Molecular Observation Network (MONet)

Soils are fundamental to ecosystem resiliency, regulating energy flows and system stability in response to natural and human-induced changes. Acting as a major reservoir of chemical energy, soils influence the transformation, retention, and release of key molecular components. Understanding these processes at the molecular level is essential for improving predictions of ecosystem responses and developing accurate models for resource management and conservation.

The complexity of soil ecological and biogeochemical processes, combined with the lack of standardized molecular and microscale soil data at scale across the continental United States, has led to significant uncertainties in Earth system models. Addressing these gaps is critical for advancing basic science and improving our ability to predict and manage ecosystem dynamics.

What is MONet?

The Molecular Observation Network (MONet) is an open science network developed by the Environmental Molecular Sciences Laboratory (EMSL), which is housed on the Pacific Northwest National Laboratory campus. MONet’s mission is to develop a continental-scale database of standardized molecular and microstructural data to advance the understanding and prediction of microbially and root-driven inputs in soil ecosystems and terrestrial aerosol processes. The information provided by MONet is essential for advancing the accuracy of multiscale Earth system models, growing American scientific leadership, and enabling the next generation of soil and aerosol research both at EMSL and within the broader user community.

With this mission in mind, EMSL is

building an open science community of collaborators and partners at universities and national laboratories, in agriculture and industry, and with community organizations to acquire samples from ecosystems across the United States
developing a national, high volume/high quality FAIR (findable, accessible, interoperable, and reusable) database that will provide open access to rich and unique data for scientists, modelers, and experimenters to advance basic science
integrating MONet biogeochemical and microbial process data streams into scaling relations to parameterize key variables for multiscale and larger-scale Earth system models.

To make this possible, MONet is standardizing molecular and microscale sample collection protocols and innovating high-throughput, automated analysis and processing workflows.

The Molecular Observation Network (MONet) is generating gold-standard, standardized, AI-ready data at regional and continental scales to enhance American innovation and scientific leadership in Earth systems models, advancing our ability to recover critical minerals and establish a predictive understanding of environmental impacts on energy system reliability and security.

Big data is critical to this task, and MONet is designed from the ground up to deliver it. A data visualization tool is available to help researchers interact with the data collected during the MONet pilot 1000 Soils Project or upload their own datasets to try beta release tools that may be formalized within EMSL's data portal.

Data Types and Training

Soil samples submitted to the MONet user program will be analyzed using an extensive suite of advanced techniques to produce different data types, including the following:

high-resolution molecular composition of soil organic matter
metagenomic sequencing
3-D microstructure
dissolved solutes
respiration, microbial biomass, and potential enzyme activity.

Data Collection

Types of data being collected by the Molecular Observation Network

Data Availability

Consistent with open science principles, data are published on EMSL Science Central™, where they are publicly available without embargo according to the EMSL Data Policy.

MONet data are being generated, quality-checked, and uploaded to the Science Central™ portal by proposal call and data type, with the inclusion of ion cyclotron resonance (ICR) datasets as well as X-ray computed tomography and metagenomes (“other datasets” in the table in the next section). The first available data for fiscal year (FY) 2024 projects will be univariate biogeochemistry data available in the spring and summer of 2025. Review an Excel spreadsheet of the MONet data delivery schedule.

For metagenome data generated at the Joint Genome Institute (JGI), filtered reads, assemblies, annotations, and metagenome-assembled genomes (MAGs) will be provided for download on the JGI Data Portal. Metagenome data will also be made available through the Integrated Microbial Genomes and Metagenomes platform for comparative analysis.

MONet data schedule — (Graphic by Stephanie King | Pacific Northwest National Laboratory)

How to Acknowledge EMSL and JGI for MONet Data

“Soil data were provided by the Molecular Observation Network (MONet) at the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), a DOE Office of Science user facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830. The work (proposal: 10.46936/10.25585/60008970) conducted by the U.S. Department of Energy, Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science user facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. A subset of soil cores was obtained by the National Ecological Observatory Network’s Research Support Services which is a program sponsored by the U.S. National Science Foundation and operated under cooperative agreement by Battelle.

The Molecular Observation Network (MONet) database is an open, FAIR, and publicly available compilation of the molecular and microstructural properties of soil. Data in the MONet open science database can be found at https://sc-data.emsl.pnnl.gov/.”

Please remember to include the MONet Data Consortium as a co-author when utilizing MONet data in your publication.

The MONet Team

John Bargar

John Bargar, EMSL
Overall questions

Emily Graham

Emily Graham, EMSL
Omics

Odeta Qafoku

Odeta Qafoku, EMSL
Soil interfaces

Yuri Corilo

Yuri Corilo, EMSL
Data analysis

Sarah Leichty

Sara Leichty, EMSL
Project management (EMSL)

Tanja Woyke

Tanja Woyke, JGI
Deputy for User Programs

Christa Pennacchio

Christa Pennacchio, JGI
Project management (JGI)

Strategic Partners

The Joint Genome Institute (JGI) will perform and prepare sequencing, metagenome analyses, assembly files, annotation, and bins of MONet samples. Data will be available for download from the EMSL MONet database and through JGI’s portals.

The National Science Foundation's National Ecological Observatory Network will provide a national network of field and observational sites to facilitate sampling and continuous sensing opportunities.

The National Microbiome Data Collaborative will support accessibility of MONet microbiome metadata.

Publications

Ghimire, S., Y. Zhang, J. Huang, E.L.W. Majumder, A.E. Hartemink, E.B. Graham, O. Qafoku, J. Andrews, and Z.B. Freedman. 2025. "Using mid-infrared spectroscopy to estimate soil microbial properties at the continental scale." Applied Soil Ecology 211 (106110). https://www.sciencedirect.com/science/article/pii/S0929139325002483.

Cheng, S., M. Mudunuru, M.M. Bowman, Q. Zhao, J. Toyoda, W. Kew, Y. Corilo, O. Qafoku, J.R. Bargar, S. Karra, and E.B. Graham. 2025. "Scaling High-Resolution Soil Organic Matter Composition to Improve Predictions of Potential Soil Respiration Across the Continental United States." Geophysical Research Letters 52 (4). https://doi.org/10.1029/2024GL113091.

Bowman, M. M., A. E. Heath, T. Varga, A. K. Battu, R. K. Chu, J. Toyoda, T. E. Cheeke, S. S. Porter, K. B. Moffett, B. LeTendre, O. Qafoku, J. R. Bargar, D. M. Mans, N. J. Hess, and E. B. Graham. 2023. "One thousand soils for molecular understanding of belowground carbon cycling." Frontiers in Soil Science (3). https://doi.org/10.3389/fsoil.2023.1120425.

Chakrawal, A., O. Qafoku, S. Karra, J. R. Bargar, E. B. Graham. 2025. "Challenges in integrating dissolved organic matter chemodiversity into kinetic models of soil respiration." Soil Biology and Biochemistry 211 (109954). https://www.sciencedirect.com/science/article/pii/S0038071725002482

Videos

2023 Molecular Observation Network Community Science Meeting Training Videos

EMSL LEARN Webinar Series: MONet Proposal Submission: Tips for Success

Learn details for MONet's quarterly soil sample submissions calls.

EMSL LEARN Tutorials: Molecular Observation Network Series

Explore how to submit a proposal to an open call and how to collect a soil sample.

EMSL Science Overview