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The shallow-sea hydrothermal vent at Guishan Islet, located off the coast of Taiwan, serves as a remarkable natural site for studying microbial ecology in extreme environments. In April 2019, we investigated the composition of prokaryotic picoplankton communities, their gene expression profiles, and the dissolved inorganic carbon uptake efficiency. Our results revealed that the chemolithotrophs Thiomicrorhabdus spp. contributed to the majority of primary production in the waters affected by the hydrothermal vent plume. The metatranscriptomic analysis aligned with the primary productivity measurements, indicating the significant gene upregulations associated with carboxysome-mediated carbon fixation in Thiomicrorhabdus. Synechococcus and Prochlorococcus served as the prokaryotic photoautotrophs for primary productivity in the waters with lower influence from hydrothermal vent emissions. Thiomicrorhabdus and picocyanobacteria jointly provided organic carbon for sustaining the shallow-sea hydrothermal vent ecosystem. In addition to the carbon fixation, the upregulation of genes involved in the SOX (sulfur-oxidizing) pathway, and the dissimilatory sulfate reduction indicated that energy generation and detoxification co-occurred in Thiomicrorhabdus. This study improved our understanding of the impacts of shallow-sea hydrothermal vents on the operation of marine ecosystems and biogeochemical cycles.

Throughout the western tropical Pacific Ocean, eddies and currents play an important role in biogeochemical cycling. Many studies have investigated the effects of hydrography on vertical patterns of picophytoplankton and heterotrophic bacterial abundance in mesoscale eddies. There is a lack of field observations to determine what impact dynamic hydrological systems of eddies have on prokaryotic community activity (growth and mortality rates). An objective of this study was to examine how anticyclonic eddies influence picoplankton abundance and activity (growth and mortality rates). To meet this purpose, heterotrophic bacterial and picophytoplankton growth and mortality rates were examined by modified dilution experiments conducted at the surface, deep chlorophyll maximum (DCM), and 200 m depth outside (OE) and inside of warm eddies core (EC) in the west Pacific Ocean. A high heterotrophic bacterial grazing rate was found in the EC region in the present study. Furthermore, the picophytoplankton grazing rate in EC was frequently greater than the grazing rate in OE. Furthermore, the higher grazing rates in the EC region cause a lower proportion of viral lysis to account for heterotrophic bacteria and picophytoplankton mortality. The results of our experiments suggest that downwelling in EC might increase picophytoplankton growth and grazing rates, increasing the carbon sink in the warm eddy and potentially increasing ocean carbon storage.

In mesoscale eddies, the chemical properties and biological composition are different from those in the surrounding water due to their unique physical processes. The mechanism of physical–biological coupling in warm-core eddies is unclear, especially because no studies have examined the effects of environmental factors on bacteria and viruses. The purpose of the present study was to examine the influence of an anticyclonic warm eddy on the relationship between bacterial and viral abundances, as well as viral activity (viral production), at different depths. At the core of the warm eddy, the bacterial abundance (0.48 to 2.82 × 105 cells mL−1) fluctuated less than that outside the eddy (1.12 to 7.03 × 105 cells mL−1). In particular, there was a four-fold higher viral–bacterial abundance ratio (VBR) estimated within the eddy, below the layer of the deep chlorophyll maximum, than outside the eddy. An anticyclonic warm eddy with downwelling at its center may contribute to viruses being transmitted directly into the deep ocean through adsorption on particulate organic matter while sinking. Overall, our findings provide valuable insights into the interaction between bacterial and viral abundances and their ecological mechanisms within a warm eddy.

The first investigations of seasonal N2O variations and water-to-air fluxes in the Tamsui River estuary and its adjacent sea were carried out in this study. In the Tamsui River estuary, the concentration of N2O decreased with increasing salinity. The seasonal variations of N2O concentrations in the estuary were 46.8–148.5 nM in autumn, 15.9–82.5 nM in spring, 11.0–42.0 nM in summer and 13.1–120.6 nM in winter. When salinity regressed to zero, N2O concentration was highest in autumn, followed by winter, spring, and summer, which might be influenced by the DO and NO3− concentrations as well as temperature. Because of mountains occlusion, the seasonal variations in wind speed were not large in the Tamsui River estuary. Seasonal variations of N2O fluxes in the estuary were 10.9–35.6 μmol m−2 d−1 in autumn, 2.8–15.1 μmol m−2 d−1 in spring, 2.4–9.5 μmol m−2 d−1 in summer and 2.7–26.8 μmol m−2 d−1 in winter. In the adjacent sea of Tamsui River estuary, seasonal average N2O concentrations in the surface seawater were 10.3 ± 0.2 nM in autumn, 11.6 ± 1.2 nM in spring, 11.4 ± 0.7 nM in summer and 13.8 ± 0.9 nM in winter, with no significantly seasonal changes while wind speed varied greatly seasonally. Seasonal variations of average N2O fluxes in Tamsui River estuary’s adjacent sea were 40.3 ± 0.7 μmol m−2 d−1 in autumn, 19.7 ± 2.1 μmol m−2 d−1 in spring, 20.9 ± 1.3 μmol m−2 d−1 in summer and 49.0 ± 3.3 μmol m−2 d−1 in winter. As a result, seasonal variations in N2O fluxes in the estuary were dominated by N2O concentrations in the water, whereas in the sea, it was dominated by wind speed. Overall, the Tamsui River estuary and its adjacent sea were net sources of atmospheric N2O with annual average fluxes 10.6 ± 6.7 and 32.5 ± 14.5 μmol m−2 d−1, respectively.

ABSTRACT Trade-offs between competitive ability and resistance to top-down control manifest the “kill-the-winner” hypothesis that explains how mortality caused by protists and viruses can promote bacterial diversity. However, the existence of such trade-offs has rarely been investigated in natural marine bacterial communities. To address this question, we conducted on-board dilution experiments to manipulate top-down control pressure (protists only or protists plus viruses [protists+viruses] combined) and then applied 16S rRNA gene high-throughput sequencing techniques to assess the responses of each bacterial taxon. Dilution experiments enabled us to measure the top-down-control-free growth rate as the competitive ability and top-down-control-caused mortality as the reverse of resistance to top-down control. Overall, bacterial taxa with higher top-down-control-free growth rates were accompanied by lower top-down-control-caused resistance. Furthermore, competition-resistance trade-offs were stronger and more consistent when top-down control was caused by protists+viruses combined than by protists only. When protists+viruses were diluted, the bacterial rank abundance distribution became steepened and evenness and richness were decreased. However, when protists were diluted, only richness decreased. Our results indicate the existence of competition-resistance trade-offs in marine microbes and demonstrate the positive impacts of such trade-offs on bacterial diversity. Regardless, the strength of the competition-resistance trade-offs and the impacts on bacterial diversity were contingent on whether top-down control was caused by protists+viruses combined or protists only. IMPORTANCE We addressed the “kill-the-winner” hypothesis from the perspective of its principle (the competition-resistance trade-off) in marine bacterial communities incubated in situ. Our results supported the existence of competition-resistance trade-offs and the positive effect on bacterial community diversity. The study linked theoretical expectations and complex natural systems and provided new knowledge regarding how top-down controls and competition trade-offs shaped natural bacterial communities.

ABSTRACT The presence of more species in the community of a sampling site (α diversity) typically increases ecosystem functions via nonrandom processes like resource partitioning. When considering multiple communities, we hypothesize that higher compositional difference (β diversity) increases overall functions of these communities. Further, we hypothesize that the β diversity effect is more positive when β diversity is increased by nonrandom assembly processes. To test these hypotheses, we collected bacterioplankton along a transect of 6 sampling sites in the southern East China Sea in 14 cruises. For any pairs of the 6 sites within a cruise, we calculated the Bray-Curtis index to represent β diversity and summed bacterial biomass as a proxy to indicate the overall function of the two communities. We then calculated deviation of observed mean pairwise phylogenetic similarities among species in two communities from random to represent the influences of nonrandom processes. The bacterial β diversity was found to positively affect the summed bacterial biomass; however, the effect varied among cruises. Cross-cruise comparison indicated that the β diversity effect increased with the nonrandom processes selecting for phylogenetically dissimilar species. This study extends biodiversity-ecosystem functioning research to the scale of multiple sites and enriches the framework by considering community assembly processes. IMPORTANCE The implications of our analyses are twofold. First, we emphasize the importance of studying β diversity. We expanded the current biodiversity-ecosystem functioning framework from single to multiple sampling sites and investigated the influences of species compositional differences among sites on the overall functioning of these sites. Since natural ecological communities never exist alone, our analyses allow us to more holistically perceive the role of biodiversity in natural ecosystems. Second, we took community assembly processes into account to attain a more mechanistic understanding of the impacts of biodiversity on ecosystem functioning.

The nutrient-scarce, warm, and high-salinity Kuroshio current has a profound impact on both the marine ecology of the northwestern Pacific Ocean and the global climate. This study aims to reveal the seasonal dynamics of picoplankton in the subtropical Kuroshio current. Our results showed that one of the picocyanobacteria, Synechococcus, mainly distributed in the surface water layer regardless of seasonal changes, and the cell abundance ranged from 104 to 105 cells mL−1. In contrast, the maximum concentration of the other picocyanobacteria, Prochlorococcus, was maintained at more than 105 cells mL−1 throughout the year. In the summer and the autumn, Prochlorococcus were mainly concentrated at the water layer near the bottom of the euphotic zone. They were evenly distributed in the euphotic zone in the spring and winter. The stirring effect caused by the monsoon determined their distribution in the water column. In addition, the results of 16S rRNA gene diversity analysis showed that the seasonal changes in the relative abundance of Synechococcus and Prochlorococcus in the surface water of each station accounted for 20 to 40% of the total reads. The clade II of Synechococcus and the High-light II of Prochlorococcus were the dominant strains in the waters all year round. Regarding other picoplankton, Proteobacteria and Actinobacteria occupied 45% and 10% of the total picoplankton in the four seasons. These data should be helpful for elucidating the impacts of global climate changes on marine ecology and biogeochemical cycles in the Western Boundary Currents in the future.

To elucidate the trophic link between classical and microbial food webs in the coastal ecosystem of Matsu Island during the warmer (27.5°C) and colder (16°C) months, we estimated the impact of mesozooplankton and microzooplankton grazing on > 20 μm and < 20 μm phytoplankton groups, respectively. In the warmer months, the > 20 μm fraction of Chl a accounted for more than 70% of the total Chl a; however, the Chl a > 20 μm fraction contributed little to the total phytoplankton biomass, at about 16%, in the colder months. Overall, the < 20 μm fraction represented 26 and 90% of the < 200 μm daily primary production in the warmer and colder months, respectively. Furthermore, the grazing loss of mesozooplankton on microzooplankton was 4.7 mgC m-3 d-1 in the warmer months; however, no significant loss rate was measured in the colder months. The results showed that large autotrophs (> 20 μm) were available for direct mesozooplankton ingestion, which indicated that they could be considered as an important link in the complex food web structures, particularly during the warmer season.

Globally, the continental shelf occupies less than 10% of the total sea surface, but supports substantial primary production and fisheries. Photosynthetic picoeukaryotes (PPE) are important primary producers in marine ecosystems, and chlorophytes make a significant contribution to PPE abundance. Although the distribution of chlorophytes has been widely studied, little is known about how their community composition varies along the coastal-offshore gradient in subtropical continental shelf waters. To better understand their spatial variations, we employed metabarcoding data of 18S rRNA V4 gene to examine chlorophyte composition within the surface and deep chlorophyll maximum (DCM) layers over the continental shelf in the East China Sea (ECS) with high-resolution sampling. Our results indicate a higher chlorophyte diversity in the surface layer than in the DCM. In addition, we found that chlorophytes in oligotrophic Kuroshio surface water were the most diverse, with a higher percentage of Chloropicophyceae, prasinophyte clade V, prasinophyte clade IX, Palmophyllophyceae and Chlorodendrophyceae. In more eutrophic waters along the coast and within the DCM layer, chlorophytes were dominated by Mamiellophyceae. A significant spatial variation in community composition occurred along the nutrient gradient in the subtropical continental shelf ecosystem, varying from Mamiellophyceae-dominant in coastal water to Chloropicophyceae-dominant in offshore water. Furthermore, at a low saline coastal station, which had the lowest chlorophyte diversity, Picochlorum (Trebouxiophyceae) was dominant. Overall, chlorophyte diversity was positively correlated with temperature, and negatively correlated with silicate concentration. This study revealed that terrestrial input into continental systems influences chlorophyte diversity in the subtropical northwestern Pacific Ocean.

The transient impact of flooding on the community composition of marine picoeukaryotes (PEs, cell size ≤5 μm) in the East China Sea (ECS) was revealed in this study. In a summer without flooding (i.e., July 2009), photosynthetic picoeukaryotes (PPEs) were more abundant in the area covered by the Changjiang River diluted water (CDW, salinity ≤31) than in the non-CDW affected area. According to the 18S ribosomal RNA phylogeny, Alveolata (all from the superclass Dinoflagellata) was the main community component accounting for 72 to 99% of the community at each sampling station during the nonflooded summer. In addition to Dinoflagellata, diatoms or Chlorophyta also contributed a considerable proportion to the PE assemblage at the stations close to the edge of CDW coverage. In July 2010, an extreme flooding event occurred in the Changjiang River basin and led to the CDW covering nearly half of the ECS. In the flooded summer, the abundance of PPEs in the CDW-covered area decreased significantly to less than 1 × 104 cells ml-1. Compared to that during the nonflooded summer, the diversity of the PE composition was increased. While Dinophyceae still dominated the surface waters, Syndiniophyceae, which were represented by the uncultured Marine Alveolata Group (MALV)-I and MALV-II, accounted for a substantial amount in the Dinoflagellata superclass relative to this community composition in the nonflooded summer. Furthermore, a variety of plankton, including Cryptophyta, Haptophyta, Picobiliphyta, the uncultured Marine Stramenopiles (MASTs) and heterotrophic nanoflagellates, were observed. The nutrition modes of these PEs have been reported to be mixotrophic or heterotrophic. Therefore, it was inferred that the potentially mixotrophic and heterotrophic PE compositions might be favored in the marginal sea in the flooded summer.

Methane (CH4) is an important greenhouse gas, and its concentrations in aquatic areas are heavily influenced by anthropogenic activities, especially human-induced eutrophication, polluted river discharge and wastewater treatment plant (WWTP) effluents. Although coastal areas and estuaries contribute large amounts of global oceanic CH4 emissions, the relative contributions of different sources have not been well determined. The Tamsui River located in northern Taiwan is an urban river flowing through populated cities and thus likely carries large amounts of contaminants, such as nutrients and organic matter to the estuary. In this study, we characterized the spatial distribution and seasonal variations in CH4 in the Tamsui River estuary adjacent marine areas. The sea-to-air CH4 fluxes were also estimated to quantify the strength of the study area as an atmospheric CH4 source. Our results showed that CH4 concentrations in coastal sea areas were influenced by WWTP effluents, sediment and freshwater inputs. Thus, river discharge and nutrient levels as well as strong vertical mixing and disturbances might increase CH4 concentrations and emissions. The seasonal surface CH4 concentrations and sea-to-air CH4 fluxes were 13.7 ± 18.7 nM and 41.7 ± 68.0 μmol m-2 d-1 in autumn; 29.3 ± 19.8 nM and 61.3 ± 44.6 μmol m-2 d-1 in spring; 21.8 ± 13.9 nM and 37.0 ± 26.2 μmol m-2 d-1 in summer; and 27.0 ± 21.4 nM and 85.9 ± 75.4 μmol m-2 d-1 in winter.

Hypoxia and upwelling co-occur in the summer, and well-mixed water typically reaches the subsurface in the East China Sea (ECS), especially off the Changjiang River estuary. The impact of upwelling on hypoxia and, therefore, on the ecosystem in the ECS is not known. This study demonstrates both positive and negative effects of upwelling on hypoxia and its impact on the ecosystem. With upwelling, the spatial extent of hypoxic water increases with a lower pH but waters with high regenerated nutrients and fugacity of CO2 (fCO2), which are normally confined to the near-bottom, are found just up to 5–10 m below the surface. This upwelled high nutrient water can enhance phytoplankton growth in this region. On one occasion in August 2014, upwelling reached to the surface and lasted for 3 weeks, with the area of coverage ranging from 326.8 to 24,368.0 km2. During this event, the water was mixed thoroughly throughout the water column, with high concentrations of nutrients, chlorophyll a, and slightly undersaturated dissolved oxygen but saturated fCO2, alongside a normal pH. This event may have served as an important pathway from the ocean to the atmosphere for the regenerated CO2. It also provided a productive and suitable environment for marine life and ventilation to alleviate low-oxygen stress in this hypoxic but upwelling region in the ECS.

In contrast to other seagrass meadows where seawater carbonate chemistry generally shows strong diel variations with higher pH but lower partial pressure of CO2 (pCO2) during the daytime and lower pH but higher pCO2 during nighttime due to the alternation in photosynthesis and respiration, the seagrass meadows of the inner lagoon (IL) on Dongsha Island had a unique diel pattern with extremely high pH and low pCO2 across a diel cycle. We suggest that this distinct diel pattern in pH and pCO2 could be associated with the enhancement of total alkalinity (TA) production coupled to carbonate sediment dissolution in a semienclosed lagoon. The confinement of the IL may hamper water exchange and seagrass detritus export to the adjacent open ocean, which may result in higher organic matter loading to the sediments, and longer residence time of the water in the IL, accompanied by microbial respiration (both aerobic and anaerobic) that may reduce carbonate saturation level to drive carbonate dissolution and thus TA elevation, thereby forming such a unique diel pattern in carbonate chemistry. This finding further highlights the importance of considering TA production through metabolic carbonate dissolution when evaluating the potential of coastal blue carbon ecosystems to buffer ocean acidification and to absorb atmospheric CO2, in particular in a semienclosed setting.

Predator and prey α-diversities are often positively associated; yet, understandings of the underlying mechanisms require manipulative experiments and thus remain unclear. We attempt to address this issue by deciphering how α-diversity of predator and prey influences each other’s community assembly processes, which subsequently determine their α-diversity. The occurrence of assembly processes was indicated by the mean pairwise taxonomic index within a community (αMPTI), assuming assembly processes left traceable imprints on species’ phylogeny. Specifically, αMPTI quantifies deviations of observed phylogenetic distances from that of random, so that it can be used to hint at the occurrence of non-random/deterministic assembly processes. Larger αMPTI of a community implies the occurrence of weaker homogenizing deterministic assembly processes, which suggests that this community might be comprised of less similar species and thus has higher α-diversity. We hypothesize that higher predator and prey α-diversity would be positively associated with each other’s αMPTI, which would then be positively associated with their α-diversity. To test the hypothesis, we calculated Shannon diversity and αMPTI for heterotrophic nanoflagellates (HNF; predator) and bacteria (prey) communities in the East China Sea (ECS). The HNF Shannon diversity was found to be positively associated with αMPTI of bacteria, which was then positively associated with bacterial Shannon diversity. In contrast, bacterial Shannon diversity did not correlate with HNF’s αMPTI. We argue that top-down control is one of the explanations to the positive α-diversity association among trophic levels in microbes of the ECS.

Prey availability plays an important role in determining larval fish survival. Numerous studies have found close relationships between the density of mesozooplankton and larval fishes; however, emerging studies suggest that small-size zooplankton are more important prey for some larval fish species. One arising question is whether the size of zooplankton determines the relationship between zooplankton and larval fish community in natural environments. To address this question, we collected small-size (50-200 μm) zooplankton, mesozooplankton (> 330 μm), and larval fish using three different mesh-size (50, 330, 1000 μm, respectively) nets in the East China Sea, and examined their relationships in density. Both meso- and small-size zooplankton densities showed positive relationships with larval fish density, while the relationship is much stronger for the small-size zooplankton. Specifically, the smallest size classes (50-75 and 75-100 μm) of small-size zooplankton showed the highest positive relationships with larval fish density. Temperature, salinity, and chlorophyll-a concentration did not significantly explain larval fish density. Based on these findings, we demonstrate the importance of considering prey size when investigating prey availability for larval fishes.

Dissolved primary production (DPP), particulate primaryproduction (PPP), and the subsequent bacterial production (BP) and respiration (BR) were reported for the first time in the NW Pacific. The study area of the subtropical southern East China Sea covers different water types, including oligotrophic Kuroshio and Taiwan Strait waters, as well as nutrient-rich China coastal and upwelled Kuroshio subsurface waters. On an areal basis, DPP and PPP ranged from 67–1649 and 160–1182 mgC m–2 d–1, respectively, showing high values in the upwelling area. The contribution of DPP to total primary production (percent extracellular release; PER) averaged 40.8 ± 12.2% with >50% in the upwelling stations. The BP and BR ranged from 48–245 and 709–2822 mgC m–2 d–1, respectively, showing patterns similar to those of primary production. Bacterial growth efficiency (BGE) averaged 5.7 ± 1.4%, representing the lower end of global ocean values. Phytoplankton and bacteria were well coupled in the upwelling area, whereas primary production could not sustain the bacterial carbon demand (BCD) at other stations. The slope of the log–log relationship between DPP and PPP was >1, indicating that the microbial loop may receive relatively less organic carbon supply in the future warmer, less productive ocean.

The short-term variabilities in temperature, salinity, nitrate, chlorophyll a (Chl a), and carbonate chemistry data (i.e., pH, partial pressure of CO2 (pCO2), total alkalinity, and dissolved inorganic carbon) were concurrently investigated in the shallow (∼50 m) and deep (∼300 m) water areas around Dongsha Atoll of the northern South China Sea (NSCS). The results show that surface temperature and pCO2 were lower but that upward nitrate flux and Chl a were higher in the upper euphotic zone at the shallow-water area than those at the deep-water area. We suggest that the observed contrasting biogeochemical properties between the two areas could be attributed to the impact of topography-flow interaction. As tidal currents (or any other horizontal currents) interacted with the shallow topography, they may induce vertical isotherm displacements (e.g., internal tides/internal waves) that may enhance turbulent mixing, and thus can transport more nutrient-replete subsurface water into the euphotic zone and stimulate phytoplankton production. The stimulated biological production and the cooling effect induced by topography-flow interaction may collectively drive surface pCO2 down in the shallow water area. Though the present short-term hydrological and CO2 data, which to our knowledge were concurrently investigated for the first time in the NSCS, reveal that the topography-flow interaction could be a favorable mechanism for atmospheric CO2 uptake around Dongsha Atoll, more long-term observations are still needed to confirm that the similar processes can repetitively take place in topography-flow interaction prevalent areas.

In spite of the fact that the interactions between environmental parameters and prokaryotic and viral abundance have been explored in various aquatic environments, only a few independent estimates of viral production and decay in the estuarine region have been explored. In this study, data were analyzed for viral and prokaryotic abundance, viral production, and viral decay in a subtropical Danshui estuary in summer 2021. Prokaryotic abundance varied from 2.4 ± 0.6 × 105 to 12 ± 2.3 × 105 cells mL−1, and viral abundance ranged from 2.3 ± 0.9 × 105 to 6.9 ± 1.3 × 105 viruses mL−1 during the study period. Viral abundance was significantly correlated with prokaryotic abundance and chlorophyll a concentration. Furthermore, studies of changes in viral to prokaryotic abundance ratio (VPR) ranged from 0.42 ± 0.11 to 2.0 ± 0.25. Viral decay values were 2.1 ± 0.5 and 2.1 ± 0.3 × 104 virus mL−1h−1, and non-significant differences were observed between the inner estuary and coastal water region. Viral decay almost balanced gross viral production in this study. The dilution experiments revealed non-significant net viral production in July; thus, a lower VPR might be explained in this estuarine environment.

Seasonal variations in the picophytoplankton community structure (Synechococcus spp. and picoeukaryotes) were studied by flow cytometry in the coastal ecosystem of the subtropical western Pacific from October 2019 to September 2020. Synechococcus spp. was dominant in abundance during the study period, with its density ranging from 0.05 to 5.6 × 104 cells mL−1; its maximum occurred in July 2020. Picoeukaryotes were less abundant, with their density ranging from 0.2 to 13.6 × 103 cells mL−1. Their highest abundance was recorded in January 2020. The growth rates of Synechococcus spp. and picoeukaryotes ranged from −0.39 to 1.42 d−1 and 0.38 to 2.46 d−1, respectively, throughout the study period. Overall, the growth rate of the picoeukaryotes was significantly higher than that of Synechococcus spp. It is interesting to note that the grazing mortality of Synechococcus spp. and picoeukaryotes during the warmer period (April to September) was relatively low. Based on this study, we suggest that mixotrophic nanoflagellates lowered their feeding activity that obtained nutrients from prey and instead used additional nutrients during the incubation experiments. Our study demonstrated that a shift in the picophytoplankton community composition and grazing activity of predacious nanoflagellates in cold and warm periods can impact on the seasonal dynamics of the microbial food web.

Viruses are known to be important agents of prokaryotic loss in diverse environments. However, only few studies to date have examined seasonal variations in virus-prokaryote interactions in marine environments. This study measured viral and prokaryotic abundance between January and November 2015 to assess seasonal variations in the relation between viruses and prokaryotes (heterotrophic bacteria, Synechococcus spp., and picoeukaryotes) in eutrophic semi-enclosed and less productivity open coastal waters. Viruses and prokaryotes were found to be significantly more abundant in productive semi-enclosed coastal waters. Using side scatter and green DNA dye complex fluorescence, we analyze flow cytometry (FCM) data to clearly distinguish between two groups of viruses, VLP1 and VLP2. VLP1, the most dominant, ranged from 84 - 89% and 67 - 78% in semi-enclosed and open coastal waters, respectively. Lower virus-to-bacteria ratios (VBR) were observed at semi-enclosed coastal waters (0.9 - 6.1), due to turbidity values of these two coastal waters being significantly different (4.5 - 6.2 NTU and 0.5 - 1.2 NTU, respectively) in summer, probably a result of higher suspended matter causing removal of viruses from the surface waters.

The first data set of seasonal marine environment and euphotic zone integrated primary production (IP) variations in the Taiwan Strait was reported. The measured annual IP was 123 ± 86 gC m–2 year–1 (338 ± 235 mgC m–2 day–1), and its seasonal variations can be described with a left-skewed normal distribution curve. The average seasonal IP values from the highest to the lowest were summer (664 ± 270 mgC m–2 day–1), autumn (350 ± 118 mgC m–2 day–1), spring (202 ± 110 mgC m–2 day–1), and winter (137 ± 68 mgC m–2 day–1). The lowest IP was during the nutrient-rich winter because it had a short insolation duration, low incident photosynthetic active radiation (PAR) and low light transmission (shallow euphotic zone depth) due to strong vertical mixing. In contrast to the winter, the highest IP was during the nutrient-depleted summer, which had a long insolation duration, high incident PAR and high light transmission (deeper euphotic zone depth). In addition, the heterotrophic nutrients from upwelling in the south might also support the highest IP in summer. As three primary water masses exist in the Taiwan Strait and three of them have different characteristics, different mixing ratios of water masses may cause different chemical and hydrographic conditions, which leads to different levels of Chl a concentrations and primary production. It is worth to mention that offshore wind farm (OWF) construction in the Changyun Rise (CYR) of the Taiwan Strait is on-going. As primary production is the foundation for a marine ecosystem and supports the food web and fish stock, the results of this research can not only be used as the baseline for evaluating the OWF impact on the marine ecosystem but also be used for assessing their influence on fishery resources.

Viral production (VP) and bacterial mortality by viral lysis critically influence the production and mortality of aquatic bacteria. Although bacterial production, mortality by viral lysis, and viral density have been found to exhibit diel variations, the diel change in viral production has rarely been investigated. In this study, we conducted two diel dilution incubation experiments in a semi-enclosed, nutrient-rich coastal region in northeastern Taiwan to estimate the diel viral production and the mortality by viral lysis. We also compared two methods (linear regression between viral density and time versus arithmetic mean of VP during incubation) of estimating viral production. We found that viral production estimated by linear regression and bacterial mortality by viral lysis were higher during the daytime than during the nighttime. A possible explanation for the high viral production at daytime is that the bacterial community was composed of cell types with higher burst sizes at daytime. We further argued that the classical linear regression method can be used only when viral density significantly linearly increases with time, which does not always occur in dilution incubations. This study offered observations of diel variation in viral dynamics and discussed the methods estimating viral production in a marine environment.

Climate warming can directly affect biological processes in marine environments. Here, we investigated if warming (+2 °C) can change dynamics in viral and prokaryotic populations in the cold seasons in natural seawaters. We monitored the changes in viral production and prokaryotic growth rate. The prokaryotic average gross growth rates were 0.08 and 0.34 h−1 in November and 0.06 and 0.41 h−1 in December in the in situ and warming experiments, respectively. We found that warming water temperature resulted in a significant increase in prokaryotic growth rates. In warming experiments, the overall viral production rate was about 0.77–14.4 × 105 viruses mL−1 h−1, and a rough estimate of prokaryotic mortality was about 5.6–6.8 × 104 cells mL−1 h−1. Based on our estimation, burst sizes of about 21 and 14 viruses prokaryotes−1 were measured under the experimental warming period. Moreover, the results found that an increased water temperature in the subtropical western Pacific coastal waters increases prokaryotic growth rates, enhances viral production, and changes the carbon fluxes in the trophic interactions of microbes.

In oceanic communities, picophytoplankton often dominates phytoplankton biomass and productivity. Diel variations in picophytoplankton abundance and growth have been well documented. In the current study, we used flow cytometry to assess the short-term variations (3 h) of the abundance of the most dominant picophytoplankton, Synechococcus spp. and picoeukaryotes, in the coastal regions of northeastern Taiwan. To explore the change in growth and mortality rate in the daytime and over 24 h incubation, we performed a two-point modified dilution experiment for measuring growth, viral lysis, and nanoflagellate grazing rate. In this study, the growth rates of picoeukaryotes were 0.21 and 0.06 h−1, and those of Synechococcus spp. were 0.15 and 0.06 h−1 for daytime and 24 h incubation, respectively, and the values were higher at significant levels in the daytime than those for 24 h incubation. These growth rate values of picoeukaryote and Synechococcus spp. after incubation for 24 h were approximately underestimated at 71% and 55%, respectively. This finding suggests that estimates based on 24 h sampling may not accurately reflect the true growth rate of these populations on ecologically relevant timescales.

Copepods have been known to be able to cause an increase in phytoplankton through trophic cascades, as copepods consume heterotrophic protists that feed on phytoplankton. However, how the intensity of copepod-induced trophic cascades varies with environmental conditions remains elusive. We hypothesized that a higher proportion of large phytoplankton in the phytoplankton size distribution, a higher stoichiometric quality of phytoplankton, and a higher temperature could mitigate the intensity of a trophic cascade through increasing direct grazing on phytoplankton by copepods. To explore this issue, we quantified the intensity of a trophic cascade as the difference in phytoplankton concentration reduction by grazing using in situ incubations with and without copepods in the East China Sea. We then investigated the relationship between the intensity of trophic cascades versus the slope of the normalized biomass size spectrum (NBSS) of the phytoplankton community, the C:N ratio of particulate organic matter (POM), and temperature. We found that the intensity of trophic cascades weakly decreased with the NBSS slope and increased with temperature; however, both relationships were not statistically significant. We did not find a clear relationship between the strength of the trophic cascades and the C:N ratio of POM. Our results do not support the hypothesis that the proportion of large phytoplankton, the stoichiometric quality of phytoplankton, and the temperature affect trophic cascades. Instead, we suggest that other critical factors, such as protist abundance, play a role in affecting trophic cascades in the plankton food web in the East China Sea. We further propose some issues which should be addressed when conducting in situ shipboard incubation.

The response of marine phytoplankton primary productivity to available light (photosynthesis-irradiance relationship, PB-E curve) is the principle physiology of plant that is particularly important in the estimation of primary production and in physical-biogeochemical modeling. In this study, we conducted on-board incubation experi­ments to examine photosynthesis-irradiance relationships in samples collected from the subtropical shelf of the East China Sea during a winter cruise. Depth and spatial variation of the maximum photosynthesis rate normalized to chlorophyll a (PBm) and the initial slope (α) of the PB-E curve parameters were insignificant in the East China Sea. The vertical homogeneity was due to the strong winter mixing. However, spatial homogeneity could be possibly caused by different factors. With relatively low solar radiation in the winter, strong vertical mixing deteriorated light dose and may lead to homogeneously low photosynthetic parameters. In addition, differential inhibitions by temperature and nutrient availability may potentially cause the spatial homogeneity. The mean values of PBm and α were 2.82 ± 0.50 gC (gChl)-1 h-1 and 0.010 ± 0.002 gC (gChl)-1 h-1 (μmol photons m-2 s-1)-1, respectively. Using the photosynthetic-irradiance model (PB-E curve model), the estimated value of shelf-averaged euphotic zone inte­grated primary production was 186 ± 117 mgC m-2 d-1. With an overestimate of satel­lite-derived primary production, field observations will be required.

This study investigated the spatial variation in the components of a microbial food web (viruses, picoplankton, nanoflagellates, and ciliates) in different hydrographic environments in the Taiwan Strait during winter. Water temperature and salinity varied spatially, with lower temperatures (15.3−22.8 °C) and salinities (32.2−33.4 psu) in the northern part of the Taiwan Strait, largely affected by runoff from the coast of China. Concentrations of nutrients and Chl a were significantly higher in the northern part than that in the southern part of the study area. Synechococcus spp., nanoflagellate, and ciliate abundance also varied significantly, with the northern strait having higher abundances of these communities. In contrast, a higher abundance of bacteria was found in the southern part of the Taiwan Strait. The results of this study, which describes two different ecosystems in the Taiwan Strait, suggest that during winter, a “viral loop” might play an important role in controlling bacterial production in the southern part of the Taiwan Strait, while nanofalgellate grazing of picophytoplankton may contribute mainly to the flux of energy in the northern part.

To understand the biogeochemical impact of typhoons in marginal seas, 16 sea-going expeditions were conducted from 2007 to 2009, covering all four seasons and including periods following the passage of several typhoons in the southern East China Sea (SECS). Higher surface nitrate and chlorophyll a (Chl a) concentrations were measured in winter and spring, but surface nitrate (< 0.1 μM) and Chl a (0.47 ± 0.17 mg m–3) concentrations were low in summer under nontyphoon conditions. In comparison, elevated surface nitrate (0.2–2.3 μM) and Chl a concentrations (1.11 ± 0.40 mg m–3) were recorded in the SECS several days after the passage of each of three typhoons in 2008. The results demonstrate that nutrient-rich waters are brought to the surface after the passage of typhoons, after which phytoplankton flourish. Most importantly, elevated particulate organic carbon (POC) fluxes (552 ± 28 mg C m–2 d–1) were observed after Typhoon Jangmi, about a threefold increase from the monthly mean value (184 ± 37 mg m–2 d–1). These field investigations demonstrate that typhoons can have a profound effect on nutrient supply, phytoplankton growth, and POC fluxes in marginal seas.

Mesoscale eddies in the subtropical oligotrophic ocean are ubiquitous and play an important role in nutrient supply and oceanic primary production. However, it is still unclear whether these mesoscale eddies can efficiently transfer CO2 from the atmosphere to deep waters via biological pump because of the sampling difficulty due to their transient nature. In 2007, particulate organic carbon (POC) fluxes, measured below the euphotic zone at the edge of warm eddy were 136-194 mg-C m-2 d-1 which was greatly elevated over that (POC flux = 26-35 mg-C m-2 d-1) determined in the nutrient-depleted oligotrophic waters in the Western North Pacific (WNP). In 2010, higher POC fluxes (83-115 mg-C m-2 d-1) were also observed at the boundary of mesoscale eddies in the WNP. The enhanced POC flux at the edge of eddies was mainly attributed to both large denuded diatom frustules and zooplankton fecal pellets based on scanning electron microscopy (SEM) examination. The result suggests that mesoscale eddies in the oligotrophic waters in the subtropical WNP can efficiently increase the oceanic carbon export flux and the eddy edge is a crucial conduit in carbon sequestration to deep waters.

Little is known about microbial processes and the effect that viruses have on Synechococcus spp. in aquatic environments. This study investigated diel variations in the Synechococcus spp. abundance in three size-fractionated water samples (200, 10, and 2 μmμm fractions). Experiments diluting Synechococcus spp. with virus-free water (30 kDa filtrate) in winter months were performed. We found Synechococcus spp. to be more abundant in virus-diluted water than in the other fractions during night time. These results suggest that protozoan grazing did not contribute importantly to a reduction in Synechococcus spp. abundance but that viral lysis more likely caused Synechococcus spp. mortality in these marine coastal waters during winter.

Viruses play an important role in aquatic environments in bacteria and phytoplankton mortality and also in carbon and nutrient recycling through the lysis of living cells. However, the effects of nitrogen regenerated by viral lysis on the growth of picophytoplankton are rarely studied. This study investigated whether the presence of viruses has a positive effect on the daytime frequency of cell division in Synechococcus spp. in the coastal waters of the western subtropical Pacific Ocean. Using cell incubation with natural viral loads and reduced virus treatments, we characterized the abundance and frequency of cell division in Synechococcus spp. over time. Our results clearly showed that during the daytime as much as 30% of Synechococcus spp. were dividing in natural virus-containing samples, a proportion six times that found in the virus-diluted treatment groups (5%). These results suggest that viruses can exert significant effects on nutrient regeneration, enhancing daytime cell division rates in Synechococcus spp.

We monitored the abundance and biomass of nanoflagellates and their potential prey, heterotrophic bacteria, and Synechococcus spp. five times during the summers in 2010 and 2011. We used size-fractionation to measure growth and grazing rates of heterotrophic bacteria and Synechococcus spp. Temporal changes in surface water chlorophyll a (Chl a) concentrations during our study were caused by an influx of nutrient-rich water upwelling into the surface water. The bacterial growth rates ranged from 0.01 to 0.08 h-1 and grazing rates from 0 to 0.06 h-1. Bacterial growth rate had a positive relationship with Chl a concentration. Furthermore, growth and grazing rates of Synechococcus spp. ranged from 0.01 to 0.09 and 0 to 0.02 h-1, respectively. During the study period about 68% of the bacterial production and 41% of the Synechococcus spp. production was grazed by nanoflagellates in the southern East China Sea upwelling region, thus, a large fraction of bacterial biomass is transferred to higher trophic levels via nanoflagellate grazing.

We incorporate tidal currents into a previously validated, three-dimensional, subtidal circulation model to assess tidal effects on the circulation in and around the East China Sea. Of particular interest is the tide-enhanced Changjiang plume dispersal and circulation in the southern East China Sea. The modeling results show that without tides, the Changjiang plume in summer presents itself as a stagnant, expansive pool in regions bordering the northern East China Sea and Yellow Sea, too far north and too accumulating relative to observations. The winter plume dispersal pushed by the north-northeast monsoon follows the China coastline southeastward as a coastal current that matches more closely with observations with or without tides. Incorporating the effect of tides brings the model closer to observation, especially in summer. During summer the Taiwan Warm Current shifts to lower latitudes, enhances upwelling off southeast China and induces a southward tidal residual coastal flow off southeast China. Tides also induce the observed seaward detachment of the summer plume. In winter, the prevailing north-northeast monsoon suppresses the Taiwan Warm Current to the minimum. However, if the winter monsoon is weakened for a few weeks, the Taiwan Warm Current reappears and these three mechanisms begin to operate as in summer. CTD surveys and satellite observations south of the Changjiang River estuary contribute to a better understanding of the tidal effects on regional ocean currents.

The abundance of Synechococcus in the East China Sea (ECS) was tracked during two sets of cruises in 1997 - 1998 and 2004. These data were combined with information from the literature to examine the hypothesis wherein variations in Synechococcus abundance were linked to the magnitude of seasonal temperature ranges. An index of the amplitude of Synechococcus seasonal abundance relative to their minimum abundance (ΔN/Nmin) was well correlated with the range of sea surface temperature (ΔT). These results suggest that the regional range of temperature is a relatively good predictor for the relative seasonal change in Synechococcus abundance within many environments.

Severe tropical storms play an important role in triggering phytoplankton blooms, yet direct field observation of evidence of the effects of a typhoon is very rare. Sea surface temperature (SST), nitrate concentration, chlorophyll a (chl a) concentration, and particulate organic carbon (POC) flux were measured before and shortly after Typhoon Jangmi which affected the southern East China Sea (SECS) on September 28 ~ 29, 2008. In situ SST (27.5 ~ 28.0°C) on September 19 ~ 21, decreased to ~24.0°C (October 3 ~ 6) in the SECS 4 ~ 7 days after the passage of Typhoon Jangmi. In situ nitrate and chl a concentrations 7-days (on October 6) after the passage of Jangmi were 1.9 μM and 1.61 mg m-3, respectively, much higher than those (nitrate: 0.3 μM and chl a: 0.73 mg m-3) concentrations before the typhoon (September 21). The enhanced chl a concentration is thus caused by a nutrient supply via vertical mixing or upwelling in the euphotic zone. The POC flux 7-days after Jangmi¡¦s passage was 552 ± 28 mg-C m-2 d-1, a ~2.5-fold increases before the typhoon (224 ± 33 mg-C m-2 d-1, on September 21). Our results suggest that typhoons indeed can stimulate efficient POC export out of the euphotic zone, while it is still poorly understood with regard to the total effects of a typhoon on nutrient dynamics and detailed carbon sequestration due to sampling difficulty. Therefore, successional sea-going observations ought to be conducted in the affected area after the passage of typhoons.

This study examined the seasonal dynamics of the bacteria, Synechococcus spp. and their nanoflagellate grazers in the Danshui River estuary in northern Taiwan and compared the variations in microbes (bacteria, Synechococcus spp. and nanoflagellate) dynamics under different (clear vs. stormy) weather conditions. Temporal variations in chlorophyll a concentrations, bacterial production, bacteria and Synechococcus spp. abundance were related to temperature, with higher values during the warmer seasons. Spatial variations in Synechococcus spp. were related to chlorophyll a concentrations and in bacterial production and abundance related to chlorophyll a concentrations when temperature is above 20¢XC (April, August, and October). Spatial variations in nanoflagellates were related to oscillations in bacterial abundance or production during non-rainy periods. We conclude that heavy freshwater input to the estuary carries a large quantity of riverine bacteria which might disrupt the relationship between bacterial and nanoflagellate abundance during rainfall events.

To investigate the spatial and temporal variation of phytoplankton and copepods, eight seasonal cruises (January 2005 ~ Oc to ber 2006) were conducted in a subtropical coast site that encom passed 19 sampling stations. The results in dicated that the temperature (18.4 - 29.7°C) varied more than 10°C seasonally, while nutrient concentrations (ni trate: 0.4 - 6.3 mM, phosphate: 0.1 - 0.8 mM, and silicate 2.1 - 12.1 mM) were in versely corre lated with temperature. Diatoms (2792 - 1602437 cells m-3) constituted > 90% of the phytoplankton as semblages and dinoflagellates (226 - 10029 cells m-3) represented only ~10% of the algaebiomass. Copepod abun dance (8 - 1031 ind. m-3) varied positively with that of diatom and tempeature. Therelative abundance of Temora spp. (1 - 712 ind. m-3) varied from < 2% in win ter to > 69% in summer; that of Paracalanus spp. (0.1 - 176 ind. m-3) were > 25% in spring and au tumn and Calanus spp. (0.5 - 24 ind. m-3) dom i nated in win ter and spring, but ac counted for only ~10% of the to tal copepods. Both di a tom den sity and copepod abun dance were positively correlated with temperature, indicating these two plank tongroups were left bot tom-up control. The copepod abun dance positively co-aried with diatoms in 2005, but not in 2006. Fur ther sea son-to-sea son analysis showed that the diatomvs. copepodratios changed positively only when the medusa abun dance changed greatly (> 40-fold) between consecutive sea sons. During periods when the medusa abundance varied less than 10-fold between seasons, there is no relationship between the ratios and the medusa abun dance. This study suggests that the stability of the medusa abundance from season to season could be important in regulating the ecological linkage between diatoms and their predators ¡V copepods.

Trace metal (Cd, Cu, and Ni) dis tri bu tions and be hav iors in sur face waters of the East China Sea continental shelf were investigated during an expeditioncon ducted in June 2004. Dissolved and particulate trace metal con centrations, as well as fractions of dissolved trace metals, fraction ated based on their different chemical affinities to ion exchangers, were determined using ultra-clean techniques and graphite furnace atomic absorption spectrometry (GFAAS). Large variations of dissolved (< 0.45 mm) metal concentrations in the East China Sea shelf waters were found (n = 16) and ranged between 0.036 - 0.287 nM for Cd, 0.87 - 8.66 nM for Cu, and 2.66 - 6.04 nM for Ni. Particulate metal contributions were highest near the river mouth. Dis solved Cd and Ni were pre dominantly present (98% for Cd and 86% for Ni) as Chelex-labile fractions in the shelf waters.

The vertical distributions of managanese at a station in the southern Okinawa Trough were investigated bi-monthly by analyzing the dissolved manganese in filtered seawaters. The analysis of every survey showed the elevated concentrations of dissolved manganese between depths of 600 and 900 m, with the peak at about 800 m and a maximum concentration of 5-8 nM. Repeated observations showed that the dissolved manganese maximum always appeared within a narrow range of £m£cbetween 27.1 and 27.2. The results not only confirmed the previous report of a mid-depth Mn maximum, but also revealed that the dissolved manganese is one of the major forms in the mid-depth manganese maximum. In this study, we conclude that a persistent mid-depth maximum of dissolved manganese exits in the southern Okinawa Trough off northeastern Taiwan.

Throughout the western tropical Pacific Ocean, eddies and currents play an important role in biogeochemical cycling. Many studies have investigated the effects of hydrography on vertical patterns of picophytoplankton and heterotrophic bacterial abundance in mesoscale eddies. There is a lack of field observations to determine what impact dynamic hydrological systems of eddies have on prokaryotic community activity (growth and mortality rates). An objective of this study was to examine how anticyclonic eddies influence picoplankton abundance and activity (growth and mortality rates). To meet this purpose, heterotrophic bacterial and picophytoplankton growth and mortality rates were examined by modified dilution experiments conducted at the surface, deep chlorophyll maximum (DCM), and 200 m depth outside (OE) and inside of warm eddies core (EC) in the west Pacific Ocean. A high heterotrophic bacterial grazing rate was found in the EC region in the present study. Furthermore, the picophytoplankton grazing rate in EC was frequently greater than the grazing rate in OE. Furthermore, the higher grazing rates in the EC region cause a lower proportion of viral lysis to account for heterotrophic bacteria and picophytoplankton mortality. The results of our experiments suggest that downwelling in EC might increase picophytoplankton growth and grazing rates, increasing the carbon sink in the warm eddy and potentially increasing ocean carbon storage. [ABSTRACT FROM AUTHOR]