September 20, 2023
Journal Article

Exploring the determinants of organic matter bioavailability through substrate-explicit thermodynamic modeling


Microbial decomposition of organic matter (OM) in river corridors is a major driver of nutrient and energy cycles in natural ecosystems. Recent advances in omics technologies enabled high-throughput generation of molecular data that could be used to inform biogeochemical models. With high-resolution OM data becoming more readily available, in particular, the substrate-explicit modeling has emerged as a promising approach due to its ability to predict OM degradation and respiration rates from chemical formulae of compounds. This model implicitly assumes that all detected compounds are bioavailable, and that aerobic respiration is driven solely by thermodynamics. Despite promising demonstrations in previous studies, these assumptions may not be universally valid because OM degradation is a complex process governed by multiple factors. To identify key drivers of OM respiration, we performed a comprehensive analysis of diverse river systems using Fourier-transform ion cyclotron resonance mass spectrometry OM data and associated respiration measurements collected by the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium. In support of our argument, we found that the incorporation of all compounds detected in the samples into the thermodynamic theory-based substrate-explicit modeling resulted in a poor correlation between the predicted and measured respiration rates. The data-model consistency was significantly improved by the selective use of a small subset (i.e., only about 5%) of OM identified using an optimization method. Through a subsequent comparative analysis of the subset of OM (which we presume as bioavailable) against the full set of compounds, we identified three major traits that potentially determine OM bioavailability, including: (1) thermodynamic favorability of aerobic respiration, (2) the number of C atoms contained in OM, and (2) carbon/nitrogen (C/N) ratio. Interestingly, we found that the first two factors serve as ‘filters’ in that the compounds with undesirable properties in any of these traits are strictly excluded from the bioavailable fraction. Among the remaining unfiltered OM, the (C/N) ratio played a key role in determining their bioavailability. This work highlights the importance of accounting for the complex interplay among multiple key traits to increase the predictive power of biogeochemical and ecosystem models.

Published: September 20, 2023


Ahamed F., Y. You, A. Burgin, J.C. Stegen, T.D. Scheibe, and H. Song. 2023. Exploring the determinants of organic matter bioavailability through substrate-explicit thermodynamic modeling. Frontiers in Water 5. PNNL-SA-184205. doi:10.3389/frwa.2023.1169701

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