Bioprospecting for polyesterase activity relevant for PET degradation in marine Enterobacterales isolates

Denisse Galarza–Verkovitch; Onur Turak; Jutta Wiese; Tanja Rahn; Ute Hentschel; Erik Borchert; Denisse Galarza–Verkovitch; Onur Turak; Jutta Wiese; Tanja Rahn; Ute Hentschel; Erik Borchert

doi:10.3934/microbiol.2023027

AIMS Microbiology

2023, Volume 9, Issue 3: 518-539. doi: 10.3934/microbiol.2023027

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Bioprospecting for polyesterase activity relevant for PET degradation in marine Enterobacterales isolates

1.
GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
2.
Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany

Received: 22 March 2023 Revised: 24 May 2023 Accepted: 07 June 2023 Published: 15 June 2023

Plastics have quickly become an integral part of modern life. Due to excessive production and improper waste disposal, they are recognized as contaminants present in practically all habitat types. Although there are several polymers, polyethylene terephthalate (PET) is of particular concern due to its abundance in the environment. There is a need for a solution that is both cost-effective and ecologically friendly to address this pollutant. The use of microbial depolymerizing enzymes could offer a biological avenue for plastic degradation, though the full potential of these enzymes is yet to be uncovered. The purpose of this study was to use (1) plate-based screening methods to investigate the plastic degradation potential of marine bacteria from the order Enterobacterales collected from various organismal and environmental sources, and (2) perform genome-based analysis to identify polyesterases potentially related to PET degradation. 126 bacterial isolates were obtained from the strain collection of RD3, Research Unit Marine Symbioses-GEOMAR-and sequentially tested for esterase and polyesterase activity, in combination here referred to as PETase–like activity. The results show that members of the microbial families Alteromonadaceae, Shewanellaceae, and Vibrionaceae, derived from marine sponges and bryozoans, are the most promising candidates within the order Enterobacterales. Furthermore, 389 putative hydrolases from the α/β superfamily were identified in 23 analyzed genomes, of which 22 were sequenced for this study. Several candidates showed similarities with known PETases, indicating underlying enzymatic potential within the order Enterobacterales for PET degradation.
- marine bacteria,
- order Enterobacterales,
- PETase-like activity,
- sponges,
- bryozoans
Citation: Denisse Galarza–Verkovitch, Onur Turak, Jutta Wiese, Tanja Rahn, Ute Hentschel, Erik Borchert. Bioprospecting for polyesterase activity relevant for PET degradation in marine Enterobacterales isolates[J]. AIMS Microbiology, 2023, 9(3): 518-539. doi: 10.3934/microbiol.2023027

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Abstract

Plastics have quickly become an integral part of modern life. Due to excessive production and improper waste disposal, they are recognized as contaminants present in practically all habitat types. Although there are several polymers, polyethylene terephthalate (PET) is of particular concern due to its abundance in the environment. There is a need for a solution that is both cost-effective and ecologically friendly to address this pollutant. The use of microbial depolymerizing enzymes could offer a biological avenue for plastic degradation, though the full potential of these enzymes is yet to be uncovered. The purpose of this study was to use (1) plate-based screening methods to investigate the plastic degradation potential of marine bacteria from the order Enterobacterales collected from various organismal and environmental sources, and (2) perform genome-based analysis to identify polyesterases potentially related to PET degradation. 126 bacterial isolates were obtained from the strain collection of RD3, Research Unit Marine Symbioses-GEOMAR-and sequentially tested for esterase and polyesterase activity, in combination here referred to as PETase–like activity. The results show that members of the microbial families Alteromonadaceae, Shewanellaceae, and Vibrionaceae, derived from marine sponges and bryozoans, are the most promising candidates within the order Enterobacterales. Furthermore, 389 putative hydrolases from the α/β superfamily were identified in 23 analyzed genomes, of which 22 were sequenced for this study. Several candidates showed similarities with known PETases, indicating underlying enzymatic potential within the order Enterobacterales for PET degradation.

Acknowledgments

The here presented work was carried out as a master thesis project by Denisse Galarza–Verkovitch. Ute Hentschel and Erik Borchert acknowledge financial support from the BMBF funded project PLASTISEA (GA no.: 031B0867A). The authors are grateful to Leon X. Steiner for support with the MinION genome sequencing pipeline. The authors are grateful to Samantha Chase for language editing.

Conflict of interest

The authors declare no conflict of interest.

Author contributions

DGV: experiment performing, data analysis, figure and/or table preparation, manuscript writing; OT: experiment performing and data analysis; JW: data analysis, maintenance of strain collection; TR: figure and/or table preparation, uploaded genomic sequences; UH: supervised the project; EB: conceived and designed the experiments, experiment performing, figure and/or table preparation. All authors contributed and reviewed the different drafts of the manuscript and approved the final version.

Data availability

The sequenced genomes have been deposited under the BioProject ID PRJNA944971 at NCBI, the respective BioSample numbers are SAMN33769435 to SAMN33769414 and the accession numbers JARLUH000000000 to JARLVC000000000. 16S rRNA gene accession numbers are listed in supplementary material table S1.

Use of AI tools declaration

The authors declare they have not used Artificial Intelligence (AI) tools in the creation of this article.

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