Soil health and One Health implications in the anthropocene: a perspective on microbiome engineering

Abstract Background Climate change and Anthropocene pressures accelerate soil degradation, threatening agricultural productivity, ecosystems, and human health. Within the One Health framework, soils are critical living systems. However, while physical and chemical dimensions of soil health are well studied, the biological dimension—particularly microbiome functional diversity—remains heavily underutilized in climate-resilient agriculture. Rationale We argue that microbiome functional diversity is the missing biological foundation linking Soil Health and One Health. Rather than viewing microbiomes as isolated components, we propose they be treated as interconnected functional networks regulating resilience across soil, plant, animal, and human systems. We position microbiome engineering as a strategic research priority to translate ecological knowledge into sustainable agricultural solutions. Key Directions Synthesizing discussions from the Chile–Sweden ACCESS Forum, we identify vital research priorities: exploring microbiomes from harsh, ancient, and extreme environments; developing synthetic microbial communities (SynComs); and integrating high-resolution mass spectrometry, multi-omics, microscale soil models, and extended genotype approaches. These tools offer unprecedented pathways to manipulate microbial functions that enhance nutrient cycling, carbon sequestration, stress tolerance, and pollutant remediation. Conclusion Advancing microbiome functional diversity from ecological discovery to functional microbiome engineering represents a critical, actionable step toward achieving climate-resilient agroecosystems and fulfilling the global objectives of the One Health framework in the Anthropocene.