Environmental diversity of bacteria and archaea

Systematic Biology

Volumn 50, Issue 4, 2001, Pages 470-478

  DeLong, Edward F ^a   Pace, Norman R ^b  

^a MONTEREY BAY AQUARIUM RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

Archaea; Bacteria; Biodiversity; Evolution; Microbial; Phylogeny

Indexed keywords

ARCHAEBACTERIUM; BACTERIUM; CLASSIFICATION; ECOSYSTEM; GENETIC VARIABILITY; GENETICS; MICROBIOLOGY; PHYLOGENY; REVIEW;

ARCHAEA; BACTERIA; ECOSYSTEM; ENVIRONMENTAL MICROBIOLOGY; PHYLOGENY; VARIATION (GENETICS);

EID: 0035527414     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/106351501750435040     Document Type: Article

References (38)

1. 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.
2. BARNS, S. M., C. F. DELWICHE, J. D. PALMER, AND N. R. PACE. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93:9188-9193.
3. BÉJÀ, O., M. T. SUZUKI, E. V. KOONIN, L. ARAVIND, A. HADD, L. P. NGUYEN, R. VILLACORTA, M. AMJADI, C. GARRIGUES, S. B. JOVANOVICH, ET AL. 2000. Construction and analysis of Bacterial Artificial Chromosome libraries from a natural microbial assemblage, Environ. Microbiol. 2:516-529.
4. BROWN, J. R., AND W. F. DOOLITTLE. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 16:456-502.
5. DELONG, E. F. 1998a. Archaeal means and extremes. Science 280:542-543.
6. DELONG, E. F. 1998b. Everything in moderation: Archaea as "nonextremophiles". Curr. Opin. Genet. Develop. 8:649-654.
7. DELONG, E. F., L. L. KING, R. MASSANA, H. CITTONE, A. MURRAY, C. SCHLEPER, and S. G. WAKEHAM. 1998. Dibiphytanyl ether lipids in nonthermophilic crenarchaeotes. Appl. Environ. Microbiol. 64:1133-1138.
8. DELONG, E. F., C. SCHLEPER, R. FELDMAN, AND R. V. SWANSON. 1999b. Application of genomics for understanding the evolution of hyperthermophilic and non-thermophilic Crenarchaeota, Biol. Bull. 196:363-366.
9. DELONG, E. F., L. T. TAYLOR, T. L. MARSH, AND C. M. PRESTON. 1999a. Visualization and enumeration of marine planktonic archaea and bacteria using polyribonucleotide probes and fluorescence in situ hybridization. Appl. Environ. Microbiol. 65:5554-5563.
10. DELONG, E. F., G. WICKHAM, and N. R. PACE. 1989. Phylogenetic stains: Ribosomal RNA-based probes for identification of single microbial cells. Science 243:1360-1363
11. DOOLITTLE, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2128.
12. HOEFS, M. J. L., S. SCOUTEN, J. W. DE LEEUW, L. L. KING, S. G. WAKEHAM, and J. S. DAMSTÉ. 1997. Ether lipids of planktonic archaea in the marine water column, Appl. Environ. Microbiol. 63:3090-3095.
13. HUGENHOLTZ, P., B. M. GOEBEL, AND N. R. PACE. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
14. IWABE, N., K. KUMA, M. HASAGAWA, S. OSAWA, AND T. MIYATA. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA 86:9355-9359.
15. MURRAY, A. E., C. M. PRESTON, R. MASSANA, L. T. TAYLOR, A. BLAKIS, K. Y. WU, AND E. F. DELONG. 1998. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters off Anvers Island, Antarctica. Appl. Environ. Microbiol. 64:2585-2595.
16. MULLINS, T. D., T. B. BRITSCHGI, R. L. KREST, AND S. J. GIOVANNONI. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr. 40:148-158.
17. OCHMAN, H., J. G. LAWRENCE, AND E. A. GROISMAN. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
18. PACE, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-740.
19. PACE, N. R., D. A. STAHL, D. J. LANE, AND G. J. OLSEN. 1986. The analysis of microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9:1-55.
20. POLTZ, M.F., AND C.M. CAVANAUGH. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730
21. PRESTON, C. M., K. Y. WU, T. F. MOLINSKI, AND E. F. DELONG. 1996. A psychrophilic crenarchaeon inhabits a marine sponge, Cenarchaeum symbiosum, gen. nov. sp. nov. Proc. Natl. Acad. Sci. USA 93:6241-6246.
22. REYSENBACH, A. L., L. J. GIVER, G. S. WICKHAM, and N. R. PACE. 1992. Differential amplification of rRNA genes by the polymerase chain reaction. Appl. Environ. Microbiol. 58:3147-3148.
23. 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, ET AL. 2000. Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2541-2547.
24. SCHLEPER, C., E. F. DELONG, C. M. PRESTON, R. A. FELDMAN, K. Y. WU, AND R. V. SWANSON. 1998. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 180: 5003-5009.
25. SCHMIDT, T. M., E. F. DELONG, AND N. R. PACE. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378.
26. SHIZUYA, H., B. BIRREN, U. J. KIM, V. MANCINO, T. SLEPAK, Y. TACHIIRI, AND M. SIMON. 1992. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Sci. USA 89:8794-8797.
27. STAHL, D. A., D. J. LANE, G. J. OLSEN, AND N. R. PACE. 1984. Analysis of hydrothermal vent associated symbionts by ribosomal RNA sequences. Science 224:409-411.
28. 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.
29. STEIN, J. L., T. L. MARSH, K. Y. WU, H. 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.
30. SUZUKI, M. T., AND S. J. GIOVANNONI. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
31. 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.
32. WINTZINGERODE, F. V., U. B. GOBEL, AND E. STACKEBRANDT. 1997. Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.
33. WANG, G. C. Y., AND Y. WANG. 1996. The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species. Microbiology 142:1107-1114.
34. WOESE, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
35. WOESE, C. R., AND G. E. FOX. 1977. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. USA 74:5088-5090.
36. WOESE, C. R., O. KANDLER, AND M. L. WHEELIS. 1990. Towards a system of organisms; proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579.
37. WOESE, C. R., L. J. MAGRUM, AND G. E. FOX. 1978. Archaebacteria. J. Mol. Evol. 11:245-252.
38. ZUCKERANDL, E., AND L. PAULING. 1965. Molecules as documents of evolutionary history. J. Theoret. Biol. 8:357-366.