Soil microbes are source of plastic-degrading enzymes

Microplastic, in the form of polyethylene terephthalate (PET), is a significant pollutant in marine environments. “Mangrove ecosystems are particularly vulnerable to the accumulation of fossil-derived plastics,” says KAUST researcher Diego Javier Jiménez Avella. “These ecosystems are natural sinks, but they are also potentially promising reservoirs of novel lignocellulose- and plastic-transforming enzymes.”

Jiménez, a research scientist in Alexandre Rosado’s team, led an international project that showed adding lignocellulose in the form of rice husks to mangrove soils increased the likelihood of recovering potential PET-degrading enzymes such as PETases^[1].

The project began in 2021, when Jiménez initiated a study of the microbial transformation of plastics with his former research group at Universidad de los Andes (UniAndes) in Bogotá, Colombia. The team sought to understand how microbial communities derived from mangrove soils respond to inputs of microplastics, plant biomass and seawater.

Initially, the researchers tried to identify plastic-degrading microorganisms by adding PET particles. Because of the difficulty in degrading PET, they tried an alternative treatment, adding plant biomass rich in lignocellulose, which contains polymers with ester linkages, similar to those found in PET molecules.

Seawater was included as a strategy to increase the chances of finding PET-degrading capabilities by mixing marine- and terrestrial-derived microbial communities. Unexpectedly, this addition proved vital for the desiccation patterns and salinity gradients within the microcosm experiments.

“Without planning it, the incubation conditions created a gradient of desiccation and salinity — an unforeseen factor that ultimately proved crucial to our findings,” says Jiménez.

The project continued when Jiménez moved to KAUST to join Rosado’s team in 2023. María Fernanda Peña-Valencia, his master’s student at UniAndes, worked on genome analyses, which provided key insights into the functional potential of salt-tolerant microorganisms enriched during the microcosm experiments.

“These results helped us better understand how specific microbial groups adapt and thrive under the experimental conditions,” says Jiménez. “A real turning point came when we expanded our analysis to gene catalogs derived from the full metagenomic dataset.”

Using high-throughput metagenomic sequencing to identify the different microbial species, the team found that conditions of desiccation and increasing salinity favor salt-tolerant PETases. The gradual evaporation of seawater and associated increase in salinity acted as strong selective pressures, particularly in the lignocellulose treatment.

Surprisingly, they discovered a higher number of potential PETases in the lignocellulose treatments compared to those amended with PET particles themselves. The researchers identified putative salt-tolerant PETases belonging to a new family of enzymes and characterized them using AI-based tools and 3D structure comparisons.

The study identified potential PETases found in soil bacteria. These enzymes can remain active under extreme conditions such as high temperatures and low pH, which makes them particularly interesting for industrial applications, explains Rosado.

PET is the only plastic that has been enzymatically recycled at an industrial scale. Over the past few decades, research efforts have focused on screening and engineering PETases, aiming to identify variants that can operate efficiently in both environmental and industrial settings.

“We still need to identify efficient thermophilic and salt-tolerant PETases for the industrial biocatalysis of PET,” Rosado says.

“Our work suggests that disrupting microbiomes with polyester-rich substrates can be an effective pathway for the discovery of PETases that can be used as scaffolds for protein engineering and biotechnological applications,” he concludes.

In future, the researchers plan to produce the enzymes and test them directly on PET under industrial conditions. They aim to develop a cocktail of enzymes able to degrade PET under harsh conditions of high temperature and salinity.