To study the diversity and metabolic activity of microbial eukaryotes in the water column of the South China Sea, genomic DNA and RNA were co-extracted from samples collected down to bathyal depth at two sites. V9 regions of both SSU rDNA and SSU rRNA were amplified and sequenced using high throughput sequencing. Our study revealed: 1) rDNA and rRNA datasets showed significant differences in microbial eukaryote community composition, with the variability between the two datasets for the same sample exceeding that between samples within each dataset, indicating that nucleic acid source overrode environmental factors in determining the composition of microeukaryotes; 2) despite the differences in community composition between the two datasets, both rDNA and rRNA revealed similar depth-related distribution patterns of microbial eukaryotes; 3) using the ratio of rRNA : rDNA as a proxy of relative metabolic activity, a depth-related pattern was found for the relative metabolic activity of some but not all groups of microbial eukaryotes, with the highest activity for the groups with depth-related pattern usually found in the middle water layers; and 4) the presence of live and active photoautotrophic microbial eukaryotes in the deep ocean was confirmed, indicating that they play an important role in controlling the deep-sea organic carbon pool. Overall, our study sheds light on the diversity and activity of microbial eukaryotes in the water column of a tropical oligotrophic ocean and their potential contributions in the downward transportation of organic material from the surface ocean to the deep via the biological pump.

Organic carbon produced by nitrifiers plays an important role in maintaining the microbial metabolism in the aphotic ocean layer with carbon and energy scarcity. However, the contribution of nitrifiers to organic carbon processing remains unclear. To explore how nitrification impacts the material cycle in the starved ecosystem, we set up an ultra-large volume, long-term incubation experiment. Seawater collected from the Halifax coastal ocean was pumped into the Aquatron Tower Tank located at Dalhousie University, Canada, and was incubated under dark conditions for 73 days. The results indicated that the relative abundance of nitrifiers increased and nitrification was strengthened in the dark system where energy and organic carbon were scarce. The importance of nitrogenous compounds in particulate materials increased over the course of the incubation. Correlation analysis showed that the relative abundances of nitrifiers and particulate organic compounds containing nitrogen were significantly and positively correlated. Furthermore, network analysis suggested that metabolic processes related to nitrogenous and aromatic compounds are most important to particle associated bacteria. This study suggests that the nitrifiers could produce a series of organic compounds that result in the alteration of organic matter composition by promoting the degradation of recalcitrant aromatic compounds, which has important implications for organic matter processing in the starved dark ecosystem.

Marine protists are essential for globally critical biological processes, including the biogeochemical cycles of matter and energy. However, compared with their prokaryotic counterpart, it remains largely unclear how environmental factors determine the diversity and distribution of the active protistan communities on the regional scale. In the present study, the biodiversity, community composition, and potential drivers of the total, abundant, and rare protistan groups were studied using high throughput sequencing on the V9 hyper-variable regions of the small subunit ribosomal RNA (SSU rRNA) along an estuary to basin transect in the northern South China Sea. Overall, Bacillariophyta and Cercozoa were abundant in the surface water; heterotrophic protists including Spirotrichea and marine stramenopiles 3 (MAST-3) were more abundant in the subsurface waters near the heavily urbanized Pearl River estuary; Chlorophyta and Pelagophyceae were abundant at the deep chlorophyll maximum depth, while Hacrobia, Radiolaria, and Excavata were the abundant groups in the deep water. Salinity, followed by water depth, temperature, and other biological factors, were the primary factors controlling the distinct vertical and horizontal distribution of the total and abundant protists. Rare taxa were driven by water depth, followed by temperature, salinity, and the concentrations of PO₄³⁻. The active protistan communities were mainly driven by dispersal limitation, followed by drift and other ecological processes.