A view to a kill: System-level analysis of metabolism in an algicidal bacterium

Genevieve Parkey

Mentors: Dr. Ali Navid and Dr. Helena Van Tol, Biochemical and Biophysical Systems Group, Lawrence Livermore National Laboratory.

Date/Time: August 24, 2021 at 1:00pm

Abstract: To answer many of the Lawrence Livermore National Laboratory’s mission-related biological questions, system-level analyses of natural ecosystems are conducted. During these investigations, new bacteria are often discovered, which leads to many questions. One important question that may need to be answered is, “what do each one of the newly discovered bacteria need to survive?” This summer, my project focused on working to answer this question for a newly identified bacterium called Rickettsia-like diatom killer, better known as RLDK. This is a bacterium that attaches to Phaeodactylum triconutum, a model microalga that can be harvested for biofuel, and kills the algae for reasons still unknown to us. This is an important problem because as climate change continues to be a problem, we are trying to get more of our energy needs met by biofuels. Phaeodactylum triconutum is being used for this, and a bacterium that kills it will prevent the algae from being harvested.

Using the Metagenome-Assembled Genome of the bacterium, we annotated it and built automatically generated draft genome-scale metabolic models of the organism. These models correlate genes with different pathways and reactions present in the organism and provide insight into the metabolism of the bacterium. By focusing on the essential exchange reactions in the models, we gathered information on the metabolic capabilities and needs of the bacterium. We generated the lists of essential exchange reactions using cobrapy, a genome-scale metabolic modeling package for python, and then examined the pathways that correspond to the reactions to see whether or not they’re operational in the organism. So far, we have found that it is probably be able to produce Histidine, which has been proven by experimental colleagues to regulate its algicidal activity. However, our initial hypothesis had been that perhaps the bacterium kills the algae for Histidine, and this finding disproves that. We have also found that RLDK might be able to produce Cysteine, Niacin, and Riboflavin.

Discovering that this bacterium can produce these metabolites is just the beginning of understanding this organism. Using the metabolic models, other critical metabolites can be uncovered that can or cannot be produced, and more research will also give insight into the role of possible transporters in its membrane, as well as other features. This will help determine why RLDK is killing the algae and causing crashes in ponds where it is grown and harvested for biofuel production on an industrial scale.