Desert soil microbiome

Land degradation or desertification is a pressing global issue. Microorganisms are the cornerstone of soil ecosystems and physicochemical functions. Yet, the detailed dynamics and functional role of soil microbiome during the long-term restoration of desert ecosystems remain unknown. We collected 1920 topsoil samples from two sites of up to 17 years of restoration near Tengger Desert and profiled the microbiome, metabolome, and physicochemical properties. We found that traditional surface irrigation promoted long-term desert microbiome stability and functional diversity compared to industrialized drip irrigation. The microbiome and metabolome dynamics signaled a systematic transition from an extreme oligotrophic to a complex copiotrophic lifestyle over time, influenced by physicochemical factors, especially the hydraulic properties. Conversely, structural equation modeling and mediation analyses show that the soil microbiome, including fungi, could affect soil physicochemical properties, likely through metabolites. The extensive longitudinal remodeling of the microbiome and metabolome centered around decreased relative activity of autotrophic functions, including carbon and nitrogen fixation, and increased relative activity of catabolic functions and diverse secondary functions, such as defense-immune systems, quorum sensing, and mobility. Finally, the soil microbiome was evolving to adapt to the changing environment. We present the comprehensive dynamic soil taxonomical, functional, ecological, physicochemical, and evolutionary landscapes during long-term desert restoration. We demonstrate that the microbes and the metabolites are the key facilitators, which could be further exploited to expedite the process.