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Highlights: [•] No statistical evidence of no-tillage and minimum tillage increasing N2O emissions from well-drained soil. [•] Municipal green-waste compost and cattle slurry more than doubled N2O emissions in a wet season. [•] Ploughing out grass/clover was a major stimulus of N2O emissions in an organic system. [•] High rainfall during the growing season enhanced soil management effects on N2O. [ABSTRACT FROM AUTHOR]

Soil is increasingly under environmental pressures that alter its capacity to fulfil essential ecosystem services. To maintain these crucial soil functions, it is important to know how soil microorganisms respond to disturbance or environmental change. Here, we summarize the recent progress in understanding the resistance and resilience (stability) of soil microbial communities and discuss the underlying mechanisms of soil biological stability together with the factors affecting it. Biological stability is not solely owing to the structure or diversity of the microbial community but is linked to a range of other vegetation and soil properties including aggregation and substrate quality. We suggest that resistance and resilience are governed by soil physico-chemical structure through its effect on microbial community composition and physiology, but that there is no general response to disturbance because stability is particular to the disturbance and soil history. Soil stability results from a combination of biotic and abiotic soil characteristics and so could provide a quantitative measure of soil health that can be translated into practice. [ABSTRACT FROM AUTHOR]

Abstract: 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. [Copyright &y& Elsevier]

Summary: 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. [Copyright &y& Elsevier]

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

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

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

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

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

A personal narrative is presented which explores the author's experience in conducting experiments on the impact of plant and earthworm additions on the physical and biological properties of subsoil.

The need for sustainable intensification of agricultural production has ushered in a growing awareness of soil health and a requirement to identify with some certainty how changes to land management will affect soil. From an agricultural perspective, the active management of soil health needs to balance the production of a healthy and profitable crop with environmental protection and improvement. However, the extreme spatial and temporal heterogeneity of soils, and the complexity of biological, physical and chemical interactions therein, makes predicting management effects on soil health challenging. Although the general principles underlying effects on soil health are well understood, they still need interpretation in a local context and the inclusion of site‐specific details. Approaches from landscape ecology provide a potential framework to integrate consideration of the structural (pools, patterns), dynamic and functional (processes, flows) aspects of the soil system. These approaches allow the crucial transition from a "descriptive and general" understanding toward a "detailed and site‐specific" prediction to be made. Using this conceptual framework, we have taken knowledge of the effects of fixed site factors (soil type and climatic zone), cropping systems and farm management practices on a range of soil physical, chemical and biological parameters for UK lowland agricultural systems, and have developed a predictive framework that shows semi‐quantitatively the effects of typical management choices on soil health and crop yield. [ABSTRACT FROM AUTHOR]

Purpose: Roots bridge aboveground and belowground systems, and play a pivotal role in structuring root-associated organisms via influencing food resources and habitat conditions. Most studies focused on the relationships between plant identity and root-associated organisms, however, little is known about how root traits affect nematode communities within the rhizosphere. Methods: We investigated the relationships between root traits of four plant species and nematode abundance, community structure and trophic complexity in an ex-arable field. Results: While the relative abundance of herbivores was negatively associated with specific root length (SRL), specific root area (SRA), root length density (RLD) and root C: N ratio, free-living nematodes were positively affected by these traits, implying a multifaceted effect of root traits on root-associated organisms. Importantly, we found that finer root systems promoted the complexity of rhizosphere nematode community, by increasing the relative abundance of high trophic-level nematodes (i.e., omnivores and predators) and enhancing nematode diversity. Conclusions: Our findings suggest that root traits could comprehensively shape soil community structure and interactions, and provide new insights into soil biodiversity conservation and functional maintenance. [ABSTRACT FROM AUTHOR]

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

Abstract: 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 96days 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. [Copyright &y& Elsevier]

Abstract: 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 100g soil), nematode richness (D′>1.0 vs >0.4) and function (>1.0 vs >0.05mg CO2 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. [Copyright &y& Elsevier]

The impact of earthworms (Metaphire guillelmi) on nematode and enchytraeid abundance was investigated in soil with added maize (Zea mays L., 'suyu 19') residues in a laboratory experiment. Soil mixed with maize residues and earthworms was placed inside a mesh bag of different mesh size (1 mm or 5 µm), and then surrounded by an outside laver of soil mixed only with maize residues (i.e., no earthworms). The 1-mm diam. mesh would allow the movements of nematodes, enchytraeids, and soluble nutrients between the inner and outer soil but prevent the movements of earthworms. While the 5-µm diam. mesh would prevent the migration of earthworms, nematodes, and enchytraeids. The presence of earthworms significantly decreased the abundance of nematodes and enchytraieds in the inner soils of the different mesh-size treatments compared with that in the outer soils during the 7-wk incubation, except for enchytraeids at 1 wk. The presence of earthworms increased protozoan abundance in the inner soil. There was no significant difference in microbial biomass C between inner and outer soils at the end of experiment. Thus, abundant food resources (microbial biomass and protozoa) in the presence of earthworms indicate that competition for food and forced migration was not the main mechanism for decreased enchytraeid and nematode abundance. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The article discusses a study on the effects of bacterial-feeding nematodes on plant growth. For the study, researchers examined the impact of various nematode species on the activity of auxin-producing rhizobacteria and rice root growth. They found that rice seedlings cultivated in soils woth bacterial-feeding nematodes developed a more highly branched and longer root system.

Abstract: In agricultural systems, soils are subjected to a range of stresses which may affect soil physical and biological properties and compromise the ability of the soil to function. How the soil responds to stress both initially and over time defines resistance and resilience respectively and is key to sustainable soil management. As soil organic matter (OM) is a fundamental soil property, we hypothesised that resilience would be controlled, in part, by this. As soil OM is itself affected by long-term soil management, we therefore sought to establish a direct link between this and resilience to physical and biological stresses. Fifteen soils were taken from a range of arable and grassland sites in England, including the Broadbalk and Highfield long-term experiments at Rothamsted. The soils were subjected to physical (uniaxial compaction stress) or biological (transient heat stress or persistent Cu stress) stresses in the laboratory and the effects on general physical (void ratio) and biological (substrate-induced respiration) functions were monitored over a recovery period of up to 28 days. Wet–dry and freeze–thaw cycles were also imposed on the soils following the initial recovery after compression. The initial recovery of void ratio following compression was greater in grassland soils (0.28–0.80) than arable soils (0.16–0.58) which was probably related to the elastic effect of particulate OM and the redistribution of the greater water content in the former soils. Wet–dry and freeze–thaw cycles had an additional effect in soils with clay contents greater than 26%. The transient heat stress reduced respiration rates in the grassland soils by up to 45%. Grassland soils are less likely to have been subjected to heat stress in the field since they carry a greater vegetation covering than arable soils. The more persistent Cu stress reduced respiration rates in arable soils by up to 85% but only up to 30% in grassland soils. The difference was ascribed to the greater microbial biomass and diversity in grassland soils and buffering by the OM. We defined resistance and resilience indices as the absolute value of the measured soil functions at maximum stress and after the recovery period respectively. Reasonable linear regressions (adjusted R 2 up to 0.68) were established for resistance or resilience as a function of soil OM content, used as a proxy index of soil management. Expressed in this way, grassland soils were more resistant and resilient to the physical and biological stresses than the arable soils. Linear relationships were also found to link physical and biological resistance and resilience (adjusted R 2 up to 0.96). An arable soil with 65% clay was found to be highly resilient also. We found large differences in physical and biological resilience to stress between arable and grassland soils. We attributed this primarily to the effect of soil management on the OM content, although we recognised the importance of clay content. [Copyright &y& Elsevier]

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

Discusses the impact of protozoan grazing on bacterial community structure in soil microcosms. Growth of protozoa; Abundance of bacteria; Size of bacterial cell; Mineralization of nitrogen.

Biochar application is perceived as a promising agricultural technology, but risk evaluation on the soil ecosystem has focused exclusively on soil microbes, whether microfood-web is likewise influenced by biochar remains unclear. We carried out a pot experiment planted with rapeseed for 2 years to test how biochar application (0, 20, 60 t ha−1), with or without nitrogen (N) fertilizer (0, 60, 120 t ha−1), affected soil microbes and microfauna (protists and nematodes). We observed that a high amount of biochar (60 t ha−1) increased crop productivity, microbial activity, and biomass carbon (C) and N, as well as the abundance of flagellates (protists), but decreased the abundances of bacterivorous, fungivorous, and herbivorous nematodes as well as the abundance of amoebae (protists). High biochar addition rates also shifted nematode community composition toward a fungivore dominance, and favored herbivores by decreasing the ratio of microbivorous to herbivorous nematodes. However, N fertilizer and its interaction with biochar generally had no effect on microbial activity and biomass as well as the abundance of protist and nematode. A structural equation model revealed that the effects of biochar on soil biota were largely direct, which might depend on biochar properties (e.g., pore size and alkalinity), whereas indirect effects, mediated by crop, soil pH, soil moisture, and polycyclic aromatic hydrocarbon (PAH) concentration, generally had no effect on soil biota. We conclude that biochar is a suitable soil amendment for increasing crop growth, but its detrimental effect on multitrophic levels of soil fauna calls for an identification of the optimal application rate and size fraction that could minimize potential negative effects on certain soil communities. [ABSTRACT FROM AUTHOR]

Abstract 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. Highlights • C cycling is more resistant and resilient to Cu and heat than N cycling • Resistance and resilience are primarily improved by the addition of crop residues • C and N processes can recover from heat rather than Cu [ABSTRACT FROM AUTHOR]

Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this, protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in soil studies. Recent methodological advances, particularly in molecular biology techniques, have made the study of soil protists more accessible, and have created a resurgence of interest in soil protistology. This ongoing revolution now enables comprehensive investigations of the structure and functioning of soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive review, we provide a synthesis of research gaps that should be prioritized in future studies of soil protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics that will establish soil protistology as a hub discipline connecting different fundamental and applied fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers in biology. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 h) 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 nir S (by 997 %). Soil pH had a significant (P < 0.001) selection effect on the phylotypes of bacterial communities and ammonium oxidizing 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. • Soil pH had significant impacts on C and N functions and underpinning bacterial communities. • The optimal pH for C and N functions and bacterial communities varied. • Neutral soils harboured greater resilience of C and N cycling to Cu and heat stresses. • Microbial composition is a central factor governing functional resilience. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 < 0.05) except for mineral nitrogen. Multivariate analyses further indicated that soil properties particularly pH, root primary and secondary defense metabolites were negatively associated with root gall. Moreover, soil microbial activity, pH and IAA concentration were the main soil properties positively associated with plant defense metabolites production and biomass for both susceptible and resistant cultivars. Overall, vermicompost could significantly suppress root pests via modulating soil properties as well as plant defenses, particularly for the susceptible plant. [ABSTRACT FROM AUTHOR]

Energy dynamics within ecological communities are important in delivering ecosystem services. However, it remains elusive how the energy fluxes within soil food webs respond to agricultural fertilization regimes. Here, we studied the effects of long-term organic amendments and mineral fertilizers on the energetic structure of soil nematodes from a food-web perspective. We replicated our experiment in a rice paddy and in an upland maize cropping system. Results showed that the abundance of most trophic groups was higher in organically amended soils compared with mineral fertilizer treatments in both systems. Organic amendments, but not mineral fertilizers, increased the energy flux of total nematodes and most trophic groups compared with the no-fertilizer treatment. Furthermore, organic amendments increased the relative allocation of energy flux to microbivores but decreased the relative allocation to herbivores, supporting a higher flow uniformity than mineral fertilizers. We further found that organic amendments favored a higher total energy flux by supporting a greater nematode diversity, while sustained a higher flow uniformity by altering nematode community composition. Taken together, the result provides the evidence that a complex and species-rich community could transfer more energy to support ecosystem services. A broader perspective on linkages of biodiversity and energy dynamics spanning multitrophic groups is crucial for sustainable management, particularly in the light of non-random species loss under future environmental change. [Display omitted] • Organic amendments increased total energy flux and flow uniformity. • High flow uniformity resulted from increasing relative energy flux of microbivores. • Energy fluxes and flow uniformity were positively linked with nematode diversity. • Effect of diversity decline on energy loss was stronger in paddy than upland fields. [ABSTRACT FROM AUTHOR]

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 < 0.05) reduced soil carbon and nitrogen but increased soil microbial biomass carbon and nitrogen. PGPR also significantly increased the yield of tomato and spinach under the low dose of vermicompost, but only significantly increased tomato yield under the high dose of vermicompost. There were strongly synergistic effects between vermicompost and PGPR on crop quality, with crop nitrate concentration being significantly decreased, while the vitamin C in tomato and soluble protein in spinach was significantly increased. Our results revealed the high potential of integrating vermicompost and microbial agents to substitute for regular chemical fertilization practices. [ABSTRACT FROM AUTHOR]

Energy flux in food webs, i.e., energy consumption by different trophic groups and describing their energetic structure, has been proposed as a powerful tool to understand the relationships between biodiversity and multiple ecosystem functions (ecosystem multifunctionality). Here we examined how different fertilization regimes affected the energy flux across multitrophic levels of soil nematodes in the paddy rice and upland maize fields. We considered 13 ecosystem functions of four ecological processes related to plant productivity, nutrient cycling processes and drivers, and functional stability, which are central to energy and nutrient flow across trophic levels. To confirm whether multitrophic flux would underpin the relationships between biodiversity and multifunctionality, we compared energy flux with other approaches including taxonomic diversity, functional diversity and community composition. Results showed that organic fertilizer supported 33–340% greater multitrophic energy flux of soil nematode community and enhanced 41–264% of ecosystem multifunctionality in both fields compared with mineral fertilizer treatments. Organic fertilization enhanced ecosystem multifunctionality by favoring energy flux in multitrophic levels of soil nematodes, while fertilization-mediated changes in other facets of biodiversity were less related to multifunctionality. Our study provides empirical evidence that energy flux within food webs can be used to understand the impacts of environmental change drivers on ecosystem multifunctionality. • Organic fertilization increased ecosystem multifunctionality. • Energy flux of soil nematodes was positively related to multifunctionality. • Energy flux underpinned the link between biodiversity and multifunctionality. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Highlights: [•] Soil iron and aluminum minerals showed great affinity for the laccase. [•] Adsorbed laccases retained 26–64% of the activity of the free enzyme, and showed increased K m values and decreased V max values versus the free laccase. [•] Mineral adsorption enhanced catalytic activity of laccase under extra acid conditions and decreased the thermal stability. [•] Mineral adsorption increased E a and ΔH a values of laccase. [•] Mineral adsorption improved the resistance to proteolysis and extended the lifespan of laccase. [Copyright &y& Elsevier]

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 [ABSTRACT FROM AUTHOR]

Abstract: We examine the potential of trait-based parameters of taxa for linking above- and below-ground ecological networks (hereafter ‘green’ and ‘brown’ worlds) to understand and predict community dynamics. This synthesis considers carbon, nitrogen and phosphorus-related traits, the abundance of component species and their size distribution across trophic levels under different forms of management. We have analysed existing and novel databases on plants, microbes and invertebrates that combine physico-chemical and biological information from (agro)ecosystems spanning the globe. We found (1) evidence that traits from above- and below-ground systems may be integrated in the same model and (2) a much greater than expected stoichiometric plasticity of plants and microbes which has implications for the entire food-web mass–abundance scaling. Nitrogen and phosphorus are primary basal resources (hence, drivers) and more retranslocation of P than of N from leaves will lead to higher N:P in the litter and soil organic matter. Thus, under nutrient-rich conditions, higher foliar concentrations of N and P are reflected by lower N:P in the brown litter, suggesting less P retranslocated than N. This apparent stoichiometric dichotomy between green and brown could result in shifts in threshold elemental ratios critical for ecosystem functioning. It has important implications for a general food-web model, given that resource C:N:P ratios are generally assumed to reflect environmental C:N:P ratios. We also provide the first evidence for large-scale allometric changes according to the stoichiometry of agroecosystems. Finally, we discuss insights that can be gained from integrating carbon and nitrogen isotope data into trait-based approaches, and address the origin of changes in Δ13C and Δ15N fractionation values in relation to consumer–resource body-mass ratios. [Copyright &y& Elsevier]

Abstract: 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. [Copyright &y& Elsevier]

Abstract: The commercial cultivation of genetically modified (GM) crops in the European Union (EU) necessitates, according to EU legislation, the setting up of a General Surveillance (GS) system that should be able to detect unanticipated effects of GM crops on the environment. Although the applicant is responsible for setting up GS as well as for reporting the results, EU Member States may implement additional supporting surveillance programmes. Devising a GS system to detect unanticipated effects is not straightforward and requires clearly defined protection goals, suitable indicators that are linked to measurable parameters and an objective system for assessing the data. This paper describes a number of recommendations for the development of a General Surveillance system of the soil ecosystem specifically focussed on the situation in the Netherlands. The overarching protection goal of General Surveillance is ‘soil quality’, which is translated into more practical terms of ecosystem services that are relevant for soil quality, and that can be used to select measurable parameters and thus make a link with actual measurements. Ultimately, if and when effects on ecosystem services are detected, decision makers will have to decide whether these effects are acceptable or not. As a support for these decision-making processes, this paper discusses the modalities for the development of a stakeholder participation model. The model involves three groups of persons: the land users, the soil scientists and the decision makers. For reasons of cost effectiveness, a GS system of the soil ecosystem will have to make use of existing networks. The Dutch Soil Quality Network (DSQN) offers an existing infrastructure for soil sampling for GS. Finally, the GS system may be extended to contain data from the Dutch Ecological Monitoring Network, earth observation systems as well as other data resources such as farmers questionnaires or reports form organisations involved in nature conservation. Ideally these data are compiled by a Central Reporting Office (CRO) and maintained in a Geographic Information System (GIS) based database. [Copyright &y& Elsevier]

Abstract: 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. [Copyright &y& Elsevier]

Abstract: 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. [Copyright &y& Elsevier]

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

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. [Display omitted] • Structure complexity of soil micro-food webs showed hump-shaped responses to grazing intensity. • The carbon\nitrogen ratio of plant root was decreased by grazing compared to no grazing scenarios. • Moderate grazing strengthened the herbivory and fungal pathways of nematode community. • The abundance of herbivores and fungivores were positively correlated with plant root quantity and quality. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We investigated if the activity of soil invertebrates (protozoa and earthworms) affected the performance of barley and if effects propagated higher up the above-ground food chain into herbivores (cereal aphid, Sitobion avenae ). Barley plants were grown individually in microcosms containing defaunated soil and grass residues. Plants were grown in soil containing: a) no added fauna, b) protozoa, c) earthworms, or d) protozoa and earthworms. After 7 weeks growth at 20°C three adult cereal aphids were added to each plant on separate leaves. The aphids were allowed to grow and reproduce for another 2 weeks before the experiment was destructively sampled. Amounts of mineral N in the soil and leached from the microcosms were significantly reduced by the presence of soil animals. Correspondingly plant biomass and total plant N content were increased significantly by soil animals, protozoa in particular. The different mechanisms responsible for changes in nutrient turnover in presence of protozoa and earthworms are discussed. Aphid performance was strongly influenced by the presence of protozoa, but not by earthworms. In the presence of protozoa the numbers and biomass of adult and juvenile aphids were significantly increased. These effects are likely due to an increased N content in barley plants and consequently increased nitrogen availability to aphids. The results underline that the detritivore and herbivore systems are intimately linked. [ABSTRACT FROM AUTHOR]

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. • We studied the resistance and resilience of C and N processes and microbial communities to Cu and heat stress. • The relationship between functional and genetic stability was not constant, varying between stresses and time. • C mineralization was more resistant and resilient to Cu compared to denitrification and ammonia oxidation. [ABSTRACT FROM AUTHOR]

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. • Acquisitive plants promoted nematode abundance and K-strategist nematodes. • Conservative plants supported mainly r-strategist nematodes. • Root length density was the key root trait for regulating soil nematodes. [ABSTRACT FROM AUTHOR]

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. • Earthworms enhanced multifunctionality by indirect rather than direct effects • Earthworms shifted functional composition toward bacterial-dominated community • Multifunctionality was unrelated to changes in soil biodiversity, structure, and pH Liu et al. study a 13-year-old field experiment to show that earthworms are beneficial to agroecosystems from a multifunctional perspective. This work incorporates the concerns of negative effects of earthworms in recently published syntheses and highlights the potential pathways in which earthworms contribute to sustainable agriculture. [ABSTRACT FROM AUTHOR]