Microbial Eukaryote Diversity and Activity in the Water Column of the South China Sea Based on DNA and RNA High Throughput Sequencing

Abstract

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 rRNA gene and its transcript (cDNA) were amplified and sequenced using high throughput sequencing. Our study revealed: (1) DNA and RNA 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 DNA and RNA revealed similar depth-related distribution patterns of microbial eukaryotes; (3) using the ratio of RNA: DNA 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.

Pigmented microbial eukaryotes fuel the deep sea carbon pool in the tropical Western Pacific Ocean

“…In a recent study, high throughput sequencing of both 18S rRNA and its gene also revealed the presence of active phototrophic microbial eukaryotes in the deep South China Sea. In the same study it was reported that, using RNA/DNA ratio as a proxy, the relative activities of some phototrophic Stramenopiles (e.g., Chrysophyceae, Synurophyceae, Dictyochophyceae and Pelagophyceae) in the deep waters were almost equal with those in the shallow waters (Xu et al ., ).…”

“…Total RNA was extracted from each cryopreserved filter membrane using AllPrep DNA/RNA kit (Qiagen, USA) following the protocols of Sun and colleagues () and Xu and colleagues (). Extracted RNA was quantified using a Nanodrop ND‐2000 Spectrophotometer (Labtech International, USA) and the integrity was assessed by 1.5% agarose gel electrophoresis.…”

“…Chrysophytes are reported to be capable of phagotrophy, osmotrophy and phototrophy (Holen and Boraas 1995). Chrysophytes have been reported in the deep South China Sea (Xu et al, 2017b) and were identified as the second most abundant class in deep-sea protistan communities (Pernice et al, 2015b). Combined with their prevalence in the deep sea globally, it has been proposed that chrysophytes may be important bacterivores in deep waters (Pernice et al, 2015b).…”

“…The ubiquitous presence of healthy photosynthetic cells (mainly diatoms) and 16S rRNA gene sequences of photosynthetic cells (cyanobacteria and algal chloroplasts) at depths of up to 4000 m in the dark ocean on a global scale has been reported (Agusti et al ., ). Finally, based on the sequencing both of the 18S rRNA and its gene, active phototrophic microbial eukaryotes were confirmed to be present in the deep waters of the South China Sea (Xu et al ., ). Although these pioneering studies have revealed the presence of phototrophic microbial eukaryotes in deep oceans, knowledge of their source, community structure, biogeography and function remain largely unknown.…”

Marked changes in diversity and relative activity of picoeukaryotes with depth in the global ocean

“…In addition, as the ribosomal content is regulated to match the protein synthesis needs during population growth and acclimation (Blazewicz et al 2013), the rRNA:rDNA ratio for a given taxon has been used as a proxy for their relative activity. This approach has been applied to microbial 85 eukaryotes in a few epipelagic (Hu et al 2016, Massana et al 2015 and vertical-profile (Jing et al 2018, Xu et al 2017 regional studies, but it has not yet been applied at the global scale.…”