Metagenome-Assembled Genomes of Four Southern Ocean Archaea Harbor Multiple Genes Linked to Polyethylene Terephthalate and Polyhydroxybutyrate Plastic Degradation

ABSTRACT Here, we present four archaeal metagenome-assembled genomes (MAGs) (three Thaumarchaeota MAGs and one Thermoplasmatota MAG) from a polar upwelling zone in the Southern Ocean. These archaea harbor putative genes encoding enzymes such as polyethylene terephthalate (PET) hydrolases (PETases) and polyhydroxybutyrate (PHB) depolymerases, which are associated with microbial degradation of PET and PHB plastics.

N itrosopumilus and Marine Group (MG) II archaea affiliated with the phyla Thaumarchaeota and Thermoplasmatota, respectively, are widely distributed in shallow depths of the oceans (1)(2)(3)(4)(5). However, except for their capacity to sequester nitrogen and carbon in the oceans (1,6,7), their metabolic functions, including those linked to the biodegradation of plastic polymers, remain largely unclear. To reduce this knowledge deficit, we present four draft genomes of Nitrosopumilus and MG II archaea from the Southern Ocean. We further explore their metabolic potential linked to the degradation of polyethylene terephthalate (PET) and polyhydroxybutyrate (PHB).

FIG 1
Predicted plastic-polymer-degrading genes, with their orientations indicated, for contiguous sequences of archaeal MAGs from a polar upwelling zone in the Southern Ocean. The predicted genes are shown as arrows, indicating contigs in ascending order. The secondary structure and domains were compared to references in the PDB mmCIF70 and Pfam-A databases, respectively, using HHpred, which yielded high similarity of .95% probability. Labels above the arrows represent contig identification numbers, as specified in the protein-coding sequence from Prodigal. The numbers before and after the underscore represent the sequence position in the genome and the gene position within the contig, respectively. Labels below the arrows show the distance between the annotated start and end, equated as the gene size and represented by the relative length of each arrow.
Data availability. Raw sequence reads (SRA accession numbers SRR17224336 and SRR17224335) are available in the NCBI GenBank database under BioProject accession number PRJNA785751. The archaeal MAGs were assigned BioSample numbers SAMN23575727 to SAMN23575730, as well as GenBank accession numbers JAJPRB000000000, JAJPRC000000000, JAJPRD000000000, and JAJPRE000000000. The versions described in this paper are the first versions (JAJPRB010000000, JAJPRC010000000, JAJPRD010000000, and JAJPRE010000000).

ACKNOWLEDGMENTS
We thank the crew aboard the SA Agulhas II during the October-November 2019 SCALE Expedition.
We acknowledge financial support from the National Research Foundation of South Africa (NRF) (grants UID 110717, UID 129225, UID 136491, and UID 148867). We acknowledge funding received from the European Union Horizon 2020 research and innovation program as part of the AtlantECO project (grant agreement 862923). We also thank the Centre for High Performance Computing (Cape Town, South Africa) and the Centre for Bioinformatics and Computational Biology, University of Pretoria, for providing computational resources. We thank the Technology Innovation Agency (TIA) for supporting the project.