• Animal Bioscience
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• 제35권8호
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• pp.1162-1173
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• 2022

Objective: This study aimed to investigate the fermentation profiles, bacterial community and predicted metabolic characteristics of Sudangrass (Sorghum sudanense Stapf.) during ensiling. Methods: First-cutting Sudangrass was harvested at the vegetative stage and ensiled in laboratory-scale silos (1 L capacity). Triplicate silos were sampled after 1, 3, 7, 15, 30, and 60 days of ensiling, respectively. The bacterial communities on day 3 and 60 were assessed through high-throughput sequencing technology, and 16S rRNA-gene predicted functional profiles were analyzed according to the Kyoto encyclopedia of genes and genomes using Tax4Fun. Results: The Sudangrass silages showed good fermentation quality, indicated by higher lactic acid contents, and lower pH, butyric acid and ammonia nitrogen contents. The dominant genus Lactococcus on day 3 was replaced by Lactobacillus on day 60. The metabolism of amino acid, energy, cofactors and vitamins was restricted, and metabolism of nucleotide and carbohydrate was promoted after ensiling. The 1-phosphofructokinase and pyruvate kinase of bacterial community seemed to play important roles in stimulating the lactic acid fermentation, and the promotion of arginine deiminase could help lactic acid bacteria to tolerate the acidic environment. Conclusion: High-throughput sequencing technology combined with 16S rRNA gene-predicted functional analyses revealed the differences during the early and late stages of Sudangrass ensiling not only for distinct bacterial community but also for specific functional metabolites. The results could provide a comprehensive insight into bacterial community and metabolic characteristics to further improve the silage quality.

• Journal of Species Research
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• 제12권2호
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• pp.165-173
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• 2023

Bacterial communities inhabiting islands play a vital role in the functioning and formation of a unique, isolated ecosystem. Nevertheless, there has been a lack of systematic research on the indigenous microbiological resources of the islands in Korea. To excavate microbial resources for further studies on the metabolism and biotechnological potential, a standard dilution plating was applied to coastal seawater samples collected from islands along the west coast of the Korean Peninsula, including Deokjeokdo, Baengnyeongdo, and Daebudo in 2022. A total of 2,007 bacterial strains were isolated from the samples as single colonies and identified using 16S rRNA gene sequence analyses. A total of 20 strains, with ≥98.7% 16S rRNA gene sequence similarity to bacterial species having validly published names but not reported in Korea, were designated as unrecorded bacterial species in Korea. The unrecorded bacterial strains were phylogenetically diverse and belonged to four phyla, five classes, 12 orders, 17 families, and 18 genera. The unreported species were assigned to Algimonas, Amylibacter, Notoacmeibacter, Roseibium, and Terasakiella of the class Alphaproteobacteria; Alteromonas, Congregibacter, Marinagarivorans, Marinicella, Oceanospirillum, Psychromonas, Thalassotalea, Umboniibacter, and Vibrio of the class Gammaproteobacteria; Lutibacter and Owenweeksia of the class Flavobacteriia; Paenibacillus of the class Bacilli; and Pelagicoccus of the class Opitutae. The taxonomic characteristics of the unreported species, including morphology, biochemistry, and phylogenetic position are provided in detail.

• Journal of Ecology and Environment
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• 제41권3호
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• pp.99-106
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• 2017

Background: Plants over-expressing Arabidopsis ABF3 (abscisic acid-responsive element-binding factor 3) have enhanced tolerance to various environmental stresses, especially drought. Using terminal restriction fragment length polymorphism (T-RFLP) analysis, we compared the rhizosphere-associated structures of microbial communities for transgenic potato containing this gene and conventional "Jopoong" plants. Results: During a 2-year field experiment, fungal richness, evenness, and diversity varied by year, increasing in 2010 when a moderate water deficit occurred. By contrast, the bacterial richness decreased in 2010 while evenness and diversity were similar in both years. No significant difference was observed in any indices for either sampling time or plant line. Although the composition of the microbial communities (defined as T-RF profiles) changed according to year and sampling time, differences were not significant between the transgenic and control plants. Conclusions: The results in this study suggest that the insertion of ABF3 into potato has no detectable (by current T-RFLP technique) effects on rhizosphere communities, and that any possible influences, if any, can be masked by seasonal or yearly variations.

• Journal of Microbiology and Biotechnology
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• 제26권5호
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• pp.883-890
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• 2016

Marine sediments are a microbial biosphere with an unknown physiology, and the sediments harbor numerous distinct phylogenetic lineages of Bacteria and Archaea that are at present uncultured. In this study, the structure of the archaeal and bacterial communities was investigated in the surface and subsurface sediments of Jeju Island using a next-generation sequencing method. The microbial communities in the surface sediments were distinct from those in the subsurface sediments; the relative abundance of sequences for Thaumarchaeota, Actinobacteria, Bacteroides, Alphaproteobacteria, and Gammaproteobacteria were higher in the surface than subsurface sediments, whereas the sequences for Euryarchaeota, Acidobacteria, Firmicutes, and Deltaproteobacteria were relatively more abundant in the subsurface than surface sediments. This study presents detailed characterization of the spatial distribution of benthic microbial communities of Jeju Island and provides fundamental information on the potential interactions mediated by microorganisms with the different biogeochemical cycles in coastal sediments.

• Journal of Microbiology
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• 제37권1호
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• pp.1-9
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• 1999

The Biolog redox technology was carried out for evaluation of acidification effect on microbial communities at each stage of pH gradient microcosm. While the number of heterotrophic bacterial population and activities of extracellular enzyme decreased as the pH decreased, the number of total bacteria in the microcosm was not affected. The average color development of sample at each pH-gradient showed a sigmoidal curve, and at higher pH, more overall color development appeared in Biolog plates. Average color development value in Biolog plates was stabilized at 50 hours as an optimum incubation time. The color production in the Biolog plates was caused by cell density at above pH 5.0, but by cell activity below pH 4.0. Principal component analysis of color responses revealed distinctive patterns among the pH-gradient microcosm samples.

• Journal of Microbiology and Biotechnology
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• 제28권6호
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• pp.976-986
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• 2018

Knowledge about the gut bacterial communities associated with insects is essential to understand their roles in the physiology of the host. In the present study, the gut bacterial communities of a laboratory-reared insecticide-susceptible (IS), and a field-collected insecticide-resistant (IR) population of a major rice pest, the brown planthopper Nilaparvata lugens, were evaluated. The deep-sequencing analysis of the V3 hypervariable region of the 16S rRNA gene was performed using Illumina and the sequence data were processed using QIIME. The toxicological bioassays showed that compared with the IS population, IR population exhibited 7.9-, 6.7-, 14.8-, and 18.7-fold resistance to acephate, imidacloprid, thiamethoxam, and buprofezin, respectively. The analysis of the alpha diversity indicated a higher bacterial diversity and richness associated with the IR population. The dominant phylum in the IS population was Proteobacteria (99.86%), whereas the IR population consisted of Firmicutes (46.06%), followed by Bacteroidetes (30.8%) and Proteobacteria (15.49%). Morganella, Weissella, and Enterococcus were among the genera shared between the two populations and might form the core bacteria associated with N. lugens. The taxonomic-to-phenotypic mapping revealed the presence of ammonia oxidizers, nitrogen fixers, sulfur oxidizers and reducers, xylan degraders, and aromatic hydrocarbon degraders in the metagenome of N. lugens. Interestingly, the IR population was found to be enriched with bacteria involved in detoxification functions. The results obtained in this study provide a basis for future studies elucidating the roles of the gut bacteria in the insecticide resistance-associated symbiotic relationship and on the design of novel strategies for the management of N. lugens.

• Journal of Microbiology and Biotechnology
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• 제21권4호
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• pp.333-340
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• 2011

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P<0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.

• Journal of Microbiology and Biotechnology
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• 제26권7호
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• pp.1320-1332
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• 2016

Light hydrocarbons accumulated in subsurface soil by long-term microseepage could favor the anomalous growth of indigenous hydrocarbon-oxidizing microorganisms, which could be crucial indicators of underlying petroleum reservoirs. Here, Illumina MiSeq sequencing of the 16S rRNA gene was conducted to determine the bacterial community structures in soil samples collected from three typical oil and gas fields at different locations in China. Incubation with n-butane at the laboratory scale was performed to confirm the presence of "universal microbes" in light-hydrocarbon microseepage ecosystems. The results indicated significantly higher bacterial diversity in next-to-well samples compared with background samples at two of the three sites, which were notably different to oil-contaminated environments. Variation partitioning analysis showed that the bacterial community structures above the oil and gas fields at the scale of the present study were shaped mainly by environmental parameters, and geographic location was able to explain only 7.05% of the variation independently. The linear discriminant analysis effect size method revealed that the oil and gas fields significantly favored the growth of Mycobacterium, Flavobacterium, and Pseudomonas, as well as other related bacteria. The relative abundance of Mycobacterium and Pseudomonas increased notably after n-butane cultivation, which highlighted their potential as biomarkers of underlying oil deposits. This work contributes to a broader perspective on the bacterial community structures shaped by long-term light-hydrocarbon microseepage and proposes relatively universal indicators, providing an additional resource for the improvement of microbial prospecting of oil and gas.

• 한국물환경학회지
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• 제23권5호
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• pp.676-682
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• 2007

The bacterial number, extracellular enzyme activities and structure of bacterial community which are major constituent of aquatic ecosystem within the artificial vegetation island (AVI) were compared to those of the nearby pelagic lake waters in order to evaluate the possibility of the AVI as a eco-technological measure for water quality improvement and restoration of littoral zone in man-made reservoirs. There was not a significant difference in the total number of bacteria, but the number of active (viable) bacteria within the AVI was about 0.7 to 4.1 times higher than nearby pelagic lake water. The ratio of the number of active bacteria versus the total number of bacteria was also higher in the AVI than nearby pelagic lake water. The activities of ${\beta}$-glucosidase and phosphatase were 1.0 to 13.1 and 0.8 to 7.3 times higher respectively in the AVI than nearby pelagic lake water, showing that microorganisms were more active within the AVI. The bacterial communities of the two waters, examined by FISH method, did not indicate a clear difference in the springtime when the growth of macrophytes was immature, but during summer and fall it showed a clear difference indicating the formation of distinct bacterial community within the AVI compared to nearby lake water. From the results of this study, we conclude that AVI can contribute to make up the littoral ecosystem which show rapid cycling of matters through active detritus food chain in the dam reservoirs which have unstable aquatic ecosystem due to short hydraulic residence time and to strengthen the self-purification capacity of the lake.

• Journal of Ecology and Environment
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• 제31권4호
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• pp.309-316
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• 2008

To develop a monitoring method for soil microbial communities in rice paddy fields, we used terminal restriction fragment length polymorphism (T-RFLP) to compare soil bacterial community structure in rice paddy fields experiencing different management practices: organic practices, conventional practices without a winter barley rotation, and conventional practices with a winter barley rotation. Restriction fragment length profiles from soils farmed using organic practices showed very different patterns from those from conventional practices with and without barley rotation. In principal component analyses, restriction fragment profiles in organic practice samples were clearly separated from those in conventional practice samples, while principal component analysis did not show a clear separation for soils farmed using conventional practices with and without barley rotation. The cluster analysis showed that the bacterial species compositions of soils under organic practices were significantly different from those under conventional practices at the 95% level, but soils under conventional practice with and without barley rotation did not significantly differ. Although the loadings from principal component analyses and the Ribosomal DNA Project II databases suggested candidate species important for soils under organic farming practices, it was very difficult to get detailed bacterial species information from terminal restriction fragment length polymorphism. Rank-abundance diagrams and diversity indices showed that restriction fragment peaks under organic farming showed high Pielou's Evenness Index and the reciprocal of Simpson Index suggesting high bacterial diversity in organically farmed soils.