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Precision Metagenomics in a Low-End Computation Infrastructure: A Tool to Augment Research on Bioremediation of Plastic and Microplastic Contamination
Summary
This study used precision metagenomic analysis of landfill soil to identify microorganisms with plastic-degrading capabilities without needing to culture them in a lab. The approach identified three distinct microbial groups with potential to break down synthetic polymers, pointing toward biological strategies for managing plastic waste at landfill sites.
Technology for management of plastic wastes, through microbial degradation, is an urgent need of the hour. An alternative to the time and resource extensive culture dependent approach was explored, where a culture independent method using precision computation was adopted in a low-end computation infrastructure. A landfill metagenome data was retrieved from the NCBI SRA database and screened using MG-RAST, SqueezeMeta and ANVIO-7 for identification of potential plastic degraders. Three distinct micro-organisms, namely Streptomyces albidoflavus strain UYFA156, Saccharomonospora viridis strain DSM 43017, Streptomyces albidoflavus strain W68 have been confirmed to contain genes for PET Hydrolase, a protein perceived beneficial for the degradation of Poly (ethylene terephthalate). Enzymes involving degradation of other recalcitrant were also traced.Culture independent computational approaches necessitates immense computational resources. The technical challenges of using the high-performance pipelines with limited computational resources have been explored and mitigation strategies of the same have been discussed herewith.