Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input

Applied and Environmental Microbiology

Volumn 66, Issue 3, 2000, Pages 956-965

  Cho, Jang Cheon ^a   Kim, Sang Jong ^a  

^a Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

GROUND WATER; RIBOSOME DNA;

AQUIFER; BACTERIUM; GROUNDWATER POLLUTION; LIVESTOCK; MICROBIAL COMMUNITY; SPECIES DIVERSITY; WASTEWATER;

AQUIFER; ARTICLE; BACTERIUM; BACTEROIDES; BIODIVERSITY; DNA SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RUMINANT STOMACH; UNINDEXED SEQUENCE; WASTE WATER;

ANIMALS; ANIMALS, DOMESTIC; BACTERIA; BACTEROIDES; BACTEROIDETES; DNA, RIBOSOMAL; ECOLOGY; FECES; GEOLOGIC SEDIMENTS; GRAM-POSITIVE BACTERIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PROTEOBACTERIA; RNA, RIBOSOMAL, 16S; WASTE PRODUCTS; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS); BACTEROIDES; CYTOPHAGA; FLEXIBACTER; POSIBACTERIA;

EID: 0034008944     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.66.3.956-965.2000     Document Type: Article

References (63)

1. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Amann, R., J. Snaidr, M. Wagner, W. Ludwig, and K.-H. Schleifer. 1996. In situ visualization of high genetic diversity in a natural microbial community. J. Bacteriol. 178:3496-3500.
3. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microhiol. Rev. 59:143-169.
4. Atlas, R. M., A. Horowitz, M. Krichevsky, and A. K. Bej. 1991. Response of microbial populations to environmental disturbance. Microb. Ecol. 22:249-256.
5. Barns, S. M., S. L. Takala, and C. R. Kuske. 1999. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl. Environ. Microbiol. 65:1731-1737.
6. Berardesco, G., S. Dyhrman, E. Gallagher, and M. P. Shiaris. 1998. Spatial and temporal variation of phenanthrene-degrading bacteria in intertidal sediments. Appl. Environ. Microbiol. 54:2560-2565.
7. Bonnie, L. M., J. R. Cole, C. T. Parker, J. G. M. Garrity, N. Larsen, B. Li, T. G. Lilburn, M. J. McCaughey, G. J. Olsen, R. Overbeek, S. Pramanik, T. M. Schmidt, J. M. Tiedje, and C. R. Woese. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27:171-173.
8. Bowman, J. P., S. A. McCammon, M. V. Brown, D. S. Nichols, and T. A. McMeekin. 1997. Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl. Environ. Microbiol. 63:3068-3078.
9. Carpenter-Boggs, L., A. C. Kennedy, and J. P. Reganold. 1998. Use of phospholipid fatty acids and carbon source utilization patterns to track microbial community succession in developing compost. Appl. Environ. Microbiol. 64:4062-4064.
10. Chandler, D. P., S. Li, C. M. Spadoni, G. R. Drake, D. L. Balkwill, J. K. Fredrickson, and F. J. Brockman. 1997. A molecular comparison of culturable aerobic heterotrophic bacteria and 16S rDNA clones derived from a deep subsurface sediment. FEMS Microbiol. Ecol. 23:131-144.
11. Cho, J.-C., and S.-J. Kim. 1999. Viable, but non-culturable, state of a green fluorescence protein-tagged environmental isolate of Salmonella typhi in groundwater and pond water. FEMS Microbiol. Lett. 170:257-264.
12. Cho, J.-C., H. B. Cho, and S.-J. Kim. Heavy contamination of a subsurface aquifer and a stream by livestock wastewater in a stock farming area, Wonju, Korea. Environ. Pollut., in press.
13. Clement, B. G., L. E. Kehl, K. L. DeBord, and C. L. Kitts. 1998. Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J. Microbiol. Methods 31: 135-142.
14. Del Val, C., J. M. Barea, and C. Azcón-Aguilar. 1999. Diversity of arbuscular mycorrhizal fungus populations in heavy-metal-contaminated soils. Appl. Environ. Microbiol. 65:718-723.
15. Dojka, M. A., P. Hugenholtz, S. K. Haack, and N. R. Pace. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:3869-3877.
16. Dunbar, J., S. Takala, S. M. Barns, J. A. Davis, and C. R. Kuske. 1999. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl. Environ. Microbiol. 65:1662-1669.
17. Eichner, C. A., R. W. Erb, K. N. Timmis, and I. Wagner-Döbler. 1999. Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community. Appl. Environ. Microbiol. 65:102-109.
18. Embley, T. M., and E. Stackebrandt. 1996. The use of 16S rRNA sequences in microbial ecology, p. 39-62. In W. Pickup and J. R. Saunders (ed.). Molecular approaches in environmental microbiology. Ellis Horwood, London, United Kingdom.
19. Felske, A., A. D. L. Akkermans, and W. M. DeVos. 1998. Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints. Appl. Environ. Microbiol. 64:4581-4587.
20. Felske, A., A. Wolterink, R. V. Lis, and A. D. L. Akkermans. 1998. Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl. Environ. Microbiol. 64:871-879.
21. Frostegård, Å., S. O. Petersen, E. Bååth, and T. H. Nielsen. 1997. Dynamics of a microbial community associated with manure hot spots as revealed by phospholipid fatty acid analyses. Appl. Environ. Microbiol. 63:2224-2231.
22. Ghiorse, W. C., and J. T. Wilson. 1988. Microbial ecology of the terrestrial subsurface. Adv. Appl. Microbiol. 33:107-172.
23. Goody, D. C, P. J. A. Withers, H. M. McDonald, and P. J. Chilton. 1998. Behaviour and impact of cow slurry beneath a storage lagoon. II. Chemical composition of chalk porewater after 18 years. Water Air Soil Pollut. 107:51-72.
24. Haldeman, D. L., and P. S. Amy. 1993. Diversity within a colony morphotype: implications for ecological research. Appl. Environ. Microbiol. 59:933-935.
25. Hastings, R. C., M. T. Ceccherini, N. Miclaus, J. R. Saunders, M. Bazzicalupo, and A. J. McCarthy. 1997. Direct molecular biological analysis of ammonia oxidizing bacteria populations in cultivated soil plots treated with swine manure. FEMS Microbiol. Ecol. 23:45-54.
26. Head, I. M., J. R. Saunders, and R. W. Pickup. 1998. Microbial evolution, diversity, and ecology: a decade of rihosomal RNA analysis of uncultivated microorganisms. Microb. Ecol. 35:1-21.
27. Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
28. Hurlbert, S. H. 1971. The non-concept of species diversity: a critique and alternative parameters. Ecology 52:577-586.
29. Insam, H., K. Amor, M. Renner, and C. Crepaz. 1996. Changes in functional abilities of the microbial community during composting of manure. Microb. Ecol. 31:77-87.
30. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York, N.Y.
31. Ka, J. O., W. E. Holben, and J. M. Tiedje. 1994. Genetic and phenotypic diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria isolated from 2,4-D-treated field soils Appl. Environ. Microbiol. 60:1106-1115.
32. Kowalchuk, G. A., J. R. Stephen, W. D. Boer, J. I. Prosser, T. M. Embley, and J. W. Woldendorp. 1997. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Prateobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63:1489-1497.
33. Kowalchuk, G. A., Z. S. Naoumenko, P. J. L. Derikx, A. Felske, J. R. Stephen, and I. A. Arkhipchenko. 1999. Molecular analysis of ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria in compost and composted materials. Appl. Environ. Microbiol. 65:396-403.
34. Krebs, C. J. 1989. Ecological methodology. Harper & Row, New York, N.Y.
35. Kuske, C. R., S. M. Barns, and J. D. Busch. 1997. Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Appl. Environ. Microbiol. 63:3614-3621.
36. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.). Nucleic acid techniques in bacterial systematics. John Wiley and Sons, New York, N.Y.
37. Lee, D.-H., Y.-G., Zo, and S.-J. Kim. 1996. Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl. Environ. Microbiol. 62:3112-3120.
38. Lee, J.-Y., and K.-K. Lee. 1999. Analysis of the quality of parameter estimates from repeated pumping and slug tests in a fractured porous aquifer system in Wonju, Korea. Ground Water 37:692-700.
39. Ludwig, W., S. H. Bauer, M. Bauer, I. Held, G. Kirchhof, R. Schulze, I. Huber, S. Spring, A. Hartmann, and K. H. Schleifer. 1997 Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett. 153:181-190.
40. Madson, E. L., and W. C. Ghiorse. 1993. Groundwater microbiology: subsurface ecosystem process, p. 167-213. In T. E. Ford (ed.). Aquatic microbiology: an ecological approach. Blackwell Sciences, Boston, Mass.
41. Martinez-Murcis, A. J., S. G. Acinas, and F. Rodriguez-Valeria. 1995 Evaluation of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments. FEMS Microbiol. Ecol. 14:219-232.
42. McCaig, A. E., L. A. Glover, and J. I. Prosser. 1999. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl. Environ. Microbiol. 65:1721-1730.
43. McDougald, D., S. A. Rice, D. Weichart, and S. Kjelleberg. 1998. Nonculturability: adaptation or debilitation? FEMS Microbiol. Ecol. 25:1-9.
44. Mover, C. L., F. C Dobbs, and D. M. Karl. 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. Appl. Environ. Microbiol. 60:871-879.
45. Muyzer, G., E. C. DeWaal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
46. Nübel, U., F. Garcia-Pichel, M. Kühl, and G. Muyzer. 1999. Quantifying microbial diversity: morphotypes, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats. Appl. Environ. Microbiol. 65:422-430.
47. Nüsslein, K., and J. M. Tiedje. 1998. Characterization of the dominant and rare members of a young Hawaiian soil bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis of its guanine and cytosine composition. Appl. Environ. Microbiol. 64:1283-1289.
48. Odum, E. P. 1983. Basic ecology. Saunders College Publishing. Philadelphia, Pa.
49. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
50. Sanders, H. L. 1968. Marine benthic diversity: a comparative study. Am. Nat. 102:243-282.
51. Schwieger, F., and C. C. Tebbe. 1998. A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl. Environ. Microbiol. 64:4870-4876.
52. Spoelstra, S. F. 1978. Enumeration and isolation of anaerobic microbiota of piggery wastes. Appl. Environ. Microbiol. 35:841-846.
53. Staley, J. T. 1997. Biodiversity: arc microbial species threatened? Curr. Opin. Biotechnol. 8:340-345.
54. Tajima, K. R. I. Aminov, T. Nagamine, K. Ogata, M. Nakamura, H. Matsui, and Y. Benno. 1999. Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol. Ecol. 29:159-169.
55. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
56. Torsvik, V., K. Salte, R. Sørheim, and J. Goksøyr. 1990. Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl. Environ. Microbiol. 56:776-781.
57. Torsvik, V., F. L. Daae, R.-A. Sandaa, and L. Øvreås. 1998. Novel techniques for analysing microbial diversity in natural and perturbed environments. J. Biotechnol. 64:53-62.
58. Ward, D. M. 1998. A natural species concept for prokaryotes. Curr. Opin. Microbiol. 1:271-277.
59. Whitford, M. F., R. J. Foster, C. E. Beard, J. Gong, and R. M. Teather. 1998. Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe 4:153-163.
60. Wintzingerode, F. V., U. B. Göbel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.
61. Wise, M. G., J. V. McArthur, and L. J. Shimkets. 1997. Bacterial diversity of a Carolina bay as determined by 16S rRNA gene analysis: confirmation of novel taxa. Appl. Environ. Microhiol. 63:1505-1514.
62. Withers, P. J. A., H. M. McDonald, K. A. Smith, and C. Chumbley. 1998. Behaviour and impact of cow slurry beneath a storage lagoon. I. Groundwater contamination 1975-1982. Water Air Soil Pollut. 107:35-49.
63. Wolin, M. J. 1979. The rumen fermentation: a model for interactions in anaerobic ecosystems. Adv. Microb. Ecol. 3:49-78.