Chemical and microbiological in situ characterization of benthic communities in sediments with different contamination levels

Journal of Soils and Sediments

Volumn 3, Issue 3, 2003, Pages 188-196

  Lachmund, Christine ^a   Köcher, Beate ^a   Manz, Werner ^a   Heininger, Peter ^a  

^a FEDERAL INSTITUTE OF HYDROLOGY   (Germany)

Author keywords

Cell extraction; Desulfobacteriaceae; Elbe; Fluorescene in situ hybridization; Lotic sediments; Microbial communities; Oder; River sediments; Sediment biofilms; Sulfate reducing bacteria (SRB); Water Framework Directive

Indexed keywords

BIOFILM; ECOTOXICOLOGY; FLUVIAL DEPOSIT; MICROBIAL COMMUNITY; SEDIMENT POLLUTION;

BACTERIA (MICROORGANISMS); DESULFOBACTERACEAE;

EID: 0141992612     PISSN: 14390108     EISSN: None     Source Type: Journal    
DOI: 10.1065/jss2003.09.086     Document Type: Article

References (40)

1. Ackermann F (1980): A procedure for correcting the grain size effect in heavy metal analyses of estuarine and coastal sediments. Environ Technol Lett 1, 518-527
2. Amann R, Krummholz L, Stahl DA (1990): Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic and environmental studies in microbiology. J Bacteriol 172, 762-770
3. ARGE (1996): Arbeitsgemeinschaft für die Reinhaltung der Elbe: Umgang mit belastetem Baggergut an der Elbe. Zustand und Empfehlungen. Wassergütestelle Elbe. Hamburg, 25
4. Bak F, Pfenning N (1991) : Sulfate-reducing bacteria in littoral sediments of Lake Constance. FEMS Microb Ecol 85, 43-52
5. Bakersmans C, Madsen EL (2002): Detection in coal tar waste-contaminated groundwater of mRNA transcripts related to naphthalene dioxygenase by fluorescent in situ hybridization with tyramide signal amplification. J Microb Meth 50, 75-84
6. Barton LL (Editor) (1995): Sulfate-reducing bacteria. Biotechnology Handbooks 8, ISBN 0-306-44857-2
7. Böckelmann U, Manz W, Neu TR, Szewzyk U (2000): Characterisation of the microbial community of lotic organic aggregates ('river snow') in the Elbe River of Germany by cultivation and molecular methods. FEMS Microb Ecol 33, 157-170
8. Christensen H, Poulsen LK (1994): Detection of Pseudomonas in soil by rRNA targeted in situ hybridization. Soil Biol Biochem 26, 1093-1096
9. Claus E, Heininger P (2002): Anwendung differenzierter Untersuchungsmethoden zur Sedimentbewertung. UWSF - Z Umweltchem Ökotox 14 (1) 3-7
10. Claus E, Heininger P, Pelzer J (in preparation): Ecotoxicological risk of Oder river sediments
11. Coates JD, Woodward J, Allen J, Philp P, Lovley DR (1997): Anaerobic degradation of polycyclic aromatic hydrocarbons and alkanes in petroleum-contaminated marine harbour sediments. Appl Environ Microb 63, 3589-3593
12. Daims H, Brühl A, Schleifer K-H, Wagner M (1999): The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microb 22, 434-444
13. Fuchs BM, Glöckner FO, Wulf J, Amann R (2000): Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labelled oligonucleotide probes. Appl Environ Microb 66, 3603-3607
14. Heininger P, Pelzer J (1998): Trends und Verteilungsmuster in der Schadstoffbelastung von Sedimenten aus östlichen Bundeswasserstraßen. Acta hydrochim Hydrobiol 26, 218-225
15. Heininger P, Pelzer J, Claus E, Tippmann P (1998): Trends in river sediment contamination and toxicity -case of the Elbe river. Wat Sci Tech 37, 6-7, 95-102
16. Kämpfer P, Erhart R, Beimfohr C, Wagner M, Amann R (1996): Characterization of bacterial communities from activated sludge: Culture-dependent numerical identification versus in situ identification using group- and genus-specific rRNA-targeted oligonucleotide probes. Microb Ecol 32, 101-121
17. Kenzaka T, Yamaguchi N, Tani K, Nasu M (1998): rRNA-targeted fluorescent in situ hybrization analysis of bacterial community structure in river water. Microb 144, 2085-2093
18. Kim J, Rhee G-Y (1997): Population dynamics of polychlorinated biphenyl-dechlorinating microorganisms in contaminated sediments. Appl Environ Microb 63, 1771-1776
19. Langworthy DE, Stapleton RD, Sayler GS, Findlay RH (1998): Genotypic and phenotypic responses of a riverine microbial community o polycyclic aromatic hydrocarbon contamination. Appl Environ Microb 64, 3422-3428
20. Lindahl V. (1996): Improved soil dispersion procedures for total bacteria counts, extraction of indigenous bacteria and cell survival. J Microb Meth 25, 279-286
21. Llobet-Brossa E, Rossello-Mora R, Amann R (1998): Microbial community composition of wadden sea sediments as revealed by fluorescence in situ hybridization. Appl Environ Microb 64, 2691-2696
22. Manz W (1999): In situ analysis of microbial biofilms by rRNA-targeted oligonucleotide probing. Meth Enzymol 310, 79-91
23. Manz W, Eisenbrecher M, Neu TR, Szewzyk U (1998): Abundance and spatial organization of gram-negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides. FEMS Microb Ecol 25, 43-61
24. Manz W, Szewzyk U, Ericsson P, Amann R, Schleifer K-H, Stenström T-A (1993): In situ identification of bacteria in drinking water and adjoining biofilms by hybridization with 16S and 23S rRNA-directed fluorescent oligonucleotide probes. Appl Environ Microb 59, 2293-2298
25. Manz W, Wagner M, Kalmbach S (2001): Assessment of metabolic potential of biofilm-associated bacteria. Meth Enzymol 336, 265-276
26. Manz W, Wendt-Potthoff K, Neu T, Szewzyk U, Lawrence JR (1999): Phylogenetic composition, spatial structure and dynamics of lotic bacterial biofilms investigated by fluorescent in situ hybridization and confocal laser scanning microscopy. Microb Ecol 37, 225-237
27. Marxen J (1996): Measurement of bacterial production in stream-bed sediments via leucine incorporation. Microb Ecol 21, 3131-325
28. Ouverney CC, Fuhrman JA (1997): Increase in fluorescence intensity of 16S rRNA in situ hybridization in natural samples treated with chloramphenicol. Appl Environ Microb 63, 2735-2740
29. Rabus R, Fukui M, Wilkes H, Widdel F (1996): Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in a anaerobic enrichment culture utilising alkylbenzenes from crude oil. Appl Environ Microb 62, 3605-3613
30. Ravenschlag K, Sahm K, Amann R (2001): Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Appl Environ Microb 67, 387-395
31. Richtlinie 2000/60/EG des Europäischen Parlaments und des Rates vom 23. Oktober 2000. Amtsblatt der Europäischen Gemeinschaften, L 327/1
32. Sandaa R-A, Torsvik V, Enger O, Daae FL, Castberg T, Hahn D (1999): Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution. FEMS Microb Ecol 30, 237-251
33. Sass H, Cypionka H, Babenzien H-D (1997): Vertical distribution of sulfate-reducing bacteria at the oxic-anoxic interface in sediments of the oligotrophic Lake Stechlin. FEMS Microb Ecol 22, 245-255
34. Shi Y, Zwolinski MD, Schreiber ME, Bahr JM, Sewell GW, Hickley WJ (1999): Molecular analysis of microbial community structures in pristine and contaminated aquifers: field and laboratory microcosm experiment. Appl Environ Microb 65, 2143-2150
35. Staley JT, Konopka A (1985): Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39, 321-346
36. Törnblom E (1996): Bacterial production and total community metabolism in sediments of a eutrophic lake. Arch Hydrobiol Spec Issues Advanc Limnol 48, 207-216
37. Utgikar VP, Harmon SM, Chaudhary N, Tabak HH, Govind R, Haines JR (2002): Inhibition of sulfate-reducing bacteria by metal sulfide formation in bioremedation of acid mine drainage. Environ Toxicol 17, 40-48
38. Wagner M, Amann R, Lemmer H, Schleifer K-H (1993): Probing activated sludge with oligonucletides specific for Proteobacteria: Inadequacy of culture-dependent methods for describing microbial community structure. Appl Environ Microbiol 59, 1520-1525
39. Wellsbury P, Herbert RA, Parkes RJ (1996): Bacterial activity and production in near-surface estuarine and freshwater sediments. FEMS Microb Ecol 19, 203-214
40. Zarda B, Hahn D, Chatzinotas A, Schönhuber W, Neff A, Amann R, Zeyer J (1997): Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch Microbiol 168, 185-192