Lambda-PFLOTRAN 1.0: a workflow for incorporating organic matter chemistry informed by ultra high resolution mass spectrometry into biogeochemical modeling

Muller, Katherine A.; Jiang, Peishi; Hammond, Glenn E.; Ahmadullah, Tasneem; Song, Hyun-Seob; Kukkadapu, Ravi; Ward, Nicholas; Bowe, Madison; Chu, Rosalie K.; Zhao, Qian; Garayburu-Caruso, Vanessa A.; Roebuck, Alan; Chen, Xingyuan

doi:10.5194/gmd-17-8955-2024

Title: Lambda-PFLOTRAN 1.0: a workflow for incorporating organic matter chemistry informed by ultra high resolution mass spectrometry into biogeochemical modeling

Journal Article · 18 December 2024 · Geoscientific Model Development (Online)

DOI: https://doi.org/10.5194/gmd-17-8955-2024 · OSTI ID:2483358

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^[1]; Ahmadullah, Tasneem ^[1]; Song, Hyun-Seob ^[2];

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^[3]; Bowe, Madison ^[3]; Chu, Rosalie K. ^[1]; Zhao, Qian ^[1];

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^[3];

^[1]

Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Univ. of Nebraska, Lincoln, NE (United States)
Pacific Northwest National Laboratory (PNNL), Sequim, WA (United States)

Organic matter (OM) composition plays a central role in microbial respiration of dissolved organic matter and subsequent biogeochemical reactions. Here, a direct connection of organic matter chemistry and thermodynamics to reactive transport simulators has been achieved through the newly developed Lambda-PFLOTRAN workflow tool that succinctly incorporates carbon chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate organic matter degradation and the resulting biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow, executed through a Jupyter notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow and transport code PFLOTRAN. The workflow consists of the following five steps: configuration, thermodynamic (lambda) analysis, sensitivity analysis, parameter estimation, and simulation output and visualization. Two test cases are provided to demonstrate the functionality of the Lambda-PFLOTRAN workflow. The first test case uses laboratory incubation data of temporal oxygen depletion to fit lambda parameters (i.e., maximum utilization rate and microbial carrying capacity). A slightly more complex second test case fits multiple lambda formulation and soil organic matter release parameters to temporal greenhouse gas generation measured during a soil incubation. Overall, the Lambda-PFLOTRAN workflow facilitates upscaling by using molecular-scale characterization to inform biogeochemical processes occurring at larger scales.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth & Environmental Systems Science (EESS)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 2483358

Report Number(s):: PNNL-SA--194808

Journal Information:: Geoscientific Model Development (Online), Journal Name: Geoscientific Model Development (Online) Journal Issue: 24 Vol. 17; ISSN 1991-9603

Publisher:: Copernicus Publications, EGUCopyright Statement

Country of Publication:: United States

Language:: English

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