Natural Microbial Community Compositions Compared by a Back-Propagating Neural Network and Cluster Analysis of 5S rRNA.

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. Most aquatic environments contain bacteria freely suspended in the water column and bacteria associated with particulate material. These two community types provide different metabolic contributions to the total bacterial community depending on environmental conditions. In oligotrophic ocean waters, free-living bacteria can dominate in numbers and biomass and account for most of the secondary production (13). However, in environments that are characterized by substantial particle loads, attached bacteria make more significant contributions in cell numbers and total productivity (13, 20). In addition, they can exhibit morphological and metabolic characteristics that are distinct from those of freely suspended bacteria (7, 15, 29). The Chesapeake Bay is a eutrophic estuary characterized by significant amounts of organic and inorganic particulate material. Typically, particle loads are greater in the upper bay due to the large influx of fresh water. The bay exhibits seasonal circulation patterns, with a highly stratified water column in the summer followed by vertical mixing in the cooler winter months. It contains extensive, abundant, and active bacterial communities, which degrade phytodetritus and contribute to the formation of anoxic zones in bottom waters of the midbay region during the summer. Tritiated thymidine uptake experiments have shown that attached bacteria make a relatively minor contribution to total bacterial secondary production in the Chesapeake Bay (12). However, attached bacteria were found to be more active on a per-cell basis in summer, and they made significant contributions to the hydrolysis of a model dipeptide, MCA-leucine (14).