PNNL

The Science

River corridors contain complex mixtures of dissolved organic matter (DOM) that support aquatic life and drive elemental cycling. However, many DOM molecules remain unidentified because current instruments cannot assign precise chemical formulas to all detected signals. These uncharacterized molecules, a.k.a. “chemical dark matter,” represent a major gap in understanding the fundamentals of DOM chemistry within river corridors. A multi-institutional team of researchers re-analyzed data from 551 DOM samples previously published on ESS-DIVE. The samples were from stream/river sediments and water across three continents. Data were generated using ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry. The chemical diversity and composition of dark matter was compared with that of identifiable molecules (i.e., “known matter”), and it was found that dark matter had smaller molecules but more distinct chemical differences between locations (i.e., higher diversity). Dissolved organic carbon (DOC) was the main factor influencing the effects of dark matter on DOM diversity. Including dark matter in analyses changed key diversity metrics, revealing that DOM dark matter is an important, but largely neglected, component of DOM chemistry across global river corridors.

The Impact

Understanding the full composition of organic material in river corridors is essential for interpreting and ultimately predicting ecosystem processes. By quantifying how uncharacterized molecules contribute to molecular diversity, this research filled a major knowledge gap in river corridor chemistry. It was one of the first comprehensive studies to measure how dark matter influences the diversity and composition of DOM in both waters and sediments. The results showed that ignoring dark matter can distort understanding of how DOC concentration is linked to DOM chemistry, particularly in sediments. The study also established an approach that will enable scientists to integrate dark matter into analyses of organic molecules going forward. This approach opens possibilities to more deeply integrate complex organic mixtures with other system components (e.g., microbial communities) to facilitate stronger representation of molecular properties within system-scale models (e.g., reactive transport) that are used to upscale processes and predict future ecosystem function.

Summary

DOM in river corridors includes thousands of molecules with varying chemical properties, but a significant portion lacks a confidently assigned molecular formula and is collectively referred to as chemical dark matter. Using ultrahigh-resolution mass spectrometry and statistical modeling, a multi-institutional team of researchers analyzed 279 water and 272 sediment samples from 97 rivers across North America, Asia, and Europe. They compared molecular diversity, composition, and mass between identifiable molecules (i.e., known matter) and dark matter. The study revealed that dark matter generally had lower molecular weight but greater differences between sites. DOC was the strongest driver of these characteristics, showing opposite effects in water and sediment: as DOC increased, dark matter’s influence decreased in water and reversed direction within sediments. The researchers inferred that photochemical reactions modulate these effects in surface waters while microbial transformations are a cause for the patterns in sediments. Including dark matter in data analyses altered diversity and compositional estimates up to ~30%, indicating that even small, uncharacterized fractions can influence broader interpretations of organic matter. The work provides a global-scale benchmark for considering the role of chemical dark matter in river corridor DOM. In particular, it provides a framework that can be further developed through expansion to diverse ecosystems and deeper investigations into microbial–DOM interactions.

The initial draft of the text above was created using ChatGPT (version 5.5 or lower, OpenAI). The language and content were subsequently edited by the author for grammar, clarity, and accuracy, and the final document was reviewed by the author. 

Research Contact(s)

James Stegen, Pacific Northwest National Laboratory

Funding

This research was supported by the Department of Energy, Office of Science, Biological and Environmental Research Program, Environmental System Science Program. This contribution originates from the River Corridor Scientific Focus Area project at Pacific Northwest National Laboratory (PNNL). A portion of this research was performed at the Environmental Molecular Sciences Laboratory user facility, located at PNNL. PNNL is operated by Battelle Memorial Institute for the Department of Energy. 

Related Links

• Data are available at the ESS-DIVE (https://data.ess-dive.lbl.gov/view/doi:10.15485/1603775; https://data.ess-dive.lbl.gov/view/doi:10.15485/1729719)
• River Corridor Hydrobiogeochemistry Science Focus Area PNNL webpage