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Eukaryotic plankton play an important role in the wetland lake ecosystems. However, the size structure and species composition of eukaryotic plankton in shallow wetland lake ecosystems remains largely unexplored. To address this gap, our study employed high-throughput sequencing and quantitative PCR techniques to investigate the size structure (pico-0.7–5 μm and nano-5–20 μm) and species composition of eukaryotic plankton in two shallow wetland lakes in China during August 2016. Our findings reveal that the diversity index values of the pico-size fraction were significantly higher than those of the nano-size fraction. Additionally, there was a significant difference in community structure between these two size fractions. Furthermore, different dominant taxa were associated with each particle size, with certain lineages being enriched exclusively in one of the size fractions. In particular, biomarkers differed between the pico- and nano- fractions. The abundance of the 18S rDNA gene did not differ significantly between the two fractions. However, there was a significant difference in the abundance of gene transcripts. Moreover, the pico- fraction exhibited a significantly higher rRNA: rDNA ratio compared to the nano- fraction. It is important to note that certain taxa had lower absolute abundance in specific samples, despite their higher relative abundance. [ABSTRACT FROM AUTHOR]

Introduction: Eukaryotic plankton plays crucial roles in ecosystem processes, impacting aquatic ecosystem stability. This study focuses on Danjiangkou Reservoir, a canyon lake in central China, that acts as the water source of the Mid-route of the South-to-North Water Diversion Project. Methods: In this study, high-throughput 18S rDNA gene sequencing was employed to investigate eukaryotic plankton community at four water depths (0.5 m, 5 m, 10 m, and 20 m). The environmental factors including pH, water temperature (WT), nitrate nitrogen (NO3--N), ammonia nitrogen (NH4+-N), total nitrogen (TN), conductivity (Cond), and dissolved oxygen (DO) in reservoir areas were measured, and their correlations with abundance and diversity of eukaryotic plankton were analyzed. Results: The results showed the presence of 122 genera of eukaryotic plankton from 38 phyla. Eukaryotic plankton communities were mainly composed of Eurytemora, Thermocyclops, Sinocalanus, Mesocyclops, and Cryptomonas. In particular, significant differences in the diversity of eukaryotic plankton communities were found in vertical distribution. The diversity and abundance of eukaryotic plankton communities in 7 sampling sites decreased with the increase of depth from 0.5 to 10 m, while the diversity and abundance of plankton communities increased at 20 m. RDA analysis indicated that pH, depth, WT, NH4+-N, DO, Cond, and NO3--N could influence the vertical distribution of the eukaryotic plankton community in the Danjiangkou Reservoir. Among these eukaryotic plankton, Eurytemora, Thermocyclops, and Volvox were negatively correlated with pH and WT and positively correlated with depth. Discussion: This study revealed a novel perspective on the distribution of the eukaryotic plankton community in Danjiangkou Reservoir, particularly in terms of vertical variation, which will be helpful to comprehensively understand ecological processes and to further ensure the water quality safety in this canyon-style reservoir. [ABSTRACT FROM AUTHOR]

IntroductionEukaryotic plankton plays crucial roles in ecosystem processes, impacting aquatic ecosystem stability. This study focuses on Danjiangkou Reservoir, a canyon lake in central China, that acts as the water source of the Mid-route of the South-to-North Water Diversion Project.MethodsIn this study, high-throughput 18S rDNA gene sequencing was employed to investigate eukaryotic plankton community at four water depths (0.5 m, 5 m, 10 m, and 20 m). The environmental factors including pH, water temperature (WT), nitrate nitrogen (NO3−-N), ammonia nitrogen (NH4+-N), total nitrogen (TN), conductivity (Cond), and dissolved oxygen (DO) in reservoir areas were measured, and their correlations with abundance and diversity of eukaryotic plankton were analyzed.ResultsThe results showed the presence of 122 genera of eukaryotic plankton from 38 phyla. Eukaryotic plankton communities were mainly composed of Eurytemora, Thermocyclops, Sinocalanus, Mesocyclops, and Cryptomonas. In particular, significant differences in the diversity of eukaryotic plankton communities were found in vertical distribution. The diversity and abundance of eukaryotic plankton communities in 7 sampling sites decreased with the increase of depth from 0.5 to 10 m, while the diversity and abundance of plankton communities increased at 20 m. RDA analysis indicated that pH, depth, WT, NH4+-N, DO, Cond, and NO3−-N could influence the vertical distribution of the eukaryotic plankton community in the Danjiangkou Reservoir. Among these eukaryotic plankton, Eurytemora, Thermocyclops, and Volvox were negatively correlated with pH and WT and positively correlated with depth.DiscussionThis study revealed a novel perspective on the distribution of the eukaryotic plankton community in Danjiangkou Reservoir, particularly in terms of vertical variation, which will be helpful to comprehensively understand ecological processes and to further ensure the water quality safety in this canyon-style reservoir.

The size structure of microeukaryotic plankton communities exerts a fundamental control on marine ecosystem functions, such as food web dynamics and element flows. The global expansion of nitrogen (N) and phosphorus (P) nutrient pollutants into estuaries and coastal waters is causing public health and environmental concerns associated with microeukaryotic plankton activities. In the context of eutrophication, understanding how size structure and biotic activities of microeukaryotic plankton communities responds to anthropogenic nutrient inputs is vital to evaluate the future fate of coastal ecosystems. Here, we conducted onboard incubation experiments to provide the first investigation of how size structure and co-occurrence network of microeukaryotic plankton communities change under the dynamic nutrient conditions in the Pearl River Estuary. Our study revealed (1) a transition from P limitation to N limitation or potential NP co-limitation for the growth of pigmented protists along the Pearl River-South China Sea continuum, and isohaline ∼ 31.5 being the geographic boundary; (2) P availability drove the microeukaryotic plankton community size structure that the increased P inputs favored the dominance of nano-sized (3–20 μm) protists due to the increased relative abundance of Chlorophyta; (3) increased P inputs enhanced the species competition among phototrophic protists and improved the network stability of microeukaryotic plankton communities. In the future, if there is an increase in anthropogenic input of P in the Pearl River Estuary during summer, which would alleviate the pressure of P-deficiency, it is expected to increase the biomass of microeukaryotic plankton, with a dominance of nano-sized Chlorophyta. Altogether, this study advances our understanding of the geographic nutrient limitation pattern for pigmented protist plankton in the Pearl River Estuary, an urbanized estuarine ecosystem. Moreover, it enhances our knowledge regarding the response of marine microeukaryotic plankton communities to future environmental changes.

We compared the genetic diversity and relative abundance of eukaryotic plankton in Daya Bay using two genetic markers(18S rRNA V4 and V9 regions) to amplify the eDNA and high-throughput sequencing technology. 56 classes, 101 orders of zooplankton and 52 classes, 69 orders of phytoplankton were detected using 18S rDNA V4 markers. And 47 classes, 81 orders of zooplankton and 56 classes, 101 orders of phytoplankton were detected using 18S rDNA V9 markers. Both 18S rDNA V4 and V9 regions results performed well to coverage communities and provided similar eukaryotic plankton distribution patterns at class taxonomic level. Maxillopoda is the dominant group of zooplankton, while Dinophyceae, Coscinodiscophyceae and Mamiellophyceae are the dominant groups of phytoplankton. Especially, two genetic markers amplification results present the similar diversity and relative abundance of Dinophyceae at order taxonomic level. The results of 18S rDNA V9 region presented higher abundance of Coscinodiscophyceae than that of V4. The results showed that the diversity of zooplankton amplification by 18S rDNA V4 primers was higher than that of 18S rDNA V9 primers, while that of phytoplankton amplification by 18S rDNA V9 primers was higher than that of 18S rDNA V4 primers. In this study, we first report high abundance parasitic Syndiniales and Mamiellales in Daya Bay [ABSTRACT FROM AUTHOR]

The diversity and community assembly mechanisms of eukaryotic plankton in coastal waters is so far not clear. In this study, we selected the coastal waters of Guangdong-Hong Kong-Macao Greater Bay Area, which is a highly developed region in China, as the research area. By use of high-throughput sequencing technologies, the diversity and community assembly mechanisms of eukaryotic marine plankton were studied in which a total of 7,295 OTUs were obtained, and 2,307 species were annotated by doing environmental DNA survey of 17 sites consist of surface and bottom layer. Ultimately, the analysis reveals that the species abundance of bottom layer is, by and large, higher than that in the surface layer. In the bottom, Arthropoda is the first largest group, accounting for more than 20% while Arthropoda and Bacillariophyta are dominant groups in surface waters accounting for more than 40%. It is significant of the variance in alpha-diversity between sampling sites, and the difference of alpha-diversity between bottom sites is greater than that of surface sites. The result suggests that the environmental factors that have significant influence on alpha-diversity are total alkalinity and offshore distance for surface sites, and water depth and turbidity for bottom sites. Likewise, the plankton communities obey the typical distance-decay pattern. Analysis about community assembly mechanisms reveals that, overall, dispersal limitation is the major pattern of community formation, which accounts for more than 83% of the community formation processes, suggesting that stochastic processes are the crucial assembly mechanism of the eukaryotic plankton community in the study area.

Eukaryotic plankton are important parts of the aquatic ecosystem and their community composition and spatiotemporal distribution patterns are affected by environmental factors. The Liujiaxia Reservoir is located at the northeastern edge of the Tibetan Plateau and is a vital resource for communities and agriculture in the region. Revealing the plankton diversity and their correlation with environmental factors is essential for understanding the ecological processes and mechanisms by which plankton contribute to, and maintain the ecosystem function of, the Liujiaxia Reservoir and beyond. This study investigated the detailed spatiotemporal distribution patterns and assembly mechanisms of eukaryotic plankton communities in Liujiaxia Reservoir for three periods during 2021. Significant spatial and temporal variations of abundance and community distribution of eukaryotic plankton were demonstrated. In addition, environmental factors such as water transparency, total phosphorus, total nitrogen, ammonia nitrogen, and pH were confirmed to have the most significant impact on the distribution of these communities in the reservoir. The dominant eukaryotic plankton group was Pyrrophyta, and the species interactions were predominantly cooperative. The trophic level index indicated excellent overall water quality in the reservoir. Deterministic processes were demonstrated as the predominant factors governing the assembly of eukaryotic plankton communities. This study provides valuable insight into the eukaryotic plankton community structure in the Liujiaxia Reservoir and reveals the complex relationships between plankton communities, environmental factors, and water quality.IMPORTANCEBased on 18S rDNA high-throughput sequencing, the spatiotemporal distribution patterns and assembly mechanisms of eukaryotic plankton communities were investigated. This study provides valuable insight into the eukaryotic plankton community structure in the Liujiaxia Reservoir in the northeastern edge of the Tibetan Plateau, and the relationships between eukaryotic plankton communities, environmental factors, and water quality. Through the dynamic changes of these communities, the water quality of the reservoir was assessed to provide basic data for the protection of its biodiversity. The findings of the present study will help to improve knowledge and understanding of the ecological processes and mechanisms by which plankton contribute to ecosystem function in the Liujiaxia Reservoir and beyond.

The cell size of microbial eukaryotic plankton normally ranges from 0.2 to 200 µm. During the past decade, high-throughput sequencing of DNA has been revolutionizing their study on an unprecedented scale. Nonetheless, it is currently unclear whether we can accurately, effectively, and quantitatively depict the microbial eukaryotic plankton community using size-fractionated filtration combined with environmental DNA (eDNA) molecular methods. Here we assessed the microbial eukaryotic plankton communities with two filtering strategies from two subtropical reservoirs, that is one-step filtration (0.2–200 µm) and size-fractionated filtration (0.2–3 and 3–200 µm). The difference of 18S rRNA gene copy abundance between the two filtering treatments was less than 50% of the 0.2–200 µm microbial eukaryotic community for 95% of the total samples. Although the microbial eukaryotic plankton communities within the 0.2–200 µm and the 0.2–3 and 3–200 µm size fractions had approximately identical 18S rRNA gene copies, there were significant differences in their community composition. Furthermore, our results demonstrate that the systemic bias introduced by size-fractionation filtration has more influence on unique OTUs than shared OTUs, and the significant differences in abundance between the two eukaryotic plankton communities largely occurred in low-abundance OTUs in specific seasons. This work provides new insights into the use of size-fractionation in molecular studies of microbial eukaryotes populating the plankton. [ABSTRACT FROM AUTHOR]

Planktonic eukaryotes are important components of aquatic ecosystems, and analyses of the whole eukaryotic planktonic community composition and function have far-reaching significance for water resource management. We aimed to understand the spatiotemporal variation and drivers of eukaryotic plankton distribution in the Middle Route Project of the South-to-North Water Diversion in Henan Province, China. Specifically, we examined planktonic assemblages and water quality at five stations along the canal and another one located before the dam in March, June, September, and December 2019. High-throughput sequencing revealed that the eukaryotic plankton community was primarily composed of 53 phyla, 200 genera, and 277 species, with Cryptophyta, Ciliophora, and norank_k_Cryptophyta being the dominant phyla. Redundancy analysis of the eukaryotic community and environmental factors showed that five vital factors affecting eukaryotic plankton distribution were oxidation-reduction potential, nitrate nitrogen, pH, total phosphorus, and water flow velocity. Furthermore, the geographical distribution of eukaryotic communities was consistent with the distance decay model. Importantly, environmental selection dominantly shaped the geographical distribution of the eukaryotic community. In summary, our study elucidates the ecological response of planktonic eukaryotes by identifying the diversity and ecological distribution of planktonic eukaryotes in trans-basin diversion channels.

Eukaryotic communities play an important role in the coastal ecosystem of Xiangshan Bay, a narrow semi-closed bay famous for fisheries and marine farming. However, information on the diversity and composition of eukaryotic communities in Xiangshan Bay remains unclear. In this study, the metabarcoding approach was utilized to comprehensively investigate the eukaryotic plankton community structure and dominant taxa, particularly eukaryotic microalgae, in the Xiangshan Bay over a period of four months in 2018. The results showed that the three major phyla were Arthropoda, Chlorophyta, and Bacillariophyta. The richness indices revealed that species richness peaked in February and was at its lowest in May. Diversity indices showed that the samples collected in May had the lowest diversity. Centropages was detected in the samples of all months, however, its highest dominance was observed in the samples collected in February. In addition, compared to other months, a greater proportion of eukaryotic microalgae was witnessed in March. The three eukaryotic algae with highest abundances in March were Cyclotella , Prorocentrum , and Thalassiosira. Moreover, high diversity of pico-sized (0.2–2.0 μm) phytoplankton (which are often easily missed by microscopy) was discovered in this study by using metabarcoding approach. This study highlights the strength and significance of the metabarcoding approach to uncover a large number of eukaryotic species which remains undetectable during application of conventional approaches. The findings of this study reveals that the eukaryotic community structure varies noticeably in both time and space throughout sampling period, with temperature being the most important environmental factor influencing these changes. This study lays a solid foundation to understand eukaryotic plankton composition, temporal and spatial dynamics and the distribution mechanism of eukaryotic plankton community in Xiangshan Bay, providing theoretical reference for further studies related to marine ecology. • This study highlights the significance of the metabarcoding approach to uncover a large number of microeukaryotic species. • In this study, the three major phyla were Arthropoda, Chlorophyta, and Bacillariophyta. • Temperature was the most significant impact on eukaryotic communities in the Xiangshan Bay. [ABSTRACT FROM AUTHOR]

Eukaryotic plankton are important parts of the marine biome and play an important role in maintaining the stability of marine ecosystems. In order to characterize the eukaryotic plankton communities in the South Yellow Sea Cold Water Mass (CWM) and the South Yellow Sea nearshore waters (NW) in October 2019, Illumina high–throughput sequencing was performed using the 18S rDNA V9 region as the target gene. Environmental factors (depth, pH, salinity, temperature, Chl a, nitrate, nitrite, ammonium, silicate, phosphate) in two sea areas were measured, and their correlations with abundance and diversity of eukaryotic plankton were analyzed. A total of 807 species of plankton were identified, of which 663 species in 24 categories were from the CWM area, and 614 species in 26 categories were from NW. The total phytoplankton abundance in CWM waters was higher than that in NW. Dinophyta and Bacillariophyta were the most abundant phyla of phytoplankton in the two areas. Arthropoda and Cnidaria were the major zooplankton taxa. The dominant fungal population was mainly Basidiomycota. Both the CWM and NW have effects on dissolved inorganic nutrient concentrations and plankton abundance. Environmental factor correlation analysis showed that the concentration of dissolved inorganic nutrients within the CWM increased with water depth and the abundance of plankton gradually increased. Ammonium salts, nitrates, phosphates, silicates and water depth were important factors affecting phytoplankton growth. Phytoplankton abundance increased with increasing concentrations of inorganic nutrients. Bacillariophyta showed a strong positive correlation with silicates and depth. Depth and microscopic phytoplankton abundance were important factors influencing the structure of the zooplankton community.

[Display omitted] • Isohaline ∼31.5 is the geographic boundary of P-limited Pearl River Diluted Water and N-limited South China Sea Water. • Increased phosphorus inputs promote the dominance of nano-sized Chlorophyta in the Pearl River Estuary in summer. • Increased phosphorus inputs induce species competitions among pigmented protists in the Pearl River Estuary in summer. • Increased phosphorus inputs stabilize microeukaryotic plankton co-occurrence network in the Pearl River Estuary in summer. The size structure of microeukaryotic plankton communities exerts a fundamental control on marine ecosystem functions, such as food web dynamics and element flows. The global expansion of nitrogen (N) and phosphorus (P) nutrient pollutants into estuaries and coastal waters is causing public health and environmental concerns associated with microeukaryotic plankton activities. In the context of eutrophication, understanding how size structure and biotic activities of microeukaryotic plankton communities responds to anthropogenic nutrient inputs is vital to evaluate the future fate of coastal ecosystems. Here, we conducted onboard incubation experiments to provide the first investigation of how size structure and co-occurrence network of microeukaryotic plankton communities change under the dynamic nutrient conditions in the Pearl River Estuary. Our study revealed (1) a transition from P limitation to N limitation or potential NP co-limitation for the growth of pigmented protists along the Pearl River-South China Sea continuum, and isohaline ∼ 31.5 being the geographic boundary; (2) P availability drove the microeukaryotic plankton community size structure that the increased P inputs favored the dominance of nano-sized (3–20 μm) protists due to the increased relative abundance of Chlorophyta; (3) increased P inputs enhanced the species competition among phototrophic protists and improved the network stability of microeukaryotic plankton communities. In the future, if there is an increase in anthropogenic input of P in the Pearl River Estuary during summer, which would alleviate the pressure of P-deficiency, it is expected to increase the biomass of microeukaryotic plankton, with a dominance of nano-sized Chlorophyta. Altogether, this study advances our understanding of the geographic nutrient limitation pattern for pigmented protist plankton in the Pearl River Estuary, an urbanized estuarine ecosystem. Moreover, it enhances our knowledge regarding the response of marine microeukaryotic plankton communities to future environmental changes. [ABSTRACT FROM AUTHOR]

Freshwater systems are characterized by an enormous diversity of eukaryotic protists and prokaryotic taxa. The community structures in different lakes are thereby influenced by factors such as habitat size, lake chemistry, biotic interactions, and seasonality. In our study, we used high throughput 454 sequencing to study the diversity and temporal changes of prokaryotic and eukaryotic planktonic communities in three Austrian lakes during the ice-free season. In the following year, one lake was sampled again with a reduced set of sampling dates to observe reoccurring patterns. Cluster analyses (based on SSU V9 (eukaryotic) and V4 (prokaryotic) OTU composition) grouped samples according to their origin followed by separation into seasonal clusters, indicating that each lake has a unique signature based on OTU composition. These results suggest a strong habitat-specificity of microbial communities and in particular of community patterns at the OTU level. A comparison of the prokaryotic and eukaryotic datasets via co-inertia analysis (CIA) showed a consistent clustering of prokaryotic and eukaryotic samples, probably reacting to the same environmental forces (e.g., pH, conductivity). In addition, the shifts in eukaryotic and bacterioplanktonic communities generally occurred at the same time and on the same scale. Regression analyses revealed a linear relationship between an increase in Bray–Curtis dissimilarities and elapsed time. Our study shows a pronounced coupling between bacteria and eukaryotes in seasonal samplings of the three analyzed lakes. However, our temporal resolution (biweekly sampling) and data on abiotic factors were insufficient to determine if this was caused by direct biotic interactions or by reacting to the same seasonally changing environmental forces.

Freshwater systems are characterized by an enormous diversity of eukaryotic protists and prokaryotic taxa. The community structures in different lakes are thereby influenced by factors such as habitat size, lake chemistry, biotic interactions, and seasonality. In our study, we used high throughput 454 sequencing to study the diversity and temporal changes of prokaryotic and eukaryotic planktonic communities in three Austrian lakes during the ice-free season. In the following year, one lake was sampled again with a reduced set of sampling dates to observe reoccurring patterns. Cluster analyses (based on SSU V9 (eukaryotic) and V4 (prokaryotic) OTU composition) grouped samples according to their origin followed by separation into seasonal clusters, indicating that each lake has a unique signature based on OTU composition. These results suggest a strong habitat-specificity of microbial communities and in particular of community patterns at the OTU level. A comparison of the prokaryotic and eukaryotic datasets via co-inertia analysis (CIA) showed a consistent clustering of prokaryotic and eukaryotic samples, probably reacting to the same environmental forces (e.g., pH, conductivity). In addition, the shifts in eukaryotic and bacterioplanktonic communities generally occurred at the same time and on the same scale. Regression analyses revealed a linear relationship between an increase in Bray-Curtis dissimilarities and elapsed time. Our study shows a pronounced coupling between bacteria and eukaryotes in seasonal samplings of the three analyzed lakes. However, our temporal resolution (biweekly sampling) and data on abiotic factors were insufficient to determine if this was caused by direct biotic interactions or by reacting to the same seasonally changing environmental forces. [ABSTRACT FROM AUTHOR]

Eukaryotic plankton are pivotal members of marine ecosystems playing crucial roles in marine food webs and biogeochemical cycles. However, understanding the patterns and drivers of their community assembly remains a grand challenge. A study was conducted in the northern South China Sea (SCS) to address this issue. Here, 49 samples were collected and size-fractionated from discrete depths at continental shelf and continental slope in the northern SCS over a diel cycle. From high throughput sequencing of the 18S rDNA gene V4 region, 2463 operational taxonomic units (OTUs) were retrieved. Alveolata and Opisthokonta overwhelmingly dominated the assemblages in the abundance (44.76%, 31.08%) and species richness (59%, 12%). Biodiversity was higher in the slope than the shelf and increased with depth. Temperature and salinity appeared to be the most important deterministic drivers of taxon composition. Community structure was influenced by multiple factors in the importance order of: environmental factors (temperature + salinity) > spatial factor > water depth > sampling time. Furthermore, the neutral model explained more variations in the smaller-sized (0.22–3 μm) community (24%) than larger-sized (3–200 μm) community (16%) but generally explained less variations than did deterministic processes. Additionally, our data indicated that the larger plankton might be more environmentally filtered and less plastic whereas the smaller plankton had stronger dispersal ability. This study sheds light on the differential contributions of the deterministic process and stochastic process and complexities of assembly mechanisms in shaping the community assembly of micro-nano and pico-eukaryotic biospheres in a subtropical ocean. [Display omitted] • Alveolata and Opisthokonta dominated the assemblages in the abundance and species richness. • Abundance and species richness were higher in the continental slope than the continental shelf. • Temperature and salinity appeared to be the most important deterministic drivers of taxon composition. • The neutral model explained more variations in the smaller-sized community than larger-sized community. [ABSTRACT FROM AUTHOR]

The diversity and community assembly mechanisms of eukaryotic plankton in coastal waters is so far not clear. In this study, we selected the coastal waters of Guangdong-Hong Kong-Macao Greater Bay Area, which is a highly developed region in China, as the research area. By use of high-throughput sequencing technologies, the diversity and community assembly mechanisms of eukaryotic marine plankton were studied in which a total of 7,295 OTUs were obtained, and 2,307 species were annotated by doing environmental DNA survey of 17 sites consist of surface and bottom layer. Ultimately, the analysis reveals that the species abundance of bottom layer is, by and large, higher than that in the surface layer. In the bottom, Arthropoda is the first largest group, accounting for more than 20% while Arthropoda and Bacillariophyta are dominant groups in surface waters accounting for more than 40%. It is significant of the variance in alpha-diversity between sampling sites, and the difference of alpha-diversity between bottom sites is greater than that of surface sites. The result suggests that the environmental factors that have significant influence on alpha-diversity are total alkalinity and offshore distance for surface sites, and water depth and turbidity for bottom sites. Likewise, the plankton communities obey the typical distance-decay pattern. Analysis about community assembly mechanisms reveals that, overall, dispersal limitation is the major pattern of community formation, which accounts for more than 83% of the community formation processes, suggesting that stochastic processes are the crucial assembly mechanism of the eukaryotic plankton community in the study area., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Yan, Zhu, Zhang, Jiang, Wang, Wei, Wang, Shao, Liu and Wang.)

Metabarcoding technology using high-throughput sequencing has revolutionized the current understanding of the diversity and ecology of eukaryotic microorganisms. The aim of the present study was to investigate vertical and seasonal variation in eukaryotic plankton communities and to assess the diversity of eukaryotic plankton, using 18S rRNA sequencing, over a depth gradient in subtropical waters affected by the Kuroshio Current. In particular, the present study focused on the diversity and ecology of Alveolata and Rhizaria taxa, which include a variety of plankton species with fragile skeletons or soft bodies. Three vertically distinct eukaryotic communities were identified: the Kuroshio-influenced epipelagic zone (<200 m), the North Pacific Intermediate Water (NPIW)-dominated mesopelagic zone (500–1000 m), and the bathypelagic zone (2000–3000 m). The operational taxonomic unit (OTU) richness was greatest near the surface (<200 m depth), gradually decreasing with increasing depth, and lowest in deeper layers, and OTU diversity (Pielou's evenness and Shannon-Wiener diversity indices) were lowest in the mesopelagic layer (500–1000 m depth). Hidden diversity was observed in both groups in both the surface and deeper layers of the western North Pacific, as well as in the NPIW, which was characterized by the lowest salinity and oxygen concentrations in the study area. In the NPIW, the Rhizaria yielded relatively more sequence reads than other taxa. Furthermore, specific taxa, such as Collodaria (Radiolaria), Syndiniales (dinoflagellates), and Oligohymenophorea (ciliates), were predominant, according to OTU richness and the relative abundance of sequence reads. These findings indicate that a unique ecosystem was formed over time in the NPIW-isolated water mass. • Eukaryotic community zoned vertically, Kuroshio epi-, NPIW meso- and bathypelagic. • Eukaryotic plankton diversity was remarkably low in the NPIW. • Collodaria, Syndiniales and Oligohymenophorea were predominant in the NPIW. • Acantharia, Nassellaria, Spumellaria and Phaeodaria OTUs peaked at 100 m depth. • Taxopodia, Nassellaria and "Other Cercozoa" reads peaked in the deepest layer. [ABSTRACT FROM AUTHOR]

The cell size of microbial eukaryotic plankton normally ranges from 0.2 to 200 μm. During the past decade, high-throughput sequencing of DNA has been revolutionizing their study on an unprecedented scale. Nonetheless, it is currently unclear whether we can accurately, effectively, and quantitatively depict the microbial eukaryotic plankton community using size-fractionated filtration combined with environmental DNA (eDNA) molecular methods. Here we assessed the microbial eukaryotic plankton communities with two filtering strategies from two subtropical reservoirs, that is one-step filtration (0.2-200 μm) and size-fractionated filtration (0.2-3 and 3-200 μm). The difference of 18S rRNA gene copy abundance between the two filtering treatments was less than 50% of the 0.2-200 μm microbial eukaryotic community for 95% of the total samples. Although the microbial eukaryotic plankton communities within the 0.2-200 μm and the 0.2-3 and 3-200 μm size fractions had approximately identical 18S rRNA gene copies, there were significant differences in their community composition. Furthermore, our results demonstrate that the systemic bias introduced by size-fractionation filtration has more influence on unique OTUs than shared OTUs, and the significant differences in abundance between the two eukaryotic plankton communities largely occurred in low-abundance OTUs in specific seasons. This work provides new insights into the use of size-fractionation in molecular studies of microbial eukaryotes populating the plankton., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Ma, Logares, Xue and Yang.)

Phytoplankton are primary producers and can be important indicators of environmental change. To monitor the plankton species composition of environmental seawater samples, we developed a molecular method composed of colony polymerase chain reaction (PCR), polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and sequencing. A clone library of the ribosomal small subunit RNA gene (18S rDNA) in the nuclear genome was constructed by environmental PCR using a newly designed primer set and clones were directly amplified by colony PCR. To select unique putative clones, we choose a PCR-RFLP method that employed two restriction enzymes ( MseI and Tsp509I). After the PCR-RFLP pattern was evaluated, selected clones were sequenced and analyzed. In this study, we revealed the hidden biodiversity in environmental seawater containing a wide range of taxonomic groups in the Alveolata (Ciliphora and Dinophyceae), Euglenozoa, Stramenopiles (Bacillariophyta), and Viridiplantae (Chlorophyta) without the need to conduct extensive colony isolation techniques. Moreover, we found species of fungi and Metazoa (Arthropoda, Annelida, and Mollusca). Therefore, this improved molecular method can be used to generate a robust database describing the species diversity of environmental samples and provide useful information regarding the dynamics of the eukaryotic plankton community structure. [ABSTRACT FROM AUTHOR]

Eukaryotic plankton are important parts of the marine biome and play an important role in maintaining the stability of marine ecosystems. In order to characterize the eukaryotic plankton communities in the South Yellow Sea Cold Water Mass (CWM) and the South Yellow Sea nearshore waters (NW) in October 2019, Illumina high–throughput sequencing was performed using the 18S rDNA V9 region as the target gene. Environmental factors (depth, pH, salinity, temperature, Chl a, nitrate, nitrite, ammonium, silicate, phosphate) in two sea areas were measured, and their correlations with abundance and diversity of eukaryotic plankton were analyzed. A total of 807 species of plankton were identified, of which 663 species in 24 categories were from the CWM area, and 614 species in 26 categories were from NW. The total phytoplankton abundance in CWM waters was higher than that in NW. Dinophyta and Bacillariophyta were the most abundant phyla of phytoplankton in the two areas. Arthropoda and Cnidaria were the major zooplankton taxa. The dominant fungal population was mainly Basidiomycota. Both the CWM and NW have effects on dissolved inorganic nutrient concentrations and plankton abundance. Environmental factor correlation analysis showed that the concentration of dissolved inorganic nutrients within the CWM increased with water depth and the abundance of plankton gradually increased. Ammonium salts, nitrates, phosphates, silicates and water depth were important factors affecting phytoplankton growth. Phytoplankton abundance increased with increasing concentrations of inorganic nutrients. Bacillariophyta showed a strong positive correlation with silicates and depth. Depth and microscopic phytoplankton abundance were important factors influencing the structure of the zooplankton community. [ABSTRACT FROM AUTHOR]