• Environmental Analysis Health and Toxicology
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• v.25 no.1
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• pp.1-10
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• 2010

Monitoring toxicity levels in specific biological compartments is necessary to evaluate the ecotoxicological risk associated with soil environmental pollution. Gene expression, as potential biomarker, is increasingly used as rapid early warning systems in environmental monitoring and ecological risk assessment procedures. Various representative species are currently used for the purpose of assessing soil toxicity, however, investigations on toxicological assessments using endpoint based on gene-level have been limited. In this review, we will present the current trends in organisms and endpoints used in soil toxicity study and report gene expression related to toxicity using soil organism, and C. elegans as promising organisms for this approach.

• Proceedings of the Korean Geotechical Society Conference
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• 2005.03a
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• pp.338-345
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• 2005

Recently, surface-wave methods have been widely used for site investigation due to economic advantage and improved reliability. Specially, the Spectral-Analysis-of-Surface-Wave (SASW) method has been used to evaluate soil properties in geotechnical engineering. In determination of subgrade stiffness by SASW measurements, only the vertical Rayleigh waves have been used. This study proposed a framework to determine shear-wave velocity profiles by using vertical and horizontal Rayleigh waves and Love wave all together. In addition, the Common-Array-Profiling(CAP) SASW method was employed, which subgrade stiffness of profile the local material under two fixed receivers. The procedure proposed in this study was verified by comparing the shear-wave velocity profiles with the shear-wave velocity profiles of downhole testing at two geotechnical sites.

• Journal of Microbiology and Biotechnology
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• v.19 no.1
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• pp.51-54
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• 2009

Myxobacteria, Gram-negative soil bacteria, are a well-known producer of bioactive secondary metabolites. Therefore, this study presents a methodological approach for the high-throughput screening of secondary metabolites from 4 wild-type Myxococcus xanthus strains. First, electrospray ionization mass spectrometry (ESI-MS) was performed using extracellular crude extracts. As a result, 22 metabolite peaks were detected, and the metabolite profiling was then conducted using the m/z value, retention time, and MS/MS fragmentation pattern analyses. Among the peaks, one unknown compound peak was identified as analogous to the myxalamid A, B, and C series. An analysis of the tandem mass spectrometric fragmentation patterns and HR-MS identified myxalamid K as a new compound derived from M. xanthus. In conclusion, LC-MS/MS-based chemical screening of diverse secondary metabolites would appear to be an effective approach for discovering unknown microbial secondary metabolites.

• Korean Journal of Soil Science and Fertilizer
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• v.42 no.4
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• pp.307-316
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• 2009

Soil microbial activity and diversity are affected by organic sources applied to improve soil quality and fluctuate seasonally. We investigated the effects of municipal compost (MC), poultry litter (PL), and cover crops of spring oats and red clover (RC) on soil enzyme activities, and soil bacterial community-level physiological profiling (CLPP) in a Mexico silt loam in North Central Missouri, USA. Temporal patterns of these parameters were observed by periodic five soil sampling from spring to fall over a two year period. MC increased soil dehydrogenase (DH) activity consistently beginning about three months after MC application; fluorescein diacetate (FDA) hydrolytic activity significantly began to increase by the September of the first year but fluctuated during the following period. DH activity responded more directly to the amount or properties of organic residues in soils while FDA hydrolysis and CLPP were generally influenced by composition of organic sources, and enzyme activities and CLPP showed seasonal variation, which depended on organic sources and soil moisture. MC and cover crops may be useful organic sources for enhancing general soil microbial activity and altering soil microbial diversity, respectively. Because microbial activities and diversity are dynamic and subject to seasonal changes, the effects of organic amendments on these parameters should be investigated frequently during a growing season.

• Geophysics and Geophysical Exploration
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• v.13 no.1
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• pp.102-108
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• 2010

The internal structure of a river embankment must be delineated as part of investigations to evaluate its safety. Geophysical methods can be most effective means for that purpose, if they are used together with geotechnical methods such as the cone penetration test (CPT) and drilling. Since the dyke body and subsoil in general consist of material with a wide range of grain size, the properties and stratification of the soil must be accurately estimated to predict the mechanical stability and water infiltration in the river embankment. The strength and water content of the levee soil are also parameters required for such prediction. These parameters are usually estimated from CPT data, drilled core samples and laboratory tests. In this study we attempt to utilise geophysical data to estimate these parameters more effectively for very long river embankments. S-wave velocity and resistivity of the levee soils obtained with geophysical surveys are used to classify the soils. The classification is based on a physical soil model, called the unconsolidated sand model. Using this model, a soil profile along the river embankment is constructed from S-wave velocity and resistivity profiles. The soil profile thus obtained has been verified by geotechnical logs, which proves its usefulness for investigation of a river embankment.

• Korean Journal of Soil Science and Fertilizer
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• v.49 no.2
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• pp.144-156
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• 2016

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

• Geomechanics and Engineering
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• v.7 no.4
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• pp.459-475
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• 2014

In this study, a CPT-based p-y analysis method was proposed for the displacement analysis of laterally loaded piles. Key consideration was the continuous soil profiling capability of CPT and cone resistance profiles that do not require artificial assumption or simplification for input parameter selection. The focus is on the application into offshore mono-piles embedded in clays. The correlations of p-y function components to the effective cone resistance were proposed, which can fully utilize CPT measurements. A case example was selected from the literature and used to validate the proposed method. Various parametric studies were performed to examine the effectiveness of the proposed method and investigate the effect of property profile and its depth resolution on the p-y analysis. It was found that the calculation could be largely misleading if wrongly interpreted sub-layer condition or inappropriate resolution of input soil profile was involved in the analyses. It was also found that there is a significant influence depth that dominates overall load response of pile. The soil profile and properties within this depth range affect most significantly calculated load responses, confirming that the soil profile within this depth range should be identified in more detail.

• Journal of Microbiology and Biotechnology
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• v.17 no.4
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• pp.560-570
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• 2007

The effective and accurate assessment of the total microbial community diversity is one of the primary challenges in modem microbial ecology, especially for the detection and characterization of unculturable populations and populations with a low abundance. Accordingly, this study was undertaken to investigate the diversity of the microbial community during the biodegradation of cis- and trans-dichloroethenes in soil and wastewater enrichment cultures. Community profiling using PCR targeting the l6S rRNA gene and denaturing gradient gel electrophoresis (PCR-DGGE) revealed an alteration in the bacterial community profiles with time. Exposure to cis- and trans-dichloroethenes led to the disappearance of certain genospecies that were initially observed in the untreated samples. A cluster analysis of the bacterial DGGE community profiles at various sampling times during the degradation process indicated that the community profile became stable after day 10 of the enrichment. DNA sequencing and phylogenetic analysis of selected DGGE bands revealed that the genera Acinetobacter, Pseudomonas, Bacillus, Comamonas, and Arthrobacter, plus several other important uncultured bacterial phylotypes, dominated the enrichment cultures. Thus, the identified dominant phylotypes may play an important role in the degradation of cis- and trans-dichloroethenes.

• Journal of Microbiology and Biotechnology
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• v.17 no.5
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• pp.784-791
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• 2007

The present work aims to use a biofilter technology(aerated submerged filters) for the aerobic transformation at laboratory-scale of olive washing water(OWW) generated in the first steps of olive oil processing, as well as the genetic profiling and identification to the species level of the bacteria involved in the formation of the biofilm, by means of TGGE. Chemical parameters, such as biological oxygen demand at five days($BOD_5$) and chemical oxygen demand(COD), decreased markedly(up to 90 and 85%, respectively) by the biological treatment, and the efficiency of the process was significantly affected by aeration and inlet flow rates. The total polyphenol content of inlet OWW was only moderately reduced(around 50% decrease of the inlet content) after the biofilter treatment, under the conditions tested. Partial 16S rRNA genes were amplified using total DNA extracted from the biofilm and separated by TGGE. Sequences of isolated bands were mostly affiliated to the $\alpha-subclass$ of Proteobacteria, and often branched in the periphery of bacteria] genera commonly present in soil(Rhizobium, Reichenowia, Agrobacterium, and Sphingomonas). The data obtained by the experimentation at laboratory scale provided results that support the suitability of the submerged filter technology for the treatment of olive washing waters with the purpose of its reutilization.

• Geomechanics and Engineering
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• v.9 no.3
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• pp.313-328
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• 2015

In the present study, a CPT-based p-y analysis method was proposed for offshore mono-piles embedded in sands. Static and cyclic loading conditions were both taken into account for the proposed method. The continuous soil profiling capability of CPT was an important consideration for the proposed method, where detailed soil profile condition with depth can be readily incorporated into the analysis. The hyperbolic function was adopted to describe the non-linear p-y curves. For the proposed hyperbolic p-y relationship, the ultimate lateral soil resistance $p_u$ was given as a function of the cone resistance, which is directly introduced into the analysis as an input data. For cyclic loading condition, two different cyclic modification factors were considered and compared. Case examples were selected to check the validity of the proposed CPT-based method. Calculated lateral displacements and bending moments from the proposed method were in good agreement with measured results for lateral displacement and bending moment profiles. It was observed the accuracy of calculated results for the conventional approach was largely dependent on the selection of friction angle that is to be adopted into the analysis.