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For decades, the term “rhizosphere fauna” has been used as a synonym to denote agricultural pests among root herbivores, mainly nematodes and insect larvae. We want to break with this constrictive view, since the connection between plants and rhizosphere fauna is far more complex than simply that of resource and consumer. For example, plant roots have been shown to be neither defenceless victims of root feeders, nor passive recipients of nutrients, but instead play a much more active role in defending themselves and in attracting beneficial soil microorganisms and soil fauna. Most importantly, significant indirect feed-backs exist between consumers of rhizosphere microorganisms and plant roots. In fact, the majority of soil invertebrates have been shown to rely profoundly on the carbon inputs from roots, breaking with the dogma of soil food webs being mainly fueled by plant litter input from aboveground. In this review we will highlight areas of recent exciting progress and point out the black boxes that still need to be illuminated by rhizosphere zoologists and ecologists.

A potato crop (Solanum tuberosum L. cv. Maris piper) was grown in a soil to which N was added, as NH4NO3, with or without added C, as sucrose or straw. Shortly after amendment the soil, in all treatments, contained only relatively low levels of mineral N. However, these levels increased later. The increase, which was greatest in the absence of added C and least with added sucrose, occurred before the emergence of the plant canopy. The addition of C to the soil had no effect on plant yield, measured either as dry matter or total N content. The potential nitrification rate was high early in the season, and decreased significantly as the plants developed. The potential denitrification rate showed two significant peaks in activity, possibly related to plant development, the first to the development of new roots and the second to root senescence. It seems probable that the amount of C released by the potato plants was only about one-quarter of that required for the maximum microbial activity.

The root-knot nematode Meloidogyne incognita is a major pathogen of a range of important crops. Currently, control is typically achieved by the use of nematicides. However, recent work suggests that manipulating the ability of roots to slough off border cells, which then act as a decoy to the nematode, can significantly decrease damage to the roots. We investigated the attractiveness of border cells to M. incognita and the response of the nematode to border cells in close proximity. We found very limited attraction, in that nematodes did not preferentially alter direction to move toward the border cells, but a large and significant increase in nematode speed was observed once they were in the immediate vicinity of border cells. We discuss the results in the context of physical and biological mechanisms in relation to the control of pathogenic nematodes.

International audience; Genetically modified (GM) crops have become a real option in modern agriculture. They offer advantages for agricultural production, but they also raise concerns about their ecological and economic impacts. Decisions about GM crops are complex and call for decision support. This paper presents a qualitative multi-attribute model for the assessment of ecological and economic impacts at a farm-level of GM and non-GM maize crops. The model is applied for one agricultural season. This is an ex-ante model developed according to DEX methodology. In this model, cropping systems are defined by four groups of features: (1) crop sub-type, (2) regional and farm-level context, (3) crop protection and crop management strategies, and (4) expected characteristics of the harvest. The impact assessment of cropping systems is based on four groups of ecological and two groups of economic indicators: biodiversity, soil biodiversity, water quality, greenhouse gasses, variable costs and production value. The evaluation of cropping systems is governed by expert-defined rules. The paper describes the structure and components of the model, and presents three practical applications of the model, assessing both hypothetical and real-life cropping systems. In an overall assessment of the ecological and economic outcomes the model ranked cropping systems in the order: organically managed > GM systems including Bt and HT traits > conventionally managed maize. The paper discusses contributions of the model to decision-making practice and highlights methodological lessons learned during its development. (C) 2008 Elsevier B.V. All rights reserved

The effects of soil structure and microbial community composition on microbial resistance and resilience to stress were found to be interrelated in a series of experiments. The initial ability of Pseudomonas fluorescens to decompose added plant residues immediately after a copper or heat stress (resistance) depended significantly on which of 26 sterile soils it was inoculated into. Subsequent studies showed that both the resistance and subsequent recovery in the ability of P. fluorescens to decompose added plant residues over 28 days after stress (resilience) varied significantly between a sandy and a clay-loam soil. Sterile, sandy and clay-loam soil was then inoculated with a complex microbial community extracted from either of the soils. The resulting microbial community structure depended on soil type rather than the source of inoculum, whilst the resistance and resilience of decomposition was similarly governed by the soil and not the inoculum source. Resilience of the clay-loam soil to heat stress did not depend on the water content of the soil at the time of stress, although the physical condition of the soil when decomposition was measured did affect the outcome. We propose that soil functional resilience is governed by the physico-chemical structure of the soil through its effect on microbial community composition and microbial physiology.

Plants of barley (Hordeum vulgare), ryegrass (Lolium perenne), pea (Pisum sativum) or turnip (Brassica campestris rapifera) were grown in pots of unfertilised soil for 10 weeks together with unplanted control pots. A wide range of soil microbiological parameters was measured on bulk soil samples 2, 4, 7 and 10 weeks after seedlings were transplanted. There was no effect of planting or differential effect of plant species upon respiration rate, microbial biomass N, or biomass of microbial predators, but these parameters all varied significantly over time. Respiration, biomass N and nematode biomass all increased, whilst protozoan biomass decreased. Microbial biomass C showed no significant temporal changes or effect of planting. There was evidence for differential plant effects on potential nitrification and denitrification. Nitrification rates were depressed, compared with the fallow, in all treatments except the pea, at some time in the experiment. Conversely denitrification rates were enhanced in all treatments, except the grass, at specific times. Denitrification rates were greater in the pea treatment than the fallow on all occasions. These results demonstrate that plants do not necessarily influence the gross microbiology of the soil, but may affect physiologically distinct sub-components of the microbial biomass.

The biomass of microbial-feeding nematodes and protozoa was measured in the rhizospheres of peas, barley, grass and turnips grown for 10 weeks in pots containing a clay-loam soil; in the rhizospheres of peas and barley grown for 3 weeks in a sandy soil; and in the rhizosphere of barley grown for 11 weeks in an unfertilised and a fertilised clay-loam soil. The nematode biomass was consistently larger in the rhizosphere of all plants in both soils than in the bulk soil, but the protozoa biomass showed a rhizosphere effect only under pea and fertilised barley. The biomass of nematodes in the rhizosphere (1.2–22.3 μg dry weight g-1 dry soil) was greater than the biomass of protozoa (0.1–3.2 μg g-1), and greater under pea>barley>grass>turnip. It is suggested that nematodes are more able to exploit low bacterial densities than protozoa and that they initially migrate into the rhizosphere from the bulk soil. In samples of potato rhizosphere from field-grown plants, the nematode biomass was also greater than the active and total protozoan biomass. It is argued that in the rhizosphere the biomass of microbially feeding nematodes exceeds that of protozoa and that nematodes are more important in terms of nutrient cycling.

The use of colloidal silica as a medium for the extraction of nematodes by flotation was examined in order to rationalise the diverse range of methods currently in use. Significantly more nematodes were extracted from small samples of rhizosphere soil and estuarine sediment by using colloidal silica (Ludox HS30 diluted to 1.10 g cm -3 with water) than by density-gradient centrifugal flotation in sucrose, a modified Baermann funnel extraction or by repeated decantation. No benefit was gained by using polyvinylpyrrolidone coated silica (Percoll), by initial mixing of the sample with kaolin or by using density-gradient centrifugation rather than centrifugation of a sample/Ludox mixture. Increasing the amount of sample mixed with a given amount of Ludox gave a linear increase in nematodes recovered up to a critical point (0.036 g rhizosphere sample and 0.221 g estuarine sample ml -1 Ludox). Rhizosphere nematodes passed through a 53 μm mesh and the sample/Ludox mixture required centrifugation so that the sample could be filtered through a 15 μm mesh. Estuarine nematodes were retained by a 53 μm mesh and simple sedimentation of the sample/Ludox mixture was sufficient for extraction.

A glasshouse experiment was undertaken to provide baseline data on the variation between conventional maize (Zea mays L.) varieties and genetically modified maize plants expressing the insecticidal Bacillus thuringiensis protein (Bt, Cry1Ab). The objective was to determine whether the variation in soil parameters under a range of conventional maize cultivars exceeded the differences between Bt and non-Bt maize cultivars. Variations in plant growth parameters (shoot and root biomass, percentage carbon, percentage nitrogen), Bt protein concentration in shoots, roots and soil, soil nematode abundance and soil microbial community structure were determined. Eight paired varieties (i.e. varieties genetically modified to express Bt protein and their near-isogenic control varieties) were investigated, together with a Bt variety for which no near-isogenic control was available (NX3622, a combined transformant expressing both Bt and herbicide tolerance) and a conventional barley (Hordeum vulgare L.) variety which was included as a positive control. The only plant parameter which showed a difference between Bt varieties and near-isogenic counterparts was the shoot carbon to nitrogen ratio; this was observed for only two of the eight varieties, and so was not attributable to the Bt trait. There were no detectable differences in the concentration of Bt protein in plant or soil with any of the Bt-expressing varieties. There were significant differences in the abundance of soil nematodes, but this was not related to the Bt trait. Differences in previously published soil nematode studies under Bt maize were smaller than these varietal effects. Soil microbial community structure, as determined by phospholipid fatty acid (PLFA) analysis, was strongly affected by plant growth stage but not by the Bt trait. The experimental addition of purified Cry1Ab protein to soil confirmed that, at ecologically relevant concentrations, there were no measurable effects on microbial community structure.

Publisher Summary This chapter discusses microfaunal interactions in the rhizosphere. The living plant is the basis of existence for several groups of organisms both above- and belowground. In the rhizosphere, bacteria are more important decomposer organisms than fungi, because of the large supply of easily decomposable organic matter. Therefore, interactions between bacteria and their microfaunal grazers are of more consequence than those of fungi and their grazing animals. Microfaunal populations in the rhizosphere often reach a maximum on the older portions of the root system rather than the root tip itself. Microfauna have significant direct effects on rhizosphere C- and N-flow through the action of plant–parasitic nematodes. Indirect interactions of microfaunal grazing seem even more important than direct effects because of nutrient release. The strong top-down regulation of rhizosphere bacteria by grazing gives a central role to nematodes and protozoa in the interactions between plant roots and their colonizing microorganisms. The outcome of the symbiosis between mycorrhizal fungi and the plant is normally regarded as positive for the plant, as it is supplied with nutrients from the mycorrhiza. Foliar herbivory is reported to inhibit mycorrhizal fungi in most cases. The interactions between rhizosphere organisms and foliar herbivores must be mediated by plant responses. The interactions between plants and microfauna in the rhizosphere are not simply limited to the mineralizing activities of the fauna, nor are they unidirectional with the fauna impacting solely on the plant. Rhizosphere microfauna provide a useful focus on the study of the complex interactions.

Summary The ability of soil to resist and recover from anthropogenic and environmental stresses defines stability and resilience, respectively; an understanding of this ability is critical to sustainable land-use. In this study of 26 soils from across Scotland, we examine the influence of soil properties and antecedent conditions on physical and biological resilience to stress. The sites studied covered a wide range of soil types and land management, including serpentine soil from the Shetland Islands, a catena on the Highland Boundary Fault, and young aeolian sandy soils on the east coast. Biological resilience was measured as CO2 evolution from soil with added plant residues after either a transient (heat) or a persistent (copper) stress. Measures of physical resilience were: (i) compression and expansion indices following rapid uniaxial compression (to 50 kPa) and relaxation; and (ii) void ratio changes due to an overburden stress and subsequent cycles of wetting and drying. Evolution of CO2 from soil with added plant residues after heat or copper stress ranged from 23% to >100% that of the unperturbed soil, while the air-filled void ratio after the overburden stress ranged from 70% to >100% that of the unperturbed soil. Soils were grouped into quartiles based on their resistance to and recovery after each of the four prescribed stresses. Soil organic carbon (SOC) content correlated strongly with resilience after biological and physical stresses, particularly resistance to Cu stress (r ¼ 0.72) and recovery from compression (r ¼ 0.67), whereas there were no strong correlations between resilience following heat and any of the measured soil characteristics, although both land use and soil class were helpful in separating the responses. Resistance to compression was negatively correlated with SOC (r ¼ –0.63).

Summary An important goal of the European Commission-funded ECOGEN project is to develop a computer-based decision support system (DSS) for the assessment of economic and ecological impacts of using genetically modified crops. In ecological impact assessment, special emphasis is put on soil biology and estimating soil quality from the observed biological parameters. Methodologically, we have addressed this goal using model-based DSS, taking the approach of qualitative multi-attribute modelling. The approach is based on developing various hierarchical multi-attribute models that consist of qualitative attributes and utility (aggregation) functions, represented by decision rules. The model presented in this paper assesses the impact of cropping systems on soil quality and can subsequently be used to assess crop management options. It was developed as a collaboration between ECOGEN soil experts and decision analysts, and consists of 34 attributes, hierarchically structured into eight levels. There are 21 input attributes, most of which measure the richness and biomass of representative soil organisms. The assessment of soil quality is based on two main indicators: (1) soil diversity (assessed through microfauna, mesofauna and macrofauna richness) and (2) soil functioning (in terms of leaching, comminution, mineralisation and plant growth). In the paper, we address the methodological aspects of the model and its development, and describe the components of the model (attributes, value scales, decision rules and weights). We present initial results of its application to the assessment of crop management on soil quality in the case of using conventional and Bacillus thuringiensis (Bt)-maize at three field sites in France and Denmark. Our finding was that soil quality was unaffected even though several input attributes had changed. We also analyse the sensitivity of the model and discuss its current and potential contribution to soil quality management. The model is operational (available through a web page) and can be used for the assessment, comparison and analysis of realistic management scenarios. Furthermore, it provides an effective means of synthesising a lot of data, encoding knowledge about soil-quality factors, supporting communication among experts, answering ‘what-if’ and ‘so-what’ questions, and supporting the evaluation of new agricultural practices.

Soils from field sites at Foulum (DK), Narbons (FR) and Varois (FR) planted with genetically modified maize expressing either the insecticidal Bacillus thuringiensis protein (Bt) or herbicide tolerance (HT), as described elsewhere in this volume, were analysed for nematodes, protozoa and microbial community structure. These analyses were mirrored in single-species testing and in mesocosm experiments, and were coordinated with field samples taken for microarthropods, enchytraeids and earthworms so allowing for cross-comparison and a better understanding of the results observed in the field. Over the first 2 years of the field experiments (in 2002 and 2003), the effect of Bt-maize was within the normal variation expected in these agricultural systems. Sampling in 2004 and 2005 was expanded to include the effects of tillage (i.e. reduced tillage versus conventional tillage) and also the use of HT-maize. Tillage had major effects regardless of soil type (Varois or Foulum), with reduced-tillage plots having a greater abundance of microfauna and a different microbial community structure (measured both by phospholipid fatty-acid analysis (PLFA) and by community-level physiological profiling (CLPP)) from conventionally titled plots. Grass, as a contrasting cropping system to maize, also had an effect regardless of soil type and resulted in greater microfaunal abundance and an altered microbial community structure. Differences in crop management, which for the Bt-maize was removal of the insecticide used to control European corn borer and for HT-maize was a change in herbicide formulation, were only tested at single sites. There were differences in microbial community structure (CLPP but not PLFA) and sporadic increases in protozoan abundance under the Bt-crop management. The HT-maize cropping system, which covered a shorter period and only one site, showed little change from the conventional system other than an altered microbial community structure (as measured by PLFA only) at the final harvest. The Bt-trait had a minimal impact, with fewer amoebae at Foulum in May 2003, fewer nematodes at Foulum in May 2004 but more protozoa at Varois in October 2002 and an altered microbial community structure (PLFA) at Foulum in August 2005. These were not persistent effects and could not be distinguished from varietal effects. Based on the field evaluations of microfauna and microorganisms, we conclude that there were no soil ecological consequences for these communities associated with the use of Bt- or HT-maize in place of conventional varieties. Other land management options, such as tillage, crop type and pest management regime, had significantly larger effects on the biology of the soil than the type of maize grown. (C) 2007 Elsevier GmbH. All rights reserved.

The effects of maize expressing the Bacillus thuringiensis Cry1Ab protein (Bt maize) on soil microarthropods were assessed in the field at four European locations (two in Denmark and two in France) that differ in their climatic conditions or soil properties. Each site was considered as a separate experiment, with separate statistical comparison. Effects of farming practices using Bt maize were compared with conventional farming practices using near-isogenic non-Bt maize and also (at some of the sites) other conventional varieties. Furthermore, at one field site (Foulum, Denmark), the effects of Bt crops were studied in both conventional tillage and reduced tillage contexts. At another field site (Askov, Denmark), Bt maize effects were also compared to the effects of the chemical insecticide dimethoate. Moreover, at three of the field sites (all except Narbons, France), the possibility of a localised Bt effect around the rhizosphere compared to the bulk soil was assessed by sampling within and between maize rows. There were some significant negative effects of Bt maize on microarthropods in soils with a high clay content. Significant differences of the same magnitude also occurred between different conventional varieties of maize, but the effect of dimethoate appeared clearly greater than Bt effects. It is thus debatable if the Bt maize effect is an effect of the Bt toxin or just an effect of the maize variety. Based on the results, it can be concluded that the effect of Bt maize on soil microarthropods was small and within the normal variation expected in conventional agricultural systems. (C) 2007 Elsevier GmbH. All rights reserved.

The effects of maize (Zea mays L.), genetically modified to express the CrylAb protein (Bt), and an insecticide on soil microbial and faunal communities were assessed in a glasshouse experiment. Soil for the experiment was taken from field sites where the same maize cultivars were grown to allow comparison between results under glasshouse conditions with those from field trials. Plants were grown in contrasting sandy loam and clay loam soils, half were sprayed with a pyrethroid insecticide (deltamethrin) and soil samples taken at the five-leaf stage, flowering, and maturity. The main effect on all measured parameters was that of soil type and there were no effects of Bt trait or insecticide on plant growth. The Bt trait resulted in more soil nematodes and protozoa (amoebae), whereas insecticide application increased plant Bt concentration and altered nematode community structure. The only significant effects on soil microbial community structure, microarthropods, and larvae of a nontarget root-feeding Dipteran, were due to soil type and plant growth stage. The results indicate that, although there were statistically significant effects of the Bt trait on soil populations, they were small. The relative magnitude of the effect could best be judged by comparison with the insecticide treatment, which was representative of current best practice. The Bt trait had no greater effect than the insecticide treatment. Results from this glasshouse experiment were in broad agreement with conclusions from field experiments using the same plant material grown in the same soils.

International audience; Field trials were established at three European sites (Denmark, Eastern France, SouthWest France) of genetically modified maize (Zea mays L.) expressing the CryIAb Bacillus thuringiensis toxin (Bt), the nearisogenic non-Bt cultivar, another conventional maize cultivar and grass. Soil from Denmark was sampled at sowing (May) and harvest (October) over two years (2002, 2003); from E France at harvest 2002, sowing and harvest 2003; and from SW France at sowing and harvest 2003. Samples were analysed for microbial community structure (2003 samples only) by community-level physiological-profiling (CLPP) and phospholipid fatty acid analysis (PLFA), and protozoa and nematodes in all samples. Individual differences within a site resulted from: greater nematode numbers under grass than maize on three occasions; different nematode populations under the conventional maize cultivars once; and two occasions when there was a reduced protozoan population under Bt maize compared to non-Bt maize. Microbial community structure within the sites only varied with grass compared to maize, with one occurrence of CLPP varying between maize cultivars (Bt versus a conventional cultivar). An overall comparison of Bt versus non-Bt maize across all three sites only revealed differences for nematodes, with a smaller population under the Bt maize. Nematode community structure was different at each site and the Bt effect was not confined to specific nematode taxa. The effect of the Bt maize was small and within the normal variation expected in these agricultural systems.

Interrelations of fungal mycelium with other soil biota are of paramount importance in forestry and soil ecology. Here we present the results of statistical analysis of a comprehensive data set collected in the first (and the only) British fungus sanctuary over a period of four months. The variables studied included a number of soil properties, bacteria, protozoan flagellates, ciliates and amoebae, microbial and plant feeding nematodes, various microarthropods, and two fungal biomarkers--glomalin and ergosterol. One way ANOVA showed that the dynamics of the microbiota studied was influenced by seasonal changes. Superimposed on these changes, however, was variability due to biological interactions and habitat characteristics. Two fungal biomarkers, ergosterol and glomalin, were differently influenced by other biota and abiotic variables. The results indicate that the dynamics of soil fungi is influenced not only by soil microarthropods, but also by those found in forest litter. The overall outcome, therefore, is likely to be very complex and will depend upon specific conditions of any particular ecosystem.

Soil collected from an upland pasture was manipulated experimentally in ways shown previously to alter microbial community structure. One set of soil was subjected to chloroform fumigation for 0, 0.5, 2, or 24 h and the other was sterilised by gamma-irradiation and inoculated with a 10(-2), 10(-4), 10(-6), or 10(-8) dilution of a soil suspension prepared from unsterilized soil. Following incubation for 8 months, to allow for the stabilization of microbial biomass and activity, the resulting microbial community structure (determined by PCR-DGGE of bacterial specific amplification products of total soil DNA) was assessed. In addition, the functional stability (defined here as the resistance and resilience of short-term decomposition of plant residues to a transient heat or a persistent copper perturbation) was determined. Changes in the active bacterial population following perturbation (determined by RT-PCR-DGGE of total soil RNA) were also monitored. The manipulations resulted in distinct shifts in microbial community structure as shown by PCR-DGGE profiles, but no significant decreases in the number of bands. These shifts in microbial community structure were associated with a reduction in functional stability. The clear correlation between altered microbial community structure and functional stability observed in this upland pasture soil was not evident when the same protocols were applied to soils in other studies. RT-PCR-DGGE profiles only detected a shift in the active bacterial population following heat, but not copper, perturbation. We conclude that the functional stability of decomposition is related to specific components of the microbial community.

Total DNA was directly extracted from microbial populations in grassland soils taken from three geographically distinct upland sites at Garrigill, Aber and Sourhope, UK. Within each site, grasslands were categorised using the National Vegetation Classification into distinct vegetation sequences, namely unimproved, semi-improved and improved. Microbial community DNA was extracted from the different soils and analysed by determining (percent guanine+yctosine) %G+C profiles by thermal denaturation, and by cross hybridisation to measure the degree of similarity between the DNA extracted from the different soils. The %G+C profiles indicated that the microbial community structure within the different grasslands at Garrigill was significantly different. No significant differences in %G+C were detected under the different grasslands at Aber and Sourhope. However, significant differences in %G+C profiles derived from spatially-distinct replicate quadrats taken within grasslands were detected within the semi-improved grasslands at each site, and the unimproved grassland at Aber. Cross hybridisation analysis revealed significant differences between the improved, semi-improved and unimproved grasslands within all sites, with similarity values ranging from 51 to 94%. Significant differences were also detected between replicate quadrats within grassland types by this technique. These results provide evidence for great spatial variation in community DNA (i.e. genetic composition of microbial communities) within these grasslands.

Plants respond strongly to environmental heterogeneity, particularly below ground, where spectacular root proliferations in nutrient–rich patches may occur. Such ‘foraging’ responses apparently maximize nutrient uptake and are now prominent in plant ecological theory. Proliferations in nitrogen–rich patches are difficult to explain adaptively, however. The high mobility of soil nitrate should limit the contribution of proliferation to N capture. Many experiments on isolated plants show only a weak relation between proliferation and N uptake. We show that N capture is associated strongly with proliferation during interspecific competition for finite, locally available, mixed N sources, precisely the conditions under which N becomes available to plants on generally infertile soils. This explains why N–induced root proliferation is an important resource–capture mechanism in N–limited plant communities and suggests that increasing proliferation by crop breeding or genetic manipulation will have a limited impact on N capture by well–fertilized monocultures.

Nematodes and protozoa assist nitrogen mineralization by consuming bacteria, and this may increase the amount of nitrogen taken up by plants so that it exceeds the amount lost by root exudation. One of the methods used to determine bacterial consumption by protozoan grazers in aquatic ecosystems, namely progressive dilution of the grazing pressure, was tested in a sandy soil. The result suggests that a basic assumption of the technique, that grazing is directly proportional to the dilution factor, is untrue for soils, possibly because the increase in moisture content with increasing dilution enhances grazer activity.

An experimental system was used in which slurry could be placed in the central section of a tube, between two cores of packed, sieved soil. The system simulated the direct injection of slurry into soil and there was movement of water and substrate from the slurry into the surrounding soil. The effects of initial soil moisture, soil nitrate concentration and slurry type, on communities of nematodes and protozoa in soil sections adjacent to and away from the slurry were investigated. Protozoa increased rapidly in the soil layer adjacent to the slurry, but responded more quickly following the addition of pig slurry than cattle slurry. Pig slurry also specifically stimulated ciliates, especially larger Hypotrich ciliates. Nematodes, however, were stimulated to a greater extent by cattle than pig slurry. It is argued that pig slurry contained a greater proportion of readily-available C than cattle slurry. There was also a substantial increase in nematode numbers in soil up to 12 cm from the slurry. This was attributed to the migration of nematodes away from the soil section adjacent to the slurry. A separate experiment was conducted with gel-stabilised cattle slurry, which restricted the movement of water and substrate from the slurry. In this case there was no stimulation of microfauna in soil more than 2 mm from the soil-slurry interface, the largest changes occurred within the slurry phase.

The operation of particular biological systems, whether ecosystem or microcosm, depends on the interplay of three general factors — environment, biological community structure (diversity), and biological activity (function). The role of diversity, particularly of micro-organisms, and the relationship between microbial diversity and function is largely unknown. The application of molecular biological techniques has shown that microbial communities, particularly in soil, are very complex (Torsvik et al., 1990; Ritz et al., 1997) and understanding this relationship is not straightforward. We set out in this paper to outline some of the concepts involved in the study of microbial diversity, and to present an overview of the relationship between diversity and function.

Broad-scale approaches seek to integrate information on whole microbial communities. It is widely recognized that culture techniques are too selective and unrepresentative to allow a realistic assessment of the overall structure of microbial communities. Techniques based on fatty acid or metabolic profiles determine the phenotypic composition of the community. Complementary information about the genotypic structure of soil microbial communities necessitates analysis of community DNA. To determine broad-scale differences in soil microbial community structure (i.e., differences at the whole community level, rather than specific differences in species composition), we have applied a community hybridization technique to determine the similarity and relative diversity of two samples by cross hybridization. In previous studies this assay failed with whole-soil community DNA. Usable hybridization signals were obtained using whole-soil DNA, in this study, by digesting the DNA with restriction enzymes before the labeling with a random-primer reaction. The community hybridization technique was tested using a graded series of microbial fractions, increasing in complexity, all isolated from the same soil sample. This demonstrated that single bacterial species and a mixture of cultivable bacteria were less complex and only 5% similar to whole-community DNA or bacteria directly extracted from the soil. Extracted bacterial and whole-community DNA were 75% similar to each other and equally complex. When DNA was extracted from four different agricultural soils, their similarities ranged from 35 to 75%. The potential usefulness of community hybridization applied to soil microbial communities is discussed.

1. With the current trend in agricultural practice to increase the importance of indigenous and added organic matter in the build-up of soil fertility, a better understanding of the dynamics of decomposition activity around organic resources is required. In this study the changes in microbial activity and populations of protozoa and nematodes were followed in decomposing barley root material buried in soil cores, and in three soil fractions with increasing distance from the root material. 2. Respiratory activity was maximal during the first week and decreased throughout the experiment, and at the last sampling after 392 days no significant effect of the roots on respiration was observed. 3. Following root addition microbial activity (dehydrogenase activity and potential denitrification rate) increased rapidly in the root material and in soil up to 1.8 mm from the roots. Microbial activity peaked after 4 days followed by a peak in protozoan numbers after 2 weeks and a peak in the number of nematodes after 6 weeks. 4. Growth potential of bacteria, as indicated by enzyme synthesis during a potential denitrification assay, and average bacterial cell size was larger on the roots than in the soil suggesting a more active bacterial biomass in this fraction. 5. The root effect was very local, and was limited mainly to the soil fraction adjacent to the roots; soil 1.8-5.4 mm from the roots and soil more than 5.4 mm from the roots was hardly affected by the resource. 6. These results demonstrate distinct successional patterns in the microbial food web with a sequence of population development from micro-organisms to protozoa and nematodes.

The plant ectoparasitic nematode Longidorus elongatus induces distinct changes in the root-tip nuclei of perennial ryegrass (Lolium perenne L.). There was an initial shift in DNA content into the 4C category, followed by further increases with values intermediate between 8C and 16C present after eight days. Nuclear size was reduced after six days due to increased nuclear division during hyperplasia. Nuclear DNA content and size decreased in galls older than eight days as a result of nuclear disintegration induced by L. elongatus. In cells near to the feeding site, nuclei became split into several, small globules. In more distant nuclei DNA-containing material became dispersed throughout the cytoplasm. In the oldest galls, cells were largely devoid of nuclei.

The nitrogenous and carbohydrate components of ryegrass and faeces from larvae of Tipula paludosa Meigen, fed on ryegrass ( Lolium perenne L.), were compared. Proteins in ryegrass were efficiently digested and uric acid was the major nitrogenous excretory product. The alkaline midgut (pH 9.1) was considered to enhance the digestibility of hemicellulose, by removing inhibitory acetyl groups, and of cellulose by altering its crystallinity. T. paludosa larvae assimilated 50% of ryegrass cellulose, and 50% of an isolated 14 C-labelled cellulose, whereas 86% of hemicellulose was digested.

Sitka spruce litter was subjected to two freeze-thaw cycles and then packed into 40 glass leaching columns. Twenty columns were each inoculated with 200 enchytraeid worms isolated from fresh untreated litter and the remaining 20 used as controls. The columns were continuously leached with distilled H2O for 16 weeks at 20°C. Leachates were collected weekly and litter harvested after 0, 4, 8 and 16 weeks. Phosphate, K+, Ca2+ and Mg2+ started to leach immediately and by the end of 16 weeks the accumulated amounts of each element released were significantly greater (P < 0.05) in columns with worms than those without. Ammonium and nitrate did not appear in leachates until after 8 weeks. At the end of the experiment, significantly more (P < 0.001) mineral-N had been leached from the inoculated litter, 18.1 mg compared with 12.7 mg N column−1 in the uninoculated control. Amounts of mineral-N extracted from the litters were similar in both treatments but total net production of mineral-N was approx. 10% greater in the worm inoculated material. The N and P contents of the added worms were relatively small and the enhanced leaching was attributed to a grazing effect of the worms that reduced nutrient immobilization in the microbial biomass.

The DNA content and size of individual nuclei from galls of perennial ryegrass root-tips induced by X. diversicaudatum and L. elongatus were measured. Feeding by X. diversicaudatum increased the DNA content of the nuclei by varying amounts. No regular doubling pattern of the DNA content was discernible. The DNA values varied up to between 32-64C. Generally the size of the nuclei was not increased, although some were larger than control nuclei. The modified nuclei probably have an altered metabolic function, which increases the food value of the gall to the nematode. Some bi-nucleate cells were also observed, which probably result from mitosis without cytokinesis. A preliminary examination of nuclei from galls induced by L. elongatus revealed similar nuclear changes, but no bi-nucleate cells were found.

SUMMARY An interference method is described for measuring section thickness in the range 0·3–45 μm. An incident illumination objective incorporating a beam splitter and adjustable reference mirror is used to generate interference fringes by reflection from the upper surfaces of sections on glass slides. Sections do not require a reflective coating. The lateral displacement of the zero-order fringe generated using white light is measured in terms of sodium light fringes and photographic enlargement of the fringes allows measurement to ± 30 nm. The method is simple in operation and allows rapid assessment of any local distortions over the entire section area.

Xiphinema diversicaudatum induced similar morphological changes in root-tips of strawberry, a good host, and ryegrass, a poorer host. After nematodes had fed for 1, 2, and 4 days the feeding site became surrounded by multinucleate hypertrophied cells with amoeboid-shaped nuclei, enlarged nucleoli and dense cytoplasm. Cell complexes also developed in association with the stelar initials in strawberry but not in rycgrass. There was an increase in the proportion of cytoplasm, from 47% to 56% of the root-tip volume, and a reduction in the proportion of vacuole from 40% to 28% after 1 day in strawberry. There was no change in the proportion of these components in ryegrass after nematodes had fed for 1 day. The total volume of the root-tip increased more in strawberry (8.5 x ) than in ryegrass (3.6 x ), but the concentrations of RNA and protein progressively decreased. Total RNA and protein both increased 3.4 x after 4 days in strawberry, but in ryegrass protein increased 2.7 x and RNA 5.4 x after 4 days. These results support an earlier hypothesis that strawberry nuclei are more transcriptionally active than ryegrass nuclei, and suggest that the metabolism of the two host plants had responded differently to feeding by X. diversicaudatum.

Amendments with glucose significantly reduced the amount of nitrate leached from a sandy soil amended with nitrate. The decrease was most likely caused by immobilisation of the nitrate into microbial cells. Populations of ciliates and flagellates and amoebae, but not nematodes, increased 7–14 days following glucose amendments. Mineralisation of the immobilised nitrate occurred during this period. Some of the mineralised nitrogen appeared to be available to ryegrass plants only if the roots exploited most of the soil during the period of maximum predator activity. After 28 days, 44% of the organic N remaining in the soil after leaching was taken up by the plants. The difference developed over the last 2 weeks when amoebal populations were large.

Numbers of the ciliate protozoan Colpoda steinii Maupas were increased by the presence of a nematode (Rhabditis sp.), in soil and liquid culture. The development of nematode numbers was inhibited by the ciliate. Observations of hatching nematodes, together with counts of total and viable numbers of the bacterium Pseudomonas fluorescens, indicate that Rhabditis sp. increased bacterial productivity but that the activity of C. steinii inhibited feeding by the nematode. When the two bacterial grazers were present in combination C. steinii benefited from increased bacterial productivity induced by Rhabditis sp. Both grazers increased the mineralization of NH4+-N when added separately to soil, and this was further increased when nematodes and ciliates were present in combination. There was no effect of grazing on levels of bicarbonate-soluble phosphate (Pi), while nematodes had a variable effect on levels of soil NO3−-N.

Eukaryotic cells were extracted from mineral soil by shaking in 50 mM Tris buffer, pH 7.5. This extracted a greater biovolume of cells than shaking in a range of surfactants, blending or sonication. An aliquot of soil suspension was incubated with iodonitrotetrazolium (INT) and then loaded onto a linear density gradient prepared from Percoll and phosphate buffer. After centrifugation. the majority of mineral particles had sedimented but most of the cells were retained in the supernatant. These cells were stained and mounted on a membrane filter for epifluorescence microscopy. Metabolically active protozoa were readily identified as having a well defined cytoplasm and cell wall, stained with acridine orange, a distinct nucleus or nuclei, stained with 4′,6′-diamidino-2-phenylindole, and containing crystals of INT-formazan. This combination of stains was the most reliable for detecting protozoa. Algal cells were easily identified by the red autofluorescence of their chlorophyll. The most-probable-number technique and our proposed method both ranked the protozoan populations from a range of soils in the same order. It is argued that the described technique gives a more accurate measure of active protozoan biomass and a recommended procedure is given.

Experiments in liquid culture indicated that nitrification was increased in the presence of bacteriophagous protozoa. There were significant accumulations of NO − 3 and NO − 2 in media containing (NH 4 ) 2 SO 4 only in the presence of amoebae and ciliates. Increasing the concentration of NH + 4 -N from 1 to 10μml −1 in the absence of protozoa did not increase nitrification, indicating that enhanced nitrification was due to the presence of protozoa rather than the excretion of NH + 4 by protozoa. The interaction between protozoa and nitrification was also studied during 4 weeks in an amended clay-loam soil held at 15°C. The addition of the biocides, cycloheximide and Triton X-100 reduced both protozoan populations and nitrification. Nitrification was significantly enhanced when protozoan numbers were increased by the addition of supplementary nutrients or extra bacteria.

Reproduction by Xiphinema diversicaudatum on strawberry (good host) and raspberry (poor host) and by Longidorus elongatus on strawberry (good host) and turnip (poor host) was examined in a glasshouse pot trial at 18°C. Populations of X. diversicaudatum increased 32-fold on the good host and those of L. elongatus 34-fold, while on the poor host populations of both nematodes increased 8-fold. The observed generation times for X. diversicaudatum were 23 weeks on strawberry and greater than 23 weeks on raspberry, and for L. elongatus were 17 weeks on strawberry and 21 weeks on turnip. The generation times were extrapolated into field conditions. There were more females with eggs, and more eggs per female on the good host than on the poor host. The total volume of nematode supported by a host plant only increased appreciably when L3, L4 or adults were present in the sample, and the good host supported 5 times the volume of X. diversicaudatum and 8 times the volume of L. elongatus than did the poor host. More galls were formed on the root system of the good host, by X. diversicaudatum and by L. elongatus, than on the poor host. The ratio of galls/nematode was such that on strawberry X. diversicaudatum induced more galls, a maximum of 0.31 galls/nematode, than L. elongatus, a maximum of 0.14 galls/nematode.

Longidorus elongatus and L. leptocephalus fed only at the root-tip of perennial ryegrass growing in agar. Galls were usually fed upon by several nematodes. Feeding behaviour was similar for L. elongatus and L. leptocephalus; the root-tip was penetrated by rapid thrusts with the stylet to several cells deep within the root, following which there was a period of inactivity when the nematodes were thought to be salivating. Ingestion followed and continued for long periods without pause, with the odontostyle-tip in the same cell. During most feeds there were two or three periods of ingestion, separated by short (c. 2 min) periods of inactivity. Calculations based on measurements of the oesophageal bulb chamber, assuming 10% pumping efficiency, indicate that a volume equivalent to more than 40 cells may be extracted by a single nematode feeding for 1 h. Ultrastructural studies of galls formed during 8 days by L. elongatus showed that there were many empty cells in which the walls were holed. It is suggested that these holes result from action of the nematode saliva and that their formation eased removal of the contents of cells distant from the odontostyle-tip.

The possibility is examined that carbon (C) released into the soil from a root could enhance the availability of inorganic nitrogen (N) to plants by stimulating microbial activity. The release of soluble C compounds from roots is assumed to occur by one of two general processes: cortical cell death or exudation from intact cells. On the basis of several assumptions chosen to allow maximal amounts of N mineralisation to be calculated, greater amounts of net N mineralisation are theoretically possible at realistic soil C:N ratios of bacteria are grazed by predators such as protozoa, than if bacteria alone are active. More N is mineralised when the substrate released from the root has a high C:N ratio (as in cell death) than when it is relatively N-rich. The amounts of N that a root might realistically cause to be mineralised are unlikely to account entirely for high nitrate inflow rates that have been measured experimentally. However there are circumstances in which the loss of C from roots is essential if any N is to be mineralised and obtained by plants.

Feeding by the nematode X. diversicaudatum caused a progressive increase in the DNA content and size of strawberry nuclei. After four days feeding, nuclei had DNA values intermediate between 8C and 16C and had increased in size from a mean of 17 micron2 for control root tips to 49 micron2. Multinucleate cells were present after two and four days feeding. There were no ultrastructural differences in the composition of nuclei from control and parasitized root tips, but strawberry nuclei consisted mainly of dispersed chromatin whereas ryegrass nuclei contained a large proportion of condensed chromatin.

SUMMARY Amounts of the individual carbohydrate components derived from uniformly 14Clabelled grass added to soil were monitored in incubations lasting for up to 2 years. Decomposition was enhanced by the presence of the earthworms. Allolobophora caliginosa and Lumbricus rubellus and the cranefly larvae Tipula paludosa. After 28 d larvae had increased the loss of 14C-arabinose by 8.8% (compared to soil without larvae), -xylose by 15%, -non cellulose glucose by 5.3% and -cellulose glucose by 12.5%. Earthworms had increased the loss of 14C-xylose by 5%, -galactose by 21% and -total glucose by 11% after 6 months, and by another 29%, 14% and 8% respectively after 12 months. The losses of 14C, initially about 60% from soil with tipulid larvae after 1 month, and 50% from soil with earthworms after 3 months, became progressively less. Total 14C losses in the presence of earthworms were 66% after 12 months and 60% after 2 years, respectively. Increased decomposition is considered to be the result of the mixing of soil and substrate by the invertebrates, rather than an effect of their digestive capabilities.

Summary Soil fungi are considered to be an important food source for earthworms. Selection experiments were carried out in order to study the preferences of earthworm species for a variety of soil fungi. Nine fungal species (Cladosporium cladosporioides, Rhizoctonia solani, Mucor sp., Trichoderma viride, Fusarium nivale, Phlebia radiata, Glaeophyllum trabeum, Coniophora puteana, Coriolus versicolor) were grown separately in centrifuge tubes on sterilized sand with potato dextrose. Tubes containing different fungal species, 8–9 per experiment, were arranged in a food choice arena. The preference for the fungi of 5 different earthworm species (Lumbricus terrestris, Lumbricus castaneus, Aporrectodea caliginosa, Aporrectodea rosea, Octolasion cyaneum) was tested by adding one specimen per chamber. Removal of sand from the tubes within 6 days was used as the indicator of preference by earthworms. The food preference of earthworms irrespective of ecological group followed a general pattern. F. nivale and C. cladosporioides were the preferred fungal species, followed by fast-growing species such as Mucor sp. and R. solani. In contrast, basidiomycetes were generally refused. The epigeic species L. rubellus had the strongest preference for a single fungal species, in contrast the endogeic species A. rosea fed more evenly on different fungal species. We conclude that early successional fungal species are used as cues by earthworms to detect fresh organic resources in soil.

International audience; The effects of maize expressing the Bacillus thuringiensis Cry1Ab protein (Bt maize) on decomposition processes under three different European climatic conditions were assessed in the field. Farming practices using Bt maize were compared with conventional farming practices using near-isogenic non-Bt maize lines under realistic agricultural practices. The litter-bag method was used to study litter decomposition and nitrogen mineralization dynamics of wheat straw. After 4 months incubation in the field, decomposition and mineralization were mainly influenced by climatic conditions with no negative effect of the Bt toxin on decomposition processes.