Stilianos Louca Wins 2017 Science & SciLifeLab Prize for Young Scientists

A sample of marine microorganisms off the Pacific coast of Canada. | Stilianos Louca

Stilianos Louca has been named the 2017 Grand Prize winner of the Science & SciLifeLab Prize for Young Scientists, for work that makes sense of how microbial communities and geophysical processes influence the Earth's chemistry.

Louca's winning essay, "Probing the metabolism of microorganisms," which will appear in the December 8 issue of Science, highlights how his team's research efforts have important implications for various microbial-driven industrial processes, such as bioremediation of acid mine drainage, where a stable microbial community can help clean up polluted areas. His work also classifies more than 30,000 ocean microorganisms by how they consume energy, which could help researchers learn more about the production of organic matter in the oceans and its impact on the global carbon cycle.

"Tracking how microbes gobble up energy in the ocean and the interplay between environment and species interactions, as Dr. Louca has done in his work, will provide new approaches to bioremediation and a greater understanding of ocean chemistry," said Barbara Jasny, deputy editor of Science.

The prize recognizes promising early-career scientists who conduct groundbreaking life-science research and includes a grand-prize award of $30,000. It is supported by Science for Life Laboratory, a coordinated effort among four universities in Sweden and the journal Science, which is published by AAAS.

While microorganisms are known to fuel many of the biochemical changes that occur in ecosystems like the ocean, soil and human gut, researchers' understanding of their specific role has remained a mystery, in part because of the microbes' diversity. "Until 15 years ago, it was very hard to even identify most microorganisms in an environment, let alone determine what they may be doing metabolically," Louca said. "The vast majority of bacteria, for example, have never been cultured in the lab. The use of advanced [genetic] sequencing technology is now changing that, by allowing us to not only identify microorganisms, but also to estimate what metabolic processes they may be involved in."

Louca, a postdoctoral researcher at the Biodiversity Research Centre in Vancouver, predicted that similar environments would promote the growth and activity of similar energy-consuming cellular pathways among the microbes, even if the species using each pathway were different.

To test his hypothesis, he sequenced the DNA of entire microbial communities living in the foliage of bromeliad plants. He estimated the species composition of the microbial communities as well as the abundances of various energy pathways encoded in the microbial genomes, discovering that each bromeliad hosted a distinct community of microbial species.

Interestingly, these different microbial communities showed a striking similarity in terms of the abundances of genes involved in various pathways, including those with a role in fermentation, oxygen respiration and carbon fixation. This observation suggested that environmental constraints largely determined the growth of these pathways and had much less influence over which species happened to represent each pathway in a bromeliad.

To further validate these findings, Louca analyzed DNA sequencing data from an international ocean microbiome survey in combination with oceanographic data from satellite imaging. He classified more than 30,000 marine microorganisms into various metabolic groups based on the pathways that they use to gain energy, distinguishing between organisms that consume the potent greenhouse gas methane and organisms that eat sulfide, a toxic gas found in parts of the ocean, for example.

Louca pioneered an approach that allowed him to quickly pinpoint the metabolic functions of microorganisms based on their species. He developed a mathematical model suggesting biological interactions among organisms may be the reason that related species do not always share the same metabolism. He then used this platform to study how microbial communities change over space or time, due to processes that are separate from selection for specific metabolic functions.

Using computer simulations, mathematical modeling and statistical methods, Louca showed that environmental conditions strongly predicted the distribution of metabolic groups across the world's oceans. In contrast, environmental conditions poorly predicted which microbial species were associated with each metabolic group in each location.

This was a perplexing finding, because ocean currents can transport microorganisms across large distances, and yet the same pathways were represented by different organisms in different locations of the ocean. Louca discovered that additional mechanisms, based on interactions between species, seem to influence which species get to perform these pathways in each location.

"Many environmentally relevant processes mediated by microorganisms may remain stable even if the specific microbial taxa involved in them change over time. For example, in biofuel-producing bioreactors it may be nearly impossible to control which microorganisms will be dominant at any moment in time, however the overall performance of the bioreactor may be controlled much more easily," Louca said.

Louca is interested in pursuing several follow up experiments in ecosystems beyond the ocean. "If we want to model biogeochemical processes in an ecosystem, or the chemical transitions over Earth's history, it seems that we can go to great lengths by simply focusing on genes and the metabolic pathways that they encode, rather than considering each microbial species," he said.

Louca will receive the award for his research in the field of Ecology and Environment in Stockholm, Sweden, on December 11, during an award ceremony and dinner at the Grand Hôtel in the Hall of Mirrors, which hosted the first Nobel Prize ceremony in 1901.

"SciLifeLab is a proud sponsor and co-organizer of this young scientist award. As a national hub for molecular biosciences in Sweden, we cover both health and environmental applications of biosciences. The innovative science performed and elegantly described by this year's winners provide inspiration to our community of young scientists and we are happy to see Science magazine propagate this globally," said SciLifeLab Director Olli Kallioniemi.

The Science & SciLifeLab Prize for Young Scientists is an annual prize aimed at rewarding young scientists at an early stage of their careers. The categories for this annual award are Cell and Molecular Biology, Ecology and Environment, Genomics and Proteomics, and Translational Medicine. Applicants for the prize submitted a 1000-word essay that was judged by an independent editorial team organized by the journal Science. Its content was evaluated on the quality of research and the applicants' ability to articulate how their work would contribute to the scientific field.

The 2017 award also recognizes three category winners, who will receive $10,000 and have their essays published in the journal Science online:

Jared Mayers : For his essay on translational medicine, "Metabolic markers as cancer clues." Mayers is a resident in internal medicine at Brigham and Women's Hospital in Boston, working toward a career that balances basic science research with clinical practice. After completing his undergraduate degree at Williams College, he earned his M.D. from Harvard Medical School and his Ph.D. in biology from the Massachusetts Institute of Technology. His research interests center on identifying and understanding the mechanisms driving whole body metabolic alterations and tissue interactions in early disease states. Outside of the hospital and lab, he enjoys running and spending time with his family.

Kelley Harris : For her essay on genomics and proteomics, "Reading the genome like a history book." Harris studied mathematics as an undergraduate at Harvard and transitioned into genomics during a postgraduate year at the Wellcome Trust Sanger Institute. She then earned a Ph.D. in mathematics at UC Berkeley, with a designated emphasis in computational biology, where she continued building statistical methods that describe how genome sequences evolve. In January 2018, Harris will finish her postdoctoral fellowship at Stanford and become an assistant professor of genome sciences at the University of Washington.

Mijo Simunovic : For his essay on cell and molecular biology, "Biology and physics rendezvous at the membrane." Simunovic earned his Ph.D. in theoretical chemistry from The University of Chicago, and his Ph.D. in experimental physics from University of Paris. In his scientific work, he pursues complex biological problems that are fundamentally driven by physics. At The Rockefeller University as a Junior Fellow of the Simons Society, he uses stem cells to build experimental models of the human embryo, aimed at elucidating the earliest events in human development. Simunovic is passionate about teaching, having served as a teaching consultant at the University of Chicago and and an instructor for undergraduate bio-physics courses in Chicago and New York.

SciLifeLab, or Science for Life Laboratory, is a national hub for molecular biosciences in Sweden, with the mission to provide enabling infrastructures for life science research, create a collaborative research community and translate research towards society benefits. SciLifeLab was established in 2010 and comprises more than 1,200 researchers and personnel.