16S rRNA Restriction fragment length polymorphism analysis of bacterial diversity as a biomarker of ecological health in polluted sediments from New Bedford Harbor, Massachusetts, USA

Marine Pollution Bulletin

Volumn 38, Issue 8, 1999, Pages 663-675

  Sorci, Jonathan J ^a   Paulauskis, Joseph D ^a   Ford, Timothy E ^a  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

16S ribosomal RNA (rRNA); Biomarkers; Ecological health; New Bedford Harbor, Massachusetts, USA; Polymerase chain reaction (PCR); Restriction fragment length polymorphism (RFLP)

Indexed keywords

BIOLOGICAL MARKER; DNA FRAGMENT; METAL; POLYCHLORINATED BIPHENYL; RIBOSOME RNA;

BACTERIUM; BIOMARKER; ECOSYSTEM HEALTH; MOLECULAR ANALYSIS; POLYMERASE CHAIN REACTION; SEDIMENT POLLUTION; SPECIES DIVERSITY;

ARTICLE; BACTERIUM; BIODIVERSITY; CLUSTER ANALYSIS; GENETIC DISTANCE; NONHUMAN; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEDIMENT; UNITED STATES; WATER POLLUTION; WATER POLLUTION INDICATOR;

UNITED STATES;

BACTERIA (MICROORGANISMS); OTUS;

EID: 0032868907     PISSN: 0025326X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0025-326X(98)90199-0     Document Type: Article

References (85)

1. Amann, R., Ludwig, W. and Schleifer, H.-H. (1995) Phylogenetic identification and in-situ detection of individual microbial cells without cultivation. Microbiological Reviews 59, 143-169.
2. Atlas, R. M. (1984) Diversity of microbial communities. Advances in Microbial Ecology 7, 1-47.
3. Atlas, R. M., Horowitz, A., Krichevsky, M. I. and Bej, A. K. (1991) Response of microbial populations to environmental stress. Microbial Ecology 22, 249-256.
4. Atlas, R. M. and Bartha, R. (1993) Microbial communities and ecosystems. In Microbial Ecology: Fundamentals and Applications. Benjamin Cummings, New York, pp. 140-145.
5. Avaniss-Aghajani, E., Jones, K., Chapman, D. and Brunk, C. (1994) A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. Bio Techniques 17, 144-149.
6. Boivin-Jahns, V., Bianchi, A., Ruimy, R., Garci, J., Daumass, S. and Christen, R. (1995) Comparison of phenotypical and molecular methods for the identification of bacterial strains isolated from a deep subsurface environment. Applied and Environmental Microbiology 61, 3400-3406.
7. Britschgi, T. B. and Giovannoni, S. J. (1991). Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Applied and Environmental Microbiology 57, 1707-1713.
8. Brosius J., Palmer M. L., Kennedy P. J. and Noller H. F. (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proceedings of the National Academy of Sciences, USA 75, 4801-4805.
9. Bruce, K. D., Hiorns, W. D., Hobman, J. L., Osborn, A. M., Strike, P. and Ritchie, D. A. (1992) Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413-3416.
10. Brunk, C. F., Avaniss-Aghjani, E. and Brunk, C. A. (1996) A computer analysis of primer and probe hybridization potential with bacterial small-subunit rRNA sequences. Applied and Environmental Microbiology 62, 872-879.
11. Dallinger, R. (1994) Invertebrate organisms as biological indicators of heavy metal pollution. Applied Biochemistry and Biotechnology 48, 27-31.
12. Dallinger, R. (1996) Metallothionein research in terrestrial invertebrates: synopsis and perspectives. Comparative Biochemistry and Physiology, Part C Pharmacology, Toxicology, and Endocrinology 113, 125-133.
13. DeLong, E. F., Franks, D. G. and Alldredge, A. L. (1993) Phylogenetic diversity of aggregate-attached versus free-living marine bacterial assemblages. Limnology and Oceanography 38, 924-934.
14. Depledge, M. H., Aagaard, A. and Gyorkos, P. (1995) Assessment of trace metal toxicity using molecular, physiological and behavioural biomarkers. Marine Pollution Bulletin 31, 19-27.
15. De Pomerai, D. (1996) Heat-shock proteins as biomarkers of pollution. Human Experimental Toxicology 15, 279-285.
16. Doyle, J. J. (1991) Evolution of higher-plant glutamine systhetase genes: Tissue specificity as a criterion for predicting orthology. Molecular Biology and Evolution 8, 366-377.
17. Doyle, J. J. and Doyle, J. L. (1993) Chloroplast DNA phylogeny of the papilionoid legume tribe phaseoleae. Systematic Botany 18, 309-327.
18. Etxeberria, M., Gajaraville, M. P. and Marigomez, I. (1995) Changes in digestive cell lysosomal structure in mussels as biomarkers of environmental stress in the Urdaibai Estuary (Biscay Coast, Iberian Peninsula). Marine Pollution Bulletin 31, 599-603.
19. Ford, T. E. (1994) Pollutant effects on the microbial ecosystem. Environmental Health Perspectives 102, 45-48.
20. Ford, T. E., Sorci, J. J. and Shine, J. J. (1994) Microbial transport of toxic metals. In Trace Substances, Environment and Health, ed C. R. Cothern. Science Reviews, Northwood, UK, pp. 9-20.
21. Fuhrman, J. A., Lee, S. H., Masuchi, Y., Davis, A. A. and Wilcox, R. M. (1994) Characterization of marine prokaryotic communities via DNA and RNA. Microbial Ecology 28, 133-145.
22. Fuhrman, J. A., McCallum, K. and Davis, A. A. (1993) Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Applied and Environmental Microbiology 59, 1294-1302.
23. Giovannoni, S. J., Britschgi, T. B., Moyer, C. L. and Field, K. G. (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60-63.
24. Goksoyr, A. (1995) Use of cytochrome P450 1A (CYP1A) in fish as a biomarker of aquatic pollution. Archives of Toxiocology Supplement 17, 80-95.
25. Gray, J. P. and Herwig, R. P. (1996) Phylogenetic analysis of the bacterial communities in marine sediments. Applied and Environmental Microbiology 62, 4049-4059.
26. Hervieu, F., Bannerot, H. and Pelletier, G. (1994) A unique cytoplasmic male sterility (CMS) determinant is present in three Phaseolus species characterized by different mitochondrial genomes. Theoretical and Applied Genetics 88, 314-320.
27. Holsinger, K. E. and Jansen, R. K. (1993) Phylogenetic analysis of restriction site data. Methods in Enzymology 224, 439-455.
28. Hugenholtz, P. and Pace, N. R. (1996) Identifying microbial diversity in the natural environment: A molecular phylogenetic approach. Trends in Biotechnology 14, 190-197.
29. Kreamer, G. L., Squibb, K., Gioeli, D., Garte, S. J. and Wirgin, I. (1991) Cytochrome P450IA mRNA expression in feral Hudson River tomcod. Environmental Research 55, 64-78.
30. Laguerre, G., Rigottier-Gois, L. and Lemanceau, P. (1994) Fluorescent Pseudomonas species categorized by using polymerase chain reaction (PCR)/restriction fragment analysis of 16S rDNA. Molecular Ecology 3, 479-487.
31. Lane, D. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, eds E. Stackebrandt and M. Goodfellow. Wiley, New York, p. 133.
32. Lee, S.-Y., Bollinger, D. and Ogram, A. (1996a) Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method. Applied and Environmental Microbiology 62, 3787-3793.
33. Lee, T. E., Riddle, B. R. and Lee, P.L. (1996b) Speciation in the desert pocket mouse (Chaetodipus penicillatus Woodhouse). Journal of Mammalogy 77, 58-68.
34. Lee, D. H., Zo, Y. G. and Kim, S. J. (1996c) Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Applied and Environmental Microbiology 62, 3112-3120.
35. Le Guennec, R., Reynes, J., Mallie, M., Pujol, C., Janbon, F. and Bastide, J.-M. (1995) Fluconazole- and intraconazole-resistant Candida albicans strains from AIDS patients: Multilocus enzyme electrophoresis analysis and antifungal susceptibilities. Journal of Clinical Microbiology 33, 2732-2737.
36. Lewicka, K., Mallie, M. and Bastide, J.-M. (1995) Genetic variability in the Saccharomyces sensu stricto complex revealed by multilocus enzyme electrophoresis. International Journal of Systematic Bacteriology 45, 538-543.
37. Livingstone, D. R. (1993) Biotechnology and pollution monitoring: Use of molecular biomarkers in the aquatic environment. Journal of Chemical Technology and Biotechnology 57, 195-211.
38. Mason, B. H. (1966) Composition of the earth. Nature 211, 616-618.
39. Mes, T. H. M. and Hart, H. T. (1996) The evolution of growth-forms in the Macaronesian genus Aeonium (Crassulaceae) inferred from chloroplast DNA RFLPs and morphology. Molecular Ecology 5, 351-363.
40. Miller, J. C. (1991) RESTSITE: A phylogenetic program that sorts raw restriction data. Journal of Heredity 82, 262-263.
41. Moyer, C. L., Dobbs, F. C. and Karl, D. M. (1994) Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Applied and Environmental Microbiology 60, 871-879.
42. Moyer, C. L., Tiedje, J. M., Dobbs, F. C. and Karl, D. M. (1996) A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: Efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Applied and Environmental Microbiology 62, 2501-2507.
43. Mutwakil, M. H. A. Z., Reader, J. P., Holdich, D. M., Smithurst, P. R., Candido, E. P. M., Jones, D., Stringham, E. G. and de Pomerai, D. I. (1997) Use of stress-inducible transgenic nematodes as biomarkers of heavy metal pollution in water samples from an English river system. Archives of Environmental Contamination and Toxicology 32, 146-153.
44. Najimi, S., Bouhaimi, A., Daubeze, M., Zekhnini, A., Pellerin, J., Narbonne, J. F. and Moukrim, A. (1997) Use of acetylcholinesterase in Perna perna and Mytilus galloprovincialis as a biomarker of pollution in Agadir Marine Bay. Bulletin of Environmental Contamination and Toxicology 58, 901-908.
45. Nei, M. 1987. Phylogenetic trees. In Molecular Evolutionary Genetics. Columbia University Press, New York, pp. 292-313.
46. Nei, M. and Li, W.-H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences USA 76, 5269-5273.
47. Nei, M. and Miller, J. C. (1990) A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics 125, 873-879.
48. Neilan, B. A., Jacobs, D. and Goodman, A. E. (1995) Genetic diversity and phylogeny of toxic cyanobacteria determined by DNA polymorphisms within the Phycocyanin locus. Applied and Environmental Microbiology 61, 3875-3883.
49. Noble, P. A., Bidle, K. D. and Fletcher, M. (1997) Natural microbial community compositions compared by a back-propagating neural network and cluster analysis of 5S rRNA. Applied and Environmental Microbiology 63, 1762-1770.
50. Olsen, G. J., Lane, D. L., Giovannoni, S. J. and Pace, N. R. (1986) Microbial ecology and evolution: A ribosomal RNA approach. Annual Review of Microbiology 40, 337-365.
51. Pace, N. R., Stahl, D. A., Lane, D. J. and Olsen, G. J. (1986) The analysis of natural microbial populations by ribosomal RNA sequences. Advances in Microbial Ecology 9, 1-55.
52. Parekh, N. R., Hartmann, A., Charnay, M.-P. and Fournier, J.-C. (1995) Diversity of carbofuran-degrading soil bacteria and detection of plasmid-encoded sequences homologous to the mcd gene. FEMS Micobial. Ecology 17, 149-160.
53. Peterson, G. S., Ankley, G. T. and Leonard, E. N. (1996) Effect of bioturbation on metal-sulfide oxidation in surficial freshwater sediments. Environmental Toxicology and Chemistry 15, 2147-2155.
54. Phillips, C. A. (1994) Geographic distribution of mitochondrial DNA variants and the historical biogeography of the spotted salamander. Ambystoma maculatum. Evolution 48, 597-607.
55. Phillips, C. A., Dimmick, W. W. and Carr, J. L. (1996) Conservation genetics of the common snapping turtle (Chelydra serpentina). Conservation Biology 10, 397-405.
56. Pruell, R. J., Norwood, C. B., Bowen, R. D., Boothman, W. S., Rogerson, P. F., Hackett, M. and Butterworth, B. C. (1990) Geochemical study of sediment contamination in New Bedford Harbor, Massachussetts. Marine Environmental Research 29, 77-101.
57. Riddle, B. R., Honeycutt, R. L. and Lee, P. L. (1993) Mitochondrial DNA phylogeography in northern grasshopper mice (Onychomys leucogaster) - the influence of Quaternary climatic oscillations on populations dispersion and divergence. Molecular Ecology 2, 183-193.
58. Rogers, J. and Kidd, K. K. (1996) Nucleotide polymorphism, effective population size, and dispersal distances in the yellow baboons (Papio hamadryas cynocephalus) of Mikumi National Park, Tanzania. American Journal of Primatology 38, 157-168.
59. Sambrook, J., Fritsch, E.F. and Maniatis, T. 1989. Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
60. Sanders, B. M. and Martin, L. S. (1993) Stress proteins as biomarkers of contaminant exposure in archived environmental samples. Science of the Total Environmental 139-140, 459-470.
61. Schmidt, T. M., DeLong, E. F. and Pace, N. R. (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. Journal of Bacteriology 173, 4371-4378.
62. Shine, J. P., Ika, R. V. and Ford, T. E. (1995) Multivariate statistical examination of spatial and temporal patterns of heavy metal contamination in New Bedford Harbor marine sediments. Environmental Science and Technology 29, 1781-1788.
63. Sneath, P.H.A. and Sokal, R.R. 1973. Numerical Taxonomy. W.H. Freeman, San Fransisco, CA, pp. 230-234.
64. Sole, M., Porte, C. and Albaiges, J. (1995) The use of biomarkers for assessing the effects of organic pollution in mussels. Science of the Total Environment 159, 147-153.
65. Sorci, J.J. 1998. Bacterial diversity and heavy metal gene expression in polluted marine sediments from New Bedford Harbor, Massachusetts. Doctoral Dissertation, Harvard University.
66. Stackebrandt, E. and Goebel, B. M. (1994) Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology 44, 846-849.
67. Steffan, R. J. and Atlas, R. M. (1991) Polymerase chain reaction: applications in environmental microbiology. Annual Review of Microbiology 45, 137-161.
68. Suzuki, M.T. and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Applied and Environmental Microbiology 62, 625-630.
69. Tam, Y. K., Kornfield, I. and Ojeda, F. P. (1996) Divergence and zoogeography of mole crabs, Emerita spp (Decapoda: Hippidae), in the Americas. Marine Biology 125, 489-497.
70. Tarr, C. L. and Fleishcer, R. C. (1993) Mitochondrial-DNA variation and evolutionary relationships in the Amakihi complex. Auk 110, 825-831.
71. Taylor, S. R. (1964) Abundance of chemical elements in the continental crust - a new table. Geochimica et Cosmochimica Acta 28, 1273-1285.
72. Tebbe, C. C. and Vahjen, W. (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appied and Environmental Microbiology 59, 2657-2665.
73. Tsai, Y. and Olson, B. H. (1991) Rapid method for direct extraction of DNA from soils and sediments. Applied and Environmental Microbiology 57, 1070-1074.
74. US Environmental Protection Agency, (1984) Guidelines establishing test procedures for the analysis of pollutants; final regulations. EPA methods 608, 3540/3550, and 8080. Federal Register, Vol. 49, No. 209, pp. 89-104.
75. U.S. Environmental Protection Agency. 1990. New Bedford Harbor NPL site estuary and lower harbor/bay operable unit: Administrative Record, Vol. VI, p. 5-5.
76. van der Oost, R., Goksoyr, A., Celander, M., Heida, H. and Vermeulen, N. P. E. (1996) Biomonitoring of aquatic pollution with ferral eel (Anguilla anguilla). I Biomarkers: Pollution-induced biochemical responses. Aquatic Toxicology 36, 189-222.
77. van der Oost, R., Vindimian, E., van den Brink, P. J., Satumalay, K., Heida, H. and Vermeulen, N. P. E. (1997) Biomonitoring of aquatic pollution with ferral eel (Anguilla anguilla). III Statistical analyses of relationships between contaminant exposure and biomarkers. Aquatic Toxicology 39, 45-75.
78. Vermeulen, A., Desprez, B., Lancelin, D. and Bannerot, H. (1994) Relationships among Cichorium species and related genera as determined by analysis of mitochondrial RFLPS. Theoretical and Applied Genetics 88, 159-166.
79. Ward, D. M., Bateson, M. M., Weller, R. and Ruff-Roberts, A. L. (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. Advances in Microbial Ecology 12, 219-257.
80. Ward, D. M., Weller, R. and Bateson, M. M. (1990) 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community. FEMS Microbiological Reviews 75, 105-116.
81. Weaver, G. (1984) PCB Contamination in and around New Bedford, Mass. Environmental Science and Technology 18, 22A-27A.
82. Weidner, S., Arnold, W. and 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. Applied and Environmental Microbiology 62, 766-771.
83. Williams, G.M. and Weisburger, J.H. 1993. Chemical Carcinogenesis. In Casarett and Doull's Toxicology: The Basic Science of Poisons, eds M. O. Amdur, J. Doull, and C. D. Klaassen, pp.127-210. Pergamon Press, New York.
84. Woese, C. R. (1987) Bacterial evolution. Microbiological Reviews 51, 221-271.
85. Zhou, J., Bruns, M. A. and Tiedje, J. M. (1996) DNA recovery from soils of diverse compositon. Applied and Environmental Microbiology 62, 316-322.