Researchers identify potential microbes and genes that permanently impact chemicals

New study identifies microbes that potentially play important roles in breaking down harmful per- and polyfluoroalkyl chemicals (PFAS) – also known as forever chemicals – and identifies functional genes that may be involved in biological transformation of these compounds.

Although microorganisms are known to facilitate the transformation of PFAS, the key microorganisms and genes responsible for these processes remain largely unknown.

The article published in the Environmental science and technology The journal is pioneering the use of bioinformatics tools traditionally used in medical fields and applying them for the first time to the study of PFAS biotransformation.

“The goals are to help other researchers understand which microbes may impact the fate of PFAS in the environment and to develop microbial transformation technologies to treat these contaminants as we do other contaminants” , said Natalie Cápiro, assistant professor in the Department of Biological and Environmental Engineering at the University of California. College of Agriculture and Life Sciences and lead author of the study.

“Biological treatment of contaminants does not require much infrastructure, it is more economical and can be applied in hard-to-reach places,” Cápiro said. It's best used in areas that won't be developed soon, because microbes are slow compared to physicochemical methods, she explained.

“The study provides clues to upcoming scientists working in the field of PFAS biotransformation, to help them better understand what they are trying to target,” said Sheng Dong, a postdoctoral researcher in Cápiro’s lab and lead author of the article.

Other researchers conducting experimental work could now use this information to verify that some of these genes are associated with these transformation pathways, Dong said.

Scientists have previously documented environmental microbial communities capable of processing human-made PFAS chemicals, found in food packaging, water-resistant clothing, nonstick cookware, and foams that extinguish fuel-related fires.

Once they enter the environment, including water, they bioaccumulate in organisms and move up the food chain in increasing concentrations. They have been linked to reduced fertility, developmental problems in children, high cholesterol, and various cancers.

Currently, permanent chemicals can be removed from water using activated carbon filters and other sequestration treatment techniques. In soils, current technologies include physical methods such as high temperature thermal and excavation to remove these compounds from the environment. Some microbes can break the extremely strong carbon-fluorine bonds found in PFAS chemicals, which can then transform the compounds.

“These compounds are man-made and their analogues in nature are not as widespread and do not have the same complexity,” Cápiro said.

People started using PFAS chemicals less than 100 years ago. Since then, exposure to chemicals may have given microbes the opportunity to adapt and develop pathways to transform them.

In the study, researchers collected soil samples from contaminated sites where microbial communities had been exposed to the compounds for many decades.

First, Dong and colleagues used network analysis methods based on the relative abundance of microbial community members in samples, where PFAS biotransformation was observed, to determine relationships between microorganisms.

“We think that microbes work as a team, it’s not just one,” Dong said. “We looked for patterns and whether certain microbes were still present.” They also took into account distinct soils collected in different geographic locations and the presence of various PFAS compounds.

In a second part of the study, researchers used a metagenome prediction tool, based on marker gene sequencing, to explore potential functional genes (and the enzymes they express) that contribute to the biotransformation of PFAS . Marker gene sequencing targets a small portion of the genome unique to each microbial taxonomic group, and Dong and colleagues then applied bioinformatics approaches to predict the rest of the genome.

Co-authors include Peng-Fei Yan, a postdoctoral researcher in Cápiro's lab.