Culturability of stream bacteria assessed at the assemblage and population levels

Microbial Ecology

Volumn 51, Issue 3, 2006, Pages 365-374

  Lemke, Michael J ^a,b   Leff, Laura G ^a  

^a KENT STATE UNIVERSITY   (United States)

^b UNIVERSITY OF ILLINOIS AT SPRINGFIELD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; CULTIVATION; LOTIC ENVIRONMENT; POPULATION DYNAMICS;

ACINETOBACTER CALCOACETICUS; ARTICLE; BURKHOLDERIA CEPACIA; CULTURAL ANTHROPOLOGY; FLUORESCENCE IN SITU HYBRIDIZATION; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY; POPULATION; PSEUDOMONAS PUTIDA; RIVER;

ACINETOBACTER CALCOACETICUS; BACTERIOLOGICAL TECHNIQUES; BURKHOLDERIA CEPACIA; CULTURE; IN SITU HYBRIDIZATION, FLUORESCENCE; POPULATION; PSEUDOMONAS PUTIDA; RIVERS;

ACINETOBACTER CALCOACETICUS; BACTERIA (MICROORGANISMS); BURKHOLDERIA CEPACIA; PSEUDOMONAS PUTIDA;

EID: 33745094100     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-006-9026-z     Document Type: Article

References (62)

1. Albright, LJ, Masuda, KV, Ennis, GL, Schreier, H (1980) Microbial dynamics of two sub-arctic Canadian rivers. Water Res 14: 1353-1362
2. Amann, RI, Krumholz, L, Stahl, DA (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172: 762-770
3. Bell, CR, Holder-Franklin, MA, Franklin, M (1980) Heterotrophic bacteria in two Canadian rivers - I. Seasonal variations in the predominant bacterial populations. Water Res 14: 440-460
4. Besemer, K, Moeseneder, MM, Arrieta, JM, Herndl, GJ, Peduzzi, P (2005) Complexity of bacterial communities in a river-floodplain system (Danube, Austria). Appl Environ Microbiol 71: 609-620
5. Bouvier, T, del Giorgio, PA (2003) Factors influencing the detection of bacterial cells using fluorescence in situ hybridization (FISH): A quantitative review of published reports. FEMS Microbiol Rev 44: 3-15
6. Braun-Howland, EB, Vescio, PA, Nierzwicki-Bauer, SA (1993) Use of simplified cell blot technique and 16S rRNA-directed probes for identification of common environmental isolates. Appl Environ Microbiol 59: 3219-3224
7. Buchanan-Mappin, JM, Wallis, PM, Buchanan, AG (1986) Enumeration and identification of heterotrophic bacteria in groundwater and in a mountain stream. Can J Microbiol 32: 93-98
8. Burger, J, Snodgrass, JW (2000) Oral deformities in several species of frogs from the Savannah River site, USA. Environ Toxicol Chem 19: 2519-2524
9. Colwell RR, Grimes DJ (Eds.) (2000) Nonculturable Microorganisms in the Environment. Am Soc Microbiol, Washington, DC
10. Colwell, RR, West, A, Maeval, D, Remmers, EF, Elliot, EL, Carlson, NE (1984) Ecology of pathogenic vibrios in Chesapeake Bay. In: Colwell, RR (Eds.) Vibrios in the Environment. Wiley, Chichester
11. Créach, V, Baudoux, A-C, Bertu, G, Le Rouzic, B (2003) Direct estimate of active bacteria: CTC use and limitations. J Microbiol Methods 52: 19-28
12. Crump, BC, Armbrust, EV, Baross, JA (1999) Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean. Appl Environ Microbiol 65: 3192-3204
13. Cuney, C, Dukan, L, Fraysse, L, Ballesteros, M, Dukan, S (2005) Investigation of the first events leading to loss of culturability during Escherichia coli starvation: Future nonculturable bacteria from a subpopulation. J Bacteriol 187: 2244-2248
14. Daubner, I (1969) The effect of some ecological factors on bacteria in water. Verh-Int Ver Limnol 17: 731-743
15. DeLong, EF, Wickham, GS, Pace, NR (1989) Phylogenetic stains: Ribosomal RNA based probes for the identification of single cells. Science 243: 1360-1363
16. Eiler, A, Bertilsson, S (2004) Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes. Environ Microbiol 6: 1228-1243
17. Gauthier, MJ (2000) Environmental parameters associated with the viable but nonculturable state. In: Colwell, RR, Grimes DJ (Eds.) Nonculturable Microorganisms in the Environment. ASM Press, Washington, DC
18. Glöckner, FO, Fuchs, BM, Amann, R (1999) Bacterioplankton compositions of lakes and oceans: A first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65: 3721-3726
19. Goulder, R (1980) Seasonal variation in heterotrophic activity and population density of planktonic bacteria in a clean river. J Ecol 68: 349-363
20. Gray, E (1951) The ecology of the bacteria of Hobson's Brook, a Cambridgeshire chalk stream. J Gen Microbiol 5: 840-859
21. Grimes, DJ, Cowell, RR (1986) Viability and virulence of Escherichia coli suspended by membrane chamber in semitropical ocean water. FEMS Microbiol Lett 34: 161-165
22. Hahn, D, Amann, RI, Ludwig, W, Akkermans, ADL, Schleifer, K-H (1992) Detection of micro-organisms in soil after in situ hybridization with rRNA-targeted, fluorescently labeled oligonucleotides. J Gen Microbiol 138: 879-887
23. Hiorns, WD, Methé, BA, Nierzwickibauer, SA, Zehr, JP (1997) Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences. Appl Environ Microbiol 63: 2957-2960
24. Hudson, JJ, Roff, JC, Bujrnison, BK (1992) Bacterial productivity in forested and open streams in southern Ontario. Can J Fish Aquat Sci 49: 2412-2422
25. Janssen, PH, Yates, PS, Grinton, BE, Taylor, PM, Sait, M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the division Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 68: 2391-2396
26. Kell, DB, Kaprelyants, AS, Weichart, DH, Harwood, CR, Barer, MR (1998) Viability and activity in readily culturable bacteria: A review and discussion of the practical issues. Antonie van Leeuwenhoek 73: 169-187
27. Langley TM, Marter WL (1973) The SRP plant site. Publication DP-1323, Savannah River Laboratory, E. I. DuPont de Nemours and Co., Aiken, SC
28. Leff, LG, Brown, BJ, Lemke, MJ (1999) Spatial and temporal changes in bacterial assemblages of the Cuyahoga River. Ohio J Sci 99: 44-48
29. Leff, LG, Kernan, RM, McArthur, JM, Shimkets, LJ (1995) Identification of aquatic Burkholderia (Pseudomonas) cepacia by hybridization with species-specific rRNA gene probes. Appl Environ Microbiol 61: 1634-1636
30. Leff, LG, Leff, AA, Lemke, MJ (1997) Seasonal changes in planktonic bacterial assemblages of two Ohio streams. Freshw Biol 39: 129-134
31. Leff, LG, Meyer, JL (1991) Biological availability of dissolved organic carbon to bacteria along the Ogeechee River continuum. Limnol Oceanogr 36: 315-323
32. Lemke, MJ, Brown, BJ, Leff, LG (1997) The response of three bacterial populations to pollution in a stream. Microb Ecol 34: 224-231
33. Lemke, MJ, Leff, LG (1999) Bacterial populations in an anthropogenically disturbed stream: Comparisons of different seasons. Microb Ecol 38: 234-243
34. Lemke, MJ, McNamara, CJ, Leff, LG (1997) Comparison of methods for concentration of bacterioplankton for in situ hybridization. J Microbiol Methods 29: 23-29
35. Liu, J, Leff, LG (2002) Temporal changes in the bacterioplankton of a Northeast Ohio (USA) river. Hydrobiologia 489: 151-159
36. Lyautey, E, Lacoste, B, Ten-Hage, L, Rols, J-L, Garabetian, F (2005) Analysis of bacterial diversity in river biofilms using 16S rDNA PCR-DGGE: Methodological settings and fingerprint interpretation. Water Res 39: 380-388
37. Madigan, MT, Martinko, JM, Park, J (2003) Brock Biology of Microorganisms. Prentice Hall, Upper Saddle River, NJ
38. Manz, W, Szewzyk, U, Eriksson, 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 Microbiol 59: 2293-2298
39. Manz, W, Wagner, M, Amann, R, Schleifer, K-H (1994) In situ characterization of the microbial consortia active in two wastewater treatment plants. Water Res 28: 1715-1723
40. Marxsen, J (1980) Untersuchungen zur okologie der Bakterien in der flibenden welle von bachen. II. die zahl der bacterien im jahrelauf. Arch Hydrobiol Suppl 58: 26-55
41. McDougald, D, Rice, SA, Weichardt, D, Kjellerbert, S (1998) Non-culturability: Adaptation of debilitation? FEMS Microbiol Ecol 25: 1-9
42. McNamara, CJ, Lemke, MJ, Leff, LG (2002) Culturable and non-culturable fractions of bacterial populations in sediments of a South Carolina stream. Hydrobiologia 482: 151-159
43. Methé, BA, Hiorns, WD, Zehr, JP (1998) Contrasts between marine and freshwater bacterial community composition: Analyses of communities in Lake George and six other Adirondack lakes. Limnol Oceanogr 43: 368-374
44. Nuttall, D (1982) The populations, characterization and activity of suspended bacteria in the Welsh River Dee. J Appl Bacteriol 53: 49-59
45. Oliver, JD (2005) The viable but nonculturable state in bacteria. J Microbiol 43: 93-100
46. Osgood, MP, Boylen, CW (1990) Seasonal variation in bacterial communities in Adirondack streams exhibiting pH gradients. Microb Ecol 20: 211-230
47. Porter, KG, Feig, YS (1980) The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25: 943-948
48. Poulsen, LK, Ballard, G, Stahl, DA (1993) Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl Environ Microbiol 59: 1354-1360
49. Rappé, MS, Gionvannoni, SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57: 369-394
50. Relman, DA (1999) The search for unrecognized pathogens. Science 284: 1308
51. Roszak, DB, Colwell, RR (1987) Survival strategies off bacteria in the natural environment. Microbiol Rev 51: 365-379
52. Sambrook, J, Fritsch, EF, Maniatis, T (1989) Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Plainview, NY
53. Schleifer, KH, Amman, R, Ludwig, W, Rothemund, C, Springer, N, Dorn, S (1992) Nucleic acid probes for the identification and in situ detection of pseudomonas. In: Galli E, Silver S, Witholt B (Eds.) Pseudomonas: Molecular Biology and Biotechnology. Am Soc Microbiol, Washington, DC, pp 127-134
54. Shimkets, LJ, Asher, SJ (1988) Use of recombination techniques to examine the structure of the csg locus of Myxococcus xanthus. Mol Gen Genet 211: 63-71
55. Staley, JT, Kanopka, A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39: 321-346
56. Tamaki, H, Sekiguchi, Y, Hanada, S, Nakamura, K, Nomura, N, Matsummura, M, Kamagata, Y (2005) Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microbiol 71: 2162-2169
57. US Department of Energy (1991) Savannah River Site Environmental Report for 1991. Westinghouse Savannah River Co., Aiken, SC
58. Wagner, M, Amann, R, Lemmer, H, Schleifer, K-H (1993) Probing activated sludge with oligonucleotides specific for proteobacteria: Inadequacy of culture-dependent methods for describing microbial community structure. Appl Environ Microbiol 59: 1520-1525
59. Wainright, SC, Couch, CA, Meyer, JL (1992) Fluxes of bacteria and organic matter into a blackwater river from river sediments and floodplain soils. Freshw Biol 28: 37-48
60. Weis, P, Schweitzer, B, Amann, R, Simon, M (1996) Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow). Appl Environ Microbiol 62: 1998-2005
61. Workman, SW, McLeod, KW (1990) Vegetation of the Savannah River Site: Major community types. Savannah River Site Nat Res Park Prog, Aiken, SC
62. Zavarzin, GA, Stackebrandt, E, Murray, RGE (1991) A correlation of phylogenetic diversity in the Proteobacteria with the influences of ecological forces. Can J Microbiol 37: 16