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Science snapshots from Berkeley Lab

Learning methane-reducing tricks from bacteria and the launch of a microbiome catalog

DOE/Lawrence Berkeley National Laboratory

Research News

How to Reduce Greenhouse Gas? Tips from a Methane-Eating Microbe
Advanced X-ray techniques yield insights into a bacterial enzyme that turns methane gas into liquid fuel
By Aliyah Kovner

Scientists have determined the structure of a unique enzyme, produced by a species of methane-eating bacteria, that converts the greenhouse gas into methanol - a highly versatile liquid fuel and industrial product ingredient.

Their new study, published in the Journal of the American Chemical Society, is the first to report the structure of the enzyme, called soluble methane monooxygenase (sMMO), at room temperature in both its reduced and oxidized forms. This detailed structural information will help researchers design efficient catalysts for industrial methane to methanol conversion processes.

"We were able to reveal the structure of sMMO and see how the environment of the two iron atoms in the enzyme's active site changes and supports the catalysis of this challenging chemical reaction," said author Jan Kern, a Berkeley Lab bioscientist. The process "involves breaking a carbon-hydrogen bond and insertion of an oxygen - converting a hydrocarbon into an alcohol. Additionally, our results showed the value of using an X-ray free electron laser (XFEL) in situations where traditional crystallography is not possible, in this case due to the reactive metals within the center of the enzyme."

Studying such enzymes by traditional X-ray methods typically gives incorrect results because of radiation damage. By using XFEL, the researchers were able to get accurate structural information in the two oxidation states.

Bacteria that metabolize methane (methanotrophs) are found in soil and aquatic environments with little to no oxygen. In these anaerobic habitats, the bacteria play a critical role as carbon recyclers; they convert methane (CH4) into more useful molecules that they and other organisms depend on.

This research was a collaboration between scientists at Berkeley Lab, University of Minnesota, Stockholm University, SLAC, and the Diamond Light Source.


Uncovering Novel Genomes from Earth's Microbiomes
Genome resource expands known diversity of bacteria and archaea by 44%
By Massie Ballon

Despite advances in sequencing technologies and computational methods in the past decade, researchers have uncovered genomes for just a small fraction of Earth's microbial diversity. Because most microbes cannot be cultivated under laboratory conditions, their genomes can't be sequenced using traditional approaches. Identifying and characterizing the planet's microbial diversity is key to understanding the roles of microorganisms in regulating nutrient cycles, as well as gaining insights into potential applications they may have in a wide range of research fields.

Now, thanks to a massive project involving more than 200 scientists from the DOE Joint Genome Institute and DOE Systems Biology Knowledgebase (KBase), a repository of 52,515 microbial draft genomes generated from environmental samples around the world has been made public. This new resource, known as the Genomes from Earth's Microbiomes (GEM) catalog, expands the known diversity of bacteria and archaea by 44%.

"Using a technique called metagenome binning, we were able to reconstruct thousands of metagenome-assembled genomes (MAGs) directly from sequenced environmental samples without needing to cultivate the microbes in the lab," said Stephen Nayfach, a JGI scientist and first author of the study describing the GEM catalog published today in Nature Biotechnology. "What makes this study really stand out from previous efforts is the remarkable environmental diversity of the samples we analyzed," he added.

Metagenomics is the study of the microbial communities (microbiomes) in the environmental samples without needing to isolate individual organisms, using various methods for processing, sequencing and analysis.

Much of the data in the catalog had been generated from environmental samples sequenced by the JGI through the Community Science Program and was already available on the JGI's Integrated Microbial Genomes & Microbiomes (IMG/M) platform. But the team behind GEM wanted to make this data more organized and accessible to the international microbial community.

The large team worked to sort and label the vast pool of metagenomic data so that users could search the resulting catalog for features of interest - such as the presence of genes needed to produce interesting compounds - and predict how these unculturable microbes interact with the environment and other organisms.

"With this dataset I can see where every microbe is found, and how abundant it is. This is a great resource for the community that is going to facilitate many more studies," said co-author Kostas Konstantinidis, who is already using the catalog in his own research on how microbes respond to climate change.

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Founded in 1931 on the belief that the biggest scientific challenges are best addressed by teams, Lawrence Berkeley National Laboratory and its scientists have been recognized with 14 Nobel Prizes. Today, Berkeley Lab researchers develop sustainable energy and environmental solutions, create useful new materials, advance the frontiers of computing, and probe the mysteries of life, matter, and the universe. Scientists from around the world rely on the Lab's facilities for their own discovery science. Berkeley Lab is a multiprogram national laboratory, managed by the University of California for the U.S. Department of Energy's Office of Science.

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