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Peering into cells: The BSISB Program

A Creature From an Alkaline Spring Could Improve Biofuel Processing

Paul Preuss

A visiting scientist at Berkeley Lab tests double-threat microorganisms that can tolerate alkali and break down cellulose.

The only truly practical biofuels will be those made from abundant feedstocks like switchgrass, wheat straw, and other woody plants, whose cell walls consist of lignocellulose. After pretreatment to remove or reduce the lignin, the sugary remains of cellulose and hemicellulose are fermented by microorganisms to yield the biofuel.

“Each additional step in the process adds to the cost,” says Michael Cohen, a professor of biology at Sonoma State University who has discovered bacteria that could, with a little help from bioengineers at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), increase the efficiency and reduce the cost of biofuel processing. “The species of bacteria we’re testing may be able to combine two important steps into one.”

Cohen found the unique strain of bacteria, which can tolerate high alkalinity and degrade cellulose at the same time, in a strange and isolated part of California called The Cedars, located inland from Timber Cove in the state’s Outer Coast Range. The site’s deep canyons and rocky serpentine barrens, all but invisible from the area’s few public roads, create a biological island that is home to living things rarely seen elsewhere.

Although industrial pretreatments for reducing lignin range from steam explosions to acid baths (low pH), Cohen knew that some of the most effective technologies soak the feedstock not in acid but its opposite, highly alkaline liquid (high pH), which breaks up the woody matrix to release the digestible hydrocarbons, the sugars. Only then are the bugs – microbes – added to do the fermenting.

Read more: A Creature From an Alkaline Spring Could Improve Biofuel Processing

Synchrotron Infrared Unveils a Mysterious Microbial Community

Berkeley Lab scientists join an international collaboration to understand how archaea and bacteria work together deep in a cold sulfur spring

Paul Preuss

 

In the fall of 2010, Hoi-Ying Holman of the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) was approached by an international team researching a mysterious microbial community discovered deep in cold sulfur springs in southern Germany.

“They told me what they were doing and said, ‘We know what you contributed to the oil-spill research,’” recalls Holman, who heads the Chemical Ecology group in Berkeley Lab’s Earth Sciences Division. “They wondered if I could help them determine the biochemistry of their microbe samples.”

Holman had co-authored a report in Science about bacteria in the Gulf of Mexico that thrived on the Deepwater Horizon oil plume. Using infrared spectromicroscopy at the Berkeley Synchrotron Infrared Structural Biology (BSISB) facility, which she directs at the Advanced Light Source (ALS), Holman helped determine how the novel bug obtained energy by eating the spilled crude. No stranger to subsurface bioscience, Holman would soon add a new actor to her cast of remarkable microbes.

“Strings of pearls” (arrow and upper inset), whose pearls are up to three millimeters in diameter, were found where SM1 Euryarchaea live in close association with bacteria in the cold sulfidic streams of Germany’s Sippenauer Moor. Part of a pearl (lower inset) reveals colonies of microscopic spherical SM1 surrounded by filamentous bacteria.

Strings of pearls (arrow and upper inset), whose "pearls" are up to three millimeters in diameter, were found where SM1 Euryarchaea live in close association with bacteria in the cold sulfidic streams of Germany’s Sippenauer Moor. Part of a pearl (lower inset) reveals colonies of microscopic spherical SM1 surrounded by filamentous bacteria. (Moissl-Eichinger group. Click on image for best resolution.)

 

Read more: Synchrotron Infrared Unveils a Mysterious Microbial Community

Waves of Berkeley Lab Responders Deploy Omics to Track Deepwater Horizon Oil Spill Cleanup Microbes

In the aftermath of the Deepwater Horizon oil spill in the Gulf of Mexico two years ago, various strategies were deployed to prevent 4.9 million barrels of light crude oil from fouling the waters and reaching the shores. A team of Lawrence Berkeley National Laboratory (Berkeley Lab) researchers found that nature also played a role in the dispersal process as marine microbial communities responded to the oil plume that made its way from the wellhead at a depth of 5,000 feet to the surface of the water.

“There was oil on the surface and oil below, but no oil in between,” said microbial ecologist Terry Hazen, former head of the Ecology Department at Berkeley Lab and now holder of the University of Tennessee-Oak Ridge National Laboratory Governor’s Chair. In a report published a few months after the oil spill, Hazen’s team reported that the microbes in the water were partly responsible for the oil’s disappearance. While several studies have since confirmed that various microbes played a role in the dispersal of the oil in the Gulf, understanding the composition of the microbial community and the roles of its members has not fully achieved until now.

Foxtail millet

Photo: A surface slick in the Gulf of Mexico, taken ~1.5 km from the
Deepwater Horizon wellhead (Olivia Mason, LBNL).

To learn more about the microbial community’s response to the oil spill, researchers led by Berkeley Lab senior scientist Janet Jansson availed themselves of the expertise and resources at two of the Lab’s national user facilities, the U.S. Department of Energy Joint Genome Institute (DOE JGI) and the Advanced Light Source (ALS). The work done by the Lab’s disaster response team demonstrated Ernest Lawrence’s pioneering vision of team science. The findings, published in two separate articles, track a series of microbial species dominating the community in the waters at various time points to remove different fractions of the oil.

As reported in an article published online June 21, 2012 in The ISME Journal, the team describes using a combination of genomics techniques to study the way the microbes responded to the influx of oil. They focused on the community’s expressed functional information or metatranscriptome. In addition, they isolated single cells to identify the predominant microbial members in the deep ocean oil plume. Using the latter technique, they were able to assemble a draft genome of what they say is the first deep-sea, oil-eating bacterium from a single cell.

Read more: Waves of Berkeley Lab Responders Deploy Omics to Track Deepwater Horizon Oil Spill Cleanup Microbes

KWMRHoi-Ying Holman and Gregory Enns were interviewed by local radio station KWMR for their Hot Tech / Cool Science show on May 17, 2012.  They discussed the recent cellular studies observing protein phosphorylation.  You can listen to the broadcast here:

Berkeley Lab scientists demonstrate the promise of synchrotron infrared spectroscopy of living cells for medical applications

APRIL 30, 2012
Berkeley Lab scientists observed phosphorylation in living PC12 cells stimulated by nerve growth factor as they differentiated and sent out neuron-like neurites. The researchers imaged individual cells and simultaneously obtained absorption spectra using synchrotron radiation from the Advanced Light Source. Cells not stimulated with nerve growth factor did not differentiate and showed different infrared absorption spectra.

Berkeley Lab scientists observed phosphorylation in living PC12 cells stimulated by nerve growth factor as they differentiated and sent out neuron-like neurites. The researchers imaged individual cells and simultaneously obtained absorption spectra using synchrotron radiation from the Advanced Light Source. Cells not stimulated with nerve growth factor did not differentiate and showed different infrared absorption spectra.

Knowing how a living cell works means knowing how the chemistry inside the cell changes as the functions of the cell change. Protein phosphorylation, for example, controls everything from cell proliferation to differentiation to metabolism to signaling, and even programmed cell death (apoptosis), in cells from bacteria to humans. It’s a chemical process that has long been intensively studied, not least in hopes of treating or eliminating a wide range of diseases. But until now the close-up view – watching phosphorylation work at the molecular level as individual cells change over time – has been impossible without damaging the cells or interfering with the very processes that are being examined.

“To look into phosphorylation, researchers have labeled specific phosphorylated proteins with antibodies that carry fluorescent dyes,” says Hoi-Ying Holman of the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). “That gives you a great image, but you have to know exactly what to label before you can even begin.”

Holman and her coworkers worked with colleagues from the San Diego and Berkeley campuses of the University of California to develop a new technique for monitoring protein phosphorylation inside single living cells, tracking them over a week’s time as they underwent a series of major changes.

“Now we can follow cellular chemical changes without preconceived notions of what they might be,” says Holman, a pioneer in infrared (IR) studies of living cells who is director of the Berkeley Synchrotron Infrared Structural Biology program at Berkeley Lab’s Advanced Light Source (ALS) and head of the Chemical Ecology Research group in the Earth Sciences Division . “We’ve monitored unlabeled living cells by studying the nonperturbing absorption of a wide spectrum of bright synchrotron infrared radiation from the ALS.”

The researchers report their results in the American Chemical Society journal Analytical Chemistry.

Read more: Molecular Spectroscopy Tracks Living Mammalian Cells in Real Time as They Differentiate

 

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