Phylogenetic legacy drives soil microbial turnover via ecological sorting under long-term nitrogen enrichment

To investigate the genomic mechanisms underlying soil microbiome turnover under chronic nitrogen (N) deposition, we leveraged a decade-long N-addition gradient experiment in a semi-arid grassland. We integrated deep shotgun metagenomic sequencing with metagenome-derived 16S rRNA (mi-tag) profiling to track community dynamics. To capture the genetic blueprints of the surviving taxa without confounding short-term phenotypic plasticity, we recovered 286 high-quality metagenome-assembled genomes (MAGs) specifically from the extreme N-enrichment endpoint (N50). Using microbial orders (spanning 42 orders) as the primary phylogenetic unit, we categorized lineages into expanding ("Winners") and declining ("Losers") groups based on their abundance trajectories along the N gradient. By evaluating these representative MAGs, we systematically compared foundational genomic architectures (i.e., genome size and GC content) and the completeness of functional modules (i.e., motility versus complex carbon degradation pathways) between Winners and Losers. This genome-resolved framework was explicitly designed to test whether community turnover is driven by active genome streamlining and physiological trade-offs, or by the passive ecological sorting of ancestrally conserved trait packages.