Timeframe is a critical factor in understanding the impact of climate change on the evolution of microbial community structure and ecological memory. Here, we demonstrate how bacterial functions have left lasting imprints through their inherent gene-regulatory network traits under alternating wet and dry climatic conditions over loess-paleosol geological time scales. In the drier loess soil, Gammaproteobacteria possess symbiotic nitrogen-fixing genes that promote microbial structural and functional succession over the ten-thousand-year scale and support a nitrogen fixation-comammox-nitrate reduction cycle and nitrogen memory, according to analysis of samples in Luochuan, China. The unique and extreme conditions of the paleoclimate environment can be reflected in the microbial community composition. Nitrogen deficiency in drier loess soil has facilitated shifts in bacterial phyla community composition, driving the evolutionary functional pathways and strong legacy effects. Our findings highlighting the crucial role of specific traits of Gammaproteobacteria as driving forces for stabilizing microbial systems in arid soils.