Dong Han Choi

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.

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 dddP—the most abundant DMS-producing gene—in 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 biraphid benthic diatom, Navicula ramosissima (Naviculales, Bacillariophyceae)

Abstract 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.

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.

The reduction in the biomass of cyanobacterial N 2 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.

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

Abstract 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.

Phytoplankton and Primary Production

The northern part of the East Sea (Japan Sea) is dominated by the cold waters of the Liman Current, whereas in the southern part, the dominant current is the Tsushima Warm Current. Together with these major current systems, subpolar fronts and mesoscale eddies that form in the region exert a strong influence on the phytoplankton ecosystem in the East Sea. These conspicuous physical forcings are manifested as often clearly discernible features in temporal and spatial distributions, composition, abundance, biomass and production of phytoplankton. In short, diatoms and dinoflagellates are found to be the most diverse phytoplankton groups and are occasionally responsible for blooms in coastal waters. Diatoms are also abundant in frontal areas and in the rings of warm core eddies. Picophytoplankton groups are also found to be important phytoplankton in the East Sea, especially in warm seasons, and photosynthetic picoeukaryotes and Synechococcus show distinct seasonal and vertical distribution patterns. Recent field measurements indicated that the spatial distribution of primary productivity in the Ulleung Basin (UB) of the East Sea ranged from 172 to 358 g C m−2 year−1. This range of primary productivity is relatively higher than in other regions in the East Sea. The East Sea is a body of dynamic “non-oceanic” water with its own particular oceanic characteristics. Coastal upwelling and mesoscale eddies over a wide range of horizontal scales contribute to the high primary productivity in the UB. This vibrant primary production provides the foundation for a biological “hot” spot and strong support for an energetic biological pump cycle in the East Sea. Despite much progress in expanding knowledge of phytoplankton ecology in the East Sea, more studies on diversity, productivity, niche, and physiological adaptation to dynamic environments should be conducted to better understand ecological roles of phytoplankton in changing oceans.

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

Abstract 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.

Draft genome sequence of Rubidibacter lacunae strain KORDI 51-2(T), a cyanobacterium isolated from seawater of Chuuk lagoon.

A photoautotrophic cyanobacterium, Rubidibacter lacunae was reported in 2008 for the first time. The type strain, KORDI 51-2T, was isolated from seawater of Chuuk lagoon located in a tropical area. Although it belonged to a clade exclusively comprised of extremely halotolerant strains by phylogenetic analyses, R. lacunae is known to be incapable of growth at high salt concentration over 10%. Here we report the main features of the genome of R. lacunae strain KORDI 51-2T. The genome of R. lacunae contains a gene cluster for phosphonate utilization encoding three transporters, one regulator and eight C-P lyase subunits.

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.