Natural microbial community compositions compared by a back-propagating neural network and cluster analysis of 5S rRNA

Applied and Environmental Microbiology

Volumn 63, Issue 5, 1997, Pages 1762-1770

  Noble, Peter A ^a,b   Bidle, Kay D ^a,c   Fletcher, Madilyn ^a,b  

^a UNIVERSITY OF MARYLAND   (United States)

^b UNIVERSITY OF SOUTH CAROLINA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA;

AQUATIC FAUNA; ARTICLE; ARTIFICIAL NEURAL NETWORK; AUTORADIOGRAPHY; BACTERIAL COUNT; BACTERIUM CULTURE; CLUSTER ANALYSIS; ESTUARY; GEL ELECTROPHORESIS; RNA ANALYSIS;

CLUSTER ANALYSIS; COMMUNITY COMPOSITION; ESTUARY; MICROBIAL COMMUNITY; NEURAL NETWORK;

USA, CHESAPEAKE BAY;

EID: 0030613389     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.63.5.1762-1770.1997     Document Type: Article

References (33)

1. Aleksander, I., and H. Morton. 1991. An introduction to neural computing, p. 1-20. Chapman & Hall, Ltd., London, England.
2. Azam, F., and B. C. Cho. 1987. Bacterial utilization of organic matter in the sea, p. 261-281. In M. Fletcher, T. R. G. Gray, and J. G. Jones (ed.), Ecology of microbial communities. Cambridge University Press, Cambridge, England.
3. Beale, R., and T. Jackson. 1990. Neural computing: an introduction. IOP Publishing Ltd., New York, N.Y.
4. Bell, J. T. 1990. Carbon flow through bacterioplankton in the mesohaline Chesapeake Bay. M.S. thesis. University of Maryland, College Park.
5. Bertone, S., M. Giacomini, C. Ruggiero, C. Piccarolo, and L. Calegari. 1996. Automated systems for identification of heterotrophic marine bacteria on the basis of their fatty acid composition. Appl. Environ. Microbiol. 62:2122-2132.
6. Bidle, K. D., and M. Fletcher. 1995. Comparison of free-living and particle-associated bacterial communities in the Chesapeake Bay by stable low-molecular-weight RNA analysis. Appl. Environ. Microbiol. 61:444-952.
7. Caron, D. A., P. G. Davis, L. P. Madin, and J. M. Sieburth. 1982. Heterotrophic bacteria and bacteriovorous protozoa in oceanic macroaggregates. Science 218:795-797.
8. Carson, C. A., J. M. Keller, K. K. McAdoo, D. Wang, B. Higgins, C. W. Bailey, J. G. Thorne, B. J. Payne, M. Skala, and A. W. Hahn. 1995. Escherichia coli O157:H7 restriction pattern recognition by artificial neural networks. J. Clin. Microbiol. 33:2894-2898.
9. Cho, B. C., and F. Azam. 1988. Major role of bacteria in biogeochemical fluxes in the ocean's interior. Nature 332:441-443.
10. Everitt, B. S. 1974. Cluster analysis. Wiley and Sons, New York, N.Y.
11. Freeman, R., R. Goodacre, P. R. Sisson, J. G. Magee, A. C. Ward, and N. F. Lightfoot. 1994. Rapid identification of species within the Mycobacterium tuberculosis complex by artificial neural network analysis of pyrolysis mass spectra. J. Med. Microbiol. 40:170-173.
12. Griffith, P., F. Shiah, K. Gloersen, H. W. Ducklow, and M. Fletcher. 1994. Activity and distribution of attached bacteria in Chesapeake Bay. Mar. Ecol. Prog. Ser. 108:1-10.
13. Griffith, P. C., D. J. Douglas, and S. C. Wainright. 1990. Metabolic activity of size-fractionated microbial plankton in estuarine, nearshore, and continental shelf waters of Georgia. Mar. Ecol. Prog. Ser. 59:263-270.
14. Griffith, P. C., and M. Fletcher. 1991. Hydrolysis of protein and model dipeptide substrates by attached and nonattached marine Pseudomonas sp. strain NCIMB 2021. Appl. Environ. Microbiol. 57:2186-2191.
15. Hodson, R. E., A. E. Maccubbin, and L. R. Pomeroy. 1981. Dissolved adenosine triphosphate utilization by free-living and attached bacterioplankton.
16. Hoefle, M. G. 1998. Identification of bacteria by low molecular weight RNA profiles: a new chemotaxonomic approach. J. Microbiol. Methods 8:235-248.
17. Hoefle, M. G. 1990. RNA chemotaxonomy of bacterial isolates and natural bacterial communities, p. 129-159. In J. Overbeck and R. J. Chrost (ed.), Aquatic microbial ecology - biochemical and molecular approaches. Springer-Verlag, Berlin, Germany.
18. Hoefle, M. G. 1992. Bacterioplankton community structure and dynamics after large-scale release of nonindigenous bacteria as reveale by low-molecular-weight-RNA analysis. Appl. Environ. Microbiol. 58:3387-3394.
19. Horton, P.B., and M. Kanehisa. 1992. An assessment of neural networks and statistical approaches for prediction of E. coli promoter sites. Nucleic Acids Res. 20:4331-4338.
20. Kirchman, D., and R. Mitchell. 1982. Contribution of particle-bound bacteria to total microheterotrophic activity in five ponds and two marshes. Appl. Environ. Microbiol. 43:200-209.
21. Kramer, J. G., and F. L. Singleton. 1992. Variations in rRNA content of marine Vibrio spp. during starvation-survival and recovery. Appl. Environ. Microbiol. 58:201-207.
22. Masters, T. 1993. Practical neural network recipes in C++. Academic Press, New York, N.Y.
23. Neidhardt, F. C., J. L. Ingraham, and M. Schaechter. 1990. Physiology of the bacterial cell: a molecular approach, Sinauer Associates, Inc., Sutherland, Mass.
24. Rao, V. B., and H. V. Rao. 1993. C++ neural networks and fuzzy logic. MIS Press, New York, N.Y.
25. Raskin, L., R. I. Amann, L. K. Poulsen, B. E. Rittman, and D. A. Stahl. 1995. Use of ribosomal RNA-based molecular probes for characterization oi complex microbial communities in anaerobic biofilms. Water Sci. Technol. 31: 261-272.
26. Roszak, D. B., and R. R. Colwell. 1987. Survival strategies of bacteria in the natural environment. Microbiol. Rev. 51:365-379.
27. Rumelhart, D. E., G. E. Hinton, and R. J. Williams. 1986. Learning internal representation by error back propagation, p. 318-362. In D. E. Rumelhart and J. L. McCleland (ed.), Parallel distributed processing. M.I.T. Press, Cambridge, Mass.
28. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press. Cold Spring Harbor, N.Y.
29. Smith, D. C., M. Simon, A. L. Alldredge, and F. Azam. 1992. Intense hydrolytic enzyme activity on marine aggregates and implications for rapid particle dissolution. Nature 359:139-142.
30. Somerville, C. C., I. T. Knight, W. L. Straube, and R. R. Colwell. 1989. Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl. Environ. Microbiol. 55:548-554.
31. Specht, T., J. Wolters, and V. A. Erdmann. 1990. Compilation of 5S rRNA and 5S rRNA gene sequences. Nucleic Acids Res. 18(Suppl.):2215-2235.
32. Sprinzel, M., J. Moll, F. Meissner, and T. Hartmann. 1985. Compilation of tRNA sequences. Nucleic Acids Res. 13:r1-r49.
33. Tollenaere, T. 1990. SuperSAB: fast adaptive back propagation with good scaling properties. Neural Networks 3:561-573.