A census of rRNA genes and linked genomic sequences within a soil metagenomic library

Applied and Environmental Microbiology

Volumn 69, Issue 5, 2003, Pages 2684-2691

  Liles, Mark R ^a   Manske, Brian F ^a   Bintrim, Scott B ^a,b   Handelsman, Jo ^a   Goodman, Robert M ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b DOW AGROSCIENCES LLC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; GENES; RNA; SOILS;

BACTERIAL ARTIFICIAL CHROMOSOMES (BAC) CLONES;

MICROBIOLOGY;

FOLIC ACID; GENE PRODUCT; RIBOSOME RNA;

GENOME; MICROBIOLOGY; SOIL MICROORGANISM;

ARCHAEBACTERIUM; ARTICLE; BACILLUS; BACTERIAL CHROMOSOME; CELL CYCLE; CELL DIVISION; COMPARATIVE STUDY; CONTROLLED STUDY; DNA REPAIR; EUKARYOTE; FLEXIBACTERACEAE; GENE AMPLIFICATION; GENE IDENTIFICATION; GENE LIBRARY; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; GRAM NEGATIVE BACTERIUM; MICROBIAL GENETICS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; POLYMERASE CHAIN REACTION; SOIL; TRANSCRIPTION REGULATION; UNINDEXED SEQUENCE;

BACTERIA; CHROMOSOMES, ARTIFICIAL, BACTERIAL; DNA, BACTERIAL; DNA, RIBOSOMAL; GENES, BACTERIAL; GENOMIC LIBRARY; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

ACIDOBACTERIUM; ALPHAPROTEOBACTERIA; ARCHAEA; BACTEROIDETES; EUKARYOTA; FIRMICUTES; FLEXIBACTERACEAE; GAMMAPROTEOBACTERIA; NEGIBACTERIA; PROKARYOTA; PROTEOBACTERIA; SPHINGOBACTERIALES; VERRUCOMICROBIA;

EID: 0038185214     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.5.2684-2691.2003     Document Type: Article

References (43)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
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. Barns, S. M., R. E. Fundyga, M. W. Jeffries, and N. R. Pace. 1994. Remarkable Archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91:1609-1613.
4. 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.
5. Beja, O., L. Aravind, E. V. Koonin, M. T. Suzuki, A. Hadd, L. P. Nguyen, S. B. Jovanovich, C. M. Gates, R. A. Feldman, J. L. Spudich, E. N. Spudich, and E. F. DeLong. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902-1906.
6. Beja, O., M. T. Suzuki, E. V. Koonin, L. Aravind, A. Hadd, L. P. Nguyen, R. Villacorta, M. Amjadi, C. Garrigues, S. B. Jovanovich, R. A. Feldman, and E. F. DeLong. 2000. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2:516-529.
7. Beja, O., E. N. Spudich, J. L. Spudich, M. Leclerc, E. F. DeLong. 2001. Proteorhodopsin phototrophy in the ocean. Nature 411:786-789.
8. Beja, O., E. V. Koonin, L. Aravind, L. T. Taylor, H. Seitz, J. L. Stein, D. C. Bensen, R. A. Feldman, R. V. Swanson, and E. F. DeLong. 2002. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68:335-345.
9. Beja, O., M. T. Suzuki, J. F. Heidelberg, W. C. Nelson, C. M. Preston, T. Hamada, J. A. Eisen, C. M. Fraser, and E. F. DeLong. 2002. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415:630-633.
10. Bintrim, S. B., T. J. Donohue, J. Handelsman, G. P. Roberts, and R. M. Goodman. 1997. Molecular phylogeny of Archaea from soil. Proc. Natl. Acad. Sci. USA 94:277-282.
11. Burgmann, H., M. Pesaro, F. Widmer, and J. Zeyer. 2001. A strategy for optimizing quality and quantity of DNA extracted from soil. J. Microbiol. Methods 45:7-20.
12. Dojka, M. A., J. K. Harris, and N. R. Pace. 2000. Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl. Environ. Microbiol. 66:1617-1621.
13. Goodman, R. M., and M. R. Liles. April 2001. Template specific termination in a polymerase chain reaction. U.S. Patent 6,248,567.
14. Handelsman, J., M. R. Rondon, S. F. Brady, J. Clardy, and R. M. Goodman. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5:R245-R249.
15. Head, I. M., J. R. Saunders, and R. W. Pickup. 1998. Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb. Ecol. 35:1-21.
16. Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of cultureindependent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
17. 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.
18. Janssen, P. H., P. S. Yates, B. E. Grinton, P. M. Taylor, and M. Sait. 2002. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl. Environ. Microbiol. 68:2391-2396.
19. Kishimoto, N., Y. Kosako, and T. Tano. 1991. Acidobacterium capsulatum gen. nov., sp. nov.: an acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Curr. Microbiol. 22:1-7.
20. Klappenbach, J. A., J. M. Dunbar, and T. M. Schmidt. 2000. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66:1328-1333.
21. 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.
22. Lane, D. J., B. Pace, G. J. Olsen, D. A. Stahl, M. L. Sogin, and N. R. Pace. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analysis. Proc. Natl. Acad. Sci. USA 82:6955-6959.
23. Liesack, W., F. Bak, J. U. Kreft, and E. Stackebrandt. 1994. Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. Arch. Microbiol. 162:85-90.
24. Lonergan, D. J., H. L. Jenter, J. D. Coates, E. J. P. Phillips, T. M. Schmidt, and D. R. Lovley. 1996. Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria. J. Bacteriol. 178:2402-2408.
25. 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.
26. Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker, Jr., P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt, and J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29:173-174.
27. Medlin, L., H. J. Elwood, S. Stickel, and M. L. Sogin. 1988. The characterization of enzymatically amplified eukaryotic 16S-like ribosomal RNA-coding regions. Gene 71:491-500.
28. Pace, N. R., D. A. Stahl, D. J. Lane, and G. J. Olsen. 1986. The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9:1-55.
29. Quaiser, A., T. Ochsenreiter, H.-P. Klenk, A. Kletzin, A. H. Treusch, G. Meurer, J. Eck, C. W. Sensen, and C. Schleper. 2002. First insight into the genome of an uncultivated crenarchaeote from soil. Environ. Microbiol. 4:603-611.
30. Rondon, M. R., P. R. August, A. D. Bettermann, S. F. Brady, T. H. Grossman, M. R. Liles, K. A. Loiacono, B. A. Lynch, I. A. MacNeil, C. Minor, C. L. Tiong, M. Gilman, M. S. Osburne, J. Clardy, J. Handelsman, and R. M. Goodman. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2541-2547.
31. Sait, M., P. Hugenholtz, and P. H. Janssen. 2002. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ. Microbiol. 4:654-666.
32. Sakai, Y., J. Ishikawa, S. Fukasaka, H. Yurimoto, R. Mitsui, H. Yanase, and N. Kato. 1999. A new carboxylesterase from Brevibacterium linens IFO 12171, responsible for the conversion of 1,4-butanediol diacrylate to 4-hydroxybutyl acrylate: purification, characterization, gene cloning, and gene expression in Escherichia coli. Biosci. Biotech. Biochem. 63:688-697.
33. Salzberg, S. R., A. L. Delcher, S. Kasif, and O. White. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26:544-548.
34. Simon, H. M., J. A. Dodsworth, and R. M. Goodman. 2000. Crenarchaeota colonize terrestrial plant roots. Env. Microbiol. 2:495-505.
35. Staley, J. T., and A. Konopka. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39:321-346.
36. Stein, J. L., T. L. Marsh, K. Y. Wu, T. Shizuya, and E. F. DeLong. 1996. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 178:591-599.
37. Torsvik, V., J. Goksoyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782-787.
38. Torsvik, V., J. Goksoyr, F. L. Daae, R. Sørheim, J. Michalsen, and K. Salte. 1994. Use of DNA analysis to determine the diversity of microbial communities, p. 39-48. In K. Ritz, J. Dighton, and K. E. Giller (ed.), Beyond the biomass. John Wiley and Sons, Chichester, England.
39. Torsvik, V., R. Sorheim, and J. Goksoyr. 1996. Total bacterial diversity in soil and sediment communities-a review. J. Ind. Microbiol. 17:170-178.
40. Vergin, K. L., E. Urbach, J. L. Stein, E. F. DeLong, B. D. Lanoil, and S. J. Giovannoni. 1998. Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl. Environ. Microbiol. 64:3075-3078.
41. von Wintzingerode, F., O. Landt, A. Ehrlich, and U. B. Gobel. 2000. Peptide nucleic acid-mediated PCR clamping as a useful supplement in the determination of microbial diversity. Appl. Environ. Microbiol. 66:549-557.
42. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63-65.
43. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.