Myung-Soo Han

Integrated Method for Single-Cell DNA Extraction, PCR Amplification, and Sequencing of Ribosomal DNA from Harmful Dinoflagellates Cochlodinium polykrikoides and Alexandrium catenella

A simplified technique was developed for DNA sequence-based diagnosis of harmful dinoflagellate species. This protocol integrates procedures for DNA extraction and polymerase chain reaction (PCR) amplification into a single tube. DNA sequencing reactions were performed directly, using unpurified PCR products as the DNA template for subsequent sequencing reactions. PCR reactions using DNA extracted from single cells of Cocodinium polykrikoides and Alexandrium catenella successfully amplified the target ribosomal DNA regions. DNA sequencing of the unpurified PCR products showed that DNA sequences corresponded to the expected locus of ribosomal DNA regions of both A. catenella and C. polykrikoides (each zero genetic distance and 100% sequence similarity). Using the protocol described in this article, there was little DNA loss during the purification step, and the technique was found to be rapid and inexpensive. This protocol clearly resolves the taxonomic ambiguities of closely related algal species (such as Alexandrium and Cochlodinium), and it constitutes a significant breakthrough for the molecular analysis of nonculturable dinoflagellate species.

Growth inhibition of bloom‐forming cyanobacterium Microcystis aeruginosa by rice straw extract

Aims:  To inhibit the growth of the bloom‐forming cyanobacterium Microcystis aeruginosa using a rice straw extract.

HETEROSIGMA AKASHIWO (RAPHIDOPHYCEAE) RESTING CELL FORMATION IN BATCH CULTURE: STRAIN IDENTITY VERSUS PHYSIOLOGICAL RESPONSE 1,2

In this study, we examined the impact of environmental perturbation on the movement of the toxic bloom‐forming alga Heterosigma akashiwo (Hada) Hada ex Y. Hara et Chihara [syn. H. carterae (Hulburt) F.J.R. Taylor] between vegetative and resting cell phases of the life history. Resting state induction, in batch culture, was most effective when vegetative cells were subjected to low temperature (10° C) and darkness for extended time periods. Heterosigma cells in stasis had neither a cell wall nor scales but were surrounded by a calyx, most probably of polysaccharide composition. The resting cell was completely immobile, although both flagella remained attached. Heterosigma resting cells did not require a maturation period before successful activation to the vegetative state could occur. Cell division and motility were impacted sequentially during both the induction and activation phases of resting cell development. Our data show that Heterosigma had an obligate light requirement for resting cell activation. In replete medium, very low light fluences of 5 μmol photons·m−2·s−1 were as effective as 60 μmol photons·m−2·s−1 in the initiation of activation. Such sensitivity to extremely low light might give Heterosigma a competitive advantage for bloom formation in nature. Reduced nitrate levels significantly shortened the temporal transition of vegetative cells into the resting cell phase of the life history. Additionally, when resting cells induced in nitrate‐limited medium were activated under nitrate‐replete condition, the efficiency of the activation response was directly correlated to light availability. Both vegetative and resting cells maintained a haploid DNA complement. Rapid amplified polymorphic DNA (RAPD) analysis demonstrated variation in genetic identity among axenic Heterosigma strains. Strain identity influenced success in resting cell induction and survival in stasis. To date, no defined sexual cycle has been described. These observations are discussed in terms of population fitness. The data presented in this report provide a model algal system wherein the molecular events that govern long‐term stasis in an obligately autotrophic organism can now be assessed.

Informative characteristics of 12 divergent domains in complete large subunit rDNA sequences from the harmful dinoflagellate genus, Alexandrium (Dinophyceae)

ABSTRACT. The genus Alexandrium includes organisms of interest, both for the study of dinoflagellate evolution and for their impacts as toxic algae affecting human health and fisheries. Only partial large subunit (LSU) rDNA sequences of Alexandrium and other dinoflagellates are available, although they contain much genetic information. Here, we report complete LSU rDNA sequences from 11 strains of Alexandrium, including Alexandrium affine, Alexandrium catenella, Alexandrium fundyense, Alexandrium minutum, and Alexandrium tamarense, and discuss their segmented domains and structure. Putative LSU rRNA coding regions were recorded to be around 3,400bp long. Their GC content (about 43.7%) is among the lowest when compared with other organisms. Furthermore, no AT‐rich regions were found in Alexandrium LSU rDNA, although a low GC content was recorded within the LSU rDNA. No intron‐like sequences were found. The secondary structure of the LSU rDNA and parsimony analyses showed that most variation in LSU rDNA is found in the divergent (D) domains with the D2 region being the most informative. This high D domain variability can allow members of the diverse Alexandrium genus to be categorized at the species level. In addition, phylogenetic analysis of the alveolate group using the complete LSU sequences strongly supported previous findings that the dinoflagellates and apicomplexans form a clade.

Deep level transient spectroscopy in plasma-assisted molecular beam epitaxy grown Al0.2Ga0.8N/GaN interface and the rapid thermal annealing effect

We investigated deep-level traps formed in Al0.2Ga0.8N/GaN heterostructures grown using plasma-assisted molecular beam epitaxy and by performing deep level transient spectroscopy (DLTS). Two electron traps with activation energies of Ec−150 meV and Ec−250 meV were observed, and their capture cross-sections (σT) were estimated to be 2.0×10−18 cm2 and 1.1×10−17 cm2, respectively. Different behaviors in the dependence of DLTS on filling pulse length confirm that the traps originated from N vacancies and dislocations. The amplitude of the dislocation-induced DLTS signal was reduced significantly by high-temperature rapid thermal annealing under N2 ambient after hydrogen treatment due to the reduction in dislocation density.

Sequence-based diagnostics and phylogenetic approach of uncultured freshwater dinoflagellate Peridinium (Dinophyceae) species, based on single-cell sequencing of rDNA

The armoured dinoflagellate Peridinium is widely distributed in freshwater environments worldwide and contains a large number of species. Their identity, however, has remained elusive, since the small cells tend to be morphologically similar. To help resolve this, a sequence-based diagnostics for uncultured Peridinium cells from field samples was applied, using single-cell PCR and direct DNA sequencing of the PCR products. Single cells were isolated randomly from field samples, and PCR successfully amplified the target rDNA regions from the crude lysates. Phylogenetic trees showed that all the cells were strongly grouped into the same clade (> 99% bootstrap value), including the previously identified P. bipes f. occultatum, and apparently separated from relatives such as P. cinctum, P. volzii and P. willei. All 17 isolates were genotypically identified as P. bipes f. occultatum, based on over than 99% of sequence similarities, and the organism was responsible for water blooms at different seasons in Korean waters. The sequence-based typing could clearly resolve P. bipes f. occultatum from the various Peridinium cells, and that the method is accurate and more labor-saving than the conventional method to monitor Peridinium species. This protocol may be useful for the application of molecular tools to uncultured Peridinium cells.

Monitoring of algicidal bacterium, Alteromonas sp. Strain A14 in its application to natural Cochlodinium polykrikoides blooming seawater using fluorescence in situ hybridization

The red tide of dinoflagellate, Cochlodinium polykrikoides has frequently occurred in coastal waters, causing severe damage to fisheries. In the present study, the algicidal bacterium Alteromonas sp. A14 isolated from the southern coast of Korea was applied to a red tide of C. polykrikoides in a laboratory experiment. In the experiment, the abundance of the strain A14 was monitored using fluorescence in situ hybridization. Inoculation of the A14 at a final cell density of 9.0×105 cells/ml caused a significant decrease in C. polykrikoides abundance from 1,830 to 700 cells/ml during 2 days, while abundances of harmless diatoms rapidly increased from 3 days. Abundances of both A14 and other bacteria increased to 1 day. After 1 day, with flagellate abundance increased, bacterial abundance decreased. Finally, algicidal bacterial abundance decreased to 3.5×104 cells/ml. In the biological control of harmful algal blooms, in addition to decrease in target algal abundance and not occurrence of other harmful blooms, decrease in abundance of utilized organism is also important. This study emphasizes the importance of monitoring the inoculated bacterium when applying bacterium to natural seawater.

Molecular genetic divergence of the centric diatom Cyclotella and Discostella (Bacillariophyceae) revealed by nuclear ribosomal DNA comparisons

The centric diatom Cyclotella, including the recently separated Discostella, is commonly present in freshwater and several species are important bio-indicators. Here, we describe molecular characteristics of the nuclear rDNA, spanning 18S to D1/D2 region of the 28S rDNA, of two genera Cyclotella and Discostella, particularly using Korean isolates of C. meneghiniana, Discostella sp. c.f. D. pseudostelligera. Molecular and morphological analyses showed that our isolates had nearly identical genotypes in rDNA and similar morphology as compared to presumably the same species from other geographical areas. Phylogenetic analyses of individual 18S and partial 28S rDNAs of Cyclotella sensu lato showed that all sequences were separated into two clades: one containing Cyclotella, the other Discostella including C. ocellata and C. bodanica. Statistical tests with pairwise genetic distance scores showed that the two genera were significantly different (one-factor ANOVA, p < 0.01). In addition, divergence in the partial 28S rDNA was significantly high (p < 0.01) as compared to 18S rDNA. This provides evidence that the two genera, Cyclotella and Discostella, belong to genetically well-separated groups. In addition, 28S rDNAs is a more suitable molecular marker for the discrimination of Cyclotella sensu lato.

Fixation of Chattonella antiqua and C. marina (Raphidophyceae) using Hepes-buffered paraformaldehyde and glutaraldehyde for flow cytometry and light microscopy

Katano T., Yoshida M., Lee J., Han M.-S. and Hayami Y. 2009. Fixation of Chattonella antiqua and C. marina (Raphidophyceae) using Hepes-buffered paraformaldehyde and glutaraldehyde for flow cytometry and light microscopy. Phycologia 48: 473–479. DOI: 10.2216/08-102.1. Chattonella antiqua and C. marina are harmful algal species that cause massive fish kills in coastal environments. Generally, Chattonella cells cannot be preserved well by fixation because of their fragile nature. In the present study, we developed a new fixative for Chattonella. Phosphate-buffered saline, which is generally used as a buffer for fixative, caused precipitation after fixation. In contrast, Hepes or sodium cacodylate prevented the precipitation. Moreover, these buffers worked well in the fixation to preserve cell morphology. Since Hepes is not as noxious as cacodylate, we selected Hepes as the buffer for the fixative. Cell counting revealed that the decrease in cell numbers by fixation was negligible and did not start until at least 8 days after fixation. We successfully analysed the DNA amount in fixed cells of Chattonella by flow cytometry. The present study demonstrated that Hepes-buffered paraformaldehyde and glutaraldehyde are superior to other fixatives for flow cytometry and light microscopy.

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.