Around the Pier: Scripps Student's Work Distinguishing Bacterial Species Honored

Scripps Institution of Oceanography at University of California San Diego graduate student Nastassia Patin is this year’s recipient of the Edward A. Frieman Prize for Excellence in Graduate Student Research.

The prize is awarded to one distinguished Scripps Oceanography graduate student who has excelled in his or her area of research, judged by a recent publication.

Patin’s paper, “Competitive strategies differentiate closely related species of marine actinobacteria,” was published in The International Society for Microbial Ecology Journal in August 2015.

The bacterial strains used for the study were isolated from marine sediment that was collected during a research cruise to the Yucatan Peninsula in summer 2012.

Using traditional methods for looking at bacterial species, the two Patin identified would have been considered one organism.

“Now, we have shown that they are, ecologically, quite distinct,” she said.

Patin said it’s easy to overlook the importance of the microdiversity that can be found within these small groups.

“Hopefully, these results will make people rethink how they analyze sequencing data and take a closer look at what they may be lumping together,” she said. “It’s kind of a microcosm of what people are always trying to look for in microbiology, which is how sequence data relates to ecology.”

The excitement of discovery in science is what draws Patin to the bench, or the field, each day.

“I’ve been interested in marine science for a long time, and became interested in microbiology as an undergrad. It has been a long journey to where I am now, with my interests changing and developing over the years,” said Patin.

Patin’s advisor, Scripps marine biologist Paul Jensen, is quick to commend her work ethic and unmistakable drive.

“This is all Nastassia’s work,” he said. “Nastassia designed all of the experiments, analyzed all of the data, and put it into a paper. This is her baby.”

“One of the holy grails of microbial ecology is to understand the relationships between molecular phylogeny and ecological function,” Jensen added. “What people don’t know is how to ask what groupings in phylogenetic trees are meaningful and distinct from each other.”

Patin has been able to zoom in and examine “the tips of those trees, to the finest resolution,” and find ecological differences, said Jensen. “If you apply what she found to everything we know about bacterial diversity, there are going to be orders of magnitude more groups of species than anyone suspected.”

These ecological discoveries will help scientists to better understand the mechanisms underlying bacterial production of natural products, for example, antibiotics and cytotoxic compounds that could be used in potential cancer treatment drugs.

“With all of the genome sequencing data we have now, we know that one strain has the potential to make 20 or 30 compounds based on sequence clusters in their genome,” said Patin, “yet only a few of these compounds are seen in the lab.”

One goal is to determine what natural triggers could incite bacteria to make these molecules, and to use that knowledge for drug development. Work like Patin’s is essential if this is what we hope to achieve. “A lot of [determining natural product triggers] lies in understanding the basic ecology of the whole microbial community and what reasons make them turn on those pathways.”

Patin was still shocked when she heard that she had been selected for the Frieman Prize. “Being at Scripps, I am surrounded by brilliant and productive students, so actually winning was a huge surprise. I am always so inspired by my fellow students here, so it’s an honor to be recognized among them.”

Patin will present a short talk about her paper at Scripps Day on June 10.

The award is named for Edward Frieman (1926-2013), the eighth director of Scripps Oceanography.  It was established in 1996 on Frieman’s 70^th birthday.

For more information on the Frieman Prize, or to see past winners, please visit: https://scripps.ucsd.edu/people/awards/edward-frieman-prize-excellence-graduate-student-research

­– Samantha Jones is a third-year biomedical sciences PhD student at the University of California San Diego.

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