• Korean Journal of Microbiology
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• v.38 no.3
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• pp.192-197
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• 2002

Fluorescent in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes was used to compare the community structures of free-living and aggregated bacteria at thawing period in Lake Baikal. Targeted groups were Eubacteria, $\alpha$-, $\beta$-, $\gamma$- proteobacteria groups, Cytophaga-Flavobacterium group and Planctomycetales. Total bacterial numbers of free-living bacteria were ranged from $0.2{\times}10^6\cells{\cdot}ml^-1$ to $3.2{\times}10^6\cells{\cdot}ml^-1$, which were decreasing with depth, while the aggregated bacterial numbers were dramatically increasing from $0.4{\times}10^4 to 3.3{\times}10^4 \cells{\cdot}ml^-1$ with depth. The ratios of EUB probe binding cells to DAPI counts were ranged from 52.3 to 74.1% in free-living bacteria, and from 39.6 to 66.7% in the aggregated bacteria, respectively. Community structures of the aggregated bacteria were very different from each free-living bacteria at every depth. At 25 m depth, where the chlorophyll a concentration was highest, both structures were quite different from those of surface layers, rendering the fact that the community structures might be affected by phytoplankton. The vertical profile of community structure of aggregated bacteria is particular. The proportion of $\beta$-proteobacteria group was increasing with depth and it was 51.8% at 100 m, but the dominant group was $\gamma$-pro-teobacteria group at 250 m. Taken together, the biodiversity and succession of aggregated bacteria are quite different from free-living bacteria.

• Journal of Microbiology
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• v.42 no.4
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• pp.357-360
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• 2004

For determining the process of bacterial aggregation, glucose was added into water from Lake Baikal which had been stored for seven months. In the presence of a higher concentration of glucose, the abun­dance of single bacteria and aggregates were higher, but the biovolumes of both bacteria were similar. Theses results mean that both free-living and aggregated bacteria have similar maximum sizes and that aggregates are forming with available organic materials. With available organic materials, the biovol­ume of aggregates becomes larger.

• Korean Journal of Microbiology
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• v.36 no.4
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• pp.292-298
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• 2000

For scrutinizing the changes of aggregated bacteria in Lake Paldang, the FISH method was applied by using the rhodamine labeled probes, and total bacteria, chloropyll a concentrations and nutrients concentrations were measured. The aggregates were collected with sediment traps. The T-N, T-P, chlorophyll a concentrations of aggregates were higher 5-15 times, 81-140 and 49-66 times than water samples, respectively. Also, the bacterial numbers of aggregates were 200 times higher than those of water smaples. The ratios of each groups of water sample were 2.1-7.4% for $\alpha$-group, 4.5-8.3% for $\beta$-group, 2.1-7.4% for $\gamma$-group, 2.1-6.1% for Cytophaga-Flavobacterium group and 0.1-2.5% for 'other'group, respectively. While, in aggregates, the ratios of $\alpha$-, $\beta$-, $\gamma$- and Cytophaga-Flavobacterium groups were very small and most abundant group was 'other' bacteria. With these results, the aggregated bacteria in Lake Paldang had a particular group composition of bacteria.

• Journal of Photoscience
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• v.9 no.2
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• pp.347-349
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• 2002

Synthetic zinc chlorins possessing a hydrophylic polyoxyethylene chain at the 17 -position were prepared. An amphiphilic zinc chlorin possessing a single chIorin moiety showed absorption maxima at 675 nm in an aqueous medium, indicating that the zinc chIorin did not form large aggregates but a dimeric structure. In contrast, amphiphilic zinc chlorin dyads in which two zinc chlorin moieties were connected with a hydrophilic polyoxyethylene linkage showed red-shifted absorption band around 720-740 nm in an aqueous medium. The result indicated that the amphiphilic zinc chlorin dyad self-aggregated to form chlorosome-like oligomer.

• ALGAE
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• v.21 no.2
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• pp.235-243
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• 2006

Benthic sediment samples ranging from poorly aggregated sand to complex, stratified mats were collected from six hypersaline ponds from March and July 1995 in the British Virgin Islands. Assemblages were analyzed with respect to species composition and abundance within visibly distinct layers in each mat sample. In individual ponds there was no apparent association between changing depth and the development of the benthic mats. Some species were present in all samples (e.g. Oscillatoria sp.) while others were restricted to single sites (e.g. Johannesbaptistia pellucida). Primary species included Microcoleus chthonoplastes, Phormidium spp., Coccochloris stagnina, and purple sulfur bacteria. Quantitative analysis of community structure included cluster and principal component analysis. Samples from individual ponds were often clustered; however, this was subject to seasonal variation. Mats collected in March were generally thicker and contained more layers than those in July. Variation among sites was not explained by the measured variation in environmental factors such as average pond salinity, depth, and oxygen concentration (mg/L). This study provides a detailed analysis of mat communities in hypersaline ponds and compares them with similar mat communities from other areas.

• Journal of Photoscience
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• v.9 no.2
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• pp.66-69
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• 2002

Zinc chlorin 1 possessing tertiary 3$^1$_hydroxy and 13$^1$-oxo groups was synthesized as a model for the antenna chlorophylls of photosynthetic green bacteria. Self-aggregation of 1 in nonpolar organic solvents was examined and compared to 2 and 3 possessing a secondary and primary 3$^1$_hydroxy group, respectively. Zinc chlorin 1 self-aggregated in I％(v/v) CH$_2$Cl$_2$-hexane to form oligomers and showed a red-shifted Qy maximum at 704 nm compared to the monomer (648 nm in CH$_2$CI2$_2$). This red-shift is larger than that of 3$^1$S-2 (648 to 697 nm) and comparable to that of3$^1$R-2 (648 to 705 nm), but smaller than that of 1 (648 to 740 nm), indicating that while a single 3$^1$-methyl group (primary to secondary OH) suppressed tight and/or extended aggregation, the additional 3$^1$-methyl group (secondary to tertiary OH) did not further suppress aggregation. The relative stability of the aggregates was in the order 3> 3$^1$R-2∼ 1 > 3$^1$S-2 as determined by visible spectral analyses. Molecular modeling calculations on oligomers of zinc chlorins 1, 3$^1$ R-2 and 3 gave similar well-ordered energy-minimized structures, while 3 stacked more tightly than 3$^1$ R- 2 and 1. In contrast, 3$^1$S-2 gave a relatively disordered (twisted) structure. The calculated oligomeric structures could explain the visible spectral data of 1-3 in nonpolar organic solvents. Moreover, self- aggregation of synthetic zinc 13$^1$_oxo-hlorins 4-6 possessing a 2-hydroxyethyl, 3-hydroxypropyl and 3- hydroxy-I-propenyl group at the 3-position in nonpolar organic solvents was discussed.

• The Plant Pathology Journal
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• v.29 no.4
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• pp.374-385
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• 2013

Environmental stresses induce several plant pathogenic bacteria into a viable but nonculturable (VBNC) state, but the basis for VBNC is largely uncharacterized. We investigated the physiology and morphology of the copper-induced VBNC state in the plant pathogen Ralstonia solanacearum in liquid microcosm. Supplementation of $200{\mu}M$ copper sulfate to the liquid microcosm completely suppressed bacterial colony formation on culture media; however, LIVE/DEAD BacLight bacterial viability staining showed that the bacterial cells maintained viability, and that the viable cells contain higher level of DNA. Based on electron microscopic observations, the bacterial cells in the VBNC state were unchanged in size, but heavily aggregated and surrounded by an unknown extracellular material. Cellular ribosome contents, however, were less, resulting in a reduction of the total RNA in VBNC cells. Proteome comparison and reverse transcription PCR analysis showed that the Dps protein production was up-regulated at the transcriptional level and that 2 catalases/peroxidases were present at lower level in VBNC cells. Cell aggregation and elevated levels of Dps protein are typical oxidative stress responses. $H_2O_2$ levels also increased in VBNC cells, which could result if catalase/peroxidase levels are reduced. Some of phenotypic changes in VBNC cells of R. solanacearum could be an oxidative stress response due to $H_2O_2$ accumulation. This report is the first of the distinct phenotypic changes in cells of R. solanacearum in the VBNC state.

• Environmental Engineering Research
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• v.11 no.3
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• pp.127-133
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• 2006

Aerobic floc-like sludge was formed in a batch reactor and the effect of cations on the formation of aerobic floc-like sludge was studied. In order to enhance the formation (rate) of aerobic floc-like sludge, cations such as $K^+$, $Na^+$, $Ca^{2+}$, and $Mg^{2+}$ were added to the seed sludge. It was found that $Ca^{2+}$ had positive effect on the formation of floc-like sludge, as measured by sludge volume index (SVI) for settle ability. The formation of floc-like sludge was confirmed by the microscopic observation after DAPI staining. The scattered forms of sludge samples at the initial stage became aggregated to form floes after $Ca^{2+}$ addition. To ensure the functions of sludge floes in a treatment plant, the gradient of ionic species around the surfaces of floc-like sludge was monitored by ion selective microelectrodes for ${NH_4}^+,\;{NO_3}^-$, and pH. The effective concentration of $Ca^{2+}$ ion to form floc-like sludge was determined to be 750 mg/L (0.15 mg $Ca^{2+}/mg$ MLSS). Under the effective $Ca^{2+}$ condition, the SVI value was the lowest and large distribution of nitrifying bacteria at the outer surface was observed in the aerobic floc-like sludge. From the results, it was found that the calcium ion functioned as an agent for the formation of aerobic floc-like sludge, resulting in the enhanced nitrification.

• Journal of the Korea Organic Resources Recycling Association
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• v.32 no.2
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• pp.27-35
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• 2024

It was known that crude oil can be mainly divided into saturates, aromatics, resins, and asphaltenes. If microbial biodegradation of asphaltenes is effectively viable, additional oil production will be expected from depleted oil reservoir. Meanwhile, biodegradation can be applied to other aspects, such as the bioremediation of spilled oil. In this case, the biodegradation of asphaltenes also plays an important role. It has been already reported that asphaltenes are decomposed by bacterial consortia. However, the biodegradation mechanism of asphaltenes has not been clearly presented. The major reason is that the molecular structure of asphaltenes is complicated and is mainly in a aggregated form. In this paper, it was presumed that the biodegradation process of asphaltenes may follow the microbial oxidation mechanism of saturates and aromatics which are easier biodegradable than asphaltenes among the crude oil components. In other words, the biodegradation process was explained by serial stages; the contact between asphaltenes and bacteria in the presence of biosurfactants, and the decomposition of alkyl groups and fused-rings within the asphaltene structure.

• The Plant Pathology Journal
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• v.34 no.5
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• pp.381-392
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• 2018

Clavibacter michiganensis subsp. michiganesis (Cmm) is a quarantine-worthy pest in $M{\acute{e}}xico$. The implementation and validation of new technologies is necessary to reduce the time for bacterial detection in laboratory conditions and Raman spectroscopy is an ambitious technology that has all of the features needed to characterize and identify bacteria. Under controlled conditions a contagion process was induced with Cmm, the disease epidemiology was monitored. Micro-Raman spectroscopy ($532nm\;{\lambda}$ laser) technique was evaluated its performance at assisting on Cmm detection through its characteristic Raman spectrum fingerprint. Our experiment was conducted with tomato plants in a completely randomized block experimental design (13 plants ${\times}$ 4 rows). The Cmm infection was confirmed by 16S rDNA and plants showed symptoms from 48 to 72 h after inoculation, the evolution of the incidence and severity on plant population varied over time and it kept an aggregated spatial pattern. The contagion process reached 79% just 24 days after the epidemic was induced. Micro-Raman spectroscopy proved its speed, efficiency and usefulness as a non-destructive method for the preliminary detection of Cmm. Carotenoid specific bands with wavelengths at 1146 and $1510cm^{-1}$ were the distinguishable markers. Chemometric analyses showed the best performance by the implementation of PCA-LDA supervised classification algorithms applied over Raman spectrum data with 100% of performance in metrics of classifiers (sensitivity, specificity, accuracy, negative and positive predictive value) that allowed us to differentiate Cmm from other endophytic bacteria (Bacillus and Pantoea). The unsupervised KMeans algorithm showed good performance (100, 96, 98, 91 y 100%, respectively).