Plastic-degrading potential across the global microbiome correlates with recent pollution trends

Abstract

Poor recycling has accumulated millions of tons of plastic waste in terrestrial and marine environments. While biodegradation is a plausible route towards sustainable management of plastic waste, the global diversity of plastic-degrading enzymes remains poorly understood. Taking advantage of global environmental DNA sampling projects, here we construct HMM models from experimentally-verified enzymes and mine ocean and soil metagenomes to assess the global potential of microorganisms to degrade plastics. By controlling for false positives using gut microbiome data, we compile a catalogue of over 30,000 non-redundant enzyme homologues with the potential to degrade 10 different plastic types. While differences between the ocean and soil microbiomes likely reflect the base compositions of these environments, we find that ocean enzyme abundance might increase with depth as a response to plastic pollution and not merely taxonomic composition. By obtaining further pollution measurements, we reveal that the abundance of the uncovered enzymes in both ocean and soil habitats significantly correlates with marine and country-specific plastic pollution trends. Our study thus uncovers the earth microbiome’s potential to degrade plastics, providing evidence of a measurable effect of plastic pollution on the global microbial ecology as well as a useful resource for further applied research.

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes

“…Although there is a growing number of MAG reconstruction pipelines ( 43–49 ), a simple comparison of studies that used differing methods for MAG generation revealed that metaGEM consistently recovers more high quality genomes per sample, both from gut microbiome ( 11–13 ) and ocean ( 50–52 ) metagenomes ( Supplementary Figure S3 ). Indeed, metaGEM has already been applied in one of our recent studies to interrogate the plastic-degrading potential of the global microbiome ( 53 ). Regarding tool selection for specific tasks such as short read quality filtering, assembly, binning, etc., there are a number of published stand-alone candidate tools to choose from in the literature.…”

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes

“…Although there is a growing number of MAG reconstruction pipelines [32][33][34][35][36][37][38] , a simple comparison of studies that used differing methods for MAG generation revealed that metaGEM consistently recovers more high quality genomes per sample, both from gut microbiome [11][12][13] and ocean [39][40][41] metagenomes (Supplementary figure 3). Indeed, metaGEM has already been applied in one of our recent studies to interrogate the plastic-degrading potential of the global microbiome 42 .…”

<em> </em>Current Research on Microbe-Plastic Interactions in the Marine Environment

“…Interestingly, the isolation and characterisation of aquatic plastic degraders are less frequent 239 , which is probably related to the extra challenge that aquatic environments, such as the oceans, represent (e.g., low nutrient concentration and temperature) compared with soil and compost. In soil and compost, high nutrient availability, humidity and temperature are often conditions in which microorganisms thrive, positively impacting any potential biodegradation processes 240 .…”