• 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.

• Journal of Animal Science and Technology
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• v.65 no.5
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• pp.951-970
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• 2023

This study utilized Italian ryegrass silage (IRGS) - based total mixed ration (TMR) as feedstuff and evaluated its effects on rumen fermentation, growth performance, blood parameters, and bacterial community in growing Hanwoo heifers. Twenty-seven Hanwoo heifers (body weight [BW], 225.11 ± 10.57 kg) were randomly allocated to three experimental diets. Heifers were fed 1 of 3 treatments as follows: TMR with oat, timothy, and alfalfa hay (CON), TMR with 19% of IRGS (L-IRGS), and TMR with 36% of IRGS (H-IRGS). Feeding high levels of IRGS (H-IRGS) and CON TMR to heifers resulted in a greater molar proportion of propionate in the rumen. The impact of different TMR diets on the BW, average daily gain, dry matter intake, and feed conversion ratio of Hanwoo heifers during the growing period did not differ (p > 0.05). Furthermore, the blood metabolites, total protein, albumin, aspartate aminotransferase, glucose, and total cholesterol of the heifers were not affected by the different TMR diets (p > 0.05). In terms of rumen bacterial community composition, 264 operational taxonomic units (OTUs) were observed across the three TMR diets with 240, 239, and 220 OTUs in CON, L-IRGS, and H-IRGS, respectively. IRGS-based diets increased the relative abundances of genera belonging to phylum Bacteroidetes but decreased the abundances of genus belonging to phylum Firmicutes compared with the control. Data showed that Bacteroidetes was the most dominant phylum, while Prevotella ruminicola was the dominant species across the three TMR groups. The relative abundance of Ruminococcus bromii in the rumen increased in heifers fed with high inclusion of IRGS in the TMR (H-IRGS TMR). The relative abundance of R. bromii in the rumen significantly increased when heifers were fed H-IRGS TMR while P. ruminicola increased in both L-IRGS and H-IRGS TMR groups. Results from the current study demonstrate that the inclusion of IRGS in the TMR is comparable with the TMR containing high-quality forage (CON). Thus, a high level of IRGS can be used as a replacement forage ingredient in TMR feeding and had a beneficial effect of possibly modulating the rumen bacterial community toward mainly propionate-producing microorganisms.

• Journal of Environmental Health Sciences
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• v.34 no.4
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• pp.327-332
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• 2008

To determine structure and activities of microbial communities in a food wastewater treatment system, biofilm of RABC (rotating activated Bacillus contactor) and samples of aeration tanks were analyzed. Heterotrophic bacterial concentrations were similar between biofilm and stage 1 aeration tank and decreased 2-log at stage 3 aeration tank as dissolved oxygen decreased, however portions of Bacillus groups were increased at stage 3 aeration tank. It was revealed by quantitative and qualitative analysis of metabolic fingerprinting patterns of Biolog GN2 plate that RABC represented much higher activities and a different microbial community structure compared to aeration tanks. Metabolic fingerprinting showed the carbon sources that isolated Bacillus groups could or could not use, were used similarly meaning that not only Bacillus groups but also other microbial groups would contribute to the treatment of wastewater.

• Journal of Animal Science and Technology
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• v.59 no.12
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• pp.28.1-28.8
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• 2017

Background: Major amino acids in pig diets are Lys, Met, Thr, and Trp, but little is known about the requirements for the other essential amino acids, especially on odorous compounds and microbial characteristics in feces of growing-finishing pigs. To this end, different levels of amino acid composition added to diets to investigate the effects of amino acid composition on microbial characteristics and odorous compounds concentration. Methods: A total eight (n = 8) barrows (Landrace ${\times}$ Yorkshire ${\times}$ Duroc) with an average bodyweight of $89.38{\pm}3.3kg$ were individually fed diets formulated by Korean Feeding Standards 2007 (old version) or 2012 (updated with ideal protein concept) in metabolism crates with two replication. After 15-day adaptation period, fresh faecal samples were collected directly from pigs every week for 4 weeks and analysed for total volatile fatty acids (VFA), phenols and indoles by using gas chromatography. The nitrogen was determined by Kjeldahl method. Bacterial communities were detected by using a 454 FLX titanium pyrosequencing system. Results: Level of VFA tended to be greater in 2012 than 2007 group. Among VFAs, 2012 group had greater (p < 0.05) level of short chain fatty acids (SCFA) than control.Concentration of odorous compounds in feces was also affected by amino acid composition in pig diet. Levels of ammonium and indoles tended to be higher in 2012 group when compared with 2007 group.Concentration of phenols, p-cresol, biochemical oxygen demand, and total Kjeldahl nitrogen, however, were lower (P < 0.05) in 2012 treatment group compare to 2007. The proportion of Firmicute phylum were decreased, while the Bacteriodetes phylum proportion increased and bacterial genera includingCoprococcus, Bacillus, and Bacteroides increased (p < 0.05) in 2012 compare to 2007 group. Conclusion: Results from our current study indicates that well balanced amino acid composition reduces odor by modulating the gut microbial community. Administration of pig diet formulated with the ideal protein concept may help improve gut fermentation as well as reduce the odor causing compounds in pig manure.

• Korean Journal of Soil Science and Fertilizer
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• v.42 no.4
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• pp.257-265
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• 2009

The long-term effects of soil management history on microbial communities are still poorly understood. Our objectives were to determine the impact of long-term application of soil amendments on microbial communities in rice paddy fields. The treatments selected were control where crops were grown without any nutrient application (CON); nitrogen-phosphorus-potassium (NPK); NPK plus compost (CNPK); NPK plus lime (LNPK); and NPK plus silicate (WNPK). The long-term addition of organic and inorganic amendments significantly changed soil chemical properties. The amount of organic carbon increased in the treatments with fertilizer and amendments over that in the soil without inputs. However, we could not observe the differences of bacterial population among the treatments, but the number of aerobic bacteria increased by the addition of amendments. Isolates from the rice paddy soils before irrigation were Dactylosporangium, Ewingella, Geobacillus, Kocuria, Kurthia, Kytococcus, Lechevalieria, Micrococcus, Micromonospora, Paenibacillus, Pedobacter, Pseudomonas, Pseudoxanthomonas, Rhodococcus, Rothia, Sphingopyxis, Stenotrophomonas, and Variovorax. Dominant genera were Arthrobacter, Kocuria, Kurthia, and Bacillus in the long-term field. Microbial biomass was the highest in the compost treatment (CNPK), and was the lowest in the CON. Dehydrogenase activity in soils treated with rice compost straw was the highest and the activity showed an increasing trend according to treatment as follows: CON < WNPK < NPK = LNPK < CNPK. These results demonstrate that soil management practice, such as optimal application of fertilizer and amendment, that result in accumulations of organic carbon may increase microbial biomass and dehydrogenase activity in long-term rice paddy soils.

• Microbiology and Biotechnology Letters
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• v.38 no.4
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• pp.448-454
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• 2010

This study investigated the effect of PCE and TCE as electron acceptors on the bacterial composition of dechlorinating communities. The enrichment cultures reductively dechlorinating PCE and TCE were developed from three environment samples using acetate as electron donor. The cultures were prepared by sequential enrichment, which was seeded with sediment and dredged soil. Denatured gradient gel electrophresis (DGGE) of 16S rRNA gene fragment was used to compare the microbial communities of these three enrichment cultures. After incubation for 4 weeks, the removal efficiencies of PCE and TCE were highest from Yeocheon site (87.37% and 84.46%, respectively). PCE and TCE as electron acceptors affected the bacterial diversity and community profiles in the enrichment cultures. DGGE analysis showed that the dominant bacteria in PCE and TCE enrichment were belonged to Clostridium sp., Desulfotomaculum sp., and uncultured bacteria.

• Journal of Ginseng Research
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• v.40 no.1
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• pp.28-37
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• 2016

Background: Panax ginseng cannot be cultivated on the same land consecutively for an extended period, and the underlying mechanism regarding microorganisms is still being explored. Methods: Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) and BIO-LOG methods were used to evaluate the microbial genetic and functional diversity associated with the P. ginseng rhizosphere soil in various cultivation ages and modes. Results: The analysis of microbial diversity using PCR-DGGE showed that microbial communities were significantly variable in composition, of which six bacterial phyla and seven fungal classes were detected in P. ginseng soil. Among them, Proteobacteria and Hypocreales dominated. Fusarium oxysporum, a soilborne pathogen, was found in all P. ginseng soil samples except R0. The results from functional diversity suggested that the microbial metabolic diversity of fallow soil abandoned in 2003was the maximum and transplanted soil was higher than direct-seeding soil and the forest soil uncultivated P. ginseng, whereas the increase in cultivation ages in the same mode led to decreases in microbial diversity in P. ginseng soil. Carbohydrates, amino acids, and polymers were the main carbon sources utilized. Furthermore, the microbial diversity index and multivariate comparisons indicated that the augmentation of P. ginseng cultivation ages resulted in decreased bacterial diversity and increased fungal diversity, whereas microbial diversity was improved strikingly in transplanted soil and fallow soil abandoned for at least one decade. Conclusion: The key factors for discontinuous P. ginseng cultivation were the lack of balance in rhizosphere microbial communities and the outbreak of soilborne diseases caused by the accumulation of its root exudates.

• Journal of Microbiology and Biotechnology
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• v.29 no.10
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• pp.1644-1655
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• 2019

Saccharomyces cerevisiae (S. cerevisiae) and glucagon-like peptide-2 (GLP-2) have been employed to improve the intestinal development of weaned animals. The goal of this study was to determine whether either exogenous S. cerevisiae or GLP-2 elicits major effects on fecal microbiotas and cytokine responses in weaned piglets. Ninety-six piglets weaned at 26 days were assigned to one of four groups: 1) Basal diet (Control), 2) empty vector-harboring S. cerevisiae (EV-SC), 3) GLP-2-expressing S. cerevisiae (GLP2-SC), and 4) recombinant human GLP-2 (rh-GLP2). At the start of the post-weaning period (day 0), and at day 28, fecal samples were collected to assess the bacterial communities via sequencing the V1-V2 region of the 16S-rRNA gene, and piglets' blood was also sampled to measure cytokine responses (i.e., IL-$1{\beta}$, TNF-${\alpha}$, and IFN-${\gamma}$). This study revealed that, on the one hand, although S. cerevisiae supplementation did not significantly alter the growth of weaned piglets, it induced increases in the relative abundances of two core genera (Ruminococcaceae_norank and Erysipelotrichaceae_norank) and decreases in the relative abundances of two other core genera (Lachnospiraceae_norank and Clostridiale_norank) and cytokine levels (IL-$1{\beta}$ and TNF-${\alpha}$) (p < 0.05, Control vs EV-SC; p < 0.05, rh-GLP2 vs GLP2-SC). On the other hand, GLP-2 supplementation had no significant influence on fecal bacterial communities and cytokine levels, but it produced better body weight and average daily gain (p < 0.05, Control vs EV-SC; p < 0.05, rh-GLP2 vs GLP2-SC). Therefore, altered fecal microbiotas and cytokine response effects in weaned piglets were due to S. cerevisiae rather than GLP-2.

• Korean Journal of Environmental Biology
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• v.29 no.3
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• pp.225-235
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• 2011

The change of microbial communities during cyanobacterial bloom was comparatively analyzed by 16S rDNA PCR-DGGE in Daechung Reservoir during 2003~2005. Morphological analysis showed that Cyanophyceae dominated algal community in the bloom. Dominant cyanobacteria were Microcystis, Planktothrix (Oscillatoria), Phormidium and Anabaena. We used 16S rDNA-denaturing gradient gel electrophoresis (DGGE) profiles and phylogenetic affiliations of the DGGE bands to analyze the community structure and diversity of the predominant microbial community. The DGGE band patterns demonstrated that the most frequent bands were identified as Microcystis during the monitoring periods, Planktothrix also dominated on September 2003 and 2004, whereas Anabaena was showed a peak on September 2005 and Aphanizomenon on August 2003. DGGE and phylogenetic analysis provided us new information that could not be obtained by traditional, morphological analysis. The relationship between cyanobacteria and other aquatic bacteria can be traced and their genetic diversity also identified in detail.