Substrate competition over 320 days maintains extracellular electron transfer and parallel genomic evolution in Shewanella oneidensis MR-1

Abstract

Electroactive microorganisms are integral to biogeochemical cycles through extracellular electron transfer and have potential applications in environmental remediation. However, their long-term competitive interactions and evolutionary dynamics with non-electroactive microorganisms remain poorly understood. In this study, we conducted a 320-day cultivation experiment in which monocultures of the electroactive Shewanella oneidensis MR-1, the non-electroactive Citrobacter freundii An1, and their cocultures were compared under three single electron acceptor conditions: anaerobic (no exogenous electron acceptor), ferrihydrite, or oxygen. After 320 d, S. oneidensis MR-1 presented the highest relative abundance of 30.94% ± 0.74% in the ferrihydrite cocultures. S. oneidensis MR-1 maintained ferrihydrite reduction capacity after cultivation under all three conditions, indicating the long-term stability of its extracellular electron transfer. Moreover, no other phenotypic evolution was observed in S. oneidensis MR-1 after ferrihydrite or anaerobic cultivation. In contrast, both monocultured and cocultured S. oneidensis MR-1 exhibited enhanced adaptation to oxygen, characterized by increased growth rates, metabolic activity, and reduced cell aggregation. Notably, substrate consumption increased in monocultures but decreased in cocultures, suggesting an optimization of metabolic efficiency in the latter. Genome sequencing revealed mutations in genes associated with cell division, adenosine triphosphate synthesis, lactate metabolism, and flagellar/pilus expression in S. oneidensis MR-1. Interestingly, the ferrihydrite-adapted groups also exhibited enhanced adaptation to oxygen. 83.96% of mutations were shared across all culture systems and enriched in environmental signal-sensing pathways, indicating that parallel genomic evolution facilitated cross-environmental adaptation. Our findings reveal the ecological evolution of electroactive microorganisms in diverse redox environments and establish a foundation for engineering electroactive communities.

Graphical abstract

Keywords

Extracellular electron transfer / Electroactive microorganisms / Substrate competition / Evolution / Shewanella / Citrobacter

Highlight

	● Shewanella oneidensis MR-1 maintained extracellular electron transfer after 320 d.
	● Ferrihydrite respiration aided S. oneidensis MR-1 survival under competition.
	● Oxygen cultivation enhanced S. oneidensis MR-1’s adaptation to oxygen.
	● Shared mutations (83.96%) revealed cross-environmental parallel evolution.
	● Metabolic efficiency was a key strategy in coculture competition.

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