Soil microbial community analysis using denaturing gradient gel electrophoresis

The most biological diversity on this planet is probably harbored in soils. Understanding the diversity and function of the microbiological component of soil poses great challenges that are being overcome by the application of molecular biological approaches. This review covers one of many approaches being used: separation of polymerase chain reaction (PCR) amplicons using denaturing gradient gel electrophoresis (DGGE). Extraction of nucleic acids directly from soils allows the examination of a community without the limitation posed by cultivation. Polymerase chain reaction provides a means to increase the numbers of a target for its detection on gels. Using the rRNA genes as a target for PCR provides phylogenetic information on populations comprising communities. Fingerprints produced by this method have allowed spatial and temporal comparisons of soil communities within and between locations or among treatments. Numerous samples can be compared because of the rapid high throughput nature of this method. Scientists now have the means to begin addressing complex ecological questions about the spatial, temporal, and nutritional interactions faced by microbes in the soil environment.

Soil microbial community analysis using terminal restriction fragment length polymorphisms

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a polymerase chain reaction (PCR)-fingerprinting method that is commonly used for comparative microbial community analysis. The method can be used to analyze communities of bacteria, archaea, fungi, other phylogenetic groups or subgroups, as well as functional genes. The method is rapid, highly reproducible, and often yields a higher number of operational taxonomic units than other, commonly used PCR-fingerprinting methods. Sizing of terminal restriction fragments (T-RFs) can now be done using capillary sequencing technology allowing samples contained in 96- or 384-well plates to be sized in an overnight run. Many multivariate statistical approaches have been used to interpret and compare T-RFLP fingerprints derived from different communities. Detrended correspondence analysis and the additive main effects with multiplicative interaction model are particularly useful for revealing trends in T-RFLP data. Due to biases inherent in the method, linking the size of T-RFs derived from complex communities to existing sequence databases to infer their taxonomic position is not very robust. This approach has been used successfully, however, to identify and follow the dynamics of members within very simple or model communities. The T-RFLP approach has been used successfully to analyze the composition of microbial communities in soil, water, marine, and lacustrine sediments, biofilms, feces, in and on plant tissues, and in the digestive tracts of insects and mammals. The T-RFLP method is a user-friendly molecular approach to microbial community analysis that is adding significant information to studies of microbial populations in many environments.

Distribution characteristics of (CS)-C-137 in wind-eroded soil profile and its use in estimating wind erosion modulus

Due to its inert reaction in soil system and distinctive vertical distribution in soil profile, caesium-137 (Cs-137) has been used as a tracer to assess wind erosion. In this study, 62 soil samples were collected from 4 sampling sites in Taipusi County, Inner Mongolia; Caesium-137 activities for those soil samples were measured using a gamma-ray spectrometry in Sichuan University, Chengdu. Distribution pattern of Cs-137 in vertical soil profile was different for different land use and land cover types. Caesium-137 was distributed homogeneously in plow layer of cropland, and negatively exponential in low to medium cover grassland. Distribution pattern in high covered grassland was represented by a peak at 2-4 cm soil depth followed by a negative exponential curve. Based on those findings, simplified mass balance model was chosen to estimate the rate of wind erosion for cropland, while profile distribution model was used for grassland. Estimated wind erosion rates were 7990, 4270 and 1808 Mg(.)km(-2.)a(-1) for cropland, low cover grassland and medium cover grassland, respectively. Wind erosion intensity correlated negatively with plant cover.

The thermo-visco-plastic instability analysis of saturated soil

A theoretical analysis of instability of saturated soil is presented considering the simple shearing of a heat conducting thermo-visco-plastic material. It is shown that the instability is mainly the consequence of thermal softening which overcomes the strain hardening and the other type of instability is controlled by strain softening. The effects of other factors such as permeability to the instability are discussed in this paper.

On the shear instability of saturated soil

In this paper. the dynamic instability of simple shear of saturated soil is discussed. The governing equations are obtained based on mixture theory in which the inertia effect and the compressibility of grains are considered. Perturbation method is used to analyze and it is shown that two types of instability may exist. One of them is dominated by pore-pressure-softening, while the other by strain-softening.

An Analytical Solution for Three-Dimensional Diffraction of Plane P-Waves by a Hemispherical Alluvial Valley with Saturated Soil Deposits

An analytical solution for the three-dimensional scattering and diffraction of plane P-waves by a hemispherical alluvial valley with saturated soil deposits is developed by employing Fourier-Bessel series expansion technique. Unlike previous studies, in which the saturated soil deposits were simulated with the single-phase elastic theory, in this paper, they are simulated with Biot's dynamic theory for saturated porous media, and the half space is assumed as a single-phase elastic medium. The effects of the dimensionless frequency, the incidence angle of P-wave and the porosity of soil deposits on the surface displacement magnifications of the hemispherical alluvial valley are investigated. Numerical results show that the existence of a saturated hemispherical alluvial valley has much influence on the surface displacement magnifications. It is more reasonable to simulate soil deposits with Biot's dynamic theory when evaluating the displacement responses of a hemispherical alluvial valley with an incidence of P-waves.

Comparison of the Dynamic Response of a Saturated Soil Between Two Models

By comparing the dynamic responses of saturated soil to Biot's and Yamamoto's models, the properties of the two models have be pointed out. First of all, an analysis has been made for energy loss of each model from the basic equations. Then the damping of elastic waves in coarse sand and fine sand with loading frequency and soil's parameters have been calculated and the representation of viscous friction and Coulomb friction in the two models has been concluded. Finally, the variations of loading wave damping and stress phase angles with water depth and soil's parameters have been obtained as loading waves range in ocean waves.

Numerical Study on Rainfall Infiltration in Rock-Soil Blocks

A mathematical model for the rain infiltration in the rock-soil slop has been established and solved by using the finite element method. The unsteady water infiltrating process has been simulated to get water content both in the homogeneous and heterogeneous media. The simulated results show that the rock blocks in the rock-soil slop can cause the wetting front moving fast. If the rain intensity is increased, the saturated region will be formed quickly while other conditions are the same. If the rain intensity keeps a constant, it is possible to accelerate the generation of the saturated region by properly increasing the vertical filtration rate of the rock-soil slop. However, if the vertical filtration rate is so far greater than the rain intensity, it will be difficult to form the saturated region in the rock-soil slop. The numerical method was verified by comparing the calculation results with the field test data.

土壤传热特性的实验研究(Experimental Study of Soil Heat Diffusivity)

发展了测定实验室土样热扩散率的方法,介绍了研制的实验装置和建议的操作程序。给出的实验结果表明土壤热扩散率随土壤空隙率、含水量和温度等许多参数而变化。

The evolution of shear bands of saturated soil

The development of the shear bands of saturated soil in coupling-rate- and pore-pressure-dependent simple shear has been discussed, using a simple model and a matching technique at the moving boundary of a shear band. Tt is shown that the development of shear bands are dominated by the coupling-rate and pore-pressure effect of the material. The strength of the soil acts as a destabilizer, whilst pore pressure diffusion makes the band expand. The theory is discussed and some computational solutions have been presented.

Numerical Simulation of Gaseous Detonation of H_2-O_2 Mixture with Detailed Chemical Reaction Model

采用高精度的ENO格式和基于基元化学反应的真实化学反应模型求解氢氧混合气体一维爆轰波的精细结构。采用直接起爆方法得到稳定传播的爆轰波,计算的爆轰波阵面参数和实验相当符合。对爆轰波反应区化学反应的研究表明,参与反应的不同组分具有不同类型的变化特征。网格尺寸影响的研究表明,计算结果的精度随着网格尺寸的增加而增加,并能保持较好的收敛性。移动网格研究结果表明,网格运动速度和爆轰速度接近时,两者的相互作用对计算结果产生一定影响。