Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient

Applied and Environmental Microbiology

Volumn 69, Issue 9, 2003, Pages 5563-5573

  Feris, Kevin ^a   Ramsey, Philip ^a   Frazar, Chris ^a   Moore, Johnnie N ^a   Gannon, James E ^a   Holben, William E ^a  

^a UNIVERSITY OF MONTANA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMASS; CONTAMINATION; ECOSYSTEMS; GROUNDWATER; HEAVY METAL COMPOUNDS; MICROSCOPIC EXAMINATION; RNA; SEDIMENTS; SURFACE WATERS;

HYPORHEIC ZONES;

BACTERIOLOGY;

RNA 16S;

COMMUNITY STRUCTURE; ECOLOGICAL IMPACT; HEAVY METAL; HYPORHEIC ZONE; MICROBIAL COMMUNITY; POLLUTION EXPOSURE;

ARTICLE; BIOMASS; CYANOBACTERIUM; GRAM NEGATIVE BACTERIUM; MICROFLORA; MOLECULAR CLONING; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; RIVER ECOSYSTEM; RNA GENE; WATER CONTAMINATION;

ALPHAPROTEOBACTERIA; BACTERIA; BASE SEQUENCE; BETAPROTEOBACTERIA; CYANOBACTERIA; DNA PRIMERS; GAMMAPROTEOBACTERIA; GEOGRAPHY; METALS, HEAVY; MONTANA; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; WATER MICROBIOLOGY; WATER POLLUTANTS, CHEMICAL;

BACTERIA (MICROORGANISMS); CYANOBACTERIA; GAMMAPROTEOBACTERIA; NEGIBACTERIA; PROTEOBACTERIA;

EID: 0141815904     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.9.5563-5573.2003     Document Type: Article

References (79)

1. Admiraal, W., H. Blanck, M. Buckert-De Jong, H. Guasch, N. Ivorra, V. Lehmann, B. A. H. Nystrom, M. Paulsson, and S. Sabater. 1999. Short-term toxicity of zinc to microbenthic algae and bacteria in a metal polluted stream. Water Res. 33:1989-1996.
2. Bååth, E., M. Diaz-Ravina, A. Frostegard, and C. D. Campbell. 1998. Effect of metal-rich sludge amendments on the soil microbial community. Appl. Environ. Microbiol. 64:238-245.
3. Baker, M. A., C. N. Dahm, and H. M. Valett. 1999. Acetate retention and metabolism in the hyporheic zone of a mountain stream. Limnol. Oceanogr. 44:1530-1539.
4. Barlocher, F., and J. H. Murdoch. 1989. Hyporheic biofilms: a potential food source for interstitial animals. Hydrobiologia 184:61-67.
5. Battin, T. J., A. Wille, B. Sattler, and R. Psenner. 2001. Phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream. Appl. Environ. Microbiol. 67:799-807.
6. Böckelmann, D. B. U. 2001. Description and characterization of bacteria attached to lotic organic aggregates (river snow) in the Elbe River of Germany and the South Saskatchewan River of Canada. Dissertation. Technischen Universität Berlin, Berlin, Germany.
7. Bond, P. L., G. K. Druschel, and J. F. Banfield. 2000. Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems. Appl. Environ. Microbiol. 66:4962-4971.
8. Bond, P. L., S. P. Smriga, and J. F. Banfield. 2000. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ. Microbiol. 66:3842-3849.
9. Boulton, A., S. Findlay, P. Marmonier, E. Stanley, and H. Valett. 1998. The functional significance of the hyporheic zone in streams and rivers. Annu. Rev. Ecol. Syst. 29:59-81.
10. Brookes, P. C., and S. P. McGrath. 1986. Effects of heavy metal accumulation in field soils treated with sewage-sludge on soil microbial processes and soil fertility, p. 327-343. In Conference proceedings, FEMS Symposium. Federation of European Microbiological Societies, Delft, The Netherlands.
11. Brugger, A., B. Wett, I. Kolar, B. Reitner, and G. Herndl. 2001. Immobilization and bacterial utilization of dissolved organic carbon entering the riparian zone of the alpine Enns River, Austria. Aquat. Microb. Ecol. 24:129-142.
12. Brunke, M., and T. Gonser. 1997. The ecological significance of exchange processes between rivers and ground water. Freshw. Biol. 37:1-33.
13. Burton, G. J., A. Drotar, J. Lazorchak, and L. Bahls. 1987. Relationship of microbial activity and Ceriodaphnia responses to mining impacts on the Clark Fork River, Montana. Arch. Environ. Contam. Toxicol. 16:523-530.
14. Chang, Y.-J., A. D. Peacock, P. E. Long, J. R. Stephen, J. P. Mckinley, S. J. Macnaughton, A. K. M. A. Hussain, A. M. Saxton, and D. C. White. 2001. Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site. Appl. Environ. Microbiol. 67:3149-3160.
15. Chapman, D. C. I. 1992. Assessment of injury to fish populations: Clark Fork River NPL sites. Montana Department of Natural Resources, Helena.
16. Craft, J., J. Stanford, and M. Pusch. 2002. Microbial respiration within a floodplain aquifer of a large gravel-bed river. Freshw. Biol. 47:251-261.
17. Dahlin, S., E. Witter, A. Mart, A. Turner, and E. Baath. 1997. Where's the limit? Changes in the microbiological properties of agricultural soils at low levels of metal contamination. Soil Biol. Biochem. 29:1405-1415.
18. Diaz-Ravina, M., and E. Bååth. 1996. Development of metal tolerance in soil bacterial communities exposed to experimentally increased metal levels. Appl. Environ. Microbiol. 62:2970-2977.
19. Domsch, K. 1984. Effects of pesticides and heavy metals on biological processes in soil. Conf. Biol. Proc. Soil Fert. 76:367-378.
20. Edwards, K. J., T. M. Gihring, and J. F. Banfield. 1999. Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment Appl. Environ. Microbiol. 65:3627-3632.
21. Feris, K. P., P. W. Ramsey, C. F. Frazar, M. C. Rillig, J. E. Gannon, and W. E. Holben. Structure and seasonal dynamics of hyporheic zone microbial communities in free-stone rivers of the western United States. Microb. Ecol., in press. [Online.] http://link.springer-ny.com/link/service/journals/00248 /contents/02/0100/s00248-002-0100-xch002.html.
22. Findlay, S. 1995. Importance of surface-subsurface exchange in stream ecosystems: the hyporheic zone. Limnol. Oceanogr. 40:159-164.
23. Findlay, S., and W. Sobczak. 1996. Variability in removal of dissolved organic carbon in hyporheic sediments. J. N. Am. Benthol. Soc. 15:35-41.
24. Findlay, S., D. Strayer, C. Goumbala, and K. Gould. 1993. Metabolism of streamwater dissolved organic carbon in the shallow hyporheic zone. Limnol. Oceanogr. 38:1493-1499.
25. Fischer, H., M. Pusch, and J. Schwoerbel. 1996. Spatial distribution and respiration of bacteria in stream-bed sediments. Arch. Hydrobiol. 137:281-300.
26. Franken, R., R. Storey, and D. Williams. 2001. Biological, chemical and physical characteristics of downwelling and upwelling zones in the hyporheic zone of a north-temperate stream. Hydrobiologia. 444:183-195.
27. Frazar, C. F. 2002. Microbial community production and tolerance in heavy metals polluted sediment. Masters thesis. The University of Montana-Missoula, Missoula.
28. Frostegard, A., A. Tunlid, and E. Bååth. 1996. Changes in microbial community structure during long-term incubation in two soils experimentally contaminated with metals. Soil Biol. Biochem. 28:55-63.
29. Frostegard, A., A. Tunlid, and E. Bååth. 1993. Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl. Environ. Microbiol. 59:3605-3617.
30. Glockner, F. O., E. Zaichikov, N. Belkova, L. Denissova, J. Pernthaler, A. Pernthaler, and R. Amann. 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.
31. Grimm, N. B., and S. G. Fisher. 1984. Exchange between interstitial and surface water: implications for stream metabolism and nutrient cycling. Hydrobiologia 111:219-228.
32. Guasch, H., M. Paulsson, and S. Sabater. 2002. Effect of copper on algal communities from oligotrophic calcareous streams. J. Phycol. 38:241-248.
33. Hahn, M. W., and M. G. Hofle. 1999. Flagellate predation on a bacterial model community: interplay of size-selective grazing, specific bacterial cell size, and bacterial community composition. Appl. Environ. Microbiol. 65:4863-4872.
34. Hare, L. 1992. Aquatic insects and trace metals: bioavailability, bioaccumulation, and toxicity. Crit. Rev. Toxicol. 22:327-369.
35. Hughes, M. F. 2002. Arsenic toxicity and potential mechanisms of action. Toxicol. Lett. 133:1-16.
36. Jones, J. B., S. G. Fisher, and N. B. Grimm. 1995. Nitrification in the hyporheic zone of a desert stream ecosystem. J. N. Am. Benthol. Soc. 14:249-258.
37. Kandeler, E., D. Tscherko, K. Bruce, M. Stemmer, P. Hobbs, R. Bardgett, and W. Amelung. 2000. Structure and function of the soil microbial community in microhabitats of a heavy metal polluted soil. Biol. Fert. Soils 32:390-400.
38. Kinner, N. E., R. W. Harvey, K. Blakeslee, G. Novarino, and L. D. Meeker. 1998. Size-selective predation on groundwater bacteria by nanoflagellates in an organic-contaminated aquifer. Appl. Environ. Microbiol. 64:618-625.
39. Kisand, V., R. Cuadros, and J. Wikner. 2002. Phylogeny of culturable estuarine bacteria catabolizing riverine organic matter in the northern Baltic Sea. Appl. Environ. Microbiol. 68:379-388.
40. Knight, B. P., S. P. Mcgrath, and A. M. Chaudri. 1997. Biomass carbon measurements and substrate utilization patterns of microbial populations from soils amended with cadmium, copper, or zinc. Appl. Environ. Microbiol. 63:39-43.
41. Komulainen, M., and J. Mikola. 1995. Soil processes as influenced by heavy metals and the composition of soil fauna. J. Appl. Ecol. 32:234-241.
42. Konopka, A., T. Zakharova, M. Bischoff, L. Oliver, C. Nakatsu, and R. F. Turco. 1999. Microbial biomass and activity in lead-contaminated soil. Appl. Environ. Microbiol. 65:2256-2259.
43. Lee, W. J., and D. J. Patterson. 2002. Abundance and biomass of heterotrophic flagellates, and factors controlling their abundance and distribution in sediments of Botany Bay. Microb. Ecol. 43:467-481.
44. Lepowski, W. 1998. Arsenic crisis in Bangladesh. Chem. Eng. News 76:27-29.
45. Lipton, J., H. Bergman, D. Chapman, T. Hillman, M. Kerr, J. N. Moore, and D. Woodward. 1993. Aquatic resource injury assessment report: Upper Clark Fork River Basin. State of Montana Natural Resource Damage Program. Montana Department of Natural Resources, Helena.
46. Malard, F., J. V. Ward, and C. T. Robinson. 1999. An expanded perspective of the hyporheic zone. Verh. Internat. Verein. Limnol. 27:1-7.
47. McCormick, F., B. Hill, L. Parrish, and W. Willingham. 1994. Mining impacts on fish assemblages in the Eagle and Arkansas Rivers, Colorado. J. Freshw. Ecol. 9:175-180.
48. Mills, A. L., and L. M. Mallory. 1987. The community structure of sessile heterotrophic bacteria stressed by acid mine drainage. Microb. Ecol. 14:219-232.
49. Moore, J. N., and S. N. Luoma. 1990. Hazardous wastes from large-scale metal extraction: a case study. Environ. Sci. Technol. 24:1278-1285.
50. Mulholland, P. J., E. R. Marzolf, J. R. Webster, D. R. Hart, and S. P. Hendricks. 1997. Evidence that hyporheic zones increase heterotrophic metabolism and phosphorous uptake in forest streams. Limnol. Oceanogr. 42:443-451.
51. Naegeli, M. W., and U. Uehlinger. 1997. Contribution of the hyporheic zone to ecosystem metabolism in a prealpine gravel-bed river. J. N. Am. Benthol. Soc. 16:794-804.
52. Nagorski, S. A., and J. N. Moore. 1999. Arsenic mobilization in the hyporheic zone of a contaminated stream. Water Resour. Res. 35:3441-3450.
53. Obbard, J., D. Sauerbeck, and K. Jones. 1994. Dehydrogenase activity of the microbial biomass in soils from a field experiment amended with heavy metal contaminated sewage sludges. Sci. Total Environ. 142:157-162.
54. Palmborg, C., A. Nordgren, and E. Baath. 1998. Multivariate modelling of soil microbial variables in forest soil contaminated by heavy metals using wet chemical analyses and pyrolysis GC/MS. Soil Biol. Biochem. 30:345-357.
55. Philippi, T. E. 1993. Multiple regression: herbivory, p. 183-210. In S. M. Scheiner and J. Gurevitch (ed.), Design and analysis of ecological experiments. Chapman and Hall, New York, N.Y.
56. Pusch, M. 1997. Community respiration in the hyporheic zone of a riffle-pool sequence, p. 51-56. In J. Gibert, J. Mathieu, and F. Fournier (ed.), Groundwater/surface water ecotones: biological and hydrological interactions and management options. Cambridge University Press, Cambridge, United Kingdom.
57. Pusch, M. 1996. The metabolism of organic matter in the hyporheic zone of a mountain stream, and its spatial distribution. Hydrobiologia 323:107-118.
58. Pusch, M., D. Fiebig, I. Brettar, H. Eisenmann, B. K. Ellis, L. A. Kaplan, M. A. Lock, M. W. Naegeli, and W. Traunspurger. 1998. The role of microorganisms in the ecological connectivity of running waters. Freshw. Biol. 40:453-495.
59. Pusch, M., and J. Schwoerbel. 1994. Community respiration in hyporheic sediments of a mountain stream (Steina, Black Forest). Arch. Hydrobiol. 130:35-52.
60. Ranjard, L., E. Brothier, and S. Nazaret. 2000. Sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking. Appl. Environ. Microbiol. 66:5334-5339.
61. Ranjard, L., S. Nazaret, F. Gourbiere, J. Thioulouse, P. Linet, and A. Richaume. 2000. A soil microscale study to reveal the heterogeneity of Hg(II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprints. Microb. Ecol. 31:107-115.
62. Sandaa, R., V. Torsvik, O. Enger, F. Daae, T. Castberg, and D. Hahn. 1999. Analysis of bacterial communities in heavy metal contaminated soils at different levels of resolution. FEMS Microbiol. Ecol. 30:237-251.
63. Sandaa, R.-A., V. Torsvik, and O. Enger. 2001. Influence of long-term heavy-metal contamination on microbial communities in soil. Soil Biol. Biochem. 33:287-295.
64. Sandaa, R.-A., Ø. Enger, and V. L. Torsvik. 1999. Abundance and diversity of Archaea in heavy-metal-contaminated soils. Appl. Environ. Microbiol. 65:3293-3297.
65. Sanguinetti, C. J., E. Dias Neto, and A. J. G. Simpson. 1994. Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. BioTechniques 17:914-921.
66. Shi, W., J. Becker, M. Bischoff, R. F. Turco, and A. E. Konopka. 2002. Association of microbial community composition and activity with lead, chromium, and hydrocarbon contamination. Appl. Environ. Microbiol. 68:3859-3866.
67. Smoot, J. C., and R. H. Findlay. 2001. Spatial and seasonal variation in a reservoir sedimentary microbial community as determined by phospholipid analysis. Microb. Ecol. 42:350-358.
68. Southam, G., and T.J. Beveridge. 1992. Enumeration of thiobacilli within pH-neutral and acidic mine tailings and their role in the development of secondary mineral soil. Appl. Environ. Microbiol. 58:1904-1912.
69. Stanford, J. A., and J. V. Ward. 1993. An ecosystem perspective of alluvial rivers: connectivity and the hyporheic corridor. J. N. Am. Benthol. Soc. 12:48-60.
70. Stephen, J. R., Y.-J. Chang, S. J. Macnaughton, G. A. Kowalchuk, K. T. Leung, C. A. Flemming, and D. C. White. 1999. Effect of toxic metals on indigenous soil β-subgroup proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metal-resistant bacteria. Appl. Environ. Microbiol. 65:95-101.
71. Traina, S. J., and V. Laperche. 1999. Contaminant bioavailability in soils, sediments, and aquatic environments. Proc. Natl. Acad. Sci. USA 96:3365-3371.
72. Valett, H. M., S. G. Fisher, and E. H. Stanley. 1990. Physical and chemical characteristics of the hyporheic zone of a Sonoran Desert stream. J. N. Am. Benthol. Soc. 16:239-247.
73. Vervier, P., and R. J. Naiman. 1992. Spatial and temporal fluctuations of dissolved organic carbon in subsurface flow of the Stillaguamish (Washington, USA). Arch. Hydrobiol. 123:401-412.
74. Wenderoth, D., and H. Reber. 1999. Correlation between structural diversity and catabolic versatility of metal affected prototrophic bacteria in soil. Soil Biol. Biochem. 31:345-352.
75. White, D. C., and D. B. Ringelberg. 1998. Signature lipid biomarker analysis, p. 255-272. In R. S. Burlage (ed.), Techniques in microbial ecology. Oxford University Press, New York, N.Y.
76. Wielinga, B., J. K. Lucy, J. N. Moore, O. F. Seastone, and J. E. Gannon. 1999. Microbiological and geochemical characterization of fluvially deposited sulfidic mine tailings. Appl. Environ. Microbiol. 65:1548-1555.
77. Wielinga, B. W., S. G. Benner, C. M. Brick, J. M. Moore, and J. E. Gannon. 1994. Geomicrobiological profile through the hyporheic zone in a historic mining flood plain, p. 267-276. In Proceedings of the Second International Conference on Groundwater Ecology. American Water Resources Association, Herndon, Va.
78. Yu, Z., and W. W. Mohn. 1999. Killing two birds with one stone: simultaneous extraction of DNA and RNA from activated sludge biomass. Can. J. Microbiol. 45:269-272.
79. Zhou, J., B. Xia, D. S. Treves, L.-Y. Wu, T. L. Marsh, R. V. O'Neill, A. V. Palumbo, and J. M. Tiedje. 2002. Spatial and resource factors influencing high microbial diversity in soil. Appl. Environ. Microbiol. 68:326-334.