Fecal Bacteroidales diversity and decay in response to variations in temperature and salinity

Applied and Environmental Microbiology

Volumn 77, Issue 8, 2011, Pages 2563-2572

  Schulz, Christopher J ^a   Childers, Gary W ^a  

^a SOUTHEASTERN LOUISIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; DECAY RATE; FECAL POLLUTION; HIGHER TEMPERATURES; HOST ORGANISM; OPERATIONAL TAXONOMIC UNITS; PHYLOGENETIC DIVERSITY; POSITIVE EFFECTS; QUANTITATIVE PCR; RIVER WATER; WATER QUALITY INDICATORS;

CLONING; GENES; POLYMERASE CHAIN REACTION; RNA; SALINITY MEASUREMENT; WATER POLLUTION; WATER QUALITY;

DECAY (ORGANIC);

BIOLOGICAL MARKER; FRESH WATER; RNA 16S;

BACTERIUM; BIOMARKER; CELL ORGANELLE; DATA SET; ESTIMATION METHOD; GENETIC ANALYSIS; HIGH TEMPERATURE; LINEARITY; MICROCOSM; NUMERICAL MODEL; PHYLOGENETICS; PHYSIOLOGICAL RESPONSE; POLYMERASE CHAIN REACTION; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; RIVER WATER; SALINITY; SPECIES DIVERSITY; SURVIVAL; TAXONOMY; TEMPERATURE EFFECT; THRESHOLD; WATER QUALITY;

ARTICLE; BACTEROIDES; CHEMISTRY; FECES; GENETICS; HEAT; HOST RANGE; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; POLYMERASE CHAIN REACTION; SALINITY; SEWAGE; SURVIVAL; WATER POLLUTANT; WATER POLLUTION;

BACTEROIDES; BIOLOGICAL MARKERS; FECES; FRESH WATER; HOST SPECIFICITY; HOT TEMPERATURE; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SALINITY; SEWAGE; SURVIVAL ANALYSIS; WATER POLLUTANTS; WATER POLLUTION;

BACTERIA (MICROORGANISMS); BACTEROIDALES;

EID: 79955579268     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01473-10     Document Type: Article

References (41)

1. Acinas, S. G., R. Sarma-Rupavtarm, V. Klepac-Ceraj, and M. F. Polz. 2005. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol. 71:8966-8969.
2. Anderson, K. L., J. E. Whitlock, and V. J. Harwood. 2005. Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments. Appl. Environ. Microbiol. 71:3041-3048.
3. Ashelford, K. E., N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman. 2006. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol. 72:5734-5741.
4. Bae, S., and S. Wuertz. 2009. Rapid decay of host-specific fecal Bacteroidales cells in seawater as measured by quantitative PCR with propidium monoazide. Water Res. 43:4850-4859.
5. Baranyi, J., and T. A. Roberts. 1994. A dynamic approach to predicting bacterial growth in food. Int. J. Food Microbiol. 23:277-294.
6. Baranyi, J., and T. A. Roberts. 1995. Mathematics of predictive food microbiology. Int. J. Food Microbiol. 26:199-218.
7. Baranyi, J., T. A. Roberts, and P. J. McClure. 1993. A non-autonomous differential equation to model bacterial growth. Food Microbiol. 10:43-59.
8. Bell, A., et al. 2009. Factors influencing the persistence of fecal Bacteroides in stream water. J. Environ. Qual. 38:1224-1232.
9. Bernhard, A. E., and K. G. Field. 2000. Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic markers from fecal anaerobes. Appl. Environ. Microbiol. 66:1587-1594.
10. Chick, H. 1908. An investigation of the laws of disinfection. J. Hyg. 8:92-157.
11. Crane, S. R., and J. A. Moore. 1986. Modeling enteric bacterial die-off: a review. Water Air Soil Pollut. 27:411-439.
12. DeSantis, T. Z., Jr., et al. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34:W394-W399.
13. DeSantis, T. Z., Jr., et al. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069-5072.
14. Dick, L. K., et al. 2005. Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl. Environ. Microbiol. 71:3184-3191.
15. Dick, L. K., and K. G. Field. 2004. Rapid estimation of numbers of fecal Bacteroidetes by use of a quantitative PCR assay for 16S rRNA genes. Appl. Environ. Microbiol. 70:5695-5697.
16. Dick, L. K., E. A. Stelzer, E. E. Bertke, D. L. Fong, and D. M. Stoeckel. 2010. Relative decay of Bacteroidales microbial source tracking markers and cultivated Escherichia coli in freshwater microcosms. Appl. Environ. Microbiol. 76:3255-3262.
17. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Department of Genetics, University of Washington, Seattle.
18. Fogarty, L. R., and M. A. Voytek. 2005. Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species. Appl. Environ. Microbiol. 71:5999-6007.
19. Gonzalez, J. M. 1995. Modelling enteric bacteria survival in aquatic systems. Hydrobiologia 316:109-116.
20. Gourmelon, M., et al. 2007. Evaluation of two library-independent microbial source tracking methods to identify sources of fecal contamination in French estuaries. Appl. Environ. Microbiol. 73:4857-4866.
21. Kildare, B. J., et al. 2007. 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: a Bayesian approach. Water Res. 41:3701-3715.
22. Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
23. Kreader, C. A. 1998. Persistence of PCR-detectable Bacteroides distasonis from human feces in river water. Appl. Environ. Microbiol. 64:4103-4105.
24. Lane, D. J. 1991. 16S/23S rRNA sequencing. John Wiley and Sons, West Sussex, England.
25. Layton, A., et al. 2006. Development of Bacteroides 16S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Appl. Environ. Microbiol. 72:4214-4224.
26. Ley, R. E., et al. 2008. Evolution of mammals and their gut microbes. Science 320:1647-1651.
27. Muirhead, R. W., R. P. Collins, and P. J. Bremer. 2005. Erosion and subsequent transport state of Escherichia coli from cowpats. Appl. Environ. Microbiol. 71:2875-2879.
28. Okabe, S., N. Okayama, O. Savichtcheva, and T. Ito. 2007. Quanitification of host-specific Bacteroides-Prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Appl. Microbiol. Biotechnol. 74:890-901.
29. Okabe, S., and Y. Shimazu. 2007. Persistence of host-specific Bacteroides-Prevotella 16S rRNA genetic markers in environmental waters: effects of temperature and salinity. Appl. Microbiol. Biotechnol. 76:935-944.
30. Pachepsky, Y. A., et al. 2006. Transport and fate of manure-borne pathogens: modeling perspective. Agric. Water Manag. 86:81-92.
31. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
32. Schloss, P. D., et al. 2009. Introducing mothur: open source, platformindependent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.
33. Seurinck, S., D. Tom, V. Willy, and D. S. Steven 2005. Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater. Environ. Microbiol. 7:249-259.
34. Shanks, O. C., et al. 2006. Basin-wide analysis of the dynamics of fecal contamination and fecal source identification in Tillamook Bay, Oregon. Appl. Environ. Microbiol. 72:5537-5546.
35. Silkie, S. S., and K. L. Nelson. 2009. Concentrations of host-specific and generic fecal markers measured by quantitative PCR in raw sewage and fresh animal feces. Water Res. 43:4860-4871.
36. Stoeckel, D. M., and V. J. Harwood. 2007. Performance, design, and analysis in microbial source tracking studies. Appl. Environ. Microbiol. 73:2405-2415.
37. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
38. Thompson, J. R., L. A. Marcelino, and M. F. Polz. 2002. Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res. 30:2083-2088.
39. Walters, S. P., and K. G. Field. 2009. Survival and persistence of human and ruminant-specific faecal Bacteroidales in freshwater microcosms. Environ. Microbiol. 11:1410-1421.
40. Walters, S. P., K. M. Yamahara, and A. B. Boehm. 2009. Persistence of nucleic acid markers of health-relevant organisms in seawater microcosms: implications for their use in assessing risk in recreational waters. Water Res. 43:4929-4939.
41. Whitman, R. L., M. B. Nevers, G. C. Korinek, and M. N. Byappanahalli. 2004. Solar and temporal effects on Escherichia coli concentration at a Lake Michigan swimming beach. Appl. Environ. Microbiol. 70:4276-4285.