Biogeochemical factors regulating photosynthetically dissolved organic carbon produced by phytoplankton in the Taiwan Strait.

The distribution and mechanisms of photosynthetically dissolved organic carbon (PDOC) released by marine phytoplankton are frequently neglected and inadequately understood because most studies on carbon sequestration capacity have focused on photosynthetic particulate organic carbon. In this study, percentage extracellular release (PER) and its environmental influencing factors were investigated for 10 cruises in the Taiwan Strait during 2006-2023. The results indicated that the PER increased horizontally from the nearshore to the off-shelf and vertically from the surface to the bottom within the euphotic zone. PER tends to be low in eutrophic waters such as upwellings and estuaries and high in oligotrophic waters. The study revealed that the average contribution of PDOC to total primary productivity (TPP) in the Taiwan Strait could reach 18.2 ± 11.7%, which is similar to the previously estimated global oceanic values. PDOC production satisfied approximately 25% the carbon requirements of heterotropic bacteria (HB). A detailed analysis of the PER combined with model simulations proved that the distribution of the PER in the Taiwan Strait was caused by the joint contribution of irradiance, size-fractionated phytoplankton, and nutrient stoichiometry. Our results contradict the view that the PER is a constant factor that is unaffected by TPP. However, there was a significant negative correlation between the PER and TPP. The PDOC was always lower than the bacterial carbon demand for a broad range of bacterial growth efficiencies, suggesting a weak coupling between phytoplankton exudation and bacterial metabolism. This challenges the idea that there is a well-coupled relationship between bacteria and phytoplankton present on the continental shelf. These findings indicate significant discrepancies in PDOC mechanisms and the quantitative importance of nearshore eutrophic and off-shelf oligotrophic environments. Consequently, it is unwise to use uniform PERs without differentiation under trophic conditions when reevaluating and appraising marine carbon fixation.

Dynamics of benthic microeukaryotic communities in a mangrove wetland invaded by Spartina alterniflora: Effects of vegetation, seasonality, and sediment depth.

Benthic microeukaryotes are crucial mediators of biogeochemical cycles in coastal wetland ecosystems, yet their spatial and temporal variability remains poorly understood. This study delineates the diversity patterns of benthic microeukaryotes in a Spartina alterniflora-invaded mangrove ecosystem in Fujian, China. Using high-throughput sequencing of 18S rRNA gene transcripts, we identified the influences of vegetation, seasonality, and sediment depth on microeukaryotic communities. We discovered that vegetation cover significantly affects community composition, primarily driven by nutrient concentrations and pH. The community structure of microeukaryotes varied seasonally and vertically, correlating with changes in sediment temperature, pH, salinity, and fucoxanthin concentration. Notably, invasive Spartina alterniflora habitats showed enhanced heterotrophic interactions, suggesting that invasive species can reshape benthic microeukaryotic co-occurrence patterns. Seasonal co-occurrence patterns revealed dominant Bacillariophyta assemblages exhibited distinct network modules enriched in the cold (spring) and warm (summer and fall) seasons, respectively, which indicated potential ecological niche differentiation. Our findings reveal the complex relationships between environmental factors and benthic microeukaryotic diversity, offering insights into microbial responses to natural and invasive vegetation influences.

Diversity, community structure, and quantity of eukaryotic phytoplankton revealed using 18S rRNA and plastid 16S rRNA genes and pigment markers: a case study of the Pearl River Estuary.

Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change. In this study, eukaryotic phytoplankton in the Pearl River Estuary, South China Sea were investigated using nuclear 18S rRNA and plastid 16S or 23S rRNA genes and pigment analysis. It was found that 18S abundance poorly explained the variations in total chlorophyll a (Chl-a). However, the ratios of log-transformed 18S abundance to Chl-a in the major phytoplankton groups were generally environment dependent, suggesting that the ratio has potential as an indicator of the physiological state of phytoplankton. The richness of 18S-based operational taxonomic units was positively correlated with the richness of 16S-based amplicon sequence variants of the whole phytoplankton community, but insignificant or weak for individual phytoplankton groups. Overall, the 18S based, rather than the 16S based, community structure had a greater similarity to pigment-based estimations. Relative to the pigment data, the proportion of haptophytes in the 18S dataset, and diatoms and cryptophytes in the 16S dataset, were underestimated. This study highlights that 18S metabarcoding tends to reflect biomass-based community organization of eukaryotic phytoplankton. Because there were lower copy numbers of plastid 16S than 18S per genome, metabarcoding of 16S probably approximates cell abundance-based community organization. Changes in biomass organization of the pigment-based community were sensitive to environmental changes. Taken together, multiple methodologies are recommended to be applied to more accurately profile the diversity and community composition of phytoplankton in natural ecosystems. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-023-00186-x.

From the Sunlit to the Aphotic Zone: Assembly Mechanisms and Co-Occurrence Patterns of Protistan-Bacterial Microbiotas in the Western Pacific Ocean.

We know little about the assembly processes and association patterns of microbial communities below the photic zone. In marine pelagic systems, there are insufficient observational data regarding why and how the microbial assemblies and associations vary from photic to aphotic zones. In this study, we investigated size-fractionated oceanic microbiotas, specifically free-living (FL; 0.22 to 3 µm) and particle-associated (PA; >3 µm) bacteria and protists (0.22 to 200 µm) collected from the surface to 2,000 m in the western Pacific Ocean, to see how assembly mechanisms and association patterns changed from photic to aphotic zones. Taxonomic analysis revealed a distinct community composition between photic and aphotic zones that was largely driven by biotic associations rather than abiotic factors. Aphotic community co-occurrence was less widespread and robust than its photic counterparts, and biotic associations were crucial in microbial co-occurrence, having a higher influence on photic than aphotic co-occurrences. The decrease in biotic associations and the increase in dispersal limitation from the photic to the aphotic zone affect the deterministic-stochastic balance, leading to a more stochastic-process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to our understanding of how and why microbial assembly and co-occurrence vary from photic to aphotic zones, offering insight into the dynamics of the protistan-bacterial microbiota in the western Pacific's photic and aphotic zones. IMPORTANCE We know little about the assembly processes and association patterns of microbial communities below the photic zone in marine pelagic systems. We discovered that community assembly processes differed between photic and aphotic zones, with all three microbial groups studied (protists and FL and PA bacteria) being more influenced by stochastic processes than in the photic zone. The decrease in organismic associations and the increase in dispersal limitation from the photic to the aphotic zone both have an impact on the deterministic-stochastic balance, resulting in a more stochastic process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to the understanding of how and why microbial assembly and co-occurrence change between photic and aphotic zones, offering insight into the dynamics of the protist-bacteria microbiota in the western Pacific oceans.

Water masses and their associated temperature and cross-domain biotic factors co-shape upwelling microbial communities.

Disentangling the drivers and mechanisms that shape microbial communities in a river-influenced coastal upwelling system requires considering a hydrologic dimension that can drive both deterministic and stochastic community assembly by generating hydrological heterogeneity and dispersal events. Additionally, ubiquitous and complex microbial interactions can play a significant role in community structuring. However, how the hydrology, biotic, and abiotic factors collectively shape microbial distribution in the hydrologically complicated river plume-upwelling coupling system remains unknown. Through underway sampling and daily observations, we employed 16S and 18S ribosomal RNA sequencing to disentangle drivers and mechanisms shaping the protist-bacteria microbiota in a river-influenced coastal upwelling system. Our findings indicate that the composition of microbial communities was water mass specific. Collectively, water mass, local water chemistry (mostly temperature) and biotic interaction (mostly cross-domain biotic interaction) shaped the protistan-bacterial communities. In comparison to protists, bacteria were more influenced by abiotic factors such as temperature than by cross-domain biotic factors, implying a stronger coupling of geochemical cycles. Both deterministic and stochastic processes had an effect on the distribution of microbial communities, but deterministic processes were more important for bacteria and were especially pronounced for upwelling communities. The co-occurrence network revealed strong associations between the protistan assemblages Orchrophyta and Ciliophora and the bacterial assemblages Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which may reflect predation and mutualism interactions. Overall, this study emphasizes the importance of taking water masses, temperature and domains of life into account when seeking to understand the drivers and assemblies of protist-bacteria microbiome dynamics in coastal upwelling systems, which is especially true given the complex and dynamic nature of the coastal ecosystem.

Contrasting Community Assembly Mechanisms Underlie Similar Biogeographic Patterns of Surface Microbiota in the Tropical North Pacific Ocean.

Marine microbiota are critical components of global biogeochemical cycles. However, the biogeographic patterns and ecological processes that structure them remain poorly understood, especially in the oligotrophic ocean. In this study, we used high-throughput sequencing of 16S and 18S rRNA genes to investigate the distribution patterns of bacterial and microeukaryotic communities and their assembly mechanisms in the surface waters of the tropical North Pacific Ocean. The fact that both the bacterial and the microeukaryotic communities showed similar distribution patterns (i.e., similar distance-decay patterns) and were clustered according to their geographic origin (i.e., the western tropical North Pacific and central tropical North Pacific) suggested that there was a significant biogeographic pattern of microbiota in the North Pacific Ocean. Indices of alpha diversity such as species richness, phylogenetic diversity, and the Shannon diversity index also differed significantly between regions. The correlations were generally similar between spatial and environmental variables and the alpha and beta diversities of bacteria and microeukaryotes across the entire region. The relative importance of ecological processes differed between bacteria and microeukaryotes: ecological drift was the principal mechanism that accounted for the structure of bacterial communities; heterogeneous selection, dispersal limitation, and ecological drift collectively explained much of the turnover of the microeukaryote communities. IMPORTANCE Bacteria and microeukaryotes are extremely diverse groups in the ocean, where they regulate elemental cycling and energy flow. Studies of marine microbial ecology have benefited greatly from the rapid progress that has been made in genomic sequencing and theoretical microbial ecology. However, the spatial distribution of marine bacteria and microeukaryotes and the nature of the assembly mechanisms that determine their distribution patterns in oligotrophic marine waters are poorly understood. In this study, we used high-throughput sequencing methods to identify the distribution patterns and ecological processes of bacteria and microeukaryotes in an oligotrophic, tropical ocean. Our study showed that contrasting community assembly mechanisms underlaid similar biogeographic patterns of surface bacterial and microeukaryotic communities in the tropical North Pacific Ocean.

Elevated pCO2 changes community structure and function by affecting phytoplankton group-specific mortality.

The rise of atmospheric pCO2 has created a number of problems for marine ecosystem. In this study, we initially quantified the effects of elevated pCO2 on the group-specific mortality of phytoplankton in a natural community based on the results of mesocosm experiments. Diatoms dominated the phytoplankton community, and the concentration of chlorophyll a was significantly higher in the high-pCO2 treatment than the low-pCO2 treatment. Phytoplankton mortality (percentage of dead cells) decreased during the exponential growth phase. Although the mortality of dinoflagellates did not differ significantly between the two pCO2 treatments, that of diatoms was lower in the high-pCO2 treatment. Small diatoms dominated the diatom community. Although the mortality of large diatoms did not differ significantly between the two treatments, that of small diatoms was lower in the high-pCO2 treatment. These results suggested that elevated pCO2 might enhance dominance by small diatoms and thereby change the community structure of coastal ecosystems.

Protistan-Bacterial Microbiota Exhibit Stronger Species Sorting and Greater Network Connectivity Offshore than Nearshore across a Coast-to-Basin Continuum.

Little is known regarding how community assembly and species association vary with habitat and depth. Here, we examined the assembly and association of protistan and bacterial communities across a coast-shelf-slope-basin gradient of the South China Sea using high-throughput sequencing of the V3 and V4 regions of the rRNA gene transcript. Our study revealed that homogenizing dispersal and drift exerted an influence on protistan communities comparable to that on bacterial communities. In contrast, selection and dispersal limitation exerted contrasting effects on the two microbial communities. Community assembly was governed to a greater degree by selection than by dispersal limitation in the bacterial community, and this was much lower in the protistan community. Moreover, this organismal assembly pattern was robust with habitat and depth. However, the relative importance of selection to dispersal limitation varied with habitat and depth in both communities, where horizontally it was higher offshore than nearshore and vertically it was lower in the bottom or deep chlorophyll maximum (DCM) than on the surface. The offshore possessed more microbial network complexity and more associations among microbial taxa than the nearshore, and vertically, the bottom possessed more complexity than the surface and the DCM. Moreover, temperature is strongly associated with the composition and co-occurrence of microbial communities, implying that temperature plays a dominant role in the selection of the protistan-bacterial microbiome across a coast-to-basin continuum. This study contributes to our understanding of the assembly mechanism and species association of protistan-bacterial microbiota across multiple habitats and depths. IMPORTANCE Microbial organisms play a crucial role in global nutrient cycling. Few studies have attempted to simultaneously investigate the community assembly of microeukaryotes and prokaryotes and their association patterns in oceanic waters. This is especially true regarding how they vary with habitats and depths despite the fact that they are essential for developing a more holistic understanding of marine ecosystems. This study revealed the differential actions of selection and dispersal limitation and species association across a coast-to-basin continuum on the marine protistan-bacterial microbiome. Moreover, temperature was identified as a crucial factor driving the structure and co-occurrence of protistan and bacterial communities. The results emphasize that the differences in community assembly and association patterns between nearshore and offshore of the main constituents of the ocean microbiota should be considered to understand their current and future configurations. This is especially crucial in the context of climate change, as the response of ocean microbiota to nearshore and offshore temperature changes remains unknown.

Biogeographic Role of the Kuroshio Current Intrusion in the Microzooplankton Community in the Boundary Zone of the Northern South China Sea.

Kuroshio Current intrusion (KCI) has significant impacts on the oceanographic conditions and ecological processes of the Pacific-Asian marginal seas. Little is known to which extent and how, specifically, the microzooplankton community can be influenced through the intrusion. Here, we focused on ciliates that often dominated the microzooplankton community and investigated their communities using high-throughput sequencing of 18S rRNA gene transcripts in the northern South China Sea (NSCS), where the Kuroshio Current (KC) intrudes frequently. We first applied an isopycnal mixing model to assess the fractional contribution of the KC to the NSCS. The ciliate community presented a provincial distribution pattern corresponding to more and less Kuroshio-influenced stations. Structural equation modeling revealed a significant impact of the KCI on the community, while environmental variables had a marginal impact. KCI-sensitive OTUs were taxonomically diverse but mainly belonged to classes Spirotrichea and Phyllopharyngea, suggesting the existence of core ciliates responding to the KCI. KCI-sensitive OTUs were grouped into two network modules that showed contrasting abundance behavior with the KC fraction gradient, reflecting differential niches (i.e., winner and loser) in the ciliate community during the Kuroshio intrusion scenarios. Our study showed that the Kuroshio intrusion, rather than environmental control, was particularly detrimental to the oligotrophic microzooplankton community.

Blackfordia virginica blooms shift the trophic structure to smaller size plankton in subtropical shallow waters.

The hydromedusa Blackfordia virginica is an invasive species that has disrupted coastal marine food webs throughout the world. Here, we report the response of plankton community to B. virginica blooms in a subtropical lagoon in China. Chlorophyll-a concentrations increased after the peak of B. virginica abundance, which was coincident with high concentrations of ammonium. An increase of the biomass and composition of pico- and nano-phytoplankton during the bloom resulted from bottom-up effects due to the nutrients excreted by B. virginica. The average size and grazing rates of microzooplankton concurrently decreased. The negative correlation between the abundances of B. virginica and microzooplankton was accurately simulated by a generalized linear model and redundancy analysis. This study provided empirical evidence of the impacts of the B. virginica bloom on the food web and the mechanisms responsible for those effects. These impacts may lead to serious ecological and environmental consequences for the lagoonal ecosystem.

The legacy of trace metal deposition from historical anthropogenic river management: A regional driver of offshore sedimentary microbial diversity.

River management, both modern and historical, have dramatically modified offshore environments. While numerous studies have described the modern impacts, very few have evaluated the legacies remaining from hundreds of years ago. Herein, we show trace metal enrichment in the surface sediment of the abandoned Yellow River Delta, hypothesized to be associated with ancient river management. Essentially, anthropogenic modification caused the river to shift, creating a 12.4×103 km2 area with elevated trace metals; characterized by clear metal deposition gradients. Geographical factors related to the ancient river mouth had the most significant influences on Zn (explained by distance to the river mouth, DTM) and Cd (DTM and sediment salinity), while the sediment absorptive capacity was associated with the reallocation of Cu (clay, silt, and iron), Ni (clay and iron), and Pb (silt and iron). Trace metal legacies showed stronger influences on prokaryotic diversity than on micro-eukaryotic diversity, with the former best described by changes in rare, rather than dominant families and classes, and explainable by an "overlapping micro-niche" model. The ancient river's legacies provide evidence of longer-term human disturbance over hundreds of years; as its impacts on associated benthic microbiomes have led to lessons for modern-day waterway management of benthic ecosystems.

Temporal and spatial variations of alkaline phosphatase activity related to phosphorus status of phytoplankton in the East China Sea.

Phosphorus (P) is a potential limiting nutrient for primary production in the East China Sea (ECS). Four cruises over four seasons were conducted during 2009-2011 to evaluate the dynamics of alkaline phosphatase (AP) activity (APA) and the P status of phytoplankton in the ECS. Sampling for bulk and single-cell APA assays was performed across the ECS, which included the Changjiang River diluted water (CDW), the mid-shelf surface water (MSW), and the Kuroshio surface water (KSW) masses. The results showed that the distribution patterns of APA varied between water masses and with season. Higher APA was normally observed in the CDW, which was influenced by the Changjiang River plume. In the CDW, phytoplankton were P-stressed during the late spring with an average bulk APA of 20.4 ± 19.5 nmol h-1 L-1, which strengthened during the late summer (average APA maximizing at 106.2 ± 133.3 nmol h-1 L-1) and remained severe during the late autumn (average APA of 48.7 ± 34.1 nmol h-1 L-1) until reducing during the winter (average APA of 9.1 ± 13.6 nmol h-1 L-1). The variation patterns of APA and the P status of phytoplankton in the MSW were similar but with slight variations. In the KSW, a certain amount of APA occurred during the late spring and late autumn (averages of 18.7 ± 19.8 and 23.1 ± 18.7 nmol h-1 L-1, respectively). Single-cell APA coincided with the bulk APA to exhibit the temporal and spatial P-stress status of the dominant micro-phytoplankton. Phytoplankton were the main AP producers in the CDW, especially during the late summer, while pico-plankton contributed most to AP in the MSW and KSW. Our results suggest that phytoplankton suffer P-stress in most seasons, and emphasize the importance of AP in the recycling of organic P to support primary production in the P-deficient ECS.

Patterns of Relative and Quantitative Abundances of Marine Bacteria in Surface Waters of the Subtropical Northwest Pacific Ocean Estimated With High-Throughput Quantification Sequencing.

Bacteria play a pivotal role in shaping ecosystems and contributing to elemental cycling and energy flow in the oceans. However, few studies have focused on bacteria at a trans-basin scale, and studies across the subtropical Northwest Pacific Ocean (NWPO), one of the largest biomes on Earth, have been especially lacking. Although the recently developed high-throughput quantitative sequencing methodology can simultaneously provide information on relative abundance, quantitative abundance, and taxonomic affiliations, it has not been thoroughly evaluated. We collected surface seawater samples for high-throughput, quantitative sequencing of 16S rRNA genes on a transect across the subtropical NWPO to elucidate the distribution of bacterial taxa, patterns of their community structure, and the factors that are potentially important regulators of that structure. We used the quantitative and relative abundances of bacterial taxa to test hypotheses related to their ecology. Total 16S rRNA gene copies ranged from 1.86 × 108 to 1.14 × 109 copies L-1. Bacterial communities were distributed in distinct geographical patterns with spatially adjacent stations clustered together. Spatial considerations may be more important determinants of bacterial community structures than measured environmental variables. The quantitative and relative abundances of bacterial communities exhibited similar distribution patterns and potentially important determinants at the whole-community level, but inner-community connections and correlations with variables differed at subgroup levels. This study advanced understanding of the community structure and distribution patterns of marine bacteria as well as some potentially important determinants thereof in a subtropical oligotrophic ocean system. Results highlighted the importance of considering both the quantitative and relative abundances of members of marine bacterial communities.

Water mass-driven spatial effects and environmental heterogeneity shape microeukaryote biogeography in a subtropical, hydrographically complex ocean system - A case study of ciliates.

The relative importance of geographic distance and depth in shaping microeukaryote community composition on a regional scale remains unclear, especially how that composition is related to the movement of water masses. Here, we collected 156 water samples across the Taiwan Strait, which is characterized by complex topography and dynamic circulation, to investigate the composition of the ciliate community with high-throughput sequencing of the 18S rRNA gene transcript. Ciliate alpha diversity exhibited strong correlations with water chemistry, food abundance, and geographic distance; approximately 50% of the variance of the diversity could be explained by dissolved oxygen concentrations, chlorophyll a concentrations, bacterial abundance, and latitude. The sampling sites could be divided into three provinces based on the compositions of the ciliate communities, which exhibited a distinctly nonuniform spatial distribution pattern on a regional scale (587 km). Geographic distance, environmental conditions, and depth were identified as principal determinants of the ciliate community within the Strait. Geographic distance was the most influential factor. The effect of geographic distance seems to mainly reflect the movement of water masses that strongly constrain dispersal and contribute to environmental heterogeneity that accounts for 86.0% and 5.5%, respectively, of community variance across the Strait. Overall, this study revealed that ciliate biogeography as a function of depth and environmental gradients is linked on a regional scale to the water masses that the ciliates inhabit. This result expands our knowledge of the drivers of microeukaryote community composition across regions within which there are water mass movements and strong spatial and environmental gradients.

Diversity Distribution and Assembly Mechanisms of Planktonic and Benthic Microeukaryote Communities in Intertidal Zones of Southeast Fujian, China.

The intertidal zone occupies the shore between the high and low tide marks and is subjected both to natural forces and anthropogenic activities. Compared with the coastal ecosystem, studies comparing diversity and community structure of intertidal planktonic and benthic microeukaryotes are limited. Therefore, the ecological processes mediating their assemblies remain poorly understood. Environmental rRNA from two size fractions (nano- and micro-sized) of plankton and from seasonally collected (spring and summer) benthos, together with water and sediment chemistry and concentrations of heavy metals, were used to explore diversity and community structure of microeukaryotes in intertidal zones of southeast Fujian Province, China. Benthic microeukaryotes harbored significantly higher alpha-diversity than those of the plankton, whereas no distinct patterns of organism size/seasonal distribution were observed for either community. Community compositions differed significantly between planktonic and benthic microeukaryotes, with the former presenting size-fractionated discrepancies and the latter showing seasonal variation. Community turnover between planktonic and benthic microeukaryotes was mainly driven by stramenopiles and alveolates. Distance-decay patterns were found in both communities, with the rate of community turnover being higher for planktonic than benthic microeukaryotes. Among the environmental factors measured, the concentration of Cd and the water content of sediment were closely associated with benthic community variations, whereas none of the factors measured was identified as being responsible for planktonic community variation. Phylogenetic null model analysis indicated that dispersal limitation was the most crucial ecological process mediating community assembly for both planktonic and benthic microeukaryotes in intertidal zones, with heterogeneous selection making a higher contribution to community variation of benthic than planktonic microeukaryotes. Stochastic processes, mainly dispersal limitation, were found to prevail in both communities. This study thus provides new insights into the diversity distribution and assembly mechanism of microeukaryotes in intertidal zones.

Integrated Space-Time Dataset Reveals High Diversity and Distinct Community Structure of Ciliates in Mesopelagic Waters of the Northern South China Sea.

Little is known about diversity distribution and community structure of ciliates in mesopelagic waters, especially how they are related to spatial and temporal changes. Here, an integrative approach, combining high-throughput cDNA sequencing and quantitative protargol stain, was used to analyze ciliate communities collected temporally along a transect from coastal to oceanic regions at depths ranging from the surface to 1000 m. The mesopelagic zone exhibited comparable alpha diversity to surface water which was consistent over temporal variation, with high diversity occurring at the interface with the euphotic zone. Comparison with the northeastern and the western Pacific Ocean revealed consistency of this vertical distribution of ciliates across oceanic basins. Mesopelagic ciliates harbored distinct community structure without significant seasonal differences, with the vertical variations driven largely by members of the classes Spirotrichea and Oligohymenophorea. Operational taxonomic units (OTUs) affiliated with Scuticociliatia, Astomatida and Apostomatida, members of which are known to be bacterivorous and/or commensal/parasitic species, were more abundant in mesopelagic waters than above, implying they are an important component of food webs in the mesopelagic zone. A combination of depth, geographic distance and environment shaped the ciliate communities, with depth being the most influential factor. Phylogenetic null modeling analysis further indicated that 57.1 and 33.3% of mesopelagic community variation was governed by dispersal limitation and heterogeneous selection, respectively, probably due to the marked biochemical and physical gradients down the water column. This suggests that ciliate community structure in the mesopelagic zone is mainly controlled by stochastic processes. Collectively, this study reports mesopelagic ciliates exhibited high diversity and distinct community structure across spatiotemporal scales and informs the processes mediating ciliate assembly in the mesopelagic zone. These should be fully considered in future studies to build a more comprehensive understanding of mesopelagic microbial assemblages.

Responses of marine phytoplankton communities to environmental changes: New insights from a niche classification scheme.

Predicting changes of phytoplankton communities in response to global warming is one of the challenges of ecological forecasting. One of the constraints is the paucity of general principles applicable to community ecology. Based on a synecological analysis of a decadal-scale database, we created a niche habitat classification scheme relating nine phytoplankton groups to fifteen statistically refined realized niches comprised of three niche dimensions: temperature, irradiance, and nitrate concentrations. The niche scheme assigned the nine phytoplankton groups to three types of niches: a cold type, a warm type, and a type associated with high irradiance and high nitrate concentrations. The fact that phytoplankton groups in cold niches were governed by irradiance and those in warm niches by nitrate is consistent with general ecological theories, but the fact that diatoms were the only dominant group in high-irradiance, high-nitrate niches challenges the idea based on autecological studies that diatoms are generally better adapted to low-irradiance, high-nutrient conditions. When combined with an irradiance model, the niche scheme revealed that photoinhibition of Prochlorococcus, which is predicted from autecological studies, is a function of temperature. We used the niche scheme to predict the responses of phytoplankton communities to environmental changes due to seawater warming and eutrophication. The results of the study suggest that a synecological analysis of large databases from field studies facilitates identification of general principles of community ecology that can be used to forecast responses of biological communities to environmental changes.

Contrasting patterns of genetic structure and phylogeography in the marine agarophytes Gelidiophycus divaricatus and G. freshwateri (Gelidiales, Rhodophyta) from East Asia.

The evolutionary and population demographic history of marine red algae in East Asia is poorly understood. Here, we reconstructed the phylogeographies of two upper intertidal species endemic to East Asia, Gelidiophycus divaricatus and G. freshwateri. Phylogenetic and phylogeographic inferences of 393 mitochondrial cox1, 128 plastid rbcL, and 342 nuclear ITS2 sequences were complemented with ecological niche models. Gelidiophycus divaricatus, a southern species adapted to warm water, is characterized by a high genetic diversity and a strong geographical population structure, characteristic of stable population sizes and sudden reduction to recent expansion. In contrast, G. freshwateri, a northern species adapted to cold temperate conditions, is genetically relatively homogeneous with a shallow population structure resulting from steady population growth and recent equilibrium. The overlap zone of the two species roughly matches summer and winter isotherms, indicating that surface seawater temperature is a key feature influencing species range. Unidirectional genetic introgression was detected at two sites on Jeju Island where G. divaricatus was rare while G. freshwateri was common, suggesting the occurrence of asymmetric natural hybrids, a rarely reported event for rhodophytes. Our results illustrate that Quaternary climate oscillations have left strong imprints on the current day genetic structure and highlight the importance of seawater temperature and sea level change in driving speciation in upper intertidal seaweed species.

The impact of giant jellyfish Nemopilema nomurai blooms on plankton communities in a temperate marginal sea.

This study focused on the bloom-developing process of the giant jellyfish, Nemopilema nomurai, on phytoplankton and microzooplankton communities. Two repeated field observations on the jellyfish bloom were conducted in June 2012 and 2014 in the southern Yellow Sea where blooms of N. nomurai were frequently observed. We demonstrated that the bloom was made up of two stages, namely the developing stage and the mature stage. Total chlorophyll a increased and the concentrations of inorganic nutrients decreased during the developing stage, while both concentrations maintained stable and at low levels during the mature stage. Our analysis revealed that phosphate excreted by growing N. nomurai promoted the growth of phytoplankton at the developing stage. At the mature stage, size compositions of microzooplankton were altered and tended to be smaller via a top-down process, while phytoplankton compositions, affected mainly through a bottom-up process, shifted to be less diatoms and cryptophytes but more dinoflagellates.

Protist diversity and community assembly in surface sediments of the South China Sea.

Protists are pivotal components of marine ecosystems in terms of their high diversity, but protist communities have been poorly explored in benthic environments. Here, we investigated protist diversity and community assembly in surface sediments in the South China Sea (SCS) at a basin scale. Pyrosequencing of 18S rDNA was performed for a total of six samples taken from the surface seafloor at water depths ranging from 79 to 2,939 m. We found that Cercozoa was the dominant group, accounting for an average of 39.9% and 25.3% of the reads and operational taxonomic units (OTUs), respectively. The Cercozoa taxa were highly diverse, comprising 14 phylogenetic clades, six of which were affiliated with unknown groups belonging to Filosa and Endomyxa. Fungi were also an important group in both read- (18.1% on average) and OTU-derived (9.3% on average) results. Moreover, the turnover patterns of the protist communities were differently explained by species sorting (53.3%), dispersal limitation (33.3%), mass effects (0%), and drift (13.3%). In summary, our findings show that the basin-wide protist communities in the surface sediments of the SCS are primarily dominated by Cercozoa and are mainly assembled by species sorting and dispersal limitation.