NSF EarthCube-funded Scientists Release Planet Microbe
Recently Published Study Details the Global Oceanographic Tool
The NSF-funded EarthCube initiative’s Planet Microbe contains thousands of samples collected from all five of Earth’s oceans and most seas.
August 17, 2020
By: Kimberly Mann Bruch
Because 70 percent of Earth is comprised of oceans, their changes have a great impact on our entire planet. Many oceanographic changes often go unnoticed for years, decades, and sometimes centuries; however, slight variances in sea microbes (microscopic organisms) can provide researchers with tremendous insight to long-term change.
To explain the collection, observation, and documentation of these smallest oceanographic organisms, National Science Foundation funded EarthCube researchers published Planet Microbe: A Platform for Marine Microbiology to Discover and Analyze Interconnected ‘Omics and Environmental Data in the July 31, 2020 database issue of Nucleic Acids Research Journal.
The journal article not only explains Planet Microbe, but also discusses how contextual information is fundamental to understanding the microbial genomic content of marine ecosystems. The project, which demonstrates a future direction in marine metagenomic research, delivers an automated system that enables scientists to ask new questions of existing data. In particular, virtual datasets can be used broadly by the geosciences community to refine global ecological models, to inform citizen science efforts and policy, and derive critical information on temporal and spatial data associated with ocean microbes.
“Our lab focuses on understanding the mechanisms that drive marine microbial interactions, and in particular the interplay between viruses and their hosts that drive ocean processes,” said Planet Microbe Principal Investigator Bonnie Hurwitz, associate professor of biosystems engineering at the University of Arizona. “We are also interested in delivering these analysis capabilities to scientists to ask their own questions for the diverse data we have collected and Planet Microbe allows us to connect datasets together through community-driven standards to positively impact earth system models for the future.”
“Our goal was to create a web-based platform for scientists to share environmental data sets from world-wide ocean research endeavors,” said Planet Microbe Principal Investigator Bonnie Hurwitz, associate professor of biosystems engineering at the University of Arizona. “Researchers collect water samples measuring an array of characteristics ranging from conductivity and temperature to depth and salinity. With Plant Microbe, scientists’ data sets can easily be uploaded and shared with one another.”
So far, Planet Microbe encompasses more than 2300 samples collected from multiple projects around the world. Most of the samples are from surface water, with 45 percent collected between zero and ten meters depth. In addition to a thorough search feature, Planet Microbe allows users - including scientists, educators, citizen scientists, and policy makers - to run computational tools on samples across systems. This provides findable, accessible, interoperable, and reusable (FAIR) data that allows for large-scale analyses across multiple studies.
“This project is a tremendous resource to researchers, policymakers, and citizen scientists. Previous generations were limited to data they themselves collected or summary data in publications. With Planet Microbe, anyone can find samples for their area of interest, with just a few clicks,” said EarthCube Office Principal Investigator Christine Kirkpatrick, division director of Research Data Services at the San Diego Supercomputer Center. “This creates new research and educational opportunities because this data has been made easy to reuse. It’s also exciting to see this leveraging and integrating other EarthCube resources, and NSF computation investments in XSEDE and CyVerse.”
This research was funded by NSF (OCE-163614 and CISE-1640775), Simons Foundation SCOPE (329108), Simons Foundation muSCOPE (481471), Gordon and Betty Moore Foundation (8751 and 3777).
EarthCube is a community-driven activity sponsored by the National Science Foundation to transform research in the academic geosciences community. EarthCube aims to create a well-connected environment to share data and knowledge in an open, transparent, and inclusive manner, thus accelerating our ability to better understand and predict the Earth’s systems. EarthCube membership is free and open to anyone in the Geosciences, as well as those building platforms to serve the Earth Sciences. The EarthCube Office is led by the San Diego Supercomputer Center (SDSC) on the UC San Diego campus.
Kimberly Mann Bruch, San Diego Supercomputer Center Communications, firstname.lastname@example.org
Lynne Schreiber, San Diego Supercomputer Center EarthCube Office, email@example.com
Planet Microbe: https://www.planetmicrobe.org/
San Diego Supercomputer Center: https://www.sdsc.edu/
UC San Diego: https://ucsd.edu/
National Science Foundation: https://www.nsf.gov/