Summary
Soil is a complex and dynamic biological system, and still in 2003 it is difficult to determine the composition of microbial communities in soil. We are also limited in the determination of microbially mediated reactions because present assays for determining the overall rate of entire metabolic processes (such as respiration) or specific enzyme activities (such as urease, protease and phosphomonoesterase activity) do not allow any identification of the microbial species directly involved in the measured processes. The central problem posed by the link between microbial diversity and soil function is to understand the relations between genetic diversity and community structure and between community structure and function. A better understanding of the relations between microbial diversity and soil functions requires not only the use of more accurate assays for taxonomically and functionally characterizing DNA and RNA extracted from soil, but also high-resolution techniques with which to detect inactive and active microbial cells in the soil matrix.

Soil seems to be characterized by a redundancy of functions; for example, no relationship has been shown to exist between microbial diversity and decomposition of organic matter. Generally, a reduction in any group of species has little effect on overall processes in soil because other microorganisms can take on its function.

The determination of the composition of microbial communities in soil is not necessary for a better quantification of nutrient transformations. The holistic approach, based on the division of the systems in pools and the measurement of fluxes linking these pools, is the most efficient. The determination of microbial C, N, P and S contents by fumigation techniques has allowed a better quantification of nutrient dynamics in soil. However, further advances require determining new pools, such as active microbial biomass, also with molecular techniques. Recently investigators have separated 13C- and 12C-DNA, both extracted from soil treated with a 13C source, by density-gradient centrifugation. This technique should allow us to calculate the active microbial C pool by multiplying the ratio between labelled and total DNA by the microbial biomass C content of soil. In addition, the taxonomic and functional characterization of 13C-DNA allows us to understand more precisely the changes in the composition of microbial communities affected by the C-substrate added to soil.

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Microbial diversity and soil functions

https://biblio.ugent.be/publication/395350/file/1130210.pdf

Comparison of multiple methods for quantification of microbial biofilms grown in microtiter plates

Phytoremediation and rhizoremediation of organic soil contaminants : Potential and challenges

Remediation of soils contaminated with polycyclic aromatic hydrocarbons (PAHs).

On a role

Fluorescein diacetate (FDA) hydrolysis is widely accepted as an accurate and simple method for measuring total microbial activity in a range of environmental samples, including soils. Colourless fluorescein diacetate is hydrolysed by both free and membrane bound enzymes, releasing a coloured end product fluorescein which can be measured by spectrophotometry. The current method for measuring FDA hydrolysis in soils is limited in its application. FDA activity was very low in sandy and clayey soils. The low activity observed for these soil types was made difficult to measure by the original authors’ choice of solvent for terminating the hydrolysis reaction. Acetone (50% v/v) was found to be most efficient at stopping the hydrolysis reaction. During this study acetone (50% v/v) was found to cause a decrease of approximately 37% in the absorbance of fluorescein produced by the soil samples measured. Although this colour loss is independent of initial fluorescein concentration, it makes the measurement of FDA hydrolytic activity extremely difficult in soils with low microbial activity i.e. sandy and/or clayey soils. Chloroform/methanol (2:1 v/v) was found to successfully stop the hydrolysis reaction for up to 50 min in a range of soil samples without causing the loss of colour observed with acetone. By changing the solvent used for terminating the hydrolysis reaction, low activity soils could be measured successfully. Other parameters of the hydrolysis reaction were optimised for the measurement of soil samples including effect of pH, optimum temperature of incubation, amount of soil, time of incubation, amount of substrate and preparation of suitable standards. A new, more sensitive method is proposed adapted from the original method, which provides a more accurate determination of FDA hydrolysis in a wide range of soils.

/pdf/development-of-a-sensitive-and-rapid-method-for-the-cnbldelspv.pdf

Development of a sensitive and rapid method for the measurement of total microbial activity using fluorescein diacetate (FDA) in a range of soils

Influence of diesel fuel on seed germination

Effects of polycyclic aromatic hydrocarbons on germination and subsequent growth of grasses and legumes in freshly contaminated soil and soil with aged PAHs residues.

Herbicide safeners: uses, limitations, metabolism, and mechanisms of action.

It has been disputed whether, when potato starch gelatinises and absorbs water, it generates an osmotic or matric pressure that makes the potato cells become round and separate from one another. Starch suspensions heated at 100°C in dialysis bags absorbed water, suggesting that starch swelling pressure does exist. It was quantified by heating starch suspensions at 85°C in a chamber which absorbed water through a membrane and contained an argon bubble whose volume was measured. This gave starch swelling pressures around 100 kPa, increasing non-linearly with starch concentration. A comparable estimate (a few hundred kPa) of starch swelling pressure within cooked potato tissue was obtained from the fact that it largely prevented the tissue contraction expected due to loss of turgor pressure in the first 1.5 min of boiling. A slight expansion thereafter was attributed to the combined effect of starch swelling pressure and cell wall and middle lamella degradation.

Harry J. Duncan

Papers

Development of a sensitive and rapid method for the measurement of total microbial activity using fluorescein diacetate (FDA) in a range of soils

Influence of diesel fuel on seed germination

Effects of polycyclic aromatic hydrocarbons on germination and subsequent growth of grasses and legumes in freshly contaminated soil and soil with aged PAHs residues.

Herbicide safeners: uses, limitations, metabolism, and mechanisms of action.

The textural analysis of cooked potato. 2. Swelling pressure of starch during gelatinisation