Thermodynamic Modeling of pH Impacts on Subsurface Microbial Consortia

Authors

• Jackfin K C, University of Nebraska-LincolnFollow

First Advisor

Hyun-Seob Song

Committee Members

Karrie Weber, Forrest M. Kievit

Date of this Version

6-2026

Document Type

Thesis

Citation

A thesis presented to the faculty of the Graduate College at the University of Nebraska in partial fulfillment of requirements for the degree of Master of Science

Major: Agricultural and Biological Systems Engineering

Under the supervision of Professor Hyun-Seob Song

Lincoln, Nebraska, June 2026

Comments

Copyright 2026, Jackfin K C. Used by permission

Abstract

Underground hydrogen storage is affected by microbial consumption, and the different minerals present in the subsurface. However, most studies consider either biotic or abiotic factors in isolation and hence, the conditions that drive a self-sustaining storage remain poorly understood. This thesis uses a genome-informed thermodynamic model developed by Kharel et al. (2026) in which pH is the central variable coupling hydrogenotrophic microbial metabolism, inter-species competition, and carbonate mineral buffering. The model includes four hydrogen-consuming species: methanogen (Methanobacterium), acetogen (Acetoanaerobium), aerobic acetate oxidizer (Pseudomonas stutzeri), and sulfate reducer (Nitratidesulfovibrio) by conditioning each organism's activity on the Gibbs free energy of its catabolic reaction, across four carbonate minerals (calcite, dolomite, magnesite, siderite). This study presents several important findings. First, community composition drives pH response: hydrogenotrophic metabolism drove the system progressively more alkaline as methanogens and acetogens consumed CO₂, whereas adding an aerobic acetate oxidizer reversed this rise by regenerating CO₂, identifying aerobic heterotrophs as natural moderators of pH. Second, total H₂ consumption was nearly same from single-species simulations to the progressive four-species consortium (adding Acetoaneorbium, Pseudomonas and Nitratidisulfovibrio to the Methanobacterium only system). However, the community composition and mineralogy shifted the product spectrum (methane, acetate, hydrogen sulfide) without changing the total hydrogen consumption. Third, mineral type is a major control of pH: shifting from calcite to siderite raised final pH of the system and made the sulfate reducer dominant, suppressing methanogenesis. A kinetics-based inference of environmentdependent microbial interactions and their dynamic variation (KIDI) analysis showed that the community shifted from competition-dominated to facilitation-dominated with rising pH, with one CO₂ mediated interaction strengthening significantly, the reason being that dissolved CO₂ becomes limiting for the anaerobes at high pH which makes the CO₂ regenerated by the aerobe increasingly valuable. Together these results indicate that pH could have significant effects on microbial metabolism and mineral kinetics.

Advisor: Hyun-Seob Song