Data Analysis
These results do not support our original hypothesis that the pond would have a greater microbial diversity than the stream. Our data do not provide definitive evidence either in favor or against our original hypothesis. None the less two significant findings did emerge from the data.
Our data showed there was more genetic diversity in the 5 stream species of bacteria than there was between the 14 pond species we analyzed. A second important result obtained from our data was that most of the bacteria we found in both the stream and the pond were related to pseudomonas bacteria. This makes sense since Pseuodomonas is a common aquatic bacteria.
One problem that arose was that the sequences generated from the two primers on the end of the cloned fragment, did not overlap which left an unidentified area of nucleotides between them. Suggestions for further research would be to use primers that select for a smaller region of the template. A second problem involved the fact that our sample size was quite small. Increasing sample size would provide greater confidence in the results achieved in subsequent studies.
Our data was analyzed by combining ten taxa selected from Margulis and Schwartz (1998) with the species we collected. We used the CLUSTAL and PHYLIP programs, and included two members of the domain Archaea (Methanococcus and Halobacteroides) as outgroups for purposes of comparison. The two approaches used in the data analysis take fundamentally different tacts. CLUSTALW looks for an overall alignment of nucleotide sequences, with no regard for coding/noncoding segments. PHYLIP is an analysis tool that focuses on shared derived characteristics.
The analysis revealed that the bacteria collected as part of our study fell into two main groups, the organisms collected at our pond site and the organisms found at our stream location. Our findings raise some interesting questions. Why are the 16S ribosomal genomes of the bacteria found in the stream different from those from the pond? Can these differences be linked to variations in microbial ecology?
Our group is especially grateful to Dr. Rob DeSalle who spent a great deal of
time cleaning up our data so that it could be put into the CLUSTAL and PHYLIP
programs for analysis. Thanks also go to John Sacco and Gene McNicholas who
provided invaluable computer assistance.
F
Figure 1. Cladistic tree demonstrating the genomic relationships among the bacterial populations generated from left-hand primer.
Figure 2. Cladistic tree generated from right-handed primer.
Reference:
Margulis, Lynn and K. V. Schwartz. 1998. Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth (Third edition). W. H. Freeman and Co. New York.