Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

Wang, Feipeng; Xie, Yuyuan; Wu, Wenxue; Sun, Ping; Wang, Lei; Huang, Bangqin

doi:10.3389/fmicb.2018.03259

Cited by 20 publications

(15 citation statements)

References 74 publications

(104 reference statements)

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“…Moreover, Wang et al (2019) found abundant MALV-II in the subtropical northwestern Pacific Ocean in the spring. However, overrepresentation of the 18S rDNA sequence numbers of MALV-II than their rRNA counterparts was also observed.…”

Section: Discussionmentioning

confidence: 93%

“…The appearance of MALV‐II implied that host–parasite interactions might often occur in this region in winter. Moreover, Wang et al () found abundant MALV‐II in the subtropical northwestern Pacific Ocean in the spring. However, overrepresentation of the 18S rDNA sequence numbers of MALV‐II than their rRNA counterparts was also observed.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, while tiny phytoplankton are expected to predominate in this area as the surface of the Kuroshio is nutrient deficient, relative information is still lacking (Chen, Chen, Jan, & Tuo, ; Chung et al, ). Recent studies on the community assemblage of picoeukaryotes claimed to be conducted in the Kuroshio Current, but their sampling sites were actually located in the northwestern Pacific Ocean, close to the mainstream of the Kuroshio Current (Wang et al, ; Wu et al, ). In this paper, we describe the temporal changes in the abundance of photosynthetic picoeukaryotes in the subtropical Kuroshio Current.…”

Section: Introductionmentioning

confidence: 99%

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Spatial variation of abundant picoeukaryotes in the subtropical Kuroshio Current in winter

et al. 2020

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To understand the importance of picoeukaryotes in the biogeochemical cycle in the subtropical Kuroshio Current, a year‐round survey of the hydrography and the distribution of picoeukaryotes were conducted in four oceanographic cruises from October 2012 to July 2013. In comparison with other seasons, the highest abundancy of photosynthetic picoeukaryotes, with concentrations >104 cells/ml, was observed around the eastern boundary of the Kuroshio in the winter. Accordingly, the composition of picoeukaryotes in this cold season was further studied by a metabarcoding analysis of the 18S rRNA gene. The majority of picoeukaryotes comprised Alveolata, followed by Haptophyta and Stramenopiles. Their composition was diverse in the waters affected by the Kuroshio and in the offshore province. For Haptophyta, in contrast to clade A prevailing in the Kuroshio waters, clade B1, which was considered the host of uncultivated diazotrophic cyanobacterium group A (UCYN‐A), appeared only in the offshore area. Similarly, in Stramenopiles, Pseudo‐nitzschia spp. and MAST‐1D, respectively, dominated in the Kuroshio‐influenced and offshore areas. While Alveolata was the most abundant group, the distributions of all lineages were similar. The association between picoeukaryote succession and hydrographic change is yet to be fully understood. Our results will assist future studies on the community composition of picoplankton and their relationship with marine ecology in the region.

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Spatial variation of abundant picoeukaryotes in the subtropical Kuroshio Current in winter

et al. 2020

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“…S3 ) and after removal of metazoan OTUs and OTUs < 1% total reads, the final OTU count was 201 with variable distributions per population per sample (Table 2 ). Compared to protist communities collected and size-fractionated by filtration, reportedly composed of > 1,000 OTUs 38 – 42 , the low OTU richness is a reminder that our cell sorting protocol allowed the focused targeting of small pigmented eukaryote populations. The low OTU counts (3–42) for each population (Table 2 ) further reflect the accuracy of the sorting method and the near taxonomic purity of some of the sorted populations.…”

Section: Resultsmentioning

confidence: 99%

Small pigmented eukaryote assemblages of the western tropical North Atlantic around the Amazon River plume during spring discharge

Charvet

Kim

Subramaniam

et al. 2021

Sci Rep

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Small pigmented eukaryotes (⩽ 5 µm) are an important, but overlooked component of global marine phytoplankton. The Amazon River plume delivers nutrients into the oligotrophic western tropical North Atlantic, shades the deeper waters, and drives the structure of microphytoplankton (> 20 µm) communities. For small pigmented eukaryotes, however, diversity and distribution in the region remain unknown, despite their significant contribution to open ocean primary production and other biogeochemical processes. To investigate how habitats created by the Amazon river plume shape small pigmented eukaryote communities, we used high-throughput sequencing of the 18S ribosomal RNA genes from up to five distinct small pigmented eukaryote cell populations, identified and sorted by flow cytometry. Small pigmented eukaryotes dominated small phytoplankton biomass across all habitat types, but the population abundances varied among stations resulting in a random distribution. Small pigmented eukaryote communities were consistently dominated by Chloropicophyceae (0.8–2 µm) and Bacillariophyceae (0.8–3.5 µm), accompanied by MOCH-5 at the surface or by Dinophyceae at the chlorophyll maximum. Taxonomic composition only displayed differences in the old plume core and at one of the plume margin stations. Such results reflect the dynamic interactions of the plume and offshore oceanic waters and suggest that the resident small pigmented eukaryote diversity was not strongly affected by habitat types at this time of the year.

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“…Compared to DNA, RNA is unstable in extracellular conditions, microbial community structures inferred from rRNA sequencing (hereafter RNA sequencing) can exclude sequences from dissolved extracellular pool, dormant cells and dead materials (Not et al, 2009). Thus, the RNA-based approach was used to identify the active species or groups in environmental samples (Massana et al, 2015;Hu et al, 2016;Wang et al, 2019). The RNA: DNA ratio (calculated by relative sequence abundance) has been used as an index for the relative metabolic activity in protist (Hu et al, 2016;Wu and Liu, 2018).…”

Section: Introductionmentioning

confidence: 99%

Diversity, Composition, and Activities of Nano- and Pico-Eukaryotes in the Northern South China Sea With Influences of Kuroshio Intrusion

et al. 2021

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Nano- and pico-eukaryotes play important roles in the diversity and functions of marine ecosystems. Warm, saline, and nutrient-depleted water that originates in the Kuroshio Current seasonally intrudes into the northern South China Sea (NSCS) from autumn to spring. To clarify the mechanisms in shaping the community structure of nano- and pico-eukaryotes as well as impacts of the Kuroshio intrusion on the NSCS ecosystem, genomic DNA and RNA were co-extracted from samples collected at two depths from nine stations, and then the V9 region of 18S rDNA and rRNA was sequenced with high-throughput sequencing. Our results showed that Dinophyceae was the most diverse and abundant nanoeukaryotic group during the study period revealed by both DNA and RNA surveys. In contrast, the relative read abundance of MAST, Pelagophyceae, and Dinophyceae in the size fraction of picoeukaryotes might be largely underestimated by the DNA survey. The RNA survey was the more reliable method to investigate the eukaryotic community structure. Environmental filtering played an important role in shaping the community structure, and the sampling depth became the governing factor of the beta diversity under the environmental setting of stratification during the study period. The spatial variations in the diversity of nanoeukaryotes were subject to the dispersal limitation under the size rule. The effects of the Kuroshio intrusion on the nanoeukaryotic community structure might also be explained by the dispersal limitation. Overall, neutral processes are critical in shaping the community structure of nanoeukaryotes. The relative metabolic activities of nanoeukaryotes were relatively stable in accordance with the high similarity of community structure between sampling sites. The responses of the relative metabolic activities of picoeukaryotes to environmental factors displayed two distinct patterns: positive correlations with salinity and nutrients and negative with temperature for Dinophyceae, MAST, and Pelagophyceae, while reversed patterns for Mamiellophyceae and Radiolaria. Our findings improve the understanding of the nano- and pico-eukaryotic communities in the NSCS and the mechanisms of their assembly.

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Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing

Cited by 20 publications

References 74 publications

Spatial variation of abundant picoeukaryotes in the subtropical Kuroshio Current in winter

Spatial variation of abundant picoeukaryotes in the subtropical Kuroshio Current in winter

Small pigmented eukaryote assemblages of the western tropical North Atlantic around the Amazon River plume during spring discharge

Diversity, Composition, and Activities of Nano- and Pico-Eukaryotes in the Northern South China Sea With Influences of Kuroshio Intrusion

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