Comparison of inorganic nitrogen concentrations in airborne particles at inshore and offshore sites in the Yellow Sea (2017-2019): Long-range transport and potential impact on marine productivity.

Atmospheric deposition of nitrogen is one of the most important external nutrient sources. We investigated the concentrations of NO3- and NH4+ in airborne particles at both an offshore and an inshore site in the Yellow Sea. At the offshore site, devoid of local sources and located downwind from the highly developed areas of Korea and China, the concentrations of atmospheric particulate NO3- and NH4+ were ∼88 ± 101 nmol m-3 and ∼102 ± 102 nmol m-3, respectively, likely due to the transboundary long-range transport of pollutants. The inshore site showed a concentration ∼2 times higher than the offshore site. Considering not only dry inorganic nitrogen deposition but also wet and organic material deposition, the total atmospheric nitrogen deposition was estimated to contribute roughly 10 % to the new production in the Yellow Sea.

Impact of vertical stratification on the 2020 spring bloom in the Yellow Sea.

The Yellow Sea is one of the world's most abundant marine resources, providing food and economic benefits to the Korean and Chinese populations. In spring 2020, a decrease in the intensity of phytoplankton bloom was observed. While one study attributed this decline to a decrease in nutrient associated with the COVID-19 pandemic, our previous research proposed weakened thermal stratification accompanied by a surface cooling anomaly as the cause. However, the relationship between the marine environment and ecosystem has not been fully elucidated. Using observations and marine physical-biogeochemical model data, we identified the weakened stratification as a critical factor for suppressing the 2020 spring bloom. Intense vertical mixing hindered the accumulation of nutrient and chlorophyll-a concentrations within the euphotic zone, resulting in a diminished phytoplankton bloom. In contrast, reduced nitrate and phosphate concentrations in 2020 were insignificant compared to those in 2017-2019, despite the notable decline in PM2.5 in March 2020 due to COVID-19. In April 2020, nutrient levels fell within the range of interannual variability based on long-term observations, reflecting a negligible effect on the spring phytoplankton bloom. Our findings provide insight into the importance of marine physical factors on the phytoplankton biomass in the Yellow Sea.

Monthly and seasonal variations in the surface carbonate system and air-sea CO2 flux of the Yellow Sea.

Surface carbonate chemistry in the Yellow Sea was investigated based on discrete seawater samples collected from 2017 to 2020 at the Socheongcho Ocean Research Station (S-ORS; 37.423°N, 124.738°E). Records of carbon parameters, including seawater CO2 partial pressure (pCO2), revealed considerable seasonal variations, with amplitudes comparable to those observed across the western part of the Yellow Sea. The study site acted as a modest sink (-0.13 mol C m-2 yr-1) for atmospheric CO2. Biological processes (primary production and respiration) and physical conditions (temperature and degree of stratification) determined seawater pCO2, which fluctuated on an intraseasonal timescale between oversaturated and undersaturated with respect to atmospheric pCO2. Variation in pCO2 was significant in summer, depending on the biological carbon drawdown and tidal mixing-induced upwelling (increased pCO2 up to ~1000 µatm). The intraseasonal variability in seawater pCO2 may bias estimated air-sea CO2 fluxes, if measurements with a coarser (seasonal) time resolution are used.

Changes in the characteristics of organic matter associated with hydrodynamics and phytoplankton size structure in the central-eastern Yellow Sea.

The central-eastern Yellow Sea is an important region for transporting organic matter (OM) to the Pacific Ocean, however, there is limited information available regarding the characteristics and sources of OM in this area. The present study investigated the concentrations and stable isotopic compositions of carbon (δ13C) and nitrogen (δ15N) for particulate matter and sediment in the central-eastern Yellow Sea during April 2019. The physicochemical properties (i.e., salinity, temperature, fluorescence, and nutrients), size-fractionated phytoplankton biomass (Chl-a), and concentration and fluorescence characteristics of dissolved organic matter (DOM) were also determined. The satellite SST and Chl-a data indicated that mixing cold and warm water masses were observed. Phytoplankton blooms occurred a few days before our sampling campaign. Considering the high concentration of suspended solids in the bottom layer, resuspended sediment caused by tidal currents could be a major source of OM in coastal areas. The δ13C values of particulate organic matter (POM) in the coastal area were higher (-23 to -22‰) than those of OM from terrestrial sources (approximately -28 to -27‰). Instead, the lowest δ13C values were observed in the central part of our study area, where the relative abundance of picophytoplankton was high. These results indicated that phytoplankton-derived OM after phytoplankton spring blooms in the coastal area could be the primary source of OM rather than terrestrial origins. In addition, the source of OM that presented low δ13C values could be picophytoplankton-derived OM. The characteristics of DOM were related to biological processes (mediated by phytoplankton and bacteria) and resuspension of sedimentary organic matter. We did not detect an influx of large amounts of terrestrial OM in coastal sediments. Overall, the source and characteristics of OM appeared to be influenced by the hydrodynamics and the distribution properties of lower trophic-level organisms in the central-eastern Yellow Sea during the spring season.

Heavy metal pollution assessment in coastal sediments and bioaccumulation on seagrass (Enhalus acoroides) of Palau.

Heavy metals in coastal sediments and seagrass (Enhalus acoroides) were studied to assess the pollution level and to understand the bioaccumulation of metals on different organs. The mean of metal concentrations in sediments were in the following order: Cr > Ni > As>Zn > Cu > Co > Pb > Cd > Hg. The results of principal component analysis indicate that Cr, Ni, Cu, Zn, As and Hg are derived from natural sources but Cd and Pb seems to be of anthropogenic sources. Cr, Ni, Cu, Zn, Cd and Pb in the coastal sediments were at low ecological risk level. As and Hg presented the highest ecological risk among all metals. The mean concentrations of Cr, Ni, Cu, Zn, Cd, and Hg were higher in leaves of E. acoroides than in roots. Significant correlations (p < 0.05) for Cr, Ni, Cu, Zn, and Pb in between sediments and in E. acoroides both leaves and roots. High bioconcentration factor (BCF) were calculated for Zn, Cd, and Hg.

Shimiella gen. nov. and Shimiella gracilenta sp. nov. (Dinophyceae, Kareniaceae), a Kleptoplastidic Dinoflagellate from Korean Waters and its Survival under Starvation.

A small dinoflagellate, ~13 µm in cell length, was isolated from Jinhae Bay, Korea. Light microscopy showed that it was similar to the kleptoplastidic dinoflagellate Gymnodinium gracilentum nom. inval. rDNA sequences were obtained and its anatomy and morphology described using light and scanning and transmission electron microscopy. Phylogenetic analyses indicated that it belonged to the family Kareniaceae. However, its large subunit (LSU) rDNA sequences were 5.2-9.5% different from those of the other five genera in the family, and its clade was clearly divergent from that of each genus. Its overall morphology was different from those of the other five genera in the family and from Gymnodinium. Unlike Gymnodinium, this dinoflagellate did not have a horseshoe-shaped apical groove, nuclear envelope chambers, or a nuclear fibrous connective (NFC). It had an apical line of narrow amphiesmal vesicles and an elongated apical furrow crossing the apex. Cells were covered with polygonal amphiesmal vesicles arranged in 16 rows. Starved cells did not contain their own plastids, eyespots, pyrenoids, peridinin, or fucoxanthin. However, they could survive without added prey for approximately one month using chloroplasts from the cryptophyte prey Teleaulax amphioxeia, indicating kleptoplastidy. Because this taxon is genetically distinct at the generic rank from the other genera in Kareniaceae, it is placed in Shimiella gen. nov., and because G. gracilentum was invalid, the new bionomial S. gracilenta sp. nov. is proposed.

Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria.

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton.

Daily variation in the prokaryotic community during a spring bloom in shelf waters of the East China Sea.

To understand prokaryotic responses during a spring bloom in offshore shelf waters, prokaryotic parameters were measured daily at a station located in the middle of the East China Sea over a six-week period from March 25 to May 19. The site experienced a phytoplankton bloom in late April, triggering changes in prokaryotic abundance and production after a lag of approximately one week. Before the bloom, changes in prokaryotic composition were small. Both during the bloom and in the post-bloom period, successive changes among bacterial groups were apparent. A SAR11 group became more dominant during the bloom period, and diverse groups belonging to the Flavobacteriia occurred dominantly during both the bloom and post-bloom periods. However, bacterial community changes at the species level during the bloom and post-bloom periods occurred rapidly in a time scale of a few days. Especially, NS5, NS4 and Formosa bacteria belonging to Flavobacteriia and bacteria belonging to Halieaceae and Arenicellaceae families of Gammaproteobacteria showed a successive pattern with large short-term variation during the period. The changes in prokaryotic composition were found to be related to phytoplankton biomass and composition, as well as seawater temperature and variations in nutrients.

Remote quantification of Cochlodinium polykrikoides blooms occurring in the East Sea using geostationary ocean color imager (GOCI).

Accurate and timely quantification of widespread harmful algal bloom (HAB) distribution is crucial to respond to the natural disaster, minimize the damage, and assess the environmental impact of the event. Although various remote sensing-based quantification approaches have been proposed for HAB since the advent of the ocean color satellite sensor, there have been no algorithms that were validated with in-situ quantitative measurements for the red tide occurring in the Korean seas. Furthermore, since the geostationary ocean color imager (GOCI) became available in June 2010, an algorithm that exploits its unprecedented observation frequency (every hour during the daytime) has been highly demanded to better track the changes in spatial distribution of red tide. This study developed a novel red tide quantification algorithm for GOCI that can estimate hourly chlorophyll-a (Chl a) concentration of Cochlodinium (Margalefidinium) polykrikoides, one of the major red tide species around Korean seas. The developed algorithm has been validated using in-situ Chl a measurements collected from a cruise campaign conducted in August 2013, when a massive C. polykrikoides bloom devastated Korean coasts. The proposed algorithm produced a high correlation (R2=0.92) with in-situ Chl a measurements with robust performance also for high Chl a concentration (300mg/m3) in East Sea areas that typically have a relatively low total suspended particle concentration (<0.5mg/m3).

Variation of Synechococcus Pigment Genetic Diversity Along Two Turbidity Gradients in the China Seas.

Synechococcus are important and widely distributed picocyanobacteria that encompass a high pigment diversity. In this study, we developed a primer set (peBF/peAR) for amplifying the cpeBA operon sequence from Synechococcus genomic DNA to study Synechococcus pigment diversity along two turbidity gradients in the China seas. Our data revealed that all previously reported pigment types occurred in the South (SCS) and East (ECS) China Seas. In addition, a novel pigment genetic type (type 3f), represented by the high phycourobilin Synechococcus sp. strain KORDI-100 (Exc495:545 = 2.35), was detected. This pigment genetic type differs from the 3c/3d types not only for a very high PUB/PEB ratio but also for a different intergenic spacer sequence and gene organization of the phycobilisome. Synechococcus of different pigment types exhibited clear niche differentiation. Type 2 dominated in the coastal waters, whereas type 3c/3d and 3f were predominant in oceanic waters of the SCS in summer. In the ECS, however, type 3a was the major pigment type throughout the transect. We suggest that in marine environment, various pigment types often co-occur but with one type dominant and PUB/PEB ratio is related to geographic distribution of Synechococcus pigment types. The two marginal seas of China have markedly different Synechococcus pigment compositions.

Identification of benthic diatoms isolated from the eastern tidal flats of the Yellow Sea: Comparison between morphological and molecular approaches.

Benthic diatoms isolated from tidal flats in the west coast of Korea were identified through both traditional morphological method and molecular phylogenetic method for methodological comparison. For the molecular phylogenetic analyses, we sequenced the 18S rRNA and the ribulose bisphosphate carboxylase large subunit coding gene, rbcL. Further, the comparative analysis allowed for the assessment of the suitability as a genetic marker for identification of closely related benthic diatom species and as potential barcode gene. Based on the traditional morphological identification system, the 61 isolated strains were classified into 52 previously known taxa from 13 genera. However, 17 strains could not be classified as known species by morphological analyses, suggesting a hidden diversity of benthic diatoms. The Blast search on NCBI's Genebank indicated that the reference sequences for most of the species were absent for the benthic diatoms. Of the two genetic markers, the rbcL genes were more divergent than the 18S rRNA genes. Furthermore, a long branch attraction artefact was found in the 18S rRNA phylogeny. These results suggest that the rbcL gene is a more appropriate genetic marker for identification and classification of benthic diatoms. Considering their high diversity and simple shapes, and thus the difficulty associated with morphological classification of benthic diatoms, a molecular approach could provide a relatively easy and reliable classification system. However, this study suggests that more effort should be made to construct a reliable database containing polyphasic taxonomic data for diatom classification.

The reduction in the biomass of cyanobacterial N2 fixer and the biological pump in the Northwestern Pacific Ocean.

The comparison of sediment trap data with physical and biogeochemical variables in the surface water column of the Tropical Northwestern Pacific Ocean (TNWPO) indicated that the magnitude of the springtime biological pump has reduced with time due to a corresponding decrease in the biomass of cyanobacterial N2 fixer. The decrease in the biomass of N2 fixer likely resulted from a reduction in phosphate concentrations in response to surface water warming and consequent shoaling of the mixed layer depth during the study period (2009-2014). The same reduction in biological pump was also observed during summer. However, the cause of the summer reduction remains uncertain and is worth assessing in future studies. Our findings have major implications for predicting future trends of the biological pump in the TNWPO, where significant warming has occurred.

Complete mitochondrial genome of Skeletonema marinoi (Mediophyceae, Bacillariophyta), a clonal chain forming diatom in the west coast of Korea.

The complete mitochondrial DNA of common planktonic diatom, Skeletonema marinoi JK029 was sequenced and characterized. The circular mitogenome contains 62 genes in 38 515 bp (29.7% GC), including 35 protein-coding, 2 rRNA, and 25 tRNA genes. Total 80% of protein-coding genes have usual ATG start codon and 20% have alternative start codons. The GC content of tRNA genes (39.8%) is relatively higher than those of the rRNA (32.9%) and CDS (29.3%). There are four cases of gene overlapping between neighboring genes, i.e., rrs-trnM, rps2-rps4, nad1-tatC, and rps11-trnY. Newly determined mitogenome of S. marinoi was compared with available seven diatoms and eight stramenopiles by using the maximum-likelihood analysis. The 34-CDS concatenated data (8528 amino acids) support the monophyly of Bacillariophyta. However, mitogenome data showed different higher class-levels clustering with previous study. These results suggested that additional mitogenome data will provide useful information for mitochondrial genome diversity and evolution of the diatoms and stramenopiles.

Repeat region absent in mitochondrial genome of tube-dwelling diatom Berkeleya fennica (Naviculales, Bacillariophyceae).

The complete mitochondrial DNA of tube-dwelling diatom, Berkeleya fennica was sequenced and characterized. The circular mitogenome contains 63 genes in 35,509 bp (29.7% GC), including 36 protein-coding, 25 tRNA, 2 rRNA genes. Most of the protein-coding (27) genes have usual ATG start codon, except 9 genes such as ATA for rps8; ATC for rps14; ATT for rps12 and orf51; GTG for nad5; TTA for cox3, nad4 and orf147; and TTG for cob. The nad11 and rrs are the only interrupted genes in the mitogenome. Gene content and synteny of B. fennica are very similar to Phaeodactylum tricoruntum (NC_016739). Absence of repeat region in B. fennica resulted in mitogenome size difference to P. tricoruntum. A new mitogenome will provide useful information for mitochondrial genome diversity and evolution of the diatoms.

Complete mitochondrial genome of Upogebia yokoyai (Decapoda, Crustacea) from Jejudo, Korea.

The complete mitochondrial DNA of an ecologically important crustacean mud shrimp, Upogebia yokoyai (Decapoda, Crustacea) was sequenced. We used next generation sequencing strategy for total genomic DNA and organelle genome pipeline for mitogenome assembly. A newly determined mitogenome was 16,063 bp in total length with 28% of GC content. Thirty-seven genes were identified including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. We found ten case of overlapping between neighboring genes. Based on genome comparison, the mitogenome of U. yokoyai shows general crustacean gene content and identical synteny to the sister species, such as U. major and U. pusilla. Our results will provide useful information for mitochondrial genome diversity and evolution of the Crustacea.

Complete mitochondrial genome of biraphid benthic diatom, Navicula ramosissima (Naviculales, Bacillariophyceae).

The complete mitochondrial DNA of biraphid benthic diatom, Navicula ramosissima TA439 was sequenced and characterized. The circular mitogenome contains 67 genes in 48,652 bp (31.1% GC), including 41 protein-coding, 24 transfer RNA (tRNA) and 2 rRNA genes. Twenty-four protein-coding sequences (CDS, 59%) have start with ATG codon and 17 CDS start with alternatives such as ATA (5), ATT (6), TTA (5) and TTG (1). The GC content of tRNA genes (42.1%) is relatively higher than those of the rRNA (35.2%) and CDS (30.5%). Three genes are consisted of multiple exons and introns, i.e. cox1 (three exons, two introns), rps11 (two exons, one intron), rrl (four exons, three introns). Phylogeny of diatoms based on mitogenome data (34 CDS, 8530 amino acids combined) supports the monophyly of Naviculales, including N. ramosissima (Naviculaceae), Berkeleya fennica (Berkeleyaceae), Fistulifera solaris (Stauroneidaceae) and Phaeodactylum tricornutum (Phaeodactylaceae). Mitogenome data may be useful for phylogenetic study of the diatoms and stramenopiles.

Pyrosequencing revealed SAR116 clade as dominant dddP-containing bacteria in oligotrophic NW Pacific Ocean.

Dimethyl sulfide (DMS) is a climatically active gas released into the atmosphere from oceans. It is produced mainly by bacterial enzymatic cleavage of dimethylsulfoniopropionate (DMSP), and six DMSP lyases have been identified to date. To determine the biogeographical distribution of bacteria relevant to DMS production, we investigated the diversity of dddP­the most abundant DMS-producing gene­in the northwestern Pacific Ocean using newly developed primers and the pyrosequencing method. Consistent with previous studies, the major dddP-containing bacteria in coastal areas were those belonging to the Roseobacter clade. However, genotypes closely related to the SAR116 group were found to represent a large portion of dddP-containing bacteria in the surface waters of the oligotrophic ocean. The addition of DMSP to a culture of the SAR116 strain Candidatus Puniceispirillum marinum IMCC1322 resulted in the production of DMS and upregulated expression of the dddP gene. Considering the large area of oligotrophic water and the wide distribution of the SAR116 group in oceans worldwide, we propose that these bacteria may play an important role in oceanic DMS production and biogeochemical sulfur cycles, especially via bacteria-mediated DMSP degradation.

Complete mitochondrial genome of Pacific abalone (Haliotis discus hannai) from Korea.

We have sequenced and characterized the complete mitochondrial DNA of an economically and ecologically important Pacific abalone, Haliotis discus hannai (Haliotidae, Gastropoda). The mitogenome of the Pacific abalone is 16,886 nt total length with a 39.6% G+C composition. Thirty-seven genes were identified including 13 protein-coding, 2 rRNA and 22 tRNA genes. We compared the mitogenome of the Pacific abalone to a putative relative species, H. rubra.

Direct linkage between dimethyl sulfide production and microzooplankton grazing, resulting from prey composition change under high partial pressure of carbon dioxide conditions.

Oceanic dimethyl sulfide (DMS) is the enzymatic cleavage product of the algal metabolite dimethylsulfoniopropionate (DMSP) and is the most abundant form of sulfur released into the atmosphere. To investigate the effects of two emerging environmental threats (ocean acidification and warming) on marine DMS production, we performed a large-scale perturbation experiment in a coastal environment. At both ambient temperature and ∼ 2 °C warmer, an increase in partial pressure of carbon dioxide (pCO2) in seawater (160-830 ppmv pCO2) favored the growth of large diatoms, which outcompeted other phytoplankton species in a natural phytoplankton assemblage and reduced the growth rate of smaller, DMSP-rich phototrophic dinoflagellates. This decreased the grazing rate of heterotrophic dinoflagellates (ubiquitous micrograzers), resulting in reduced DMS production via grazing activity. Both the magnitude and sign of the effect of pCO2 on possible future oceanic DMS production were strongly linked to pCO2-induced alterations to the phytoplankton community and the cellular DMSP content of the dominant species and its association with micrograzers.

Application of pyrosequencing method for investigating the diversity of synechococcus subcluster 5.1 in open ocean.

Synechococcus are distributed throughout the world's oceans and are composed of diverse genetic lineages. However, as they are much less abundant than Prochlorococcus in oligotrophic open oceans, their in-depth genetic diversity cannot be investigated using commonly used primers targeting both Prochlorococcus and Synechococcus. Thus, in this study, we designed a primer specific to the 16S-23S rRNA internal transcribed spacer (ITS) of the Synechococcus subcluster 5.1. Using the primer, we could selectively amplify Synechococcus sequences in oligotrophic seawater samples. Further, we showed that a barcoded amplicon pyrosequencing method could be applicable to investigate Synechococcus diversity using sequences retrieved in GenBank and obtained from environmental samples. Allowing sequence analyses of a large number of samples, this high-throughput method would be useful to study global biodiversity and biogeographic patterns of Synechococcus in marine environments.