Cataloging the microbes that manage the health of river systems

Database provides details on river microbes in 90% of US continental watersheds.

The Science

In a recent Nature paper, researchers describe a dataset of microbial genomes sampled from rivers covering 90% of the watersheds in the continental United States. They also provided multiple access points to the information. The team harnessed a community-science program to collect samples from across the country to standardize the process. They noted this may be the first publicly available, river-focused microbial resource that provides information at multiple scales from genes to the community level.

The Impact

Rivers are transport systems, and their health is heavily reliant on the energy and nutrient flows that the microbes in these bodies of water help regulate. However, the microbes also interact with compounds like fertilizers and microplastics that might be added to the water along the way, impacting its quality and in turn affecting environmental and human health, energy production and agriculture. Understanding the compositions of river microbiomes—who the core microbes are and what they do—can help researchers develop predictive watershed scale models to manage river ecosystems. One application for the information is the development of river health diagnostic systems to monitor for and identify land use or water quality changes.

Summary

Rivers are key components of watershed ecosystems, where rain or snow drain into such bodies of water before heading out to bays and oceans. While river microbes are critical to monitoring and maintaining the health of these systems, these communities remain understudied. Through the JGI’s Community Science Program, Colorado State University researchers led a consortium to study river microbiomes. To understand the microbiology of watershed systems, they utilized over 160 river water samples collected through WHONDRS, a community science river sampling program at Pacific Northwest National Laboratory. The JGI sequenced over 1,000 metagenomes and established standardized sequencing protocols so that researchers could compare results across the varying sampling locations. Metatranscriptomic information was also generated.

The 3.8 trillion bases or Terabases of sequencing data, along with geochemical and geospatial measurements collected at each sampling site, were compiled into the Genome Resolved Open Watershed database (GROWdb). The team also provided several access points for these datasets. As part of a larger microbiome data integration hub, these datasets are searchable from the National Microbiome Data Collaborative. The published river microbiome datasets are also available through the DOE Systems Biology Knowledgebase, allowing researchers to immediately explore and reuse the data from the GROWdb for comparative analyses with their own data on the KBase platform, without having to download anything.

The collaborative consortium behind the GROWdb project demonstrates not only how researchers can successfully partner with DOE user facilities and resources on such large-scale multi-omic data efforts, but also how data integration and sharing could work across platforms.