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Ocean microbes offer clues to environmental resilience

Researchers at the University of Colorado Boulder and Oak Ridge National Laboratory have developed a new way to identify genetic changes that help tiny oxygen-producing microbes survive in extreme environments. The findings outline a new experimental approach for learning how microbes and other types of cells, including human cells, respond and adapt to environmental stress.

Their research, in the Proceedings of the National Academy of Sciences, will also help scientists engineer faster-growing synthetic strains of microbes that could be used to develop new bio-derived fuels, chemicals and materials.

The multidisciplinary group of engineers and biochemists used a gene silencing system called CRISPR interference (CRISPRi) to turn down the activity of every gene in the genome of Synechococcus sp. PCC 7002, an ocean-dwelling cyanobacteria species. Cyanobacteria perform photosynthesis, much like plants.

"Because these organisms produce a large share of Earth's oxygen, understanding how they respond to a changing climate is critical," said Andrew Hren, a Ph.D. student in the Fox Group and the paper's first author.

The team explored how cyanobacteria responded to different light and temperature conditions found at various ocean depths. They discovered that making small changes in how certain genes are turned on or off can help the cells adapt better to extreme environmental conditions like heat, cold or drought.

"Our work shows how small genetic changes can yield large improvements in fitness when we push microbes to the edge of their comfort zone," said Jerome Fox, an associate professor of chemical and biological engineering at the University of Colorado Boulder and a co-lead author on the study with Carrie Eckert at ORNL, a former senior scientist fellow in the Renewable and Sustainable Energy Institute (RASEI).

"Our findings also highlight the value of using CRISPRi to turn the activity of genes down, but not off, as intermediate adjustments tended to provide the greatest survival advantage in extreme conditions."

The work was inspired by the late Jeff Cameron, an associate professor in the Department of Biochemistry and fellow at RASEI, Fox said.

"Jeff's enthusiasm for cyanobacteria was infectious," Fox added. "He taught us everything we know and served as a critical resource on experimental design."

The researchers plan to continue studying cyanobacteria to further understand how the microbes absorb light and convert it into energy to develop new technologies—such as engineered microbes that produce renewable chemicals and other useful products.