• Korean Journal of Soil Science and Fertilizer
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• v.45 no.6
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• pp.1073-1085
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• 2012

Soil microbial communities are immensely diverse and complex with respect to species richness and community size. These communities play essential roles in agricultural soil because they are responsible for most of the nutrient cycles in the soil and influence the plant diversity and productivity. However, the majority of these microbes remain uncharacterized because of poor culturability. Next-generation sequencing techniques have revolutionized many areas of biology by providing cheaper and faster alternatives to Sanger sequencing. Among them, amplicon pyrosequencing is a powerful tool developed by 454 Life Sciences for assessing the diversity of complex microbial communities by sequencing PCR products or amplicons. This review summarizes the current opinions in amplicon sequencing of soil microbial communities, and provides practical guidance and advice on sequence quality control, aligning, clustering, OTU- and taxon-based analysis. The last section of this article includes a few representative studies conducted using amplicon pyrosequencing.

• Journal of Veterinary Science
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• v.22 no.3
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• pp.37.1-37.14
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• 2021

Background: Ticks are one of the most common external parasites in dogs, and are associated with the transmission of a number of major zoonoses, which result in serious harm to human health and even death. Also, the increasing number of pet dogs and pet owners in China has caused concern regarding human tick-borne illnesses. Accordingly, studies are needed to gain a complete understanding of the bacterial composition and diversity of the ticks that parasitize dogs. Objectives: To date, there have been relatively few reports on the analysis of the bacterial community structure and diversity in ticks that parasitize dogs. The objective of this study was to investigate the microbial composition and diversity of parasitic ticks of dogs, and assessed the effect of tick sex and geographical region on the bacterial composition in two tick genera collected from dogs in China. Methods: A total of 178 whole ticks were subjected to a 16S ribosomal RNA (rRNA) next generation sequencing analysis. The Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene was used to characterize the bacterial communities of the collected ticks. Sequence analysis and taxonomic assignment were performed using QIIME 2 and the GreenGene database, respectively. After clustering the sequences into taxonomic units, the sequences were quality-filtered and rarefied. Results: After pooling 24 tick samples, we identified a total of 2,081 operational taxonomic units, which were assigned to 23 phyla and 328 genera, revealing a diverse bacterial community profile. The high, moderate and low prevalent taxa include 46, 101, and 182 genera, respectively. Among them, dominant taxa include environmental bacterial genera, such as Psychrobacter and Burkholderia. Additionally, some known tick-associated endosymbionts were also detected, including Coxiella, Rickettsia, and Ricketssiella. Also, the potentially pathogenic genera Staphylococcus and Pseudomonas were detected in the tick pools. Moreover, our preliminary study found that the differences in microbial communities are more dependent on the sampling location than tick sex in the tick specimens collected from dogs. Conclusions: The findings of this study support the need for future research on the microbial population present in ticks collected from dogs in China.

• Journal of Microbiology and Biotechnology
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• v.29 no.10
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• pp.1580-1590
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• 2019

Capsaicinoids in red pepper powder are known to show anti-bacterial effects; however, their effects during kimchi fermentation are not known. This study aimed to investigate the effects of various concentrations of capsaicinoids on kimchi fermentation. Five sets of kimchi samples were prepared using 0 mg/kg (control), $98.34{\pm}5.34mg/kg$ (mild), $243.47{\pm}3.71mg/kg$ (medium), $428.63{\pm}30.78mg/kg$ (hot), and $1,320.49{\pm}28.27mg/kg$ (extreme) capsaicinoid. The characteristics of each kimchi sample, including pH, acidity, organic acid, sugars, sugar alcohol, capsaicinoid content, and microbial community were periodically investigated during fermentation. Kimchi with red pepper powder shows significantly higher acidity than control kimchi, whereas pH values were the same. Organic acid in kimchi with red pepper powder was higher than in control kimchi, probably caused by higher lactic acid bacteria (LAB) counts in kimchi samples with red pepper powder. Our results show that addition of red pepper powder decreased Leuconostoc spp. counts in the bacterial community. In particular, Lactobacillus sakei and Leuconostoc gelidum counts increased and decreased, respectively, with increasing capsaicinoid content of red pepper powder added to kimchi. Overall, the results of this study indicate that physicochemical properties and LAB such as L. sakei and L. gelidum are influenced by capsaicinoid content. However, further studies are necessary to investigate the effects of the percentage of red pepper powder in kimchi on fermentation to provide practical guidelines for producing standardized kimchi.

• Korean Journal of Organic Agriculture
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• v.23 no.4
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• pp.767-779
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• 2015

soil microbial activities and diversities in a newly reclaimed soil. Soil chemical properties, population of microbe, microbial biomass, and properties of microbial community were investigated under 4 different treatment (animal manure compost+green manure, chemical fertilizer, and without fertilizer). The experiment was conducted for 3 years from 2012 to 2014. The most of chemical properties in the animal manure compost+green manure treatment were increased continually compare to chemical fertilizer and without fertilizer. The population of bacteria and fungi were higher in the animal manure compost+green manure treatment, however, there was no difference on actinomyces. Soil microbial biomass C content was higher in the animal manure compost+green manure treatment than in chemical fertilizer and without fertilizer. Biolog examination showed that catabolic diversities of bacterial communities were higher in the treatment of animal manure compost+green manure. It was showed that principle component analysis of the Biolog data differentiated the organic matter amended soils from NPK and control. These results indicated that application of animal manure compost+green manure had a beneficial effect on soil microbial properties.

• Asian-Australasian Journal of Animal Sciences
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• v.12 no.1
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• pp.129-138
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• 1999

If rumen bacteria can be manipulated to utilize nutrients (i.e., ammonia and plant cell wall carbohydrates) more completely and efficiently, the need for protein supplementation can be reduced or eliminated and the digestion of fiber in forage or agricultural residue-based diets could be enhanced. However, these approaches require a complete and accurate description of the rumen community, as well as methods for the rapid and accurate detection of microbial density, diversity, phylogeny, and gene expression. Molecular ecology techniques based on small subunit (SSU) rRNA sequences, nucleic acid probes and the polymerase chain reaction (PCR) can potentially provide a complete description of the microbial ecology of the rumen of ruminant animals. The development of these molecular tools will result in greater insights into community structure and activity of gut microbial ecosystems in relation to functional interactions between different bacteria, spatial and temporal relationships between different microorganisms and between microorganisms and reed panicles. Molecular approaches based on SSU rRNA serve to evaluate the presence of specific sequences in the community and provide a link between knowledge obtained from pure cultures and the microbial populations they represent in the rumen. The successful development and application of these methods promises to provide opportunities to link distribution and identity of gastrointestinal microbes in their natural environment with their genetic potential and in situ activities. The use of approaches for assessing pupulation dynamics as well as for assessing community functionality will result in an increased understanding and a complete description of the gastrointestinal communities of production animals fed under different dietary regimes, and lead to new strategies for improving animal growth.

• Journal of Soil and Groundwater Environment
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• v.25 no.2
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• pp.16-23
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• 2020

In this work, ²²²Rn activity, major dissolved ions, and microbial community in ground- and surface waters were investigated to characterize groundwater inflow to the stream located in an urban area, Daejeon, Korea. The measured ²²²Rn activities in groundwater and stream water ranged from 136 to 231 Bq L^-1 and 0.3 to 48.8 Bq L^-1, respectively. The spatial distributions of ²²²Rn activity in the stream strongly suggested groundwater inflow to the stream. The change of geochemical composition of the stream water indicated the effect of groundwater discharge became more pronounced as the stream flows downstream. Furthermore, microbial community composition of the stream water had good similarity to that of groundwater, which is another evidence of groundwater discharge. Although groundwater inflow could not be estimated quantitatively in this study, the results can provide useful information to understand interactions between groundwater and surface water, and determine hydrological processes governing groundwater recharge and hydrogeological cycles of dissolved substances such as nutrients and trace metals.

• Journal of Life Science
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• v.34 no.4
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• pp.254-263
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• 2024

Korean jang is a food made using fermented soybeans, and the typical products include gochujang (GO), doenjang (DO), cheonggukjang (CH), and ganjang (GA). In this study, 16S rRNA metagenome analysis was performed on a total of 200 types of GO, DO, CH, and GA using next-generation sequencing to analyze the microbial community of fermented soybean foods and compare taxonomic (biomarker) differences. Alpha diversity analysis showed that in the CHAO index, the species richness index tended to be significantly higher compared to the DO and GA groups (p<0.001). The results of the microbial distribution analysis of the GO, DO, CH, and GA products showed that at the order level, Bacillales was the most abundant in the GO, DO, and CH groups, but Lactobacillales was most abundant in the GA group. Linear discriminant analysis effect (LEfSe) analysis was used to identify biomarkers at the family and species levels. Leuconostocaceae, Thermoactinomycetaceae, Bacillaceae, and Enterococcaceae appeared as biomarkers at the family level, and Bacillus subtilis, Kroppenstedtia sanguinis, Bacillus licheniformis, and Tetragenococcus halophilus appeared at the species level. Permutational multivariate analysis of variance (PERMANOVA) analysis showed that there was a significant difference in the microbial community structure of the GO, DO, CH, and GA groups (p=0.001), and the microbial community structure of the GA group showed the greatest difference. This study clarified the correlation between the characteristics of Korean fermented foods and microbial community distribution, enhancing knowledge of microorganisms participating in the fermentation process. These results could be leveraged to improve the quality of fermented soybean foods.

• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.704-715
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• 2006

Oil spill was found in 1999 from a diesel storage facility located near the top of Baekun Mountain in Uiwang City. Application of bioremediation techniques was very relevant in removing oil spills in this site, because the geological condition was not amenable for other onsite remediation techniques. For efficient bioremediation, bacterial communities of the contaminated site and the uncontaminated control site were compared using both molecular and cultivation techniques. Soil bacterial populations were observed to be stimulated to grow in the soils contaminated with diesel hydrocarbon, whereas fungal and actinomycetes populations were decreased by diesel contamination. Most of the dieseldegrading bacteria isolated from contaminated forest soils were strains of Pseudomonas, Ralstonia, and Rhodococcus species. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that the profiles were different among the three contaminated sites, whereas those of the control sites were identical to each other. Analysis of 16S rDNA sequences of dominant isolates and clones showed that the bacterial community was less diverse in the oil-contaminated site than at the control site. Sequence analysis of the alkane hydroxylase genes cloned from soil microbial DNAs indicated that their diversity and distribution were different between the contaminated site and the control site. The results indicated that diesel contamination exerted a strong selection on the indigenous microbial community in the contaminated site, leading to predominance of well-adapted microorganisms in concurrence with decrease of microbial diversity.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.3
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• pp.377-384
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• 2012

This study was carried out to evaluate effect of temperature condition on nitrogen mineralization of organic matter, distribution of microbial group by PLFA profiles, and soil microbial community in non-volcanic ash soil. Dried soil 30 g mixed well each 2 g of pellet (OFPE) organic fertilizers, pig manure compost (PMC), and food waste compost (FWC). And then had incubated at $10^{\circ}C$, $20^{\circ}C$, and $30^{\circ}C$, respectively. Nitrogen mineralization rate increased with increasing temperature and that was in the order of FWC>OFPE>PMC. Distribution ratio of microbial group by PLFA profiles showed that was different significantly according to incubation temperature and the type of organic matter. As incubating time passed, density of microbial group decreased gradually. The Gram-bacteria PLFA/Gram+ bacteria PLFA, Fungi PLFA/Bacteria PLFA, and Unsaturated PLFA/saturated PLFA ratios were decreased according to the increasing temperature gradually. Principal component analysis using PLFA profiles showed that microbial community structures were composed differently by temperature factor at both 75 days ($10^{\circ}C$) and 270 days ($30^{\circ}C$). In conclusion, Soil microbial community structure showed relative sensitivity and seasonal changes as affected by temperature and organic matter type.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.4
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• pp.467-474
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• 2012

This study was carried out to evaluate effect of temperature condition on nitrogen mineralization of organic matter, distribution of microbial group by PLFA profiles, and soil microbial community structure in volcanic ash soil. Dried soil 30 g mixed well each 2 g of pellet (OFPE) organic fertilizers, pig manure compost (PMC), and food waste compost (FWC). And then had incubated at $10^{\circ}C$, $20^{\circ}C$, and $30^{\circ}C$, respectively. Nitrogen mineralization rate increased with increasing temperature and that was in the order of FWC>OFPE>PMC. Distribution ratio of microbial group by PLFA profiles were different significantly caused by incubation temperature and the type of organic matter. As incubating time passed, density of microbial group decreased gradually. The Gram-bacteria PLFA/Gram+ bacteria PLFA, Fungi PLFA/Bacteria PLFA, and Unsaturated PLFA/saturated PLFA ratios were decreased according to the increasing temperature gradually. But cy19:0/$18:1{\omega}7c$ ratio increased both FWC and PMC treatment. Principal component analysis using PLFA profiles showed that microbial community structure made up clearly at both 75 days ($10^{\circ}C$) and 270 days ($30^{\circ}C$) by temperature factor. As incubating time passed, microbial community structure shifted gradually.