DNA PROBES AND MARINE MICROBIOLOGY

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Provided by Jed Fuhrman, University of Southern California

Summary Papers

Amann, R. I., Ludwig, W., & Schleifer, K.-H. (1995). Phylogenetic
identification and in situ detection of individual cells without
cultivation. Microb. Rev., 59, 143-169.

Fuhrman, J. A., Lee, S. H., Masuchi, Y., Davis, A. A., & Wilcox, R. M.
(1994). Characterization of marine prokaryotic communities via DNA and
RNA. Microbial Ecology, 28, 133-145.

Giovannoni, S., & Cary, S. C. (1993). Probing marine systems with
ribosomal RNAs. Oceanography, 6, 95-104.

Olsen, G. J., Lane, D. L., Giovannoni, S. J., & Pace, N. R. (1986).
Microbial ecology and evolution: A ribosomal RNA approach. Ann. Rev.
Microbiol., 40, 337-365.

Pace, N. R., Stahl, D. A., Lane, D. L., & Olsen, G. J. (1986). The
analysis of natural microbial populations by rRNA sequences. Adv.
Microbiol. Ecol., 9, 1-55.


Recent significant papers (there are no old classics)

Amann, R. I., Krumholz, L., & Stahl, D. A. (1990). Fluorescent
oligodeoxynucleotide probing of whole cells for determinative,
phylogenetic and environmental studies in microbiology. J. Bact., 172,
762-770.

Britschgi, T., & Giovannoni, S. J. (1991). Phylogenetic analysis of a
natural marine bacterioplankton population by rRNA gene cloning and
sequencing. Appl. Environ. Microbiol., 57, 1707-1713.

DeLong, E. F. (1992). Archaea in coastal marine environments. Proc. Natl.
Acad. Sci., USA, 89, 5685-5689.

Fuhrman, J. A., McCallum, K., & Davis, A. A. (1992). Novel major
archaebacterial group from marine plankton. Nature, 356, 148-149.

Fuhrman, J. A., McCallum, K., & Davis, A. A. (1993). Phylogenetic
diversity of marine subsurface microbial communities from the Atlantic and
Pacific Oceans. Appl. Environ.
Microbiol., 59(5), 1294-1302.

Hicks, R. E., Amann, R. I., & Stahl, D. A. (1992). Dual staining of
natural bacterioplankton with 4',6-diamidino-2-phenylindole and
fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA
sequences. Appl. Environ. Microbiol., 58, 2158-2163.


Hofle, M. G. (1992). Bacterioplankton community structure and dynamics
after large-scale release of nonindigenous bacteria as revealed by
low-molecular-weight-RNA analysis. Appl. Environ. Microbiol., 58,
3387-3394.

Muyzer, G., Waal, E. D. d., & Uitterlinden, A. G. (1993). Profiling of
complex microbial populations by denaturing gradient gel electrophoresis
analysis of polymerase chain reaction-amplified genes coding for 16S rRNA.
Appl. Environ. Microbiol., 59, 695-700.

Schmidt, T. M., DeLong, E. F., & Pace, N. R. (1991). Analysis of a Marine
Picoplankton Community by 16S rRNA Gene Cloning and Sequencing. J.
Bacteriol., 173, 4371-4378.

Voytek, M. A., & Ward, B. B. (1995). Detection of ammonium-oxidizing
bacteria of the beta subclass of the class Proteobacteria in aquatic
samples with PCR. Appl. Environ. Microbiol., 61, 1444-1450.


Papers relating to potential problems or controversies

Liesack, W., Weyland, H., & Stackebrandt, E. (1991). Potential risks of
gene amplification by PCR as determined by 16S rDNA analysis of a
mixed-culture of strict barophilic bacteria. Microb. Ecol., 21, 191-198.

Rehnstam, A. S., Backman, S., Smith, D. C., Azam, F., & Hagstrom, A.
(1993). Bloom of sequence-specific culturable bacteria in the sea. FEMS
Microbiol. Ecol., 102, 161-166.

Suzuki, M. T., & Giovannoni, S. J. (1996). Bias Caused by Template
Annealing in the Amplification of Mixtures of 16s rRNA Genes by PCR. Appl. Environ. Microbiol., 62(2), 625-630.

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