• Asian-Australasian Journal of Animal Sciences
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• v.28 no.4
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• pp.584-591
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• 2015

This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level). Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.

• Korean Journal of Environmental Biology
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• v.40 no.1
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• pp.54-69
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• 2022

We conducted a field survey from 2018 to 2020 to analyze the spatial distribution of phytoplankton communities at 13 stations in the East Sea. The diatom Chaetoceros curvisetus appeared as the dominant species in winter, and small flagellates less than 20 ㎛ prevailed in all seasons except winter. The seasonal average range of the micro (>20 ㎛), nano (20 ㎛≥Chl-a>3 ㎛), and picophytoplankton (≤3 ㎛) was 20.6-26.2%, 27.1-35.9%, and 40.8-49.0%, respectively. The composition ratio of nano and picophytoplankton was high at the surface mixed layer from spring to autumn when the water columns were strongly stratified. Especially, the stability of the water mass was increased when the summer surface water temperature was higher than that of the previous year. As a result, the nutrient inflow from the lower layer to the surface was reduced as the ocean stratification layer was strengthened. Therefore, the composition ratio of nano and picophytoplankton was the highest at 77.9% at the surface mixed layer. In conclusion, the structure of the phytoplankton community in the East Sea has been miniaturized, which is expected to form a complex microbial food web structure and lower the carbon transfer rate to the upper consumer stage.

• Korean Journal of Ecology and Environment
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• v.41 no.2
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• pp.174-187
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• 2008

In an effort to identify structure and function of microbial loop in Paldang reservoir, we monitored environmental and biological factors at Kyungan stream (station K), Paldang dam (station P) and the confluence of North and South Han River (station M) from March to December, 2005. DOC concentration was higher in March to May and November than the others. Nutrient concentration in station K detected relatively higher than that of two stations. Both of phosphate and silicate gradually increased at all stations until September, after then decreased. The highest Chl-$\alpha$ concentration was observed at all stations in April, and November. The carbon biomass of bacteria and HNF were relatively higher in March, May and August than the others, whereas that of the ciliate showed no significant difference in monthly fluctuation. Nevertheless, the significant relationships revealed between ciliate (P<0.001) and HNF (P<0.05) and bacterial density. Tintinnopsis cratera, Didinium sp., Vorticella sp., Paramecium sp. and Strombidium sp. were dominant species in ciliate community. The dominant species of phytoplankton were Stephanodiscus hantzschii and Cyclotella meneghiniana at almost stations in Spring, Summer and Autumn. However, Aulacoseira granulata accounted for >95% of phytoplankton biomass at station P and M in Autumn. The carbon biomass of zooplankton was highest at station P and M in June, and relatively higher biomass observed at all stations in August, October and November. Diaphanosoma brachyurum and Bosmina longirostris were dominant in stations P and M of June and in all stations of October and November, respectively. The maximum growth (A. granulata: $0.17\;d^{-1}$, S. hantzschii: $0.14\;d^{-1}$) and grazing rate (A. granulata: 1.93 preys $d^{-1}$, S. hantzschii: 1.63 preys $d^{-1}$) of Bosmina longirostris revealed in algal preys as Aulacoseira granulata and Stephanodiscus hantzschii. In conclusion, these results suggest that bacteria and phytoplankton can play the most crucial source as prey within microbial food chain in Spring and Summer and grazing food chain in Autumn, respectively.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.116-124
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• 2006

In this study was performed to analyze quantitatively the number of viable but non-culturable bacteria in the Pine and Quercus forest soil by improved direct viable count (DVC) and plate count (PC) methods. The number of living bacteria of Pine and Quercus forest soil by PC method were less then 1% of DVC method. This result showed that viable but non-culturable (VBNC) bacteria existed in the forest soil with high percentage. Diversity and structure of VBNC bacterial populations in forest soil were analyzed by direct extracting of DNA and 16S rDNA-ARDRA from Pine and Quercus forest soil. Each of them obtained 111 clones and 108 clones from Pine and Quercus forest soil. Thirty different RFLP types were detected from Pine forest soil and twenty-six different RFLP types were detected from Quercus forest soil by HeaIII. From ARDRA groups, dominant clones were selected for determining their phylogenetic characteristics based on 16S rDNA sequence. Based on the 16S rDNA sequences, dominant clones from ARDRA groups of Pine forest soil were classified into 7 major phylogenetic groups ${\alpha}$-proteobacteria (12 clones), ${\gamma}$-proteobacteria (3 clones), ${\delta}$-proteobacteria (1 clone), Flexibacter/Cytophaga (1 clone), Actinobacteria (4 clones), Acidobacteria (4 clones), Planctomycetes (5 clones). Also, dominant clones from ARDRA groups of Quercus forest soil were classified into 6 major phylogenetic groups : ${\alpha}$-proteobacte,ia (4clones), ${\gamma}$-proteobacteria (2 clones), Actinobacteria (10 clones), Acidobacteria (8 clones), Planctomycetes (1 clone), and Verrucomicobia (1 clone). Result of phylogeneric analysis of microbial community from Pine and Quercus forest soils were mostly confirmed at uncultured or unidentified bacteria, VBNC bacteria of over 99% existent in forest soil were confirmed variable composition of unknown micro-organism.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.140-147
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• 2009

In this study, anaerobic enrichment cultivation was performed with the sediments from the Gimpo and Inchon areas. Lactate as an electron donor and PCE as an electron acceptor was injected into the serum bottle with an anaerobic medium. After the incubation of 8 weeks, the reductive dechlorination of PCE was observed in 7 sites among 16 sites (43%). Three enrichment cultures showed completely dechlorination of PCE to ethene, while four enrichment culture showed transformation of PCE to cis-DCE. The bacterial community structure was analyzed by PCR-DGGE. Dechlorinating bacteria were detected by species-specific primers. The dominant species in seven anaerobic enrichments were found to belong to the genus of Dehalococcoides sp. and Geobacter sp., and Dehalobacter sp.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.248-253
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• 2004

To scrutinize the physiological diversity by BIOLOG microplate, the carbon source utilization patterns of 168 strains of oligotrophic bacteria and 132 strains of psychrotrophic bacteria isolated from Lake Baikal during 2000 and 2002 were investigated. Eighty-six percent (56 strains) of oxidase test positive group (GN-NENT group) and 89 % (92 strains) of oxidase test negative group (GN-ENT group) among oligotrophic bacteria, and 82% (85 strains) of oxidase test negative group among psychrotrophic bacteria were able to utilize $\alpha$-D-glucose as a sole-carbon-source, and 93% (26 strains) of oxidase test positive group among psychrotrophic bacteria were able to utilize bromosuccinic acid as a sole-carbon-source. However, most strains except few oligotrophic bacteria with oxidase test negative group were not able to utilize $\alpha$-D-lactose as a sole-carbon-source. Most dominant genus among 300 strains was Pseudomonas (49 strains). Other dominant genera belonged to Salmonella, Serratia, Buttiauxella, Pantoea, Yersinia, Brevundimonas, Hydrogenophaga, Photorhabdus, Sphingomonas, and Xenorhabdus. Our results by BIOLOG identification system were able to provide basic data to determine community-level carbon source utilization patterns and to accomplish the efficient and reliable identification for microbial community structure in Lake Baikal.

• Research in Plant Disease
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• v.30 no.2
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• pp.165-175
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• 2024

The Korean fir tree (Abies koreana), an endemic species of South Korea, is experiencing a severe decline in population due to climate change. Studies on the conservation of Korean fir have been extensive, yet research regarding its correlation with rhizosphere bacterial communities remains scarce, warranting further investigation. In this study, metagenome amplicon sequencing targeting the 16S rRNA V4 region was conducted to examine the presence of specific bacterial communities in Korean fir and to investigate potential differences based on habitat types (rhizosphere of native or cultivated trees, soil of dead trees, and bulk soil) and seasonal variations (April, June, September, November). Here we show that although we could not identify specific taxa highly specifically with Korean fir, the rhizosphere bacterial community in native trees exhibited less variability in response to seasonal changes compared to that in bulk soils. Suggesting the establishment of relatively stable bacterial populations around the Korean fir natural habitat. Further research on other types of rhizosphere and/or microbes is necessary to investigate the distinct relationship of Korean fir with microbial communities.

• Journal of Marine Bioscience and Biotechnology
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• v.16 no.1
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• pp.63-86
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• 2024

This study analyzed the distribution, diversity, and density variation of algal clusters in a freshwater reservoir from an oceanic island and a traditional inland water system to gain insights on future marine freshwater resource management. In the Paldang water system (Han River), despite the upstream Paldang Dam and the downstream Jamsil underwater reservoir being in the same meteorological zone, their algae density patterns varied inversely. The distinct algal cluster structure (diversity/dominance) of Paldang was altered in the downstream reservoir, suggesting that physical devices aid algae management in traditional water systems. In contrast, 24 out of 35 genera (63.2%) identified in the Jeolgol Reservoir (Baeknyeong Island) were unique, lacking regulatory mechanisms, and existing in a complex ecotone. The desmid Chlorophyceae Cosmarium, adapted to higher photosynthetic stress and low temperatures, dominated in January (38.04%) and August (86.45%) during the periods of extreme photosynthetic stress. Jeolgol's annual algal cluster structure (H' 2.097; D 0.259; S' 35) demonstrated higher stability than Paldang (H' 1.125; D 0.448; S' 13) and the Jamsil underwater reservoir (H' 1.078; D 0.469; S' 12), maintaining an H' above 1.5 even during midwinters. No evidence of TN/TP inflow from surrounding soils was observed, even during torrential rainfalls, with phosphorus being the limiting factor for algal growth. TOC, BOD, chlorophyll-a, and turbidity peaked during Cosmarium bloom. Future climate change is expected to cause fluctuations in algal clusters and related water quality factors. The complex transitional nature of the Jeolgol Reservoir, its algal diversity, and the interspecies interactions contribute to the high stability of its algal community.

• Korean Journal of Environmental Biology
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• v.24 no.2 s.62
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• pp.172-178
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• 2006

The dynamics of bacterial populations belonging to $\alpha\;\beta\;\gamma-subclass$ proteobacteria, Cytophaga-Flavobacterium (CF) group and sulfate reducing bacteria (SRB) in water column of the middle reaches of Nakdong River depending on sediment harvesting were analyzed by fluorescent in situ hybridization (FISH) at sediment harvesting site (near the Seongju bridge) and non-sediment harvesting site (near the Gumi bridge). In addition, some physico-chemical parameters such as temperature, pH, $chi-\alpha$ and electrical conductivity were measured. Regarding the number of total cell counts, cells stained by DAPI, there were no substantial quantitative differences between both sites, but those fluctuation at sediment Harvesting site was greater. And also the ratios of CFgroup and SRB to total cell counts tend to increase at sediment harvesting site with higher $chl-\alpha$, maybe due to the resuspension of sediment into water column. But the total proportion of all determined bacterial populations to total cell counts were greater at non-sediment harvesting site, compared with those at sediment harvesting site. Since the detectibility of bacteria by FISH depends on their metabolic activity, those lower proportion at the sediment harvesting site implies that sediment harvesting may lead to malfunction of those bacteria respect to nutrient recycling and subsequently negative effects on microbial food web.

• Journal of Life Science
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• v.28 no.10
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• pp.1179-1185
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• 2018

Recently, Sargassum horneri, the marine weed inhabiting the shoreline, beach, and littoral sea area, has caused serious damage to intensive aquaculture farms particularly those around Jeju Island, South Korea. The purpose of this study was to investigate the diversity of microorganisms in Sargassum horneri and to provide basic data on ecological problems by identifying microbial functions. A total of 88 isolates were identified by 16S rRNA sequencing. Proteobacteria was the dominant phylum accounting for 88%, including class ${\alpha}-proteobacteria$, six genera, and ten species. The dominating genus, Pseudobacter, accounted for 40% in Pseudorhodobacter, 20% in Paracoccus, and the remaining at 10% each were Rhizobium, Albirhodobacter, Skermanella, and Novosphingobium. Class ${\beta}-proteobactera$ included five genera and ten species. Genus Hydrogenophaga accounted for 50%, while genus Azoarcus accounted for 20%, and the remaining Oxalicibacterium, Duganella, and Xenophilus were 10% each. Class ${\gamma}-proteobacteria$ with 13 genera and 57 species, accounted for 74% in phylum Proteobacteria, 23% in Shewanella, 19% in Cobetia, 12% in Pseudomonas, 4% each in Vibrio and Serratia, and 2% each in Rheinheimera, Raoultella, Pantoea, Acinetobacter, Moraxella, and Psychrobacter genera. In addition, Actinobacteria with two species of Nocardioides genera accounted for 50%, and Bacteroidetes accounted for 33%, with three genera and five species that included Lacihabitans and Mariniflexile. The remaining Dyadobacter, Cellulophaga, and Ferruginibacter genera each accounted for 11%.