Structure of bacterial communities in diverse freshwater habitats

Canadian Journal of Microbiology

Volumn 58, Issue 3, 2012, Pages 326-335

  Aizenberg Gershtein, Yana ^a   Vaizel Ohayon, Dalit ^b   Halpern, Malka ^a  

^a UNIVERSITY OF HAIFA   (Israel)

^b Mekorot Israel National Water COLTD   (Israel)

Author keywords

Bacterial populations; Drinking water; Firmicutes; Proteobacteria; Raw water

Indexed keywords

DRINKING WATER; FRESH WATER; GENOMIC DNA; GROUND WATER; RNA 16S;

BACTERIUM; BIOINDICATOR; COMMUNITY STRUCTURE; DRINKING WATER; ELECTROKINESIS; FECES; FRESHWATER ECOSYSTEM; GENOMICS; MICROBIAL COMMUNITY; PHYLOGENETICS; PHYLOGENY; SAMPLING; TOLERANCE;

ACTINOBACTERIA; ARTICLE; AUTUMN; BACTERIUM DETECTION; BACTEROIDETES; COMMUNITY STRUCTURE; DENATURING GRADIENT GEL ELECTROPHORESIS; FIRMICUTES; FRESHWATER ENVIRONMENT; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEOBACTERIA; UNINDEXED SEQUENCE; WATER MANAGEMENT; WATER SAMPLING;

BACTERIA; BACTERIAL LOAD; BACTERIAL PHYSIOLOGICAL PHENOMENA; BIODIVERSITY; DNA, BACTERIAL; DRINKING WATER; ECOSYSTEM; FRESH WATER; GROUNDWATER; ISRAEL; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEOBACTERIA; RNA, RIBOSOMAL, 16S; SEASONS; WATER MICROBIOLOGY;

ISRAEL;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; ENTEROBACTERIACEAE; FIRMICUTES; PROTEOBACTERIA;

EID: 84857868658     PISSN: 00084166     EISSN: 14803275     Source Type: Journal    
DOI: 10.1139/W11-138     Document Type: Article

References (28)

1. Amann, R.I., Ludwig, W., and Schleifer, K.H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59(1): 143-169. PMID: 7535888.
2. Araya, R., Tani, K., Takagi, T., Yamaguchi, N., and Nasu, M. 2003. Bacterial activity and community composition in stream water and biofilm from an urban river determined by fluorescent in situ hybridization and DGGE analysis. FEMS Microbiol. Ecol. 43(1): 111-119. doi:10.1111/j.1574-6941.2003.tb01050.x. PMID: 19719701.
3. Bai, X., Wu, F., Zhou, B., and Zhi, X. 2010. Biofilm bacterial communities and abundance in a full-scale drinking water distribution system in Shanghai. J. Water Health, 8(3): 593-600. doi:10.2166/wh.2010.048. PMID:20375488.
4. Balkwill, D.L., Fredrickson, J.K., and Romine, M.F. 2006. Sphingomonas and related genera. In The prokaryotes. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K.H. Schleifer, and E. Stackebrandt. Springer Press, New York, USA. pp. 605-629.
5. Bergogne-Bérézin, E., and Towner, K.J. 1996. Acinetobacter sp. as nosocomial pathogens: microbiological, clinical, and epidemiological features. Clin. Microbiol. Rev. 9(2): 148-165. PMID: 8964033.
6. Chun, J., Lee, J.H., Jung, Y., Kim, M., Kim, S., Kim, B.K., and Lim, Y.W. 2007. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 57(10): 2259-2261. doi:10.1099/ijs.0.64915-0. PMID:17911292.
7. Eichler, S., Christen, R., Holtje, C., Westphal, P., Botel, B., Brettar, I., et al. 2006. Composition and dynamics of bacterial communities of a drinking water supply system as assessed by RNA- and DNAbased 16S rRNA gene fingerprinting. Appl. Environ. Microbiol. 72(3): 1858-1872. doi:10.1128/AEM.72.3.1858-1872.2006.PMID:16517632.
8. Felske, A., Rheims, H., Wolterink, A., Stackebrandt, E., and Akkermans, A.D. 1997. Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiology, 143(9): 2983-2989. PMID: 9308181.
9. Gauthier, V., Redercher, S., and Block, J.C. 1999. Chlorine inactivation of Sphingomonas cells attached to goethite particles in drinking water. Appl. Environ. Microbiol. 65(1): 355-357. PMID:9872809.
10. Hahn, M.W., and Schauer, M. 2007. 'Candidatus Aquirestis calciphila' and 'Candidatus Haliscomenobacter calcifugiens', filamentous, planktonic bacteria inhabiting natural lakes. Int. J. Syst. Evol. Microbiol. 57(5): 936-940. doi:10.1099/ijs.0.64807-0.PMID:17473236.
11. Hansen, C.K., Diderichsen, B., and Jørgensen, P.L. 1992. CelA from Bacillus lautus PL236 encodes a novel cellulose-binding endo-b- 1,4-glucanase. J. Bacteriol. 174(11): 3522-3531. PMID:1592807.
12. Haveman, S.A., and Pedersen, K. 2002. Distribution of culturable microorganisms in fennoscandian shield ground water. FEMS Microbiol. Ecol. 39(2): 129-137. doi:10.1111/j.1574-6941.2002. tb00914.x. PMID:19709192
13. Hoefel, D., Monis, P.T., Grooby, W.L., Andrews, S., and Saint, C.P. 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. PMID: 15960678.
14. Kawai, M., Matsutera, E., Kanda, H., Yamaguchi, N., Tani, K., and Nasu, M. 2002. 16S ribosomal DNA-based analysis of bacterial diversity in purified water used in pharmaceutical manufacturing processes by PCR and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 68(2): 699-704. doi:10.1128/AEM.68. 2.699-704.2002. PMID:11823209.
15. Lane, D.J., Pace, B., Olsen, G.J., Stahl, D.A., Sogin, M.L., and Pace, N.R. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. U.S.A. 82(20): 6955-6959. doi:10.1073/pnas.82.20.6955. PMID:2413450.
16. Lee, D.G., Lee, J.H., and Kim, S.J. 2005. Diversity and dynamics of bacterial species in a biofilm at the end of the Seoul water distribution system. World J. Microbiol. Biotechnol. 21(2): 155-162. doi:10.1007/s11274-004-2890-0.
17. Li, D., Yang, M., Li, Z., Qi, R., He, J., and Liu, H. 2008. Change of bacterial communities in sediments along Songhua River in northeastern China after a nitrobenzene pollution event. FEMS Microbiol. Ecol. 65(3): 494-503. doi:10.1111/j.1574-6941.2008.00540.x. PMID:18616580.
18. Madigan, M.T., Martinko, J.M., Dunlap, P.V., and Clark, D.P. 2009. Brock biology of microorganisms. Pearson Education, San Francisco, Calif., USA.
19. Martiny, A.C., Albrechtsen, H.J., Arvin, E., and 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. PMID:16332854.
20. Mulder, E.G., and Deinema, M.H. 2006. The genus Haliscomenobacter. In The prokaryotes. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K.H. Schleifer, and E. Stackebrandt. Springer Press, New York, USA. pp. 602-604.
21. Muyzer, G., De Waal, E.C., and Uitterlinden, A.G. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59(3): 695-700. PMID:7683183.
22. Poitelon, J.-B., Joyeux, M., Welté, B., Duguet, J.-P., Prestel, E., Lespinet, O., and DuBow, M.S. 2009. Assessment of phylogenetic diversity of bacterial microflora in drinking water using serial analysis of ribosomal sequence tags. Water Res. 43(17): 4197-4206. doi:10.1016/j.watres.2009.07.020. PMID:19665751.
23. Regan, J.M., Harrington, G.W., and Noguera, D.R. 2002. Ammoniaand 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. PMID:11772611.
24. Stackebrandt, E., and Ebers, J. 2006. Taxonomic parameters revisited: tarnished gold standards. Microbiol. Today, 33: 152-155.
25. Ultee, A., Souvatzi, N., Maniadi, K., and Konig, K. 2004. Identification of the culturable and nonculturable bacterial population in ground water of a municipal water supply in Germany. J. Appl. Microbiol. 96(3): 560-568. doi:10.1111/j.1365- 2672.2004.02174.x. PMID:14962136.
26. Williams, M.M., Domingo, J.W.S., Meckes, M.C., Kelty, C.A., and Rochon, H.S. 2004. Phylogenetic diversity of drinking water bacteria in a distribution system simulator. J. Appl. Microbiol. 96 (5): 954-964. doi:10.1111/j.1365-2672.2004.02229.x. PMID: 15078511.
27. Yu, Y., Breitbart, M., McNairnie, P., and Rohwer, F. 2006. FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics, 7(1): 57. doi:10.1186/1471-2105-7-57. PMID:16464253.
28. Zwart, G., Crump, B.C., Kamst-van Agterveld, M.P., Hagen, F., and Han, S.-K. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat. Microb. Ecol. 28: 141-155. doi:10.3354/ ame028141.