Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates

Fons A de Vogel; Cathleen Schlundt; Robert E Stote; Jo Ann Ratto; Linda A Amaral-Zettler

doi:10.3390/microorganisms9010186

Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates

Microorganisms. 2021 Jan 16;9(1):186. doi: 10.3390/microorganisms9010186.

Authors

Fons A de Vogel^{1

2}, Cathleen Schlundt³, Robert E Stote⁴, Jo Ann Ratto⁴, Linda A Amaral-Zettler^{1

3

5}

Affiliations

¹ Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, The Netherlands.
² Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.115, 3508 TC Utrecht, The Netherlands.
³ Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
⁴ U.S. Army Combat Capabilities Development Command Soldier Center, 10 General Greene Avenue, Natick, MA 01760, USA.
⁵ Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, The Netherlands.

Abstract

Biodegradable and compostable plastics are getting more attention as the environmental impacts of fossil-fuel-based plastics are revealed. Microbes can consume these plastics and biodegrade them within weeks to months under the proper conditions. The biobased polyhydroxyalkanoate (PHA) polymer family is an attractive alternative due to its physicochemical properties and biodegradability in soil, aquatic, and composting environments. Standard test methods are available for biodegradation that employ either natural inocula or defined communities, the latter being preferred for standardization and comparability. The original marine biodegradation standard test method ASTM D6691 employed such a defined consortium for testing PHA biodegradation. However, the taxonomic composition and metabolic potential of this consortium have never been confirmed using DNA sequencing technologies. To this end, we revived available members of this consortium and determined their phylogenetic placement, genomic sequence content, and metabolic potential. The revived members belonged to the Bacillaceae, Rhodobacteraceae, and Vibrionaceae families. Using a comparative genomics approach, we found all the necessary enzymes for both PHA production and utilization in most of the members. In a clearing-zone assay, three isolates also showed extracellular depolymerase activity. However, we did not find classical PHA depolymerases, but identified two potentially new extracellular depolymerases that resemble triacylglycerol lipases.

Keywords: PHA depolymerases; Plastisphere; biodegradation standard test methods; comparative genomics; plastic biodegradation; polyhydroxyalkanoate (PHA) cycle.