In a teaspoon of soil, billions of microbes are hard at work recycling nutrients, pulling carbon out of the atmosphere, and even helping plants ward off disease. Or, according to Berkeley Kauffman, a senior engineering associate, only some of the microbes may be doing the work.
Scientists like Kauffman are working to figure out how to decode complex communities that we can’t see with the naked eye–making the system a functional genomics black box. Diving into an organism’s DNA and understanding how it relates to function and evolution can reveal important clues to what currently stands as a microscopic mystery. “It turns out that when you look even closer, you start seeing different levels of activity, or patterns of gene expression, in the different players,” he said.
Kauffman and the Joint Genome Institute’s (JGI) Micro-scale Applications group, led by Rex Malmstrom, are working to uncover which microbial species are metabolically active in an environmental sample. As in most enmeshed ecosystems, individual roles aren’t always crystal clear. By parsing things down to the microscopic level, researchers can begin to understand not only who’s there but what they’re up to in their community, which according to Kauffman, helps us define fundamental questions about what a particular species does and where it belongs on the tree of life.
“One of the focuses of my group, of my work, is to continue finding ways to open those black boxes,” Kauffman said.
From the Sea to Land
Born in North Carolina, Kauffman’s preferred first name, Berkeley, was inspired by his mother’s fondness for the beautiful birch trees of the northeast. He moved to San Francisco in his early teens and with Ocean Beach next to his high school, Kauffman grew up surfing and fishing and fell in love with all things marine.
After graduation, he headed to Puerto Rico to sail around the Caribbean. “Even though I get seasick on boats, I can’t stay away from them,” Kauffman admitted. “I’ve spent a lot of time on the water and it introduced me to science.”
Upon completing an undergraduate degree in marine science and a graduate degree in chemical oceanography, Kauffman pivoted towards biochemistry and eventually earned a doctoral degree from Tulane University in Louisiana. “I wanted to take a deeper dive into the human side of science,” he said. “But now, I get to bring it all together and answer ecological questions.”
For Kauffman and his family, the Bay Area always felt like home. So after he finished defending his dissertation in the south, Kauffman and his family headed west. He became familiar with Berkeley Lab during his studies and, in 2019, applied for a role with JGI. “I really liked the vibe of the group, it was a good balance of research and development with a bit of production work too,” he said.
Serving the User
Kauffman and his team process a variety of microbial community samples sourced from environments ranging from hot springs and forest soils to Antarctic lakes and plant roots. As a DOE Office of Science user facility, JGI works with scientists around the world who are interested in uncovering the genetic makeup of natural microbial communities. This information helps users begin to understand the microbial makeup of their samples and, with additional tools and techniques, unlock the secrets of their function.
When a sample arrives, Kauffman receives it and begins processing it. He and the team use an established protocol with an instrument called a flow cytometer to distinguish different components in a sample. This technique rapidly sorts through a liquified version of the sample to separate the cells based on specific characteristics like size, shape, or molecular makeup. The cells of interest are genetically sequenced and that information is returned to the user, helping them to identify which microbial species are present in their sample and which genes they carry.
“At the JGI, we have access to some of the best robots and technology that exists,” Kauffman said. “It’s really rewarding to be able to help our users who don’t have these resources get the data that they need to answer their research questions.”
Although understanding everything that’s present in a sample is important information, some users are more interested in which microbes are actively working versus not. So in addition to processing samples for individual identification, Kauffman also works to develop new techniques that help users explore untapped information in their samples.
Stable isotope probing, or SIP, is a newer technique used by Berekeley and his team to link functional information, like who’s doing what, to specific microbes. To do this, the researchers spike their environmental samples with food sources that contain a carbon molecule that is heavier than usual, known as a stable isotope. The microbes eating these specific food sources pick up the heavy carbon and incorporate it into their DNA, whereas those who are eating other things, don’t.
The DNA from these samples is extracted and sent to Kauffman who adds it to a super concentrated salt (cesium chloride) solution and spins it in a centrifuge at 44,000 RPM. After several days, a gradient forms where the heavier DNA sinks further down. Kauffman then removes and sequences the DNA of the active cells, and identifies who is actually working.
Kauffman and his team are cross-functionally trained and work fluidly across the processing of samples and development of new techniques. Right now, they’re collaborating as a group to optimize the SIP pipeline, which is already available to JGI users. “Developing new pipelines and products that we can offer our users will help us continue to be relevant into the future,” Kauffman said.
Bringing together his initial interests in marine science and ecology, Kauffman enjoys the chance to interact with the users to understand the specific goals of their project. With numerous tools already available and novel ideas constantly being tested out by the team, there are different directions that the analysis can take based on what the user is looking to achieve.
“It’s fun. Having worked in ecology labs where your most expensive tool is a 400-foot measuring tape, it’s really nice to be able to bring high level technology to help answer fundamental questions posed by ecologists, oceanographers, and soil scientists,” Kauffman said.
“I can only imagine today how useful this technology is going to be in helping these labs answer their questions in the future.”
Read other profiles in the Behind the Breakthroughs series.