How waste-eating bacteria digest complex carbons
New information could lead to bacteria-based platforms that recycle
plastic and plant waste

Date:
February 6, 2023
Source:
Northwestern University
Summary:
For the first time, researchers mapped the metabolic mechanisms
in a Comamonas bacterium that digests chemicals from plastic and
plant waste.

This new information could potentially lead to novel biotechnology
platforms that harness the bacteria to help recycle plastic waste.


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FULL STORY ==========================================================================
A common environmental bacterium, Comamonas testosteroni, could someday
become nature's plastic recycling center. While most bacteria prefer to
eat sugars, C.

testosteroni, instead, has a natural appetite for complex waste from
plants and plastics.


==========================================================================
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. testosteronican 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.

* RELATED_TOPICS
o Plants_&_Animals
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========================================================================== Story Source: Materials provided by Northwestern_University. Original
written by Amanda Morris. Note: Content may be edited for style and
length.


========================================================================== Journal Reference:
1. Rebecca A. Wilkes, Jacob Waldbauer, Austin Caroll, Manuel Nieto-
Domi'nguez, Darren J. Parker, Lichun Zhang, Adam M. Guss, Ludmilla
Aristilde. Complex regulation in a Comamonas platform for diverse
aromatic carbon metabolism. Nature Chemical Biology, 2023; DOI:
10.1038/ s41589-022-01237-7 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2023/02/230206130644.htm

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