Diversity of uncultured epsilonproteobacteria from terrestrial sulfidic caves and springs

Applied and Environmental Microbiology

Volumn 74, Issue 15, 2008, Pages 4973-4977

  Porter, Megan L ^a   Engel, Annette Summers ^b  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^b LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; PHYLOGENETIC DIVERSITY;

RIBOSOME RNA;

BACTERIUM; CAVE; EVOLUTION; PHYLOGENETICS; RNA; SPECIES DIVERSITY; TERRESTRIAL ECOSYSTEM;

ARTICLE; EPSILONPROTEOBACTERIA; MICROBIAL DIVERSITY; NONHUMAN; PHYLOGENY; SPRING;

BASE SEQUENCE; DNA PRIMERS; ECOSYSTEM; ENVIRONMENT; EPSILONPROTEOBACTERIA; FRESH WATER; GEOLOGY; HOT SPRINGS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; VARIATION (GENETICS);

EPSILONPROTEOBACTERIA;

EID: 49449092854     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02915-07     Document Type: Article

References (30)

1. Angert, E. R., D. E. Northup, A. L. Reysenbach, A. S. Peek, B. M. Goebel, and N. R. Pace. 1998. Molecular phylogenetic analysis of a bacterial community in Sulphur River, Parker Cave, Kentucky. Am. Mineral. 83:1583-1592.
2. Barton, H. A., and F. Luiszer. 2005. Microbial metabolic structure in a sulfidic cave hot spring: potential mechanisms of biospeleogenesis. J. Cave Karst Stud. 67:28-38.
3. Campbell, B. J., A. S. Engel, M. L. Porter, and K. Takai. 2006. The versatile ε-proteobacteria: key players in the sulphur cycle. Nat. Rev. Microbiol. 4:458-468.
4. Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
5. Cho, J.-C., and J. M. Tiedje. 2000. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl. Environ. Microbiol. 66:5448-5456.
6. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
7. Engel, A. S., N. Lee, M. L. Porter, L. A. Stern, P. C. Bennett, and M. Wagner. 2003. Filamentous "Epsilonproteobacteria" dominate microbial mats from sulfidic cave springs. Appl. Environ. Microbiol. 69:5503-5511.
8. Engel, A. S., M. L. Porter, L. A. Stern, S. Quinlan, and P. C. Bennett. 2004. Bacterial diversity and ecosystem function of filamentous microbial mats from aphotic (cave) sulfidic springs dominated by chemolithoautotrophic "Epsilonproteobacteria." FEMS Microbiol. Ecol. 51:31-53.
9. Engel, A. S., L. A. Stern, and P. C. Bennett. 2004. Microbial contributions to cave formation: new insights into sulfuric acid speleogenesis. Geology 32: 369-372.
10. Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (v 3.2). Cladistics 5:164-166.
11. Goffredi, S., S. Johnson, and R. Vrijenhoek. 2007. Genetic diversity and potential function of microbial symbionts associated with newly discovered species of Osedax polychaete worms. Appl. Environ. Microbiol. 73:2314-2323.
12. Green, J., and B. J. M. Bohannan. 2006. Spatial scaling of microbial biodiveristy. Trends Ecol. Evol. 21:501-507.
13. Grote, J., M. Labrenz, D. Pfeiffer, G. Jost, and K. J.ürgens. 2007. Quantitative distributions of Epsilonproteobacteria and a Sulfurimonas subgroup in pelagic redoxclines of the central Baltic Sea. Appl. Environ. Microbiol. 73:7155-7161.
14. Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
15. Hirayama, H., M. Sunamura, K. Takai, T. Nunoura, T. Noguchi, H. Oida, Y. Furushima, H. Yamamoto, T. Oomori, and K. Horikoshi. 2007. Culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off Taketomi Island, Japan. Appl. Environ. Microbiol. 73:7642-7656.
16. Horner-Devine, M. C., K. M. Carney, and B. J. M. Bohannan. 2004. An ecological perspective on bacterial biodiversity. Proc. R. Soc. Lond. Ser. B Biol. Sci. 271:113-122.
17. Horner-Devine, M. C., M. Lage, J. B. Hughes, and B. J. M. Bohannan. 2004. A taxa-area relationship for bacteria. Nature 432:750-753.
18. Huber, J., D. M. Welch, H. Morrison, S. Huse, P. Neal, D. Butterfield, and M. Sogin. 2007. Microbial population structures in the deep marine biosphere. Science 318:97-100.
19. Macalady, J. L., E. H. Lyon, B. Koffman, L. K. Albertson, K. Meyer, S. Galdenzi, and S. Mariani. 2006. Dominant microbial populations in limestone-corroding stream biofilms, Frasassi cave system, Italy. Appl. Environ. Microbiol. 72:5596-5609.
20. Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker, Jr., P. R. Saxman, R. J. Farris, et al. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29:173-174.
21. Massana, R., E. F. DeLong, and C. Pedros-Alio. 2000. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl. Environ. Microbiol. 66:1777-1787.
22. Moussard, H., E. Corre, M. A. Cambon-Bonavita, Y. Fouquet, and C. Jeanthon. 2006. Novel uncultured Epsilonproteobacteria dominate a filamentous sulphur mat from the 13 degrees N hydrothermal vent field, East Pacific Rise. FEMS Microbiol. Ecol. 58:449-463.
23. Nakagawa, S., Y. Takaki, S. Shimamura, A.-L. Reysenbach, K. Takai, and K. Horikoshi. 2007. Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens. Proc. Natl. Acad. Sci. USA 104:12146-12150.
24. Papke, R. T., N. B. Ramsing, M. M. Bateson, and D. M. Ward. 2003. Geographical isolation in hot spring cyanobacteria. Environ. Microbiol. 5:650-659.
25. Posada, D., and T. R. Buckley. 2004. Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53:793-808.
26. Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
27. Schloss, P. D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
28. Stackebrandt, E., and B. M. Goebel. 1994. A place for DNA-DNA reassociation and 16S ribosomal-RNA sequence-analysis in the present species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 44:846-849.
29. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The Clustal_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
30. Yakimov, M., V. La Cono, R. Denaro, G. D'Auria, F. Decembrini, K. Timmis, P. Golyshin, and L. Giuliano. 2007. Primary producing prokaryotic communities of brine, interface and seawater above the halocline of deep anoxic Lake L'Atalante, eastern Mediterranean Sea. ISME J. 1:743-755.