Sampling, defining, characterising and modeling the rhizosphere—the soil science tool box

We review methods and models that help to assess how root activity changes soil properties and affects the fluxes of matter in the soil. Subsections discuss (1) experimental systems including plant treatments in artificial media, studying the interaction of model root and microbial exudates with soil constituents, and microcosms to distinguish between soil compartments differing in root influence, (2) the sampling and characterization of rhizosphere soil and solution, focusing on the separation of soil at different distances from roots and the spatially resolved sampling of soil solution, (3) cutting-edge methodologies to study chemical effects in soil, including the estimation of bioavailable element or ion contents (biosensors, diffusive gradients in thin-films), studying the ultrastructure of soil components, localizing elements and determining their chemical form (microscopy, diffractometry, spectroscopy), tracing the compartmentalization of substances in soils (isotope probing, autoradiography), and imaging gradients in-situ with micro electrodes or gels or filter papers containing dye indicators, (4) spectroscopic and geophysical methods to study the plants influence on the distribution of water in soils, and (5) the modeling of rhizosphere processes. Macroscopic models with a rudimentary depiction of rhizosphere processes are used to predict water or nutrient requirements by crops and forests, to estimate biogeochemical element cycles, to calculate soil water transport on a profile scale, or to simulate the development of root systems. Microscopic or explanatory models are based on mechanistic or empirical relations that describe processes on a single root or root system scale and/or chemical reactions in soil solution. We conclude that in general we have the tools at hand to assess individual processes on the microscale under rather artificial conditions. Microscopic, spectroscopic and tracer methods to look at processes in small "aliquots” of naturally structured soil seem to step out of their infancy and have become promising tools to better understand the complex interactions between plant roots, soil and microorganisms. On the field scale, while there are promising first results on using non-invasive geophysical methods to assess the plant's influence on soil moisture, there are no such tools in the pipeline to assess the spatial heterogeneity of chemical properties and processes in the field. Here, macroscopic models have to be used, or model results on the microscopic level have to be scaled up to the whole plant or plot scale. Upscaling is recognized as a major challeng

Modified micro suction cup/rhizobox approach for the in-situ detection of organic acids in rhizosphere soil solution

Root-soil interactions can strongly influence the soil solution chemistry in the rhizosphere. In the present study we propose a modification of the classical rhizobox/micro suction cup system to make it suitable for the collection and analysis of organic acids in the rhizosphere. In order to show the potential of the method, we tested the modified system with Lupinus albus L. as a model plant known to exude large amounts of citrate. The suction cups were installed through the transparent front plate of the rhizoboxes just after the emergence of cluster roots in order to allow optimal localized collection of soil solution. A small dead-volume allowed almost immediate stabilisation with formaldehyde of the sampled soil solutions in the collection container to prevent microbial degradation. The concentrations of organic acids were significantly larger in the rhizosphere soil solution of active cluster roots of Lupinus albus L. than in the bulk soil solution (about 400µM of citrate versus <0.05µM). We were able to follow the exudation process in-situ, which occurred during 2-3days. Also the concentrations of other organic acids and inorganic anions differed between the bulk soil and the rhizosphere of cluster roots, normal roots, and nodule

Bacterial, Archaeal and Fungal Succession in the Forefield of a Receding Glacier

Glacier forefield chronosequences, initially composed of barren substrate after glacier retreat, are ideal locations to study primary microbial colonization and succession in a natural environment. We characterized the structure and composition of bacterial, archaeal and fungal communities in exposed rock substrates along the Damma glacier forefield in central Switzerland. Soil samples were taken along the forefield from sites ranging from fine granite sand devoid of vegetation near the glacier terminus to well-developed soils covered with vegetation. The microbial communities were studied with genetic profiling (T-RFLP) and sequencing of clone libraries. According to the T-RFLP profiles, bacteria showed a high Shannon diversity index (H) (ranging from 2.3 to 3.4) with no trend along the forefield. The major bacterial lineages were Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Cyanobacteria. An interesting finding was that Euryarchaeota were predominantly colonizing young soils and Crenarchaeota mainly mature soils. Fungi shifted from an Ascomycota-dominated community in young soils to a more Basidiomycota-dominated community in old soils. Redundancy analysis indicated that base saturation, pH, soil C and N contents and plant coverage, all related to soil age, correlated with the microbial succession along the forefiel

The C:N:P:S stoichiometry of soil organic matter

The formation and turnover of soil organic matter (SOM) includes the biogeochemical processing of the macronutrient elements nitrogen (N), phosphorus (P) and sulphur (S), which alters their stoichiometric relationships to carbon (C) and to each other. We sought patterns among soil organic C, N, P and S in data for c. 2000 globally distributed soil samples, covering all soil horizons. For non-peat soils, strong negative correlations (p < 0.001) were found between N:C, P:C and S:C ratios and % organic carbon (OC), showing that SOM of soils with low OC concentrations (high in mineral matter) is rich in N, P and S. The results can be described approximately with a simple mixing model in which nutrient-poor SOM (NPSOM) has N:C, P:C and S:C ratios of 0.039, 0.0011 and 0.0054, while nutrient-rich SOM (NRSOM) has corresponding ratios of 0.12, 0.016 and 0.016, so that P is especially enriched in NRSOM compared to NPSOM. The trends hold across a range of ecosystems, for topsoils, including O horizons, and subsoils, and across different soil classes. The major exception is that tropical soils tend to have low P:C ratios especially at low N:C. We suggest that NRSOM comprises compounds selected by their strong adsorption to mineral matter. The stoichiometric patterns established here offer a new quantitative framework for SOM classification and characterisation, and provide important constraints to dynamic soil and ecosystem models of carbon turnover and nutrient dynamics

Contrasting Roles for TLR Ligands in HIV-1 Pathogenesis

The first line of a host's response to various pathogens is triggered by their engagement of cellular pattern recognition receptors (PRRs). Binding of microbial ligands to these receptors leads to the induction of a variety of cellular factors that alter intracellular and extracellular environment and interfere directly or indirectly with the life cycle of the triggering pathogen. Such changes may also affect any coinfecting microbe. Using ligands to Toll-like receptors (TLRs) 5 and 9, we examined their effect on human immunodeficiency virus (HIV)-1 replication in lymphoid tissue ex vivo. We found marked differences in the outcomes of such treatment. While flagellin (TLR5 agonist) treatment enhanced replication of CC chemokine receptor 5 (CCR 5)-tropic and CXC chemokine receptor 4 (CXCR4)-tropic HIV-1, treatment with oligodeoxynucleotide (ODN) M362 (TLR9 agonist) suppressed both viral variants. The differential effects of these TLR ligands on HIV-1 replication correlated with changes in production of CC chemokines CCL3, CCL4, CCL5, and of CXC chemokines CXCL10, and CXCL12 in the ligand-treated HIV-1-infected tissues. The nature and/or magnitude of these changes were dependent on the ligand as well as on the HIV-1 viral strain. Moreover, the tested ligands differed in their ability to induce cellular activation as evaluated by the expression of the cluster of differentiation markers (CD) 25, CD38, CD39, CD69, CD154, and human leukocyte antigen D related (HLA)-DR as well as of a cell proliferation marker, Ki67, and of CCR5. No significant effect of the ligand treatment was observed on apoptosis and cell death/loss in the treated lymphoid tissue ex vivo. Our results suggest that binding of microbial ligands to TLRs is one of the mechanisms that mediate interactions between coinfected microbes and HIV-1 in human tissues. Thus, the engagement of appropriate TLRs by microbial molecules or their mimetic might become a new strategy for HIV therapy or prevention

Compatibility of deformation in Two-Phase Ti-Al alloys: Dependence on microstructure and orientation relationships

A two-phase alloy of composition Ti-47.5Al-2.5Cr has been studied under two heat-treated conditions in order to obtain different microstructures. These consisted of lamellar and equiaxed distributions of y grains in which the α2 phase was distributed as long lamellae or smaller globules, respectively. The specific rotation relationships between γ/γ and γ/α2 grains have been measured, and these have been used to understand their effect on the compatibility of deformation across adjacent grains. For this, detailed analysis of active slip systems has been carried out by transmission electron microscopy (TEM) observations of deformed samples. A theoretical calculation of a geometric compatibility factor characterizing the best slip transfer across adjacent grains has been used in such a way that it has been possible to deduce the role played by the type of orientation relationship between grains in producing active deformation systems that allow the maximum compatibility of deformation.Peer Reviewe

Phosphorus Allocation to Leaves of Beech Saplings Reacts to Soil Phosphorus Availability

Decreasing phosphorus (P) concentrations in leaves of beech (Fagus sylvatica L.) across Europe raise the question about the implications for forest health. Considering the distribution of beech forests on soils encompassing a broad range of nutrient availability, we hypothesized that this tree species exhibits high phenotypic plasticity allowing it to alter mass, and nutrient allocation in response to local nutrient availability. To test this, we grew two groups of 12–15 year old beech saplings originating from sites with high and low soil P availability for 2 years in mineral soil from their own site and in soil from the other site. After two growing seasons, P concentrations in leaves and stem, as well as mass allocation to leaves and fine roots were affected by both soil and plant origin. By contrast, relative P allocation to leaves and fine roots, as well as P concentrations in fine roots, were determined almost entirely by the experimental soil. Independent of the P nutritional status defined as average concentration of P in the whole plant, which still clearly reflected the soil conditions at the site of plant origin, relative P allocation to leaves was a particularly good indicator of P availability in the experimental soil. Furthermore, a high plasticity of this plant trait was indicated by a large difference between plants growing in the two experimental soils. This suggests a strong ability of beech to alter resource allocation in response to specific soil conditions.ISSN:1664-462

Plant nutritional status explains the modifying effect of provenance on the response of beech sapling root traits to differences in soil nutrient supply

Forests dominated by beech (Fagus sylvatica L.) cover large parts of Europe where they occupy a broad ecological niche in terms of soil fertility. This indicates a large potential to adapt to different soil conditions over long time periods. Recent changes in tree mineral nutrition across Europe raise the question to what degree beech can acclimate to changing soil conditions in the short term. In this study, we aimed at assessing the plasticity of root traits and rhizosphere properties of young beech trees from populations that are adapted to either high or low nutrient supply, when growing in soils differing in their fertility. We sampled beech saplings from two forest sites of contrasting nutrient supply, most distinctly in terms of phosphorus. We grew them for 2 years in rhizoboxes in mineral soil either from their own site or from the other site. We assessed the influence of the factors “plant origin” and “current soil” on root traits and rhizosphere properties. Fine root traits related to growth (biomass, length), architecture (branching), and morphology (diameter) responded strongly to the factor “current soil.” Provenance (factor “plant origin”) modified the response. The modifying effect was consistent with an influence of the plant status in those nutrients, which were not in sufficient supply in the soil. An additional genotypic difference in the sensitivity of the beech saplings to different soil nutrient supply could not be excluded. Fine root parameters normalized for length, mass, or volume (root tip density and frequency, specific root length and area, and root tissue density) did not differ among the treatments. Differences in percentage of mycorrhizal root tips and rhizosphere parameters related to phosphorus mobilization potential (pH, abundance of organic acid anions, and phosphatase activity) were small and mainly determined by the “current soil.” Provenance had only a minor modifying effect, possibly due to differences in the ability of the plants to transfer carbon compounds from the shoot to the root and the fungal partner. Our results indicate a high plasticity of young beech trees to adapt their root system to different soil nutrient supply, thereby also taking into account internal nutrient reserves