Different methods for extracting bacteria from freshwater sediment and a simple method to measure bacterial production in sediment samples

Journal of Microbiological Methods

Volumn 41, Issue 3, 2000, Pages 249-257

  Dos Santos Furtado, André Luiz ^a   Casper, Peter ^b  

^a Institute of Biology   (Brazil)

^b LEIBNIZ INSTITUTE OF FRESHWATER ECOLOGY AND INLAND FISHERIES   (Germany)

Author keywords

Bacteria extraction; Centrifugation; Freshwater sediments; Leucine uptake; Sonication

Indexed keywords

FRESH WATER;

ARTICLE; AUTOCLAVE; BACTERIAL COUNT; BACTERIUM DETECTION; DENSITY GRADIENT CENTRIFUGATION; NONHUMAN; PRIORITY JOURNAL; SAMPLING; SEDIMENT; ULTRASOUND;

BACTERIA; CENTRIFUGATION, DENSITY GRADIENT; COLONY COUNT, MICROBIAL; FRESH WATER; GEOLOGIC SEDIMENTS; POVIDONE; SILICON DIOXIDE; SONICATION; TRITIUM; WATER MICROBIOLOGY;

EID: 0033847958     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-7012(00)00163-9     Document Type: Article

References (28)

1. Bååth E. Thymidine incorporation into macromolecules of bacteria extracted from soil homogenization-centrifugation. Soil Biol. Biochem. 24:1992;1157-1165.
2. Bååth E. Thymidine incorporation of bacteria sequentially extracted from soil using repeated homogenisation-centrifugation. Microb. Ecol. 31:1996;153-166.
3. Bakken L.R. Separation and purification of bacteria from soil. Appl. Environ. Microbiol. 49:1985;1482-1487.
4. Bakken L.R., Lindahl V. Recovery of bacterial cells from soil. van Els J.D., Trevors J.T. Nucleic Acids in the Environment: Methods and Applications. 1995;9-27 Springer.
5. Casper S.J. Monographiae Biologicae. Lake Stechlin. A temperate oligotrophic lake. Vol. 58:1985;553 Dr. W. Junk Publishers, Dordrecht, The Netherlands.
6. Danovaro R., Fabiano M., Boyer M. Seasonal changes of benthic bacteria in a seagrass bed (Posidonia oceanica) of the Ligurian Sea in relation to origin, composition and fate of the sediment organic matter. Mar. Biol. 119:1994;489-500.
7. Díaz-Raviña M., Frostegård Å., Bååth E. Thymidine, leucine and acetate incorporation into soil bacterial assemblages at different temperatures. FEMS Microbiol. Ecol. 14:1994;221-232.
8. Fry J.C. Determination of biomass. Austin B. Methods in Aquatic Bacteriology. 1988;27-72 John Wiley & Sons.
9. Fry J.C. Direct methods and biomass estimation. Methods Microbiol. 22:1990;41-85.
10. Hoff K.A. Total and specific bacterial counts by simultaneous staining with DAPI and fluorochrome-labeled antibodies. Kemp P.F., Sherr B.F., Sherr E.B., Cole J.J. Handbook of Methods in Aquatic Microbial Ecology. 1993;149-154 Lewis Publishers, Boca Raton, Florida.
11. Hollibaugh J.T., Wong P.S. Ethanol-extractable substrate pools and the incorporation of thymidine, L-leucine, and other substrates by bacterioplankton. Can. J. Microbiol. 38:1992;605-613.
12. 3H] thymidine incorporation into DNA as a method to determine bacterial productivity in stream bed sediments. Appl. Environ. Microbiol. 58:1992;3614-3621.
13. Kepner R.L., Pratt J.R. Use of fluorochromes for direct enumeration of total bacteria in environmental samples: past and present. Microbiol. Rev. 58:1994;603-615.
14. Lindahl V., Bakken L.R. Evaluation of methods for extraction of bacteria from soil. FEMS Microbiol. Ecol. 16:1995;135-142.
15. Osinga R., Kop A.J., Duineveld G.C.A., Prins R.A., van Duyl F.C. Benthic mineralization rates at two locations in the southern North Sea. J. Sea Res. 36:1996;181-191.
16. Priemé A., Sitaula J.I.B., Klemedtsson Å.K., Bakken L.R. Extraction of methane-oxidizing bacteria from soil particles. FEMS Microbiol. Ecol. 21:1996;59-68.
17. Ramsay A.J. Extraction of bacteria from soil: efficiency of shaking or ultrasonication as indicated by direct counts and autoradiography. Soil Biol. Biochem. 16:1984;475-481.
18. Rodriguez G.G., Phipps D., Ishiguro K., Ridgway H.F. Use of a fluorescent redox probe for direct visualisation of actively respiring bacteria. Appl. Environ. Microbiol. 58:1992;1801-1808.
19. Schallenberg M., Kalff J. The ecology of sediment bacteria in lakes and comparisons with other aquatic ecosystems. Ecology. 74:1993;919-934.
20. Schallenberg M., Kalff J., Rasmussen J.B. Solutions to problems in enumerating sediment bacteria by direct counts. Appl. Environ. Microbiol. 55:1989;1214-1219.
21. Simon M., Azam F. Protein content and protein synthesis rates of planktonic marine bacteria. Mar. Ecol. Prog. Ser. 51:1989;201-213.
22. Sinsabaugh R.L., Findlay S. Microbial production, enzyme activity, and carbon turnover in surface sediments of the Hudson River estuary. Microb. Ecol. 30:1995;127-141.
23. 3H-leucine. Mar. Microb. Food Webs. 6:1992;107-114.
24. Starink M., Bär-Gilissen M.-J., Bak R.P.M., Cappenberg T.E. Bacterivory by heterotrophic nanoflagellates and bacterial production in sediments of a freshwater littoral system. Limnol. Oceanogr. 41:1996;62-69.
25. Törnblom E., Pettersson K. Bacterial production and total sediment metabolism in profundal Lake Erken sediments. Arch. Hydrobiol. Spec. Issues Advanc. Limnol. 51:1998;177-183.
26. Tso S.F., Taghon G.L. Enumeration of protozoa and bacteria in muddy sediment. Microb. Ecol. 33:1997;144-148.
27. Tulonen T., Kankaala P., Ojala A. Production of bacteria in the littoral zone of two experimental mesohumic ponds. Arch. Hydrobiol. Spec. Issues Advanc. Limnol. 48:1996;217-225.
28. Tuominen L. Comparison of leucine uptake methods and a thymidine incorporation method for measuring bacterial activity in sediment. J. Microbiol. Methods. 24:1995;125-134.