Flux balance modeling to predict bacterial survival during pulsed-activity events

Nicholas A. Jose, Rebecca Lau, Tami L. Swenson, Niels Klitgord, Ferran Garcia-Pichel, Benjamin P. Bowen, Richard Baran, Trent R. Northen

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Desert biological soil crusts (BSCs) are cyanobacteria-dominated surface soil microbial communities common to plant interspaces in arid environments. The capability to significantly dampen their metabolism allows them to exist for extended periods in a desiccated dormant state that is highly robust to environmental stresses. However, within minutes of wetting, metabolic functions reboot, maximizing activity during infrequent permissive periods. iMicrocoleus vaginatus/i, a primary producer within the crust ecosystem and an early colonizer, initiates crust formation by binding particles in the upper layer of soil via exopolysaccharides, making microbial dominated biological soil crusts highly dependent on the viability of this organism. Previous studies have suggested that biopolymers play a central role in the survival of this organism by powering resuscitation, rapidly forming compatible solutes, and fueling metabolic activity in dark, hydrated conditions. To elucidate the mechanism of this phenomenon and provide a basis for future modeling of BSCs, we developed a manually curated, genome-scale metabolic model of iMicrocoleus vaginatus/i (iNJ1153). To validate this model, gas chromatography-mass spectroscopy (GC-MS) and liquid chromatography-mass spectroscopy (LC-MS) were used to characterize the rate of biopolymer accumulation and depletion in in hydrated iMicrocoleus vaginatus/i under light and dark conditions. Constraint-based flux balance analysis showed agreement between model predictions and experimental reaction fluxes. A significant amount of consumed carbon and light energy is invested into storage molecules glycogen and polyphosphate, while iβ/i-polyhydroxybutyrate may function as a secondary resource. Pseudo-steady-state modeling suggests that glycogen, the primary carbon source with the fastest depletion rate, will be exhausted if iM. vaginatus /i experiences dark wetting events 4 times longer than light wetting events.

Original languageEnglish (US)
Pages (from-to)2219-2229
Number of pages11
Issue number7
StatePublished - Apr 16 2018

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Earth-Surface Processes


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