• Journal of Ecology and Environment
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• v.34 no.3
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• pp.269-278
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• 2011

Carabid beetle community changes in paddy fields, abandoned paddy fields, and mountains were investigated to understand differences in species diversity and composition of different habitat types in small agricultural landscapes in South Korea. A total of 2,938 individuals from 37 species were identified and classified from the studied habitats. Diversity in the mountains was higher than that in abandoned paddy fields. As the number of years since abandonment increased, the diversity and stability of the carabid beetle community also increased. Abandoned paddy fields in some paddy field areas and adjoining mountainous areas, left with preconditions for management and control, have provided the opportunity to improve the diversity and habitat of small agricultural landscapes. Species composition changed continuously from the paddy fields to the mountains, in accordance with individual species habitat preferences. Abandoned paddy fields in small agricultural landscapes are believed to play an important role as transitional buffer zones between paddy fields and the adjacent mountainous areas.

• Journal of Forest and Environmental Science
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• v.38 no.1
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• pp.21-37
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• 2022

The present study was carried out to evaluate the chemical properties of soil in relation to forest structure and composition at different altitudes (900-2,600 m asl) in a part of Western Himalaya. The composite soil samples were taken from three (viz. upper, middle and lower) depths. The soils of the whole study area were acidic in nature (pH=4.90-5.51). Contents of Nitrogen (N), Phosphorus (P), Potassium (K), Carbon (C) and soil organic matter (SOM) showed much fluctuation during different seasons of year. Nitrogen content showed significant positive correlations with altitude (r=0.924, p<0.05) and different community parameters like species diversity (r=0.892, p<0.01) and species richness (r=0.941, p<0.05). Phosphorus exhibited direct correlations with carbon (r=0.637) while weak negative correlations with different community parameters like species richness & diversity, total basal cover (TBC), density and canopy cover. Carbon content and hence SOM showed direct correlations with Nitrogen (r=0.821, p<0.01); Phosphorus (r=0.637, ns) and Potassium (r=0.540, ns). But no significant relationship was observed between K content and species richness (p=0.30, r=-0.504); between K content and species diversity (p=0.14, r=-0.672); between P content and species diversity (p=0.29, r=-0.513) and species richness (p=0.23, r=-0.575). Among the different soil nutrients, only N showed a significant positive correlation with altitude while all others exhibited negative (but non-significant) correlation with it. The study revealed that the chemical properties affect and are reciprocally affected by forest structure and composition and that N rich soils of higher altitudes are best for the growth and development of forests.

• 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.24 no.3
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• pp.313-323
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• 2014

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coal-mining reclamation areas was suggested.

• Journal of Periodontal and Implant Science
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• v.52 no.5
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• pp.394-410
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• 2022

Purpose: The purpose of this study was to compare the microbial composition of 3 types of oral samples through 16S metagenomic sequencing to determine how to resolve some sampling issues that occur during the collection of sub-gingival plaque samples. Methods: In total, 20 subjects were recruited. In both the healthy and periodontitis groups, samples of saliva and supra-gingival plaque were collected. Additionally, in the periodontitis group, sub-gingival plaque samples were collected from the deepest periodontal pocket. After DNA extraction from each sample, polymerase chain reaction amplification was performed on the V3-V4 hypervariable region on the 16S rRNA gene, followed by metagenomic sequencing and a bioinformatics analysis. Results: When comparing the healthy and periodontitis groups in terms of alpha-diversity, the saliva samples demonstrated much more substantial differences in bacterial diversity than the supra-gingival plaque samples. Moreover, in a comparison between the samples in the case group, the diversity score of the saliva samples was higher than that of the supra-gingival plaque samples, and it was similar to that of the sub-gingival plaque samples. In the beta-diversity analysis, the sub-gingival plaque samples exhibited a clustering pattern similar to that of the periodontitis group. Bacterial relative abundance analysis at the species level indicated lower relative frequencies of bacteria in the healthy group than in the periodontitis group. A statistically significant difference in frequency was observed in the saliva samples for specific pathogenic species (Porphyromonas gingivalis, Treponema denticola, and Prevotella intermedia). The saliva samples exhibited a similar relative richness of bacterial communities to that of sub-gingival plaque samples. Conclusions: In this 16S oral microbiome study, we confirmed that saliva samples had a microbial composition that was more similar to that of sub-gingival plaque samples than to that of supra-gingival plaque samples within the periodontitis group.

• Korean Journal of Environmental Biology
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• v.22 no.1
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• pp.220-226
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• 2004

The restoration effects in two sorts of forests created and managed on the bases of ecological principles in Sihwa industrial complex and Mt. Surak respectively were evaluated in both viewpoints of species composition and diversity. Species composition of the forests created based on the ecological design was move similar to that of the natural forests compared wit h the forests constructed by applying the landscape architectural method. The increased species diversity in the ecologically created forest reflected the effect as well. Black locust plantation managed by applying the ecological principle showed move similar species composition to the surrounding natural forest than the forest left without any management. Furthermore, the former forest showed higher species diversity than the latter one. The methods, which create and manage a forest based on ecological principles, revealed several problems, such as lack of specialty of project operators and inspecting officers, construction regulations without the ecological background, absence of the endemic young trees to be introduced in diverse natural environment, etc. Preparation of guidance for ecological planting and systematic environmental education including revision of construction regulation were recommended as the measures to solve such problems.

• 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.

• The Korean Journal of Malacology
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• v.30 no.3
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• pp.249-258
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• 2014

Phytoplankton species composition and ecological index (diversity, evenness, richness and dominance) were analysed from April 2013 to March 2014 at 10 stations of cupped oyster, Crassostrea gigas culture area in Iwon coast, Korea. Seasonal and positional variation of phytoplankton standing crops, biomass, dominant species and water quality were distinctively different according to occasionally inflow of Iwon dam reservoired water. The composition of phytoplankton species were Bacillariophyceae 98, Dinophycease 22, Chlorophycease 13, Cyanophyceae 8, Silicofalgellate 4, Euglenophyceae 2, Cryptophyceae 1 species. The most dominant species was Bacillariophyceae as 64.0%. The highest biomass of phytoplankton recorded in September as $40,910{\times}10^3$ cell/L at the station 1, near from inland water inflow area. Ecological indices (diversity, richness, evenness, and dominance index), used for structural change of phytoplankton community and water quality (temperature, dissolved oxygen, salinity) showed difference of spatiotemporal property also.

• The Korean Journal of Mycology
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• v.51 no.4
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• pp.419-428
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• 2023

Several endophytic fungal strains were isolated from Taxus cuspidata and identified by molecular analysis of the internal transcribed spacer and RNA polymerase II second largest subunit. This study aimed to determine the relative abundance and compare the species diversity of endophytic fungal communities within needle leaves and twigs. We identified a total of 49 endophytic fungal species. Notably, two species, Trichoderma dingleyae and Xylaria cubensis, were discovered to be previously unrecorded in Korea. The fungal communities in both plant tissues demonstrated distinct species composition. Differences were observed in the relative abundance and species diversity index between needle leaves and twigs. Our findings suggest that the host plant tissues influence the species diversity of endophytic fungal communities.

• Journal of Microbiology and Biotechnology
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• v.30 no.11
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• pp.1640-1650
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• 2020

Colorectal cancer (CRC) is the leading cause of common malignant neoplasm worldwide. Many studies have analyzed compositions of gut microbiota associated with various diseases such as inflammatory bowel diseases (IBD) and colon cancer. One of the most representative bacteria involved in CRC is enterotoxigenic Bacteroides fragilis (ETBF), a species belonging to phylum Bacteroidetes. We used ETBF colonized mice with azoxymethane (AOM)/dextran sulphate sodium (DSS) and zerumbone, a compound with anti-bacterial effect, to determine whether zerumbone could restore intestinal microbiota composition. Four experimental groups of mice were used: sham, ETBF colonized AOM/DSS group, ETBF colonized AOM/DSS group zerumbone 60 mg kg-1 (ETBF/AOM/DSS + Z (60)), and only zerumbone (60 mg kg^-1)-treated group. We performed reversible dye terminators-based analysis of 16S rRNA gene region V3-V4 for group comparison. Microbiota compositions of ETBF/AOM/DSS + Z (60) group and ETBF colonized AOM/DSS group not given zerumbone were significantly different. There were more Bacteroides in ETBF/AOM/DSS + Z (60) group than those in ETBF colonized AOM/DSS group, suggesting that B. fragilis could be a normal flora activated by zerumbone. In addition, based on linear discriminant analysis of effect size (LEfSe) analysis, microbial diversity decreased significantly in the ETBF colonized AOM/DSS group. However, after given zerumbone, the taxonomic relative abundance was increased. These findings suggest that zerumbone not only influenced the microbial diversity and richness, but also could be helpful for enhancing the balance of gut microbial composition. In this work, we demonstrate that zerumbone could restore the composition of intestinal microbiota.