Biosciences Area

‘Magic Pools’ Approach Accelerates Study of Novel Bacteria

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.

Microbial Metabolism in Real World Native Biocrusts

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.

Potato blight’s chemical attack mechanism explained

Jenny Mortimer, Deputy Vice President of the Feedstocks Division at the Joint BioEnergy Institute (JBEI) and Research Scientist with the Environmental Genomics and Systems Biology (EGSB) Division at the Biosciences Area.Jenny Mortimer, Deputy Vice President of the Feedstocks Division at the Joint BioEnergy Institute (JBEI) and Research Scientist with the Environmental Genomics and Systems Biology (EGSB) Division collaborated with a team of international researchers headed by scientists from the University of Tübingen to decipher the workings of the Cytolysin toxin, which is produced by some of the world’s most devastating crop diseases. The study shows that the Cytolysin binds to a class of glycosylated sphingolipid that Mortimer’s group studies. By producing plants which have modified forms of the sphingolipid, the toxin binding specificity could be determined. The study was published in Science today, December 14, and its findings may lead to ways of better protecting crops from such pathogens in the future. Read the Science news article about the study.

Dub-seq Wins 2017 R&D100 Award

A high-throughput, cost effective method for discovering gene function in microbes under various environmental conditions is among the winners of R&D Magazine’s 2017 R&D 100 Award. The technology, called Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), was developed by Adam Arkin, Adam Deutschbauer, Vivek Mutalik, and Pavel Novichkov of the Environmental Genomics and Systems Biology (EGSB) Division. Dub-seq … Read more »

Biosciences Researcher Helps Map the Microbiome of Everything

The Earth Microbiome Project is a massively collaborative effort to characterize all microbial life on the planet. Representing Berkeley Lab, Eric Dubinsky, a guest scientist working with Gary Andersen in EGSB, as well as Neslihan Tas and Shi Wang in the Climate & Ecosystems Science Division (EESA), were among the more than 300 scientists from 161 institutions worldwide to participate in the project. Dubinsky contributed 124 soil samples and metadata he collected from Hawaii. A meta-analysis of all the microbial community samples collected thus far was published Nov. 1 in Nature. This multi-scale reference database gives global context to DNA sequence data and provides a framework for incorporating data from future studies.

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