Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake

Limnology and Oceanography

Volumn 46, Issue 3, 2001, Pages 557-572

  Urbach, Ena ^a,b   Vergin, Kevin L ^a   Young, Lei ^a   Morse, Ariel ^a   Larson, Gary L ^a   Giovannoni, Stephen J ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPLANKTON; COMMUNITY STRUCTURE; LAKE; MARINE ENVIRONMENT; PROTEOBACTERIUM; RIBOSOME RNA; SMALL SUBUNIT; TRACE METAL; UNITED STATES; WATER DEPTH;

BACTERIOPLANKTON; COMMUNITY STRUCTURE; LAKE; OLIGOTROPHIC ENVIRONMENT;

CRATER LAKE; OREGON; UNITED STATES;

EID: 0035033231     PISSN: 00243590     EISSN: None     Source Type: Journal    
DOI: 10.4319/lo.2001.46.3.0557     Document Type: Article

References (58)

1. ALFREIDER, A., J. PERNTHALER, R. AMANN, B. SATTLER, F-O. GLÖCKNER, A. WILLE, AND R. PSENNER. 1996. Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization. Appl. Environ. Microbiol. 62: 2138-2144.
2. AMERICAN PUBLIC HEALTH ASSOCIATION. 1985. Standard methods for examination of water and wastewater, 16th ed. APHA.
3. BAHR, M., J. E. HOBBIE, AND M. L. SOGIN. 1996. Bacterial diversity in an arctic lake: A freshwater SAR11 cluster. Aquat. Microb. Ecol. 11: 271-277.
4. BEL'KOVA, N. L., L. Y. DENISOVA, E. N. MANAKOVA, E. E ZAICHIKOV, AND M. A. GRACHEV. 1996. Species diversity of deep-water microorganisms of Lake Baikal: Analysis of 16S rRNA sequences. Dokl. Biol. Sci. 348: 692-695.
5. CAVENDER-BARES, K. K., E. L. MANN, S. W. CHISHOLM, M. E. ONDRUSEK, AND R. B. BIDIGARE. 1999. Differential response of equatorial Pacific phytoplankton to iron fertilization. Limnol. Oceanogr. 44: 237-246.
6. COLLIER, R., J. DYMOND, AND J. MCMANUS. 1991. Studies of hydrothermal processes in Crater Lake, OR. College of Oceanography Report #90 7. Oregon State University.
7. CRUMP, B. C., E. V. ARMBRUST, AND J. A. BAROSS. 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.
8. DELONG, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89: 5685-5689.
9. _. 1998. Archaeal means and extremes. Science 280: 542-543.
10. DOJKA, M. A., P. HUGENHOLTZ, S. K. HAAK, AND N. R. PACE. 1998. Microbial diversity in a hydrocarbon-and chlorinated-solvent -contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64: 3869-3877.
11. DYMOND, J., R. W. COLLIER, AND M. E. WATWOOD. 1989. Bacterial mats from Crater Lake, Oregon and their relationship to possible deep-lake hydrothermal venting. Nature 342: 673-675.
12. FAULKNER, K. K., C. I. MEASURES, S. E. HERBELIN, J. M. EDMOND, AND R. F. WEISS. 1991. The major and minor element geochemistry of Lake Baikal. Limnol. Oceanogr. 36: 413-423.
13. FELSENSTEIN, J. 1993. PHYLIP (Phylogeny Inference Package). Version 3.5c. Univ. of Washington-Seattle.
14. FIELD, K. G., D. GORDON, M. RAPPÉ, E. URBACH, K. VERGIN, AND S. J. GIOVANNONI. 1997. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl. Environ. Microbiol. 63: 63-76.
15. FUHRMAN, J. A., K. MCCALLUM, AND A. A. DAVIS. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 59: 1294-1302.
16. GIOVANNONI, S. J., T. B. BRITSCHGI, C. L. MOYER, AND K. G. FIELD. 1990a. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60-62.
17. _, E. F. DELONG, T. M. SCHMIDT, AND N. R. PACE. 1990b. Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Appl. Environ. Microbiol. 56: 2572-2575.
18. _, AND M. RAPPÉ. 2000. Evolution, diversity, and molecular ecology of marine prokaryotes, p. 47-84. In D. L. Kirchman [ed.], Microbial ecology of the oceans. Wiley.
19. _, M. S. RAPPÉ, K. L. VERGIN, AND N. L. ADAIR. 1996. 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria. Proc. Natl. Acad. Sci. USA 93: 7979-7984.
20. GOLDMAN, C. R. 1963. The measurement of primary productivity and limiting factors in freshwater with carbon-14, p. 103-113. In M. S. Doty [ed.], Primary productivity measurement, marine and freshwater. U.S. Atomic Energy Commission TID-7633.
21. GORDON, D. A., AND S. J. GIOVANNONI. 1996. Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 62: 1171-1177.
22. GROEGER, A. W., AND T. C. TEITJEN. 1993. Physiological responses of nutrient-limited phytoplankton to nutrient addition. Verh. Internat. Verein. Limnol. 25: 370-372.
23. HIORNS, W. D., B. A. METHÉ, S. A. NIERZWICKI-BAUER, AND J. P. ZEHR. 1997. Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences. Appl. Environ. Microbiol. 63: 2957-2960.
24. HÖFLE, M., H. HAAS, AND K. DOMINIK. 1999. Seasonal dynamics of bacterioplankton community structure in a eutrophic lake as determined by 5S rRNA analysis. Appl. Environ. Microbiol. 65: 3164-3174.
25. HUGENHOLTZ, P., C. PITULLE, K. L. HERSHBERGER, AND N. R. PACE. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180: 366-376.
26. KRUMHOLZ, L., AND P. A. STAHL. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172: 762-770.
27. 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.
28. LANE, D. J. 1991. 16S/23/S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow [eds.], Nucleic acid techniques in bacterial systematics. Wiley.
29. LANE, J. L., AND C. R. GOLDMAN. 1984. Size-fractionation of natural phytoplankton communities in nutrient bioassay studies. Hydrobiologia 118: 219-223.
30. LARSON, G. L., C. D. MCINTIRE, M. HURLEY, AND M. W. BUKTENICA. 1996a. Temperature, water chemistry, and optical properties of Crater Lake. Lake Reservoir Manag. 12: 230-247.
31. _, _, R. TRUITT, M. BUKTENICA, AND E. K. THOMAS. 1993. Zooplankton assemblages in Crater Lake. U.S. Department of the Interior. Report NPS/PNROSU/NRTR-93/03.
32. _, _, R. E. TRUITT, M. W. BUKTENICA, AND E. DARNAUGH-THOMAS. 1996b. Zooplankton assemblages in Crater Lake, Oregon, USA. Lake Reservoir Manag. 12: 281-297.
33. LI, L., C. KATO, AND K. HORIKOSHI. 1999. Bacterial diversity in deep-sea sediments from different depths. Biodivers. Conserv. 8: 659-677.
34. MAIDAK, B. L., AND OTHERS. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27: 171-173.
35. MANZ, W., R. AMANN, AND W. LUDWIG. 1992. Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: Problems and solutions. Syst. Appl. Microbiol. 15: 593-600.
36. MASSANA, R., E. F. DELONG, AND C. PEDRÖS-ALIÓ. 2000. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl. Environ. Microbiol. 66: 1777-1787.
37. _, A. E. MURRAY, C. M. PRESTON, AND E. E DELONG. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 63: 50-56.
38. MCINTIRE, C. D., G. L. LARSON, R. E. TRUITT, AND M. K. DEBACON. 1996. Taxonomic structure and productivity of phytoplankton assemblages in Crater Lake, Oregon. Lake Reservoir Manag. 12: 259-280.
39. MCMANUS, J., R. COLLIER, J. DYMOND, C. G. WHEAT, AND G. L. LARSON. 1996. Spatial and temporal distribution of dissolved oxygen in Crater Lake, Oregon. Limnol. Oceanogr. 41: 722-731.
40. _, R. W. COLLIER, AND J. DYMOND. 1993. Mixing processes in Crater Lake, Oregon. J. Geophys. Res. 98: 295-307.
41. METHÉ, B. A., W. D. HIORNS, AND J. P. ZEHR. 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.
42. _, AND J. P. ZEHR. 1999. Diversity of bacterial communities in Adirondack lakes: Do species assemblages reflect lake water chemistry? Hydrobiologia 401: 77-96.
43. MORRIS, D. P., AND B. R. HARGREAVES. 1997. The role of photochemical degradation of dissolved organic carbon in regulating the UV transparency of three lakes on the Pocono Plateau. Limnol. Oceanogr. 42: 239-249.
44. MURRAY, A. E., C. M. PRESTON, R. MASSANA, L. T. TAYLOR, A. BLAKIS, K. WU, AND E. F. DELONG. 1998. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 64: 2585-2595.
45. NELSON, P. O., J. F. REILLY, AND G. L. LARSON. 1996. Chemical solute mass balance of Crater Lake, Oregon. Lake Reservoir Manag. 12: 248-258.
46. PACE, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
47. POLZ, M. F., AND C. M. CAVANAUGH. 1997. A simple method for quantification of uncultured microorganisms in the environment based on in vitro transcription of 16S rRNA. Appl. Environ. Microbiol. 63: 1028-1033.
48. PORTER, K. G., AND Y. S. FEIG. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25: 943-948.
49. PRISCU, J. C., AND OTHERS. 1999. Geomicrobiology of subglacial ice above Lake Vostok, Antarctica. Science 286: 2141-2144.
50. RAPPÉ, M. S., P. F. KEMP, AND S. J. GIOVANNONI. 1997. Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol. Oceanogr. 42: 811-826.
51. SEMENOVA, E. A., AND K. D. KUZNEDELOV. 1998. A study of the biodiversity of Baikal picoplankton by comparative analysis of 16S rRNA gene 5′-terminal regions. Mol. Biol. 32: 754-760.
52. 3H-leucine. Mar. Microb. Food Webs 6: 107-114.
53. STACKEBRANDT, E. In press. Defining taxonomic ranks. In M. Dworkin [ed.], The prokaryotes: An evolving electronic resource for the microbiological community. http://www.prokaryotes. com [6 July 2000], Springer.
54. STRUNK, O., AND OTHERS. 1996. ARB - a software environment for sequence data. Version 2.5b. Technical Univ. of Munich.
55. SWOFFORD, D. L. 1996. PAUP*: Phylogenetic analysis using parsimony (and other methods). Version 4.0. Sinauer.
56. VINCENT, W. F., R. RAE, I. LAURION, C. HOWARD-WILLIAMS, AND J. C. PRISCU. 1998. Transparency of Antarctic ice-covered lakes to solar UV radiation. Limnol. Oceanogr. 43: 618-624.
57. WILLIAMSON, C. E., R. S. STEMBERGER, D. P. MORRIS, T. M. FROST, AND S. G. PAULSEN. 1996. Ultraviolet radiation in North American lakes: Attenuation estimates from DOC measurements and implications for plankton communities. Limnol. Oceanogr. 41: 1024-1034.
58. ZWART, G., AND OTHERS. 1998. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst. Appl. Microbiol. 21: 546-556.