Sediment Trap Study Reveals Dominant Contribution of Metazoans and Dinoflagellates to Carbon Export and Dynamic Impacts of Microbes in a Subtropical Marginal Sea

Abstract

Flux and efficiency of carbon export in the ocean has been widely studied using sediment traps, but due to limitations of traditional methods, differential contribution of different organisms is poorly understood. Here, we used DNA metabarcoding to document taxonomic composition for sediment traps deployed at a continental shelf (C6) and a continental slope (C9) site in the South China Sea. The results indicated that metazoans (mainly copepods) and dinoflagellates were the most dominant contributors overall, while dinoflagellates, diatoms, and haptophytes dominated the photosynthetic assemblage. For prokaryotes, Gammaproteobacteria dominated all samples. Furthermore, comparing the trap flora to overlying plankton revealed that metazoans and Polycystinea from Eukaryota and Gammaproteobacteria and Bacteroidetes from Prokaryota were enriched in the trap at both stations whereas haptophytes and Dinophyceae were consistently attenuated during sinking. In addition, Oceanospirillaceae and Rhodobacteraceae exhibited negative correlations with dinoflagellates, and based on overlying plankton metatranscriptomes, were most transcriptionally active lineages for metabolizing labile and semi‐labile organic carbon, potentially contributing to the Martin's decay of sinking particulate organic carbon. Using DNA and RNA sequencing technologies, this study provides novel insights into the lineage‐specific contribution and dynamic impacts of microbes to carbon export in a subtropical marginal sea.

A comparative study reveals the relative importance of prokaryotic and eukaryotic proton pump rhodopsins in a subtropical marginal sea

“…As mentioned earlier, microbial community structures based on SSU (rDNA) have been reported elsewhere [ 42 , 43 ] and data are available (BioProject numbers PRJNA782430 and Accession number CNP0001483). The high-throughput sequencing of our RNA samples yielded 881 Gb raw data, which resulted in 792.7 Gb of clean reads in total after quality processing.…”

“…Twenty samples for 16 S and 18 S rRNA gene (rDNA SSU) analysis were collected in same way as RNA samples but were immersed in DNA lysis buffer before being stored at −80 °C. The analysis of the DNA samples to characterize the microbial community structures has been reported elsewhere [ 42 , 43 ].…”

Characterization of sinking and suspended microeukaryotic communities in spring Oyashio waters

“…Phototrophic dinoflagellates, which were more abundant in sinking particles and showed stable relative abundance with depth (Figs. 5a-b and 6a-b), play a significant role in the BCP across various ecosystems (Guidi et al ., 2016; Durkin et al ., 2022; Lin et al ., 2022); Dinoflagellates are more carbon-dense than diatoms, as evident from their carbon-to-cell volume ratio (Menden-Deuer and Lessard, 2000); their sinking can sequester more carbon per volume of particles than that of diatoms. The formation of massive carbon-rich and thick-walled resting cysts during dinoflagellate blooms makes them more resistant to degradation, contributing to the intense sedimentation of organic matter (Heiskanen, 1993; Cohen et al ., 2021).…”

“…Recent advances in environmental DNA-based approaches, such as 18S rDNA metabarcoding method (Duret et al, 2020;Durkin et al, 2022), have provided comprehensive information on community composition, improving our understanding of the role of microeukaryotes in the export of carbon to the deep ocean. Small and non-mineralizing species, such as non-calcifying haptophytes and dinoflagellates, could have been underestimated in previous studies (Richardson, 2019;Lin et al, 2022). Time-series sediment trap studies at abyssal depths have documented the occurrence of various eukaryotic lineages of protists originating from surface layers (Boeuf et al, 2019;Preston et al, 2020).…”