Holocene Chronosequences Reveal the Temporal Dynamics of Antibiotic Resistance Genes during Sediment Development

Antibiotic resistance gene (ARG) dynamics have been extensively studied in anthropogenically impacted environments. However, how ARGs evolve during natural succession in pristine ecosystems remains poorly understood. In this study, we utilized metagenomic sequencing to investigate ARG dynamics across a 12,000 year sedimentary chronosequence in an intertidal zone. ARG abundance and diversity showed a significant upward trend with sediment depth, peaking in the deepest, oldest layers, as corroborated by compositional shifts linked to sediment age (PERMANOVA, <i>p</i> < 0.001). This trend reflects the natural evolution of ARGs dominated by stochastic process, as supported by the low detection rates of three human activity-related indicators and the robust fit to the neutral community model (<i>R</i>² = 0.576). Furthermore, ARG evolution was mainly attributed to alterations in microbial communities, reflected in the growing complexity of ARG-microbe interaction networks and significant procrustes correlations between microbial taxa and ARG profiles. Specially, <i>Proteobacteriota</i> and <i>Actinobacteriota</i> were identified as the key taxa driving ARG evolution, with their succession patterns closely mirroring ARG enrichment trends. Interestingly, the enrichment of MGEs in deeper sediments and their closer association with ARGs during natural succession underscore an enhanced HGT potential, highlighting the pivotal role of MGEs in driving ARG evolution. This study reveals the natural dynamics of ARGs during sedimentary processes, providing an important reference for understanding their independent natural evolution and strengthening our insight into the progression of environmental antibiotic resistance development.