An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats The extent of the diversity of microorganisms in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microorganisms is involved in important soil functions This review focuses on recent data relating how plant type, soil type, and soil management regime affect the microbial diversity of soil and the implication for the soil's disease suppressiveness The two main drivers of soil microbial community structure, ie, plant type and soil type, are thought to exert their function in a complex manner We propose that the fact that in some situations the soil and in others the plant type is the key factor determining soil microbial diversity is related to the complexity of the microbial interactions in soil, including interactions between microorganisms and soil and microorganisms and plants A conceptual framework, based on the relative strengths of the shaping forces exerted by plant and soil versus the ecological behavior of microorganisms, is proposed

Microbial diversity in soil: Selection of microbial populations by plant and soil type and implications for disease suppressiveness

Soil is a component of primary importance in crop production, even if it is often neglected, or only regarded as a physical support for the growth of plants. However, with the increasing societal concerns for the sustainability of agriculture, soil must be considered as a living system. Its quality results from the multiple interactions among physicochemical and biological components, notably the microbial communities, primordial for soil function. Crops are threatened by soil-borne diseases. These are often difficult to control, because of the “hidden” status of the pathogens and also because of the absence, noxiousness or lack of efficacy of chemical treatments. In this context, there is a renewed interest for cultural practices such as the use of organic amendments. These practices have a strong influence on soil health, which takes into account plant health, through both changes of physicochemical characteristics and influence on soil microbial communities. Cultural practices are used to improve soil health, and can, in some cases, increase soil disease suppression. The effects of these practices on soil properties have been studied, but the relationship between these properties and soil suppressiveness has not been always very clear. Many different soil descriptors, either abiotic or biotic, have been used to describe the soil health and suppressiveness, but there is a lack of identified, reliable and consistent indicators. One aim of this review is to show that, despite the age of the soil health concept and all the studies that have been conducted, there are still no guidelines for assessment of soil quality from the plant health point of view. Obviously, the extreme diversity of situations makes any generalisation from a given case-study difficult. However, based on what has already been done in related fields, a methodology to search for indicators of soil health can be proposed. In this review we will present (i) how a healthy soil can be defined and what are the concepts hidden behind the words “soil health,” (ii) which cultural practices have been used to control soil-borne diseases and their limitations, (iii) which soil parameters have been measured when studying soil suppressiveness, and which relationships have been found between these parameters, and finally (iv) how these descriptors could become indicators of soil health, using appropriate analytical and statistical methods.

Soil health through soil disease suppression: Which strategy from descriptors to indicators?

Numerous container-based studies in greenhouses or growth rooms have consistently demonstrated a suppressive effect of composts on soil-borne diseases such as damping-off and root rots (Pythium ultimum, Rhizoctonia solani, Phytophthora spp.), and wilts (Fusarium oxysporum and Verticillium dahliae). Composts have also been shown to suppress several diseases in the field, although the effects have been generally smaller and more variable than in container experiments. Several diseases of turf grass were suppressed by top-dressing with compost. These diseases are Fusarium patch (Microdochium nivale), red thread (Laetisaria fuciformis), damping-off (Pythium graminicola), brown patch (Rhizoctonia solani), dollar spot (Sclerotinia homoeocarpa) and snow mould (Typhula ishikariensis). The disease suppressive effect of compost generally increased with rate of application. Compost inclusion rates of at least 20% (v/v) were normally required to consistently obtain a disease suppressive effect, particularly in peat-b...

Suppression of soil-borne plant diseases with composts: A review

Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds

Soil organic matter is considered as a major component of soil quality because it contributes directly or indirectly to many physical, chemical and biological properties. Thus, soil amendment with composts is an agricultural practice commonly used to improve soil quality and also to manage organic wastes. We evaluated in laboratory scale experiments the response of the soilborne microflora to the newly created soil environments resulting from the addition of three different composts in two different agricultural soils under controlled conditions. At a global level, total microbial densities were determined by classical plate count methods and global microbial activities were assessed by measuring basal respiration and substrate induced respiration (SIR). Soil suppressiveness to Rhizoctonia solani diseases was measured through bioassays performed in greenhouses. At a community level, the modifications of the metabolic and molecular structures of bacterial and fungal communities were assessed. Bacterial community level physiological profiles (CLPP) were determined using Biolog™ GN microtiter plates. Bacterial and fungal community structures were investigated using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Data sets were analyzed using analysis of variance and ordination methods of multivariate data. The impact of organic amendments on soil characteristics differed with the nature of the composts and the soil types. French and English spent mushroom composts altered all the biological parameters evaluated in the clayey soil and/or in the sandy silty clay soil, while green waste compost did not modify either bacterial and fungal densities, SIR values nor soil suppressiveness in any of the soils. The changes in bacterial T-RFLP fingerprints caused by compost amendments were not related to the changes in CLPP, suggesting the functional redundancy of soil microorganisms. Assessing the density, the activity and the structure of the soil microflora allowed us not only to detect the impact of compost amendment on soil microorganisms, but also to evaluate its effect at a functional level through the variation of soil disease suppressiveness. Differences in disease suppressiveness were related to differences in chemical composition, in availability of nutrients at short term and in microbial composition due to both incorporation and stimulation of microorganisms by the compost amendments.

/pdf/response-of-soil-microbial-communities-to-compost-amendments-i5v54bxmx8.pdf

Response of soil microbial communities to compost amendments

Effects of compost addition and simulated solarisation on the fate of Ralstonia solanacearum biovar 2 and indigenous bacteria in soil.

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Effects of compost addition and simulated solarisation on the fate of Ralstonia solanacearum biovar 2 and indigenous bacteria in soil.