Oceans of Microbiomes (2021-2022)

Background 

Microbes are core components of the ecology, biochemistry and geochemistry of all ecosystems, including plants and animals. Microbiomes can include thousands of members, each with the potential to interact with their environment and other organisms, often in unique ways, ultimately influencing the functioning of the system. 

While there is a growing understanding of the diversity of microbial communities, it remains difficult to disentangle the effects of different environment variables and processes in driving the composition and functioning of these communities.

Project Description 

This project team will develop a marine microbial model system to examine the interplay between the key temporal and spatial patterns that shape microbial communities and processes in complex environments. The project will use a marine system as a test-case for analysis and collaboration, with the broader goal of understanding the complexity, functioning and variability of microbiomes across a range of systems from marine to terrestrial to human and beyond.

The project team will collect and process microbiome diversity and metagenomic samples toward unraveling the complexity (and its drivers) of the marine microbiomes. Datasets for analyses will include amplicon libraries for assessments of the fine-scale diversity of marine microbiomes, and metagenomic data to determine what biochemical pathways are enriched for different communities. 

Team members will use modern tools of bioinformatic analyses and unpack the molecular mechanisms behind the patterns of diversity observed by the 2020-2021 team.  The team will use the Galaxy platform to advance the goals of the project and ultimately to transfer this technology and approach to Duke for further research and training purposes. 

Learn more about this project team by viewing the team's video.

Anticipated Outputs

Publication on marine microbiomes; data for future proposals 

Student Opportunities

Ideally, this project team will be comprised of 2 graduate students and 5 undergraduate students. The precise background of participants is open because the study of microbiomes spans many disciplines; however, this project will appeal to microbiologists, prehealth students, engineers, computational biologists, marine scientists and microbial ecologists, among others. 

An ideal makeup for the team would include one or more members with experience in R, Python and MATLAB programming languages, DNA/RNA extraction, PCR, field sampling and computational/data analysis. A general background and strong interest in microbial ecology is also welcomed. 

Team members will be exposed to a variety of environmental and molecular sciences. Students will gain tangible skills in environmental and sequence data analysis. Graduate students will be able to develop leadership skills, while also getting exposure and training in a cutting-edge field and molecular techniques. 

Each weekly meeting will be assigned a theme/discussion point. Each major component of the project will be assigned a lead student and contributor/team lead. All meetings will be Zoom-enabled so that both Durham and Beaufort members can contribute. Additional interactions will occur using Basecamp. Tasks will be divided among members on a consensus and mutually agreeable basis.

The Freiburg Galaxy Project, housed at the University of Freiburg in Germany, is an open source, web-based platform for data-intensive bioinformatic analyses. Depending on COVID restrictions, a limited number of team members will be trained in Germany (or a colleague will travel to Duke); otherwise, we will engage in an online training forum. 

During the optional summer component, 2 students may be selected to participate in hands-on research at DUML. This component of the project will be field/laboratory-based. We expect this summer component to last approximately 2 months (per student); it could occur simultaneously or be overlapping. Any 2-month block during late May through mid-August should be fine.

Junyao Gu will serve as project manager. 

Timing

Summer 2021 – Spring 2022 

  • Summer 2021 (optional): Finalize project goals and products; finalize timeline; create team charter; collect and process samples at Marine Lab; submit for sequencing; take part in weekly meetings; two-week visit to (or by) international collaborator
  • Fall 2021: Present on summer work; revise goals as needed; take part in weekly meetings; analyze environmental data and microbiome community data; analyze metagenomic data; give oral report on findings to date; draft report 
  • Spring 2022: Present results at Bass Connections Showcase; present to Duke Microbiome Center; submit manuscript

Crediting 

Academic credit available for fall and spring semesters; summer funding available

See earlier related team, Oceans of Microbiomes (2020-2021).

 

Image: Baltic blooms, by European Space Agency, licensed under CC BY-SA 2.0

Baltic blooms.

Team Leaders

  • Junyao Gu, Nicholas School of the Environment–Marine Science and Conservation–Ph.D. Student
  • Zachary Johnson, Sanford School of Public Policy

/graduate Team Members

  • Jessica Gronniger, Marine Sci & Conservation-PHD

/yfaculty/staff Team Members

  • James Clark, Nicholas School of the Environment-Environmental Sciences and Policy
  • Lawrence David, Graduate School
  • Claudia Gunsch, Pratt School of Engineering-Civil & Environmental Engineering
  • Dana Hunt, Nicholas School of the Environment-Marine Science and Conservation
  • John Rawls, School of Medicine-Molecular Genetics and Microbiology
  • Amy Schmid, Arts & Sciences-Biology

/zcommunity Team Members

  • Wolfgang Hess, University of Freiburg
  • Claudia Steglich, University of Freiburg