Microbiology Resource of the Month: Genomes of 5 PET-Plastic-Degrading Bacterial Isolates

June 26, 2019

Announcement: Draft Genome Sequences of Five Environmental Bacterial Isolates that Degrade PET Plastic.
Reference: Genomes of a bacterial consortia that degrades polyethylene terephthalate plastic.
Plastic accumulation is a huge environmental problem. The strong nature of the synthetic polymer means it can take a plastic water bottle hundreds of years to degrade. Fortunately, there may be a microbial solution.

Because bacteria adapt so quickly to their environment, scientists have been searching for (and finding) microbes with the metabolic capabilities of digesting plastic polymers. A team of scientists, including Rosa León-Zayas and Jay Mellies, recently published the genomes of a bacterial consortia that can degrade the plastic polymer polyethylene terephthalate. We asked them about their discovery.

What is polyethylene terephthalate plastic and where is it found?

Mellies: Polyethylene terephthalate (PET) plastic is a widely-used polyester, or high-molecular weight polymer that is made from terephthalic acid (TPA) and ethylene glycol (EG). The aromatic nature of the monomer TPA adds rigidity to the structure, making it difficult for bacteria to degrade.

Polyethylene terephthalate (PET) is resistant to degradation (L), leading to accumulation of materials such as plastic water bottles (R).
Polyethylene terephthalate (PET) is resistant to degradation (L), leading to accumulation of materials such as plastic water bottles (R).

Due to its durability, PET plastic is used in beverage containers, textiles, and packaging materials. Global production of PET fibers has continued to rise, and now exceeds 40 million tons each year. While nearly half of single-use PET beverage bottles are collected for recycling, the resultant polyester fibers are destined mostly to only one additional use, for example, to be made into carpets or clothing. The remaining PET plastic ends up in our environment, in landfills and in our oceans.

Where did you isolate these bacterial samples from?

Mellies: The bacterial strains were isolated from soil samples taken at East Beach, Galveston, Texas. Several Superfund Sites exist in the Houston area, and these sites are contaminated with many different types of pollutants from the oil industry.
We hypothesized that PET-degrading bacteria would exist in soils with high levels of hydrocarbon pollution, including aromatic hydrocarbons. Back in the lab, resuspended soil samples were grown on Rhodamine B agar plates to screen for lipase activity, an enzyme associated with PET degradation, where ester bond cleavage of the carbon source, olive oil, resulted in fluorescence in the presence of UV light.     

How did you determine these 5 bacterial strains work together?

Mellies: Our first clue that the bacteria work cooperatively came simply from the isolation, that for the 2 consortia, each contained a Pseudomonas sp. and a Bacillus sp. Consistently, it’s been shown that synergistic growth between bacteria depends on substrate complexity. The full consortium, containing all 5 strains, grew faster and reduced the weight of granular PET plastic to a greater extent after 6 weeks than either of the 2 consortia or any of the individual strains.   
Team member Cameron Roberts works in the lab to enrich bacterial consortia from the original isolates. Photo courtesy R. Leon-Zayas.
Team member Cameron Roberts works in the lab to enrich bacterial consortia from the original isolates. Photo courtesy R. Leon-Zayas.

How will you use the genomes in your research?

Leon-Zayas: The genomes will be mined to determine which genes are related to enzymes that may degrade complex hydrocarbon-like compounds. We are also using the sequences of the predicted proteins as guides for the biochemical and structural analysis of the secreted proteins from the consortium, which we plan to identify using mass spectrometry techniques. The genomes will be used to understand better the processes that are actively occurring within the bacteria when they are degrading PET, in tandem with transcriptomic analyses. 

What might these bacterial genomes reveal about how these species work together to degrade PET plastic?

Leon-Zayas: We were initially looking at the genomes in order to decipher the genes that encode for enzymes that could degrade PET, such as secreted lipases and esterases. Knowing that biofilm formation is necessary for efficient degradation, we will also search for associated genes, those encoding for flagellar motility, pili, exopolysaccharide biosynthesis, and quorum sensing. Additionally, by looking at the genome as a whole, we may be able to better constrain the mechanisms by which these bacteria degrade PET, and understand the syntrophic associations between the consortium members.
For example, we plan to establish the genetic basis for how the strains cooperate metabolically in the complete degradation of PET as a sole carbon and energy source.     

How will other scientists in the research community use this resource?

Leon-Zayas: These genomes could be a great resource for the larger scientific community in numerous ways. First, the genomes can be used as a comparative resource for other researchers who are studying organisms that have the potential also to degrade complex hydrocarbons. Second, the gene sequences could be used as a basis for synthetic biologists to develop technologies that aid in the degradation of plastics, or to exploit metabolic pathways to produce economically valuable byproducts. Finally, as plastic pollution can be considered a newly formed niche in our environment, the genomes may provide a model network for how bacteria degrade plastic in a syntrophic manner. 
For more information about plastic-degrading microorganisms, listen to scientific team member Morgan Vague present their findings at an October 2018 TEDx conference:

Author: Julie Wolf, Ph.D.

Julie Wolf, Ph.D.
Dr. Julie Wolf is in science communications at Indie Bio, and is a former ASM employee.