Paper Type

Master's Thesis


College of Arts and Sciences

Degree Name

Master of Science (MS)



NACO controlled Corporate Body

University of North Florida. Department of Biology

First Advisor

Dale Casamatta

Second Advisor

Sarah Hamsher

Third Advisor

Marie Mooney

Fourth Advisor

John Hatle

Department Chair

Cliff Ross

College Dean

Lori Kuhn-Hancock


A region of Lake Huron near Alpena, Michigan (U.S.A) includes karstic sinkholes with oxygen-poor, sulfur-rich ground water that contain vibrant microbial mats resembling life in early Earth’s shallow seas. We sought to document some of this unique ? diversity including the cyanobacteria, heterotrophic bacteria, and diatoms. Using culture-based investigations, we recovered strains of a novel cyanobacterium, Anagnostidinema visiae, and by employing a polyphasic approach we described this novel species from the Middle Island Sinkhole. In the processes of characterizing this novel species, the challenges of cyanobacterial systematics became evident. This led us to create a bioinformatics tool to help in the tedious and error prone method of ITS motif analysis for species level designation of cyanobacteria. We created a web- based application called the Cyanobacterial ITS Motifs Slicer (CIMS) which finds and separates the relevant motifs in cyanobacterial ITS regions. Finally, to describe the microbial diversity present in the region, we used both metabarcoding and culture-based techniques to explore the bacterial, cyanobacterial, and diatom communities. Our multi-marker metabarcoding approach allowed us to compare our findings to those previously reported using a universal 16S rRNA marker while also being able to get a more comprehensive view of the cyanobacterial community using a cyanobacterial specific 16S primer. Furthermore, we report the first analysis of the diatom community in these sites using a diatom specific rbcL marker. Our multi-marker approach recovered more ? diversity and taxonomic range - and highlighted the importance of using a cyanobacterial specific primer when investigating cyanobacterial communities via metabarcoding. In addition, we revealed very distinct diatom communities in the three sites and note the importance of surface water mixing, light penetration, and oxygenation in shaping the microbial communities.

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