In a new Northwestern University-led study, researchers have, for the first time, deciphered the metabolic mechanisms that enable C. testosteroni to digest the seemingly undigestible. This new information could potentially lead to novel biotechnology platforms that harness the bacteria to help recycle plastic waste.

The research will be published on Feb. 6 in the journal Nature Chemical Biology.

Comamonas species are found nearly everywhere — including in soils and sewage sludge. C. testosteroni first caught researchers’ attention with its natural ability to digest synthetic laundry detergents. After further analysis, scientists discovered that this natural bacterium also breaks down compounds from plastic and lignin (fibrous, woody waste from plants).

Although other researchers have worked to engineer bacteria that can breakdown plastic waste, Aristilde believes bacteria with natural abilities to digest plastics hold more promise for large-scale recycling applications.

“Soil bacteria provide an untapped, underexplored, naturally occurring resource of biochemical reactions that could be exploited to help us deal with the accumulating waste on our planet,” said Northwestern’s Ludmilla Aristilde. “We found that the metabolism of C. testosteroni is regulated on different levels, and those levels are integrated. The power of microbiology is amazing and could play an important role in establishing a circular economy.”

The study was led by Aristilde, an associate professor of civil and environmental engineering at Northwestern’s McCormick School of Engineering, and Ph.D. student Rebecca Wilkes, who is the paper’s first author. The study included collaborators from University of Chicago, Oak Ridge National Laboratory and Technical University of Denmark.

Kicking sugar

Most projects to engineer bacteria involve Escherichia Coli because it is the most well-studied bacterial model organism. But E. Coli, in its natural state, readily consumes various forms of sugar. As long as sugar is available, E. Coli will consume that — and leave the plastic chemicals behind.

“Engineering bacteria for different purposes is a laborious process,” Aristilde said. “It is important to note that C. testosteroni cannot use sugars, period. It has natural genetic limitations that prevent competition with sugars, making this bacterium an attractive platform.”

What C. testosteroni really wants, though, is a different source of carbon. And materials such as plastic and lignin contain compounds with a ring of tasty carbon atoms. While researchers have known that C. testosteroni can digest these compounds, Aristilde and her team wanted to know how.

“These are carbon compounds with complex bond chemistry,” Aristilde said. “Many bacteria have great difficulty breaking them apart.”

Combining different ‘omics’

To study how C. testosteroni degrades these complex forms of carbon, Aristilde and her team combined multiple forms of “omics”-based analyses: transcriptomics (study of RNA molecules); proteomics (study of proteins); metabolomics (study of metabolites); and fluxomics (study of metabolic reactions). Comprehensive “multi-omics” studies are massive undertakings that require a variety of different techniques. Aristilde leads one of few labs that carries out such comprehensive studies.

By examining the relationship among transcriptomics, proteomics, metabolomics and fluxomics, Aristilde and her team mapped the metabolic pathways that bacteria use to degrade plastic and lignin compounds into carbons for food. Ultimately, the team discovered that the bacteria first break down the ring of carbons in each compound. After breaking open the ring into a linear structure, the bacteria continue to degrade it into shorter fragments.

“We started with a plastic or lignin compound that has seven or eight carbons linked together through a core six-carbon circular shape forming the so-called benzene ring,” Aristilde explained. “Then, they break that apart into shorter chains that have three or four carbons. In the process, the bacteria feed those broken-down products into their natural metabolism, so they can make amino acids or DNA to help them grow.”

Upcycling plastic waste

Aristilde also discovered that C. testosteroni can direct carbon through different metabolic routes. These routes can lead to useful by-products that can be used for industrially relevant polymers such as plastics. Aristilde and her team are currently working on a project investigating the metabolism that triggers this polymer biosynthesis.

“These Comamonas species have the potential to make several polymers relevant to biotechnology,” Aristilde said. “This could lead to new platforms that generate plastic, decreasing our dependence on petroleum chemicals. One of my lab’s major goals is to use renewable resources, such as converting waste into plastic and recycling nutrients from wastes. Then, we won’t have to keep extracting petroleum chemicals to make plastics, for instance.”

Aristilde is a member of the Institute for Sustainability and Energy at Northwestern’s Program on Plastics, Ecosystems and Public Health.

“With ongoing waves of COVID-19, long COVID has created a serious public health burden. Our findings raise the possibility that adopting more healthy behaviors may reduce the risk of developing long COVID,” said Andrea Roberts, senior research scientist in the Department of Environmental Health and senior author of the study.

The study appears online February 6, 2023, in JAMA Internal Medicine.

It’s estimated that 8-23 million Americans suffer from long COVID, which is defined as having COVID-19 symptoms four weeks or more after initial SARS-CoV-2 infection. Symptoms can include fatigue, fever, and a variety of respiratory, heart, neurological, and digestive symptoms.

The researchers analyzed data from more than 32,000 female nurses in the Nurses’ Health Study II, who reported on lifestyle in 2015 and 2017 and reported history of SARS-CoV-2 infection from April 2020 to November 2021.

During that time, more than 1,900 participants contracted COVID-19. Among these, 44% developed long COVID. Compared to women without any healthy lifestyle factors, those with five or six had 49% lower risk of long COVID. Among the six lifestyle factors, maintaining a healthy body weight and getting adequate sleep (seven to nine hours daily) were the ones most strongly associated with lower risk of long COVID. The results also showed that, even among women who developed long COVID, those with a healthier pre-infection lifestyle had 30% lower risk of having symptoms that interfered with their daily life.

The authors noted that one possible explanation for the associations they observed is that, based on prior research, an unhealthy lifestyle is associated with increased risk of chronic inflammation and immune dysregulation, which have been linked with increased risk of long COVID.

“In the past decades, scientists have accumulated evidence that healthy lifestyle is good for overall health. However, in the U.S. for example, 70% of the population do not have a healthy body weight and 30% do not sleep enough. Findings from this study suggest that simple lifestyle changes, such as having adequate sleep, may be beneficial for the prevention of long COVID,” said lead author Siwen Wang, research fellow in the Department of Nutrition.

Other Harvard Chan School authors included Yanping Li, Yiyang Yue, Changzhen Yuan, Jorge Chavarro, and Shilpa Bhupathiraju.

Support for the study came from NIH NICHD grant 3R01HD094725-02S1. Other support includes grants U01HL145386, R24ES028521, U01 CA176726, R01 CA67262, and R01 HD057368 from the NIH, the Dean’s Fund for Scientific Advancement Acceleration Award from Harvard Chan School, and Massachusetts Consortium on Pathogen Readiness Evergrande COVID-19 Response Fund Award.

“Arctic sea ice decline is among the most obvious evidence of global warming from the past several decades,” said Pengfei Zhang, assistant research professor of meteorology and atmospheric science at Penn State and lead author of the study. “Despite temperatures in the Arctic being well below freezing, sea ice decline in winter is still very significant. And our research shows atmospheric rivers are one factor in understanding why.”

Atmospheric rivers carry large amounts of water vapor in narrow, ribbon-like storm systems that can stretch for a thousand miles and produce extreme rainfall and flooding when they make landfall. These storms regularly impact midlatitude coastal regions like California, where atmospheric river events in January, for example, dropped 11 inches of rain.

Using satellite observations and climate model simulations, the scientists found these storms are increasingly reaching the Arctic — particularly the Barents and Kara seas off the northern coasts of Norway and Russia — during the winter ice-growing season. They reported their findings Monday, Feb. 6, in the journal Nature Climate Change.

“We often think that Arctic sea ice decline is a gradual process due to gradual forcings like global warming,” said L. Ruby Leung, Battelle Fellow at Pacific Northwest National Laboratory, and a co-author. “This study is important in that it finds sea ice decline is due to episodic extreme weather events — atmospheric rivers, which have occurred more frequently in recent decades partly due to global warming.”

Warm moisture carried by these storms increases downward longwave radiation, or heat emitted back to Earth from the atmosphere, and produces rain, both of which can melt the thin, fragile ice cover regrowing during the winter months.

Using satellite remote sensing images, the scientists observed sea ice retreat almost immediately following atmospheric river storms and saw the retreat persisted for up to 10 days. Because of this melting and because the storms are becoming more common, atmospheric rivers are slowing down seasonal sea-ice recovery in the Arctic, the scientists said.

“When this kind of moisture transport happens in the Arctic, the effect is not only the amount of rain or snow that falls from it, but also the powerful melting effect on the ice,” said Mingfang Ting, a professor at Lamont-Doherty Earth Observatory, Columbia University and a co-author. “This is important since we are losing Arctic sea ice fast in the past few decades that brought many unwanted consequences such as Arctic warming, erosion of Arctic coastlines, disturbance to global weather patterns and disruption to the Arctic communities and ecosystems.”

The loss of Arctic sea ice has broad implications, the scientists said. Open waters may enable new, more direct shipping routes but also trigger geopolitical concerns between countries. Additionally, freshwater melting into the salty ocean may impact oceanic circulations patterns that stabilize global temperatures.

“Those factors make this study especially important from a science perspective, but also from social and security perspectives, said Laifang Li, assistant professor of meteorology and atmospheric science at Penn State and a co-author. “Sea ice melting has a big impact for the climate system and for society, and our study finds the Arctic is an open system and that climate change is way more complicated than temperature change alone can explain.”

Using large-ensemble climate models, the scientists determined that human-induced warming has increased the rate of atmospheric river storms in the Arctic. But they also found that one major mode of natural climate variabilities — the so-called Interdecadal Pacific Oscillation — also contribute to atmospheric river changes.

“This study, together with other work that noted the presence of atmospheric rivers in the tropics, highlights that atmospheric rivers represent a global phenomenon,” said Bin Guan, Earth systems scientist at the University of California, Los Angeles and Jet Propulsion Laboratory, California Institute of Technology. “Since they were discovered relatively recently — in the 1990s, and even more recently in terms of recognizing their societal impacts — atmospheric rivers provide an opportunity for potentially coordinated research and applications globally, that is, with today’s computational and technological capabilities.”

Also contributing to this research was Gang Chen, professor at the University of California, Los Angeles.

Researchers involved on this project received support from the National Science Foundation, NASA and the Department of Energy.