Date of Award


Document Type


Degree Name

Master of Science (M.S.)


Pharmaceutical and Chemical Sciences

First Advisor

Skylar Carlson

First Committee Member

Jerry Tsai

Second Committee Member

Joseph Harrison

Third Committee Member

Paul Orwin


Natural products chemistry is the pursuit of bioactive small molecules from living organisms. These can be classified as primary metabolites if they are essential to survival, and secondary metabolites if they are accessory, playing a role in communication, defense, recruitment, etc.. Natural products have made a significant contribution to society – of 1,881 FDA-approved drugs from 1981 to 2019, 4% were pure natural products, 19% were natural products derived, and 3% were synthetic drugs with a natural products pharmacophore targeting a wide range of diseases and infections (Newman & Cragg, 2020). Pharmacophores are structural components of drugs that are responsible for the observed biological activity. Natural products often contain unique pharmacophores that exhibit potent bioactivity, thereby serving as inspiration for synthetic chemists to manufacture exciting new drug leads.

Bacteria are ubiquitous in the environment. Marine bacteria are a prolific source of chemically diverse natural products due to the high biodiversity and competition in the marine environment. In 2018, 240 new marine natural products were reported in the literature from bacteria (Carroll et al., 2020). It is hypothesized that secondary metabolites offer an advantage to the producer, however, the roles that natural products play in their environment are not as well characterized. These pursuits are classified as chemical ecology. Throughout my thesis, I aim to identify the bacteria present from these environments and begin to understand the ecological role small molecules play in their environment.

Staphylococcus aureus is notorious for causing chronic infections and resisting therapeutic treatment by forming biofilms. Biofilms are extracellular polymeric substance (EPS) matrices containing bacteria that attach to biotic and abiotic surfaces. The EPS matrix provides a refuge and anchorage to a surface, allowing biofilm inhabitants to be shielded from full strength of therapeutic treatments leading to resistance. Variovorax paradoxus is a gram-negative bacteria that also produces biofilms. It has been previously reported that V. paradoxus inhibits S. aureus biofilm formation. Preliminary data suggests V. paradoxus produces a small molecule that has biofilm inhibition activity. My work focuses on characterizing a GLP and another secondary metabolite produced by V. paradoxus that inhibits S. aureus biofilms through both molecular biology and natural products chemistry.

Caulerpa spp. is a macroalgae native to tropical and subtropical oceans. Due to global warming, the temperature of oceans continues to rise, allowing Caulerpa spp. to inhabit higher latitudes. It has been hypothesized that successful invasion occurs by outcompeting native organisms via exerting adverse effects on the surrounding environment. The secondary metabolites of this algae are well characterized however their ecological role is hardly characterized. We hypothesize that Caulerpa spp. could be chemically mediating its surface microbiome by recruiting a higher percentage of Vibrio spp.. Vibrio spp. are known pathogens to humans and marine organisms by causing infections and forming biofilms. My goal was to identify a panel of culturable Caulerpa spp. surface-associated bacteria through molecular and microbiology methods.

Microalgae are an exciting alternative source of biofuels. However, microalgae are grown in open algal ponds which are susceptible to crashing causing the total loss of an algal crop. Pond crashes are caused by a number of factors, one of which is contamination by unwanted pests such as protozoans and fungi. Previous studies focused on the use of bacterial communities as a built-in biocontrol to inhibit pests from causing algal pond crashes. Preliminary data demonstrated the addition of a bacterial community protected the microalgae Microchloropsis salina from grazing by the marine rotifer Brachionus plicatilis (Fisher et al., 2019). My work focuses on analyzing the composition of the protective bacterial community added to the microalgae that have been size filtered to observe bacterial association with algae, rotifers, or free-floating. M. salina cultures in the presence and absence of B. plicatilis were analyzed for the identification of protective bacterial species that were algae-, rotifer-associated, or free-floating. This work has been submitted to the journal Algal Research and is under review (Fisher et al., 2022).

Bacteria play a significant role in their environment. The identification of bacterial species and the role their suite of small molecules play is crucial to fully characterizing the observed interactions. My thesis surveys several means of bacterial community analysis through identification and small molecule characterization.



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