The mechanisms underlying the enrichment of deep-sea rare earth elements and yttrium (REY) enrichment are fundamental to both resource utilization and paleoenvironmental reconstruction. Iron-manganese oxides serve as highly effective scavengers, capturing REY from seawater during initial sedimentation. Meanwhile, apatite, whether of biogenic or authigenic origin, has been identified as a major host phase for REY in sediments. However, the processes governing the transfer of REY from iron-manganese oxides to apatites during early diagenesis remain poorly understood. Here, we present high-resolution geochemical, magnetic, microscopic and biological data to elucidate the synergistic upregulation of REY concentrations and microbial activity within the deep-sea sediments of the western Pacific. We substantiate that microbial iron reduction (MIR) facilitates the re-release of REY from iron-manganese oxides into pore waters, thus promoting their isomorphism in host minerals. This is evidenced by the alignment of the relative abundance of iron-reducing functional genes and their characteristic product (i.e., microbial-induced magnetite) with the trends in REY concentration in core profiles. Moreover, global climate fluctuations since the Cenozoic may be a critical factor driving the enrichment of REY in deep-sea sediments. These insights enhance our understanding of the interplay between biogeochemical processes and the fate of REY in marine systems.

deep-sea sediments, rare earth elements enrichment, microbial iron reduction, microbially-induced magnetite, climate change