Genome sequencing work illuminates microbial dark matter

The immense, invisible world of the earth’s microbial life is being illuminated by an extensive project to sequence the genomes of microbes at the single-cell level. The work is a major advancement both for scientists and for environmental engineers who rely on microbial processes to treat contaminants in the environment, according to Professor Wen-Tso Liu, co-author of a paper on the research published in the current issue of Nature.

Liu, a professor and Civil and Environmental Engineering Excellence Faculty Scholar at Illinois, is part of a team led by researchers from the U.S. Department of Energy Joint Genome Institute that included scientists from institutions in the U.S., Australia, Canada, Germany, and Greece.

Dispersed microbial sample from the terephthalate degrading reactor used in the MDM study.
Dispersed microbial sample from the terephthalate degrading reactor used in the MDM study.

The researchers applied single-cell genomics to target and sequence 201 previously uncultivated archaeal and bacterial cells from nine diverse habitats and belonging to 29 major, mostly uncharted branches of the tree of life, so-called “microbial dark matter.”

“Microbial dark matter refers to those things we don’t know in the microbial world,” Liu said. “As an example, we know a lot about animals—how to classify them—but we don’t know how to do that with microbes. This provides a really nice way to do that.”

The method the researchers developed of taking a single cell of a microbe, just 2-5 microns in size, extracting the genomic information and sequencing it is expected to have far-reaching applications for scientists, Liu said. From an engineering perspective, the work will help elucidate the biological processes engineers use in wastewater treatment, he said.

“This will open up a window for us to re-look at optimizing the processes and better treat the wastewater,” Liu said.

Liu’s part in the study involved the use of a terephthalic acid (TA)-degrading methanogenic bioreactor, the only one of its kind in the world, to study how microbes break down TA in wastewater.

One of the most synthesized chemicals in the world, TA is an important raw material for the manufacture of various plastic products, such as polyethylene terephthalate bottles, textile fibers, adhesive, coatings and packing materials. It gets into wastewater during production, and it is one of the most synthesized chemicals in the world.

The research findings yielded valuable information about the microbes’ metabolic processes in breaking down TA, and will contribute to better optimization of bioreactors that degrade TA and other environmental contaminants, Liu said.

The work, from establishing the bioreactor to sequencing microbial genomes, which has proceeded over a 10-year period, will continue with the goal of furthering our understanding of the multitude of microbes that inhabit our planet. Thus far, it has offered scientists and engineers a significant resource that will shape the study of microbial life and everything it influences for years to come, Liu said.

“Look at the galaxy. There are so many stars, and you don’t know anything about them,” Liu said. “Now imagine someone says, ‘I’ve explored them, and now I understand 10 percent of the stars.”

The paper, “Insights into the phylogeny and coding potential of microbial dark matter,” was published in the July 25 issue of Nature and is available online. This work was funded by the U.S. Department of Energy.

Contact: Wen-Tso Liu, Department of Civil and Environmental Engineering, 217/333-8442, [email protected]

Writer: Celeste Arbogast Bragorgos, director of communications, Department of Civil and Environmental Engineering, 217/333-6955.

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