Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates
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 famil...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-01-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/1/186 |
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| author | Fons A. de Vogel Cathleen Schlundt Robert E. Stote Jo Ann Ratto Linda A. Amaral-Zettler |
| author_facet | Fons A. de Vogel Cathleen Schlundt Robert E. Stote Jo Ann Ratto Linda A. Amaral-Zettler |
| author_sort | Fons A. de Vogel |
| collection | DOAJ |
| description | 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 <i>Bacillaceae</i>, <i>Rhodobacteraceae</i>, and <i>Vibrionaceae</i> 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. |
| first_indexed | 2024-03-09T04:35:21Z |
| format | Article |
| id | doaj.art-da9d98e2bc3a4ceebc60575fd47cc470 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T04:35:21Z |
| publishDate | 2021-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-da9d98e2bc3a4ceebc60575fd47cc4702023-12-03T13:29:46ZengMDPI AGMicroorganisms2076-26072021-01-019118610.3390/microorganisms9010186Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade PolyhydroxyalkanoatesFons A. de Vogel0Cathleen Schlundt1Robert E. Stote2Jo Ann Ratto3Linda A. Amaral-Zettler4Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, The NetherlandsJosephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USAU.S. Army Combat Capabilities Development Command Soldier Center, 10 General Greene Avenue, Natick, MA 01760, USAU.S. Army Combat Capabilities Development Command Soldier Center, 10 General Greene Avenue, Natick, MA 01760, USADepartment of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, The NetherlandsBiodegradable 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 <i>Bacillaceae</i>, <i>Rhodobacteraceae</i>, and <i>Vibrionaceae</i> 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.https://www.mdpi.com/2076-2607/9/1/186biodegradation standard test methodsplastic biodegradationpolyhydroxyalkanoate (PHA) cyclePHA depolymerasescomparative genomicsplastisphere |
| spellingShingle | Fons A. de Vogel Cathleen Schlundt Robert E. Stote Jo Ann Ratto Linda A. Amaral-Zettler Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates Microorganisms biodegradation standard test methods plastic biodegradation polyhydroxyalkanoate (PHA) cycle PHA depolymerases comparative genomics plastisphere |
| title | Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates |
| title_full | Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates |
| title_fullStr | Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates |
| title_full_unstemmed | Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates |
| title_short | Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates |
| title_sort | comparative genomics of marine bacteria from a historically defined plastic biodegradation consortium with the capacity to biodegrade polyhydroxyalkanoates |
| topic | biodegradation standard test methods plastic biodegradation polyhydroxyalkanoate (PHA) cycle PHA depolymerases comparative genomics plastisphere |
| url | https://www.mdpi.com/2076-2607/9/1/186 |
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