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The application of agricultural biosolids to land is likely to increase on farms as pressures intensify to manage nutrients and carbon, especially with regard to slurry. Although much work has been carried out in this area, it has tended to focus on specific aspects of the application-use cycle, without a coherent framework and notably the role of soil biology has been little studied in this context, or considered appropriately in the development and application of slurry management systems. In this review article we present a hypothesis that the configuration of the soil microbial community is determined by the history of long-term inputs to which the community has been subjected and that the resultant configuration determines the instantaneous responses of the associated soil to the presence of slurries, and posit a set of critical questions which would effectively test this.

Measurements of concentrations of easily extractable soil nitrogen (N) were carried out on samples collected at the Heron Wood Reserve, Scotland, concurrently with investigations of N associated with total microbial biomass and the abundances of bacteria, fungi, and invertebrates. Soil biota at the studied site appeared to be limited by N. There was a remarkable difference between the ambient (i.e., easily extractable N) and biomass nitrogen. The abundance data of bacteria, protozoa and nematodes significantly negatively correlated with ambient N but showed positive correlations with the total microbial N content. There were, however, remarkable differences between the correlation patterns exhibited by the fungal and the bacterial pathways, as fungi did not show any correlations with chemical variables. These differences should be taken into account whilst interpreting biological interactions both at this important site and elsewhere.

The small subunit ribosomal gene (SSU rDNA) is used in both environmental and phylogenetic studies of nematodes. However, currently described SSU rDNA primers near to the 5′ end of the gene show mismatches with a number of different nematode sequences. Here a new SSU rDNA 5′ forward primer, Nem_SSU_F74, is designed from existing database sequences and its performance compared with a previously described forward primer, SSU_F04, by sequencing from nematode assemblage DNA, in combination with a previously described reverse primer. DNA was extracted from three nematode assemblages isolated from arable soil and, in total, six clone libraries were created: three amplified with established forward primer SSU_F04 and three with the novel primer Nem_SSU_F74. Ninety six clones were sequenced from each library. Nem_SSU_F74 libraries yielded a higher number of nematode sequences than SSU_F04 libraries, and a greater number of nematode taxa were found using the novel forward primer. The most abundant sequences were common to libraries created with either forward primer. Data from a morphological survey of the same samples revealed that biomass was more closely related to molecular analysis than simple counts of nematodes. For all but one nematode order (Aphelenchida), percentage assemblage composition was not significantly different between biomass and sequences obtained with the novel forward primer Nem_SSU_F74.

To study the sustainability of arable agricultural systems we examined a wide range of biological, physical and chemical properties associated with changes in soil quality. We integrated these using a qualitative multi-attribute model supported by the software tool DEXi to achieve a holistic estimation of soil quality. We tested the relative changes in soil quality attributes resulting from the incorporation of cattle slurry or green-waste compost, or from including a ley phase in the production of arable crops. We measured: abundances and biodiversity of the soil biota, physical properties and nutrient concentrations; twice in 2006 and thrice in 2007. These data were used to generate a model of soil quality, which showed that the addition of organic matter or a ley phase did increase soil quality. However, to fully understand the soil system results should be derived from a number of functionally related observations as there were opposing trends in individual observations. Increases in some beneficial attributes (such as decomposition, soil nutrient status and physical condition) were associated with an increased risk of nutrient losses from leaching and gaseous emissions. Assessing soil quality with only a few indicators may not identify these trade-offs. The multi-attribute modelling approach could identify the pathways responsible for changes in soil quality and identify possible environmentally detrimental effects.

Soil fauna, especially soil nematode communities may be used as indicators for monitoring soil biodiversity and ecological processes. A major drawback facing ecologists is the specialised taxonomic knowledge and labour intensive nature of the work required for traditional morphological identification of soil fauna. We review rapid molecular methods, including: DNA Barcoding or sequencing, PCR-DGGE, PCR-TRFLP and real-time PCR, which could enable an empirical assessment of soil nematode assemblages, in relation to their use as monitoring tools. Based on advantages of: high-throughput; ease of comparison between samples; and rapid data analysis, we argue that PCR-TRFLP is well suited to monitoring purposes.

The main threats to soils outlined in the pending Soil Framework Directive (SFD) are: contamination, loss of organic matter, erosion, compaction, sealing, salinization and desertification. The first four threats are pertinent to agricultural systems in Atlantic Europe, but vary in their extent between countries depending on the spatial soil distribution. Loss of soil biodiversity has not been included as a potential threat in the SFD due to lack of information that is currently available both spatially and temporally to facilitate any legislation to protect it. This paper gives emphasis to the four main threats outlined above associated with Agricultural systems in Atlantic Europe. Each soil threat is discussed in relation to the agricultural management calendar for cultivated and grazed grassland soils. The paper discusses current soil protection policies and possible changes to such legislation with the adoption of the SFD by member states.

Re-vegetation of trace element contaminated soils can alter the pH and chelating capacity in the rhizosphere, increasing the mobility of pollutants, which, in turn, may impact on rhizosphere ecology. In this study a short-term pot experiment was carried out in order to investigate the multi-factorial effects of: buffering capacity (sandy-loam and loam soils); pollutant load (0%, 1.3%, and 4% of pyrite sludge), and the presence/absence of plant (Lolium perenne L. and Medicago sativa L.) on the mobility of trace elements, soil biochemical functionality (hydrolase activities), and biological diversity (bacterial and nematode communities). The experiment was carried out with representative soils from the Guadiamar basin (SW Spain), an area where the Aznalcóllar mining spill affected over 4000ha. Results indicated that the development of rhizospheres in polluted soils (coarse-textured) increases the mobilization of trace elements. In general the presence of roots has stimulatory effects on soil quality indicators such as hydrolase activities and both bacterial and nematode communities. However, the presence of high amount of metals interferes with these beneficial effects. This study provided evidence about the complexity of the impact of growing plants on trace element polluted soils. Trace element mobilization, hydrolase activities and bacterial and nematode communities in the rhizosphere are dependent on plant species, soil type, and pollution dose.

The effects of bacterial-feeding nematodes on nitrification and the ammonia-oxidizing bacteria (AOB) community composition were studied in soil microcosms. Sterilized soils were inoculated with mixed soil bacteria (obtained by filtering) or with bacteria and bacterial-feeding nematodes, after which the dynamic inorganic nitrogen concentration was measured weekly. After 28 days of incubation, denaturing gradient gel electrophoresis (DGGE) based on PCR amplification of the amoA gene was used to analyze the AOB community composition. In addition, a clone library from the amoA gene fragments was established using clones randomly selected and sequenced from the two treatments. The results showed that the presence of bacterial-feeding nematodes led to significantly greater NH4+ and NO3− contents over the entire incubation period, indicating that bacterial-feeding nematodes promoted both N mineralization and nitrification. The results of DGGE showed that the AOB community composition was significantly changed in the presence of bacterial-feeding nematodes. Furthermore, the sequencing results suggested that Nitrosospira sp. was the dominant species in the treatment without nematodes, while Nitrosomonas sp. and Nitrosospira sp. were the dominant species in the treatment with nematodes. Such changes in the AOB community may be one of explanation of the important role that nematodes play in promoting nitrification.

Re-vegetation of eroded soil restores organic carbon concentrations and improves the physical stability of the soil, which may then extend the range of microhabitats and influence soil microbial activity and functional stability through its effects on soil bacterial community structure. The objectives of this study were (i) to evaluate the restorative effect of re-vegetation on soil physical stability, microbial activity and bacterial community structure; (ii) to examine the effects of soil physical microhabitats on bacterial community structure and diversity and on soil microbial functional stability. Soil samples were collected from an 18-year-old eroded bare soil restored with either Cinnamomum camphora (“Eroded Cc”) or Lespedeza bicolour (“Eroded Lb”). An uneroded soil planted with Pinus massoniana (“Uneroded Pm”) and an eroded bare soil served as references. The effect of microhabitats was assessed by physical destruction with a wet shaking treatment. Soil bacterial community structure and diversity were measured using a terminal restriction fragment length polymorphism (T-RFLP) approach, while soil microbiological stability (resistance and resilience) was determined by measuring short-term (28 days) decomposition rate of added barley (Hordeum vulgare) powder following copper and heat perturbations. The results demonstrated that re-vegetation treatment affected the recovery of physical and biological stability, microbial decomposition and the bacterial community structure. Although the restored soils overshot the Uneroded Pm sample in physical stability, they had lower microbial decomposition and less resilience to copper and heat perturbations than the Uneroded Pm samples. Soil physical destruction by shaking had the same effect on soil physical stability, but different effects on soil microbial functional stability. There were significant effects of vegetation treatment and perturbation type, and interactive effects among vegetation treatment, shaking and perturbation type on bacterial community structure. The destruction of aggregate structure increased resilience of the Eroded Lb sample and also altered its bacterial community structure. Both copper and heat perturbations resulted in significantly different community structure from the unperturbed controls, with a larger effect of copper than heat perturbation. Bacterial diversity (Shannon index) increased following the perturbations, with a more profound effect in the Uneroded Pm sample than in the restored soils. The interactive effects of vegetation treatment and shaking on microbial community and stability suggest that soil aggregation may contribute to the generation of bacterial community structure and mediation of biological stability via the protection afforded by soil organic carbon. Differential effects of re-vegetation treatment suggest that the long-term effects are mediated through changes in the quality and quantity of C inputs to soil.

Two contrasting phases of work are described that help inform the development and requirements of a soil monitoring system: firstly, the development and application of a multi-criterion analysis of soil quality indicators grounded in the basic natural sciences; and secondly, scrutiny of the outcome of that process by a wide range of non-specialist but key stakeholders at a workshop. This process ensures that the final monitoring design meets both the scientific rigour expected from a monitoring system and as far as possible meets the aspirations of policy and regulatory stakeholders. Individual indicators of soil quality were evaluated in terms of their applicability against a number of important environmental and logistical parameters and therefore their overall fitness for purpose. These included relevance to different soil types, functions, habitats and threats to soil, the inherent variability of soil, and a range of technical aspects such as analytical complexity, precision and reproducibility of analytical results and whether a standard operating procedure (SOP) existed for the technique. A tiered approach to soil monitoring was supported by workshop delegates. This will require indicators that are suitable and effective at national, site-specific and process-level scales. In addition, the opportunities for synchronizing soil monitoring with air and water quality monitoring should be considered and the potential for integrating on-site measurements with remote methods should be researched further. It was considered by workshop attendees that soil monitoring should be rooted in pedological principles (i.e. recognizing defined soil horizons) to ensure that results can be extrapolated from individual sites and to retain flexibility.

The long-term (18 years) effects of re-vegetating eroded soil on soil microbial biomass, community structure and diversity were investigated in a forest soil derived from Quaternary clay in the Red Soil Ecological Experimental Station of the Chinese Academy of Sciences. Large areas of land in this region of China have been subjected to severe soil erosion, characterised by the removal of the fertile surface soil and even the exposure of parental rock in some areas due to a combination of deforestation and heavy rainfall. The effects of planting eroded or uneroded soil with Pinus massoniana, Cinnamomum camphora or Lespedeza bicolor on the soil microbial community and chemical properties were assessed. Total soil microbial community DNA was extracted and bacterial 16 S rRNA gene fragments were amplified by PCR and analysed by terminal restriction fragment length polymorphism (T-RFLP). Microbial biomass carbon (Cmic) was measured by chloroform fumigation-extraction. Following the restoration there were significant increases in both Cmic and bacterial diversity (Shannon index), and significant changes in bacterial community structure. Erosion factors were significant only in minor dimensions suggesting that the restoration had been largely successful in terms of bacterial community structure. Compared with uneroded soil, Cmic recovered in L. bicolor and P. massoniana restored eroded plots and was significantly greater under these tree species than C. camphora, although soils in C. camphora restored plots displayed the highest bacterial diversity. The recovery of microbial biomass and diversity in the eroded plots was, to large extent, accompanied by the development of the same bacterial community structure as in the uneroded plots with erosion having relatively little effect on bacterial community structure.

The effect of earthworms on soil hydrolases (protease, urease, invertase, and alkaline phosphatase) and dehydrogenase activities was investigated in maize residue amended rice–wheat rotation agro-ecosystem. Experimental plots in the rotation had five treatments, i.e. incorporation or mulching of maize residues with or without added earthworms and an untreated control. The application of maize residues to soil without earthworms significantly enhanced the five soil enzyme activities compared with the control treatment during rice and wheat cultivation. The presence of earthworms further significantly enhanced protease activity in the soils with both incorporated and mulched maize residues during two cultivation seasons, but only significantly increased alkaline phosphatase activity in the soil with incorporated maize residue during the rice cultivation season. Invertase activity was significantly enhanced by the presence of earthworms in the soil with maize residue incorporation during two cultivation seasons. There were no changes in dehydrogenase activity when earthworms were present. Additionally, the five enzyme activities in earthworm casts were significant higher than those in the surrounding soil, especially dehydrogenase and invertase activities. Whatever the treatment, the values obtained for the enzyme activities in both soil and casts, except for dehydrogenase activity in earthworm casts, were significantly higher under wheat than those in rice-cultivated soil. These results indicate that the presence of earthworms strongly affected soil enzyme activities, depending on the method of organic residue application, and the enhanced enzyme activities of earthworm casts probably contributed to the surrounding soil enzyme activities.

The influence of earthworms on nematodes and protozoan communities was determined during the wheat phase of a six year rice–wheat rotation agro-ecosystem. Experimental plots in the rotation had five treatments, i.e. incorporation or mulching of maize residues with or without added earthworms and a control. The addition of maize residues to soil strongly affected the abundance and community structure of nematodes and protozoa in the absence of earthworms. The presence of earthworms gave significantly lower total nematode numbers at all soil depths following maize residue incorporation than the same treatment without earthworms, and also gave lower (although not significantly) total nematode numbers in the upper soil layer following maize residue mulching than the same treatment without earthworms. This was mainly due to a significant decrease in bacterial-feeding nematode numbers. Earthworms also strongly affected the distribution of the number of total nematodes and two trophic groups (bacterial and plant feeders) with soil depth. In the presence of earthworms, total protozoan and flagellate numbers significantly increased at all soil depths following both incorporation and mulching of maize residues, while numbers of amoebae increased only when maize residues were mulched. Additionally, in earthworm casts total nematode numbers (mainly bacterial and fungal feeders) were significantly higher, whereas total protozoa numbers (mainly flagellates and amoebae) were significantly lower than that in soil from 0 to 5 cm layer. These results indicated that earthworm activity could affect the abundance and community structure of microfauna, and change their distribution between soil layers and cast material, depending on the mode of application of organic residues.

Policy makers rely on risk-based maps to make informed decisions on soil protection. Producing the maps, however, can often be confounded by a lack of data or appropriate methods to extrapolate using pedotransfer functions. In this paper, we applied multi-objective regression tree analysis to map the resistance and resilience characteristics of soils onto stress. The analysis used a machine learning technique of multiple regression tree induction that was applied to a data set on the resistance and resilience characteristics of a range of soils across Scotland. Data included both biological and physical perturbations. The response to biological stress was measured as changes in substrate mineralization over time following a transient (heat) or persistent (copper) stress. The response to physical stress was measured from the resistance and recovery of pore structure following either compaction or waterlogging. We first determined underlying relationships between soil properties and its resistance and resilience capacity. This showed that the explanatory power of such models with multiple dependent variables (multi-objective models) for the simultaneous prediction of interdependent resilience and resistance variables was much better than a piecewise approach using multiple regression analysis. We then used GIS techniques coupled with an existing, extensive soil data set to up-scale the results of the models with multiple dependent variables to a national level (Scotland). The resulting maps indicate areas with low, moderate and high resistance and resilience to a range of biological and physical perturbations applied to soil. More data would be required to validate the maps, but the modelling approach is shown to be extremely valuable for up-scaling soil processes for national-level mapping.

The effects of management in maintaining high rice yield with less water have received increasing attention in sub-tropical regions where seasonal drought is very severe. To test whether water management affects soil ecological process we compared the soil nematode communities in paddy field soils following water management treatments imposed during late rice cropping. The treatments were continuously flooded rice cultivation (CF), non-continuously flooded rice cultivations without (ZM) and with (M) rice straw mulching. A sequential extraction procedure involving Baermann extraction (Baermann) followed by centrifugal sugar flotation (centrifugation) was used to extract the whole nematode community. Based on the analysis of nematode abundance, genera composition, trophic groups and other ecological indices (Margalef richness index, Shannon index, maturity index, enrichment index and structure index), water management significantly affected the nematode community, with the non-continuously flooded condition, in particular combination with rice straw mulching (M), stimulating nematode development. There was a high abundance, richness, and structure in the nematode community in mulched treatments, indicating improved biodiversity and biological interactions. We hypothesize that soil microclimate and available food resources are affected by water management and directly or indirectly influence the establishment of different nematode communities. We suggested that studies aiming to test natural or anthropogenic influences on nematodes might be distorted by sole use of the Baermann method. Although the Baermann step in a sequential extraction procedure gave valuable information on nematode responses to soil treatments, it was not sufficient to detect effects on the whole nematode community. Our results demonstrate that the sequential extraction procedure is an effective tool to obtain comprehensive information on the whole nematode community, with both steps providing complementary ecologically relevant information, on how the soil ecosystem is affected by human management.

A glasshouse experiment was set up to compare processes and organisms in two soils planted with genetically modified (GM) herbicide tolerant (HT) maize treated with appropriate herbicides. This was part of a wider project (ECOGEN) looking at the consequences of GM cropping systems on soil biology using a tiered approach at laboratory, glasshouse and field scales. Soil for the experiment was taken from field sites where the same maize cultivars were grown to allow comparison between results under glasshouse and field conditions. The maize cultivars T25 (GM HT glufosinate-ammonium tolerant), Orient (non HT near isogenic control for T25) and Monumental (a conventional, non HT variety) were grown in contrasting sandy loam and clay loam soils, half were sprayed with the appropriate herbicide as used in the field and soil samples were taken at the five-leaf and flowering plant growth stage. The main effects on all measured parameters were those of soil type and plant growth stage, with four categories of subsequent interaction: (1) there were no effects of herbicide on plant growth or soil microarthropods: (2) the maize cultivar (but not the GM HT trait) had effects on the decomposition of cotton strips and the nematode community; (3) herbicide application in general altered the community level physiological profile of the microbial community and reduced both soil basal respiration and the abundance of protozoa; and (4) the specific application of glufosinate-ammonium to T25 maize altered soil microbial community structure measured by ester linked fatty acids. The results from this glasshouse experiment support the findings from the field that there are effects of herbicide application on the soil microbial and meso-faunal community but that, compared to other standard agricultural practices, the differences are relatively small.

Molecular techniques offer an alternative to time-consuming traditional methods of faunal identification based on morphology. The first stage in developing a molecular technique is to have a robust method to extract DNA. Here methods are assessed using nematodes as a model faunal group. A traditional DNA extraction, with proteinase K digestion followed by phenol chloroform extraction; sodium hydroxide extraction; and physical disruption, followed by utilisation of one of four proprietary PCR purification kits were tested for nematode DNA extraction. Nematode communities were isolated from a range of habitats (arable agriculture, sand dune, coniferous forest, permanent pasture and moorland). Template DNA concentration was measured and PCR-amplification performed to test the suitability of the extracts for downstream molecular applications. DNA extraction with phenol chloroform purification consistently yielded high-quality template DNA as did the DNA extraction followed by the Purelink PCR purification kit. T-RFLP based on a single enzyme digest was sufficient to discriminate between nematode communities extracted from all five habitats. In addition, T-RFLP demonstrated that there was little difference in perceived nematode community composition following amplification of DNA extract purified through either the Qiaquick or Purelink kits. Physical disruption of tissue followed by purification through a kit provides a rapid, reliable and relatively inexpensive method of DNA extraction, yielding high-quality template. We suggest that kit suitability should be tested for each habitat under investigation as there may be a limited bias between kits for the community DNA extracted. Application of high-throughput molecular techniques to soil microfauna increases their potential to be used as indicators in routine monitoring of soil health.

Soil nematode feeding groups are a long-established trophic categorisation largely based on morphology and are used in ecological indices to monitor and analyse the biological state of soils. Stable isotope ratio analysis (13C/12C and15N/14N, expressed asδ13C andδ15N) has provided verification of, and novel insights into, the feeding ecology of soil animals such as earthworms and mites. However, isotopic studies of soil nematodes have been limited to date as conventional stable isotope ratio analysis needs impractically large numbers of nematodes (up to 1,000) to achieve required minimum sample weights (typically >100 µg C and N). Here, micro-sample near-conventional elemental analysis–isotopic ratio mass spectrometry (μEA–IRMS) of C and N using microgram samples (typically 20 µg dry weight), was employed to compare the trophic position of selected soil nematode taxa from four feeding groups: predators (AnatonchusandMononchus), bacterial feeders (PlectusandRhabditis), omnivores (Aporcelaimidae and Qudsianematidae) and plant feeder (Rotylenchus). Free-living nematodes were collected from conventionally and organically managed arable soils. As few as 15 nematodes, for omnivores and predators, were sufficient to reach the 20 µg dry weight target. There was no significant difference inδ15N (p= 0.290) orδ13C (p= 0.706) between conventional and organic agronomic treatments but, within treatments, there was a significant difference in N and C stable isotope ratios between the plant feeder,Rotylenchus(δ15N = 1.08 to 3.22 mUr‰,δ13C = –29.58 to –27.87 mUr) and all other groups. There was an average difference of 9.62 mUr inδ15N between the plant feeder and the predator group (δ15N = 9.89 to 12.79 mUr,δ13C = –27.04 to –25.51 mUr). Isotopic niche widths were calculated as Bayesian derived standard ellipse areas and were smallest for the plant feeder (1.37 mUr2) and the predators (1.73 mUr2), but largest for omnivores (3.83 mUr2). These data may reflect more preferential feeding by the plant feeder and predators, as assumed by classical morphology-based feeding groups, and indicate that omnivory may be more widespread across detritivore groups i.e. bacterial feeders (3.81 mUr2). Trophic information for soil nematodes derived from stable isotope analysis, scaled as finely as species level in some cases, will complement existing indices for soil biological assessment and monitoring, and can potentially be used to identify new trophic interactions in soils. The isotopic technique used here, to compare nematode feeding group members largely confirm their trophic relations based on morphological studies.

The sustainable use of soils requires the protection of soil biodiversity because of its importance in the delivery of ecosystems services. However, no effective indicator exists which would allow assessment of the current state of biodiversity and is sensitive to change. This study, which is a component of the EcoFINDERS project, examines the use of mites (Acari) as a possible biological indicator of soil community composition. Thirty-six sites were sampled across 10 European countries spanning four bio-climatic zones (Alpine, Atlantic, Continental and Mediterranean) and 3 land uses (arable, grassland and forestry) for both biotic and abiotic variables. Results show a significant effect of bio-climatic zone on mite communities; in particular, the Mediterranean region had a rather distinct composition. Land use type significantly affected mite community composition and there was a distinct association with forestry. Cross-taxon congruence among soil taxa was variable and generally weak. Procrustes analysis showed that there was little similarity between the patterns of variation in mite community composition and those of other taxonomic groups (Collembola, Enchytraeidae, Nematoda and microbes). Mite and Collembola communities had the strongest correlation ( r = 0.4316, p

Soil compaction has deleterious effects on soil physical properties, which can affect plant growth, but some soils are inherently resilient, whereby they may recover following removal of the stress. We explored aspects of soil physical resilience in a field-based experiment. We subjected three soils of different texture, sown with winter wheat or remaining fallow, to a compaction event. We then monitored soil strength, as a key soil physical property, over the following 16 months. We were also interested in the associated interactions with crop growth and the microbial community. Compaction had a considerable and sustained effect in a sandy loam and a sandy clay loam soil, resulting in an increase in strength and decreased crop yields. By contrast compaction had little effect on a clay soil, perhaps due initially to the buoyancy effect of pore water pressure. Fallow clay soil did have a legacy of the compaction event at depth, however, suggesting that it was the actions of the crop, and rooting in particular, that maintained smaller strengths in the cropped clay soil rather than other physical processes. Compaction generally did not affect microbial communities, presumably because they occupy pores smaller than those affected by compaction. That the clay soil was able to supply the growing crop with sufficient water whilst remaining weak enough for root penetration was a key finding. The clay soil was therefore deemed to be much more resilient to the compaction stress than the sandy loam and sandy clay loam soils.

The interactions of genetically modified (GM) crops with soil species and ecosystems is complex, requiring both specific and broad spectrum assessments. In the ECOGEN project we undertook experiments at three scales of increasing complexity, using Bt maize expressing the Cry1Ab protein from Bacillus thuringiensis as an example. Test species were selected for laboratory-scale experiments to represent taxonomic groups that we could also monitor at glasshouse and field scales (e.g., nematodes, protozoa, micro-arthropods, earthworms, and snails). In the laboratory, single species were exposed to purified Cry1Ab protein or to Bt maize leaf powder incorporated into simplified diets under controlled conditions. In the glasshouse, multiple test species and soil microbial communities taken from ECOGEN's field sites were exposed to Bt maize plants growing under glasshouse or mesocosm conditions. In the field, evaluations were conducted on our selected indicator groups over multiple sites and growing seasons. Field evaluation included assessment of effects due to the local environment, crop type, seasonal variation and conventional crop management practice (tillage and pesticide use), which cannot be assessed in the glasshouse. No direct effects of Cry1Ab protein or Bt leaf residues were detected on our laboratory test organisms, but some significant effects were detected in the glasshouse. Total nematode and protozoan numbers increased in field soil under Bt maize relative to conventional maize, whilst microbial community structure and activity were unaffected. Field results for the abundance of nematodes and protozoa showed some negative effects of Bt maize, thus contradicting the glasshouse results. However, these negative results were specific to particular field sites and sampling times and therefore were transient. Taking the overall variation found in maize ecosystems at different sites into account, any negative effects of Bt maize at field scale were judged to be indirect and no greater than the impacts of crop type, tillage and pesticide use. Although the ECOGEN results were not predictive between the three experimental scales, we propose that they have value when used with feedback loops between the scales. This holistic approach can used to address questions raised by results from any level of experimentation and also for putting GM crop risk:benefit into context with current agricultural practices in regionally differing agro-ecosystems.

Abstract Microinvertebrate abundance was measured, together with forest soil properties and litter components in eight plots dominated by beech and birch during May to August 2001. The results were analysed using ANOVA, stepwise regression and correlation analysis. Both protozoa and nematodes were analysed according to their functional groups. The protozoa were flagellates, ciliates and naked amoebae, and the nematodes were microbial and plant feeding nematodes. Moisture levels were between 28% and 33% in soil, and 50% to 70% in litter. Population numbers were very variable between sites and dates, and showed variable levels between May and July followed by a significant increase in August.ANOVA showed significant site and date effects, mainly in the litter. Stepwise regression models and correlation analysis revealed a number of interactions among separate groups of protozoa and nematodes, as well as their interrelations with fungi and bacteria. In addition, statistical analysis of soil data revealed a number of microfaunal relationships with soil pH, moisture and organic content, whilst in the field layer a number of significant interactions with specific forest litter fractions were found.The results have revealed particularly high levels of microfaunal abundance in the litter fraction compared to the soil, with flagellates and microbial feeding nematodes showing the highest levels among the trophic groups studied. These data compare well with other studies in similar ecosystems. The invertebrates present appear to be concentrated in hotspots of biological activity. In soil, they may predominantly have been confined to the rhizosphere. In the litter, their numbers may have been enhanced by nutrient availability, which may have increased throughout the study period owing to the gradual progress of decomposition facilitated by the combination of faunal, bacterial and fungal activity.

The microbial functioning of soils following perturbation was assessed at a temperate upland grassland site, maintained by the Soil Biodiversity and Ecosystem Function Programme at Sourhope Research Station, Scotland. Published results indicated that the soil microbial communities were resilient to these initial perturbations; in this paper we tested whether they were equally resilient to a subsequent perturbation. Soil samples were taken from field plots receiving treatments that represented different forms of perturbation, viz. reseeding, application of sewage-sludge, biocide or nitrogen plus lime, and a non-perturbed control. Functional resilience following further perturbation comprising a transient heat or persistent copper perturbation was assessed over 28 days, by monitoring the short-term decomposition of added plant residues. Bacterial community structure was assessed by DGGE separation of eubacterial 16S rDNA PCR products. PCR-DGGE did not distinguish any significant difference (P>0.05) between the bacterial communities of soils under different treatments, showing differences only between treated soils and the untreated, control soils. Two days after the application of stresses, functional capability differed in soils under different treatments. Soil samples from all the treated plots were less resilient to heat stress than soil from control plots. The initial reduction in decomposition following the addition of copper differed between treatments, but function had not recovered in any of the Cu-amended soils within 28 days. Soil resilience varied according to the type and duration of stress applied, microbial activity, soil characteristics and treatment regimes. The initial resistance of function to stress was not predictive of recovery of function over time.

Although nematode community analysis is widely quoted as a useful environmental indicator, a major impediment to its wider adoption is the morphological identification of individual nematodes. Problems of taxonomy and throughput could potentially be overcome using molecular biological techniques. This study combined morphological and molecular sequencing to establish the potential for analysing nematode communities by molecular biological characterisation. Nematodes were extracted from an arable soil and the extracted nematode community divided into two for simultaneous morphological and molecular analysis. Samples were proportionately dominated (>10%) by Hoplolaimidae, Telotylenchidae, Cephalobidae and Pratylenchus, volumetrically dominated (>20%) by Anatonchus and Aporcelaimellus and genetically (>10%) dominated by sequence types clustering with Aporcelaimellus, Clarkus and Anatonchus. Nematodes from the Rhabditida and Tylenchida were under-represented in the molecular characterisation, a problem which needs to be overcome to enable routine molecular characterisation of nematode communities.

We prepared soil with greater populations of bacterial-feeding nematodes, compared to a normal field soil, to determine the effects of bacterial-feeding nematodes on the root development of tomato seedlings. Soil mixed with either pig manure or rice straw was placed in a mesh bag, and then surrounded by an outer layer of unamended soil. Nematodes were able to migrate through a 1 mm diameter mesh bag into the outer soil, thus giving greater populations than in soil surrounding a control treatment of a 5 μm diameter mesh bag, through which nematodes cannot migrate. After 28 and 35 days incubation, respectively, the outer soil contained a nine-fold increase in nematode numbers in the pig manure treatment and a six-fold in the rice straw treatment, compared to control soil. The increased nematodes were mainly bacterial-feeders, accounting for 98.2% of total nematodes in the pig manure treatment and 90.5% in the rice straw treatment. Tomato seedlings were grown in the outer soil and root parameters (total length, average diameter, total surface area, numbers of forks and numbers of tips) determined after 5 and 10 days growth at 20 °C. We found that the tomato seedlings grown in the soil containing more bacterial-feeding nematodes developed a highly branched root system with longer and thinner roots.

Studies on the effect of genetically modified Bacillus thuringiensis (Bt) crops on true soil dwelling non-target arthropods are scarce. The objective of this study was to assess the influence of a 4-week exposure to two Bt maize varieties (Cry1Ab) Cascade and MEB307 on the collembolan Protaphorura armata. For comparison three non-Bt maize varieties, Rivaldo (isogenic to Cascade), Monumental (isogenic to MEB307) and DK242, and two control diets based on baker's yeast (uncontaminated and contaminated with Bt toxin Cry1Ab) were also tested. Due to a lower C:N ratio, individuals reared on yeast performed significantly better in all of the measured endpoints than those reared on maize. P. armata performed equally well when reared on two Bt and three non-Bt maize varieties. Although there were no negative effects of Bt maize in this experiment, we recommend future studies on Bt crops to focus on species interactions in long-term, multi-species experiments. Studies on the effect of genetically modified Bacillus thuringiensis (Bt) crops on true soil dwelling non-target arthropods are scarce. The objective of this study was to assess the influence of a 4-week exposure to two Bt maize varieties (Cry1Ab) Cascade and MEB307 on the collembolan Protaphorura armata. For comparison three non-Bt maize varieties, Rivaldo (isogenic to Cascade), Monumental (isogenic to MEB307) and DK242, and two control diets based on baker's yeast (uncontaminated and contaminated with Bt toxin Cry1Ab) were also tested. Due to a lower C:N ratio, individuals reared on yeast performed significantly better in all of the measured endpoints than those reared on maize. P. armata performed equally well when reared on two Bt and three non-Bt maize varieties. Although there were no negative effects of Bt maize in this experiment, we recommend future studies on Bt crops to focus on species interactions in long-term, multi-species experiments.

Summary The composition of forest litter and understorey layer, and fungal biomass (in terms of ergosterol) were measured in eight subplots over a winter – spring period (January to April). The sampling site was positioned in a range of woodland habitats (variously dominated by beech, Fagus sylvatica ; birch, Betula pendula × pubescens , and oak Quercus petraea ) and a clear area covered with grass (dominated by Holcus lanatus ). The results were analysed together with data on bacteria and microinvertebrates available from parallel research. Levels of ergosterol in individual subplots ranged between 50 and 160 µ g g − 1 DW. Fungal biomass decreased in March, and then increased signifi cantly in April. Stepwise regression models for ergosterol indicated positive relationships with moisture content (February), bacteria (all but February and March), fl agellates (February) and plant-feeding nematodes and fl ies (January, overall). The relationships with roots, seeds, the collective variable ‘ other microinvertebrates ’ (all March), amoebae (February) and fragments (March, overall) were negative, while the relationship between fungi- and microbial-feeding nematodes changed sign between February ( − ) and March (+). Results of analysis of covariance for fungal ergosterol were signifi cant only for January and the combined dataset. In January, fungi were shown to be signifi cantly related to amoebae, bacteria and a collembolan Folsomia candida , while the only signifi cant predictor returned by the overall model was bacteria. Correlation analysis confi rmed some effects already noted, and revealed a number of further interactions. The results highlighted the complexity of factors infl uencing temporal dynamics and spatial variability of

Whole-community DNA was extracted from two pasture soils, the cultivable and directly extractable bacterial subsets of one of the soils, and two aquatic bacterioplankton communities. The percent guanine+cytosine (%G+C) base distribution, derived using thermal denaturation profiles, and parameterised using a generalised logistic equation, varied markedly between the samples. Bacterioplankton communities carried a more even distribution of %G+C than the soil communities, which had higher median %G+C. The directly extracted soil bacterial fraction had the highest median %G+C. There was a distinct trend of increasing complexity, measured using reassociation kinetics, between cultivable, extractable and total soil community DNA. Bacterioplankton communities were of a similar order of complexity to the cultivable soil bacterial fraction.

Microbial community DNA was extracted directly from an arable soil experimentally polluted with Cd, Cu, Ni, Pb or Zn, and incubated for 34 months. Broad-scale measurements of changes in microbial community structure were assessed by applying %G+C profiling and community hybridisation techniques to the DNA, and compared with phospholipid fatty acid (PLFA) profiles. %G+C profiles, statistically compared using parameterisation and principal component analysis, differed between treatments. Community hybridisation revealed a range of DNA similarities between treatments. The combination of these two techniques facilitated the interpretation of the data. The differences between the treatments determined by DNA analysis were consistent with the PLFA patterns, and revealed that: (i) microbial communities in metal contaminated soils were different from those in uncontaminated soil, (ii) the microbial community in Cu contaminated soil was different from those in soils contaminated with the other metals, and (iii) the microbial communities in soils contaminated with Pb and Ni were indistinguishable from one another.

Abstract The micro and meso-invertebrate abundance was measured, together with forest litter composition, in eight plots of differing vegetation (dominated by beech and birch) over a winter-spring period. The litter moisture content was a mean of 76% during the sampling period and the beech sites were the driest. The results were analysed using a suite of statistical techniques, together with data on protozoa, fungi and bacteria available from parallel research. Nematodes were analysed according to the trophic levels, which included microbial feeders, plant feeders and predators. The majority of arthropods found were the collembolan, Folsomia candida and cryptostigmatid mites, with very small quantities of other micro- and mesoarthropods (such as larvae and mesostigmatid mites). The microarthropod populations peaked in January and fell during subsequent months, while population numbers of nematodes showed a decrease between January and February, followed by an increase in March. ANOVA showed a significant date effect, but no site-date interactions for the population abundance of both nematodes and microarthropods. Ecological interactions of meiofauna were analysed by ANCOVA, stepwise regression, and correlation analysis. Examples of relationships revealed include positive relationships of plant-feeding nematodes (PFN) with microbial feeding nematodes (MFN), and of F. candida with cryptostigmatid mites. Other positive interactions were found for PFN, MFN, F. candida, cryptostigmatid and mesostigmatid mites with litter components, such as beech leaves and litter thickness, moisture and grass, and protozoa. Negative interactions were recorded for PFN, MFN, F. candida, cryptostigmatid and mesostigmatid mites with beech leaves, fungi, protozoa and bacteria. The results have highlighted a very complex structure of factors influencing the temporal and spatial dynamics of the forest litter community. It is suggested that temperature and moisture content particularly influence the invertebrates present. The invertebrates appear to be present in a range of microhabitats, which may have resulted in a reduced level of competition and a high level of positive interactions revealed.

We explore the potential for applying broad ecological theories to interactions between soil animals and micro-organisms to generate a predictive framework within which more hypothesis led research can be undertaken. The paper stems from discussions during a workshop at the XIVth International Symposium on Soil Zoology. The possible linkage between biodiversity and ecosystem functions forms a good example of how soil zoology research can be productively stimulated by addressing a broader ecological concept but also how the concept can be tested below ground at fundamentally different scales to those commonly used above ground. Other areas of theory rapidly developing above ground, which are yet to be fully tested below ground, include: spatial variability in food webs; indirect interactions mediated through changes in plant secondary chemistry; signalling, including tritrophic interactions; optimal foraging theory, including depletion theory when patches differ in quality as well as quantity; adaptive plasticity in life history traits in relation to temporal variability in resources; trade-offs and facultative non-symbiotic and symbiotic mutualism. We identify modelling of effects of climate change on the soil compartment of the global carbon cycle as an area in which understanding of soil fauna-microbe interaction may outstrip current ecological theory and as a major challenge facing soil biologists in the future. © 2006.

We investigated the influence of root border cells on the colonisation of seedling Zea mays roots by Pseudomonas fluorescens SBW25 in sandy loam soil packed at two dry bulk densities. Numbers of colony forming units (CFU) were counted on sequential sections of root for intact and decapped inoculated roots grown in loose (1.0 mg m−3) and compacted (1.3 mg m−3) soil. After two days of root growth, the numbers of P. fluorescens (CFU cm−1) were highest on the section of root just below the seed with progressively fewer bacteria near the tip, irrespective of density. The decapped roots had significantly more colonies of P. fluorescens at the tip compared with the intact roots: approximately 100-fold more in the loose and 30-fold more in the compact soil. In addition, confocal images of the root tips grown in agar showed that P. fluorescens could only be detected on the tips of the decapped roots. These results indicated that border cells, and their associated mucilage, prevented complete colonization of the root tip by the biocontrol agent P. fluorescens, possibly by acting as a disposable surface or sheath around the cap.

Summary Stability and resilience of a variety of soil properties and processes are emerging as key components of soil quality. We applied recently developed measures of biological and physical resilience to soils from an experimental site treated with metal-contaminated sewage sludge. Soils treated with cadmium-, copper- or zinc-contaminated, digested or undigested sewage sludge were studied. Biological stability and resilience indices were: (i) the time-dependent effects of either a transient stress (heating to 40°C for 18 hours) or a persistent stress (amendment with CuSO4) on decomposition, and (ii) the mineralization of dissolved organic carbon (DOC) released by drying–rewetting cycles. Physical stability and resilience measures were: (i) compression and expansion indices of the soils, and (ii) resistance to prolonged wetting and structural regeneration through drying–rewetting cycles. Soil total carbon and DOC levels were greater in the sludge-amended soils, but there were no differential effects due to metal contamination of the sewage sludge. Effects of metals on physical resilience were greater than effects on soil C, there being marked reductions in the expansion indices with Cd- and Cu-contaminated sludge, and pointed to changes in soil aggregation. The rate of mineralization of DOC released by drying and wetting was reduced by Zn contamination, while biological resilience was increased in the Zn-contaminated soil and reduced by Cd contamination. We argue that physical and biological resilience are potentially coupled through the microbial community. This needs to be tested in a wider range of soils, but demonstrates the benefits from a combined approach to the biological and physical resilience of soils.

Soil communities in landscapes that are rapidly changing due to a range of anthropogenic processes can be regarded as highly transient systems where interactions between competing species or trophic levels may be seriously disrupted. In disturbed communities dispersal in space and time has a role in ensuring continuity of community function. Stable communities, in undisturbed systems, are more dependent on competition and other biotic interactions between species. We predicted how food web components would respond to disturbance, based on their dispersal and colonizing abilities. During decomposition, flows of energy and nutrients generally follow either a bacterial-based path, with bacteria as the primary decomposer and bacterial-feeding fauna and their predators forming the associated food web, or a fungal-based channel. Trophic links that were generally resistant to change were the organisms of the bacterial. pathway that have high abilities to disperse in time and passively disperse in space. Organisms in the fungal pathway were less resistant to disturbance. Resource inputs to the soil system are derived from plants, either through root exudation and root turnover during active growth or from dead plant material following senescence or agricultural tillage. Disturbances to the soil system can arise as a direct action on the soil, or indirectly from effects on the above-ground plant community. Disturbance-induced changes in plant community composition will change the soil food web composition. Organisms involved in direct interactions with plants (e.g. AM-mycorrhizal fungi) were also predicted to be vulnerable to disturbance. (C) 2004 Elsevier GmbH. All rights reserved. (Less)

Can diet have a significant impact on the ability of organisms to sense and locate food? Focusing on the bacterial feeder Caenorhabditis elegans, we investigated what effect preconditioning on a range of bacterial substrates had on the subsequent chemotaxis process involved in the nematode locating other bacterial populations. Remarkably, we found that C. elegans, initially fed on a diet of Escherichia coli OP50, was significantly impaired in finding E. coli OP50 populations, compared to other available bacterial populations (P < 0.001). We found similar results for another bacterial feeding nematode species, suggesting that a general “substrate legacy” may operate across a wide range of organisms. We discuss this important finding with respect to the variation in response exhibited within a given nematode population, and the impact nematode migration has on bacterial dispersal in the environment.

We characterised the spatial structure of soil microbial communities in an unimproved grazed upland grassland in the Scottish Borders. A range of soil chemical parameters, cultivable microbes, protozoa, nematodes, phospholipid fatty acid (PLFA) profiles, community-level physiological profiles (CLPP), intra-radical arbuscular mycorrhizal community structure, and eubacterial, actinomycete, pseudomonad and ammonia-oxidiser 16S rRNA gene profiles, assessed by denaturing gradient gel electrophoresis (DGGE) were quantified. The botanical composition of the vegetation associated with each soil sample was also determined. Geostatistical analysis of the data revealed a gamut of spatial dependency with diverse semivariograms being apparent, ranging from pure nugget, linear and non-linear forms. Spatial autocorrelation generally accounted for 40-60% of the total variance of those properties where such autocorrelation was apparent, but accounted for 97% in the case of nitrate-N. Geostatistical ranges extending from approximately 0.6-6 m were detected, dispersed throughout both chemical and biological properties. CLPP data tended to be associated with ranges greater than 4.5 m. There was no relationship between physical distance in the field and genetic similarity based on DGGE profiles. However, analysis of samples taken as close as 1 cm apart within a subset of cores suggested some spatial dependency in community DNA-DGGE parameters below an 8 cm scale. Spatial correlation between the properties was generally weak, with some exceptions such as between microbial biomass C and total N and C. There was evidence for scale-dependence in the relationships between properties. PLFA and CLPP profiling showed some association with vegetation composition, but DGGE profiling did not. There was considerably stronger association between notional sheep urine patches, denoted by soil nutrient status, and many of the properties. These data demonstrate extreme spatial variation in community-level microbiological properties in upland grasslands, and that despite considerable numeric ranges in the majority of properties, overarching controlling factors were not apparent.

The community fingerprints of both the prevalent and the metabolically active microbial community were related to a quantitative estimation of microbial biomass in an arable soil, revealed by substrate-induced-respiration (SIR). Two concentrations of glucose or l -asparagine, representing those used in the SIR measurement or equivalent to those released in root exudates, were studied. Respiration rates and changes in community structure fingerprints were followed for 48 h. Bacterial and fungal community fingerprints were obtained using both reverse transcribed 16S and 18S ribosomal RNA (rRNA) regions and the corresponding rDNA as a template in PCR. Samples were then analysed by denaturing gradient gel electrophoresis (DGGE). Low concentrations of substrate amendments resulted in minor changes in rRNA or rDNA-based bacterial and fungal banding patterns during the whole 48 h incubation. High concentrations of substrates, especially l -asparagine, increased respiration rates and induced significant changes in both 16S rRNA and rDNA-community fingerprints. The prominent rRNA and rDNA bacterial community sequence types were common to all treatments, but in general the bacterial rDNA fingerprints had fewer bands than the corresponding rRNA profiles that assess the active fraction of the community. In contrast, there was little difference between fungal 18S rRNA and rDNA patterns. The number of fungal ribosomal sequence types in DGGE fingerprints was lower than the number of bacterial types. This study indicated that there was a rapid respiration response by the whole microbial community during SIR estimates in soil, but that community structure did not change during the conventional incubation period. In an extended (8–48 h) incubation with high amounts of l -asparagine increased respiration was associated with growth of the microbial community.

• Background and Aims Border cells are released from the root tips of many plant species, and can remain viable in the rhizosphere for 1 week. Whether border cells are capable of controlled glucose exchange with their environment was investigated. • Methods Border cells were removed from Zea mays L. root tips, and immersed in 14C‐labelled d‐glucose. In one experiment, the hexose transport inhibitor, phlorizin, was used to investigate active glucose uptake from a range of glucose concentrations. In another experiment, glucose efflux from border cells was monitored over time. • Key Results Glucose uptake by the border cells increased with increasing glucose concentration from 0·2 to 20 mm. At 0·2 mm glucose, uptake was mainly active, as evidenced by the approx. 60 % inhibition with phlorizin. At 2 and 20 mm glucose, however, uptake was mainly via diffusion, as phlorizin inhibition was negligible. Glucose efflux increased with time for live border cells in both 2 and 20 mm glucose. There was no clear efflux/time pattern for heat‐killed border cells. • Conclusions Border cells actively take up glucose, and also release it. Under our experimental conditions, glucose uptake and efflux were of similar order of magnitude. In the rhizosphere net glucose exchange will almost certainly depend on local soil conditions.

This study aimed to characterise soil microbial community structure and function in temperate upland grassland ecosystems. We compared the use of community level physiological profiles (CLPP), phospholipid fatty acid (PLFA) profiles and community DNA (%G+C base distribution) approaches to quantify soil microbial community structure and potential activity across a gradient of three upland grassland types at 10 geographically distinct sites within the UK. Soil microbial biomass (Cmic) was highest in unimproved (U4a) and lowest in improved (MG6) grasslands. In contrast, potential soil microbial activity (carbon utilisation) was greatest in the improved and lowest in the semi-improved (U4b) grasslands. PLFA and culturing revealed that the soil microbial community shifted from one favouring fungi to one favouring bacteria as grassland improvement increased. Canonical variate analysis (CVA) of the CLPP and PLFA data differentiated microbial communities from the grassland types and sites and the separation between grasslands was greater using PLFA than CLPP. Discrimination between grasslands was mainly due to the presence of higher concentrations of fatty acids typical for Gram −ve bacteria in improved grasslands and actinomycete and fungal fatty acids in the semi and unimproved grasslands. CVA of the %G+C data gave less discrimination of the microbial communities than the other two methods. Correlation analysis of the CVA data for each microbial analysis showed a small, but significant, level of matching between the CLPP and PLFA data suggesting these two analyses may be reporting on similar members of the microbial community. Correlation between microbial community structure and soil physio-chemical properties indicated that PLFA were highly correlated with calcium, phosphorus, sodium, nitrogen and organic matter content and pH. CLPP were highly correlated with sodium and organic matter content and pH, while %G+C content correlated with pH. Correlation between microbial community structure and plant community structure indicated that fatty acids typical for Gram −ve bacteria were highly correlated with the presence of Lolium perenne and Trifolium repens and all microbial PLFA with the presence of Vaccinium myrtillus. Correlation of plant species with CLPP indicated that the presence of a number of rushes, shrubs, herbs and grasses influenced the metabolic profiles of the microbial communities from these grasslands. The presence of herbs were found to be highly correlated with certain %G+C classes within the community DNA.

Changes in biopolymer products during transit of the intestine in two termites with contrasting feeding habits were quantified by pyrolysis mass-spectrometry. In Zootermopsis nevadensis, a wood-feeder, native lignin-derived fractions increased in the faeces, with little indication of modification or degradation, but 62% of hexose polymer and 43% of xylan were degraded. In the soil-feeding Cubitermes ugandensis, polysaccharide and alkene-derived mass ions were enriched in faeces while amino acid-derived ions were depleted, consistent with a proposed model of fermentative digestion supported by peptides released from soil organic matter.

Summary It seems possible that soil potential nitrification rates (PNRs) are determined by the size and structure of both the eubacterial and nitrifier populations. We have examined this possibility by comparing the structure of the eubacterial community with the subcomponents and dynamics of the ammonium-oxidizer population, within and between three arable fields. PNRs were significantly different between the three fields and also showed significantly different temporal patterns within each field. The use of eubacterial primers in polymerase chain reaction–denaturing gel gradient electrophoresis (PCR–DGGE) analyses indicated that the bacterial community structure in each field was significantly different from that in the others, and that the bacterial components of these communities changed with time through the season. In contrast, PCR–DGGE analyses specific to ammonium oxidizers suggested that the populations in all three fields were similar in types and did not vary with time. Competitive PCR suggested that there were large and biologically significant differences in the size of the nitrifier population between the three fields, but that within each individual field populations did not change over time. Sequencing identified the ammonium oxidizers in the Nitrosospira spp. cluster. There was also no relation between the size of the nitrifier populations and PNR. Functional expression, as PNR, apparently responded to changes in eubacterial community structure.

The abundance of heterotrophic flagellates, ciliates and naked amoebae was measured in 8 sites covered with different vegetation (beech, birch, beech-birch, birch-oak-beech, grass) from January to April 2001. The results were analysed by a suite of mathematical techniques, together with data on bacteria, fungi, nematodes, microarthropods, and the composition of forest litter and field layer, available from parallel research. The population levels ranged between 4.02 and 795 × 103, 28 and 1010, 35 and 1170 g–1 litter dry wt for flagellates, ciliates and amoebae, respectively. Temporal changes in the microbiota appeared to be affected by progressive winter cooling followed by a spring increase in temperature, and influenced by habitat characteristics and a complex multivariate interplay among ecosystem components. The population abundance in winter (January-mid March) was higher than in spring (late March–April) for all protozoa. Amoebae showed minimum values in March, followed by considerable recovery in April. However, ciliate values dropped slightly between March and April, whilst flagellate values steadily decreased throughout the whole research period, suggesting that the spring growth of ciliates and flagellates might have been arrested by increased predation and/or competition. Statistical analysis revealed a number of significant relationships between the protozoa studied and other ecosystem components. These relationships were indicative of the conditions studied and may, therefore, be useful for future reference. The results highlighted the complexity of transient multivariate interactions of protobiota in forest litter, suggesting that any interpretations of the population dynamics must take account of a full range of both temporal and spatial factors.

Abstract Two similar, sandy loam soils from the same geographical region but with distinct nematode communities were used to determine the extent to which water, soil and inoculum factors affected nematode community structure. Treatments were established in pots containing a middle layer of frozen defaunated soil, sandwiched between an inoculum that was either fresh soil from the same site ('self') or a mixture of soils to give a more diverse inoculum ('mixed'). During year 2, half the pots were watered at regular intervals while the other half received only rainfall. For individual nematode taxa, soil layer and watering regime were the main factors discriminating between treatments, while initial inoculum had a larger influence than soil type. Acrobeloides was most affected by the watering regime, being more abundant under variable water conditions, whereas Hoplolaimidae, Longidorus and Pratylenchus were more abundant in deeper soil layers in contrast to other taxa. For the community as a whole, when analysed by principal component analysis, soil factors clearly influenced composition and also indicated that the biological properties of the soils were important.

The survival of enteric pathogens in sewage sludge could lead to their transferral into the soil environment and subsequent contamination of crops and water courses. This, in turn, could increase the potential spread of gastrointestinal disease. This work aimed to determine the persistence of several microorganisms, co-introduced with sewage sludge, when exposed to varying proportions of sewage sludge to soil. Three microcosm-based studies were established, inoculated with Salmonella Dublin or an environmentally-persistent strain of Escherichia coli (quantified periodically over a period of 42 days), or indigenous sewage sludge E. coli (quantified over a period of 56 days). Treatments consisted of a mixture containing: 0, 15, 25, 50, 75 and 100% soil or sludge, depending upon the experiment. Each introduced microorganism declined significantly over time, with greater quantities of soil generally instigating greater die-off particularly in the cases of environmentally-persistent E. coli and S. Dublin. However, this relationship was not proportionally related as sludge/soil mixtures showed greater declines than pure soil treatments. In contrast, indigenous sewage sludge E. coli had a more consistent decline across all treatments. This may indicate that indigenous strains are more resilient and may be indicative of natural behaviour. Moreover, the effects of soil-borne factors on pathogen attenuation were context dependent and non-linear, possibly arising from the relative spatial distribution of introduced sludge and attendant microbes in soil.

The influence of grazing by a mixed assemblage of soil protozoa (seven flagellates and one amoeba) on bacterial community structure was studied in soil microcosms amended with a particulate resource (sterile wheat roots) or a soluble resource (a solution of various organic compounds). Sterilized soil was reinoculated with mixed soil bacteria (obtained by filtering and dilution) or with bacteria and protozoa. Denaturing gradient gel electrophoresis (DGGE) of PCR amplifications of 16S rRNA gene fragments, as well as community level physiological profiling (Biolog plates), suggested that the mixed protozoan community had significant effects on the bacterial community structure. Excising and sequencing of bands from the DGGE gels indicated that high-G+C gram-positive bacteria closely related to Arthrobacter spp. were favored by grazing, whereas the excised bands that decreased in intensity were related to gram-negative bacteria. The percentages of intensity found in bands related to high G+C gram positives increased from 4.5 and 12.6% in the ungrazed microcosms amended with roots and nutrient solution, respectively, to 19.3 and 32.9% in the grazed microcosms. Protozoa reduced the average bacterial cell size in microcosms amended with nutrient solution but not in the treatment amended with roots. Hence, size-selective feeding may explain some but not all of the changes in bacterial community structure. Five different protozoan isolates ( Acanthamoeba sp., two species of Cercomonas , Thaumatomonas sp., and Spumella sp.) had different effects on the bacterial communities. This suggests that the composition of protozoan communities is important for the effect of protozoan grazing on bacterial communities.

Four similar, agricultural soils with distinct nematode communities were used to determine the extent to which soil and inoculum factors affected nematode community structure. The soils all had a sandy loam texture from the same geographical area and had been in pasture or arable rotation for the last 10 years. Treatments were established in pots containing a middle layer of frozen defaunated soil, sandwiched between an inoculum that was either fresh soil from the same site ('self') or a mixture of soils to give a more diverse inoculum ('mixed'). Principal component analysis indicated that a single soil type given different inocula developed different community structures (i.e., the community under 'self' differed from that under 'mixed') suggesting an inoculum effect. It was also true that different soil types under a single inoculum soil also developed different community structures (i.e., community under 'mixed' differed with soil type), suggesting a soil effect. It is likely that the nematode community structure is influenced by a combination of antecedent land use, soil factors, species introductions and inter-species competition, which should be considered in any interpretation of nematode communities as a biotic indicator.

peer-reviewed Plants rely on microorganisms to mobilize organically and inorganically bound sulfur (S) and phosphorus (P) in which the plant can then readily utilize. The aim of this study was to investigate the role of S- and P-mobilizing bacteria in plant growth promotion in biochar-amended soil, which has been rarely investigated so far. Pot experiments of Lolium perenne were established on S and P limited soil with 1% or 2% biochar (Miscanthusxgiganteus) or without biochar (control) for a period of 126days. Both biochar amendments resulted in significant plant growth promotion. Rhizobacteria capable of growing with (1) S from aromatic sulfonates, (2) P from phosphate esters, (3) P from phosphonates, and (4) P from tri-calcium phosphates as sole source of S or P, respectively, were significantly more abundant in the biochar treatments. 16S rRNA gene-based rhizobacteria community analysis revealed a significant biochar treatment effect. Abundance of nematodes feeding on bacteria was also significantly increased in the biochar treatments. Diversity analysis of rhizospheric asfA and phnJ genes revealed broad sequence diversities in bacterial sulfonate and phosphonate-mineralizing capabilities. These findings suggest that biochar amendment enhances microbially mediated nutrient mobilization of S and P resulting in improved plant growth. ACCEPTED peer-reviewed