• Korean Journal of Environmental Agriculture
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• v.38 no.2
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• pp.76-82
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• 2019

BACKGROUND: For sustainable agriculture, there are various agricultural practices including low input. Over the last few decades high input of chemical fertilizer and compounds results in environmental pollution and deterioration of soil fertility. Soybean (Glycine max L.) is well known eco-friendly crop due to their symbionts. Soybean has a relationship with nitrogen fixation bacteria called rhizobia. In this research work, we investigated effects of soybean cultivation on soil microorganism activities. METHODS AND RESULTS: Experiments were conducted in pots and potato cultivation was used as reference. Soil chemical properties were analyzed considering soil nutrient over cropping period. For the soil microbial community analysis, dehydrogenase activity analysis (DHA) analyzed along with denaturing gradient gel electrophoresis. The results showed that higher soil organic matter in the soybean cultivation soil than in the potato cultivation soil. Available $P_2O_5$ concentration increased gradually in both pots but showed higher value in the potato cultivation soil. DHA value implying microbial activities showed higher value in the soybean cultivation soil over all cropping period. CONCLUSION: The cause of high microbial activity in the soybean cultivation soil was considered to the effects of some specific microorganisms related to soybean cultivation. Therefore, the availability of soybean cultivation for sustainable agriculture should be encouraged in terms of microorganism community activity in soil.

• Journal of Soil and Groundwater Environment
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• v.11 no.3
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• pp.66-77
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• 2006

This review inquired the recently applied molecular biological and biochemical methods analyzing the microbial community structure of groundwater and, as a result, summarized the functional or taxonomic groups of active microorganisms with major contaminants in groundwater. The development of gene amplification through PCR has been possible to figure out microbial population and identification. Active microbial community structures have been analyzed using a variety of fingerprinting techniques such as DGGE, SSCP, RISA, and microarray and fatty acid analyses such as PLFA and FAME, and the activity of a specific strain has been examined using FISH. Also, this review included the dominant microflora in groundwater contaminated with fuel components such as n-alkanes, BTEX, MTBE, and ethanol and chlorinated compounds such as TCE, PCE, PCB, CE, carbon tetrachloride, and chlorobenzene.

• Journal of Environmental Science International
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• v.30 no.5
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• pp.379-389
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• 2021

Soil microorganism activity in an agricultural field is affected by various factors including climate conditions, soil chemical properties, and crop cultivation. In this study, we elucidate the correlation between microorganism activity and agricultural environment factors using the dehydrogenase activity (DHA) value, which is one of the indicators of soil microbial activity. As a result, the various factors noted above were related to the DHA value. Annual rainfall, soil Mg2+, bacterial and fungal diversities, types of crops, developmental stages, seasons, and cultivation status were highly correlated with the DHA value. Furthermore, next-generation sequencing (NGS) analysis was used to identify that the type of crop affected soil microbial compositions of both bacteria and fungi. Soil used for soybean cultivation showed the highest relative abundance for Verrucomicrobia, Planctomycetes, and Acidobacteria but Actinobacteria and Firmicutes had the lowest relative abundance. In the case of soil used for potato cultivation, Actinobacteria had the highest relative abundance but Proteobacteria had the lowest relative abundance. Armatimonadetes showed the highest relative abundance in soil used for cabbage cultivation. Among the fungal communities, Mortierellomycota had the highest relative abundance for soybean cultivation but the lowest relative abundance for cabbage cultivation; further, Rozellomycota, Chytridiomycota, and Cercozoa had the highest relative abundance for cabbage cultivation. Basidiomycota had the highest relative abundance for potato cultivation but the lowest relative abundance for soybean cultivation.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2000.04a
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• pp.100-107
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• 2000

In a recently developed strategy for in-situ treatment of polychlorinated biphenyls (PCB), bioaugmentation was used in conjunction with a surfactant, sorbitan trioleate, as a carbon source for the degrader bacteria, along with the monoterpene, carvone, and salicylic acid as inducing substrates. Two bacteria were used for soil inoculants, including Arthrobacter sp. st. B1B and Ralstonia eutrophus H850. This methodology achieved 60% degradation of PCBs in Aroclor 1242 after 18 weeks in soils receiving 34 repeated applications of the degrader bacteria. However, an obvious limitation was the requirement for soil mixing after every soil inoculation. In the research reported here, bioaugmentation and biostimulation treatment strategies were modified by using the earthworm, Pheretima hawayana, as a vector for dispersal and mixing of surface-applied PCB-degrading bacteria and soil chemical amendments. Changes in microbial biomass and microbial community structure due to earthworm effects were examined using DNA extraction and PCR-DGGE of 16S rDNA. Results showed that earthworms effectively promoted biodegradation of PCBs in bioaugmented soils to the same extent previously achieved using physical soil mixing, and had a lesser, but significant effect in promoting PCB biodegradation in biostimulated soils treated with carvone and salicylic acid. The effects of earthworms were speculated to involve many interacting factors including increased bacterial transport to lower soil depths, improved soil aeration, and enhanced microbial activity and diversity.

• Journal of Korean Society on Water Environment
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• v.24 no.1
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• pp.19-29
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• 2008

Hot air sparging is a groundwater remediation technique, in which organic contaminants volatilized into hot air from the saturated to vadose zone. In the laboratory diesel (10,000 mg TPH/kg) was spiked in contaminated saturated aquifer soil. The hot air ($34.9{\pm}2.7^{\circ}C$) was injected in intermittent (Q=1,500 mL/min, 10 minute injection and 10 minute idle) modes. We performed microcosm tests using the groundwater samples to assess TPH reductive remediation activity. For Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis of eubacterial communities in sludge of wastewater treatment plants and soil of experiment site, the 16S rDNA was amplified by Polymerase Chain Reaction (PCR) from the sludge and the soil. The obtained 16S rDNA fragments were digested with Msp I and separated by electrophoresis gel. We found various sequence types for hot air sparging experiment with sludge soil samples that were closely related to Bacillus (149 bp, Firmicutes), Methlobacterium (149 bp, Euryarchaeotes), Pseudomonas (492 bp, ${\gamma}$-Proteobacteria), etc., in the clone library. In this study we find that TPH-water was reduced to 78.9% of the initial value in this experiment aquifer. The results of the present study suggests that T-RFLP method may be applied as a useful tool for the monitoring in the TPH contaminated soil fate of microorganisms in natural microbial community.

• Journal of Microbiology and Biotechnology
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• v.17 no.1
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• pp.67-73
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• 2007

The present study compared the microbial diversity and activity during the application of various bioremediation processes to crude oil-contaminated soil. Five different treatments, including natural attenuation (NA), biostimulation (BS), biosurfactant addition (BE), bioaugmentation (BA), and a combined treatment (CT) of biostimulation, biosurfactant addition, and bioaugmentation, were used to analyze the degradation rate and microbial communities. After 120 days, the level of remaining hydrocarbons after all the treatments was similar, however, the highest rate (k) of total petroleum hydrocarbon (TPH) degradation was observed with the CT treatment (P<0.05). The total bacterial counts increased during the first 2 weeks with all the treatments, and then remained stable. The bacterial communities and alkane monooxygenase gene fragment, alkB, were compared by denaturing gradient gel electrophoresis (DGGE). The DGGE analyses of the BA and CT treatments, which included Nocardia sp. H17-1, revealed a simple dominant population structure, compared with the other treatments. The Shannon-Weaver diversity index (H') and Simpson dominance index (D), calculated from the DGGE profiles using 16S rDNA, showed considerable qualitative differences in the community structure before and after the bioremediation treatment as well as between treatment conditions.

• Korean Journal of Medicinal Crop Science
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• v.24 no.4
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• pp.294-302
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• 2016

Background: Crop rotation plays an important role in improving soil chemical properties, minimizing the presence of disease pathogens, and assists in neutralizing autotoxic effects associated with allelochemicals. Methods and Results: Five rotation crops of sudan grass, soybean, peanut, sweet potato, and perilla were cultivated for one year with an aim to reduce yield losses caused by repeated cropping of ginseng. In 2-year-old ginseng grown in the same soil as a previous ginseng crop, stem length and leaf area were reduced by 30%, and root weight per plant was reduced by 56%. Crop rotation resulted in a significant decrease in electrical conductivity, $NO_3$, and $P_2O_5$ content of the soil, whereas organic matter, Ca, Mg, Fe, Cu, and Zn content remained-unchanged. Soil K content was increased following crop rotation with sudan grass and peanut only. Rotation with all alternate crops increased subsequent ginseng aerial plant biomass, whereas root weight per plant significantly increased following crop rotation with perilla only. A significant positive correlation was observed between root rot ration and soil K content, and a significant negative correlation was observed between ginseng root yield and the abundance of actinomycetes. Crop rotation affected the soil microbial community by increasing gram negative microbes, the ratio of aerobic microbes, and total microbial biomass whereas decreases were observed in actinomycetes and the ration of saturated fatty acids. Conclusions: In soil exhibiting crop failure following replanting, crop rotation for one year promoted both soil microbial activity and subsequent ginseng aerial plant biomass, but did not ameliorate the occurrence of root rot disease.

• Korean Journal of Organic Agriculture
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• v.27 no.4
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• pp.479-499
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• 2019

This study was conducted to investigate the responses of soil properties and microbial communities to different agricultural management and soil types, including organic management in Andisols (Org-A), organic management in Non-andisols (Org-NA), conventional management in Andisols (Con-A) and conventional management in Non-andisols (Con-NA) by using a pyrosequencing approach of 16S rRNA gene amplicon in Radish farms of volcanic ash soil in Jeju island. The results showed that agricultural management systems had a little influence on the soil chemical properties but had significant influence on microbial communities. In addition, soil types had significant influences on both the soil chemical properties and microbial communities. Organic farming increased the microbial density of bacteria and biomass C compared to conventional farming, regardless of soil types. Additionally, Org-NA had the highest dehydrogenase activity among treatments, whereas no difference was found between Org-A, Con-A and Con-NA and had the highest species richness (Chao 1) and diversity (Phyrogenetic diversity). Particularly, Chao 1 and Phyrogenetic diversity were increased in organic plots by 12% and 20%, compared with conventional plots, respectively. Also, regardless of agricultural management and soil types, Proteobacteria was the most abundant bacterial phylum, accounting for 21.9-25.9% of the bacterial 16S rRNAs. The relative abundance of putative copiotroph such as Firmicutes was highest in Org-NA plot by 21.0%, as follows Con-NA (13.1%), Con-A (6.7%) and Org-A (5.1%.), respectively and those of putative oligotrophs such as Acidobacteria and Planctomycetes were higher in Con-A than those in the other plots. Furthermore, LEfSe indicated that organic system enhanced the abundance of Fumicutes, while conventional system increased the abundance of Acidobacteria, especially in Non-andisols. Correlation analysis showed that total organic carbon (TOC) and nutrient levels (e.g. available P and exchangeable K) were significantly correlated to the structure of the microbial community and microbial activity. Overall, our results showed that the continuous organic farming systems without chemical materials, as well as the soil types made by long-term environmental factors might influence on soil properties and increase microbial abundances and diversity.

• Journal of Ginseng Research
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• v.40 no.2
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• pp.97-104
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• 2016

Background: Rhizobacteria play an important role in plant defense and could be promising sources of biocontrol agents. This study aimed to screen antagonistic bacteria and develop a biocontrol system for root rot complex of Panax notoginseng. Methods: Pure-culture methods were used to isolate bacteria from the rhizosphere soil of notoginseng plants. The identification of isolates was based on the analysis of 16S ribosomal RNA (rRNA) sequences. Results: A total of 279 bacteria were obtained from rhizosphere soils of healthy and root-rot notoginseng plants, and uncultivated soil. Among all the isolates, 88 showed antagonistic activity to at least one of three phytopathogenic fungi, Fusarium oxysporum, Fusarium solani, and Phoma herbarum mainly causing root rot disease of P. notoginseng. Based on the 16S rRNA sequencing, the antagonistic bacteria were characterized into four clusters, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetesi. The genus Bacillus was the most frequently isolated, and Bacillus siamensis (Hs02), Bacillus atrophaeus (Hs09) showed strong antagonistic activity to the three pathogens. The distribution pattern differed in soil types, genera Achromobacter, Acidovorax, Brevibacterium, Brevundimonas, Flavimonas, and Streptomyces were only found in rhizosphere of healthy plants, while Delftia, Leclercia, Brevibacillus, Microbacterium, Pantoea, Rhizobium, and Stenotrophomonas only exist in soil of diseased plant, and Acinetobacter only exist in uncultivated soil. Conclusion: The results suggest that diverse bacteria exist in the P. notoginseng rhizosphere soil, with differences in community in the same field, and antagonistic isolates may be good potential biological control agent for the notoginseng root-rot diseases caused by F. oxysporum, Fusarium solani, and Panax herbarum.

• Journal of Ecology and Environment
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• v.33 no.3
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• pp.261-270
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• 2010

Increasing atmospheric $CO_2$ affects the soil carbon cycle by influencing microbial activity and the carbon pool. In this study, the effects of elevated $CO_2$ on extracellular enzyme activities (EEA; ${\beta}$-glucosidase, N-acetylglucosaminidase, aminopeptidase) in salt marsh sediment vegetated with Suaeda japonica were assessed under ambient atmospheric $CO_2$ concentration (380 ppm) or elevated $CO_2$ concentration (760 ppm) conditions. Additionally, the community structure of sulfate-reducing bacteria (SRB) was analyzed via terminal restriction fragments length polymorphism (T-RFLP). Sediment with S. japonica samples were collected from the Hwangsando intertidal flat in May 2005, and placed in small pots (diameter 6 cm, height 10 cm). The pots were incubated for 60 days in a growth chamber under two different $CO_2$ concentration conditions. Sediment samples for all measurements were subdivided into two parts: surface (0-2 cm) and rhizome (4-6 cm) soils. No significant differences were detected in EEA with different $CO_2$ treatments in the surface and rhizome soils. However, the ratio of ${\beta}$-glucosidase activity to N-acetylglucosaminidase activity in rhizome soil was significantly lower (P < 0.01) at 760 ppm $CO_2$ than at 380 ppm $CO_2$, thereby suggesting that the contribution of fungi to the decomposition of soil organic matter might in some cases prove larger than that of bacteria. Community structures of SRB were separated according to different $CO_2$ treatments, suggesting that elevated $CO_2$ may affect the carbon and sulfur cycle in salt marshes.