Oceans of Microbiomes (2020-2021)


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 in order 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, but it is rooted in 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.

First, team members will examine historical data and take new measurements to develop an initial understanding of the variability of environmental parameters for the long-term sampling location and the surrounding areas. Next, the team will process, sequence and analyze data of microbiome communities from the samples collected. Data from these communities will be used to explore how the environment drives the broader composition of these communities as well as how specific members respond to environmental changes such as temperature). Finally, the team will analyze the metagenomic and metatranscriptomic data generated from the samples, with the goal of uncovering the molecular mechanisms responsible for community-level changes.

One of the leading platforms to analyze this type of vast and complex data is Galaxy. The Freiburg Galaxy Project is an open source, web-based platform for data-intensive bioinformatic analyses. The team will use this platform to advance the goals of this year’s project and ultimately to transfer this technology and approach to Duke for research and training purposes.

Anticipated Outputs

Publication on marine microbiomes; proposal for university training center in microbiome research and education


Fall 2020 – Spring 2021

  • Fall 2020: Analyze environmental data; develop sampling scheme; perform sampling/data collection; process environmental data; construct microbiome community libraries; perform initial analysis of environmental and microbiome community data
  • Spring 2021: Continue microbiome community/environment analyses; complete initial training in Galaxy; deliver final oral report; complete final written report


Image: 20140727--IMG_4406.jpg, by Ryan McMinds, licensed under CC BY 2.0


Team Leaders

  • Zackary Johnson, Nicholas School of the Environment-Marine Science and Conservation

/graduate Team Members

  • Jessica Gronniger, Marine Sci & Conservation-PHD
  • Junyao Gu, Marine Sci & Conservation-PHD

/undergraduate Team Members

  • Taylor Adams
  • Han Mu
  • Maya Suzuki
  • Cynthia Wang, Biomedical Engineering (BSE)

/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