• Korean Journal of Microbiology
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• v.38 no.1
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• pp.31-37
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• 2002

For elucidating the correlation between the eubacterial community structure and environmental parameters in Nammae Reservoir located in Kyungsan, Kyungbuk, the bacterial community structure and their structure affecting environmental parameters were analyzed using Fluorescent In Situ Hybridization (FISH) monthly over year. $\alpha$ . $\beta$ . $\gamma$-subclasses of Proteobacteria and Cytophaga-Flavobacterium (CF) group known as dominant bacterial group in freshwater were detected in 3 stations over year. The ratio of each subclass to total bacteria was determined; $\alpha$.$\beta$ . $\gamma$-subclasses and CF group varied in the range of 4.0~29.2%, 1.7~25.8%, 1.8~12.8%, 4.9~36.3%, respectively and there was no substantial differences between stations. In terms of the correlation between each group specific bacteria and environmental parameters such as temperature, SS, pH, DOC, NH$_4$-N, NO$_3$-N, PO$_4$-P, standing crops of algae, the results were as follows: 1) total bacterial numbers correlated positively with temperature, SS and DOC, 2) Eubacteria positively with DOC and Chl-$\alpha$, 3)${\gamma}$-subclass positively with DOC, and 4) CF group positively with standing crops of chlorophyceae, 5) whereas $\beta$-subclass bacteria correlated negatively with standing crop of cyanobacteria and that of total algae.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.119-125
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• 2009

To understand the ecological function of heterotrophic bacterial community in water column of large freshwater lakes in the permafrost zone, we investigated the structure and function of bacterial community in Lake Khuvsgul, Mongolia. Species composition of overall bacterial community was analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments, and bacteria that can be cultured at 10oC were isolated and characterized. Based on the depth profile of environmental parameters, thermocline and chemocline were recognized at the 5~10 m zone of the water column. The stratified DGGE profile indicated that the discontinuity of water properties might influence the structure of bacterial community: band profiles in the 0~5 m zone were diverse with large change by depth, but the profile was relatively stable at the $\geq$10 m zone, with predominance of the band identified as Acidovorax facilis. Bacterial cultures were screened for protease, cellulase, amylase and lipase activity, and 23 isolates were selected for high activity of the hydrolytic enzymes. The isolates were identified based on their 16S rRNA gene sequences. In the surface water (zero meter depth), Acidovorax defluvii and Sphingobacterium faecium with high cellulase activity were present. Flavobacterium succinicans, Mycoplana bullata and A. facilis were stably predominant isolates at 2 m, 5 m, and $\geq$10 m depths, respectively. F. succinicans isolates showed high protease activity while M. bullata isolates showed moderate levels of protease and celluase activity. A. facilis isolates showed either cellulase or lipase activity, exclusively to each other. According to the profile of growth rates of the isolates in the temperature range of $0\sim42^{\circ}C$, the surface-zone (0~5 m) isolates were facultative psychrophiles while isolates from $\geq$10 m depth were typical mesophiles. This stratification is believed to be due to stratified availability of organic materials to the bacterial decomposers. In the water column below the chemoline, the environment is extremely oligotrophic so that the trait of rapid growth in low temperature might not be demanded by deep-lake decomposers. The stratified distribution of community composition and decomposer activity in Lake Khuvsgul implies that ecological functions of bacterial community in lakes of cold region are sharply divided by water column stratification.

• Korean Journal of Microbiology
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• v.46 no.4
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• pp.366-374
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• 2010

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Spirastrella abata. A total of 164 bacterial strains associated with the sponge were cultivated using Zobell and Natural sea salt media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 95% similarities compared with known bacterial species, and the isolates belonged to four phyla, Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteriodetes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge- derived total gDNA showed five major DGGE bands, and their sequences showed more than 96% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of four phyla, including Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Spirochetes, and Chloroflexi. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with S. abata by both RFLP and DGGE methods; however, overall bacterial community in the sponge differed depending on the analysis methods.

• Korean Journal of Microbiology
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• v.51 no.4
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• pp.398-406
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• 2015

Culture-dependent ARDRA and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Halichondria panicea collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and Marine agar media. PCR amplicons of the 16S rRNA gene from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rRNA gene sequences derived from ARDRA patterns showed more than 96% similarities compared with known bacterial species, and the isolates belonged to four classes, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Firmicutes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rRNA genes amplified from the sponge-derived total gDNA showed 14 DGGE bands, and their sequences showed 100% similarities compared with the sequences available in GenBank. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven classes, including Alphaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteira, Bacteroidetes, Cyanobacteria, and Chloroflexi. According to both the ARDRA and DGGE methods, three classes, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, were commonly found in H. panicea. However, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture independent method than in culture-dependent method.

• Korean Journal of Microbiology
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• v.51 no.4
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• pp.347-354
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• 2015

Soybean is well known to be originated from Korea and far-east Asian countries, and studies of many root nodule bacteria associated with soybean have mainly-focused on nitrogen fixation, but much less study was carried out on bacterial community in the rhizosphere of soybean. In this study, we analyzed the bacterial community in rhizosphere of Korean soybean, Daepungkong using the pyrosequencing method based on the 16S rRNA gene to characterize the change of the rhizosphere community structure according to the growth stages of soybeans and to elucidate bacterial core community in rhizosphere of soybean. Our results revealed that bacterial community of rhizosphere soil differed from that of bulk soil and was composed of a total of 21 bacterial phyla. The predominant phylum in the rhizosphere of soybean was Proteobacteria (36.6-42.5%) and followed by Acidobacteria (8.6-9.4%), Bacteroidetes (6.1-10.9%), Actinobacteria (6.4-9.8%), and Firmicutes (5.7-6.3%). The bacterial core community in soybean rhizosphere was mainly composed of the operational taxonomic units (OTUs) belonging to the phylum Proteobacteria throughout all growth stages. The OTU00006 belonged to the genus Bradyrhizobium had the highest abundance and Steroidobacter, Streptomyces, Devosia were followed. These results show that bacterial core community in soybean rhizosphere was mainly composed of OTUs associated with plant growth promotion and nutrient cycles.

• Korean Journal of Microbiology
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• v.49 no.2
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• pp.150-155
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• 2013

We have conducted pyrosequencing for freshwater microbial community analyses. Fourteen sites along the Yeongsan river were selected for this study, and samples were collected monthly from May to July, 2012. Total 987,380 reads were obtained from 42 samples and used for taxonomic classification and OTU distribution analysis. Our results showed that high geographical and temporal variation in the phylum level bacterial composition, suggesting that microbial community is a very sensitive parameter affected by the surrounding environments including tributaries and land use nearby. In addition, we conducted an OTU-based Microbial Source Tracking to identify sources of fecal pollution in the same region. From this study Firmicutes was found to be the most influential taxa in this region. Here, we report that the use of pyrosequencing based microbial community analysis may give an additional information on freshwater quality monitoring, in addition to the currently used water quality parameters, such as BOD and pH.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.244-247
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• 2004

To investigate the effects of elevated $CO_2$ on the denitrifying bacterial community structure in a wetland soil, dynamics of bacterial community structure was explored in an artificial wetland ecosystem with one of three plant species (T. latifolia, S. lacustris, and 1. effusus) under two levels of $CO_2$(370 ppm or 740 ppm) after 110day incubation. For the analysis of bacterial community structure, functional genes such as nitrite reductase genes (nirS) were PCR-amplified followed by cloning of PCR products and screening by restriction fragment length polymorphism (RFLP). nirS gene fragments were amplified in all analyzed soil samples. Species richness estimated by the number of distinct phylotypes were 83 and 95 in the ambient $CO_2$ treatment and the elevated treatment, respectively. Two phylotypes (type 1 and type 2) were dominant in both of the treatments. Elevated $CO_2$ treatment increased species richness of denitrifying as well as changed a large proportion of denitrifier phylotypes compared to those of the ambient treatment. Overall, the data in this study suggested that the denitrifying communities in the wetland soil are diverse and that the richness of denitrifying bacterial community might be affected by elevated $CO_2$ treatment.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.155-162
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• 2009

A cultivation-based approach was employed to compare the culturable bacterial diversity associated with two phylogenetically closely related marine sponges, Spirastrella abata and Spirastrella panis, which have geologically overlapping distribution patterns. The bacteria associated with sponge were cultivated using MA medium supplemented with 3% sponge extracts. Community structures of the culturable bacteria of the two sponge species were analyzed with PCR-RFLP (restriction fragment length polymorphism) based on 16S rDNA sequences. The RFLP fingerprinting of 16S rDNA digested with HaeIII and MspI, revealed 24 independent RFLP types, in which 1-5 representative strains from each type were partially sequenced. The sequence analysis showed >98.4% similarity to known bacterial species in public databases. Overall, the microbial populations of two sponges investigated were found to be the members of the classes; Alphaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria. The Alphaproteobacteria were predominant in the bacterial communities of the two sponges. Gammaproteobacteria represented 38.5% of bacterial community in S. abata. Whereas only 1.6% of this class was present in S. panis. Bacillus species were dominat in S. panis. Bacillus species were found to be 44.3% of bacterial species in S. panis, while they were only 9.7% in S. abata. It is interesting to note that Planococcus maritimus (8.1%, phylum Firmicutes) and Psychrobacter nivimaris (28.9%, phylum Gammaproteobacteria) were found only in S. abata. This result revealed that profiles of bacterial communities from the sponges with a close phylogenetic relationship were highly species-specific.

• Korean Journal of Microbiology
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• v.48 no.4
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• pp.275-283
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• 2012

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Asteropus simplex collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and MA media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 94% similarities compared with known bacterial species, and the isolates belonged to five phyla, Alphaproteobacteria, Gammaproteobacteria Actinobacteria, Bacteroidetes, and Firmicutes, of which Gammaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge-derived total gDNA showed 12 DGGE bands, and their sequences showed more than 90% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven phyla, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteira, Chloroflexi, and Nitrospira. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with A. simplex by both RFLP and DGGE methods, however, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture-independent method than in culture-dependent method.

• Korean Journal of Microbiology
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• v.53 no.1
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• pp.9-19
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• 2017

We studied soil composition, $N_2O$ production, a number of denitrifying bacteria, community structure and T-RFLP patterns of denitrifying bacteria dependent on agricultural methods with the change of seasons. Analyses of the soil chemical composition revealed that total carbon and total organic carbon contents were 1.57% and 1.28% in the organic farming soil, 1.52% and 1.24% in the emptiness farming soil, and 1.40% and 0.95% in traditional farming soil, respectively. So, the amount of organic carbon was relatively high in the environment friendly farming soils than traditional farming soils. In case of $N_2O$ production, the amount of $N_2O$ production was high in May and November soils, but the rate of $N_2O$ production was fast in August soil. The average number of denitrifying bacteria were $1.32{\times}10^4MPN{\cdot}g^{-1}$ in the organic farming soil, $1.17{\times}10^4MPN{\cdot}g^{-1}$ in the emptiness farming soil, and $6.29{\times}10^3MPN{\cdot}g^{-1}$ in the traditional farming soil. It was confirmed that the environment friendly farming soil have a larger number of denitrifying bacteria than the traditional farming soil. As a result of the phylogenetic analyses, it was confirmed that six clusters were included in organic farming soil among total 10 clusters. And the result of PCA profile distribution of T-RFLP pattern on agricultural methods, the range of distribution showed wide in the organic farming method, relatively narrow in the conventional farming method, and middle in the emptiness farming method. Therefore, we could concluded that the distribution and the community structure of denitrifying bacteria were changed according to the agricultural methods and seasons.