Author Profile
Initial Publication Date: April 16, 2023

Using Ocean Plastic Research to Increase Student Engagement and Persistence in Biology

Ana Maria Barral, National University
Rachel E. Simmons, National University (co-PI)
Jeff Bowman, Scripps Institution of Oceanography
Emelia DeForce, Scripps Institution of Oceanography
Huda Makhluf, National University
Michael Maxwell, National University
Location: California

Abstract

The Improving Undergraduate STEM Education: Hispanic-Serving Institutions Program (HSI Program) aims to enhance undergraduate STEM education and build capacity at HSIs. Projects supported by the HSI Program will also generate new knowledge on how to achieve these aims. This project at National University will advance the aims of the HSI Program by adding research experiences to undergraduate biology courses. Through a collaboration with the Scripps Institution of Oceanography, this project incorporates course-based undergraduate research (CURE) biology courses for biology majors and for non-majors. The research topics focuses on plastic pollution in the ocean, particularly the microbial populations attached to floating plastic. The CURE is modular and can be adapted for undergraduate courses of different levels. In addition, a virtual adaptation was implemented during the Covid-19 epidemic lockdown phase. A version of the CURE designed for microbiology courses uses the established Tiny Earth methodology to isolate antibiotic producing bacteria from plastic debris.

Student Goals

  1. Explain the causes of plastic pollution in the ocean, types of plastic, and the types of microbes attaching to them. This goal is applicable for students in all courses.
  2. Isolate and characterize bacterial colonies with antibiotic activity from ocean plastic samples. This goal is more specific for microbiology students. This goal is an adaptation of the Tiny Earth CURE.
  3. Describe microbial populations using bioinformatics analysis (for 400-level courses)

Research Goals

  1. Explore and describe the bacterial populations attaching to different plastic types in coastal ocean waters.
  2. Isolate and identify bacteria with physiological properties such as antibiotic production and plastic degradation capacity from ocean plastic.

Context

This NSF-funded CURE started in 2018 and has involved a total of 442 students by December 2022. These included 122 students in in-person courses, and 320 in online courses due to the Covid pandemic. The CURE has modules adaptable to different courses, such as general biology lab (non-majors and majors, 100-level), microbiology (200-level), and molecular biology (400-level). The CURE was designed for National University's accelerated schedule, with the 100-level courses taking place over 4 weeks and the 200/400 level courses over 8 weeks. They can be easily adapted as modules in longer courses. No previous knowledge is required.

Target Audience: Introductory, Major, Non-major, Upper Division
CURE Duration:A few class periods

CURE Design

The central theme of the CURE is plastic pollution of the ocean and specifically microbes attaching to plastic. The topic is introduced before the laboratory activities using videos and in-class discussions. The topic of experimental design is discussed as part of the sample deployment/collection activities. Techniques needed for students to succeed are introduced at the same time or in parallel activities. Example streaking is introduced before students need to isolate their producers (microbiology). CURE data are used to introduce/practice activities (ex. 16S PCR/Blast). Existing data can provide materials for students with no/limited results.

Students' family and friends, who learn indirectly from students and potentially change behaviors (ex. use less single-use plastic) due to this research. Professional organizations and institutions interested in further studying promising bacterial candidates. Community organizations involved in plastic cleanups and other plastic pollution control measures.

Core Competencies: Analyzing and interpreting data, Asking questions (for science) and defining problems (for engineering), Planning and carrying out investigations, Using mathematics and computational thinking
Nature of Research:Basic Research, Field Research, Informatics/Computational Research, Wet Lab/Bench Research

Tasks that Align Student and Research Goals

Research Goals →
Student Goals ↓
Research Goal 1: Explore and describe the bacterial populations attaching to different plastic types in coastal ocean waters.
Research Goal 2: Isolate and identify bacteria with physiological properties such as antibiotic production and plastic degradation capacity from ocean plastic.

Student Goal 1: Explain the causes of plastic pollution in the ocean, types of plastic, and the types of microbes attaching to them. This goal is applicable for students in all courses.

Students watch a documentary (Into the gyre) that describes research activities around ocean plastic pollution directly preceding the activities of the CURE.
Students culture bacteria from ocean plastic samples, and depending on the course level characterize them (microbiology stainings, 16S PCR, bioinformatics analysis)

Students culture and describe bacteria from ocean plastic.
Students discuss processes to identify colonies with potential practical uses.


Student Goal 2: Isolate and characterize bacterial colonies with antibiotic activity from ocean plastic samples. This goal is more specific for microbiology students. This goal is an adaptation of the Tiny Earth CURE.

Students culture and describe bacteria from ocean plastic.

Students culture bacteria from ocean plastic.
Students test for antibiotic production .
Students isolate and characterize the producers.


Student Goal 3: Describe microbial populations using bioinformatics analysis (for 400-level courses)

Students extract DNA from plastic samples.
Students analyze metagenomic sequencing data.

Students identify potential antibiotic producing bacteria using microbiology techniques and 16S PCR (microbiology courses)
Students analyze DNA sequencing data (whole genome sequences or metagenomic sequences) for activities such as antibiotic production and enzymes involved in plastic degradation (400 level courses).


Instructional Materials

A good introduction to the theme of the CURE are videos such as the Into the gyre documentary and websites such as that of The SEA program.

Examples of materials have been uploaded. Lectures, handouts, and instructional files depend on the courses, but can be provided. A public Youtube playlist includes some of our instructional videos together with other applicable videos.

Our CURE is directed at ocean plastic samples deployed and collected at a specific location, but it can be adapted to any plastic or even water samples. Resources/instrumentation correspond to standard biology courses, especially for non majors. Majors' courses and microbiology courses require a thermocycler and 16S Sanger sequencing. Upper level bioinformatics analysis require metagenomic sequencing/WGS sequencing and an analysis pipeline. This part of the CURE is the least developed and greatly depend on the Scripps Institution of Oceanography knowledge, although they share the analysis in their website: https://www.polarmicrobes.org/


Antibiotic producer instructions (Microsoft Word 2007 (.docx) 24kB Jan9 23)
Example syllabus nonmajors (Microsoft Word 2007 (.docx) 37kB Jan9 23)

Assessment

Student survey (Microsoft Word 2007 (.docx) 37kB Jan9 23)
Final poster instructions (Microsoft Word 2007 (.docx) 24kB Jan9 23)
Quiz on background video (Microsoft Word 2007 (.docx) 96kB Jan9 23)

Instructional Staffing

An essential feature of the CURE is direct interaction with research scientists. This can be done informally during the field trip experience, or in a more organized way as panels (in-person) or zoom meeting (virtual). Students repeatedly mentioned the opportunity to interact with professors and graduate students as one of the highlights of the experience.

Author Experience

Ana Maria Barral, National University

My motivation was two-fold: knowledge of previous research on ocean plastic microbes (Drs. DeForce and Bowman) and experience of the transformative effect of CUREs in my teaching (been involved in GEP and SWI/Tiny Earth). In addition, the global issue of plastic pollution is relevant and very engaging for students. The CURE itself is not complicated to set up and does not require specialized knowledge (except the bioinformatics part) and can be set up in different courses. The modular nature of the CURE was inspired by the flexibility of the Tiny Earth framework (of which I have been a participant since 2013).


Read full Instructor Story »

Advice for Implementation

I have taught the CURE multiple times and it has been a great experience. Most challenging is organizing the field trip experience, especially when timing is constrained. I recommend having backup samples in case students cannot come the day planned. Implementation for non majors general biology and microbiology is not too challenging. 16S PCR can be challenging if students do not get results. It is recommended to have extra sequences so they can learn how to analyze them (can be provided). We have not completed the metagenomics bioinformatic module yet due to multiple challenges with sequences, expertise, and pipeline. Note that the CURE can be done virtually. While students expressed they wished they could do the field trip in real life, surveys still showed positive effect of the experience.

Iteration

Due to our accelerated course schedule, this aspect of the CURE is mostly applicable for students in microbiology and molecular biology courses, which run in 8 weeks. As the course schedule includes long lab hours 2x and sometimes 3x week, there is time for troubleshooting and repeating. Most issues are related to contamination and PCR. Class sizes are relatively small (24 or less) and instructors oversee student work directly.

Using CURE Data

CURE results include:
- metagenomic sequencing data, which are handled and shared by SIO personnel
- 16S PCR data
- antibiotic producing bacterial colonies


The two latter are mostly explored further with undergraduate student researchers (either grant, internally, or FWS funded). Students present their data at national/local conferences - see for example these professional and student publications:

Resources

 

The following introduction to ocean plastic microbes are relevant for faculty:

  1. Andrady, A. L. (2015). Persistence of Plastic Litter in the Oceans. In Marine Anthropogenic Litter (pp. 57–72). Springer International Publishing. https://doi.org/10.1007/978-3-319-16510-3_3
  2. Ashar, M., Fraser, M. A., Li, J., Wang, C., Huang, W., Zhang, D., & Zhang, C. (2020). Interaction between microbial communities and various plastic types under different aquatic systems. Marine Environmental Research. https://doi.org/10.1016/j.marenvres.2020.105151
  3. Austin, H. P., Allen, M. D., Donohoe, B. S., Rorrer, N. A., Kearns, F. L., Silveira, R. L., Pollard, B. C., Dominick, G., Duman, R., Omari, K. E., Mykhaylyk, V., Wagner, A., Michener, W. E., Amore, A., Skaf, M. S., Crowley, M. F., Thorne, A. W., Johnson, C. W., Lee Woodcock, H., ... Beckham, G. T. (2018). Characterization and engineering of a plastic-degrading aromatic polyesterase. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1718804115
  4. Bryant, J. A., Clemente, T. M., Viviani, D. A., Fong, A. A., Thomas, K. A., Kemp, P., Karl, D. M., White, A. E., & DeLong, E. F. (2016). Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre. MSystems, 1(3), e00024-16. https://doi.org/10.1128/mSystems.00024-16
  5. Oberbeckmann, S., & Labrenz, M. (2020). Marine Microbial Assemblages on Microplastics: Diversity, Adaptation, and Role in Degradation. Annual Review of Marine Science, 12(1), 209–232. https://doi.org/10.1146/annurev-marine-010419-010633
  6. Pinto, M., Langer, T. M., Hüffer, T., Hofmann, T., & Herndl, G. J. (2019). The composition of bacterial communities associated with plastic biofilms differs between different polymers and stages of biofilm succession. PLOS ONE, 14(6), e0217165. https://doi.org/10.1371/journal.pone.0217165
  7. Wright, R. J., Erni-Cassola, G., Zadjelovic, V., Latva, M., & Christie-Oleza, J. A. (2020). Marine Plastic Debris: A New Surface for Microbial Colonization. Environmental Science & Technology. https://doi.org/10.1021/acs.est.0c02305
  8. Zettler, E. R., Mincer, T. J., & Amaral-Zettler, L. A. (2013). Life in the "plastisphere": Microbial communities on plastic marine debris. Environmental Science and Technology, 47, 7137–7146. https://doi.org/10.1021/es401288x
  9. Into the gyre documentary 
  10. Tiny Earth website

References for students include:

  1. Into the gyre documentary 
  2. Zettler, E. R., Mincer, T. J., & Amaral-Zettler, L. A. (2013). Life in the "plastisphere": Microbial communities on plastic marine debris. Environmental Science and Technology, 47, 7137–7146. https://doi.org/10.1021/es401288x

 




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