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.

Burrowing rodents as ecosystem engineers: the ecology and management of plateau zokors Myospalax fontanierii in alpine meadow ecosystems on the Tibetan Plateau

1. Plateau zokors, Myospalax fontanierii, are the only subterranean herbivores on the Tibetan plateau of China. Although the population biology of plateau zokors has been studied for many years, the interactions between zokors and plants, especially for the maintenance and structure of ecological communities, have been poorly recognized. In the past, plateau zokors have been traditionally viewed as pests, competitors with cattle, and agents of soil erosion, thus eradication programmes have been carried out by local governments and farmers. Zokors are also widely and heavily exploited for their use in traditional Chinese medicine.2. Like other fossorial animals, such as pocket gophers Geomys spp. and prairie dogs Cynomys spp. in similar ecosystems, zokors may act to increase local environmental heterogeneity at the landscape level, aid in the formation, aeration and mixing of soil, and enhance infiltration of water into the soil thus curtailing erosion. The changes that zokors cause in the physical environment, vegetation and soil clearly affect the herbivore food web. Equally, plateau zokors also provide a significant food source for many avian and mammalian predators on the plateau. Zokor control leading to depletion of prey and secondary poisoning may therefore present problems for populations of numerous other animals.3. We highlight the important role plateau zokors play in the Tibetan plateau ecosystem. Plateau zokors should be managed in concert with other comprehensive rangeland treatments to ensure the ecological equilibrium and preservation of native biodiversity, as well as the long-term sustainable use of pastureland by domestic livestock.

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.

Wave-soil-pipe coupling effect on submarine pipeline on-bottom stability

Wave-soil-pipe coupling effect on the untrenched pipeline stability on sands is for the first time investigated experimentally. Tests are conducted in the U-shaped water tunnel, which generates an oscillatory how, simulating the water particle movements with periodically changing direction under the wave action. Characteristic times and phases during the instability process are revealed. Linear relationship between Froude number and non-dimensional pipe weight is obtained. Effects of initial embedment and loading history are observed. Test results between the wavesoil-pipe interaction and pipe-soil interaction under cyclic mechanical loading are compared. The mechanism is briefly discussed. For applying in the practical design, more extensive and systematic investigations are needed.

Experimental study on pore pressure in rock-soil slope during reservoir water level fluctuation

A test system was developed for measuring the pore pressure in porous media, and a new model was devised for the pore pressure testing in both saturated and unsaturated rock-soil. Laboratory experiments were carried out to determine the pore pressure during water level fluctuation. The variations of transient pore pressure vs. time at different locations of the simulated rock-soil system were acquired and processed, and meanwhile the deformation and failure of the model are observed. The experiment results show that whether the porous media are saturated or not, the transient pore pressure is mainly dependent on the water level fluctuation, and coupled with the variation of the stress field.