2013. Monitoring microbiological changes in drinking water systems using a fast and reproducible flow cytometric method. Water Res. 47:7131-7142.
43. Prest, E., J. Ei-Chakhtoura, F. Hammes, P. Saikaly, M. Van loosdrecht, and J. Vrouwenvelder . 2014. Combining flow cytometry and 16S rRNA gene pyrosequencing: a promising approach for drinking water monitoring and characterization. Water Res. 63:179-189.
44. Ramseier, M. K., U. Von Gunten, P. Freihofer, and F. Hammes . 2011. Kinetics of membrane damage to high (HNA) and low (LNA) nucleic acid bacterial clusters in drinking water by ozone, chlorine, chlorine dioxide, monochloramine, ferrate(VI), and permanganate. Water Res. 45:1490-1500.
45. Sartory, D. P. 2004. Heterotrophic plate count monitoring of treated drinking water in the UK: a useful operational tool. Int. J. Food Microbiol. 92:297-306.
46. Shaw, J. L., P. Monis, L. S. Weyrich, E. Sawade, M. Drikas, and A. J. Cooper . 2015. Using amplicon sequencing to characterize and monitor bacterial diversity in drinking water distribution systems. Appl. Environ. Microbiol. 81:6463-6473.
47. SLMB. 2012. Determining the total cell count and ratios of high and low nucleic acid content cells in freshwater using flow cytometry. Federal Office of Public Health, Switzerland.
48. Szewzyk, U., R. Szewzyk, W. Manz, and K.-H. Schleifer . 2000. Microbiological safety of drinking water. Ann. Rev. Microbiol. 54:81-127.
49. Uhl, W., and G. Schaule . 2004. Establishment of HPC(R2A) for regrowth control in non-chlorinated distribution systems. Int. J. Food Microbiol. 92:317-325.
50. Vaerewijck, M. J., G. Huys, J. C. Palomino, J. Swings, and F. Portaels . 2005. Mycobacteria in drinking water distribution systems: ecology and significance for human health. FEMS Microbiol. Rev. 29:911-934.
51. Vital, M., D. Stucki, T. Egli, and F. Hammes . 2010. Evaluating the growth potential of pathogenic bacteria in water. Appl. Environ. Microbiol. 76:6477-6484.
52. Vital, M., M. Dignum, A. Magic-Knezev, P. Ross, L. Rietveld, and F. Hammes . 2012. Flow cytometry and adenosine tri-phosphate analysis: alternative possibilities to evaluate major bacteriological changes in drinking water treatment and distribution systems. Water Res. 46:4665-4676.
53. Wagner, M. R., D. S. Lundberg, D. Coleman-Derr, S. G. Tringe, J. L. Dangl, and T. Mitchell-Olds . 2014. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol. Lett. 17:717-726.
54. Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole . 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
55. Wang, Y., F. Hammes, N. Boon, M. Chami, and T. Egli . 2009. Isolation and characterization of low nucleic acid (LNA)-content bacteria. ISME J. 3:889-902.
56. Wei, Y.-M., J.-Q. Wang, T.-T. Liu, W.-W. Kong, N. Chen, X.-Q. He, et al. 2015. Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene. Environ. Sci. Pollut. Res. 22:12605-12614.
57. WHO. 1999. World Health Organization-International Society of Hypertension guidelines for the management of hypertension. WHO, Geneva, Switzerland.
58. Ye, L., and T. Zhang . 2011. Pathogenic bacteria in sewage treatment plants as revealed by 454 pyrosequencing. Environ. Sci. Technol. 45:7173-7179.