Abstract
The accumulation of petroleum-based plastic waste has become a major issue for the environment. A sustainable and biodegradable solution can be found in Polyhydroxyalkanoates (PHAs), a microbially produced biopolymer. An analysis of the global phylogenetic and ecological distribution of potential PHA producing bacteria and archaea was carried out by mining a global genome repository for PHA synthase (PhaC), a key enzyme involved in PHA biosynthesis. Bacteria from the phylum Actinobacteria were found to contain the PhaC Class II genotype which produces medium-chain length PHAs, a physiology until now only found within a few Pseudomonas species. Further, several PhaC genotypes were discovered within Thaumarchaeota, an archaeal phylum with poly-extremophiles and the ability to efficiently use CO2 as a carbon source, a significant ecological group which have thus far been little studied for PHA production. Bacterial and archaeal PhaC genotypes were also observed in high salinity and alkalinity conditions, as well as high-temperature geothermal ecosystems. These genome mining efforts uncovered previously unknown candidate taxa for biopolymer production, as well as microbes from environmental niches with properties that could potentially improve PHA production. This in silico study provides valuable insights into unique PHA producing candidates, supporting future bioprospecting efforts toward better targeted and relevant taxa to further enhance the diversity of exploitable PHA production systems.
Highlights
Plastic waste pollution has become a significant issue, with plastic waste as of 2015 amounting to 6,300 million metric tons predicted to almost double to 12,000 million metric tons by 2050, with only 9% being recycled, 12% disposed of through incineration and 79% of which is sent to landfill or ending up in the natural environment (Geyer et al, 2017)
Within the maximum-likelihood tree, the bacterial PhaC protein sequences appeared to form generally distinct groupings within their respective classes in the phylogenetic tree, with Class III PhaCs showing relatively high variation in phyla compared to those seen in Class I and II PhaCs (Figure 1A)
From this subset of genomes with PhaC genotypes, 2339 Class I, 529 Class II and 1,229 Class III PhaCs were identified according to the class of the matching query sequence used in the BLAST search (Supplementary Data 5)
Summary
Plastic waste pollution has become a significant issue, with plastic waste as of 2015 amounting to 6,300 million metric tons predicted to almost double to 12,000 million metric tons by 2050, with only 9% being recycled, 12% disposed of through incineration and 79% of which is sent to landfill or ending up in the natural environment (Geyer et al, 2017). The need for biodegradable and sustainable alternatives has, become critical with microbially produced polyhydroxyalkanoates (PHAs) showing significant promise as an economically viable replacement for petroleum-based plastic (Meereboer et al, 2020). The major advantage for waste management is that PHA products are 100% biodegradable (compostable bioplastics) in the land and ocean, leaving no lasting waste management footprint. As such these biopolymers are well suited as a “green” alternative to petroleum-based plastics by being both biodegradable and non-toxic (Dietrich et al, 2017). The carbon-based “feedstocks” used in the development of efficient microbial PHA production are derived from sustainable and low-cost sources: agricultural waste (starch, lignocellulose and animal carcasses), molasses, whey, waste oils and glycerol from the production of biodiesel (Cui et al, 2016)
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