Abstract
The community compositions of free-living and particle-associated bacteria in the Chesapeake Bay estuary were analyzed by comparing banding patterns of stable low-molecular-weight RNA (SLMW RNA) which include 5S rRNA and tRNA molecules. By analyzing images of autoradiographs of SLMW RNAs on polyacrylamide gels, band intensities of 5S rRNA were converted to binary format for transmission to a back-propagating neural network (NN). The NN was trained to relate binary input to sample stations, collection times, positions in the water column, and sample types (e.g., particle-associated versus free-living communities). Dendrograms produced by using Euclidean distance and average and Ward's linkage methods on data of three independently trained NNs yielded the following results. (i) Community compositions of Chesapeake Bay water samples varied both seasonally and spatially. (ii) Although there was no difference in the compositions of free-living and particle-associated bacteria in the summer, these community types differed significantly in the winter. (iii) In the summer, most bay samples had a common 121-nucleotide 5S rRNA molecule. Although this band occurred in the top water of midbay samples, it did not occur in particle-associated communities of bottom-water samples. (iv) Regardless of the season, midbay samples had the greatest variety of 5S rRNA sizes. The utility of NNs for interpreting complex banding patterns in electrophoresis gels was demonstrated.
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- Bertone S., Giacomini M., Ruggiero C., Piccarolo C., Calegari L. Automated systems for identification of heterotrophic marine bacteria on the basis of their Fatty Acid composition. Appl Environ Microbiol. 1996 Jun;62(6):2122–2132. doi: 10.1128/aem.62.6.2122-2132.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bidle K. D., Fletcher M. Comparison of free-living and particle-associated bacterial communities in the chesapeake bay by stable low-molecular-weight RNA analysis. Appl Environ Microbiol. 1995 Mar;61(3):944–952. doi: 10.1128/aem.61.3.944-952.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Caron D. A., Davis P. G., Madin L. P., Sieburth J. M. Heterotrophic bacteria and bacterivorous protozoa in oceanic macroaggregates. Science. 1982 Nov 19;218(4574):795–797. doi: 10.1126/science.218.4574.795. [DOI] [PubMed] [Google Scholar]
- Carson C. A., Keller J. M., McAdoo K. K., Wang D., Higgins B., Bailey C. W., Thorne J. G., Payne B. J., Skala M., Hahn A. W. Escherichia coli O157:H7 restriction pattern recognition by artificial neural network. J Clin Microbiol. 1995 Nov;33(11):2894–2898. doi: 10.1128/jcm.33.11.2894-2898.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Freeman R., Goodacre R., Sisson P. R., Magee J. G., Ward A. C., Lightfoot N. F. Rapid identification of species within the Mycobacterium tuberculosis complex by artificial neural network analysis of pyrolysis mass spectra. J Med Microbiol. 1994 Mar;40(3):170–173. doi: 10.1099/00222615-40-3-170. [DOI] [PubMed] [Google Scholar]
- Griffith P. C., Fletcher M. Hydrolysis of Protein and Model Dipeptide Substrates by Attached and Nonattached Marine Pseudomonas sp. Strain NCIMB 2021. Appl Environ Microbiol. 1991 Aug;57(8):2186–2191. doi: 10.1128/aem.57.8.2186-2191.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Horton P. B., Kanehisa M. An assessment of neural network and statistical approaches for prediction of E. coli promoter sites. Nucleic Acids Res. 1992 Aug 25;20(16):4331–4338. doi: 10.1093/nar/20.16.4331. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Höfle M. G. Bacterioplankton community structure and dynamics after large-scale release of nonindigenous bacteria as revealed by low-molecular-weight-RNA analysis. Appl Environ Microbiol. 1992 Oct;58(10):3387–3394. doi: 10.1128/aem.58.10.3387-3394.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kirchman D., Mitchell R. Contribution of particle-bound bacteria to total microheterotrophic activity in five ponds and two marshes. Appl Environ Microbiol. 1982 Jan;43(1):200–209. doi: 10.1128/aem.43.1.200-209.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kramer J. G., Singleton F. L. Variations in rRNA content of marine Vibrio spp. during starvation-survival and recovery. Appl Environ Microbiol. 1992 Jan;58(1):201–207. doi: 10.1128/aem.58.1.201-207.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Roszak D. B., Colwell R. R. Survival strategies of bacteria in the natural environment. Microbiol Rev. 1987 Sep;51(3):365–379. doi: 10.1128/mr.51.3.365-379.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Somerville C. C., Knight I. T., Straube W. L., Colwell R. R. Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl Environ Microbiol. 1989 Mar;55(3):548–554. doi: 10.1128/aem.55.3.548-554.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Specht T., Wolters J., Erdmann V. A. Compilation of 5S rRNA and 5S rRNA gene sequences. Nucleic Acids Res. 1990 Apr 25;18 (Suppl):2215–2230. doi: 10.1093/nar/18.suppl.2215. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sprinzl M., Moll J., Meissner F., Hartmann T. Compilation of tRNA sequences. Nucleic Acids Res. 1985;13 (Suppl):r1–49. doi: 10.1093/nar/13.suppl.r1. [DOI] [PMC free article] [PubMed] [Google Scholar]