Sung-Cheol Koh

Paenibacillus yonginensis DCY84T induces changes in Arabidopsis thaliana gene expression against aluminum, drought, and salt stress

Current agricultural production methods, for example the improper use of chemical fertilizers and pesticides, create many health and environmental problems. Use of plant growth-promoting bacteria (PGPB) for agricultural benefits is increasing worldwide and also appears to be a trend for the future. There is possibility to develop microbial inoculants for use in agricultural biotechnology, based on these beneficial plant-microbe interactions. For this study, ten bacterial strains were isolated from Yongin forest soil for which in vitro plant-growth promoting trait screenings, such as indole acetic acid (IAA) production, a phosphate solubilization test, and a siderophore production test were used to select two PGPB candidates. Arabidopsis thaliana plants were inoculated with Paenibacillus yonginensis DCY84(T) and Micrococcus yunnanensis PGPB7. Salt stress, drought stress and heavy metal (aluminum) stress challenges indicated that P. yonginensis DCY84(T)-inoculated plants were more resistant than control plants. AtRSA1, AtVQ9 and AtWRKY8 were used as the salinity responsive genes. The AtERD15, AtRAB18, and AtLT178 were selected to check A. thaliana responses to drought stress. Aluminum stress response was checked using AtAIP, AtALS3 and AtALMT1. The qRT-PCR results indicated that P. yonginensis DCY84(T) can promote plant tolerance against salt, drought, and aluminum stress. P. yonginensis DCY84(T) also showed positive results during in vitro compatibility testing and virulence assay against X. oryzae pv. oryzae Philippine race 6 (PXO99). Better germination rates and growth parameters were also recorded for the P. yonginensis DCY84(T) Chuchung cultivar rice seed which was grown on coastal soil collected from Suncheon. Based on these results, P. yonginensis DCY84(T) can be used as a promising PGPB isolate for crop improvement.

Full-scale biological treatment of tannery wastewater using the novel microbial consortium BM-S-1

In order to develop a more effective and eco-friendly treatment technology, a full-scale tannery wastewater treatment plant with a sludge digestion system was augmented with a novel microbial consortium (BM-S-1). The aim of this study was to determine if the BM-S-1 could successfully treat the tannery wastewater in a full-scale treatment system without chemical pretreatment and to investigate effect of the augmentation on sludge production. Chemical oxygen demand (COD), total nitrogen (TN), total phosphorus (TP), chromium (Cr) and mixed liquor suspended solids (MLSS) were measured to monitor treated water quality and treatment efficiency. Microbial community structures in the treatment were also examined using pyrosequencing analysis of 16S rRNA gene and quantitative PCR (qPCR) of the nitrous oxide reductase gene (nosZ). The removal efficiencies of COD, TN, TP, and Cr were estimated to be 98.3%, 98.6%, 93.6%, and 88.5%, respectively, while the system without a continuous augmentation was broken down. The pyrosequencing analysis showed Brachymonas denitrificans to be the most dominant microbial population in the buffering tank (B; 37.5%). Potential polymeric substance degraders (Clostridia), sulfate reducers (Desulfuromonas palmitatis), and sulfur oxidizers (uncultured Thiobacillus) were dominant in the sludge digestion (SD) tank. The denitrifiers assayed by nosZ qPCR were dominant in B and SD. These microbial communities appeared to play important roles in removing nutrients and odor, and reducing sludge in the wastewater treatment plant without chemical pretreatment.

An eco-friendly treatment of tannery wastewater using bioaugmentation with a novel microbial consortium

A novel microbial consortium (BM-S-1) enriched from natural soils was successfully used to treat tannery wastewater from leather manufacturing industries in Korea on a pilot scale. The objective of this study was to determine whether augmentation with a novel microbial consortium BM-S-1could successfully treat the recalcitrant wastewater without chemical pre-treatment in a tannery wastewater treatment system. Chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) were monitored for water quality. The microbial population dynamics were analyzed using pyrosequencing, and denitrifying bacteria were quantified using real-time PCR (RT-PCR). The removal efficiencies for COD, TN and TP were greater than 91%, 79%, and 90%, respectively. The dominant phyla in the buffering tank (B), primary aeration (PA), secondary aeration (SA) and sludge digestion tank (SD) were Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes and Deinococcus-Thermus. Cluster analysis based on the UniFrac distance of the species in the different stages showed that the PA is similar to the SA, whereas the B is similar to the SD. qPCR of the nosZ genes showed the highest abundance of denitrifiers in B, which was increased 734-fold compared to the influent (I). It was hypothesized that anaerobic denitrifiers and the diverse microbial community may play important roles in the biological treatment of tannery wastewater. This technology may also contribute to the full-scale treatment of industrial wastewater containing food processing wastewater and marine sediment with high organic content.

Plant terpenes and lignin as natural cosubstrates in biodegradation of polyclorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs)

The objective of this minireview is to examine how cometabolic biodegradation of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) might be affected by plant terpenes and lignins as natural substrates abundant in nature. The topics covered, hence, are environmental significance of PCBs and PAHs, nature and distribution of plant terpenes and lignin, structural and metaoblic similarities of the natural compounds to PCBs and PAHs, and possible roles of the natural substrates in inducing the biodegradative pathways of PCBs and PAHs.

Implication of two glutathione S-transferases in the optimal metabolism of m-toluate by Sphingomonas yanoikuyae B1

A putative glutathione S-transferase (GST) gene (bphK) was identified in the meta-cleavage operon for the degradation of m-toluate by Sphingomonas yanoikuyae B1. Disruption of bphK resulted in the loss of GST activity against 1-chloro-2,4-dinitrobenzene and a much increased lag time of the mutant strain MB3 (bphK::Km) following subculture into m-toluate medium. In contrast, an increased lag time was not observed when MB3 was grown on biphenyl or m-xylene and MB3 showed normal growth on m-toluate when complemented with a subclone containing the bphK gene only. Furthermore, an additional GST activity was detected in MB3. The induction timing of this second GST activity coincided with the beginning of the exponential growth phase of MB3 on m-toluate, reached maximal activity within three hours, and then dropped sharply to the basal level. Thus, it is apparent that BphK and/or the second GST are necessary for optimal growth of B1 on m-toluate.

EFFECT OF DIAZINON ON BEHAVIOR OF JAPANESE MEDAKA (ORYZIAS LATIPES) AND GENE EXPRESSION OF TYROSINE HYDROXYLASE AS A BIOMARKER

This paper reports on the development of a biomarker used to monitor abnormal behaviors caused by diazinon in Japanese medaka (Oryzias latipes) as a model organism. Tyrosine hydroxylase (TH) activity in tissues was measured and the TH enzyme production in specific organs using a in situ cytochemical technique was monitored. These data were comparatively analyzed with those from semi-quantitative RT-PCR utilizing medaka TH gene that could be a potential biomarker for neuronal modulations and behaviors. For monitoring experiments at behavioral and molecular biological levels, the fish were treated under different sublethal conditions of diazinon (O, O-diethyl O-[6-methyl-2-(1-methylethyl)-4-pyrimidinyl] phosphorothioate) and their behavioral responses were observed. There were no significant differences in activity of TH head and body portions when the fish were exposed to lower concentrations (0.5–10 ppb) of diazinon including control treatment (0 ppb) for 24 hr. In temporal change of TH activity at 100 ppb diazinon treatment, however, the activity of body portion appeared to be inhibited during the first 30 min exposure but later seemed to recover slightly after 1 hr. TH appeared to be expressed mainly in the olfactory bulb, midbrain and brain stem regions as assessed by in situ immunohistochemistry. The treatment (1000 ppb) significantly suppressed TH protein production in the olfactory bulb, midbrain and brain stem regions. In kidney from the body portion the higher concentration treatment (1000 ppb) caused little suppression compared with the control. The RT-PCR showed that a production of TH mRNA transcript was significantly inhibited at 5 ppm diazinon treatment in the body portion. It was concluded that a suppression of TH activity would be one of the causes for the abnormal behaviors of the medaka that could be quantitatively monitored using an image processing system. This study provides molecular and neurobehavioral bases of a biomonitoring system for toxic chemicals using a model organism such as fish.

Specific biodegradation of polychlorinated biphenyls (PCBs) facilitated by plant terpenoids

The aim of this study was to examine how plant terpenoids, as natural growth substrates or inducers, would affect the biodegradation of PCB congeners. Various PCB degraders that could grow on biphenyl and several terpenoids were tested for their PCB degradation capabilities. Degradation activities of the PCB congeners, 4,4′-dichlorobiphenyl (4,4′-DCBp) and 2,2′-dichlorobiphenyl (2,2′-DCBp), were initially monitored through a resting cell assay technique that could detect their degradation products. The PCB degraders,Pseudomonas sp. P166 andRhodococcus sp. T104, were found to grow on both biphenyl and terpenoids ((S)-(−) limonene,p-cymene and α-terpinene) whereasArthrobacter sp. B1B could not grow on the terpenoids as a sole carbon source. The B1B strain grown on biphenyl exhibited good degradation activity for 4,4′-DCBp and 2,2′-DCBp, while the activity of strains P166 and T104 was about 25% that of the B1B strain, respectively. Concomitant GC analysis, however, demonstrated that strain T104, grown on (S)-(−) limonene,p-cymene and α-terpinene, could degrade 4,4′-DCBp up to 30%, equivalent to 50% of the biphenyl induction level. Moreover, strain T104 grown on (S)-(−) limonene, could also degrade 2,2′-DCBp up to 30%. This indicates that terpenoids, widely distributed in nature, could be utilized as both growth and/or inducer substrate(s) for PCB biodegradation in the environment.

Identification of potential biomarkers for diazinon exposure to Japanese Medaka (Oryzias latipes) using annealing control primers.

A new differential display-polymerase chain reaction (PCR) method based on annealing control primers was used to screen and identify potential biomarkers from differentially expressed genes (DEGs) in medaka exposed to sub-lethal concentration of diazinon (100 ppb). Among the differentially expressed genes identified, the majority were in functional categories of protein biosynthesis, transport and metabolism according to the gene ontology classification. The differential expression of ribosomal protein genes was quantified by real time PCR. The genes encoding ribosomal proteins including L3 and S17 were selected as potential biomarkers for diazinon exposure in medaka fish.

Visualizing the infection process of Xanthomonas campestris in cabbage using green fluorescent protein

The plant pathogen, Xanthomonas campestris NRRL B-1459 was chromosomally tagged with gfp, and the transformant, which was subjected to Southern hybridization showed the presence of gfp in the chromosome. The virulence-related gene of the transformant was not affected by the insertion of gfp. After inoculation into cabbage plants, the infection process was visually studied in planta. Using a fluorescence microscope, the migration and distribution of gfp-labelled bacteria was visualized in real time. As the gfp-labelled cells were easily visualized from the beginning of infection, we observed a time delay of 2 days between distribution of the Xanthomonas cells in cabbage plant and the appearance of visible necrosis.

Modeling of Recycling Oxic and Anoxic Treatment System for Swine Wastewater Using Neural Networks

A recycling reactor system operated under sequential anoxic and oxic conditions for the treatment of swine wastewater has been developed, in which piggery slurry is fermentatively and aerobically treated and then part of the effluent is recycled to the pigsty. This system significantly removes offensive smells (at both the pigsty and the treatment plant), BOD and others, and may be cost effective for small-scale farms. The most dominant heterotrophic were, in order,Alcaligenes faecalis, Brevundimonas diminuta andStreptococcus sp., while lactic acid bacteria were dominantly observed in the anoxic tank. We propose a novel monitoring system for a recycling piggery slurry treatment system through the use of neural networks. In this study, we tried to model the treatment process for each tank in the system (influent, fermentation, aeration, first sedimentation and fourth sedimentation tanks) based upon the population densities of the heterotrophic and lactic acid bacteria. Principal component analysis (PCA) was first applied to identify a relationship between input and output. The input would be microbial densities and the treatment parameters, such as population densities of heterotrophic and lactic acid bacteria, suspended solids (SS), COD, NH4+-N, or-tho-phosphorus (o-P), and total-phosphorus (T-P). Then multi-layer neural networks were employed to model the treatment process for each tank. PCA filtration of the input data as microbial densities was found to facilitate the modeling procedure for the system monitoring even with a relatively lower number of input. Neural networks independently trained for each treatment tank and their subsequent combined data analysis allowed a successful prediction of the treatment system for at least two days.