26 October 2021

Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends

Biodegradation is a plausible route toward sustainable management of the millions of tons of plastic waste that have accumulated in terrestrial and marine environments. However, the global diversity of plastic-degrading enzymes remains poorly understood. Taking advantage of global environmental DNA sampling projects, here we constructed hidden Markov models from experimentally verified enzymes and mined ocean and soil metagenomes to assess the global potential of microorganisms to degrade plastics. By controlling for false positives using gut microbiome data, we compiled a catalogue of over 30,000 nonredundant 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 increases with depth as a response to plastic pollution and not merely taxonomic composition. By obtaining further pollution measurements, we observed 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.

IMPORTANCE Utilization of synthetic biology approaches to enhance current plastic degradation processes is of crucial importance, as natural plastic degradation processes are very slow. For instance, the predicted lifetime of a polyethylene terephthalate (PET) bottle under ambient conditions ranges from 16 to 48 years. Moreover, although there is still unexplored diversity in microbial communities, synergistic degradation of plastics by microorganisms holds great potential to revolutionize the management of global plastic waste. To this end, the methods and data on novel plastic-degrading enzymes presented here can help researchers by (i) providing further information about the taxonomic diversity of such enzymes as well as understanding of the mechanisms and steps involved in the biological breakdown of plastics, (ii) pointing toward the areas with increased availability of novel enzymes, and (iii) giving a basis for further application in industrial plastic waste biodegradation. Importantly, our findings provide evidence of a measurable effect of plastic pollution on the global microbial ecology.

INTRODUCTION

The demands for plastic production are increasing annually despite plastic waste pollution presenting a major global environmental problem. The majority of plastic products end up in landfills or dispersed in the environment (1), with inadequate waste management leading to an estimated 9 to 14 million metric tons of plastic entering the ocean every year (2) on top of the already accumulated ∼150 million metric tons (3). Even plastic additives such as phthalate compounds, frequently used as plasticizers, are a major source of concern due to their overuse in a variety of different products and adverse health effects (4, 5). While some thermoplastics (polyethylene [PE], polypropylene [PP], polyethylene terephthalate [PET], polyvinyl chloride [PVC], and phthalic acid [PA]) can be recycled, contaminated and composite plastics as well as thermosets (polyurethane [PU] and vinyl esters) cannot be remolded or heated after the initial forming (6, 7). Although the durability of man-made synthetic plastics facilitates their persistence in the environment, the synthetic polymers, like natural polymers (e.g., polysaccharides), can serve as a microbial carbon source (8–10). Microorganisms thus mediate a number of plastic biodegradation reactions across different environments (11–16), and even plastics such as PET (10) and PU (17) can be transformed and metabolized by microbial species. However, despite this widespread degradation capability, the true microbial potential for plastic degradation across different global habitats is not yet fully understood.

The isolation, identification, and characterization of microorganisms with plastic-degrading potential are frequently conducted from aquatic environments (18–21), waste disposal landfills (22–25), or places that are in direct contact with the plastic, such as plastic refineries (26–28). However, growing microorganisms outside their natural environments using conventional approaches is extremely challenging (29) and limits the amount of isolated species that can be cultured and studied to as little as 1% or lower (30). Studying single microbial isolates also limits our understanding of the microbial ecology of plastic degradation, where microbial consortia have been found to act synergistically, producing more enzymes and degrading plastics more efficiently than individual species (31, 32). Likewise, localized analyses from single locations hinder our understanding of the global environmental impact of plastic materials (33). On the other hand, with advances in environmental DNA sequencing and computational algorithms, metagenomic approaches enable the study of the taxonomic diversity and identification of the functional genetic potential of microbial communities in their natural habitats (33–35). For example, global ocean sampling revealed over 40 million mostly novel nonredundant genes from 35,000 species (35), whereas over 99% of the ∼160 million genes identified in global topsoil cannot be found in any previous microbial gene catalogue (34). This indicates that global microbiomes carry an enormous unexplored functional potential, with unculturable organisms as a source of many novel enzymes (30). Identification of such enzymes involved in the biological breakdown of plastics is an important first step toward a sustainable solution for plastic waste utilization (36, 37). However, despite the availability of experimentally determined protein sequence data on plastic-degrading enzymes (10, 38–43), no large-scale global analysis of the microbial plastic-degrading potential has yet been performed.

In the present study, we explored the global potential of microorganisms to degrade plastics. We compiled a data set of all known plastic-degrading enzymes with sequence-based experimental evidence and construct a library of hidden Markov models (HMMs), which we used to mine global metagenomic data sets covering a diverse collection of oceans, seas, and soil habitats (34, 35, 44, 45). By controlling for false positives using gut microbiome data (46), we compiled a catalogue of over 30,000 nonredundant enzyme homologues with the potential to degrade 10 different plastic types. Comparison of the ocean and soil fractions shows that the uncovered enzymatic potential likely reflects the major differences related to the composition of these two environments. Further analysis of metagenome-assembled genomes in the ocean reveals a significant enrichment of plastic-degrading enzymes within members of the classes Alphaproteobacteria and Gammaproteobacteria and supports the notion that enzyme abundance increases with sea depth as a response to plastic pollution and not merely taxonomic composition (47–50). By relating the identified enzymes to the respective habitats and measured environmental variables within the soil and ocean environments, we further showed that the abundance of the uncovered enzymes significantly correlates with both marine and country-specific plastic pollution measurements (51–56), suggesting that the earth's microbiome might already be adapting to current global plastic pollution trends.

RESULTS

The global microbiome harbors thousands of potential plastic-degrading enzymes.

To probe the potential for plastic degradation across the global microbiome, we compiled a data set of known enzymes with experimental evidence of plastic-modifying or -degrading activity from published studies (10, 38–42, 57–62) and databases (43), including a total of 95 sequenced plastic enzymes spanning 17 different plastic or additive types from 56 distinct microbial species (Fig. 1A; also, see “Enzyme data set and construction of HMMs” in Materials and Methods). The types of plastics (13 types) and plastic additives (4 types of phthalate-based compounds) (Fig. 1A; additives are marked with asterisks) spanned the main types of globally produced plastics that constitute the major fraction of global plastic waste (1), except for PP and PVC, for which no representatives could be found (Fig. S1A). To enable efficient searching across global metagenomic data sets, we built HMMs (63) by including the known homologous sequences from the UniProt TrEMBL database (64) (Fig. 1B; Fig. S1B and C). Briefly, we clustered the known enzymes to obtain representative sequences (95% sequence identity) (Fig. 1A) and used these to query the UniProt TrEMBL database and obtain an expanded data set of a total of 16,834 homologous enzyme sequences (E-value < 1e−10) (Fig. S1C). Each group of enzyme sequences at a given BLAST sequence identity cutoff ranging from 60% (65) to 90% was then clustered (95% sequence identity) to obtain groups of representative sequences that were used to construct a total of 1,201 HMMs (Fig. 1A; Fig. S1; see “Enzyme data set and construction of HMMs” in Materials and Methods).