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Agricultural soils are important sources of greenhouse gases (GHGs). Soil properties and environmental factors have complex interactions which influence the dynamics of these GHG fluxes. Four arable and five grassland soils which represent the range of soil textures and climatic conditions of the main agricultural areas in the UK were incubated at two different moisture contents (50 or 80% water holding capacity) and with or without inorganic fertiliser application (70 kg N ha⁻¹ ammonium nitrate) over 22 days. Emissions of N₂O, CO₂ and CH₄ were measured twice per week by headspace gas sampling, and cumulative fluxes were calculated. Multiple regression modelling was carried out to determine which factors (soil mineral N, organic carbon and total nitrogen contents, C:N ratios, clay contents and pH) that best explained the variation in GHG fluxes. Clay, mineral N and soil C contents were found to be the most important explanatory variables controlling GHG fluxes in this study. However, none of the measured variables explained a significant amount of variation in CO₂ fluxes from the arable soils. The results were generally consistent with previously published work. However, N₂O emissions from the two Scottish soils were substantially more sensitive to inorganic N fertiliser application at 80% water holding capacity than the other soils, with the N₂O emissions being up to 107 times higher than the other studied soils.

The development of soil sustainability is linked to the improved management of soil biota, such as earthworms, and crop residues to improve soil physical structure, enhance microbial activities, and increase nutrient cycling. This study examined the impacts of maize residue (65.8C/N ratio, dry biomass 0.75 kg m−2) incorporation and earthworms (70 g Metaphire guillelmi m−2) on the resistance and resilience of soil C and N cycling to experimentally applied stresses. Field treatments were maize residue incorporation, maize residue incorporation with earthworm addition, and an unamended control. Resistance and resilience of C mineralization, ammonia oxidation, and potential denitrification were investigated over 28 days following a persistent stress of Cu (1 mg Cu soil g−1) or a transient heat stress (50 °C for 16 h). The results indicated that C mineralization was more resistant and resilient than ammonia oxidation and denitrification to either a persistent Cu or a transient heat stress. The application of maize residues significantly increased soil microbial biomass, C mineralization, ammonia oxidation and potential denitrification compared with the unamended control. Maize residues significantly improved the resistance and resilience of N processes to Cu and heat stress. The presence of earthworms significantly increased potential denitrification but had limited positive effect on functional resistance and resilience. This study suggested crop residue incorporation would strongly increase soil functional resistance and resilience to persistent and transient stresses, and thus could be a useful agricultural practice to improve soil ecosystem sustainability.

The rate of change in the relative size of SOC pools (sensitivity) due to land management may vary depending on their level of chemical and/or physical protection from decomposition, but has rarely been directly measured. The availability of archived (1975) soils from an abandoned long term tillage treatment experiment provided a unique opportunity to assess the sensitivity of SOC pools with different levels of stability to uniform land management after divergent tillage treatments. There were four initial treatments (1968–1991): 1) deep plough then no till, 2) shallow plough, 3) reduced till then rotary cultivation and 4) no till. The treatments were followed by uniform long-term grassland management (17 years) and subsequent short-term arable (two years). The sensitivity of SOC to land management was assessed by fractionation and direct comparison of archived soils and soils sampled in 2014 from this site. Both reductions and increases in SOC stocks were observed over time in comparable treatments but the overall effect was a trend towards an equilibration of SOC stocks across all plots. The labile fractions (particulate and dissolved organic matter) were sensitive to land management regardless of initial tillage treatment, but were more sensitive in the reduced till + rotary cultivation and no till treatments (2.3–5.3 times more sensitive than the whole soil) than the deep plough + no till and shallow plough treatments (1.12.2 times more sensitive than the whole soil). The chemically resistant fraction of the soils was surprisingly sensitive to land management (0.9–1.3 times more sensitive than the whole soil). This study shows that the degree of sensitivity of SOC fractions to land management can vary significantly depending on previous tillage management practices.

Earthworms could affect soil C and N cycling process to balance their energy and nutrients requirements, and they could also regulate soil microbial community structure and microbial acquisition for C and N. However, the connection between faunal and microbial stoichiometry in the coupling soil C and N cycling remains poorly understood. In a controlled laboratory experiment, we amended soil with five litters differing in litter chemistry (clover, maize stover, wheat straw, Rumex and bagasse fiber) including a no litter control and treated them without or with earthworms (Metaphire guillelmi). After 90 d incubation, we examined changes in earthworm tissue and microbial stoichiometry and different soil C and N fractions. Earthworm tissue C content was rather stable compared with the fluctuation in tissue N, implying that C is under stronger control and associated with higher demand than N. The presence of earthworm significantly enhanced CO2 emissions and decreased particulate organic carbon (POC) and soil organic carbon (SOC) contents in the low lignin litter species clover, maize stover and wheat straw. Meanwhile, earthworm presence increased N2O cumulative emissions but exerted negligible effects on particulate organic nitrogen (PON) and soil total nitrogen (TN) contents irrespective of litter species. Correspondingly, earthworm regulated microbial C and N acquisition as C to N-degrading enzyme activity ratio were nearly doubled in the low lignin litter species clover, maize stover and wheat straw, while it was decreased in the high lignin litter species Rumex and bagasse fiber. However, the structural equation modeling indicated C loss induced by earthworms was mainly attributed to their effects on soil fungi and bacteria abundance, while much less related to C-degrading enzyme activities. In conclusion, litter species controlled earthworm effects on soil C and N loss and associated microbial acquisition for C and N, highlighting the pivotal role of resource chemistry in the regulation of soil fauna impact on soil functioning and ecosystem services.

Elevated atmospheric CO2 concentrations (eCO2) often increase plant growth but simultaneously lead to the nitrogen (N) limitation in soil. The corresponding mitigation strategy such as supplementing N fertilizer and growing high-yielding cultivars at eCO2 would further modify soil ecosystem structure and function. Little attention has, however, been directed toward assessing the responses of soil food web. We report results from a long-term free air CO2 enrichment (FACE) experiment in a rice paddy agroecosystem that examined the responses of soil micro-food webs to eCO2 and exogenous nitrogen fertilization (eN) in the rhizosphere of two rice cultivars with distinctly weak and strong responses to eCO2. Soil micro-food web parameters, including microfauna (protists and nematodes) and soil microbes (bacteria and fungi from phospholipid fatty acid (PLFA) analysis), as well as soil C and N variables, were determined at the heading and ripening stages of rice. Results showed that eCO2 effects on soil micro-food webs depended strongly on N fertilization, rice cultivar and growth stage. eCO2 stimulated the fungal energy channel at the ripening stage, as evidenced by increases in fungal biomass (32%), fungi:bacteria ratio (18%) and the abundance of fungivorous nematodes (64%), mainly due to an enhanced carbon input. The eN fueled the bacterial energy channel by increasing the abundance of flagellates and bacterivorous nematodes, likely through alleviating the N-limitation of plants and rhizosphere under eCO2. While eCO2 decreased the abundance of herbivorous nematodes under the weak-responsive cultivar by 59% and 47% with eN at the heading and ripening stage, respectively, the numbers of herbivorous nematodes almost tripled (×2.9; heading) and doubled (×1.6; ripening) under the strong-responsive cultivar with eCO2 at eN due to higher root quantity and quality. Structural equation model (SEM) showed that lower trophic-level organisms were affected by bottom-up forces of altered soil resources induced by eCO2 and eN, and effects on higher trophic level organisms were driven by bottom-up cascades with 69% of the variation being explained. Taken together, strategies to adapt climate change by growing high-yielding crop cultivars under eCO2 may face a trade-off by negative soil feedbacks through the accumulation of root-feeding crop pest species.

Vertisols are characterized by their high clay content, which can hinder assessment of their soil biology. Recovery of nematodes from vertisols with active techniques has indicated that free living nematode numbers within Australian vertisols are often low. Despite this, cotton yield losses due to the reniform nematode have recently been reported in Australia. In light of this and other changes in the cotton production system, we undertook a series of experiments to determine whether passive nematode extraction techniques could be applied to high clay vertisols. Existing published passive nematode recovery methods proved to be inefficient. The use of sodium hexametaphosphate as a clay dispersant was found to further reduce effectiveness. Instead, direct extraction of soil in Ludox at 1.1 g/cm3 followed by sieving was found to be as effective at recovering nematodes using Baermann funnel extraction from fresh soil but considerably quicker and three times more effective with dried soil.

Herbivorous insect pests living in the soil represent a significant challenge to food security given their persistence, the acute damage they cause to plants and the difficulties associated with managing their populations. Ecological research effort into rhizosphere interactions has increased dramatically in the last decade and we are beginning to understand, in particular, the ecology of how plants defend themselves against soil-dwelling pests. In this review, we synthesise information about four key ecological mechanisms occurring in the rhizosphere or surrounding soil that confer plant protection against root herbivores. We focus on root tolerance, root resistance via direct physical and chemical defences, particularly via acquisition of silicon-based plant defences, integration of plant mutualists (microbes and entomopathogenic nematodes, EPNs) and the influence of soil history and feedbacks. Their suitability as management tools, current limitations for their application, and the opportunities for development are evaluated. We identify opportunities for synergy between these aspects of rhizosphere ecology, such as mycorrhizal fungi negatively affecting pests at the root-interface but also increasing plant uptake of silicon, which is also known to reduce herbivory. Finally, we set out research priorities for developing potential novel management strategies.

In terrestrial ecosystems decomposing cadavers act as resource patches affecting nutrient cycling and soil communities, but the effects on soil communities are not well known. In this study we investigated nematode community response to decomposing pig cadavers (Sus scrofa) over a one-year period. As nematodes play key roles in soil food webs and are known to respond to disturbances and nutrient enrichment, we hypothesised that they would respond to decomposing cadavers and that this response would change over time. We compared the temporal patterns of nematode density and community structure under pig cadavers, either placed directly on the ground or hung 1 m aboveground (for effects of cadaveric fluids only), with two controls, i.e., bare soil and bags filled with soil placed on the ground (fake pigs – for microclimatic effects only). In the control and fake pig treatments nematode densities, community patterns and maturity indices did not change significantly. In contrast, density increased significantly underneath the ground and hanging pigs two weeks after the beginning of the experiment, and nematode family richness, Simpson diversity and maturity index were significantly reduced in the cadaver treatments. Most nematode families responded negatively to cadavers with the notable exceptions of Rhabditidae, Neodiplogasteridae and Diplogasteroididae. The latter two were found exclusively underneath the decomposing cadavers and are promising bioindicators of vertebrate cadaver decomposition. Even though diversity, density and communities were recovering after one year, the impact of cadavers was still significant for the maturity index. These contrasting patterns illustrate how decomposing cadavers contribute to increasing local biodiversity and suggest that soil nematodes could be used as a tool to document the presence of a decomposing cadaver, or to estimate the time elapsed since death (post-mortem interval). Patterns should, however, be compared in different settings and seasons before such a tool can be validated.

Sustainable agriculture aims to manage soil and plant health while relying less on chemical inputs. The individual effect of organic amendments or resistant crop cultivars on the suppression of root pests through modulating soil and plant performance is being well documented. However, the interactions between organic amendments and crop cultivars are less well studied. A pot experiment was conducted across two tomato cultivars of distinct resistance to root-knot nematodes (RKNs, Meloidogyne incognita ) with three amendments including inorganic fertilizer (IF), conventional compost (CC) and vermicompost (VC). All treatments were inoculated with second-stage juveniles of M. incognita to simulate the root-knot nematode disease in field condition and to focus on the comparison among different soil amendment effects. Plant growth (shoot height, shoot biomass, root biomass and root C:N ratio), root defense metabolites (phenolics) and their related genes expression, and soil properties including pH, electrical conductivity, available nutrients, 3-indoleacetic acid (IAA), microbial biomass and activity were analyzed at 14 and 30 days post inoculation (dpi). Compared with inorganic fertilizer, vermicompost significantly decreased the numbers of nematode-induced galls on susceptible (Sus) and resistant (Res) cultivar roots by 77% and 42% respectively at 14 dpi, and by 59% and 46% respectively at 30 dpi. Vermicompost also significantly increased root defense metabolite concentrations, defense related gene expression, and improved soil properties ( p

One of the greatest challenges in soil ecology is to disentangle the plant-mediated bottom-up factors regulating soil biodiversity and community composition. The soil food web, fundamentally driving nearly all ecosystem functions, is controlled by the quantity and quality of root-mediated resources. Here, a trait-based approach was adopted to explore the divergence of soil nematode functional guilds and their connections to root traits belonging to distinct plant resource-use strategies. Root traits and rhizosphere nematode functional guilds were measured on four plant species in an ex-arable field. Results showed that plant species exhibiting acquisitive strategies promoted nematode abundance in contrast to species with conservative strategies. Further, the results also supported that plant resource-use strategies could regulate nematode life strategies in a bottom-up manner. However, lower proportions of opportunist nematodes in rhizosphere were found in acquisitive plants rather than conservative plants, mainly attributed to the stronger top-down regulation as a dominant control within the former than the later ones. Structure equation modeling revealed that root length density could primarily modulate nematode abundance and functional guilds mainly through changes in nitrogen availability of rhizosphere, as indicated by mineral N and enzymatic stoichiometry. Overall, our findings extend the conceptual framework based on a trait-centred view spanning plants to the soil food web, and this knowledge is critical to understand the mechanisms of ecosystem process.

Physical and biological soil stabilities (i.e. resistance and resilience) were measured on a range of arable farms across eastern Scotland under a range of management practices, with the objective of using a geographically restricted set of soils under similar land use to detect any underlying associations between soil stability, management factors and soil properties. Data were analysed using a combination of a stepwise fixed effects model selection within a linear mixed-model framework (LMM) and neural network analysis using a Kohonen self-organising map (KSOM). In general, physical and biological measures of stability were associated with both physical and biological soil properties, particularly bulk density, water retention characteristics, soil carbon and bacterial community structure. A strength of KSOM is its ability to fit more flexible models than the linear relationships of LMM. However, a weakness is that it does not have the ability of LMM to model the sampling design, which is likely to lead to overstating statistical significance. Consequently, KSOM identified more significant associations between soil properties and stability than LMM, while the latter identified significant associations at the between-farm level. The high-level land management decisions of farm type (conventional, organic, integrated), crop type or underlying soil type were not associated with stability at this regional scale, thus indicating that the effects of different management practices between farms were overridden by the soil properties on each farm. Management decisions on improving soil stability therefore need to be taken at the individual field scale.

Organic amendments not only promote soil quality and plant performance directly but also facilitate the establishment of introduced microbial agents. A field experiment with a fully factorial design was conducted using three levels of vermicompost (without vermicompost, low dose of 15 Mg ha−1 and high dose of 30 Mg ha−1), with and without plant growth-promoting rhizobacteria (PGPR) to investigate their effects in a tomato – by spinach rotation system. Our results demonstrated that applying PGPR alone had no effect on soil properties and crop performance. Vermicompost enhanced the beneficial effects of PGPR on both soil and crop, with the extent of promotion depending on the dose of vermicompost and crop types. In the presence of vermicompost, PGPR significantly (P

Biological invasion is governed by intrinsic and extrinsic factors, but few studies have explored the interactive roles of species traits and disturbance in soil microbial invasion. A microcosm experiment was conducted to compare the survival of four non-indigenous bacteria in soil previously subjected to heating disturbance (60 °C, 24 h). The survival of non-indigenous bacteria was positively correlated with their utilization capability of saccharose and glucose 3 days after inoculation, and positively with maltose, saccharose, D-mannitol, glycerol, glucose and amylose 42 days following inoculation. Disturbance increased resource availability and also reduced diversity of the native microbial community. Bacteria survival was significantly increased in disturbed soil, especially for the bacteria with weak resource utilization capability. Bacterial invasion potential was determined by resource utilization capability, with that dependence increased with incubation duration and reduced if soil was initially disturbed.

Previous results from a long-term grassland trial, located in south-east Ireland indicated conserved (homeostatic) nutrient stoichiometry of the soil microbial biomass despite widely varying soil C:N:P ratios. To determine whether this was associated with a change in microbial community structure, rather than a change in microbial physiology, this study characterized the responses of below-ground microbial and nematode community structure to P fertilization. The trial site maintained a range of P fertilisation rates (0–30 kg P ha−1 yr−1) which had been applied since 1968 and soil samples were collected in spring 2009, autumn 2010 and spring 2011. The microbial biomass demonstrated homeostatic stoichiometry over all sampling occasions, particularly of the C:P ratio, despite a 50-fold difference in soil solution C:P ratio. However, microbial and nematode community structure also varied with P fertilisation, indicating that nutrient ratios are maintained even though there were changes in microbial community structure. P fertilization induced a shift from fungal to bacterial dominated decomposition pathways, as indicated by the proportion of bacterial-feeding to fungal-feeding nematodes and bacterial: fungal phospholipid fatty acids (PLFAs). The altered microbial community structure was considered to result from bottom-up control of nutrient quality and quantity by altered vegetation structure and fertilizer inputs, as well as top-down pressures from the nematode community.

Soil management practices shown to increase carbon sequestration include reduced tillage, amendments of carbon and mixed rotations. As a means to mitigate greenhouse gases, however, the success of these practices will be strongly influenced by nitrous oxide (N 2 O) emissions that vary with soil wetness. Few seasonal data are available on N 2 O under different soil managements so we measured seasonal N 2 O emission in three field experiments between 2006 and 2009 in eastern Scotland. The experimental treatments at the three sites were (1) tillage: no-tillage, minimum tillage, ploughing to 20 cm with or without compaction and deep ploughing to 40 cm, (2) organic residue amendment: application of municipal green-waste compost or cattle slurry and (3) rotations: stocked and stockless (without manure) organic arable farming rotations. Most seasons were wetter than average with 2009 the wettest, receiving 20–40% more rainfall than average. Nitrous oxide emissions were measured using static closed chambers. There was no statistical evidence, albeit with low statistical power, that reduced tillage affected N 2 O emissions compared to normal depth ploughing. With organic residue amendments, only in the wet season in 2008 were emissions significantly increased by high rates of green-waste compost (4.5 kg N 2 O-N ha −1 ) and cattle slurry (5.2 kg N 2 O-N ha −1 ) compared to the control (1.9 kg N 2 O-N ha −1 ). In the organic rotations, N 2 O emissions were greatest after incorporation of the grass/clover treatments, especially during conversion of a stocked rotation to stockless. Emissions from the organic arable crops (1.9 kg N 2 O-N ha −1 in 2006, 3.0 kg N 2 O-N ha −1 in 2007) generally exceeded those from the organic grass/clover (0.8 kg N 2 O-N ha −1 in 2006, 1.1 kg N 2 O-N ha −1 in 2007) except in 2008 when the wet weather delayed manure applications and increased emissions from the grass/clover (2.8 kg N 2 O-N ha −1 ). Nevertheless, organic grassland was the land use providing the most effective overall mitigation. Although the magnitude of fluxes did not relate particularly well to rainfall differences between seasons, greater rainfall received during some growing seasons increased the differences between tillage, organic residue and crop rotation phase treatments, negating any possible mitigation by timing management operations in dry periods. This was partly attributed to applying tillage and manures late and/or in wet conditions. Of benefit would be different sampling strategies including closed chambers or eddy covariance with standardised methodology. Controlled soil management experiments with a wide geographic spread to specify land management for mitigation also important.

SUMMARYNitrification inhibitors are used in agriculture for the purpose of decreasing nitrogen (N) losses, by limiting the microbially mediated oxidation of ammonium (NH4+) to nitrate (NO3−). Successful inhibition of nitrification has been shown in numerous studies, but the extent to which inhibitors affect other N transformations in soil is largely unknown. In the present study, cattle slurry was applied to microcosms of three different grassland soils, with or without the nitrification inhibitor dicyandiamide (DCD). A solution containing NH4+and NO3−, labelled with15N either on the NH4+or the NO3−part, was mixed with the slurry before application. Gross N transformation rates were estimated using a15N tracing model. In all three soils, DCD significantly inhibited gross autotrophic nitrification, by 79–90%. Gross mineralization of recalcitrant organic N increased significantly with DCD addition in two soils, whereas gross heterotrophic nitrification from the same pool decreased with DCD addition in two soils. Fungal to bacterial ratios were not significantly affected by DCD addition. Total gross mineralization and immobilization increased significantly across the three soils when DCD was used, which suggests that DCD can cause non-target effects on soil N mineralization–immobilization turnover.

BACKGROUND Responses of the soil microbial and nematode community to organic and conventional agricultural practices were studied using the Teagasc Kinsealy Systems Comparison trial as the experimental system. The trial is a long-term field experiment which divides conventional and organic agriculture into component pest-control and soil treatment practices. We hypothesised that management practices would affect soil ecology and used community level physiological profiles, microbial and nematode counts, and denaturing gradient gel electrophoresis (DGGE) to characterise soil microbial communities in plots used for onion (Allium cepa L.) cultivation. RESULTS Microbial activity and culturable bacterial counts were significantly higher under fully organic management. Culturable fungi, actinomycete and nematode counts showed a consistent trend towards higher numbers under fully organic management but these data were not statistically significant. No differences were found in the fungal/bacterial ratio. DGGE banding patterns and sequencing of excised bands showed clear differences between treatments. Putative onion fungal pathogens were predominantly sequenced under conventional soil treatment practices whilst putative soil suppressive bacterial species were predominantly sequenced from the organic pest-control treatment plots. CONCLUSION Organic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation. © 2013 Society of Chemical Industry

Plant-mediated effects of aboveground herbivory on the belowground ecosystem are well documented, but less attention has been paid to agro-ecosystems and in particular how crop cultivars with different traits (i.e. resistance to pests) shape such interactions. A fully factorial experiment was conducted using four rice cultivars with different insect-resistance, with and without the aboveground herbivore Nilaparvata lugens (brown planthopper), and to test two hypotheses (1) aboveground herbivory affects the soil microbial biomass and nematode community by altering plant performance and soil resource availability and (2) herbivory effects will depend on cultivar resistance traits. Our results suggested that cultivar resistance mediated both herbivory intensity and herbivore effects on plant performance. N. lugens decreased the availability of soil resources (soluble sugars, amino acids, organic acids, dissolved organic carbon and nitrogen), microbial biomass and percentages of bacterivores when feeding on a susceptible cultivar but increased them in a resistant cultivar. However, total nematode abundance and the percentage of plant-parasitic nematodes responded in the opposite way, increasing under a susceptible cultivar and decreasing under a resistant cultivar. The development of plant-parasites under resistant cultivars before aboveground herbivory might contribute to their resistance traits. Our findings provide evidence that N. lugens significantly reversed the pattern of soil resource availability, microbial biomass and nematode community structure (abundance and trophic composition) across cultivars with distinct resistance. In the presence of aboveground pests, the agronomic use of resistant rice cultivars could also control populations of plant-parasites and promote soil resource availability, further extended to higher trophic level of soil food web.

nWe studied the effects of maize residue application on some life-cycle parameters of the earthworm Aporrectodea trapezoides in saline agricultural soils with electrical conductivity (EC) ranging from 1.58 to 7.35 dS m(-1). This experiment was carried out under controlled laboratory conditions for 150 days. Results showed that soil salinity significantly affected the growth and reproduction of earthworms, decreasing survival, numbers and mean fresh weights of adults, juveniles and cocoons. Maize residue application gave a greater survival of earthworms at all salinity levels, but the differences were only significant at an EC of 7.35 dS m(-1), although the mean weight of adult earthworms was significantly increased by maize residue application at all salinity levels. At an EC of 1.58 dS m(-1) and 3.35 dS m(-1), the application of maize residues gave significantly higher numbers of cocoons and juveniles, but in soils with 5.26 dS m(-1) and 7.35 dS m(-1) earthworms did not produce any cocoons over the experimental period, irrespective of maize residue application. These results indicated that maize residue application alleviated the negative effects of soil salinity on the growth and reproduction of A. trapezoides up to 3.35 dS m-1, above which maize residues only increased the growth but not on the reproduction of earthworms. (c) 2012 Elsevier Ltd. All rights reserved.

The utility of a high-throughput molecular characterisation (directed - terminal restriction fragment length polymorphism – dTRFLP) of soil nematode community structure was evaluated in a field trial of the effects of tillage intensity. Replicated plots were established in a field previously used for continuous, conventional tillage of spring barley ( Hordeum vulgare ) and cultivated by: zero tillage; minimum tillage; conventional tillage; deep tillage and conventional tillage with compaction. Nematodes were sampled in spring, summer and autumn for three years after treatment began. Total nematode abundance and Nematode Channel Ratio indicated changes due to the zero and minimum tillage, more nematodes and a greater proportion of fungal feeders, but effects were secondary to those of year and season. The effects of tillage were far easier to interpret when other bioindicators were also taken into account. Increases in soil carbon and fungal biomass in the upper layers of the zero and minimum tillage treatments, observed in parallel studies, corroborated the nematode data. The high-throughput molecular method proved to be well suited for multiple measurements of nematode community structure, although limitations in the resolution of nematode taxa could obscure changes in generic and species composition.

Responses of nematode assemblages and soil function (short-term decomposition) in restored and degraded soil following an experimental disturbance (copper, chloroform, heat or drying) were monitored for 65 days. We tested the hypotheses: restoration enhanced the measured soil parameters; stability to disturbance was higher in degraded soil due to induced tolerance; and whether changes of the nematode assemblage were related to soil function. Even after disturbance, greater nematode abundance (>150 vs >10 per 100 g soil), nematode richness ( D ′ > 1.0 vs >0.4) and function (>1.0 vs >0.05 mg CO 2 g −1 week −1 ) were maintained in restored than in degraded soil, respectively. An increase in nematode enrichment index (from 60 to >75) following all disturbances was attributed to the relatively high abundance of tolerant fungivores. The greater stability of the nematode structure index in degraded soil following heat and drying (120% and 125% respectively of the control), than in restored soil (90% and 30% of control) was due to a higher proportion of tolerant omnivores and carnivores. Thus some higher trophic level nematodes, with high c–p values, were tolerant to disturbance. However, stability of function was greater for restored than degraded soil, with a reduction over time in the degraded soil regardless of disturbance type. The differences in the responses of nematodes and soil function to disturbance suggest that nematodes could provide complementary insights into soil stability.

This study was conducted to investigate the effects of incubation temperature on mineralization of native pools of C from a soil with a history of manure application, compared to a non-manured soil. Net C mineralization, microbial community structure, biomass size, and metabolic quotient (qCO2) were measured. Mineralization at cooler temperatures followed zero-order kinetics, indicating a non-limiting supply of substrate. First-order kinetics dominated at warmer temperatures as substrate supply increasingly limited microbial respiration. The soil with a history of manure application had a larger microbial biomass than the non-manured soil, and higher rates of C mineralization. There was a trend toward decreased biomass sizes with increasing incubation temperature. Bacterial DNA T-RFLP profiles were affected by incubation temperature and time with a significant difference in community structure detected after soils had been incubated for 120 days, as well as after incubation at 35 °C. Fungal DNA T-RFLP profiles indicated a distinct community in soils incubated at 35 °C, regardless of the length of the incubation. The key findings from the study were that C mineralization from native pools of organic matter does not follow Arrhenius kinetics at high temperatures, and that incubation of soils outside of their normal temperature range can alter soil biological characteristics which may impact estimates of mineralization parameters.

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.

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 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 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.