UCSD Jacobs School of Engineering

New UC San Diego Study Discover Interactions Between Phototrophic Communities Are Highly Dynamic and Driven by Availability of Nutrients

Figure 1 Differential expression of metabolic pathways. Results obtained during the algal growth under monoculture and co-culture conditions. Upregulated and downregulated genes were determined using two-sided t -test, n  = 3, and a cut-off  P value of 0.05.

San Diego, Calif., Oct. 7, 2019 -- Light-driven microbial communities, otherwise known as phototrophic communities, are widespread throughout the environment. This group includes cyanobacteria and algae, microorganisms that obtain their energy through photosynthesis, and heterotrophic microorganisms that use organic carbon as food. 

Yet how these microbes interact with each other has been largely unknown. Are their interactions consistent, or do they change based on different variables? What makes one group’s relationship collaborative versus another group’s dynamic competitive? 

Researchers at University of California San Diego, along with collaborators from Johns Hopkins University and the National Renewable Energy Laboratory, are working closely to solve some of these unknowns through the integration of metatranscriptomics, metabolomics, and phenotyping with computational modeling.

Their latest study, published in Nature Microbiology, was led by senior author Dr. Karsten Zengler, professor of pediatrics and bioengineering at UC San Diego. 

The ultimate goal of the study is to better predict how microbial communities react to disruption of their diet and environment, and use that information to manipulate microbes for the benefit of human and environmental health. 

What the researchers discovered was that much of what was previously believed about microbial interactions was misleading — there is, in fact, a large amount of variability in their interplay. Many microbes are “unculturable,” meaning they can’t be grown as a single species in the laboratory. According to Zengler’s study, it now appears this could be in part because they require community interplay to thrive in the world around us.

Once thought that these relationships and interactions were “written in stone,” the team discovered that the interactions were highly dynamic and depended on a variety of factors including environmental stimuli and cell ratio. Another factor that surprised the team was that these interactions were highly strain dependent.

“This was quite shocking to see… tiny differences between strains had a huge effect on growth performance of the overall community, sometimes reverting nutrient exchanges” Dr. Zengler said. 

Testing their hypotheses in the lab using gene knockouts, where one of an organism's genes was made inoperative, the team saw changes in how the organisms interacted. A single gene change in one microbe could influence assembly and maintenance of the whole community. 

“This has implications on our understanding of dynamics in microbiomes as well as on culturability of microbes,” Dr. Zengler said. He is now looking forward to doing additional studies on other environments, including human skin, and exploring ways to manipulate microbiomes in the future.

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