Utilisation of nanopore sequencing for the discovery of novel plastic degrading enzymes in the environment

Environmental plastic pollution has led to microorganisms evolving to repurpose existing enzymatic mechanisms to utilise it as a carbon source. Such enzymes can be exploited and enhanced to generate enzymatic approaches to plastic degradation and polymerisation. This would allow plastics to be efficiently recycled, instead of down-cycling into lower grade products, allowing for a circular economy.

Although multiple enzymes able to degrade plastics such as polyethylene terephthalate (PET) have been discovered, development to allow industrial-scale deployment remains an important task. The CEI have developed a pipeline of protein engineering and large-scale production to allow such enzymes to be characterised, improved, and deployed. Our role is in the discovery of environmental organisms with novel mechanisms for degradation of a wide range of polymer substrates, which could inform enzymatic molecular engineering.

This project aims to trial a field-based approach for identification of putative plastic-degrading enzymes from the environment using Nanopore sequencing. An adaptive sampling approach will be used, comparing DNA sequences in real-time with an ever-increasing database of known plastic-degrading enzymes and precursors (e.g. cutinase), to enrich for sequencing of putative enzymes of interest. Field results will be compared with lab-based metagenomic sequencing to identify whether this approach could provide a method for screening prior to in-depth metagenomic sequencing.

There are many, as yet, undiscovered bacteria in the environment with the potential to break down plastics. The aim of this work is to develop a technique to find areas in the environment with high quantities of such bacteria. It is similar to using a metal detector to scan the land for gold, once treasure has been found then a concerted effort can be made to excavate that area. Similarly the technique proposed will be used to see which areas in the environment have high abundance of plastic degrading bacteria. The area with the highest amount can then be sampled for more in-depth analysis. The idea is that this will save time and money on expensive in depth tests, making finding plastic degrading bacteria easier - and less like looking for a needle in a hay-stack.