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.

Citation: Singleton SL, Davis EW, Arnold HK, Daniels AMY, Brander SM, Parsons RJ, Sharpton
TJ and Giovannoni SJ (2023) Identification of rare microbial colonizers of plastic materials
incubated in a coral reef environment. Front. Microbiol. 14:1259014. doi:
10.3389/fmicb.2023.1259014

Tyler Radniecki, CBEE

Born at the beginning of the COVID-19 pandemic, OSU’s wastewater surveillance efforts, led by Drs. Christine Kelly and Tyler Radniecki (both professors in the School of Chemical, Biological and Environmental Engineering), are still going strong.  On-going collaborative efforts include researching how wastewater surveillance can contribute to pandemic resilient cities (National Science Foundation), creating a national wastewater surveillance network for tracking antibiotic resistance genes, bacteria and pharmaceuticals (US Environmental Protection Agency), as well as monitoring state-wide community disease dynamics for SARS-CoV-2, influenza and RSV (Oregon Health Authority).  Additional current pilot-scale wastewater surveillance projects include monitoring for Candida auris and antibiotic resistance genes at health care facilities and identifying the presence of the markers for H5N1 influenza strain in Oregon communities. 

Throughout it all, Oregon State University’s Center of Quantitative Life Sciences (CQLS) has been a critical partner in these efforts.  CQLS wet lab staff assist with nucleic acid extractions from wastewater, library preparation and sequencing of wastewater samples.  Additionally, CQLS bioinformatics staff have helped develop and implement bioinformatic pipelines to identify wastewater surveillance targets and report relevant results to OHA and the Center for Disease Control and Prevention.  I can honestly say that every member of the CQLS staff has played a hand in our wastewater surveillance efforts. 

It is due to our collaborative efforts with CQLS that a lot of exciting advancements in wastewater surveillance have been made.  For instance, in collaboration with the OSU TRACE team, we demonstrated that wastewater surveillance is less biased than clinical surveillance at estimating COVID-19 prevalence in a community and that wastewater surveillance can identify COVID-19 hotspots and variant compositions of a community.  We have used wastewater sequence surveillance to identify COVID-19 variants in a community before they were identified in clinical samples.  Additionally, we demonstrated that wastewater sequence surveillance could accurately identify the COVID-19 variant relative abundances in the state, a critical finding as clinical COVID-19 sequencing has declined substantially from its peak.  Finally, we have used wastewater surveillance data to help evaluate the effectiveness of COVID-19 policies implemented by Oregon State University during the first two years for the pandemic.

As we continue to move forward with our wastewater surveillance work, the CQLS will remain a critical collaboration.  Together we are developing novel bioinformatic tools and pipelines to identify strains of RSV, norovirus and influenza.  Additionally, we are moving forward with new wastewater surveillance projects that will explore links between the environment and human pathogens as well as use our national wastewater surveillance network to monitor the spread climate sensitive diseases in the US.  While these endeavors remain challenging, I am grateful to have access to the CQLS to advance our goals.