Ed Davis, CQLS
In a collaboration between the Tom Sharpton and Steve Giovannoni labs in the microbiology department, graduate student Seb Singleton designed and performed a study to examine degradation of, and the communities that form biofilms on, plastics in the ocean. Plastic waste accumulation in marine environments is a growing problem that has global effects on the macro and micro scales. In order to understand the ecology surrounding plastic-colonizing bacteria in marine environments, Seb designed a 3 month-long study to examine the changes in biofilm communities as well as structural and chemical changes in the polymer surfaces on high density polyethylene (HDPE), low density polyethylene (LDPE), and polypropylene (PP). An overview of the study design is shown below in Figure 1 from the paper.
The CQLS, including sequencing using the MiSeq platform in the core lab, as well as bioinformatics consulting done by senior bioinformatics scientist Ed Davis, was integral to the successful outcome of this study. The study encountered several technical roadblocks that were overcome using novel analytical techniques that leveraged the CQLS compute infrastructure. Here is a brief summary of the findings and difficulties overcome:
- Initial Dominance: Common marine microbial families such as Alteromonadaceae, Marinomonadaceae, and Vibrionaceae were initially prevalent.
- Community Shift: A significant transition in microbial composition occurred between days 42 and 56, with Hyphomonadaceae and Rhodobacteraceae becoming more dominant. These community shifts also coincided with the passing of Tropical Storm Henri!
- Rare Taxa: 8,641 colonizing taxa (Amplicon Sequence Variants; ASVs) were identified in total, with 594 overall ASVs enriched on one or more polymer types vs. the glass control, and only 25 ASVs, including known hydrocarbon degraders, significantly enriched on specific plastics.
- Plastic types differ in the ‘rare’ taxa they recruit: Five were specifically enriched on HDPE, nine on LDPE, and eleven on PP.
- Taxonomic Assignment Difficulties: Of the 594 significant ASVs, many were unable to be classified to lower taxonomic levels using a classifier trained on the Silva database (i.e. Family and/or Genus level). An alternative classification scheme, called Cladal Taxonomic Annotation (CTA), provided additional taxonomic assignments to 171 (29%) of the significantly enriched ASVs. Most importantly, 8 of the 25 plastic-specific significantly enriched ASVs were better assigned after the CTA.
The shift in taxa over the study period are shown below in Figure 5 from the study:
Taxa enriched on one or more plastics throughout the study are shown below in Figure 7 from
the paper:
Degradation of plastics was confirmed using high resolution helium ion microscropy (HIM), and
relevant examples are shown below from Figure 4 of the paper:
This research highlights the complex interactions between microbes and plastic surfaces in
marine environments, offering insights into the ecological impact of plastic pollution.
