EGSB News

As the Arctic continues to warm at about twice the rate of the rest of the world, scientists expect its frozen soils—known as permafrost—to thaw, activating microbes capable of decomposing soil and releasing carbons and other nutrients to the atmosphere and water. Berkeley Lab scientists in the Earth and Environmental Systems Area (EESA), led by microbial ecologist Neslihan Taş, set out to learn more about how Arctic soil microbes can contribute to greenhouse gas emissions under a warming climate. Taş’s research team collaborated with Susannah Tringe, Deputy for User Programs at the Joint Genome Institute (JGI), to conduct their study, funded by the Department of Energy’s Office of Biological and Environmental Research (BER). The results were published in Nature Communications.

Several Berkeley Lab scientists will present talks at the 72nd annual meeting of the American Association for the Advancement of Science (AAAS), the world’s largest general scientific society, to be held February 15 through 19 in Austin, Texas. Among them are four representing the Biosciences Area: Mary Maxon, Blake Simmons, Trent Northen, and Susannah Tringe.

Though once thought to be “junk DNA,” enhancers are extremely important, regulating the expression of specific genes that ultimately determine a cell’s properties and functions. However, there are many more enhancers than genes and their relationship is unclear. A team of scientists in the Environmental Genomics & Systems Biology Division have turned their attention to this relationship and the overall importance of enhancers to development. By better linking the genomic complement of an organism with its expressed characteristics, their work offers new insights that further the growing field of systems biology, which seeks to gain a predictive understanding of living systems.

To characterize the functions of genes in newly discovered bacteria, microbiologists introduce mutations using mobile DNA snippets called transposons delivered via a vector. But finding an effective transposon mutagenesis system for a novel microorganism through trial and error can be a time-consuming and expensive endeavor.

To streamline the process, Environmental Genomics and Systems Biology (EGSB) Division researchers, led by Adam Deutschbauer and Adam Arkin, have developed a new technique to test hundreds of different transposon vector variants in parallel within what the investigators term “magic pools.”

The approach was detailed in mSystems, an open access journal from the American Society for Microbiology.

Biological soil crusts, or biocrusts, contain communities of microorganisms—including fungi, bacteria, and archaea—that dwell together within the uppermost millimeters of soil in arid lands. These microbes can exist for extended periods in a desiccated, dormant state, becoming metabolically active when it rains. Understanding how biocrust microbial communities adapt to their harsh environments could help shed light on the roles of soil microbes in the global carbon cycle. Berkeley Lab scientists led by Trent Northen’s group in Environmental Genomics and Systems Biology (EGSB) found that specific compounds are transformed by and strongly associated with specific bacteria in native biological soil crust. The researchers reported their findings in a paper published January 2 in Nature Communications.