Microbiological and 16S rRNA analysis of sulphite-reducing clostridia from river sediments in central Italy

BMC Microbiology

Volumn 8, Issue , 2008, Pages

  Marcheggiani, Stefania ^a   Iaconelli, Marcello ^a   D'angelo, Annamaria ^a   Pierdominici, Elio ^a   La Rosa, Giuseppina ^a   Muscillo, Michele ^a   Equestre, Michele ^a   Mancini, Laura ^a  

^a ISTITUTO SUPERIORE DI SANITÀ   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; SULFITE; BACTERIAL RNA;

ADAPTATION; ANAEROBIC BACTERIUM; ARTICLE; BACTERIAL STRAIN; BACTERIUM; BACTERIUM ISOLATION; BIOCHEMISTRY; CLOSTRIDIA PEFRINGENS; GENE SEQUENCE; GENETIC ANALYSIS; HAPLOTYPE; ITALY; MICROBIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RIVER; RNA ANALYSIS; SEASONAL VARIATION; SEDIMENT; WATER CONTAMINATION; BACTERIAL GENE; BIODIVERSITY; CLOSTRIDIUM; ENVIRONMENTAL MONITORING; FECES; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; RNA GENE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; WATER POLLUTANT;

BACILLUS CEREUS; BACTERIA (MICROORGANISMS); CLOSTRIDIA; CLOSTRIDIUM PERFRINGENS; CLOSTRIDIUM PERFRINGENS A;

BIODIVERSITY; CLOSTRIDIUM; ENVIRONMENTAL MONITORING; FECES; GENES, BACTERIAL; GENES, RRNA; GEOLOGIC SEDIMENTS; HAPLOTYPES; ITALY; MOLECULAR SEQUENCE DATA; PHYLOGENY; RIVERS; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; WATER MICROBIOLOGY; WATER POLLUTANTS;

EID: 54249142791     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-8-171     Document Type: Article

References (66)

1. Alternative microbiol indicators of faecal pollution: Current Perspective. VK Tyagi AK Chopra AA Kazmi A Kumar, (IAEH)Iran Ass Environ Health 2006 3 205 216
2. Directive 2006/7/EC 15 February 2006. Concerning the management of bathing water quality and repealing Directive 76/160/EEC. The European Parliament and the Council of European Union, Official Journal of the European Union 2006
3. The indicator system. G Berg, Indicators of Viruses in Water and Food Ann Arbor, MI: Ann Arbor Science, Berg G, 1978 1 13
4. Waterborne diseases: Update on water quality assessment and control. WOK Grabow, Water SA 1996 22 193 202
5. Clostridium perfringens and somatic coliphages as indicators of the efficiency of drinking water treatment for viruses and protozoan cysts. P Payment E Franco, Appl Environ Microbiol 1993 59 2418 2424 8368831
6. C Gleeson NF Gray, The coliform index and waterborne disease: problems of microbial drinking water assessment London: E. & F.N. Spon 1 1997
7. Enteric bacterial metabolism of stream sediment eluates. CW Hendricks, Can J Microbiol 1971 17 551 556 4928631
8. JE Grimes, The Thread of Discourse. Janua Linguarum Series Minor The Hague: Mouton 1975 207
9. Sediment bacterial indicators in an urban shellfishing subestuary of the lower Chesapeake Bay. CW Erkenbrecher, Appl Environ Microbiol 1981 42 481 492
10. Enteric bacteria survival factors. M Pommepuy JF Guillaud E Dupray A Derrien F Le Guyader M Cormier, Water Sci Technol 1992 12 93 103
11. Effect of chelating agents on the growth of Escherichia coli in seawater. GE Jones, J Bacteriol 1964 87 484 499
12. Role of bacteria and protozoa in the removal of Escherichia coli from estuarine waters. EM Enzinger RC Cooper, Appl Environ Microbiol 1976 31 758 763 776086
13. Effect of Several Clay Minerals and Humic Acid on the Survival of Klebsiella aerogenes Exposed to Ultraviolet Irradiation. G Bitton Y Henis N Lahav, Appl Microbiol 1972 23 870 874 5031559
14. Effects of salinity on sedimentation and of particulates on survival of bacteria in estuarine habitats. MM Roper KC Marshall, Geomicrobiol J 1979 1 103 116
15. Evidence that Escherichia coli accumulates glycine betaine from marine sediment. M Ghoul T Bernard M Cormier, Appl Environ Microbiol 1986 56 551 554
16. Influence of prior growth conditions on low nutrient response of Escherichia coli in seawater. MJ Gauthier PM Munro VA Breittmayer, Can J Microbiol 1989 35 379 383 2659156
17. Survival of faecal microorganisms in marine and freshwater sediments. CM Davies A Julian H Long M Donald NJ Ashbolt, Appl Environ Microbiol 1995 61 1888 1896 7646026
18. Indicatori microbiologici di inquinamento: corrispondenza acqua-sedimenti del Mar Piccolo di Taranto. RA Cavallo F Latorre MI Acquaviva MT Montagna MS Mele, Inquinamento 1996 3 54 57
19. Seasonal changes in ribosomal RNA of sulphate-reducing bacteria and sulphate reducing activity in a freshwater lake sediment. J Li KJ Purdy S Takii H Hayashi, FEMS Microbiol Ecol 1999 28 31 39 10.1111/j.1574-6941.1999.tb00558.x
20. Distribution of Clostridium perfringens in polluted lake environments. E Bezirtzoglou A Panagiou Y Savvaidis V Maipa, Anaerobe 1997 3 169 172 10.1006/anae.1997.0101 16887584
21. Microorganisms present in the ground-water environment. FH Chapelle, Ground-water microbiology and geochemistrynd Edition New York: Wiley J & Sons, Chapelle FH, 2 2000 32 57
22. Clostridium perfringens as a water pollution indicator. JW Bisson VJ Cabelli, J Water Pollut Control Fed 1980 52 241 248 6245283
23. Clostridium perfringens, a reliable indicator of stream water quality. RS Fujioka LK Shizumura, J Water Pollut Control Fed 1985 57 986 992
24. Relationships between indicators, pathogens and water quality in an estuarine system. CM Ferguson BG Coote NJ Ashbolt IM Stevenson, Wat Res 1996 30 2045 2054 10.1016/0043-1354(96)00079-6
25. Clostridium perfringens as a potential indicator for the Presence of Sewage Solids in Marine Sediments. C Skanavis WA Yanko, Mar Pollut Bull 2001 42 31 35 10.1016/S0025-326X(00)00087-4 11382981
26. Influence of Soil on Faecal Indicator Organisms in a Tidally Influenced Subtropical Environment. TJ Desmarais HM Solo-Gabriele CJ Palmer, Appl Environ Microbiol 2002 68 1165 1172 11872464 10.1128/AEM.68.3.1165-1172.2002
27. Sources of E. coli to a SubTropical Coastal Environment. H Solo-Gabriele M Wolfert T Desmarais C Palmer, App Environ Microbiol 2000 66 1 230 237
28. Distinguishing sources of fecal pollution in Australian inland and coastal waters using sterol biomarkers and microbial fecal indicators. R Leeming PD Nichols NJ Ashbolt, Research Report No. 204 Melbourne: Water Services Association of Australia 1998
29. Clostridium perfringens in animal disease: A review of current knowledge. L Niilo, Can Vet J 1980 21 141 148 6253040
30. Urban sprawl leaves its PAH signature. P Van Metre B Mahler E Furlong, Environ Sci Technol 2000 34 4064 4070 10.1021/es991007n
31. World Health Organization, Guidelines for drinking water quality. Health criteria and other supporting information Geneva: World Health Organization Second 1996 2
32. Sulfite-reducing clostridia in the sediment of high mountain lake (Laguna Grande, Gredos, Spain) as indicators of faecal pollution. S Robles JM Rodrìguez I Granados MC Guerrero, Int Microbiol 2000 3 187 91 11032313
33. Clostridium perfringens as a point-source indicator in non-point source polluted streams. DL Sorensen SG Eberl RA Dicksa, Water Res 1989 23 191 197 10.1016/0043-1354(89)90043-2
34. Water quality surveys; a guide for the collection and interpretation of water quality data. International Hydrological Decade - World Health Organization (IHD-WHO), Studies and Reports in Hydrology (UNESCO), no. 23/International Hydrological Decade, 75 - Paris (France) Geneva: World Health Organization 1978 57 54
35. Obligate anaerobic bacterial indicators. VJ Cabelli, Indicators of Viruses in Water and Food Ann Arbor, MI: Ann Arbor Science, Berg G, 1978 171 200
36. Bacterial Indicators of Pollution. VP Olivieri, Bacterial indicators of pollution Boca Raton, FL: CRC Press, Minton NP, Clarke DJ, 1982 21 41
37. Sorbitol-fermenting bifidobacteria as indicators of diffuse human faecal pollution in estuarine watersheds. MW Rhodes H Kantor, J Appl Microbiol 1999 87 528 535 10.1046/j.1365-2672.1999.00845.x 10583680
38. Bacterial evolution. CR Woese, Microbiol Rev 1987 51 221 271 2439888
39. 16S ribosomal DNA amplification for phylogenetic study. WG Weisburg SM Barns DA Pelletier DJ Lane, J Bacteriol 1991 17 697 703
40. The use of 16S and 16S-23S rDNA to easily detect and differentiate common Gram-negative orchard epiphytes. RS Jeng AM Svircev AL Myers L Beliaeva DM Hunter M Hubbes, J Microbiol Methods 2001 44 69 77 10.1016/S0167-7012(00)00230-X 11166101
41. 16S rDNA for Diagnosing Pathogens: a Living Tree. D Harmsen H Karch, ASM News 2004 19 19 24
42. 16S rRNA gene based analysis of Enterobacter sakazakii strains from different sources and development of a PCR assay for identification. A Lehner T Tasara R Stephan, BMC Microbiol 2004 4 1 43 15563736 10.1186/1471-2180-4-43
43. Investigating the role of small, acid-soluble spore proteins (SASPs) in the resistance of Clostridium perfringens spores to heat. D Raju M Waters P Setlow MR Sarker, BMC Microbiol 2006 6 50 16759397 10.1186/1471-2180-6-50
44. Genetic diversity of Clostridium perfringens type A isolates from animals, food poisoning outbreaks and sludge. A Johansson A Aspan E Bagge V Båverud Björn E Engström Karl-Erik Johansson, BMC Microbiol 2006 6 47 16737528 10.1186/1471-2180-6-47
45. Bergey's Manual of Systematic Bacteriology. AAVV, Springer, London, UK, Garrity G, 2 2005
46. Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. JB Kruskal, Psychometrica 1964 29 1 27 10.1007/BF02289565
47. Nonmetric multidimensional scaling: a numerical method. JB Kruskal, Psychometrica 1964 29 115 129 10.1007/BF02289694
48. Dating of the human-ape splitting by molecular clock of mitochondrial DNA. M Hasegawa H Kishino T Yano, J Mol Evol 1985 32 443 445 10.1007/BF02101285
49. Standard Methods for the Examination of Water and WasteWater. APHA-AWWA-WPCF, Washington DC, USA,: APHA American Public Health Association 20 1998
50. Membrane filter enumeration method for Clostridium perfringens. JW Bisson VJ Cabelli, Appl Environ Microbiol 1979 37 55 66 216310
51. A modified m-CP medium for enumerating C. perfringens from water samples. R Armon P Payment, Can J Microbiol 1988 34 78 79 2897874
52. Taxonomy of the clostridia: Ribosomal ribonucleic acid homologie among the species. JL Johnson BS Francis, J Gen Microbiol 1975 88 219 24
53. Taxonomy and Phylogeny. EP Cato E Stackebrandt, Clostridia-Biotechnology handbooks, III series New York and London: Plenum Press, Minton NP, Clarke DJ, 1989 1 26
54. The phylogeny of the genus Closridium: Proposal of five new genera and eleven new species combinations. MD Collins PA Lawson A Willems JJ Cordoba J Fernandez-Garayzabal P Garcia J Cai H Hipe JAE Frarrow, Int J Syst Bacteriol 1994 44 812 826 7981107
55. Distribution of Sewage Indicated by Clostridium perfringens at a Deep-Water Disposal Site after Cassation of Sewage Disposal. RT Hill WL Straube AC Palmisano SL Gibson RR Colwell, Appl Environ Microbiol 1996 62 1741 1746 8633872
56. Attività di controllo della qualità delle acque del bacino del Tevere. Rapporto n. 1 descrizione delle attività ed analisi di variabilità dei dati. Roma. ACEA, Azienda Comunale Energia & Ambiente, Rapporto tecnico 1996
57. Rapporto ICRAM Sedimenti - Scheda 6 - Analisi di spore di clostridi solfito-riduttori. Ministero dell'Ambiente e Tutela del Territorio 2000
58. Particle-size analysis by a modified pipette procedure. SJ Indorante LR Follmer RD Hammer PG Koenig, Soil Sci Soc Am J 1990 54 560 563
59. A new method of sampling soil suspension for particle-size analysis. N Moshrefi, Soil Sci 1993 155 245 8 10.1097/00010694-199304000-00002
60. FM Ausubel R Brent RE Kingston DD Moore GJ Seidman JA Smith K Struhl, Current Protocols in Molecular Biology New York: Green Publishing Associates and Wiley-Interscience 1989
61. Primer3 on the WWW for general users and for biologist programmers. S Rozen HJ Skaletsky, Bioinformatics Methods and Protocols: Methods in Molecular Biology Totowa, NJ: Human Press, Krawetz S, Misener S, 2000 365 386
62. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins, Nucleic Acids 1997 24 4876 4882 10.1093/nar/25.24.4876
63. Multiple sequence alignment with Clustal X. F Jeanmougin JD Thompson M Gouy DG Higgins TJ Gibson, Trends in Bioch Sci 1998 23 403 405 10.1016/S0968-0004(98)01285-7
64. The neighbor-joining method: a new method for reconstructing phylogenetic trees. N Saitou M Nei, Mol Biol Evol 1987 4 406 425 3447015
65. DL Swofford, PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0 Sunderland, Massachusetts: Sinauer Associates 2002
66. MODELTEST: testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics 1998 14 817 818 10.1093/bioinformatics/14.9.817 9918953