Cracking the dynamic code of the deep: Unexpected seasonal patterns of active protistan-bacterial microbiomes in the mesopelagic zone of the South China Sea

Disentangling microbial dynamics in the mesopelagic zone is crucial due to its role in processing sinking photic production, affecting carbon export to the deep ocean. The relative importance of photic zone processes versus local biogeochemical conditions in mesopelagic microbial dynamics, especially seasonal dynamics, is largely unknown. We employed rRNA gene transcript-based high-throughput sequencing on 189 samples collected from both the photic and mesopelagic zones, along with seasonal observations, to understand the South China Sea’s protistan-bacterial microbiota diversity, drivers, and mechanisms. Mesopelagic communities displayed unexpectedly greater seasonal but less vertical dynamics than photic counterparts. Temperature, dissolved oxygen, nutrients, and bacterial abundance drove mesopelagic communities vertically. Photic zone processes (using net community production and mixed layer depth as proxies) of past seasons, coinciding with strong monsoon periods, shaped seasonal fluctuations in mesopelagic communities, indicating a time-lag effect. Furthermore, certain microbes were identified as indicators for beta diversity by depth and season. This investigation deepens our understanding of how and why mesopelagic communities vary with season and depth. Recognizing the time-lagged effect of photic zone processes on mesopelagic communities is crucial for understanding the current and future configurations of the ocean microbiome, especially in the context of climate change and its effect on carbon export and ocean storage.