Research Abstracts Online
January - December 2011
University of Minnesota Duluth
Swenson College of Science and Engineering
PI: Randall E. Hicks
Improved Detection of Harmful Microbes in Ballast Water
The appearance of the fish virus VHS in the Great Lakes has led many to recognize that some microbes transported in the ballast water of commercial ships may be harmful invasive species. With support from the LCCMR, this researcher is sampling freshwater (“Lakers”) and ocean-going (“Salties”) commercial ships to identify harmful bacteria that are being transported in ballast water and discharged into Lake Superior. Once extracted, DNA from bacterial communities corresponding to the V6 hypervariable region of the 16S rDNA gene will be amplified. The amplicons from multiple samples will be pooled and sequenced on an Illumina/Solexa Sequencer at the National Center for Genomic Research in Santa Fe, New Mexico. Using this approach, about 20 million reads will be obtained from each sequence run. It is expected that multiple sequences runs will be completed that include more than 20 samples as part of this project. The vast amount of DNA sequence data obtained requires a supercomputer to efficiently analyze it. The 16S rDNA sequence data will be compared to reference databases to identify the taxonomic signatures of microorganisms. Local alignments, phylotype clusters, diversity estimates, and graphical representation of data will be obtained using the MOTHUR program at MSI. The resulting phylogenetic relationships that are identified will be tested by maximum-likelihood bootstrap trees (with 1,000 iterations). When completed, these analyses will give us a comprehensive picture of the bacterial structure of ballast water and the receiving water in the Duluth-Superior harbor, where ballast water is discharged. This project is being run in conjunction with Professor Michael Sadowsky’s laboratory (Soil, Water, and Climate). He has used MOTHUR to analyze similar datasets for bacterial communities in the Mississippi River. His groups’ experience with these software tools and MSI will help guide this project.
Andrew J. Reed, Research Associate