The phylogenetic and global distribution of bacterial polyhydroxyalkanoate bioplastic‐degrading genes

Abstract

Polyhydroxyalkanoates (PHAs) are a family of microbially made polyesters commercialized as biodegradable plastics. PHA production rates are predicted to increase as concerns around environmental plastic contamination and limited fossil fuel resources have increased the importance of biodegradable and biobased plastic alternatives. Microbially produced PHA depolymerases are the key enzymes mediating PHA biodegradation, but only a few PHA depolymerases have been well-characterized and screens employing metagenomic sequence data are lacking. Here, we used 3078 metagenomes to analyse the distribution of PHA depolymerases in microbial communities from diverse aquatic, terrestrial and waste management systems. We significantly expand the recognized diversity of this protein family by screening 1914 Gb of sequence data and identifying 13 869 putative PHA depolymerases in 1295 metagenomes. Our results indicate that PHA depolymerases are unevenly distributed across environments. We predicted the highest frequency of PHA depolymerases in wastewater systems and the lowest in marine and thermal springs. In tandem, we screened 5290 metagenome-assembled genomes to describe the phylogenetic distribution of PHA depolymerases, which is substantially broader compared with current cultured representatives. The Proteobacteria and Bacteroidota are key lineages encoding PHA depolymerases, but PHA depolymerases were predicted from members of the Bdellovibrionota,

Demethylation of the Antibiotic Methylarsenite is Coupled to Denitrification in Anoxic Paddy Soil

“…curvata DSM 43183, Pseudomonas aeruginosa, and Cupriavidus metallidurans CH34) were gathered as the reference sequences. Putative arsI genes in microbial genomes were identified by using the reference sequences of ArsIs as queries in a BLASTp search with a threshold e < 1 × 10 –10 . The16S rRNA gene sequences of microbes which contain both arsI and narG or napA genes were predicted using barrnap with corresponding default parameters (bacteria or archaea mode) from their genomes.…”

New approaches for the characterization of plastic-associated microbial communities and the discovery of plastic-degrading microorganisms and enzymes

“…Homology-based screens using hidden markov models (HMMs) or basic local alignment search tools (BLAST) can identify putative PDEs in silico based on shared sequence similarity to known PDEs. Homology-based screens of large datasets composed of many metagenomes have identified the global distribution of PET-degrading enzymes [76] and PHA-degrading enzymes [77] . Alongside metagenomic screens, other studies have investigated nucleotide and protein data repositories to predict new PDEs.…”

“…Despite major advancements, large fractions of metagenomes are often unbinned [84] or occur in poor quality MAGs (<50% complete) [85] . In these cases, the taxonomic origin of a PDE-encoding scaffold can be predicted using computational tools such as MEGAN [86] , which has been used to predict new PET depolymerase- [76] and PHA depolymerase-encoding lineages [77] from unbinned metagenomic data.…”

Plastics degradation by hydrolytic enzymes: Theplastics‐activeenzymes database—PAZy

“…Because we mainly focus on synthetic fossil fuel‐based plastics, enzymes degrading bioplastics such polylactide (PLAs) or polyhydroxyalkanoate‐based polymers (PHAs) were excluded in this manuscript. For the latter and their global distribution, we refer to two excellent review articles on PHA hydrolases 49,50 …”