Modelling and quantifying the effect of heterogeneity in soil physical conditions on fungal growth

Despite the importance of fungi in soil ecosystem services, a theoretical framework that links soil management strategies with fungal ecology is still lacking. One of the key challenges is to understand how the complex geometrical shape of pores in soil affects fungal spread and species interaction. Progress in this area has long been hampered by a lack of experimental techniques for quantification. In this paper we use X-ray computed tomography to quantify and characterize the pore geometry at microscopic scales (30 μm) that are relevant for fungal spread in soil. We analysed the pore geometry for replicated samples with bulk-densities ranging from 1.2–1.6 g/cm3. The bulk-density of soils significantly affected the total volume, mean pore diameter and connectivity of the pore volume. A previously described fungal growth model comprising a minimal set of physiological processes required to produce a range of phenotypic responses was used to analyse the effect of these geometric descriptors on fungal invasion, and we showed that the degree and rate of fungal invasion was affected mainly by pore volume and pore connectivity. The presented experimental and theoretical framework is a significant first step towards understanding how environmental change and soil management impact on fungal diversity in soils

Assessment of <i>Miscanthus</i> × <i>giganteus</i> derived biochar as copper and zinc adsorbent:study of the effect of pyrolysis temperature, pH and hydrogen peroxide modification

In this work, experimental and modelling investigations were conducted on biochars pyrolyzed at 350 °C and 600 °C, to determine the effect of pyrolysis temperature, hydrogen peroxide activation and pH on copper and zinc removal, in comparison with commercially available activated carbons. Characterization of biochars was performed by BET surface area, elemental analysis and FTIR spectroscopy. Experiments results demonstrated that biochar pyrolyzed at 600 °C adsorbed both copper and zinc more efficiently than biochar pyrolyzed at 350 °C. Chemical activation by H2O2 increased the removal capacity of biochar pyrolyzed at 350 °C. All investigated biochars showed a stronger affinity for copper retention, with a maximum adsorption capacity of 15.7 mg/g while zinc was 10.4 mg/g. The best adsorption performances were obtained at pH 5 and 6. Langmuir adsorption isotherm described copper adsorption process satisfactorily, while zinc adsorption was better described by Freundlich isotherm

The influence of habitat quality on the foraging strategies of the entomopathogenic nematodes Steinernema carpocapsae and Heterorhabditis megidis

Entomopathogenic nematodes (EPN) are soil-transmitted parasites and their foraging strategies are believed to range from ‘ambush’ to ‘cruise’ foragers. However, research on their behaviour has not considered the natural habitat of these nematodes. We hypothesized that EPN behaviour would be influenced by soil habitat quality and tested this hypothesis using 2 EPN species Steinernema carpocapsae (an ‘ambusher’) and Heterorhabditis megidis (a ‘cruiser’) in 2 contrasting habitats, sand and peat. As predicted from previous studies, in sand most S. carpocapsae remained at the point of application and showed no taxis towards hosts, but in peat S. carpocapsae dispersed much more and showed a highly significant taxis towards hosts. H. megidis dispersed well in both media, but only showed taxis towards hosts in sand. In outdoor mesocosms in which both species were applied, S. carpocapsae outcompeted H. megidis in terms of host finding in peat, whereas the opposite was true in sand. Our data suggest that these 2 EPN may be habitat specialists and highlight the difficulties of studying soil-transmitted parasites in non-soil media

Predicting the minimum liquid surface tension activity of pseudomonads expressing biosurfactants

Bacteria produce a variety of biosurfactants capable of significantly reducing liquid (aqueous) surface tension (γ) with a range of biological roles and biotechnological uses. In order to determine the lowest achievable surface tension (γMin), we tested a diverse collection of Pseudomonas-like isolates from contaminated soil and activated sludge, and identified those expressing biosurfactants by drop-collapse assay. Liquid surface tension reducing ability was quantitatively determined by tensiometry, with 57 isolates found to significantly lower culture supernatant surface tensions to 24.5 – 49.1 mN m−1. Differences in biosurfactant behaviour determined by foaming, emulsion and oil-displacement assays, was also observed amongst isolates producing surface tensions of 25 – 27 mN m−1, suggesting that a range of structurally-diverse biosurfactants were being expressed. Individual distribution identification (IDI) analysis was used to identify the theoretical probability distribution that best fitted the surface tension data, which predicted a γMin of 24.24 mN m−1. This was in agreement with predictions based on earlier work of published mixed–bacterial spp. data, suggesting a fundamental limit to the ability of bacterial biosurfactants to reduce surface tensions in aqueous systems. This implies a biological restriction on the synthesis and export of these agents or a physical-chemical restriction on their functioning once produced

A randomised controlled study of high intensity exercise as a dishabituating stimulus to improve hypoglycaemia awareness in people with type 1 diabetes:a proof of concept study

Aims/hypothesis Approximately 25% of people with type 1 diabetes have suppressed counterregulatory hormonal and symptomatic responses to insulin-induced hypoglycaemia, which renders them at increased risk of severe, disabling hypoglycaemia. This is called impaired awareness of hypoglycaemia (IAH), the cause of which is unknown. We recently proposed that IAH develops through habituation, a form of adaptive memory to preceding hypoglycaemia. Consistent with this hypothesis, we demonstrated restoration of defective counterregulatory hormonal responses to hypoglycaemia (referred to as dishabituation) in a rodent model of IAH following introduction of a novel stress stimulus (high intensity training [HIT]). In this proof-of-concept study we sought to further test this hypothesis by examining whether a single episode of HIT would amplify counterregulatory responses to subsequent hypoglycaemia in people with type 1 diabetes who had IAH (assessed by Gold score ≥4, modified Clarke score ≥4 or Dose Adjustment For Normal Eating (DAFNE) hypoglycaemia awareness rating 2 or 3). The primary outcome was the difference in adrenaline response to hypoglycaemia following both a single episode of HIT and rest. Methods In this randomised, crossover study 12 participants aged between 18 and 55 years with type 1 diabetes for ≥5 years and an HbA1c < 75 mmol/mol (9%) were recruited. Individuals were randomised using computer generated block randomisation to start with one episode of HIT (4 × 30 s cycle sprints [2 min recovery] at 150% of maximum wattage achieved during V˙O2peak assessment) or rest (control). The following day they underwent a 90 min hyperinsulinaemic–hypoglycaemic clamp study at 2.5 mmol/l with measurement of hormonal counterregulatory response, symptom scores and cognitive testing (four-choice reaction time and digit symbol substitution test). Each intervention and subsequent clamp study was separated by at least 2 weeks. The participants and investigators were not blinded to the intervention or measurements during the study. The investigators were blinded to the primary outcome and blood analysis results. Results All participants (six male and six female, age 19–54 years, median [IQR] duration of type 1 diabetes 24.5 [17.3–29.0] years, mean [SEM] HbA1c 56 [3.67] mmol/mol; 7.3% [0.34%]) completed the study (both interventions and two clamps). In comparison with the rest study, a single episode of HIT led to a 29% increase in the adrenaline (epinephrine) response (mean [SEM]) (2286.5 [343.1] vs 2953.8 [384.9] pmol/l); a significant increase in total symptom scores (Edinburgh Hypoglycaemia Symptom Scale: 24.25 [2.960 vs 27.5 [3.9]; p < 0.05), and a significant prolongation of four-choice reaction time (591.8 [22.5] vs 659.9 [39.86] ms; p < 0.01] during equivalent hypoglycaemia induced the following day. Conclusions/interpretation These findings are consistent with the hypothesis that IAH develops in people with type 1 diabetes as a habituated response and that introduction of a novel stressor can restore, at least partially, the adapted counterregulatory hormonal, symptomatic and cognitive responses to hypoglycaemia.Output Status: Forthcoming/Available Onlin

Reverse engineering of biochar

This study underpins quantitative relationships that account for the combined effects that starting biomass and peak pyrolysis temperature have on physico-chemical properties of biochar. Meta-data was assembled from published data of diverse biochar samples (n = 102) to (i) obtain networks of intercorrelated properties and (ii) derive models that predict biochar properties. Assembled correlation networks provide a qualitative overview of the combinations of biochar properties likely to occur in a sample. Generalized Linear Models are constructed to account for situations of varying complexity, including: dependence of biochar properties on single or multiple predictor variables, where dependence on multiple variables can have additive and/or interactive effects; non-linear relation between the response and predictors; and non-Gaussian data distributions. The web-tool Biochar Engineering implements the derived models to maximize their utility and distribution. Provided examples illustrate the practical use of the networks, models and web-tool to engineer biochars with prescribed properties desirable for hypothetical scenarios

Three-dimensional mapping of soil chemical characteristics at micrometric scale by combining 2D SEM-EDX data and 3D X-ray CT images

There is currently a significant need to improve our understanding of the factors that control a number of critical soil processes by integrating physical, chemical and biological measurements on soils at microscopic scales to help produce 3D maps of the related properties. Because of technological limitations, most chemical and biological measurements can be carried out only on exposed soil surfaces or 2-dimensional cuts through soil samples. Methods need to be developed to produce 3D maps of soil properties based on spatial sequences of 2D maps. In this general context, the objective of the research described here was to develop a method to generate 3D maps of soil chemical properties at the microscale by combining 2D SEM-EDX data with 3D X-ray computed tomography images. A statistical approach using the regression tree method and ordinary kriging applied to the residuals was developed and applied to predict the 3D spatial distribution of carbon, silicon, iron, and oxygen at the microscale. The spatial correlation between the X-ray grayscale intensities and the chemical maps made it possible to use a regression-tree model as an initial step to predict the 3D chemical composition. For chemical elements, e.g., iron, that are sparsely distributed in a soil sample, the regression-tree model provides a good prediction, explaining as much as 90% of the variability in some of the data. However, for chemical elements that are more homogenously distributed, such as carbon, silicon, or oxygen, the additional kriging of the regression tree residuals improved significantly the prediction with an increase in the R2 value from 0.221 to 0.324 for carbon, 0.312 to 0.423 for silicon, and 0.218 to 0.374 for oxygen, respectively. The present research develops for the first time an integrated experimental and theoretical framework, which combines geostatistical methods with imaging techniques to unveil the 3-D chemical structure of soil at very fine scales. The methodology presented in this study can be easily adapted and applied to other types of data such as bacterial or fungal population densities for the 3D characterization of microbial distribution

The evolution of biofilm-forming Wrinkly Spreaders in static microcosms and drip-fed columns selects for subtle differences in wrinkleality and fitness

Experimental evolution studies are used to investigate bacterial adaptive radiation in simple microcosms. In the case of the Wrinkly Spreader, a class of biofilm-forming adaptive mutants of Pseudomonas fluorescens SBW25, the current paradigm is that they are only evolutionarily successful in static microcosms where they outcompete other lineages for O2 at the air–liquid interface. However, we have isolated Wrinkly Spreaders from drip-fed glass bead columns as an example of parallel evolution. These mutants are adaptive, with competitive fitness advantages on columns of 1.28–1.78. This might be explained by the enhanced attachment characteristically shown by Wrinkly Spreaders, allowing them to resist liquid flow through the column pore network. A comparison of column and static microcosm-isolated Wrinkly Spreaders showed that many aspects of wrinkleality, including colony reversion, microcosm growth, biofilm strength and attachment, as well as fitness in static microcosms, were significantly different within and between the two groups of mutants. These findings indicate that the two environments had selected for Wrinkly Spreaders with subtly differing degrees of wrinkleality and fitnesses, suggesting that aspects of the Wrinkly Spreader phenotype may have different relative values in static microcosms and drip-fed columns

Malaria vectors resistance to commonly used insecticides in the control of malaria in Bichi, northern Nigeria

This study was carried out in 2015 to assess the level of resistance of sibling species of Anopheles gambiae complex the principal malaria vector from Bichi in Kano state to three classes of insecticides; (DDT, Permethrin and Bendiocarb) approved by World Health Organization (WHO) for vector control with the aim of obtaining baseline susceptibility and resistance data by evaluating the potency of brands of insecticides used against the mosquito vector in the area where the disease is prevalent. An. gambiae larvae collected from ecologically contrasting breeding sites were reared to adults in the laboratory. Adults from the F1 progeny were assayed for resistance using the WHO adult insecticide susceptibility bioassay protocol. The mosquitoes were exposed to DDT, permethrin and bendiocarb belonging to 3 classes of insecticides. The individual sibling species were identified molecularly and the molecular resistance mechanisms characterized by SINE and kdr PCR methods respectively. The An. gambiae populations tested revealed high level of resistance to DDT and permethrin but less resistant to bendiocarb. Analysis of the genetic composition of the vector population revealed predominance of An. coluzzii (&gt; 77%). L1014F and L1014S kdr mutations correlated to insecticide resistance phenotype expression. This study indicates differential distribution of the resistant genotype of Anopheles malaria vector between ecologically different habitats in the area. This insecticide resistance represents a threat to vector control tool and should be monitored. The information obtained could be useful in decision and planning making for vector control programs in the region.Keywords: Anopheles coluzzii, Anopheles gambiae, Insecticides, Malaria control, resistance, Susceptibilit

Quantification of the pore size distribution of soils:assessment of existing software using tomographic and synthetic 3D images

The pore size distribution (PSD) of the void space is widely used to predict a range of processes in soils. Recent advances in X-ray computed tomography (CT) now afford novel ways to obtain exact data on pore geometry, which has stimulated the development of algorithms to estimate the pore size distribution from 3D data sets. To date there is however no clear consensus on how PSDs should be estimated, and in what form PSDs are best presented. In this article, we first review the theoretical principles shared by the various methods for PSD estimation. Then we select methods that are widely adopted in soil science and geoscience, and we use a robust statistical method to compare their application to synthetic image samples, for which analytical solutions of PSDs are available, and X-ray CT images of soil samples selected from different treatments to obtain wide ranging PSDs. Results indicate that, when applied to the synthetic images, all methods presenting PSDs as pore volume per class size (i.e., Avizo, CTAnalyser, BoneJ, Quantim4, and DTM), perform well. Among them, the methods based on Maximum Inscribed Balls (Bone J, CTAnalyser, Quantim4) also produce similar PSDs for the soil samples, whereas the Delaunay Triangulation Method (DTM) produces larger estimates of the pore volume occupied by small pores, and Avizo yields larger estimates of the pore volume occupied by large pores. By contrast, the methods that calculate PSDs as object population fraction per volume class (Avizo, 3DMA, DFS-FIJI) perform inconsistently on the synthetic images and do not appear well suited to handle the more complex geometries of soils. It is anticipated that the extensive evaluation of method performance carried out in this study, together with the recommendations reached, will be useful to the porous media community to make more informed choices relative to suitable PSD estimation methods, and will help improve current practice, which is often ad hoc and heuristic