• Journal of Mushroom
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• v.22 no.1
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• pp.22-26
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• 2024

Tricholoma matsutake is a traditional favorite food in East Asia, cultivated in fairy rings called "shiro," which are found near Pinus densiflora. For effective artificial cultivation of Tri. matsutake, microorganisms from symbiotic fairy rings are co-cultivated. In this study, one bacterial isolate (Y22_B35) and two fungal isolates (Y22_F64 and Y22_F68) displayed growth-promoting effects on Tri. matsutake mycelium (158.47, 125.00, and 122.26% enhanced growth, respectively). For identification, 16S rRNA or ITS regions from the microorganisms¡¯ genomes were sequenced. Other sequences, including BenA, CaM, and RPB2 were sequenced in the fungal isolates. The bacterial isolate Y22_B35 was identified as Bacillus cereus. Y22_F64 and Y22_F68 were identified as Umbelopsis nana and Aspergillus parvulus, respectively. To identify the effects of the dominant microorganisms on Tri. Matsutake cultivation, metagenomic analyses were performed. Discovery of these Tri. matsutake mycelium growth-promoting microorganisms and metagenomics analyses are expected to contribute to our understanding of Tri. matsutake fruiting body growth and construction of biomimicry.

• Journal of The Korean Society of Grassland and Forage Science
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• v.39 no.4
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• pp.227-234
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• 2019

This study was performed to investigate the effect of heat-stressed environment on rumen microbial diversity in Holstein cows. Rectal temperature and respiration rate were measured and rumen fluid was collected under normal environment (NE; Temperature humidity index (THI)=64.6) and heat-stressed environment (HE; THI=87.2) from 10 Holstein cows (60±17.7 months, 717±64.4 kg) fed on the basis of dairy feeding management in National Institute of Animal Science. The rumen bacteria diversity was analyzed by using the Illumina HiSeq^TM 4000 platform. The rectal temperature and respiratory rate were increased by 1.5℃ and 53 breaths/min in HE compared to that in NE, respectively. In this study, HE exposure induced significant changes of ruminal microbe. At phylum level, Fibrobacteres were increased in HE. At genus level, Ruminococcaceae bacterium P7 and YAD3003, Butyrivibrio sp. AE2032, Erysipelotrichaceae bacterium NK3D112, Bifidobacterium pseudolongum, Lachnospiraceae bacterium FE2018, XBB2008, and AC2029, Eubacterium celulosolvens, Clostridium hathewayi, and Butyrivibrio hungatei were decreased in HE, while Choristoneura murinana nucleopolyhedrovirus, Calothrix parasitica, Nostoc sp. KVJ20, Anabaena sp. ATCC 33047, Fibrobacter sp. UWB13 and sp. UWB5, Lachnospiraceae bacterium G41, and Xanthomonas arboricola were increased in HE. In conclusion, HE might have an effect to change the rumen microbial community in Holstein cows.

• Microbiology and Biotechnology Letters
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• v.36 no.4
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• pp.247-259
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• 2008

Terminal-restriction fragment length polymorphism (T-RFLP) analysis, one of rapid culture-independent microbial community analysis methods, was used to determine the lactic acid bacterial complexity and dynamics during kimchi fermentation at $15^{\circ}C$ and $4^{\circ}C$. At both temperatures, the common presence of Leuconostoc mesenteroides, Lc. inhae, Lc. kimchi, Weissella koreensis, W. cibaria, Lactobacillus sakei, Lb. curvatus, Lb. plantarum, Lb. paraplantarum, Lb. pentosus, and Lb. brevis was predicted. Lc. citreum and Enterococcus faecalis were detected at $15^{\circ}C$ and $4^{\circ}C$, respectively. W. koreensis predominated during the mid stage of kimchi fermentation whereas lactobacilli were dominants during later stage. Lb. sakei and Lb. curvatus became dominants regardless of fermentation temperature but the growth of Lb. plantarum, Lb. paraplantarum, Lb. pentosus, and Lb. brevis was restricted at psychrophilic temperature. Some species of leuconostocs were maintained until the later stage of kimchi fermentation.

• Korean Journal of Microbiology
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• v.52 no.2
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• pp.157-165
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• 2016

Under flooded rice fields, methanogens produce methane which comes out through rice stalks, thus rice fields are known as one of the anthropogenic sources of atmospheric methane. Studies have shown that use of manure increases amount of methane emission from rice. To investigate mechanisms by which manure boosts methane emission, comparative soil metagenomics between inorganically (NPK) and pig manure fertilized paddy soils (PIG) were conducted. Results from taxonomy analysis showed that more abundant methanogens, methanotrophs, methylotrophs, and acetogens were found in PIG than in NPK. In addition, BLAST results indicated more abundant carbohydrate mabolisetm functional genes in PIG. Among the methane metabolism related genes, PIG sample showed higher abundance of methyl-coenzyme M reductase (mcrB/mcrD/mcrG) and trimethylamine-corrinoid protein Co-methyltransferase (mttB) genes. In contrast, genes that down regulate methane emission, such as trimethylamine monooxygenase (tmm) and phosphoserine/homoserine phosphotransferase (thrH), were observed more in NPK sample. In addition, more methanotrophic genes (pmoB/amoB/mxaJ), were found more abundant in PIG sample. Identifying key genes related to methane emission and methane oxidation may provide fundamental information regarding to mechanisms by which use of manure boosts methane emission from rice. The study presented here characterized molecular variation in rice paddy, introduced by the use of pig manure.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.5
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• pp.822-828
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• 2012

Organic fruit production has increased due to consumer's interest and government's political support for environmentally-friendly agriculture. The aim of this study was to investigate the effects of cover plants on soil microbial community and establish the fruit cultivation method by organic farming techniques. Cover plants used as an organic nutrient source in an apple orchard were rye and barley, the Gramineae and red clover and hairy vetch, the Leguminosae. In the effects of cover plants on the soil chemical characteristics, the soil pH values were higher than that of conventional organic pear orchard. The content of P showed no significant difference between control and cover plant plots. Organic matter level was similar in control and Gramineae cover plant plots, while organic matter content in cover plants belong to Leguminosae was lower than that of control plot. K content was lower in the plots treated with rye and red clover than control plot, while K content in hairy vetch treated plot was higher than control plot. Ca content was lower in control plot than in cover plant treated plots. Concentrations of Mg in the plots treated with barley and hairy vetch was lower than control plot. In August rye and red clover covered soil showed higher bacterial community density than that of control soil and barley treated soil showed highest Actinomycetes community density among treatments. Barley and hairy vetch soils showed higher level of fungi community density than that of control soil in August. In pyrosequencing analysis barley treated soil showed highest distribution ratio of Actinomycetes among treatment. Our findings might be used as basic data for choosing cover plant with effective organic matter decomposition and nutrition supply capacity.

• Microbiology and Biotechnology Letters
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• v.31 no.3
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• pp.264-270
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• 2003

A quantitative survey of the protozoa microfauna at bioreactor of advanced sewage treatment plant was carried out during a period of 11 months. In this study, 32 genera were identified, including 17 ciliates. The abundance of the important protozoa were compared with the operating parameters and water quality of the effluent of the plant using statistical procedure. Statistical analysis revealed a relationship between the abundance of some genera and removal rate. In particular, correlation analysis on the quality of effluent and protozoa indicated that Lepadella may be used as the bioindicator of TP removal and Trochilia, Entosiphon, Colepus may be used as the bioindicator of TN removal when water temperature was below $20^{\circ}C$.

• Microbiology and Biotechnology Letters
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• v.37 no.3
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• pp.189-196
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• 2009

Bacteria were isolated from roots of plants belonging to family Solanaceae and Gramineae, inhabited in Dokdo island. Fifty six endospore-forming bacteria grown on tryptic soy broth (TSB) agar medium and 23 nitrogen-fixing bacteria (NFB) grown on nitrogen free agar medium were isolated, respectively. The isolates were partially identified by analyzing the 16S rDNA and categorized into phylogenetic groups. The 16S rDNA sequences of each identified isolates were compared with sequences of each type strains to analyze phylogenetic relationship by phylogenetic tree. As a result, endospore-forming bacteria and nitrogen-fixing bacteria were classified into 4 and 6 lineage groups, respectively. Among these isolated, 18 were presumed to be novel species candidates based on the similarity (lower than 98%) analysis of the l6S rDNA sequences.

• Korean Journal of Soil Science and Fertilizer
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• v.42 no.5
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• pp.341-347
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• 2009

Soil microbial community has been changed after the treatment of anaerobic fermentation using wheat bran or rice bran was applied to the soil. In the dilution plate technique, the number of anaerobic bacteria and fungi was higher in rice bran-treated soil than in non and wheat bran-treated soil, but of yeast was higher in wheat bran-treated soil than in non and rice bran-treated soil. Specially, the fungi were not detected in the wheat bran-treated soil. Identified by 16S rDNA sequencing, the number of aerobic bacteria was similar in all treatments, the dominant bacteria was the genus Bacillus. In the phospholipid fatty acid (PLFA) technique, both Gram-positive and Gram-negative bacteria change slightly in all treatments for 20 days of fermentation process but, after 20day, increased rapidly in wheat or rice bran-treated soil. In conclusion, the microbial communities structure was dramatically changed after the treatment of wheat or rice bran to soil.

• Korean Journal of Microbiology
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• v.47 no.1
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• pp.56-65
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• 2011

Culture-independent microscopic observations and 16S rDNA analyses were applied to describe the bacterial community inherent to the biofilm structure of the RABC (Rotating Activated Bacillus Contactors) process for swine butchery wastewater treatment. The ratios of Gram-positive bacterial counts to total bacterial counts of the RABC process were significantly increased in the last aeration tank as well as returned sludge, while those of the existing A2O (Anaerobic-Anoxic-Oxic) process maintained constant from aeration tanks to returned sludge. Totally nine phyla were recovered by 16S rDNA analysis, two of which were major groups: the Proteobacteria (64.1%) and the Actinobacteria (18.4%). The third major group was the endospore-forming Firmicutes (5.4%). The remaining six minor groups are the Bacteroidetes (3.3%), the Chlorobi (2.2%), the Nitrospirae (1.1%), the Chlorofleix (1.1%), the Acidobacteria (1.1%), and the Fusobacteria (1.1%). The ratio of endospore-forming bacteria was 19.4%, which was composed of the members of the Firmicutes phylum (5.4%) and the Intrasporangiaceae family (14.0%) of the Actinobacteria phylum. Nitrifying and denitrifying related- and phosphorus accumulating related-sequences were composed of 6.5% and 5.4% of total community, respectively, these could mean the high capacity of the RABC process to remove odor compounds and reduce eutrophication by efficient removing inorganic nutrients.

• Korean Journal of Microbiology
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• v.33 no.4
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• pp.257-261
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• 1997

To scrutinize the bacterial community composition of Lake Soyang in winter, bacterial numbers belonging to Eubacteria, Proteobacteria and Cytophaga-Flavobacterium group were estimated by using 16S and 23S rRNA targeted oligonucleotide probes. Total bacterial numbers ranged from $0.7{\times}10^6$ to $1.1{\times}10^6cells{\cdot}ml^{-1}$, and vertical profile of total bacteria showed a peak at 5 m depth. The ratio of eubacteria to total bacteria were 34~90% and at 5 m and 10 m depths those were low exhibiting, 39 and 34%, respectively. The percentage of proteobacteria ${\alpha}$-group ranged 10.8~28.7%, ${\beta}$-group 4.5~53.5%, ${\gamma}$-group 4.9~35.5% and Cytophaga-Flavobacterium group 6.1~21.1%. The dominant groups were ${\beta}$-group at 0, 2 and 5 m, ${\gamma}$-group at 10 m, ${\alpha}$-group at 30 m and Cytophaga-Flavobacterium group at 50 m depth. In winter season, Lake Soyang can be divided into three layer, 0~2 m, 5~10 m and 30~50 m, by the bacteria community composition. By this method, new informations about aquatic ecosystem were developed.