Global plastic production has increased exponentially since manufacturing commenced in the 1950’s, including polymer types infused with diverse additives and fillers. While the negative impacts of plastics are widely reported, particularly on marine vertebrates, impacts on microbial life remain poorly understood. Plastics impact microbiomes directly, exerting toxic effects, providing supplemental carbon sources and acting as rafts for microbial colonisation and dispersal. Indirect consequences include increased environmental shading, altered compositions of host communities and disruption of host organism or community health, hormone balances and immune responses. The isolation and application of plastic-degrading microbes are of substantial interest yet little evidence supports the microbial biodegradation of most high molecular weight synthetic polymers. Over 400 microbial species have been presumptively identified as capable of plastic degradation, but evidence for the degradation of highly prevalent polymers including polypropylene, nylon, polystyrene and polyvinyl chloride must be treated with caution; most studies fail to differentiate losses caused by the leaching or degradation of polymer monomers, additives or fillers. Even where polymer degradation is demonstrated, such as for polyethylene terephthalate, the ability of microorganisms to degrade more highly crystalline forms of the polymer used in commercial plastics appears limited. Microbiomes frequently work in conjunction with abiotic factors such as heat and light to impact the structural integrity of polymers and accessibility to enzymatic attack. Consequently, there remains much scope for extremophile microbiomes to be explored as a source of plastic-degrading enzymes and microorganisms. We propose a best-practice workflow for isolating and reporting plastic-degrading taxa from diverse environmental microbiomes, which should include multiple lines of evidence supporting changes in polymer structure, mass loss, and detection of presumed degradation products, along with confirmation of microbial strains and enzymes (and their associated genes) responsible for high molecular weight plastic polymer degradation. Such approaches are necessary for enzymatic degraders of high molecular weight plastic polymers to be differentiated from organisms only capable of degrading the more labile carbon within predominantly amorphous plastics, plastic monomers, additives or fillers.

The number of plastic-degrading microorganisms reported is rapidly increasing, making it possible to explore the conservation and distribution of presumed plastic-degrading traits across the diverse microbial tree of life. Putative degraders of conventional high-molecular-weight polymers, including polyamide, polystyrene, polyvinylchloride, and polypropylene, are spread widely across bacterial and fungal branches of the tree of life, although evidence for plastic degradation by a majority of these taxa appears limited. In contrast, we found strong degradation evidence for the synthetic polymer polylactic acid (PLA), and the microbial species related to its degradation are phylogenetically conserved among the bacterial family Pseudonocardiaceae. We collated data on genes and enzymes related to the degradation of all types of plastic to identify 16,170 putative plastic degradation orthologs by mining publicly available microbial genomes. The plastic with the largest number of putative orthologs, 10,969, was the natural polymer polyhydroxybutyrate (PHB), followed by the synthetic polymers polyethylene terephthalate (PET) and polycaprolactone (PCL), with 8,233 and 6,809 orthologs, respectively. These orthologous genes were discovered in the genomes of 6,000 microbial species, and most of them are as yet not identified as plastic degraders. Furthermore, all these species belong to 12 different microbial phyla, of which just 7 phyla have reported degraders to date. We have centralized information on reported plastic-degrading microorganisms within an interactive and updatable phylogenetic tree and database to confirm the global and phylogenetic diversity of putative plastic-degrading taxa and provide new insights into the evolution of microbial plastic-degrading capabilities and avenues for future discovery. IMPORTANCE We have collated the most complete database of microorganisms identified as being capable of degrading plastics to date. These data allow us to explore the phylogenetic distribution of these organisms and their enzymes, showing that traits for plastic degradation are predominantly not phylogenetically conserved. We found 16,170 putative plastic degradation orthologs in the genomes of 12 different phyla, which suggests a vast potential for the exploration of these traits in other taxa. Besides making the database available to the scientific community, we also created an interactive phylogenetic tree that can display all of the collated information, facilitating visualization and exploration of the data. Both the database and the tree are regularly updated to keep up with new scientific reports. We expect that our work will contribute to the field by increasing the understanding of the genetic diversity and evolution of microbial plastic-degrading traits.

The number of publications reporting putative plastic-degrading microbes and proteins is continuously increasing, necessitating the compilation of these data and the development of tools to facilitate their analysis. We developed the PlasticDB web application to address this need, which comprises a database of microorganisms and proteins reported to biodegrade plastics. Associated metadata, such as the techniques utilized to assess biodegradation, the environmental source of microbial isolate and presumed thermophilic traits are also reported. Proteins in the database are categorized according to the plastic type they are reported to degrade. Each protein structure has been predicted in silico and can be visualized or downloaded for further investigation. In addition to standard database functionalities, such as searching, filtering and retrieving database records, we implemented several analytical tools that accept inputs, including gene, genome, metagenome, transcriptomes, metatranscriptomes and taxa table data. Users can now analyze their datasets for the presence of putative plastic-degrading species and potential plastic-degrading proteins and pathways from those species. Database URL:http://plasticdb.org.

The ubiquity of plastic debris in marine environments raises the question, what impacts do plastics have on our marine microbiota? To investigate this, we applied bacterial 16S rRNA gene and fungal ITS2 region sequencing to identify changes in microbial biofilm community compositions on marine plastic, over time. We sampled biofilm on virgin linear low-density polyethylene (LLDPE), nylon-6 (PA) and glass after 2, 6 and 12 weeks of constant immersion in Te Whakaraupō-Lyttelton Harbour, Aotearoa-New Zealand. Of the prokaryotes, Proteobacteria and Bacteroidetes were predominant in all samples and Verrucomicrobiota were most abundant in mature biofilms. Microbial communities on the three substrate types were significantly distinct from those in the surrounding seawater, regardless of age, but not between attachment substrates. Bacterial communities occurring two weeks after immersion and fungal communities at six weeks were found to vary more among substrate types than at other times; however, no significant substrate-specific communities were identified overall. Taxa closely related to previously reported plastic-biodegrading species were found in very low abundance across all substrates, including on the glass slides. Our findings suggest that microorganisms do not selectively persist on the LLDPE or PA surfaces to gain significant direct metabolic benefit, instead using these plastics primarily as an attachment surface on which they form generalist biofilm communities.

Internationally, the environmental damage caused by the improper disposal of approximately 100 Mt of plastic waste per annum is of growing concern. Attempts to address this issue have generated many hundreds of scientific studies announcing the discovery of novel plastic-degrading microorganisms and their respective enzymes. On closer inspection, however, evidence remains sparse for the microbial degradation of most of the plastic polymers produced globally. We systematically surveyed the international literature to confirm how many microorganisms proposed to degrade plastics (n = 664) cause substantial (i.e.,  20% mass) losses of virgin polymer, rather than losses of plastic additives, filler, and/or shedding of polymer micro-fragments. Additionally, we noted where degradation was only demonstrated for artificially aged polymer since physicochemical ageing procedures increase the abundance of monomers and oligomers such that they may be degraded by microbial activity. Additionally, artificial ageing may introduce functional groups to the polymer backbone, creating more locations susceptible to microbial degradation than would otherwise occur in the environment. We identified multiple studies demonstrating the effective microbial degradation of heterochain plastic polymers such as polylactic acid, polycaprolactone and polyethylene terephthalate (i.e., polymers containing elements other than carbon in the backbone structure). However, in the literature, we find no evidence for the substantial degradation of unadulterated polyethylene, polypropylene, polystyrene or polyvinyl chloride, homochain polymers which represent the overwhelming majority of global plastics production. Current research demonstrates that the pre-treatment of plastics with elevated temperature or UV-light may speed physicochemical plastic degradation, with valuable applications for downstream microbial processing. However, evidence for the microbial degradation of most plastic polymers in current circulation is lacking. We outline simple criteria that should be met before announcing the microbial degradation of plastic polymers. We hope this may help to address largely unsubstantiated expectations that microorganisms can degrade many plastic polymers in situ.