Until recently, the common view of the terrestrial nitrogen cycle had been driven by two core assumptions—plants use only inorganic N and they compete poorly against soil microbes for N. Thus, plants were thought to use N that microbes “left over,” allowing the N cycle to be divided cleanly into two pieces—the microbial decomposition side and the plant uptake and use side. These were linked by the process of net mineralization. Over the last decade, research has changed these views. N cycling is now seen as being driven by the depolymerization of N-containing polymers by microbial (including mycorrhizal) extracellular enzymes. This releases organic N-containing monomers that may be used by either plants or microbes. However, a complete new conceptual model of the soil N cycle needs to incorporate recent research on plant–microbe competition and microsite processes to explain the dynamics of N across the wide range of N availability found in terrestrial ecosystems. We discuss the evolution of thinking abou...

Nitrogen mineralization: challenges of a changing paradigm

This review discusses the analysis of whole-community phospholipid fatty acid (PLFA) profiles and the composition of lipopolysaccharides in order to assess the microbial biomass and the community structure in soils. For the determination of soil microbial biomass a good correlation was obtained between the total amount of PLFAs and the microbial biomass measured with methods commonly used for determinations such as total adenylate content and substrate-induced respiration. Generally, after the application of multivariate statistical analyses, whole-community fatty acid profiles indicate which communities are similar or different. However, in most cases, the organisms accounting for similarity or difference cannot be determined, and therefore artefacts could not be excluded. The fatty acids used to determine the biomass vary from those which determine the community structure. Specific attention has to be paid when choosing extraction methods in order to avoid the liberation of fatty acids from non-living organic material and deposits, and to exclude the non-target selection of lipids from living organisms, as well. By excluding the fatty acids which were presumed to be common and widespread prior to multivariate statistical analysis, estimates were improved considerably. Results from principal component analysis showed that determining the levels of fatty acids present in both low and high concentrations is essential in order to correctly identify microorganisms and accurately classify them into taxonomically defined groups. The PLFA technique has been used to elucidate different strategies employed by microorganisms to adapt to changed environmental conditions under wide ranges of soil types, management practices, climatic origins and different perturbations. It has been proposed that the classification of PLFAs into a number of chemically different subgroups should simplify the evaluating procedure and improve the assessment of soil microbial communities, since then only the subgroups assumed to be involved in key processes would be investigated.

http://www.evisdom.com/pdf/1150507076.pdf

Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review

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

Total soil organic matter content is a key attribute of soil quality since it has far-reaching effects on soil physical, chemical, and biological properties. However, changes in contents of organic carbon (C) and total nitrogen (N) occur only slowly and do not provide an adequate indication of important short-term changes in soil organic matter quality that may be occurring. Labile organic matter pools can be considered as fine indicators of soil quality that influence soil function in specific ways and that are much more sensitive to changes in soil management practice. Particulate organic matter consists of partially decomposed plant litter, and it acts as a substrate and center for soil microbial activity, a short-term reservoir of nutrients, a food source for soil fauna and loci for formation of water stable macroaggregates. Dissolved (soluble) organic matter consists of organic compounds present in soil solution. This pool acts as a substrate for microbial activity, a primary source of mineralizable N, sulfur (S), and phosphorus (P), and its leaching greatly influences the nutrient and organic matter content and pH of groundwater. Various extractable organic matter fractions have also been suggested to be important, including hot water-extractable and dilute acid-extractable carbohydrates, which are involved in stabilization of soil aggregates, and permanganate-oxidizable C. Measurement of potentially mineralizable C and N represents a bioassay of labile organic matter using the indigenous microbial community to release labile organic fractions of C and N. Mineralizable N is also an important indicator of the capacity of the soil to supply N for crops. It is concluded that individual labile organic matter fractions are sensitive to changes in soil management and have specific effects on soil function. Together they reflect the diverse but central effects that organic matter has on soil properties and processes. (c) 2005 Elsevier Inc.

Labile Organic Matter Fractions as Central Components of the Quality of Agricultural Soils: An Overview

The effects of irrigation-induced salinity and sodicity on the size and activity of the soil microbial biomass in vertic soils on a Zimbabwean sugar estate were investigated. Furrow-irrigated fields were selected which had a gradient of salinity and sugarcane yield ranging from good cane growth at the upper ends to dead and dying cane at the lower ends. Soils were sampled under dead and dying cane, poor, satisfactory and good cane growth and from adjacent undisturbed sites under native vegetation. Electrical conductivity (EC) and sodium adsorption ratio (SAR) of saturation paste extracts was measured, as well as the exchangeable sodium percentage (ESP). There was a significant negative exponential relationship between EC and microbial biomass C, the percentage of organic C present as microbial biomass C, indices of microbial activity (arginine ammonification and fluorescein diacetate hydrolysis rates) and the activities of the exocellular enzymes beta-glucosidase, alkaline phosphatase and arylsulphatase but the negative relationships with SAR and ESP were best described by linear functions. By contrast, the metabolic quotient increased with increasing salinity and sodicity, exponentially with EC and linearly with SAR and ESP. Potentially mineralizable N, measured by aerobic incubation, was also negatively correlated with EC, SAR and ESP. These results indicate that increasing salinity and sodicity resulted in a progressively smaller, more stressed microbial community which was less metabolically efficient. The exponential relationships with EC demonstrate the highly detrimental effect that small increases in salinity had on the microbial community. It is concluded that agriculture-induced salinity and sodicity not only influences the chemical and physical characteristics of soils but also greatly affects soil microbial and biochemical properties. (C) 2003 Elsevier Science Ltd. All rights reserved.

Effects of irrigation-induced salinity and sodicity on soil microbial activity

(Chapter Headings): Introduction. Quality Control and Quality Assurance in Applied Soil Microbiology and Biochemistry. Soil Sampling, Handling, Storage, And Analysis. Enrichment, Isolation and Counting of Soil Microorganisms. Estimation of Microbial Activities. Anaerobic Microbial Activities in Soil. Enzyme Activities. Micorbial Biomass. Community Structure. Field Methods. Bioremediation of Soil. Subject Index.

Kassem Alef

Papers

Methods in Applied Soil Microbiology and Biochemistry