• The Korean Journal of Mycology
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• v.47 no.2
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• pp.165-172
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• 2019

To investigate the diversity of aquatic fungi, we collected deposits of soil, plants, and plant litter from ponds and streams. NNIBRFG1552 was isolated from soil deposits and NNIBRFG3013 from plant deposits in Namsaengi-mot in Jeju, Korea in 2016; NNIBRFG5472 was isolated from plant litter in Bocheong-cheon, Boeun, Korea in 2018. Based on morphological characteristics and phylogenetic analysis using rDNA sequences of the internal transcribed spacer (ITS), NNIBRFG1552, NNIBRFG3013, and NNIBRFG5472 were identified as Filoporella exilis (100% similarity with KC834046), F. fistucella (99.8% with KC834047), and F. cf. annelidica (100% with KC834044), respectively. Furthermore, cultural and morphological characteristics were analyzed to confirm the molecular identification. No species of the genus Filosporella has yet been reported in Korea.

• International Journal of Industrial Entomology and Biomaterials
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• v.47 no.1
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• pp.1-11
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• 2023

The Indian golden muga silkworm, Antheraea assamensis Helfer is an economically important wild silkworm endemic to Northeastern part of India. In recent years, climate change has posed a threat to muga silk production due to the requirement that larvae be reared outdoors. Since the muga silkworm larvae are exposed to the vagaries of nature, the changing climate has increased the incidence of microbial diseases in the rearing fields. Accurate diagnosis of the disease causing pathogens and its associated epidemiology are prerequisites to manage the diseases in the rearing field. Although conventional microbial culturing methods are widely used to identify pathogenic bacteria, they would not provide meaningful information on a wide variety of silkworm pathogens. The information on use of molecular diagnostic tools in detection of microbial pathogens of wild silk moths is very limited. A wide range of molecular and immunodiagnostic techniques including denaturing gradient gel electrophoresis (DGGE), random amplified polymorphism (RAPD), 16S rRNA/ITSA gene sequencing, multiplex polymerase chain reaction (M-PCR), fluorescence in situ hybridization (FISH), immunofluorescence, and repetitive-element PCR (Rep-PCR), have been used for detecting and characterizing the pathogens of insects with economic significance. Nevertheless, the application of these molecular tools for detecting and typing entomopathogens in surveillance studies of muga silkworm rearing is very limited. Here, we discuss the possible application of these molecular techniques, their advantages and major limitations. These methods show promise in better management of diseases in muga ecosystem.

• Asian-Australasian Journal of Animal Sciences
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• v.13 no.1
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• pp.96-114
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• 2000

Genetically selected beef cattle are fed high-energy diets in intensive production systems developed in industrial countries. This type of feeding can induce rumen dysfunctions that have to be corrected by farmers to optimise cost-effectiveness. The risk of rumen acidosis can be reduced by using slowly degradable starch, which partly escapes rumen fermentation and goes on to be digested in the small intestine. Additives are proposed to stabilise the rumen pH and restrict lactate accumulation, thus favouring the growth of cellulolytic bacteria and stimulating the digestion of the dietary plant cell wall fraction. This enhances the energy value of feeds when animals are fed maize silage for example. Supplementation of lipids to increase energy intake is known to influence the population of rumen protozoa and some associated rumen functions such as cellulolysis and proteolysis. The end products of rumen fermentation are also changed. Lipolysis and hydrogenation by rumen microbes alter the form of fatty acids supplied to animals. This effect is discussed in relation with the quality of lipids in beef and the implications for human health. Conditions for optimising the amount of amino acids from microbial proteins and dietary by-pass proteins flowing to the duodenum of ruminants, and their impact on beef production, are also examined.

• Biomedical Science Letters
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• v.22 no.4
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• pp.150-159
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• 2016

Knowledge of the distribution and biodiversity of environmental bacteria and the ecosystem that influences them is crucial for predicting an ecosystem. However, bacterial culture methods can only analyze approximately 0.1% of the existing microorganisms, those that are readily cultured under laboratory conditions. By contrast, next-generation sequencing (NGS) has generally been known to obtain more diverse profiling of bacterial composition. We compared the bacterial communities using both a culture-dependent (MALDI-TOF) and culture-independent (NGS) methods. Environmental specimens were obtained from both freshwater and seawater. Water samples were also analyzed by both pyrosequencing and MiSeq sequencing, in order to select one NGS platform which could analyze comparatively more diverse microbiota. Bacterial distribution analyzed with MALDI-TOF showed no difference between the microbiota of freshwater and seawater, whereas the results analyzed with NGS distinguished between the two. The diversity indexes of MiSeq sequencing were higher than for Pyrosequencing. This indicated that MiSeq sequencing is capable of analyzing a comparatively wider diversity of bacteria. The genus of Flavobacterium and Planktophila were identified as being unique to freshwater, whereas EU801223 and OM43 were found in the seawater. Difference between the bacterial composition of the freshwater and seawater environments was identified by MiSeq sequencing analysis.

• Food Science and Biotechnology
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• v.15 no.4
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• pp.595-598
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• 2006

Semi-quantitative monitoring of Lactobacillus sake and Lactobacillus plantarum, major and minor microorganisms in kimchi, respectively, and Lactobacillus paraplantarum, recently shown to be present in kimchi, was carried out by real-time polymerase chain reaction (PCR). Changes in the 3 species during kimchi fermentation were monitored by the threshold cycle ($C_T$) of real-time PCR. As fermentation proceeded at $15^{\circ}C$, the number of L. sake increased dramatically compared to those of L. plantarum and L. paraplantarum. During fermentation at $4^{\circ}C$, the growth rates of the 3 species decreased, but the proportions of L. plantarum and L. paraplantarum in the microbial ecosystem were almost constant. Considering the $C_T$ values of the first samples and the change in the $C_T$ value, the number of L. sake is no doubt greater than those of L. plantarum and L. paraplantarum in the kimchi ecosystem. L. sake seems to be one of the major microorganisms involved in kimchi fermentation, but there is insufficient evidence to suggest that L. plantarum is the primary acidifying bacterium.

• Journal of Microbiology and Biotechnology
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• v.33 no.12
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• pp.1615-1624
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• 2023

Microcystis blooms threaten ecosystem function and cause substantial economic losses. Microorganismbased methods, mainly using cyanobactericidal bacteria, are considered one of the most ecologically sound methods to control Microcystis blooms. This study focused on gaining genomic insights into Paucibacter aquatile DH15 that exhibited excellent cyanobactericidal effects against Microcystis. Additionally, a pan-genome analysis of the genus Paucibacter was conducted to enhance our understanding of the ecophysiological significance of this genus. Based on phylogenomic analyses, strain DH15 was classified as a member of the species Paucibacter aquatile. The genome analysis supported that strain DH15 can effectively destroy Microcystis, possibly due to the specific genes involved in the flagellar synthesis, cell wall degradation, and the production of cyanobactericidal compounds. The pan-genome analysis revealed the diversity and adaptability of the genus Paucibacter, highlighting its potential to absorb external genetic elements. Paucibacter species were anticipated to play a vital role in the ecosystem by potentially providing essential nutrients, such as vitamins B₇, B₁₂, and heme, to auxotrophic microbial groups. Overall, our findings contribute to understanding the molecular mechanisms underlying the action of cyanobactericidal bacteria against Microcystis and shed light on the ecological significance of the genus Paucibacter.

• Journal of Ginseng Research
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• v.40 no.2
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• pp.127-134
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• 2016

Background: Rhizospheric fungi play an essential role in the plantesoil ecosystem, affecting plant growth and health. In this study, we evaluated the fungal diversity in the rhizosphere soil of 2-yr-old healthy Panax notoginseng cultivated in Wenshan, China. Methods: Culture-independent Illumina MiSeq and culture-dependent techniques, combining molecular and morphological characteristics, were used to analyze the rhizospheric fungal diversity. A diffusion test was used to challenge the phytopathogens of P. notoginseng. Results: A total of 16,130 paired-end reads of the nuclear ribosomal internal transcribed spacer 2 were generated and clustered into 860 operational taxonomic units at 97% sequence similarity. All the operational taxonomic units were assigned to five phyla and 79 genera. Zygomycota (46.2%) and Ascomycota (37.8%) were the dominant taxa; Mortierella and unclassified Mortierellales accounted for a large proportion (44.9%) at genus level. The relative abundance of Fusarium and Phoma sequenceswas high, accounting for 12.9% and 5.5%, respectively. In total,113 fungal isolates were isolated from rhizosphere soil. They were assigned to five classes, eight orders (except for an Incertae sedis), 26 genera, and 43 species based on morphological characteristics and phylogenetic analysis of the internal transcribed spacer. Fusarium was the most isolated genus with six species (24 isolates, 21.2%). The abundance of Phoma was also relatively high (8.0%). Thirteen isolates displayed antimicrobial activity against at least one test fungus. Conclusion: Our results suggest that diverse fungi including potential pathogenic ones exist in the rhizosphere soil of 2-yr-old P. notoginseng and that antagonistic isolates may be useful for biological control of pathogens.

• Journal of Wetlands Research
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• v.17 no.4
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• pp.332-338
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• 2015

Valuation of ecosystem services through organic carbon distribution and cycling in the Pinus densiflora forest at Mt. Worak National Park were investigated from January 2013 through December 2013. The amount of carbon allocated to above and below ground biomass was 32.17 and 8.04 ton C $ha^{-1}$. Amount of organic carbon in litter layer was 5.55 ton C $ha^{-1}$. Amount of organic carbon within 50cm soil depth was 58.62 ton C $ha^{-1}$ 50cm-$depth^{-1}$. Total amount of organic carbon in this Pinus densiflora forest was estimated to 104.38 ton C $ha^{-1}$. The estimated amount of won in this Pinus densiflora forest in terms of total organic carbon was about 10.44 million won $ha^{-1}$. The amount of carbon evolved through soil respiration was 4.44 ton C $ha^{-1}yr^{-1}$. The amount of carbon evolved through microbial respiration and root respiration was 2.18 and 2.27 ton C $ha^{-1}yr^{-1}$, respectively. The amount of organic carbon absorbed from the atmosphere of this Pinus densiflora forest was 0.44 ton C $ha^{-1}yr^{-1}$ when estimated from the difference between net primary production and microbial respiration. This amount will come to about 44,000 won $ha^{-1}$ in Korean currency.

• Journal of agriculture & life science
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• v.50 no.1
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• pp.117-124
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• 2016

Researches on soil microbial community are increasing to assess ecosystem responses to anthropogenic disturbances and to provide an indicator of ecosystem recovery. Microbial communities are able to respond more rapidly to environmental changes than plants and therefore they may provide an early indication of the ecosystem recovery trajectory. This study was conducted using 16S rRNA gene pyrosequencing of soil samples to compare soil bacterial community composition between artificially covered soils of the Baedudaegan ridgeline and their adjacent forest soils in two restoration project sites, Ihwaryeong and Yuksimnyeong, which were completed in 2012 and 2013, respectively. Richness of the Phylum level was 29.3 in Ihwaryeong and 32.3 in Yuksimnyeong. Significant difference in the richness between artificial restored soils and adjacent forest soils(p<0.01) was observed, however no significant difference was observed for site location and soil depth. Acidobacteria(37.3%) and Proteobacteria(31.1%) were more abundant than any other phylum in collected soil samples. Also, we found the significant difference in the relative abundance of the two abundant phyla between artificially restored soils and their adjacent forest soils (Proteobacteria, 38.1% in restored soils vs 24.2% in adjacent forest soils, p<0.01; Acidobacteria, 55.4% in restored soils vs 19.2% in adjacent forest soils, p<0.001). The results support the previous researches indicating that soil bacterial community composition is affected by nutritional status of soils and that Acidobacteria is also strongly influenced by pH, thus favoring soils with lower pH. This study could be utilized to monitor and evaluate restoration success of forest soil environment quantitatively.

• Animal cells and systems
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• v.7 no.4
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• pp.289-294
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• 2003

To quantify nutrient loading from emergent macrophytes through leaching in the littoral zones of Paldang Reservoir, we conducted incubation experiments using leaf litter of the emergent macrophyte, Zizaniz latifolia. To separate the leaching process from microbial decay, we used $HgCl_2$ to suppress microbial activity during the experiment. We measured electric conductivity, absorbance at 280nm, total nitrogen and dissolved inorganic nitrogen, total phosphorus and soluble reactive phosphorus, Na, K, Mg and Ca amounts in leaf litter and in water. In addition, we examined the effects of water temperature and ion concentrations of ambient water on the leaching process. A total of 6% of the initial ash-free dry mass of leaf litter was lost due to leaching during incubation (four days). Electric conductivity and A280 continued to increase and saturate during the incubation. To compare reaching rates of different nutrients, we fitted leaching dynamics with a hyperbolic saturation function [Y=AㆍX/(B+X)]. From these fittings, we found that ratios of leaching amounts to nutrient concentration in the litter were in the order of K > Na > Mg > P > Ca > N. Leaching from leaf litter of Z. latifolia was dependent on water temperature while it was not related with ion concentrations in the ambient water. Our results suggest that the leaching process of nutrients, especially phosphorus, from aquatic macrophytes provides considerable contribution to the eutrophication of the Paldang Reservoir ecosystem.