Berkeley researchers discover thousands of new microbes, complete genomes

Roy Kaltschmidt/Berkeley Lab/Courtesy
SFA project - Microbial Observatory - Rifle, Colorado. Near the town of Rifle, Colorado, lies the primary field site for Phase I of the Subsurface Systems Scientific Focus Area 2.0 (SFA 2.0, sponsored by the DOE Office of Biological and Environmental Research—BER). The site’s history as a milling facility for ores rich in uranium and other metals (such as vanadium, selenium, and arsenic) has resulted in low but persistent levels of contamination within subsurface sediments and groundwater. With the support of BER, Earth Sciences Division and their collaborators from the DOE Joint Genome Institute have conducted major investigations at the Rifle site, to facilitate integrated, field-based subsurface biogeochemical and microbial genomics research relevant to uranium mobility to improve the predictive understanding of subsurface flow and transport relevant to metal and radionuclide contaminants.

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A study published Monday from campus and Lawrence Berkeley National Laboratory researchers uncovered new information about the genetic role of individual microbes and how they work to affect our climate.

Over the course of two years, the researchers studied microbes found onsite in a Colorado aquifer under Jillian Banfield, a campus professor and geochemist at the Berkeley Lab, publishing the study in Nature Communications. Brett Baker, a professor of microbial ecology at the University of Texas at Austin, called it “the most well-studied microbial community that’s ever been published.”

Together, the Berkeley team discovered 82 new groups of microbes and reconstructed more than 2,500 microbial genomes — sequences of genes that comprise all living things. Rather than traditional methods relying on small sequences of genes, the team used terabytes of DNA data to reconstruct entire genomes from end to end — allowing them to identify the role of individual microbes and establish the most influential microorganisms in the environment.

“Our knowledge of biology is very limited by certain groups we can grow in the lab,” Baker said. “Usually we only get a few genomes from the environment.”

Generally, microbes were thought to mostly perform environmental processes on their own, but the study reveals that they actually work in concert with each other through a symbiotic, parasitic network in processes such as the carbon cycle. This information, according to Banfield, is a new insight into the scale of microbial diversity.

This activity plays a crucial role in how microbes affect natural processes such as nitrogen fixation, which can control the amount of nitrous oxide, a greenhouse gas, released into the atmosphere from fertilizers. According to Adam Arkin, a campus bioengineering professor and member of the Berkeley Lab, the study is remarkable because it allows scientists to begin to infer the ‘“web of dependencies” among microbes and successfully begins to infer their functions using their genetic sequences.

“We find that the ecosystem’s jobs are distributed amongst the community,” Arkin said. “So we don’t have an explosion of greenhouse gas.”

The most important impact of the results, according to the paper’s first author, campus postdoctoral fellow Karthik Anantharaman, is in scientists’ understanding of how microbes interact with each other and affect climate change processes. Now that they understand how microbes keep a subsurface ecosystem running — namely, the soil in their aquifer — they can use their techniques to get a better understanding of the same microbes in different environments.

Additionally, he said, their research methods have laid the groundwork for scientists to study other microbial ecosystems such as the human digestive system.

“This doesn’t represent the unknown to me,” Anantharaman said. “This represents what we will know in the future.”

Contact Ashley Wong at [email protected] and follow her on Twitter at @wongalum.