Bringing together researchers worldwide to unlock the secrets of river ecosystems through the GROWdb.
Jan 24, 2025

Community Highlight: Mikayla Borton

I’m Mikayla Borton (MB) (she/her), co-PI of the Microbial Ecosystems Lab at Colorado  State University. My passion lies in unraveling how microbes shape ecosystems, from riverbeds to wetlands, and how we can harness this knowledge to address global challenges. Recently, I led the development of the Genome Resolved Open Watersheds database (GROWdb), a functional microbiome catalog crowdsourced from North American rivers.

Mikayla Borton holds a sample from one of the rivers.

Mikayla Borton holds up a river sample.

Genome Resolved Open Watersheds (GROW) is a community effort to increase genomic representation of the world river microbiome with an emphasis on creating an ecosystem-specific publicly available genome database (GROWdb) that will be a resource for microbiologists, geochemists, hydrologists, and modelers and enable new fundamental understandings of watershed microbiology. The GROW project wouldn’t have been possible without major support from Kelly Wrighton (Colorado State University) and James Stegen (Pacific Northwest National Laboratory), along with a dedicated team of GROW collaborators spanning institutions. Working across disciplines, our team collected samples from rivers across North America and built an open-access platform that empowers the scientific community. 

How has the Department of Energy, alongside the JGI and KBase, supported the GROW project?

(MB) JGI and KBase have been the foundation of GROWdb’s success. Through JGI’s Community Science Program (Proposal ID 505780), we utilized cutting-edge sequencing technologies to process all GROWdb samples. KBase took this a step further by transforming the data into an accessible, interactive platform, moving beyond static flat files that often limit microbiome research today. This approach ensures global usability and access for all researchers, regardless of their data infrastructure. This was exemplified by our workshop at ISME19, where we trained researchers from around the world to use KBase tools with GROWdb data, demonstrating the transformative potential of open and collaborative platforms.

How has the GROW project benefited from working with KBase?

(MB) By simplifying complex genomic workflows and fostering transparency, KBase empowered a global community to collectively build and use the GROW database. The platform not only streamlines data analysis but also ensures the data could be easily accessed, visualized, and reused by scientists worldwide. This emphasis on data usability has enabled innovative applications, with 2661 downloads and reuses in KBase since publication. This collaboration exemplifies the potential of open science to break down barriers and maximize data impact.

Login to KBase to view the GROWdb Collection here: https://narrative.kbase.us/collections/GROW.

What role do you see GROW filling in open science principles? 

(MB)  By making microbial data freely accessible, we’re empowering researchers worldwide to ask new questions, uncover hidden patterns, and connect these insights to their own research endeavors. But accessibility is just the beginning, as we’ve partnered with KBase and other collaborators to ensure the data are not only available but also easily explorable and usable, even for those without extensive microbiome expertise. For example, the GROWdb Explorer was designed to enable researchers working in river systems to explore microbiome content regardless of their scientific background. Additionally, we’ve strengthened the community’s ability to leverage GROWdb data through workshops hosted with KBase, providing hands-on training in microbiome data analytics and fostering interdisciplinary collaboration.

Cache la Poudre River in Colorado, surrounded by trees and brush. The river is low enough that some rocks stick out from the water.

View of the Cache la Poudre River in Colorado.

What is one “behind the scenes” thing you want to share about your project – e.g., from collecting the data, running the analysis, publishing the results? Or, any tips on using the tool, learning more about your project, or ways to get involved?

Katie Willi, Colorado State University, sampling one of the rivers.

Katie Willi squats down to take a water sample at one of the river sample sites.

(MB) One of the most rewarding aspects of this project was bringing together contributions from a diverse team of researchers and trainees. Seeing the data come to life has been incredibly fulfilling, especially as we continue to sequence and explore new river microbiomes.

For anyone new to KBase, take full advantage of their tutorials and workshops—they’re like having a mentor right at your fingertips. And don’t hesitate to get involved! Science thrives when everyone contributes.


Links

Borton, M.A., McGivern, B.B., Willi, K.R. et al. A functional microbiome catalogue crowdsourced from North American rivers. Nature (2024). https://doi.org/10.1038/s41586-024-08240-z

GROWdb – Borton, M., Wrighton, K., Sadkhin, B., Henry, C., Wood-Charlson, E., Liu, F., Edirisinghe, J., Faria, J., & Cannon, S. (2022). GROWdb US River Systems – Samples [Data set]. Colorado State University, Fort Collins, CO. https://doi.org/10.25982/109073.30/1895615

From Reads to Function Workshop at ISME19: An Accessible Metagenomics Toolkit for Decoding Microbial Contributions to Biogeochemical Cycles. https://www.kbase.us/isme19-workshop/

Listen to the Genome Insider episode featuring the GROWdb project.

Other papers leveraging GROWdb sequencing on freshwater systems:

Fadum, J. M., et al. “Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics.” Msystems (2024). https://doi.org/10.1128/msystems.01059-23

Rodríguez-Ramos, Josué, et al. “Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream.” Frontiers in Microbiomes (2023). https://doi.org/10.3389/frmbi.2023.1199766

Stach, Tom Lennard, et al. “Complex compositional and cellular response of river sediment microbiomes to multiple anthropogenic stressors.” bioRxiv (2024). https://doi.org/10.1101/2024.06.07.597903

Funding

JGI CSP (#505780) https://doi.org/10.46936/10.25585/60001289 

 

Ellen Dow
Ellen Dow
Lawrence Berkeley National Laboratory

Ellen G. Dow, Ph.D. is a member of the outreach, communications, and user development team. Inspired by involvement in science outreach throughout graduate school, she left the bench to gain experience in informal education and cultivate community engagement from the general public to science sectors. A molecular biologist by training, Ellen applies her research experience to support scientists and develop resources for the KBase community.