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Microorganisms, the catalysts of all biogeochemical cycles on Earth, are the origin and essence of life—an invisible yet powerful force sustaining all living organisms. The health of both individual organisms and ecosystems critically depends on functional microbiomes that drive essential processes such as nutrient cycling, pathogen control, detoxification, and resilience. However, like their macroorganism counterparts, these beneficial microbes are vulnerable to environmental changes, and their decline often accelerates ecosystem degradation