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The resilience of microbial functions like carbon (C) and nitrogen (N) cycling to stress is likely heavily dependent on pH. Past research, however, has been limited to laboratory manipulations or a pH gradient resulting from differences in soil mineralogy. In this study, soils were collected from a >50-year field trial where plots have been maintained at pH 4.9, 6 and 7.1. We selected copper (Cu) and heat to represent persistent and transient stresses, respectively. Changes in C mineralization, ammonia oxidation, denitrification, and gene (16S rRNA, nirK, nirS and amoA) abundance were immediately measured after heat- (40 °C for 16 hours) and Cu- (500 µg Cu soil g-1 or 1 mg Cu soil g-1) induced stresses, during subsequent recovery over 56 days, and compared to an unstressed control. Higher soil pH significantly increased C mineralization (by 217%), ammonia oxidation (by 617%), and the gene abundances of 16S rRNA (by 77%), nirK (by 976%) and nirS (by 997%). Soil pH had a significant (P < 0.001) selection effect on the phylotypes of bacterial communities and ammonium oxidising bacteria (AOB). Ammonia oxidation was significantly (P < 0.05) more resistant and resilient to both Cu stresses in the pH 7.1 soil. C mineralization in the soil at pH 7.1 was significantly (P < 0.05) more resilient to low Cu than the soil at pH 4.9. Correspondingly, significantly (P < 0.001) distinct bacterial communities were present in these soils, indicating that bacterial composition triggered by the adaptation and tolerance to stress is a central factor governing functional resilience. Denitrification in the pH 7.1 soil was significantly (P < 0.05) more resilient to low and high Cu, compared to the soil at pH 4.9. Similarly, the abundances of nirS and nirK genes were greater in the higher pH soil. Although soil pH directly affects Cu but not heat stress, our results indicated that neutral soils harboured greater resilience of C and N cycling to both Cu (persistent) and heat (transient) stresses.

The functional performance of soil ecosystems following disturbance determines ecosystem stability, and although contributions of bacterivorous nematodes to soil ecosystems are recognized, their roles in functional stability have received little attention. The objective of this study was to evaluate the roles of bacterivorous nematodes in functional stability following stress. In a factorial laboratory experiment, soil microcosms were prepared with two levels of nematode abundance, either an enriched abundance of bacterivores (Nema soil) or background abundance of nematodes (CK soil), and three levels of stress, copper, heat, or an unstressed control. The resistance and resilience of nematode abundance, as well as soil microbial function by determining decomposition of plant residues and microbial substrate utilization pattern using a BIOLOG microplate, were followed post stress. The relative changes of two dominant bacterivores, Acrobeloides and Protorhabditis, responded differently to stresses. The resistance and resilience of Protorhabditis were greater than that of Acrobeloides to copper stress during the whole incubation period, while both bacterivores only showed higher resilience under heat stress at the end of incubation. The enrichment of bacterivores had no significant effects on the soil microbial resistance but significantly increased its resilience to copper stress. Under heat stress, the positive effect of bacterivores on soil resilience was only evident from 28 days to the end of incubation. The differences in the responses of soil function to stress with or without bacterivores suggested that soil nematodes could be conducive to ecosystem stability, highlighting the soil fauna should be taken into account in soil sustainable management.

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.

International audience; The ability of ecosystems to withstand disturbances and maintain their functions is being increasingly tested as rates of change intensify due to climate change and other human activities. Microorganisms are crucial players underpinning ecosystem functions, and the recovery of microbial communities from disturbances is therefore a key part of the complex processes determining the fate of ecosystem functioning. However, despite global environmental change consisting of numerous pressures, it is unclear and controversial how multiple disturbances affect microbial community stability and what consequences this has for ecosystem functions. This is particularly the case for those multiple or compounded disturbances that occur more frequently than the normal recovery time. The aim of this review is to provide an overview of the mechanisms that can govern the responses of microbes to multiple disturbances across aquatic and terrestrial ecosystems. We first summarize and discuss properties and mechanisms that influence resilience in aquatic and soil biomes to determine whether there are generally applicable principles. Following, we focus on interactions resulting from inherent characteristics of compounded disturbances, such as the nature of the disturbance, timing, and chronology that can lead to complex and nonadditive effects that are modulating the response of microorganisms.

Sloughing of root cap cells and exudation of mucilage plays an important role in the penetration of compacted soils by roots. For the first time we have quantified the rate of sloughing of root cap cells in an abrasive growth medium that was compacted to create mechanical impedance to root growth. The number of maize (Zea mays) root cap cells sloughed into sand increased as a result of compaction, from 1930 to 3220 d -1 per primary root. This represented a 12-fold increase in the number of cells sloughed per mm root extension (from 60 to > 700). We estimated that the whole of the cap surface area was covered with detached cells in compacted sand, compared with c. 7% of the surface area in loose sand. This lubricating layer of sloughed cells and mucilage probably decreases frictional resistance to soil penetration. The total carbon deposited by the root was estimated at c. 110 μg g -1 sand d -1 . Sloughed cells accounted for < 10% of the total carbon, the vast majority of carbon being contained in mucilage exudates.

Soils frequently experience environmental stresses that may have transient or persistent impact on important ecosystem services, such as carbon (C) and nitrogen (N) cycling. Microbial communities underpin resistance (the ability to withstand a stress) and resilience (the ability to recover from a stress) of these functions. Whilst functional stability and resilience have been studied extensively, the link to genetic stability is missing. In this study, the resistance and resilience of C mineralization, ammonia oxidation and denitrification, their associated gene abundances (16S rRNA, bacterial amoA, nirK, nirS, nosZ-I and nosZ-II) and bacterial community structures (T-RFLP 16S rRNA) were compared in two managed soils for 28 days after stressing the soils with either a persistent (1 mg Cu soil g−1) or a transient (heat at 40 °C for 16 h) stress. The average resistance of C mineralization to Cu was 60%, which was significantly greater than the resistance of ammonia oxidation (25%) and denitrification (31%) to Cu. Similarly, the average resilience of C mineralization to Cu was 52%, which was significantly greater than the resilience of ammonia oxidation (12%) and denitrification (18%) to Cu. However, this pattern was not significant after heat stress, indicating the critical role of different stressors. Changes in total bacterial community structure rather than abundance of 16S rRNA reflected the responses of C mineralization to Cu and heat. Both Cu and heat significantly decreased functional gene abundance (amoA, nirK, nirS, nosZ-I and nosZ-II), however, a significant recovery of denitrifying gene abundance was observed after 28 days following heat. There were lack of constant relationships between functional and genetic stability, highlighting that soil physiochemical properties, the nature of the stressor, and microbial life history traits combine to confer functional resistance and resilience. Genetic responses on their own are therefore inadequate in predicating changes to soil functions following stresses.

As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns., This research was supported by a grant from DOB Ecology to T.W.C., a grant from the Netherlands Organization for Scientific Research (grant 016.Veni.181.078) to S.G., grants from NSF (OPP 1115245, 1341736, 0840979) to B.J.A., by a Ramon y Cajal fellow award (RYC-2016-19939) to R.C.H., a grant from UNEP & Global Environment Facility to J.E.C., grants from NERC’s Soil Security Programme to R.D.B. (NE/M017028/1) T.C. (NE/M017036/1), a grant from FAPEMIG/FAPESP/VALE S.A.(CRA-RDP-00136-10) to L.B.C., through the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) awarded to S.R.C., a grant from CNPq PROTAX (562346/2010-4) to J.M.d.C.C., a grant from DFG (CRC990) to V.K. and S.S., a grant from the MSHE of Russia (AAAA-A17-117112850234-5) to A.A.K., grants from the Chinese Academy of Sciences (XDB15010402) and the National Natural Science Foundation of China (41877047) to Q.L., grants from the National Natural Science Foundation of China (31330011, 31170484) to W.L., grants from NERC (NE/ M017036/1) to M.M., grants from the Spanish Ministry of Innovation (CGL2009-14686-C02-01/02, CGL2013- 43675-P) to J.A.R.M., grant from the Spanish Ministry of Innovation (RYC-2016-19939) to R.C.H., grants from NSF (DEB-0450537, DEB-1145440) to P.M., T.O.P. and K. Powers, grants from the German Academic Exchange Service (PKZ 91540366) and NAFOSTED (106.05–2017.330) to T.A.D.N., by an ARC Discovery project (DP150104199) to U.N.N., by the National Key Research and Development Program of China (2016YFC0502101) and the National Natural Science Foundation of China (31370632) to K. Pan, a ERC Research Council Advanced grant (ERC-Adv 323020 SPECIALS) to W.H.v.d.P, a grant from the Natural Environment Research Council (NERC) to D.G.W., a grant from BAPHIQ (106AS-9.5.1-BQ-B3) to J.-i.Y., a grant from the Russian Foundation for Basic Research (18-29-05076) to A.V.T. The James Hutton Institute receives financial support from the Scottish Government Rural and Environment Science and Analytical Services (RESAS) division. Investigations in Northwest Russia were carried out under state order for IB KarRC RAS and are partially supported by the Russian Foundation for Basic Research (18-34-00849).

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.

Livestock grazing can affect both above- and below-ground communities, however, the effects of grazing intensity on vertical distribution of root traits and their associations with belowground food webs are still unclear. Based on a 5-year grazing intensity experiment (i.e., no grazing, moderate grazing and heavy grazing) in a Tibetan plateau meadow, we investigated how grazing-induced changes in root traits affected soil biota (microbes and nematodes) from the surface (0–10 cm) and subsurface soils (10–20 cm). Our results showed that moderate grazing increased nematode abundance and structure complexity of the soil micro-food webs compared to no and heavy grazing, and predominantly increased herbivores and fungivores regardless of soil layers. Shifts in herbivores and fungivores were mainly driven by root quantity and quality, emphasizing the stronger bottom-up effects on the lower trophic levels of nematodes. Grazing decreased the number of omnivores-predators in the surface soil compared to no grazing, which therefore weakened predation pressure on soil nematodes lower in the trophic structure, including root herbivores, while that effect was far less pronounced in the subsurface soil. Our study demonstrated that changes in root quantity and quality were highly associated with the complexity of the soil micro-food webs under grazing scenarios. These findings warranted the ideas that combined aboveground herbivore-root-soil micro-food webs as an ecological holo is essential for sustainable management of grassland.

Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 georeferenced samples to generate a mechanistic understanding of the patterns of the global abundance of nematodes in the soil and the composition of their functional groups. The resulting maps show that 4.4 ± 0.64 × 1020 nematodes (with a total biomass of approximately 0.3 gigatonnes) inhabit surface soils across the world, with higher abundances in sub-Arctic regions (38% of total) than in temperate (24%) or tropical (21%) regions. Regional variations in these global trends also provide insights into local patterns of soil fertility and functioning. These high-resolution models provide the first steps towards representing soil ecological processes in global biogeochemical models and will enable the prediction of elemental cycling under current and future climate scenarios., This research was supported by a grant from DOB Ecology to T.W.C., a grant from the Netherlands Organization for Scientific Research (grant 016.Veni.181.078) to S.G., grants from NSF (OPP 1115245, 1341736, 0840979) to B.J.A., by a Ramon y Cajal fellow award (RYC-2016-19939) to R.C.H., a grant from UNEP & Global Environment Facility to J.E.C., a grant from NERC (NE/M017036/1) to T.C., a grant from FAPEMIG/FAPESP/VALE S.A.(CRA-RDP-00136-10) to L.B.C., through the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) awarded to S.R.C., a grant from CNPq PROTAX (562346/2010-4) to J.M.d.C.C., a grant from DFG (CRC990) to V.K. and S.S., a grant from the MSHE of Russia (AAAA-A17-117112850234-5) to A.A.K., grants from the Chinese Academy of Sciences (XDB15010402) and the National Natural Science Foundation of China (41877047) to Q.L., grants from the National Natural Science Foundation of China (31330011, 31170484) to W.L., grants from NERC (NE/M017036/1) to M.M., grants from the Spanish Ministry of Innovation (CGL2009-14686-C02-01/ 02, CGL2013-43675-P) to J.A.R.M., grants from NSF (DEB-0450537, DEB-1145440) to P.M., T.O.P. and K. Powers, grants from the German Academic Exchange Service (PKZ 91540366) and NAFOSTED (106.05 – 2017.330) to T.A.D.N., by an ARC Discovery project (DP150104199) to U.N.N., by the National Key Research and Development Program of China (2016YFC0502101) and the National Natural Science Foundation of China (31370632) to K. Pan, a grant from the Natural Environment Research Council (NERC) to D.G.W., a grant from BAPHIQ (106AS-9.5.1-BQ-B3) J.-i.Y. The James Hutton Institute receives financial support from the Scottish Government Rural and Environment Science and Analytical Services (RESAS) division. Investigations in northwest Russia were carried out under state order for IB KarRC RAS and are partially supported by the Russian Foundation for Basic Research (18-34-00849). We thank E. Clark and A. Orgiazzi for review of the manuscript; and R. Bouharroud, Z. Ferji, L. Jackson and E. Mzough for providing data.

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.

A large part of Australia’s broad acre irrigation industry, which includes cotton, is farmed on heavy clay Vertosols. Recent changes in nematicide chemical availability, changes in rotations and the observation of the reniform nematode in central Queensland has highlighted that we need to improve our understanding of nematodes in these soils. We undertook preliminary investigations into distribution by depth under a cotton-cotton and cotton-maize rotation as well as vertical movement experiments in microcosms to better understand nematode distribution and movement in heavy clay soils. Analysis revealed that field populations decreased with soil sample depth, but there were also differences between rotations. In microcosm experiments, vertical movement of nematodes in these heavy clay soils was restricted, even in the presence of plant roots and moisture, both of which were hypothesised to improve nematode migration. The results imply that crop rotation currently remains a plausible option for nematode control, and that we still have a lot to learn about the ecology of nematode populations in Vertosols.

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.

The quantity and quality of plant-derived resources are the primary factors regulating soil microbial communities, however, the top-down control of soil fauna on the soil food web is still underexplored. To integrate bottom-up and top-down forces in mediating soil microbial communities, we evaluated six plant species rhizosphere microbial community structure (indicated by multiple PLFA biomarkers) and functioning (indicated by four different enzyme activities) in the presence and absence of seven adult Metaphire guillelmi earthworms. Six plant species with two legume species (Trifolium repens and Medicago sativa), two grass species (Arundo donax and Lolium perenne) and two grain crops (Triticum aestivum and Zea mays) were used varying with resource demand and nutrient acquisition strategies. We found earthworms led to increasing in similarity of rhizosphere microbial community structure across all studied plant species. For example, the variability of the fungi: bacteria and gram-positive: gram-negative ratios across six plant species was reduced in the presence of earthworms. Furthermore, earthworms generally supported enzyme production in acquiring carbon over nitrogen and phosphorus, and enhanced immobilization sink for N in microbial biomass, suggesting earthworms are more beneficial for microbes in acquiring energy as plant roots-produced enzyme mostly targeted on nutrients. In conclusion, our results revealed a context-dependent earthworm effects on microbial community structure and a general pattern of earthworms in shifting enzyme production across different plant species.

peer-reviewed Grasslands form a significant proportion of land used across the globe and future management is important. The objective of this study was to compare the long-term impact of inorganic phosphorus (Pi) fertilisation rates (P0, P15 and P30 ha−1 yr−1) under two grass management trials (grazed vs. cut and removed) on soil physicochemical properties, microbial biomass, phosphomonoesterase activity, bacterial community structure and abundance of a phosphorus (P) mineralising gene (phoD). Under grazing, microbial biomass and soil phosphorus concentrations (total and Pi) generally increased with Pi fertilisation rate, accompanied by significant differences in bacterial community structure between unfertilised (P0) and P30 soil. At the cut and removed site, although Pi was significantly greater in P30 soil, P concentrations (total and Pi) did not increase to the same extent as for grazing, with microbial biomass and bacterial community structures unresponsive to Pi fertilisation. Despite differences in soil P concentrations (total and Pi) and microbial biomass between sites, the abundance of bacterial phoD increased with increasing soil Pi across both sites, while phosphomonoesterase activity decreased. Amplicon sequencing revealed Acidobacteria were the dominant bacterial phylum across both grasslands, but significant differences in relative abundances of bacterial genera were detected at the grazed site only. The bacterial genera Gp6 and Gp16 increased significantly with Pi fertilisation under grazing. Conversely, Bradyrhizobium as well as unclassified genus-type groups belonging to Actinobacteria and Acidimicrobiales significantly decreased with Pi fertilisation, suggesting potential roles in P mobilisation when soil Pi concentrations are low. This study highlights the importance of long-term Pi fertilisation rates and aboveground vegetation removal in shaping soil bacterial community structure and microbial biomass, which in turn may impact soil fertility and plant productivity within agricultural soils.

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

The sustainable management of land for agricultural production has at its core a healthy soil, because this reduces the quantity of external inputs, reduces losses of nutrients to the environment, maximises the number of days when the soil can be worked, and has a pore structure that maximises both the retention of water in dry weather and drainage of water in wet weather. Soil health encompasses the physical, chemical, and biological features, but the use of biological indicators is the least well advanced. Sustainability also implies the balanced provision of ecosystem services, which can be more difficult to measure than single indicators. We describe how the key components of the soil food web contribute to a healthy soil and give an overview of the increasing number of scientific studies that have examined the use of biological indicators. A case study is made of the ecosystem service of water infiltration, which is quite an undertaking to measure directly, but which can be inferred from earthworm abundance and biodiversity which is relatively easy to measure. This highlights the difficulty of putting any monitoring scheme into practice and we finish by providing the considerations in starting a new soil health monitoring service in the UK and in maintaining biological monitoring in The Netherlands.

Molecular approaches are offering a supplement to, or even the possibility of replacing morphological identification of soil fauna, because of advantages for throughput, coverage and objectivity. We determined ecological indices of nematode community data from four sets of duplicate soil cores, based on morphological identification of nematodes after elutriation from 200 g soil and high throughput sequencing (HTS) targeting nematodes both after being elutriated from soils and DNA extracted directly from 10 g soil. HTS (at genus and species level) increased the taxonomic resolution compared to morphology (at family level). DNA extracted from elutriated nematodes identified more nematode taxa than when extracted from soil, due to an enrichment in nematode sequences. Each method also gave a different ecological footprint for the nematode community. Standardisation to previously determined indices based on morphological identification is needed in order to provide more meaningful information about soil quality and for ecological monitoring.

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.

There is a growing recognition of the fundamental importance of soils in supporting productive and sustainable agricultural systems. The term sustainable intensification is now widely used to characterise the importance of linking productivity with sustainability. This term recognises the need to maintain or increase food production without increasing the use of land or external inputs. In this chapter, we explore the concepts of sustainable intensification and soil quality and explain how these impact soils in different global regions. The economic impacts of improving soil quality are also considered.

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.

Summary Earthworms have been perceived as benevolent soil engineers since the time of Charles Darwin, but several recent syntheses link earthworm activities to higher greenhouse gas emissions, less soil biodiversity, and inferior plant defense against pests. Our study provides new field-based evidence of the multiple direct and indirect impacts of earthworms on ecosystem functions within an ecological multifunctionality framework (i.e., aggregated measures of the ability of ecosystems to simultaneously provide multiple ecosystem functions). Data from a 13-year field experiment describing 21 ecosystem functions showed that earthworm presence generally enhanced multifunctionality by indirect rather than direct effects. Specifically, earthworms enhanced multifunctionality by shifting the functional composition toward a soil community favoring the bacterial energy channel and strengthening the biotic associations of soil microbial and microfaunal communities. However, earthworm-mediated changes in soil physical structure, pH, and taxonomic diversity were not related to multifunctionality. We conclude that the coordinated actions of earthworms and their associated soil biota were responsible for the maintenance of multifunctionality at high levels in this rice-wheat cropping system. Management of crop residue inputs and reduction of soil physicochemical disturbances should encourage beneficial earthworm effects and support multiple ecosystem services that are vital to sustainable agriculture.

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.

Enteropathogens released into the environment can represent a serious risk to public health. Soil clay content has long been known to have an important effect on enteropathogen survival in soil, generally enhancing survival. However, clay mineral composition in soils varies, and different clay minerals have specific physiochemical properties that would be expected to impact differentially on survival. This work investigated the effect of clay materials, with a predominance of a particular mineral type (montmorillonite, kaolinite, or illite), on the survival in soil microcosms over 96 days of Listeria monocytogenes, Salmonella Dublin, and Escherichia coli O157. Clay mineral addition was found to alter a number of physicochemical parameters in soil, including cation exchange capacity and surface area, and this was specific to the mineral type. Clay mineral addition enhanced enteropathogen survival in soil. The type of clay mineral was found to differentially affect enteropathogen survival and the effect was enteropathogen-specific.

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

The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia – Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia. The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise. nonPeerReviewed

Soils provide many ecosystem services that are ultimately dependent on the local diversity and below ground abundance of organisms. Soil biodiversity is affected negatively by many threats and there is a perceived policy requirement for the effective biological monitoring of soils at the European level. The aim of this study was to evaluate and recommend policy relevant, cost-effective soil biological indicators for biodiversity and ecosystem function across Europe. A total of 18 potential indicators were selected using a logical-sieve based approach. This paper considers the use of indicators from the 'top down' (i.e. concerned with the process of indicator selection), rather than from the 'bottom up' detail of how individual indicators perform at specific sites and with specific treatments. The indicators assessed a range of microbial, faunal and functional attributes, newer nucleic acids based techniques, morphological approaches and process based measurements. They were tested at 6 European experimental sites already in operation and chosen according to land-use, climatic zone and differences in land management intensity. These were 4 arable sites, one each in Atlantic, Continental, Mediterranean and Pannonian climate zones, and 2 grassland sites, one each in Atlantic and Continental zones. At each site we sampled three replicated plots of contrasting management intensity and, while the treatments varied from site to site, their disturbance effects were quantified in terms of land use intensity. The field sampling and laboratory analysis were standardised through a combination of ISO protocols, or standard operating procedures if the former were not available. Sites were sampled twice, in autumn 2012 and spring or autumn 2013, with relative costs of the different indicators being determined each time. A breakdown of the cost effectiveness of the indicators showed the expected trade-off between effort required in the field and effort required in the laboratory. All the indicators were able to differentiate between the sites but, as no single indicator was sensitive to all the differences in land use intensity, we suggest that an indicator programme should be based upon a suite of different indicators. For monitoring under the European climatic zones and land uses of this study, indicators for ecosystem functions related to the services of water regulation, C-sequestration and nutrient provision would include a minimum suite of: earthworms; functional genes; and bait lamina. For effective monitoring of biodiversity all taxonomic groups would need to be addressed. (C) 2016 Elsevier Ltd. All rights reserved.

European Commission 036314 MTKD-CT2006-042062 MicroB3-287589-OCEAN2012 MACUMBA-CP-TP 311975 PharmaSea-CPTP 312184, EU 256596; International audience; Fertilisers, especially nitrogen (N) and phosphorus (P) supplies, are frequently used in agricultural soil management to attain high crop yields. However, the intensive application of these chemical inputs can decrease the quality of agricultural soils and increase the probability of environmental pollution. In this study, the impact of P fertilisation on the diversity of the soil bacterial community was assessed. For this, a culture-independent approach targeting 16 rRNA and phoD genes was used on DNA extracted from pasture soils subjected to three different P fertilisation regimes for a long-term (42 years). As alkaline phosphomonoesterase (ALP) is necessary for mineralisation of organic P, an inverse relationship between the level of potential ALP activity and soil available P was expected. Indeed, a lower ALP activity was observed in soil subjected to higher chemical P fertiliser input. Analysis of the prevalence of three divergent families of ALP (PhoA, PhoD and PhoX) in metagenomic datasets revealed that PhoD is the most frequent ALP in soil samples and was selected as the most representative ALP possessed by the soil bacterial communities. Diversity of the phoD phosphorus mineraliser group, as well as the total bacterial community, was both increased in response to long-term P fertilisation. Specifically, phosphorus fertilisation decreased the relative abundance of certain taxa, including Acidobacteria and Pseudomonas fluorescens. In conclusion, this study shows that P fertilisation affects the microbial diversity of soil ecosystems, which might potentially modulate the soil biogeochemical cycle.

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.

Summary 1. Nematode assemblages are commonly used as an indicator of ecosystem health; however, conventional approaches to assemblage analyses are restricted by time-consuming processing and declining availability of expertise. Molecular methods offer a rapid and cost-effective alternative. 2. We have designed a molecular profiling system, using directed terminal-restriction fragment length polymorphism (dT-RFLP), to characterise nematode assemblages by relative abundance of feeding guilds. 3. An arable soil was first characterised by cloning and sequencing of small subunit ribosomal DNA, and an enzyme digest selected to discriminate between feeding guilds. This yielded 14 different terminal-restriction fragments (T-RFs) from the sequence set, assigned to five nematode feeding guilds. 4. Robustness of the dT-RFLP methodology was tested. The greatest amount of variation between replicates occurred at the PCR stage, with little variability between replicate digests from the same PCR product or capillary runs. 5. dT-RFLP revealed changes in assemblage composition owing to organic amendments of dairycattle slurry and municipal green compost. The proportion of microbial feeding nematodes was higher in compost and slurry plots than in the no amendment control in the first sampling after organic amendment. Plant feeding nematodes composed a significantly greater proportion of the control assemblage during the growing season and post-harvest. 6. The increased throughput of molecular analysis compared with microscopy increases the feasibility of studies involving large-scale sampling and makes nematode assemblage analysis more attractive as an indicator of soil health for environmental assessment.