• Journal of Korean Society of Forest Science
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• v.106 no.2
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• pp.121-129
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• 2017

The soil microbiome plays important roles in material cycling and plant growth in forest ecosystem. Although a lot of researches on forest soil fungi in Korea have been performed, the studies on forest soil bacterial communities have been limited. In this study, we conducted next generation sequencing (NGS) targeting 16S rRNA gene to investigate the soil bacterial communities from natural red pine (Pinus densiflora) forest in Mt. Janggunbong, Bonghwa-gun, Gyeongbuk, Korea. Our results showed that the entire bacterial communities in the study sites include the phyla Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, which have been typically observed in forest soils. The composition ratio of Proteobacteria was the highest in the soil bacteria community. The results reflect that Proteobacteria is copiotroph, which generally favors relatively nutrient-rich conditions with abundant organic matter. Some rhizobia species such as Burkholderia, Bradyrhizobium, Rhizobium, which are known to contribute to soil nitrogen-fixation, exist in the study sites. As a result of correlation analysis between soil physicochemical characteristics and bacteria communities, the soil pH was significantly correlated with the soil bacteria compositions.

• Journal of Korean Society of Environmental Engineers
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• v.28 no.3
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• pp.240-248
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• 2006

In this study, a retrofitting BNR process that was modified for the economical applicability was proposed and evaluated in the pilot plant($50m^3/d$). At the same time the bacterial community structure was investigated in the pilot plant by using FISH(fluorescent in situ hybridization) method. Economically 16% of the initial construction cost for the proposed process(introduction of a biological nutrient removal process of $60,000m^3/d$ scale basis) was reduced due to the absence of a bioreactor. Water treatment efficiencies and maintenance facilities of the modified process were satisfied with the strengthened discharge permits in Korea throughout a long term pilot plant operating including a winter season. Bacterial populations in the pilot plant and in the control plant(A2/O process, B SIP(Sewage Treatment Plant)) were remained uniformly during the test period, but bacterial structure in the bioreactor was changed drastically. Proportions of ${\beta}$-proteobacteria group including soil bacteria which play a important role in wastewater treatment increased $25{\sim}607%$ in population.

• Journal of Life Science
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• v.26 no.7
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• pp.819-825
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• 2016

The present study was done to assess the diversity of the bacterial community associated with Ulva pertusa collected from Jeju Island using Restriction Fragment Length Polymorphism (RFLP) marker analysis. For RFLP analysis, a total of 145 bacterial strains associated with Ulva pertusa were screened and cultivated using Marine agar and R2A agar. The PCR amplicons of the 16S rRNA gene from all the isolated strains were digested with HaeIII and RsaI restriction enzymes and then classified into different groups according to their restriction patterns. Strains selected based on the RFLP patterns showed more than 91% 16S rRNA gene sequence similarity when compared with known bacterial species, which include 4 phyla - proteobacteria (alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria - 63%), firmicutes (11%), actinobacteria (4%), bacteroidetes (22%)–as well as 7 classes (actinobacteria, flavobacteriia, cytophagia, bacilli, α-proteobacteria, γ-proteobacteria, β-proteobacteria), 13 orders, 18 families, and 27 genera. These results confirmed a wide diversity of bacterial communities as contrasted with other regions. The newly isolated 10 strains, which show 16S rRNA sequence similarity of <97% compared to previously identified bacteria, could be noble species. Further experiments, such as morphological, physiological, and biochemical classification, are necessary to confirm the novelty of the newly isolated 10 strains.

• Journal of Wetlands Research
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• v.24 no.2
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• pp.69-82
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• 2022

In this study, we investigated the bacterial community structure in organic rice-fish mixed farming paddy soil by using high-throughput sequencing technology. The results showed that compared with the organic rice cultivated soil, the content of AP (available phosphorus) increased by 310.23 % and the content of OM (organic matter) increased by 168.83%. The most abundant phyla in paddy soils were Proteobacteria, Bacteriodetes, and Chloroflexi, whose relative abundance was above 47.83%. Among the dominant genera, the relative abundance of Limisphaera in paddy soils was observed. Alpha diversity indicated that the bacterial diversity of paddy soils was similar among each other. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Principal Coordinated Analysis (PCoA) results showed that the bacterial communities in organic rice-fish mixed farming soil and organic paddy soil were correlated to each other; the bacterial community structure was distinctively grouped by four different systems (paddy soil under organic rice-fish mixed farming system, organic rice cultivation, and conventional rice cultivation), where the first two are closely related to each other than the third one. The results provide basal support for organic agri-cultivation while improving an ecological value at the same time.

• Korean Journal of Agricultural Science
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• v.43 no.5
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• pp.777-787
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• 2016

In the present study, we aimed to investigate the effect of dietary supplementation of palm kernel meal (PKM), as a fermentable carbohydrate source, on the growth performance, meat quality, concentration of odorous compound, and changes in bacterial community in swine manure. Swine (average initial body weight of $51.36{\pm}1.02kg$) were fed diet which included three levels of PKM (0, 2 and 4%), and their manure samples were collected from the slurry pit. Growth performance and meat quality were not affected by PKM treatments (p > 0.05). Levels of phenols and indoles were decreased in the 2 and 4% PKM treatments compared to 0% PKM (control; p < 0.05). Especially, compared to the control, the 2% PKM group showed decreased levels of phenols by 35% and indoles by 34%. Among the dominant bacterial genera, the main change in relative abundance occurred in those belonging to the Firmicutes phylum in PKM treatments. Terrisporobacter and Clostridium were decreased in the PKM groups compared to the control. However, the relative abundance of Intestinibacter, AM406061_g, Coprococcus_g2, Phascolarcotobacterium, EF401875_g, Lactobacillus, and Streptococcus were increased in the PKM group compared to control. Taken together, administration of PKM had a beneficial effect on reducing production of odorous compounds in swine manure, possibly by modulating the communities of predominantly carbohydrate-utilizing bacteria in the large intestine of swine.

• The Korean Journal of Food And Nutrition
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• v.22 no.4
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• pp.492-496
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• 2009

The composition of the bacterial populations in Gorosoe(Acer mono Max.) sap was characterized during storage with different heat treatments($63^{\circ}C$ for 30 min and $73^{\circ}C$ for 15 sec). The saps were aseptically collected at 0, 15 and 30 days of storage and analyzed by dilution plating and 16S rDNA PCR-DGGE analysis. There were significant differences in the total number of colony forming units(CFUs) of bacteria between heated and nonheated saps. Bacteria of nonheated sap were present at a level of $3.4{\times}10^7CFU/m{\ell}^{-1}$, whereas living bacteria were not detected in the heated sap. According to the 16S rDNA sequence and DGGE analysis, Pseudomonas sp. was the most abundant bacterial strain in the samlpes, and the bacterial community structures become more simplified with time and were composed of the Chryseobacterium sp. with time. These results allowed us to characterize the dominant bacteria involved in Gorosoe sap and to better understand their dynamics throughout storage.

• Journal of Microbiology and Biotechnology
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• v.22 no.9
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• pp.1264-1270
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• 2012

The ecotoxicological effects of nanomaterials on animal, plant, and soil microorganisms have been widely investigated; however, the nanotoxic effects of plant-soil interactive systems are still largely unknown. In the present study, the effects of ZnO nanoparticles (NPs) on the soil-plant interactive system were estimated. The growth of plant seedlings in the presence of different concentrations of ZnO NPs within microcosm soil (M) and natural soil (NS) was compared. Changes in dehydrogenase activity (DHA) and soil bacterial community diversity were estimated based on the microcosm with plants (M+P) and microcosm without plants (M-P) in different concentrations of ZnO NPs treatment. The shoot growth of M+P and NS+P was significantly inhibited by 24% and 31.5% relative to the control at a ZnO NPs concentration of 1,000 mg/kg. The DHA levels decreased following increased ZnO NPs concentration. Specifically, these levels were significantly reduced from 100 mg/kg in M-P and only 1,000 mg/kg in M+P. Different clustering groups of M+P and M-P were observed in the principal component analysis (PCA). Therefore, the M-P's soil bacterial population may have more toxic effects at a high dose of ZnO NPs than M+P's. The plant and activation of soil bacteria in the M+P may have a less toxic interactive effect on each of the soil bacterial populations and plant growth by the ZnO NPs attachment or absorption of plant roots surface. The soil-plant interactive system might help decrease the toxic effects of ZnO NPs on the rhizobacteria population.

• Journal of Microbiology and Biotechnology
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• v.18 no.1
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• pp.5-14
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• 2008

The deep subseafloor rock in oil reservoirs represents a unique environment in which a high oil contamination and a very low biomass can be observed. Sampling this environment has been a challenge owing to the techniques used for drilling and coring. In this study, the facilities developed by the Brazilian oil company PETROBRAS for accessing deep subsurface oil reservoirs were used to obtain rock samples at 2,822-2,828 m below the ocean floor surface from a virgin field located in the Atlantic Ocean, Rio de Janeiro. To address the bacterial diversity of these rock samples, PCR amplicons were obtained using the DNA from four core sections and universal primers for 16S rRNA and for APS reductase (aps) genes. Clone libraries were generated from these PCR fragments and 87 clones were sequenced. The phylogenetic analyses of the 16S rDNA clone libraries showed a wide distribution of types in the domain bacteria in the four core samples, and the majority of the clones were identified as belonging to Betaproteobacteria. The sulfate-reducing bacteria community could only be amplified by PCR in one sample, and all clones were identified as belonging to Gammaproteobacteria. For the first time, the bacterial community was assessed in such a deep subsurface environment.

• Animal Bioscience
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• v.36 no.9
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• pp.1453-1464
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• 2023

Objective: This study investigated the changes in bacterial communities within decomposing swine microcosms, comparing soil with or without intact microbial communities, and under aerobic and anaerobic conditions. Methods: The experimental microcosms consisted of four conditions: UA, unsterilized soil-aerobic condition; SA, sterilized soil-aerobic condition; UAn, unsterilized soil-anaerobic condition; and San, sterilized soil-anaerobic condition. The microcosms were prepared by mixing 112.5 g of soil and 37.5 g of ground carcass, which were then placed in sterile containers. The carcass-soil mixture was sampled at day 0, 5, 10, 30, and 60 of decomposition, and the bacterial communities that formed during carcass decomposition were assessed using Illumina MiSeq sequencing of the 16S rRNA gene. Results: A total of 1,687 amplicon sequence variants representing 22 phyla and 805 genera were identified in the microcosms. The Chao1 and Shannon diversity indices varied in between microcosms at each period (p<0.05). Metagenomic analysis showed variation in the taxa composition across the burial microcosms during decomposition, with Firmicutes being the dominant phylum, followed by Proteobacteria. At the genus level, Bacillus and Clostridium were the main genera within Firmicutes. Functional prediction revealed that the most abundant Kyoto encyclopedia of genes and genomes metabolic functions were carbohydrate and amino acid metabolisms. Conclusion: This study demonstrated a higher bacteria diversity in UA and UAn microcosms than in SA and SAn microcosms. In addition, the taxonomic composition of the microbial community also exhibited changes, highlighting the impact of soil sterilization and oxygen on carcass decomposition. Furthermore, this study provided insights into the microbial communities associated with decomposing swine carcasses in microcosm.

• Animal Bioscience
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• v.36 no.12
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• pp.1842-1852
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• 2023

Objective: Hairy vetch is considered to improve the nutritional value of corn because of its high protein and mineral levels. To better understand the mechanism underlying hairy vetch regulated whole-plant corn silage fermentation, this experiment investigated the fermentation quality and bacterial community of whole-plant corn and hairy vetch mixture. Methods: Whole-plant corn and hairy vetch were mixed at ratios of 10:0 (Mix 10:0), 8:2 (Mix 8:2), 6:4 (Mix 6:4), 4:6 (Mix 4:6), 2:8 (Mix 2:8), and 0:10 (Mix 0:10) on a fresh weight basis. After ensiling 60 days, samples were collected to examine the fermentation dynamics, ensiling characteristics, and bacterial communities. Results: Mix 0:10, Mix 2:8, and Mix 4:6 showed poor fermentation characteristics. Mix 8:2 and Mix 6:4 silages showed high quality, based on the low pH, acetic acid, and ammonia nitrogen levels and the high lactic acid, crude protein, and crude fat contents. The bacterial diversity was affected by the mixing ratio of the two forage species. The genus Lactobacillus dominated the bacterial community in Mix 10:0 silage, whereas with the addition of hairy vetch, the relative abundance of unclassified-Enterobacter increased from 7.67% to 41.84%, and the abundance of Lactobacillus decreased from 50.66% to 13.76%. Conclusion: The silage quality of whole-plant corn can be improved with inclusion levels of hairy vetch from 20% to 40%.