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.

The spring phytoplankton bloom is a critical event in temperate oceans typically associated with the highest productivity levels throughout the year. To investigate the bloom process in the Yellow Sea, daily data on physical, chemical, and phytoplankton taxonomic group biomass, calculated via the chemotaxonomic approach, were collected from late March or early April to late May between 2018 and 2020 at the Socheongcho Ocean Research Station. During early spring (late March to mid-April), phytoplankton biomass increased, accompanied by a decrease in nutrient levels, with Bacillariophyceae and Cryptophyceae being the dominant groups. As water temperature increased, a pycnocline began to develop in late April, leading to a peak of the phytoplankton bloom dominated by chlorophytes and Cryptophyceae. Network analysis suggested that this phytoplankton bloom was caused by the onset of vertical stratification induced by increased sea surface temperature. The chlorophyte peak induced phosphate limitation above the pycnocline, resulting in succession to Prymnesiophyceae and Dinophyceae. Following pycnocline formation, phytoplankton biomass below the pycnocline was dominated by Bacillariophyceae and Cryptophyceae, with decreasing or fluctuating trends depending on phosphate concentration. Apart from these general patterns, 2019 and 2020 both had distinctive traits. The 2019 data revealed lower phosphate concentrations than the other 2 years, leading to a smaller chlorophyte peak at the surface compared to 2018 and extreme phosphate limitation above the pycnocline. This limitation resulted in decreased biomass of late successional groups, including Prymnesiophyceae and Dinophyceae. Pycnocline formation was delayed in year 2020, and stratification was significantly weaker compared to the previous 2 years. Due to the pycnocline delay, the surface chlorophyte peak did not develop and no succession to late successional groups was observed. Instead, high levels of Bacillariophyceae and Cryptophyceae biomass were observed throughout the water column with no surface bloom. Thus, among various environmental factors, increasing surface water temperature and phosphate concentrations play pivotal roles in shaping phytoplankton bloom dynamics. Distinct yearly variation points to the broader impacts of climate shifts, emphasizing the need for continued marine monitoring.

Picocyanobacteria (Prochlorococcus and Synechococcus) play an important role in primary production and biogeochemical cycles in the subtropical and tropical Pacific Ocean, but little biological information on them is currently available in the North Pacific Ocean (NPO). The present study aimed to determine the picocyanobacterial contributions to the total primary production in the regions in the NPO using a combination of a dual stable isotope method and metabolic inhibitor. In terms of cell abundance, Prochlorococcus were mostly dominant (95.7 ± 1.4%) in the tropical Pacific region (hereafter, TP), whereas Synechococcus accounted for 50.8%–93.5% in the subtropical and temperate Pacific region (hereafter, SP). Regionally, the averages of primary production and picocyanobacterial contributions were 11.66 mg C m⁻²·h⁻¹ and 45.2% (±4.8%) in the TP and 22.83 mg C m⁻²·h⁻¹ and 70.2% in the SP, respectively. In comparison to the carbon, the average total nitrogen uptake rates and picocyanobacterial contributions were 10.11 mg N m⁻²·h⁻¹ and 90.2% (±5.3%) in the TP and 4.12 mg N m⁻²·h⁻¹ and 63.5%, respectively. These results indicate that picocyanobacteria is responsible for a large portion of the total primary production in the region, with higher contribution to nitrogen uptake rate than carbon. A long-term monitoring on the picocyanobacterial variability and contributions to primary production should be implemented under the global warming scenario with increasing ecological roles of picocyanobacteria.

The CHEMTAX program has been widely used to estimate community composition based on major pigment concentrations in seawater. However, because CHEMTAX is an underdetermined optimization algorithm, underdetermined bias has remained an unsolved problem since its development in 1996. The risk of producing biased results increases when analyzing the picophytoplankton community; therefore, this study tested a new method for avoiding biased CHEMTAX results using the picophytoplankton community around the East Sea (Japan Sea). This method involves building a linear model between pigment concentration data and community composition data based on DNA sequencing to predict the pigment range for each operational taxonomic unit, based on the 95% prediction interval. Finally, the range data are transformed into an initial ratio and ratio limits for CHEMTAX analysis. Three combinations of initial ratios and ratio limits were tested to determine whether the modeled initial ratio and ratio limit could prevent underdetermined bias in the CHEMTAX estimates; these combinations were the modeled initial ratio and ratio limit, the modeled initial ratio with a default ratio limit of 500 s, and an initial ratio from previous research with the default ratio limit. The final ratio and composition data for each combination were compared with Bayesian compositional estimator-based final ratio and composition data, which are robust against underdetermined bias. Only CHEMTAX analysis using the modeled initial ratio and ratio limit was unbiased; all other combinations showed significant signs of bias. Therefore, the findings in this study indicate that ratio limits and the initial ratio are equally important in the CHEMTAX analysis of biased datasets. Moreover, we obtained statistically supported initial ratios and ratio limits through linear modeling of pigment concentrations and 16s rDNA composition data.

Herein, we evaluate the scientific basis for managing hull fouling of ships entering Korean ports, diagnose biological risks that may occur when in-water cleaning (IWC) systems remove hull fouling, and present a protocol for evaluating these risks (the Korean Infection Modes and Effects Analysis; K-IMEA). Protocol development included the selection of core elements and scenario design for IWC and the evaluation of regrowth experiments. The K-IMEA index was designed by considering the inoculation pathway of attaching organisms in all processes to ships that enter a port for in-water cleaning. A number of risk indices were defined: R1—Introduction/Establishment of alien species before in-water cleaning; R2—Establishment of alien species escaped during in-water cleaning; R3—Introduction/Establishment of alien species after in-water cleaning; and R4—Establishment of alien species in effluent water. K-IMEA regrowth experiments (R2 and R4) using the in-water cleaning effluent showed that the attachment and regrowth of prokaryotes, microalgae, and macroalgae were successfully detected. In particular, prokaryotes were observed in samples filtered through a 5 μm mesh of the in-water cleaning effluent, even at a low fouling rating (Levels 1–2). These experiments suggest a necessity to consider a secondary treatment method in addition to the primary filtration method for the treatment of in-water cleaning effluents.

The disposal of mine tailings into the marine environment is considered an essential option to secure the economic efficiency of deep-sea mining, but it might adversely affects the ecosystem. To examine the potential impacts of tailing disposal from polymetallic nodules and polymetallic sulfide mines on phytoplankton communities, addition experiments of crushed fine particles into surface seawater were conducted in the open Indian Ocean and changes in chlorophyll a fluorescence and community composition were analyzed. The addition of tailings had serious adverse effects on phytoplankton fluorescence and photosynthetic activity, regardless of mine type. The adverse effects seemed to mainly be due to the physical properties of the mine tailings. These also showed discriminatory effects on phytoplankton, resulting in great changes in community composition. The results suggest that mine tailings could have significant adverse impacts on phytoplankton assemblages, but the degree of impact greatly varies depending on the phytoplankton groups. The discriminatory impacts would cause changes in biomass, community structure, and thus ecological function.