Fluorescence in situ hybridization in soil and water ecosystems: A useful method for studying the effect of xenobiotics on bacterial community structure

Toxicological and Environmental Chemistry

Volumn 92, Issue 3, 2010, Pages 567-579

  Caracciolo, Anna Barra ^a   Bottoni, Paola ^b   Grenni, Paola ^a  

^a WATER RESEARCH INSTITUTE   (Italy)

^b ISTITUTO SUPERIORE DI SANITÀ   (Italy)

Author keywords

Bacterial phylogenetic characterization; Groundwater; Oseltamivir carboxylate (tamiflu); Simazine; Soil; Surface water; Terbuthylazine

Indexed keywords

BACTERIAL PHYLOGENETIC CHARACTERIZATION; OSELTAMIVIR CARBOXYLATE; PHYLOGENETIC CHARACTERIZATION; SIMAZINE; SOIL SURFACES; TAMIFLU; TERBUTHYLAZINE;

BACTERIA; BACTERIOLOGY; BIOCHEMISTRY; CARBOXYLATION; ECOSYSTEMS; FLUORESCENCE; FLUORESCENCE MICROSCOPY; GROUNDWATER; HERBICIDES; HYDROGEOLOGY; OLIGONUCLEOTIDES; RNA; SOCIAL SCIENCES; SOILS; SURFACE WATERS; WATER TREATMENT;

GROUNDWATER POLLUTION;

BACTERIUM; MICROBIAL COMMUNITY; PHYLOGENETICS; RNA; SOIL ECOSYSTEM; SURFACE WATER; XENOBIOTICS;

ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES (CLASS); BACTEROIDES PHYLUM; CYTOPHAGA; FLAVOBACTER; PLANCTOMYCETES; POSIBACTERIA; PROTEOBACTERIA;

EID: 77949411140     PISSN: 02772248     EISSN: 10290486     Source Type: Journal    
DOI: 10.1080/02772241003620244     Document Type: Article

References (26)

1. Accinelli, C., A. Barra Caracciolo, and P. Grenni. 2007. Degradation of the antiviral drug oseltamivir carboxylate in surface water samples. International Journal of Environmental Analytical Chemistry 87: 579-87.
2. Amann, R.I., B.J. Binder, R.J. Olson, S.W. Chisholm, R. Devereux, R., and D.A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied Environmental Microbiology 56: 1919-25.
3. Amann, R.I., L. Krumholz, and D.A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. Journal of Bacteriology 172: 762-70.
4. Amann, R.I., W. Ludwig, and K.H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Review 59: 143-69.
5. Barra Caracciolo, A., P. Grenni, R. Ciccoli, G. Di Landa, and C. Cremisini. 2005a. Simazine biodegradation in soil: Analysis of bacterial community structure by in situ hybridization. Pest Management Science 61: 863-69.
6. Barra Caracciolo, A., P. Grenni, C. Cupo, and S. Rossetti. 2005b. In situ analysis of native microbial communities in complex samples with high particulate loads. FEMS Microbiology Letters 253: 55-8.
7. Barra Caracciolo, A., P. Grenni, M.L. Saccà, S. Amalfitano, R. Ciccoli, M. Martin, M, and A. Gibello. 2010. The role of a groundwater bacterial community in the degradation of the herbicide terbuthylazine. FEMS Microbiology Ecology 71: 127-36.
8. Bottari, B., D. Ercolini, M. Gatti, and E. Neviani. 2006. Application of FISH technology for microbiological analysis: Current state and prospects. Applied Microbiology and Biotechnology 73: 485-94.
9. Curtis, T.P., and W.T. Sloan. 2005. Exploring microbial diversity: A vast below. Science 309: 1331-33.
10. Daims, H., A. Brühl, R. Amann, K.H. Schleifer, and M. Wagner. 1999. The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: Development and evaluation of a more comprehensive probe set. Systematic and Applied Microbiology 22: 434-444.
11. Eickhorst, T., and R. Tippkotter. 2008. Detection of microorganisms in undisturbed soil by combining fluorescence in situ hybridization (FISH) and micropedological methods. Soil Biology and Biochemistry 40: 1284-1293.
12. Engel, A.S., N. Lee, M.L. Porter, L.A. Stern, P. Bennett, and M. Wagner. 2003. Filamentous "Epsilonproteobacteria" dominate microbial mats from Sulfidic Cave Springs. Applied and Environmental Microbiology 69: 5503-11.
13. Grenni, P., A. Gibello, A. Barra Caracciolo, C. Fajardo, M. Nande, R. Vargas, M.L. Sacca, M.J. Martinez-Iñigo, R. Ciccoli, R, and M. Martín. 2009. A new fluorescent oligonucleotide probe for in situ detection of s-triazine-degrading Rhodococcus wratislaviensis in contaminated groundwater and soil samples. Water Research 43: 2999-3008.
14. Loy, A., F. Maixner, M. Wagner, and M. Horn. 2007. probeBase-an online resource for rRNA-targeted oligonucleotide probes: New features 2007. Nucleic Acids Research 35, no. Database issue: D800-4.
15. Ludwig, W., and K.H. Schleifer. 1994. Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiology Reviews 15: 155-73.
16. Manz, W., R. Amann, W. Ludwig, M. Vancanneyt, and K.H. Schleifer. 1996. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology 142: 1097-1106.
17. Manz, W., R. Amann, W. Ludwig, M. Wagner, and K.H. Schleifer. 1992. Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: Problems and solutions. Systematic and Applied Microbiology 15: 593-600.
18. Meier, H., R. Amann, W. Ludwig, and K.H. Schleifer. 1999. Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DNA G + C content. Systematic and Applied Microbiology 22: 186-96.
19. Morán, A.C., A. Müller, M. Manzano, and B. González. 2006. Simazine treatment history determines a significant herbicide degradation potential in soils that is not improved by bioaugmentation with Pseudomonas sp ADP. Journal of Applied Microbiology 101: 26-35.
20. Neef, A., R. Amann, H. Schlesner, and K.H. Schleifer. 1998. Monitoring a widespread bacterial group: In situ detection of Planctomycetes with 16S rRNA-targeted probes. Microbiology 144: 3257-66.
21. Pernthaler, J.F., O. Glöckner, W. Schönhuber, and R. Amann. 2001. Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. Methods in Microbiology 30: 207-26.
22. Roller, C., M. Wagner, R. Amann, W. Ludwig, and K.H. Schleifer. 1994. In situ probing of Gram-positive bacteria with high DNA G + C content using 23S rRNA- targeted oligonucleotides. Microbiology 140: 2849-58.
23. Schleifer, K.H., and E. Stackebrandt. 1983. Molecular systematics of prokaryotes. Annual Review of Microbiology 37: 143-87.
24. Stahl, D.A., and R. Amann. 1991. Development and application of nucleic acid probes. In Nucleic acid techniques in bacterial systematics, eds. E. Stackebrandt and M. Goodfellow, 205-248. Chichester, England: John Wiley and Sons.
25. Torsvik, V., and L. Øvreås. 2007. Microbial phylogeny and diversity in soil. In Modern soil microbiology. 2nd ed, eds. J.D. van Elsas, J.K. Jansson and J.T. Trevors, 23-54. Boca Raton, FL: CRC Press/Taylor and Francis.
26. Zwart, G., B.C. Crump, M.P. Kamst-van Agterveld, F. Hagen, and S.K Han. 2002. Typical freshwater bacteria: An analysis of available 16S rRNA gene sequences from plankton of freshwater lakes and rivers. Aquatic Microbial Ecology 28: 141-55.