• Korean Journal of Environmental Biology
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• v.22 no.1
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• pp.213-219
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• 2004

The bacterial community of water stream, soil and guano in Gossi cave was examined by using PCR amplified the 16S rDNA-denaturing gradient gel electrophoyesis (DGGE). In this study, the genetic diversity and the similarity of bacterial community between open area and non - open area toy cave tour were investigated, and the seasonable variation pattern was compared each other. DGGE is attractive technique, as it sepayate same length dsDNA according to sequence variation typical 16S rDNA genes. The diversity and similarity of bacterial community in cave was analyzed by GC341f and PRUN518r primer sets foy amplification of V3 region of eubacteria 16S rDNA. The specific DGGE band profile of the cave water gives the possibility that the specific bacterial cell can be adapting to the specific cave environment and living in the cave. The DGGE band profiles of all samples with guano were compared and analyzed by image analyzer, in which mutual band profile was compared to be and the band intensity of guano was the highest. From these result, it is thought that the guano was main nutrient source and influenced on the community structure of the cave environment where is nutritionally limited. Pseudomonas sp. NZ060, Pseudomonas pseudoalcaligenes, uncultured Variovorax sp. and soli bacterium NS7 were identified to be on some sample from analysing DNA sequence of some DGGE band.

• Journal of Climate Change Research
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• v.5 no.3
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• pp.249-256
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• 2014

Permafrost is frozen soil below $0^{\circ}C$ for two or more years. Surface of permafrost is called as active layer that seasonally thaws during the summer. Although the thawing of permafrost may deepen the active layer and consequently increase the microbial activity, the microbial community structure in this habitat has not yet been well described. In this study, we presented bacterial and archaeal diversity in the active layer soil from Resolute, Canada using pyrosequencing analysis. The soil sample was collected from the surface of the marsh covered with moss and Carex. A total of 7,796 bacterial reads for 40 phyla and 245 archaeal reads for 4 phyla were collected, reflecting the high diversity of bacteria. Predominant bacterial groups were Proteobacteria (37.7%) and Bacteroidetes (30.0%) in this study. Major groups in Archaea were Euryarchaeota (51.4%) and Thaumarchaeota (46.1%). Both methane producing archaea and consuming bacteria were detected in this study. Although it might be difficult to characterize microbial community with only one sample, it could be used for the basis of assessing the relative importance of the specific groups with a high resolution on the bacterial and archaeal community in this habitat.

• Journal of Soil and Groundwater Environment
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• v.25 no.1
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• pp.25-36
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• 2020

In a redox transition zone, geochemical reactions are facilitated by active bacteria that mediate reactions involving electrons, and arsenic (As) and iron (Fe) cycles are the major electron transfer reactions occurring at such a site. In this study, the effect of repetitive redox changes on soil bacterial community in As-contaminated soil was investigated. The results revealed that bacterial community changed actively in response to redox changes, and bacterial diversity gradually decreased as the cycle repeated. Proportion of strict aerobes and anaerobes decreased, while microaerophilic species such as Azospirillum oryzae group became the predominant species, accounting for 72.7% of the total counts after four weeks of incubation. Bacterial species capable of reducing Fe or As (e.g., Clostridium, Desulfitobacterium) belonging to diverse phylogenetic groups were detected. Indices representing richness (i.e., Chao 1) and phylogenetic diversity decreased from 1,868 and 1,926 to 848 and 1,121, respectively. Principle component analysis suggests that repetitive redox fluctuation, rather than oxic or anoxic status itself, is an important factor in determining the change of soil bacterial community, which in turn affects the cycling of As and Fe in redox transition zones.

• Journal of Veterinary Science
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• v.24 no.2
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• pp.27.1-27.15
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• 2023

Background: The relationships between the postpartum subacute ruminal acidosis (SARA) occurrence and predicted bacterial functions during the periparturient period are still not clear in Holstein cows. Objectives: The present study was performed to investigate the alterations of rumen fermentation, bacterial community structure, and predicted bacterial functional pathways in Holstein cows. Methods: Holstein cows were divided into the SARA (n = 6) or non-SARA (n = 4) groups, depending on whether they developed SARA during the first 2 weeks after parturition. Reticulo-ruminal pH was measured continuously during the study period. Reticulo-ruminal fluid samples were collected 3 weeks prepartum, and 2 and 6 weeks postpartum, and blood samples were collected 3 weeks before, 0, 2, 4 and 6 weeks postpartum. Results: The postpartum decline in 7-day mean reticulo-ruminal pH was more severe and longer-lasting in the SARA group compared with the non-SARA group. Changes in predicted functional pathways were identified in the SARA group. A significant upregulation of pathway "PWY-6383" associated with Mycobacteriaceae species was identified at 3 weeks after parturition in the SARA group. Significantly identified pathways involved in denitrification (DENITRIFICATION-PWY and PWY-7084), detoxification of reactive oxygen and nitrogen species (PWY1G-0), and starch degradation (PWY-622) in the SARA group were downregulated. Conclusions: The postpartum SARA occurrence is likely related to the predicted functions of rumen bacterial community rather than the alterations of rumen fermentation or fluid bacterial community structure. Therefore, our result suggests the underlying mechanisms, namely functional adaptation of bacterial community, causing postpartum SARA in Holstein cows during the periparturient period.

• 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.26 no.1
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• pp.89-98
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• 2016

Endophytes play an important role in the growth and development of the host. However, the study of endophytes is mostly focused on plants, and reports on bacteria associated with fungi are relatively rare. We studied the bacteria associated with fruiting bodies of Tricholoma matsutake picked from seven main T. matsutake-producing areas in Sichuan, China, by barcoded pyrosequencing. About 8,272 reads were obtained per sample, representing 40 phyla, 103 classes, and 495 genera of bacteria and archaea, and 361-797 operational taxonomic units were observed at a 97% similarity level. The bacterial community was always both more abundant and more diverse than the archaeal community. UniFrac analysis showed there were some difference of bacterial communities among the samples sites. Three bacterial phyla, Proteobacteria, Bacteroidetes, and Firmicutes, were dominant in all samples. Correlation analysis showed there was a significant correlation between some soil properties and bacterial community associated with T. matsutake. This study demonstrated that the bacteria associated with T. matsutake fruiting bodies were diversified. Among these bacteria, we may find some strains that can promote the growth of T. matsutake.

• 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.

• Korean Journal of Environmental Agriculture
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• v.38 no.3
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• pp.185-196
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• 2019

BACKGROUND: This study investigated the effects of rice genetically modified to be resistant against rice blast and rice bacterial blight on the soil microbial community. A comparative analysis of the effects of rice genetically modified rice choline kinase (OsCK1) gene for disease resistance (GM rice) and the Nakdong parental cultivar (non-GM rice) on the soil microbial community at each stage was conducted using rhizosphere soil of the OsCK1 and Nakdong rice. METHODS AND RESULTS: The soil chemistry at each growth stage and the bacterial and fungal population densities were analyzed. Soil DNA was extracted from the samples, and the microbial community structures of the two soils were analyzed by pyrosequencing. No significant differences were observed in the soil chemistry and microbial population density between the two soils. The taxonomic analysis showed that Chloroflexi, Proteobacteria, Firmicutes, Actinobacteria, and Acidobacteria were present in all soils as the major phyla. Although the source tracking analysis per phylogenetic rank revealed that there were differences in the bacteria between the GM and non-GM soil as well as among the cultivation stages, the GM and non-GM soil were grouped according to the growth stages in the UPGMA dendrogram analysis. CONCLUSION: The difference in bacterial distributions between Nakdong and OsCK1 rice soils at each phylogenetic level detected in microbial community analysis by pyrosequencing may be due to the genetic modification done on GM rice or due to heterogeneity of the soil environment. In order to clarify this, it is necessary to analyze changes in root exudates along with the expression of transgene. A more detailed study involving additional multilateral soil analyses is required.

• Journal of Microbiology and Biotechnology
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• v.12 no.3
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• pp.382-388
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• 2002

In order to assess the effects of organic fertilizer on soil microbial community structure and diversity in the greenhouse fields, fatty acid methyl ester (FAME) was analyzed by the MIDI (Microbial ID, Inc., Newark, DE, U.S.A.) system and enumerations were performed. In relation to bacterial division of each sample, low GC Gram-positive bacteria were predominant among bacteria cultured on aerobic bacteria media. On the other hand, alpha subdivision was predominant on proteobacteria of control and OM (organic matter) 1 treated plot, and Flavobacterium spp. existed in OM2 plot on crystal violet media of all samples. Shannon-weaver Index (H) of OM1 plot varied most by 1.9 and 5.0 among bacteria cultured on aerobic bacteria media and crystal violet media, respectively. Our results revealed that addition of the organic wastes to soil led to a highly diverse microbial community, but the excessive amounts of organic and mineral fertilizer applied in the greenhouse fields produced excess nutrients in soil and led to simplification on bacterial populations.

• Korean Journal of Microbiology
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• v.36 no.2
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• pp.136-141
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• 2000

The temporal variation of bacterial community and environmental factors, affecting on bacterial community structure were estimated monthly kom April, 1998 to May, 1999. Bacterial community structures were determined by in situ hyblidization with rRNA-targeted fluorescently labeled oligonucleotide probes (FISH) and epifluorescence microscopy; and the statistical analysis was done by SPSS program. The oligonucleotide probes used in this study were EUB338, ALFlb, GAM42a, and CF. In surface water, $\alpha$-group was related to only DOC (-0.538, p<0.05) and Chlorophyll a concentration was related to y-group (-0.630, p$\beta$-group and Cytophaga-Flavobacterium group were related to water temperature as 0.665, and 0.685 @<0.05). Between pH and $\beta$-group, there was a positive relationship (0.541, p<0.05), and Cytophaga-Flavobactevizim group was represent to correlation (0.672, p