Phylogenetic composition of rocky mountain endolithic microbial ecosystems

Applied and Environmental Microbiology

Volumn 73, Issue 11, 2007, Pages 3497-3504

  Walker, Jeffrey J ^b   Pace, Norman R ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC ENGINEERING; MATHEMATICAL MODELS; MICROORGANISMS; PHOTOSYNTHESIS; ROCKS; STATISTICAL METHODS;

ENDOLITHIC COMMUNITIES; MICROBIAL HABITATS; PHYLOGENETIC COMPOSITION; PORE SPACE;

ECOSYSTEMS;

RIBOSOME RNA;

COMMUNITY COMPOSITION; ENDOLITHON; GENE EXPRESSION; MICROBIAL ECOLOGY; PHYLOGENETICS; SPECIES DIVERSITY; STATISTICAL ANALYSIS;

ARTICLE; BIOGEOGRAPHY; ECOLOGY; ECOSYSTEM; GENE SEQUENCE; MICROBIAL DIVERSITY; MICROHABITAT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOSYNTHESIS; PHYLOGENY; PREDICTION; ROCK; SAMPLING; STATISTICAL ANALYSIS; UNITED STATES;

ALGAE, GREEN; ARCHAEA; BACTERIA; BIODIVERSITY; DNA, RIBOSOMAL; ECOSYSTEM; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOIL MICROBIOLOGY; UNITED STATES;

NORTH AMERICA; ROCKY MOUNTAINS; UNITED STATES;

EID: 34249885115     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02656-06     Document Type: Article

References (40)

1. Achenbach, L. A., J. Carey, and M. T. Madigan. 2001. Photosynthetic and phylogenetic primers for detection of anoxygenic phototrophs in natural environments. Appl. Environ. Microbiol. 67:2922-2926.
2. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
3. Barton, H. A., M. R. Taylor, and N. R. Pace. 2004. Molecular phylogenetic analysis of a bacterial community in an oligotrophic cave environment. Geomicrobiol. J. 21:11-20.
4. Beja, O., E. N. Spudich, J. L. Spudich, M. Leclerc, and E. F. DeLong. 2001. Proteorhodopsin phototrophy in the ocean. Nature 411:786-789.
5. Bell, R. A. 1993. Cryptoendolithic algae of hot semiarid lands and deserts. J. Phycol. 29:133-139.
6. Brock, T. D. 1987. The study of microorganisms in situ: progress and problems. Symp. Soc. Gen. Microbiol. 41:1-17.
7. Colwell, R. R. 1997. Microbial diversity: the importance of exploration and conservation. J. Ind. Microbiol. Biotechnol. 18:302-307.
8. Dahms, D. E. 2004. Relative and numeric age data for pleistocene glacial deposits and diamictons in and near Sinks Canyon, Wind River Range, Wyoming, USA. Arct. Antarct. Alp. Res. 36:59-77.
9. de la Torre, J. R., B. M. Goebel, E. I. Friedmann, and N. R. Pace. 2003. Microbial diversity of cryptoendolithic communities from the McMurdo Dry Valleys, Antarctica. Appl. Environ. Microbiol. 69:3858-3867.
10. DeSantis, T. Z., P. Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, et al. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34:W394-W399.
11. 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.
12. Dunbar, J., S. M. Barns, L. O. Ticknor, and C. R. Kuske. 2002. Empirical and theoretical bacterial diversity in four Arizona soils. Appl. Environ. Microbiol. 68:3035-3045.
13. Finlay, B. J. 2002. Global dispersal of free-living microbial eukaryote species. Science 296:1061-1063.
14. Friedmann, E. I., and R. Ocampo-Friedmann. 1984. Endolithic microorganisms in extreme dry environments: analysis of a lithobiontic microbial habitat, p. 177-185. In M. J. Klug and C. A. Reddy (ed.), Current perspectives in microbial ecology. American Society for Microbiology, Washington, DC.
15. Friedmann, E. I. 1982. Endolithic microorganisms in the Antarctic cold desert. Science 215:1045-1053.
16. Friedmann, E. I., and R. Ocampo. 1976. Endolithic blue-green-algae in dry valleys - primary producers in Antarctic desert ecosystem. Science 193:1247-1249.
17. Giovannoni, S. J., S. Turner, G. J. Olsen, S. Barns, D. J. Lane, and N. R. Pace. 1988. Evolutionary relationships among cyanobacteria and green chloroplasts. J. Bacteriol. 170:3584-3592.
18. 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.
19. Ingalls, A. E., S. R. Shah, R. L. Hansman, L. I. Aluwihare, G. M. Santos, E. R. Druffel, et al. 2006. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc. Natl. Acad. Sci. USA 103:6442-6447.
20. Kanagawa, T. 2003. Bias and artifacts in multitemplate polymerase chain reactions (PCR). J. Biosci. Bioeng. 96:317-323.
21. 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, NY.
22. Leininger, S., T. Urich, M. Schloter, L. Schwark, J. Qi, G. W. Nicol, et al. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806-809.
23. Ley, R. E., J. K. Harris, J. Wilcox, J. R. Spear, S. R. Miller, B. M. Bebout, et al. 2006. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl. Environ. Microbiol. 72:3685-3695.
24. Lozupone, C., and R. Knight. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235.
25. Lozupone, C., M. Hamady, and R. Knight. 2006. UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371-385.
26. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, et al. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
27. Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-740.
28. Papineau, D., J. J. Walker, S. J. Mojzsis, and N. R. Pace. 2005. Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl. Environ. Microbiol. 71:4822-4832.
29. Robertson, C. E., J. K. Harris, J. R. Spear, and N. R. Pace. 2005. Phylogenetic diversity and ecology of environmental Archaea. Curr. Opin. Microbiol. 8:638-642.
30. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
31. Spear, J. R., J. J. Walker, T. M. McCollom, and N. R. Pace. 2005. Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proc. Natl. Acad. Sci. USA 102:2555-1560.
32. Stackebrandt, E., F. A. Rainey, and N. L. Ward-Rainey. 1997. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int. J. Syst. Bacteriol. 47:479-491.
33. Sun, H. J., and E. I. Friedmann. 1999. Growth on geological time scales in the Antarctic cryptoendolithic microbial community. Geomicrobiol. J. 16:193-202.
34. Tilman, D., D. Wedin, and J. Knops. 1996. Productivity and sustainability influenced by biodiversity in grassland ecosystems. Nature 379:718-720.
35. Turner, S. 1997. Molecular systematics of oxygenic photosynthetic bacteria. Plant Syst. Evol. Suppl. 11:13-52.
36. Vestal, J. R. 1988. Carbon metabolism of the cryptoendolithic microbiota from the Antarctic Desert. Appl. Environ. Microbiol. 54:960-965.
37. Walker, J. J. 2005. Ph.D. thesis. University of Colorado, Boulder.
38. Walker, J. J., J. R. Spear, and N. R. Pace. 2005. Geobiology of a microbial endolithic community in the Yellowstone geothermal environment. Nature 434:1011-1014.
39. Warscheid, T., and J. Braams. 2000. Biodeterioration of stone: a review. Int. Biodeterior. Biodegrad. 46:343-368.
40. Whitaker, R. J., D. W. Grogan, and J. W. Taylor. 2003. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301:976-978.