• Journal of Microbiology and Biotechnology
• /
• v.20 no.2
• /
• pp.383-390
• /
• 2010

A newly isolated active producer of raw-starch-digesting amyloytic enzymes, Rhizopus microsporus var. chinensis CICIM-CU F0088, was screened and identified by morphological characteristics and molecular phylogenetic analyses. This fungus was isolated from the soil of Chinese glue pudding mill, and produced high levels of amylolytic activity under solid-state fermentation with supplementation of starch and wheat bran. Results of thin-layer chromatography showed there are two kinds of amyloytic enzymes formed by this strain, including one $\alpha$-amylase and two glucoamylases. It was found in the electron microscope experiments that the two glucoamylases can digest raw corn starch and have an optimal temperature of $70^{\circ}C$. These results signified that amyloytic enzymes secreted by strain Rhizopus microsporus var. chinensis CICIM-CU F0088 were types of thermostable amyloytic enzymes and able to digest raw corn starch.

• Journal of Microbiology and Biotechnology
• /
• v.24 no.10
• /
• pp.1301-1307
• /
• 2014

White-rot fungi of the genus Bjerkandera are cosmopolitan and have shown potential for industrial application and bioremediation. When distinguishing morphological characters are no longer present (e.g., cultures or dried specimen fragments), characterizing true sequences of Bjerkandera is crucial for accurate identification and application of the species. To build a framework for molecular identification of Bjerkandera, we carefully identified specimens of B. adusta and B. fumosa from Korea based on morphological characters, followed by sequencing the internal transcribed spacer region and 28S nuclear ribosomal large subunit. The phylogenetic analysis of Korean Bjerkandera specimens showed clear genetic differentiation between the two species. Using this phylogeny as a framework, we examined the identification accuracy of sequences available in GenBank. Analyses revealed that many Bjerkandera sequences in the database are either misidentified or unidentified. This study provides robust reference sequences for sequence-based identification of Bjerkandera, and further demonstrates the presence and dangers of incorrect sequences in GenBank.

• Animal Systematics, Evolution and Diversity
• /
• v.27 no.2
• /
• pp.159-163
• /
• 2011

DNA barcoding of Bryozoa or "moss animals" has hardly advanced and lacks reference sequences for correct species identification. To date only a small number of cytochrome c oxidase subunit I (COI) sequences from 82 bryozoan species have been deposited in the National Center for Biotechnology Information (NCBI) GenBank and Barcode of Life Data Systems (BOLD). We here report COI data from 53 individual samples of 29 bryozoan species collected from Korean seawater. To our knowledge this is the single largest gathering of COI barcode data of bryozoans to date. The average genetic divergence was estimated as 23.3% among species of the same genus, 25% among genera of the same family, and 1.7% at intraspecific level with a few rare exceptions having a large difference, indicating a possibility of presence of cryptic species. Our data show that COI is a very appropriate marker for species identification of bryozoans, but does not provide enough phylogenetic information at higher taxonomic ranks. Greater effort involving larger taxon sampling for the barcode analyses is needed for bryozoan taxonomy.

• ALGAE
• /
• v.31 no.3
• /
• pp.219-230
• /
• 2016

The Euglena deses group are common freshwater species composed of E. adhaerens, E. carterae, E. deses, E. mutabilis, and E. satelles. These species are characterized by elongated cylindrical worm-like cell bodies and numerous discoid chloroplasts with a naked pyrenoid. To understand the cryptic diversity, species delimitation and phylogenetic relationships among members of the group, we analyzed morphological data (light and scanning electron microscopy) and molecular data (nuclear small subunit [SSU] and large subunit [LSU] rDNAs and plastid SSU and LSU rDNAs). Bayesian and maximum likelihood analyses based on the combined four-gene dataset resulted in a tree consisting of two major clades within the group. The first clade was composed of two subclades: the E. mutabilis subclade, and the E. satelles, E. carterae, and E. adhaerens subclade. The E. mutabilis subclade was characterized by a lateral canal opening at the anterior end and a single pellicular stria, whereas the E. satelles, E. carterae, and E. adhaerens subclade was characterized by an apical canal opening at the anterior end of the cell and double pellicular striae. The second clade consisted of 20 strains of E. deses, characterizing by a subapical canal opening at the anterior end and double pellicular striae, but they showed cell size variation and high genetic diversity. Species boundaries were tested using a Bayesian multi-locus species delimitation method, resulting in the recognition of five cryptic species within E. deses clade.

• Journal of Mushroom
• /
• v.15 no.1
• /
• pp.8-13
• /
• 2017

An auxin-producing bacterial strain, designated 4-3, was isolated from waste button mushroom compost in Boryeong-si, Chungnam. The strain 4-3 was classified as a novel strain of Leucobacter tardus, based on chemotaxonomic and phylogenetic analyses. TLC and HPLC the isolated L. tardus strain 4-3 produced indole-3-acetic acid (IAA), the auxin. Maximum IAA productionof $94.3mg\;L^{-1}$ was detected for bacteria cultured in R2A medium with 0.1% l-tryptophan, incubated for 24 h at $35^{\circ}C$. Negative correlationwas observed between IAA production and pH of the culture medium, indicating that the increase inIAA caused acidification ofthe medium. The effect of supplementation with varying concentrations of l-tryptophan, a known precursor of IAA, was also assessed. production was maximal at 0.1% l, but decreased at lconcentrations above 0.2%. To investigate the plant growth-promoting effects of the bacterium, L. tardus strain 4-3 culture broth was used to inoculate water cultures and seed pots of mung bean. We found thatadventitious root induction and root growth were 2.2-times higher in thethan in the non-inoculated plants.

• ALGAE
• /
• v.24 no.3
• /
• pp.129-138
• /
• 2009

DNA-based discrimination of species is a powerful way for morphologically otherwise similar species, like centric diatoms. Here, the author sequenced long-range nuclear ribosomal DNAs, spanning from the 18S to the D5 region of the 28S rDNA, of Stephanodiscus, particularly including a Korean isolate. By comparisons, high DNA similarities were detected from the rDNAs of nine Stephanodiscus (>99.4% in 18S rDNA, >98.0% in 28S rDNA). Their genetic distances, however, were significantly different (Kruskal-Wallis test, p < 0.01) compared to two related genera, namely Cyclotella and Discostella. In addition, genetic distances of 18S rDNAs were significantly different (Student’s t-test, p = 0.000) against those of the 28S rDNAs according to individual genera (Cyclotella, Discostella, and Stephanodiscus). Phylogenetic analyses showed that Stephanodiscus and Discostella showed a sister taxon relationship, and their clade was separated from a cluster of Cyclotella (1.00 PP, 100% BP). This suggests that Stephanodiscus has highly conserved sequences of both 18S and 28S rDNA; however, Stephanodiscus is well-separated from other freshwater centric diatoms, such as Cyclotella and Discostella, at the generic level.

• Journal of Microbiology and Biotechnology
• /
• v.14 no.1
• /
• pp.205-211
• /
• 2004

A 16S rDNA clone library was generated to investigate the bacterial diversity in tidal flat sediment in Ganghwa Island, Republic of Korea. A total of 103 clones were sequenced and analyzed by comprehensive phylogenetic analyses. No clones were identical to any of known 16S rRNA sequences in public databases. Sequenced clones fell into thirteen lineages of the domain Bacteria: the alpha, beta, gamma, delta, and epsilon Proteobacteria, Actinobacteria, CFB group, Chloroflexi, Acidobacteria, Planctomycetes, Verrucomicrobia, and known uncultured candidate divisions (OP11, BRC1, KSB1, and WS1). Two clones were not associated with any known bacterial divisions. The majority of clones belonged to the gamma and delta Proteobacteria (46.7%). Clones of Actinobacteria were distantly related to known taxa. It is evident from 16S rDNA-based community analysis that the bacterial community in tidal flat sediment is remarkably diverse and unique among other marine environments examined so far.

• Fisheries and Aquatic Sciences
• /
• v.20 no.6
• /
• pp.8.1-8.18
• /
• 2017

Background: Metallothionein (MT) is a multifunctional protein playing important roles in homeostatic regulation and detoxification of metals. Mollusk species have been considered as useful sentinel platforms for MT-based biomarker approaches, and they have been reported to display an extraordinary structural diversity of MT proteins. However, potential diversity of molluskan MTs has not been fully explored and recent updates have suggested the need of revision of evolutionary hypothesis for molluskan MTs. Results: Based on bioinformatic analysis and phylogenetic evidences, novel divergence mechanisms and paths were hypothesized in both gastropod and bivalve MT groups. Our analyses are suggestive of the taxon- or lineage-specific domain multiplication/duplication from the ancestral or prototypic MT. Diversification and selection of molluskan MTs might be driven by the needs for acquiring metal selectiveness, specialized novel function, and improved capacity of metal detoxification under environmentally stressed conditions. Conclusion: The structural diversity and variations of molluskan MTs are significantly larger than previously understood. Undoubtedly, molluskan MTs have undergone dynamic divergent processes in their evolutionary histories, giving rise to the great diversity of domain structures in extant MT isoforms. Novel evolutionary paths for molluskan MTs newly proposed in this review could shed additional light onto the revision of the hypothesis for evolutionary differentiation of MTs in the molluskan lineage.

• Fisheries and Aquatic Sciences
• /
• v.21 no.10
• /
• pp.27.1-27.5
• /
• 2018

During a survey of marine algal flora, two gigartinalean species were collected from Pohang and Youngdeok located on the eastern coast of Korea. They share the generic morphological features of Dumontia. One is characterized by cylindrical to complanate thallus with multi- and uniaxial structure, somewhat inflated and contorted branches, and hollow medulla and cortex consisting of progressively smaller cells outwards. The other shows basically the same features as the former species but was smaller in size, as having 4-7 cm in thallus length and 1-2 mm in branch width rather than 15 and 2-5 mm. Both species are distinguished from each other only by these morphometric features. However, it is supported by molecular analysis that both species are genetically distinct. In a phylogenetic tree based on internal transcribed spacer sequence, the two species nest in the same clade as Dumontia contorta and D. alaskana, respectively. The genetic distance between both sequences within the clade was calculated as 0.0 0.2%, considered to be intra-specific for Dumontia. Based on the morphological and molecular analyses, the two Korean species are identified as D. contorta and D. alaskana described originally from Netherlands and Alaska, respectively. This is the first record of the two Dumontia species in Korea.

• Parasites, Hosts and Diseases
• /
• v.43 no.1 s.133
• /
• pp.7-13
• /
• 2005

The taxonomy of Acanthamoeba spp., an amphizoic amoeba which causes granulomatous amoebic encephalitis and chronic amoebic keratitis, has been revised many times. The taxonomic validity of some species has yet to be assessed. In this paper, we analyzed the morphological characteristics, nuclear 18s rDNA and mitochondrial 16s rDNA sequences and the Mt DNA RFLP of the type strains of four Acanthamoeba species, which had been previously designated as A. divionensis, A. parasidionensis, A. mauritaniensis, and A. rhysodes. The four isolates revealed characteristic group II morphology. They exhibited 18S rDNA sequence differences of $0.2-1.1\%$ with each other, but more than $2\%$ difference from the other compared reference strains. Four isolates formed a different clade from that of A. castellanii Castellani and the other strains in morphological group lion the phylogenetic tree. In light of these results, A. paradivionensis, A. divionensis, and A. mauritaniensis should be regarded as synonyms for A. rhysodes.