Integrating evolution and ecology on microbial dehalogenation to advance sustainable soil health

Abstract

Microbial dehalogenation governs the fate of persistent pollutants frequently detected globally-organohalides (OHs) in soils, and is a critical process for mitigating threats to ecosystem health. However, conventional research focused on rare specialist bacteria cannot account for the widespread, low-level OH turnover observed globally. This review applies a potential evolutionary ecology framework, reframing dehalogenation as a community-wide trait that originated from versatile ancestral enzymes and disseminated via horizontal gene transfer (HGT). This evolutionary history highlights the important ecological role of abundant non-specialists, such as methanogens, which capable of perform dehalogenation at certain condition as a secondary metabolic function. These organisms face metabolic trade-offs, allocating resources between primary growth and secondary dehalogenation. This resource partitioning links OH fate to major biogeochemical cycles, challenging traditional remediation approaches for complex environmental media such as soil. To advance the field, future research must quantify in situ fluxes using multi-omics and stable isotope techniques, and develop predictive models to elucidate these trade-offs. Ultimately, we advocate a shift from simple bioaugmentation to predictive ecological engineering—managing soils by manipulating environmental conditions and designing synthetic microbial consortia. This strategy aims to enhance polluted soil resilience and multifunctionality, aligning remediation with the broader goals of sustainable soil health.

Graphical abstract

Keywords

organohalides / microbial dehalogenation / non-specialist dehalogenators / evolutionary ecology / biogeochemical coupling / soil health

Highlight

	● Evolution and ecology are integrated to explain soil microbial dehalogenation.
	● Dehalogenation is reframed as a distributed trait driven by enzyme promiscuity and horizontal gene transfer.
	● Non-specialist microbes contribute significantly via metabolic trade-offs.
	● Dehalogenation is coupled with biogeochemical cycles, impacting overall soil health.
	● Predictive ecological engineering is proposed to enhance soil ecosystem resilience.

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