Unveiling the temporal dynamics and functional traits of prokaryotic and eukaryotic microbes in the coastal South China Sea

This comprehensive two-year investigation of marine microbes in the coastal South China Sea has advanced our understanding of these microbes from both community and genomic perspectives. By combining metagenomics and metatranscriptomics, we have revealed the intricate temporal dynamics and remarkable adaptability of microbial communities and phytoplankton metagenome-assembled genomes (MAGs) in response to environmental fluctuations. Seasonal variations in microbial community composition and function were observed, with cyanobacteria dominating during warmer months and photosynthetic protists more abundant during colder seasons, while photosynthesis-related pathways remained active throughout the year. These patterns highlight the influence of environmental factors such as temperature, salinity, and nitrate concentrations on microbial community composition, while temperature and silicate emerging as crucial factors shaping their functional traits. The recovery and analysis of 37 phytoplankton MAGs, including nine prokaryotic cyanobacteria and 28 eukaryotic protist MAGs from diverse phyla, provided insights into their genetic diversity and metabolic capabilities. Distinct profiles of photosynthesis-related pathways among the MAGs indicated their genetic adaptations to changing environmental conditions. This study enhances our understanding of microbial dynamics in coastal marine ecosystems and provides valuable insights into the ecological roles and responses of different microbial groups.