Bum Soo Park

Comprehensive comparisons of three pennate diatoms, Diatoma tenuae, Fragilaria vaucheriae, and Navicula pelliculosa, isolated from summer Arctic reservoirs (Svalbard 79°N), by fine-scale morphology and nuclear 18S ribosomal DNA

Here we report morphological and molecular characteristics of dominant freshwater diatoms in summer Arctic reservoirs of Svalbard (Norway), using four culture isolates, when we collected the samples in the field on 15 August 2005. Analyses of morphology and BLAST searches with 18S rDNA sequences identified them to Diatoma tenue (HYNP006, HYNP013), Navicula pelliculosa (HYNP021), and Fragilaria vaucheriae (HYNP022), respectively. Comparative studies of morphology revealed that the body shapes of the three polar diatoms were nearly identical to the known morphology of each species; however, they were considerably shorter in body length than previously described identical species from other locations. The 18S rDNA sequences of the diatoms were nearly identical to the same species from temperate and other regions. Phylogenetic analysis showed that the polar diatoms each formed a clade with their identical species and genera according to their taxonomic positions. This suggests that the polar diatoms may possess little or no genetic or morphological variation compared to more temperate strains.

Dynamics of bacterial community structure during blooms of Cochlodinium polykrikoides (Gymnodiniales, Dinophyceae) in Korean coastal waters

Recent studies of dinoflagellates have reported that blooms can be closely related to the characteristics of the associated bacteria, but studies of the correlation between the toxic dinoflagellate, Cochlodinium polykrikoides and their associated bacterial community composition has not been explored. To understand this correlation, changes in bacterial community structure through the evolution of a C. polykrikoides bloom in Korean coastal waters via clone library analysis were investigated. Although there were no apparent changes in physio-chemical factors during the onset of the C. polykrikoides bloom, the abundance of bacteria bourgeoned in parallel with C. polykrikoides densities. Alpha-, gamma-proteobacteria and Flavobacteria were found to be dominant phyletic groups during C. polykrikoides blooms. The proportion of gamma-proteobacteria was lower (11.8%) during peak of the bloom period compared to the post-bloom period (26.2%). In contrast, alpha-proteobacteria increased in dominance during blooms. Among the alpha-proteobacteria, members of Rhodobacterales abruptly increased from 38% of the alpha-proteobacteria before the bloom to 74% and 56% during the early bloom and peak bloom stages, respectively. Moreover, multiple sites concurrently hosting C. polykrikoides blooms also contained high portions of Rhodobacterales and principal component analysis (PCA) demonstrated that Rhodobacterales had a positive, significant correlation with C. polykrikoides abundances (p≤0.01, Pearson correlation coefficients). Collectively, this study reveals the specific clades of bacteria that increase (Rhodobacterales) and decrease (gamma-proteobacteria) in abundance C. polykrikoides during blooms.

Assessment of EvaGreen-based quantitative real-time PCR assay for enumeration of the microalgae Heterosigma and Chattonella (Raphidophyceae)

Heterosigma akashiwo and Chattonella species (Raphidophyceae) are difficult to detect and quantify in environmental samples because of their pleomorphic and fragile cell nature. In this study, we developed a quantitative real-time polymerase chain reaction (qRT-PCR) assay for the enumeration of these algal taxa using a new DNA-binding dye, EvaGreen. Species-specific qRT PCR primers to H. akashiwo, Chattonella antiqua, Chattonella marina, Chattonella ovata, and Chattonella subsalsa were designed to target the ITS2 rRNA gene intergenic region. Primer specificities were tested via BLAST searches. In addition, specificity was verified using empirical tests, including competitive PCR. The qRT PCR assay analyzing Ct value and the log of cell number showed a significant linear relationship (r2 ≥ 0.997). When light microscopy was used to monitor the population dynamics of targeted Raphidophyceae from Lake Shihwa, H. akashiwo was detected in ten samples and no Chattonella spp. were detected (70 samples collected from May, 2007 to January, 2008). In contrast, when the qRT-PCR assay was used, H. akashiwo was detected in 41 samples. C. antiqua, C. marina, and C. ovata were detected in eight samples. Most of the samples analyzed using qRT-PCR assays showed higher algal numbers than did those assayed via microscopy, suggesting that the enumeration of Raphidophyceae via classic microscopic methods most likely underestimates true algal concentration.

An Improved Quantitative Real-Time PCR Assay for the Enumeration of Heterosigma akashiwo (Raphidophyceae) Cysts Using a DNA Debris Removal Method and a Cyst-Based Standard Curve

The identification and quantification of Heterosigma akashiwo cysts in sediments by light microscopy can be difficult due to the small size and morphology of the cysts, which are often indistinguishable from those of other types of algae. Quantitative real-time PCR (qPCR) based assays represent a potentially efficient method for quantifying the abundance of H. akashiwo cysts, although standard curves must be based on cyst DNA rather than on vegetative cell DNA due to differences in gene copy number and DNA extraction yield between these two cell types. Furthermore, qPCR on sediment samples can be complicated by the presence of extracellular DNA debris. To solve these problems, we constructed a cyst-based standard curve and developed a simple method for removing DNA debris from sediment samples. This cyst-based standard curve was compared with a standard curve based on vegetative cells, as vegetative cells may have twice the gene copy number of cysts. To remove DNA debris from the sediment, we developed a simple method involving dilution with distilled water and heating at 75°C. A total of 18 sediment samples were used to evaluate this method. Cyst abundance determined using the qPCR assay without DNA debris removal yielded results up to 51-fold greater than with direct counting. By contrast, a highly significant correlation was observed between cyst abundance determined by direct counting and the qPCR assay in conjunction with DNA debris removal (r2 = 0.72, slope = 1.07, p < 0.001). Therefore, this improved qPCR method should be a powerful tool for the accurate quantification of H. akashiwo cysts in sediment samples.

Cyst morphology and germination in Heterosigma akashiwo (Raphidophyceae)

Abstract: Further understanding of the life history of Heterosigma akashiwo (Raphidophyceae) requires identification and isolation of cysts. In this study, we provide a more detailed description of the cyst wall, the germination pore, the structure underneath the lid of germination pore (SULG) and the germination process. The SULG is associated with cyst germination and may be a useful diagnostic feature of H. akashiwo cysts. Our refined description of cysts of H. akashiwo may allow for accurate identification in environmental samples.

A mutualistic interaction between the bacterium Pseudomonas asplenii and the harmful algal species Chattonella marina (Raphidophyceae)

Several studies on various Chattonella species have reported that bacteria may play an important role in Chattonella bloom initiation, however, no studies have described how these bacteria promote the growth of C. marina. The interaction between C. marina and bacteria was investigated for identification and characterization of potential growth-promoting bacteria. In preliminary tests, the growth promoting effect of Pseudomonas species (25 strains) was investigated and P. asplenii (≥2.27) was determined as a growth-promoting bacteria for both C. marina strains (CCMP 2049 and 2050). This bacterium exerted optimal growth-promoting effects on C. marina, causing an increase in the initial density of P. asplenii to approximately 1×107cellsmL-1, which was used as the initial density in this study. To determine whether the growth-promoting activity was direct or indirect, P. asplenii was incubated in the algal media and then a filtrate of this culture was added to both C. marina strains. The P. asplenii filtrate stimulated the growth of C. marina and maintained the growth-promoting effects after high temperature (121°C for 20min) and pressure (15psi) treatment. Thus, P. asplenii is able to promote C. marina growth through the release of a heat-resistant substance, such as inorganic nutrients. A nutrient analysis indicated that this bacterium elevated the phosphate concentration. Interestingly, P. asplenii was unable to survive in phosphate-limited media but could grow in phosphate-limited media incubating C. marina. Moreover, this bacterium could secrete significantly more phosphate in the presence of C. marina (p<0.0001). These results suggested that P. asplenii and C. marina may have a mutualistic interaction.

Relationship between dissolved organic carbon and bacterial community in the coastal waters of Incheon, Korea

Abstract Bacteria constitute a large domain of prokaryotic microorganisms present in marine ecosystems and play a significant role in energy flow and nutrient cycling. Bacterial community changes may affect organisms of higher trophic levels. We conducted field monitoring to study the relationship between dissolved organic carbon (DOC) and the bacterial community in the coastal waters of Incheon, Korea. Results showed that abiotic factors, such as temperature, salinity, dissolved oxygen (DO), pH, and dissolved inorganic nutrients, were not significantly different among the sampling sites during the study period. On the other hand, nutrient conditions were significantly different among the sites between 2012-2013 and 2014. Nitrogen was the limiting factor from 2012 to 2013, and phosphate in 2014. Biotic data showed that DOC affected both bacterial abundance and bacterial composition. A similar fluctuation pattern was observed for phytoplankton and Chlorophyll a. However, a close correlation was not observed between phytoplankton and other variables. Redundancy analysis (RDA) and Pearson correlation analysis of abiotic and biotic factors also showed that DOC concentration and bacterial abundance were correlated. Therefore, DOC appears to be an important factor affecting bacterial abundance and composition in the coastal waters of Incheon, Korea.

Improvement of cyanobacterial-killing biologically derived substances (BDSs) using an ecologically safe and cost-effective naphthoquinone derivative

In previous studies, naphthoquinone (NQ) compounds have been shown to be effective, selective, and ecologically safe algicides for controlling harmful algal blooming species (HABs) or winter bloom species, such as Stephanodiscus hantzschii. However, there are no reports on NQ-based algicides for use with cyanobacterial blooming species. In this study, we developed 31 NQ compounds to investigate algicides for mitigating cyanobacterial blooms. In addition, to better apply these compounds in the field, we reduced the number of production steps to develop a cost-effective algicide. In preliminary testing, we screened NQ compounds that showed the best algicidal activity on target cyanobacteria, including Aphanizomenon, Dolichospermum, Microcystis, Oscillatoria, and Nostoc species. The compound NQ 2-0 showed the highest algicidal activity (90%) at a low concentration (≥1μM) on target algae. These were very limiting algicidal effects of 1µM NQ 2-0 observed against non-target algae, such as diatoms (Stephanodiscus hantzschii, Cyclotella meneghiniana, Synedra acus, and Aulacoseira granulata) or green algae (Cosmarium bioculatum and Scenedesmus quadricauda), and the effect did not exceed 15-25% (except against S. quadricauda). NQ 2-0 (1μM) showed no eco-toxicity, as represented by the survival rates of Pseudokirchneriella subcapitata (100%), Daphnia magna (100%), and Danio rerio (100%). Additionally, a chronic eco-toxicity assessment showed no toxicity toward the survival, growth or reproduction of D. magna. Moreover, NQ 2-0 quickly dissipated from field water samples and had a half-life of approximately 3.2 days. These results suggest that NQ 2-0 could be a selective and ecologically safe algicide to mitigate harmful cyanobacterial blooms.