The response of epilithic bacteria to different metals regime in two upland streams: Assessed by conventional microbiological methods and PCR-DGGE

Archiv fur Hydrobiologie

Volumn 163, Issue 3, 2005, Pages 405-427

  Mahmoud, Huda M A ^a,b   Goulder, Raymond ^a   Carvalho, Gary R ^a  

^a UNIVERSITY OF HULL   (United Kingdom)

^b KUWAIT UNIVERSITY   (Kuwait)

Author keywords

Epilithic bacteria; Freshwater bacteria; Metals pollution; PCR DGGE; Upland streams

Indexed keywords

BACTERIUM; MICROBIAL COMMUNITY; ZINC;

EASTERN HEMISPHERE; ENGLAND; EURASIA; EUROPE; NORTHUMBRIA; UNITED KINGDOM; WESTERN EUROPE; WORLD;

ALPHAPROTEOBACTERIA; NITROSPIRAE;

EID: 23944454357     PISSN: 00039136     EISSN: None     Source Type: Journal    
DOI: 10.1127/0003-9136/2005/0163-0405     Document Type: Article

References (65)

1. ABEL, P. D. (1989): Water Pollution Biology. - Ellis Horwood, Ltd., Chichester.
2. - (1996): Water Pollution Biology 2nd Ed. - Taylor & Francis, London.
3. ABEL, P. D. & GREEN, D. W. J. (1981): Ecological and toxicological studies on invertebrate fauna of two rivers in the Northern Pennine Orefield. - In: SAY, P. J. & WHITTON, B. A. (eds): Heavy metals in Northern England: Environmental and Biological Aspects. - University of Durham, Department of Botany, Durham, pp. 109-122.
4. ADMIRAAL, W., BLANCK, H., BUCKERT-DE JONG, M. GUASCH, H., IVORRA, N., LEHMANN, V., NYSTROM, B. A. H., PAULSSON, M. & SABATER, S. (1999): Short-term toxicity of zinc to microbenthic algae and bacteria in a metal polluted stream. - Water Res. 33: 1989-1996.
5. ALTSCHUL, S. F., MADDEN, T. L., SCHAFFER, A. A., ZHANG, J., ZHANG, Z., MILLER, W. & LIPMAN, D. J. (1997): Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. - Nucleic Acids Res. 25: 3389-3402.
6. BAATH, E., DIAZ-RAVINA, M., FROSTEGARD, A. & CAMPBELL, C. D. (1998): Effect of metal-rich sludge amendments on the soil microbial community. - Appl. Environ. Microbiol. 64: 238-245.
7. BANO, N. & HOLLIBAUGH, J. T. (2002): Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. - Appl. Environ. Microbiol. 68: 505-518.
8. BRÜMMER, I. H. M., FEHR, W. & WAGNER-DÖBLER, I. (2000): Biofilm community structure in polluted rivers: abundance of dominant phylogenetic groups over a complete annual cycle. - Appl. Environ. Microbiol. 66: 3078-3082.
9. BRÜMMER, I. H. M., FELSKE, A. & WAGNER-DÖBLER, I. (2003): Diversity and seasonal variability of β-Proteobacteria in biofilms of polluted rivers: analysis by temperature gradient electrophoresis and cloning. - Appl. Environ. Microbiol. 69: 4463-4473.
10. BURNS, A. & RYDER, D. S. (2001): Potential for biofilms as biological indicators in Australian riverine systems. - Ecol. Manage. Restor. 2: 53-63.
11. CARIELLO, N. F., KEOHAVONG, P., SANDERSON, B. J. S. & THILLY, W. G. (1988): DNA damage produced by ethidium bromide staining and exposure to ultraviolet light. - Nucleic Acids Res. 16: 4157.
12. CHANG, Y.-J., STEPHEN, J. R., RICHTER, A. P., VENOSA, A. D., BRUGGEMANN, J., MACNAUGHTON, S. J., KOWALCHUK, G. A., HAINES, J. R., KLINE, E. & WHITE, D. C. (2000): Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method. - J. Microbiol. Methods 40: 19-31.
13. CHAPPELL, K. R. & GOULDER, R. (1994 a): Seasonal variation of epilithic extracellular enzyme activity in three diverse headstreams. - Arch. Hydrobiol. 130: 195-214.
14. _ (1994 b): Epilithic extracellular-enzyme activity in a zinc-contaminated stream. - Bull. Environ. Contam. Toxicol. 52: 305-310.
15. CHRISTNER, B. C., MOSLEY-THOMPSON, E., THOMPSON, L. G. & REEVE, J. N. (2001): Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice. - Environ. Microbiol. 3: 570-577.
16. COLWELL, F. S., HORNOR, S. G. & CHERRY, D. S. (1989): Evidence of structural and functional adaptation in epilithon exposed to zinc. - Hydrobiologia 171: 79-90.
17. CRUMP, B. C., ARMBRUST, E. V. & BAROSS, J. A. (1999): Phylogenetic analysis of particle-attached and free-living bacterial communities in the Colombia River, its estuary, and the adjacent coastal ocean. - Appl. Environ. Microbiol. 65: 3192-3204.
18. DALEY, R. J. (1979): Direct epifluorescence enumeration of native aquatic bacteria: uses, limitations, and comparative accuracy. - In: COSTERTON, J. W. & COLWELL, R. R. (eds): Native aquatic bacteria: enumeration, activity, and ecology, Special Technical publication No. 695. - American Society for Testing and Materials, Philadelphia. pp. 29-45.
19. DEAN-ROSS, D. (1990): Response of attached bacteria to zinc in artificial streams. - Can. J. Microbiol. 36: 561-566.
20. DON, R. H., WAINWRIGHT, B. J. & MATTICK, J. S. (1991): "Touchdown" PCR to circumvent spurious priming during gene amplification. - Nucleic Acids Res. 19: 4008.
21. EDWARDS, A. C. & CRESSER, M. S. (1987): Relationships between ultraviolet absorbance and total organic carbon in two upland catchments. - Water Res. 21: 49-56.
22. FELSENSTEIN, J. (1985): Confidence of limits on phylogenies: an approach using the bootstrap. - Evolution 39: 783-791.
23. FERRIS, M. J., MUYZER, G. & WARD, D. M. (1996): Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. - Appl. Environ. Microbiol. 62: 340-346.
24. FLIESSBACH, A., MARTENS, R. & REBER, H. H. (1994): Soil microbial biomass and microbial activity in soils treated with heavy metal contaminated sewage sludge. - Soil Biol. Biochem. 26: 1201-1205.
25. FORD, T., SORCI, J., IKA, R. & SHINE, J. (1998): Interactions between metals and microbial communities in New Bedford Harbor, Massachusetts. - Environ. Health Perspect. 106: 1033-1039.
26. GENTER, R. B., CHERRY, D. S., SMITH, E. P. & CAIRNS, J. (1987): Algal-periphyton population and community changes from zinc stress in stream mesocosms. - Hydrobiologia 153: 261-275.
27. GLOCKNER, F. O., ZICHIKOV, E., BELKOVA, N., DENISSOVA, L., PERNTHALER, J., PERNTHALER, A. & AMANN, R. (2000): Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. - Appl. Environ. Microbiol. 66: 5053-5065.
28. HALL, T. A. (1999): BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. - Nucleic Acids 41: 95-98.
29. HARDING, J. P. C. & WHITTON, B. A. (1976): Resistance to zinc of Stigeoclonium tenue in the field and the laboratory. - Br. Phycol. J. 11: 417-426.
30. HILLIS, D. M., MORITZ, C. & MABLE, B. K. (1996): Molecular systematics 2nd Edition. - Sinauer Associates Inc., Sunderland, Massachusetts.
31. IVORRA, N., BREMER, S., GUASCH, H., KRAAK, M. H. S. & ADMIRAAL, W. (2000): Differences in the sensitivity of benthic microalgae to Zn and Cd regarding biofilm development and exposure history. - Environ. Toxicol. Chem. 19: 1332-1339.
32. JESPERSON, A. M. & CHRISTOFFERSEN, K. (1987): Measurements of chlorophyll-a from phytoplankton using ethanol as extraction solvent. - Arch. Hydrobiol. 109: 445-454.
33. JUKES, T. H. & CANTOR, C. R. (1969): Evolution of protein molecules. - In: MUNRO, H. N. (ed.): Mammalian Protein Metabolism. - Academic Press, New York, pp. 21-132.
34. KANDELER, E., KAMPICHLER, C. & HORAK, O. (1996): Influence of heavy metals on the functional diversity of soil microbial communities. - Biol. Fertility Soils 23: 299-306.
35. KOZDROJ, J. & VAN ELSAS, J. D. (2001): Structural diversity of microorganisms in chemically perturbed soil assessed by molecular and cytochemical approaches. - J. Microbiol. Methods 43: 197-212.
36. LEHMANN, V., TUBBING, G. M. & ADMIRAAL, W. (1999): Induced metal tolerance in microbenthic communities from three lowland rivers with different metal loads. - Arch. Environ. Contam. Toxicol. 36: 384-391.
37. LOWE, R. L. & PAN, Y. (1996): Benthic algal communities as biological monitors. - In: STEVENSEN, R. J., BOTHWELL, M. L. & LOWE, R. L. (eds): Algal ecology: freshwater benthic ecosystems. - Academic Press, San Diego, pp. 705-739.
38. MAHMOUD, H. M. A. (2002): Structural and functional diversity of epilithic bacterial communities in streams: effects of pollution. PhD thesis. - University of Hull, UK.
39. MAIDAK, B. L., COLE, J. R., LILBURN, T. G., PARKER, C. T. Jr., SAXMAN, P. R., FARRIS, R. J., GARRITY, G. M., OLSEN, G. J., SCHMIDT, T. M. & TIEDJE, J. M. (2001): The RDP-II (Ribosomal Database Project). - Nucleic Acids Res. 29: 173-174.
40. MORENO, E. (1998): Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome? - FEMS Microbiol. Rev. 22: 255-275.
41. MULLINS, T. D., BRITSCHGI, T. B., KREST, R. L. & GIOVANNONI, S. J. (1995): Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. - Limnol. Oceanogr. 40: 148-158.
42. MUYZER, G. (1998): Structure, function and dynamics of microbial communities: the molecular biological approach. - In: CARVALHO, G. R. (ed.): Advances in Molecular Ecology. - IOS Press, Amsterdam, pp. 87-117.
43. MUYZER, G., DE WAAL, E. C. & UITTERLINDEN, A. G. (1993): Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16S rRNA. - Appl. Environ. Microbiol. 59: 695-700.
44. OGRAM, A. (1998): Isolation of nucleic acids from environmental samples. - In: BURLAGE, R. S., ATLAS, R., STAHL, D., GEESEY, G. & SAYLER, G. (eds): Techniques in Microbial Ecology. - Oxford University Press, Oxford, pp. 273-288.
45. OGRAM, A., SAYLOR, G. & BARKAY, T. (1987): The extraction and purification of microbial DNA from sediments. - J. Microbiol. Methods 7: 57-66.
46. O'SULLIVAN, L. A., WEIGHTMAN, A. J. & FRY, J. C. (2002): New degenerate Cytophaga-Flexibacter-Bacteroides 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon. - Appl. Environ. Microbiol. 68: 201-210.
47. OVREAS, L., FORNEY, L., DAAE, F. L. & TORSVIK, V. (1997): Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. - Appl. Environ. Microbiol. 63: 3367-3373.
48. PAULSSON, M., MANSSON, V. & BLANCK, H. (2002): Effects of zinc on the phosphorus availability to periphyton communities from the river Gota Alv. - Aquatic Toxicol. 56: 103-113.
49. PAULSSON, M., NYSTROM, B. & BLANCK, H. (2000): Long-term toxicity of zinc to bacteria and algae in periphyton communities from the river Gota Alv based on a microcosm study. - Aquatic Toxicol. 47: 243-257.
50. RIEMANN, L. & WINDING, A. (2001): Community dynamics of free-living and particle-associated bacterial assemblages during a freshwater phytoplankton bloom. - Microb. Ecol. 42: 274-285.
51. RIEMANN, L., STEWARD, G. F., FANDINO, L. B., CAMPBELL, L., LANDRY, M. R. & AZAM, F. (1999): Bacterial community composition during two consecutive NE monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes. Deep-Sea Res. Part II- Topical Stud. - Oceanogr. 46: 1791-1811.
52. SABATER, S., ARMENGOL, J., COMAS, E., SABATER, F., URRIZALQUI, I. & URRUTIA, I. (2000): Algal biomass in a distributed Atlantic river: water quality relationships and environmental implications. - Sci. Total Environ. 263: 185-195.
53. SAMBROOK, J., FRITSCH, E. F. & MANIATIS, T. (1989): Molecular Cloning: a Laboratory Manual, 2 nd Edition. - Cold Spring Harbor Laboratory Press, New York.
54. SAMBROOK, J. & RUSSELL, D. W. (2001): Molecular Cloning: a Laboratory Manual volume 2, 3 rd Edition. - Cold Spring Harbor Laboratory Press, New York.
55. SANDAA, R.-A., TORSVIK, V. & ENGER, O. (2001): Influence of long-term heavy-metal contamination on microbial communities in soil. - Soil Biol. Biochem. 33: 287-295.
56. SCHÄFER, H. & MUYZER, G. (2001): Denaturing gradient gel electrophoresis in marine microbial ecology. - In: PAUL, J. H. (ed.): Methods in Microbiology: Volume 30 Marine Microbiology. - Academic Press, London, pp. 425-468.
57. STEIN, L. Y., LA DUC, M. T., GRUNDL, T. J. & NEALSON, K. H. (2001): Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments. - Environ. Microbiol. 3: 10-18.
58. SWOFFORD, D. L. (2002): PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4. - Sinauer Associates, Sunderland, Massachusetts.
59. THOMPSON, J. D., GIBSON, T. J., PLEWNIAK, F., JEANMOUGIN, F. & HIGGINS, D. G. (1997): The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. - Nucleic Acids Res. 24: 4876-4882.
60. 14C)-leucine incorporation rate. - Microb. Ecol. 26: 201-217.
61. VAN DER GUCHT, K., SABBE, K., DE MEESTER, L., VLOEMANS, N., ZWART, G., GILLIS, M. & VYVERMAN, W. (2001): Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophic freshwater lakes. - Environ. Microbiol. 3: 680-690.
62. WEIDNER, S., ARNOLD, W. & PUHLER, A. (1996): Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. - Appl. Environ. Microbiol. 62: 766-771.
63. WETZEL, R. G. (1996): Benthic algae and nutrient cycling in lentic freshwater ecosystems. - In: STEVENSON, R. J., BOTHWELL, M. L. & LOWE, R. L. (eds): Algal ecology: fresh water benthic ecosystems. - Academic Press, San Diego, pp. 641-669.
64. WHITE, D. C., SUTTONT, S. D. & RINGELBERG, D. B. (1996): The genus Sphingomonas: physiology and ecology. - Curr. Opin. Biotech. 7: 301-306.
65. YU, W., DODDS, W. K., BANKS, K., SKALSKY, J. & STRAUSS, E. (1995): Optimal staining and sample storage time for direct microscopic enumeration of total and active bacteria in soil with two fluorescent dyes. - Appl. Environ. Microbiol. 61: 3367-3372.