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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. [ABSTRACT FROM AUTHOR]

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/cm3followed 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. [ABSTRACT FROM PUBLISHER]

Soils provide many ecosystem services that are ultimately dependent on the local diversity and belowground 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. [ABSTRACT FROM AUTHOR]

Abstract: 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. [Copyright &y& Elsevier]

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

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

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

Summary 1. Two lectins, concanavalin A (Con A) and Galanthus nivalis agglutinin (GNA), have anti-feedant properties that suggest a potential for the control of invertebrate pests of plants. We tested potato plants genetically engineered to produce each of these lectins constitutively, as well as the purified lectins, for possible non-target effects. 2. Laboratory studies with soil bacterial communities and a ciliate protozoan could detect no direct effect of either lectin over a range of concentrations. There was a significant inhibition in the host-finding response of a bacterial-feeding nematode when Con A or GNA was present in the medium at 0·5–50 µg ml-1. 3. A number of GNA- and Con A-producing potato lines had no detectable effects on the rhizosphere microbial and microfaunal populations when examined in pot trials. The incorporation of leaves from transgenic plants into soil reduced protozoan populations significantly, but there was no subsequent effect on the decomposition of added cotton strips. 4. Controlled field-release experiments demonstrated that, although GNA-producing potato lines consistently altered the physiological profile of the rhizosphere microbial community at harvest, the effect did not persist from one season to the next over a trial period of two field seasons. There was no significant effect of the best performing GNA line on the development of a subsequent barley crop. 5. A single Con A-producing line was tested in a controlled field-release. The only significant effects were transient reductions of c. 40% in soil protozoan populations and of c. 10% in potential microbial activity. [ABSTRACT FROM AUTHOR]

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

There is a current need to identify European biological indicators of biodiversity and ecosystem function that can be used for soil monitoring, in order to aid policy making. Europe, however, is subdivided into different bio-geographical (climate) zones, containing different soils and varying management practices. This work (as part of the EcoFINDERS project) set out to determine the range of variation in nematode community structure as a potential indicator across European bio-geographical zones, taking into account land use and soil characteristics. Nematodes have been suggested as biological indicators for the monitoring of soil quality due to their involvement in the delivery of functions such as carbon sequestration and recycling of nutrients as well as the provision of habitat for biodiversity. Using a molecular (directed-T-RFLP) approach for rapid nematode community structure assessment and a traditional morphological assessment at a feeding group level, we determined that nematode communities differ between bio-geographical zones and between different land uses within bio-geographical zones. Therefore, at the very large or trans-national level, the presence of any differing bio-geographical zones within the monitored area should be taken into account when sampling and analysing data. Care should be taken when making comparisons across different bio-geographical zones. [ABSTRACT FROM AUTHOR]

Soil organisms are considered drivers of soil ecosystem services (primary productivity, nutrient cycling, carbon cycling, water regulation) associated with sustainable agricultural production. Soil biodiversity was highlighted in the soil thematic strategy as a key component of soil quality. The lack of quantitative standardised data at a large scale has resulted in poor understanding of how soil biodiversity could be incorporated into legislation for the protection of soil quality. In 2011, the EcoFINDERS (FP7) project sampled 76 sites across 11 European countries, covering five biogeographical zones (Alpine, Atlantic, Boreal, Continental and Mediterranean) and three land-uses (arable, grass, forestry). Samples collected from across these sites ranged in soil properties; soil organic carbon (SOC), pH and texture. To assess the range in biodiversity and ecosystem function across the sites, fourteen biological methods were applied as proxy indicators for these functions. These methods measured the following: microbial diversity: DNA yields (molecular biomass), archaea, bacteria, total fungi and arbuscular mycorrhizal fungi; micro fauna diversity: nematode trophic groups; meso fauna diversity: enchytraeids and Collembola species; microbial function: nitrification, extracellular enzymes, multiple substrate induced respiration, community level physiological profiling and ammonia oxidiser/nitrification functional genes. Network analysis was used to identify the key connections between organisms under the different land use scenarios. Highest network density was found in forest soils and lowest density occurred in arable soils. Key taxomonic units (TUs) were identified in each land-use type and in relation to SOC and pH categorisations. Top-connected taxonomic units (i.e. displaying the most co-occurrence to other TUs) were identified for each land use type. In arable sites this was dominated by bacteria and fungi, while in grassland sites bacteria and fungi were most connected. In forest soils archaeal, enchytraeid and fungal TUs displayed the largest number of neighbours, reflecting the greatest connectivity. Multiple regression models were applied to assess the potential contribution of soil organisms to carbon cycling and storage and nutrient cycling of specifically nitrogen and phosphorus. Key drivers of carbon cycling were microbial biomass, basal respiration and fungal richness; these three measures have often been associated with carbon cycling in soils. Regression models of nutrient cycling were dependent on the model applied, showing variation in biological indicators. [ABSTRACT FROM AUTHOR]

The sustainable use of soils requires the protection of soil biodiversity because of its importance in the delivery of ecosystems services. However, no effective indicator exists which would allow assessment of the current state of biodiversity and is sensitive to change. This study, which is a component of the EcoFINDERS project, examines the use of mites (Acari) as a possible biological indicator of soil community composition. Thirty-six sites were sampled across 10 European countries spanning four bio-climatic zones (Alpine, Atlantic, Continental and Mediterranean) and 3 land uses (arable, grassland and forestry) for both biotic and abiotic variables. Results show a significant effect of bio-climatic zone on mite communities; in particular, the Mediterranean region had a rather distinct composition. Land use type significantly affected mite community composition and there was a distinct association with forestry. Cross-taxon congruence among soil taxa was variable and generally weak. Procrustes analysis showed that there was little similarity between the patterns of variation in mite community composition and those of other taxonomic groups (Collembola, Enchytraeidae, Nematoda and microbes). Mite and Collembola communities had the strongest correlation ( r = 0.4316, p < 0.001). There was also variation in the indicator values of individual mite groups. Mesostigmata were correlated with soil microbial activity, as assessed using Multiple Substrate Induced Respiration, and Prostigmata with Collembola. [ABSTRACT FROM AUTHOR]

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

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

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

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