Technical limitations have restricted investigations of rhizosphere mineralogy. Various analytical techniques were applied to assess root-mineral associations and dynamics in natural soils under corn production. Soil samples were collected between four and five weeks after planting and included rhizospheric and non-rhizospheric soils, and undisturbed block samples containing corn root systems. Analytical techniques were applied and included; X-ray diffraction, optical microscope, SEM, EDXRA with SEM, transmission electron microscope (TEM), electron energy loss spectra with TEM, high-resolution transmission electron microscope (HRTEM) and microanalysis with HRTEM. The mineralogy of the rhizosphere differed from that of the bulk soil. Within the rhizosphere, minute platy particles which were mostly vermiculitic minerals, were particularly concentrated near or on root surfaces. These platy mineral particles were not attached to the entire area, but only to certain areas of root surfaces. Therefore, we report quantitative evidence for mineralogical changes in the rhizosphere in soil environments.

Cesium uptake by plants depends on adsorption/desorption reactions in the soil, as well as root uptake processes controlled by the plant. In this study, sorption and desorption of Cs+ on reference illite (IMt-1) was investigated in the presence of oxalate to gain understanding of mechanisms by which plant root exudates may influence Cs+ bioavailability in micaceous soils. Cesium sorption on illite decreased significantly as oxalate concentration increased from 0.4 to 2 mM. Cesium desorption from illite increased significantly with increasing oxalate concentration. Desorption of Cs+ by exchange with Na+, Ca2+ and Mg2+ was significantly enhanced in the presence of oxalate as selectivity for Cs+ decreased with respect to these ions in the presence of oxalate. On the other hand, oxalate had little effect on the Cs+/K+ selectivity coefficient. This suggests that oxalate treatments increase the relative proportion of exchange sites that are not highly selective for Cs+ and K+; e.g. ‘planar’ sites. The results indicate that oxalate plays an important role in Cs+ binding on illite and, therefore, plant rhizosphere chemistry is likely to alter Cs+ bioavailability in micaceous soils.

Rhizoctonia solani Kühn and Pythium aphanidermatum Edson cause cabbage seedling damping-off, resulting in severe yield losses. The current study demonstrates the production of toxic volatile organic compounds (VOCs) by two strains of Bacillus mycoides and the evaluation of a potential use of B. mycoides as a biocontrol agent to control cabbage damping-off. Two VOCs, dimethyl disulphide and ammonia, were found to reduce radial growth, cause hyphal deformation and result in organelle degeneration in both R. solani and P. aphanidermatum. Pathogen hyphae, after being exposed to VOCs, showed poor rigidity, shrinkage, curling and swelling. The amount of VOCs produced by B. mycoides and the antagonistic activity against plant pathogens varied, depending on the type of medium used to culture bacteria. Application of B. mycoides cell suspensions to cultivation medium promotes growth of five different plant species tested. Experiments conducted in greenhouses revealed that B. mycoides did not reduce damping-off incidence caused by R. solani. However, B. mycoides reduced damping-off incidence induced by P. aphanidermatum by as much as 45% on cabbage seedlings. The results provide valuable information on the feasibility of utilizing B. mycoides as a biocontrol agent in controlling cabbage damping-off.

This study examines the effect of German camomile (Matricaria camomilla L.) cultivation on the weathering of minerals present in the clay fraction of five different soil series modified or not unmodified (control) with cattle manure. A factorial experiment was performed in a randomized complete block design (RCBD) with three replications. At harvest time the rhizosphere soil was separated from bulk soil and the mineralogy was examined by X-ray diffraction (XRD). Trioctahedral chlorite transformed to hydroxy-interlayer vermiculite (HIV), while kaolinite disappeared. The presence of HIV was identified by an increase in the intensity ratio of the 1.0 and 1.4 nm peaks after Na-citrate pretreatment and K-saturation. It is suggested that Al3+ is released during dissolution of kaolinite and subsequently enters into the interlayer sheet of chlorite, and consequently the brucite layer disappears. This was verified by a significant Mg2+ increase in the soil solution in three out of five experiments at harvest time compared to pre-planting. The pots amended with manure showed the same changes as the pots without manure. The results of this study may explain the presence of unexpected clay minerals in regions with unsuitable conditions for their formation.

Rhizobacteria are being evaluated for promotion of plant growth and for biological control of weeds, insects, diseases, and nematodes. Although considerable efforts have been allocated to this approach to biological control, commercial success remains elusive yet intriguing. In this review, the root biology of downy brome and winter wheat is described as an initial model of the information needed for other plant hosts. A limited review of rhizobacteria in disease management is presented to demonstrate the potential and some limitations with rhizobacteria as biocontrol agents. Several techniques are described to improve the survival of a rhizobacterium to suppress downy brome. To achieve success with rhizobacteria in pest management, more information is needed on the root biology of the host plants and the ecology of the rhizobacteria.

Greenhouse studies were conducted to determine the following: if treating henbit or downy brome with glyphosate increased populations of Fusarium solani f. sp. pisi and Pythium ultimum in soil and rhizosphere soil; if treating henbit or downy brome with glyphosate increased root colonization and infection by F. solani f. sp. pisi or P. ultimum; and, if henbit and downy brome are hosts of F. sohni f. sp. pisi or P. ultimum. Pythium ultimum populations increased only in soil containing glyphosate-treated henbit. Fusarium solani f. sp. pisi and P. ultimum populations increased in rhizosphere soil from glyphosate-treated henbit, while only P. ultimum populations increased in rhizosphere soil from glyphosate-treated downy brome. These results suggest that peas planted in soil where either downy brome or henbit had been treated with glyphosate could be exposed to higher populations of F. solani f. sp. pisi and P. ultimum. Root colonization and infection, plant height, and root weight data indicated that henbit and downy brome are alternate hosts of P. ultimum. F. sohni f. sp. pisi colonized, but did not readily infect roots of downy brome and henbit.

Soil microbial community structure and activity are linked to plant communities. Weeds may alter their soil environment, selecting for specific rhizosphere microbial communities. Rhizosphere modification occurs for many crop and horticultural plants. However, impacts of weeds in agroecosystems on soil biology and ecology have received less attention because effective weed management practices were developed to minimize their impacts on crop production. The recent development of herbicide resistance (HR) in several economically important weeds leading to widespread infestations in crop fields treated with a single herbicide has prompted a re-evaluation of the effects of weed growth on soil biology and ecology. The objective of this article is to review the potential impacts of herbicide-resistant weeds on soil biological and ecological properties based on reports for crops, weeds, and invasive plants. Persistent weed infestations likely establish extensive root systems and release various plant metabolites through root exudation. Many exudates are selective for specific soil microbial groups mediating biochemical and nutrient acquisition processes. Exudates may stimulate development of microbial groups beneficial to weed but detrimental to crop growth or beneficial to both. Changes in symbiotic and associative microbial interactions occur, especially for arbuscular mycorrhizal fungi (AMF) that are important in plant uptake of nutrients and water, and protecting from phytopathogens. Mechanisms used by weeds to disrupt symbioses in crops are not clearly described. Many herbicide-resistant weeds including Amaranthus and Chenopodium do not support AMF symbioses, potentially reducing AMF propagule density and establishment with crop plants. Herbicides applied to control HR weeds may compound effects of weeds on soil microorganisms. Systemic herbicides released through weed roots may select microbial groups that mediate detrimental processes such as nutrient immobilization or serve as opportunistic pathogens. Understanding complex interactions of weeds with soil microorganisms under extensive infestations is important in developing effective management of herbicide-resistant weeds.

Pseudomonas fluorescens strain D7 (P. f. D7; NRRL B-18293) is a root-colonizing bacterium that inhibits downy brome (Bromus tectorum L. BROTE) growth. Before commercialization as a biological control agent, strain D7 must be tested for host plant specificity. Agar plate bioassays in the laboratory and plant–soil bioassays in a growth chamber were used to determine the influence of P. f. D7 on germination and root growth of 42 selected weed, cultivated or native plant species common in the western and midwestern United States. In the agar plate bioassay, all accessions of downy brome were inhibited by P. f. D7. Root growth of seven Bromus spp. was inhibited an average of 87% compared with that of controls in the agar plate bioassay. Root growth of non-Bromus monocots was reduced by 0 to 86%, and only 6 out of 17 plant species were inhibited 40% or greater. Among all plant species, only downy brome root growth from two accessions was significantly inhibited by P. f. D7 in plant–soil bioassays (42 and 64%). P. f. D7 inhibited root growth and germination in agar plate bioassays more than in plant–soil bioassays. Inhibition in plant–soil bioassays was limited to downy brome, indicating promise for P. f. D7 as a biocontrol agent that will not harm nontarget species.

Cultivation-independent analyses were carried out to compare the bacterial community structure found in the rhizospheres of a transplastomic tobacco plant carrying the antibiotic resistance marker-gene aadA and its non-engineered parental line. PCR- and reverse transcriptase PCR-amplifications of 16S rRNA and their corresponding genes were carried out with primers targeting the domain Bacteria. The diversity of PCR-products amplified from total nucleic acids extracted from rhizospheres of 10-week-old plants, which had been grown in potting soil in the greenhouse, was visualized by genetic profiling using the single-strand conformation polymorphism (SSCP) technique. The SSCP profiles generated from DNA extracted with two different protocols, one including total RNA and the other only DNA, did not show any differences. The SSCP profiles amplified from RNA and DNA were also highly similar to each other, indicating that the dominant bacteria detected were metabolically active. High similarities were seen between the SSCP profiles from the transplastomic and the non-engineered plants, except for a single band that consistently occurred with samples from the non-engineered plants (six replicates), but not, or only weakly, with their engineered counterparts. DNA sequencing and database analysis revealed that the partial rRNA gene matched to a Flavobacterium sp. Other bands of the SSCP-profiles, related to Burkholderia and Bordetella were variable between individual plants but not affected by the transplastomic modification. Thus, the transplastomic modification caused a relative decline of a specific Flavobacterium population but not of other bacteria. Further studies including additional tobacco cultivars, soils and conditions of cultivation would be desirable, to elucidate the ecological importance of this difference.

The influence of variation in the concentration of dissolved inorganic carbon (DIC) in the form of CO2 and HCO3− in the root media on the C and N metabolism of Lycopersicon esculentum cv. F144 was investigated under both saline and non-saline conditions. Tomato seedlings were grown in hydroponic culture (pH 6.5) with or without NaCl, and the root solution was aerated with either ambient CO2 (360 μmol mol−1) or CO2-enriched air (5000 μmol mol−1). Nitrate uptake and root tissue NO3− concentrations were increased slightly by elevated rhizosphere DIC concentrations in both control and salinity-treated plants. This was associated with 46% higher nitrate reductase activity in the roots of control plants supplied with elevated DIC than in those supplied with ambient DIC. The activity of phosphoenolpyruvate carboxylase (PEPc) in vitro in control and salinity-treated plants was unaffected by the supply of elevated rhizosphere DIC concentrations. However, PEPc activity in vitro was considerably higher than the rates of PEPc activity in vivo reported previously, indicating that PEPc activity was not in itself a limitation on the provision of anaplerotic C. Therefore elevated DIC concentration in the rhizosphere stimulated the uptake of NO3− and provided alternative C skeletons for the assimilation of the NH4+ resulting from NO3− reduction into amino acids within the roots. Salinity stimulated root glutamine synthetase (GS) activity up to double that in control plants. Furthermore, elevated DIC caused an increase in leaf and root GS activity of control plants while inhibiting GS activity in the roots of salinity-treated plants. Glutamine[ratio ]2- oxoglutarate aminotransferase (GOGAT) activity of salinity-treated plants was doubled by elevated rhizosphere DIC concentrations. These changes in GS and GOGAT activity must reflect changes in amino acid synthesis. Under saline conditions the xylem transport of NO3− is partly blocked and a larger root assimilation develops, requiring not only the transamination of 2-oxoglutarate to glutamate but also that of oxaloacetate to aspartate and the transamidation of aspartate to asparagine.

Rice (Oryza sativa) plants were grown with their roots sandwiched between thin layers of phosphorus-deficient soil from which they were separated by fine mesh, and root-induced changes in the soil affecting phosphate solubility were measured. The concentrations of low molecular weight organic anions in the thin layers, particularly citrate, increased in the presence of the plants. Apparent rates of citrate excretion from the roots, calculated from the quantities in the soil and rates of decomposition calculated with a first order rate constant measured independently, varied from 337–155 nmol g−1 root f. wt h−1 over the course of plant growth, equivalent to 2–3% of plant d. wt. Rates of excretion were similar for NH4+ and NO3−-fed plants. The soil pH decreased from its initial value by up to 0.6 units for the NH4+-fed plants and increased by up to 0.4 units for the NO3−-fed ones. The contribution of organic anion excretion to the pH changes was small compared with that of the inorganic cation-anion balance in the plants. The extent to which the observed excretion of citrate and root-induced pH changes could account for the observed phosphate solubilization and uptake was assessed using a mathematical model. Previous work had shown that phosphate solubilization by rice in this soil could not be explained by enhanced phosphatase activity in the rhizosphere, and the roots were not infected with mycorrhizas. The model allows for the diffusion of the solubilizing agent (citrate or H+) away from the roots, its decomposition by soil microbes (citrate only); its reaction with the soil in solubilizing phosphate and diffusion of the solubilized phosphate to the roots. The model contains no arbitrary assumptions and uses only independently measured parameter values. The agreement between the measured time course of phosphorus uptake and that predicted for solubilization by citrate was good. Root-induced acidification by NH4+-fed plants resulted in additional solubilization, the acidification enhancing the solubilizing effect of citrate. However, the final phosphorus uptake by NH4+-fed plants was no greater than that of NO3−-fed plants, presumably because the acidification inhibited plant growth. The mechanism of solubilization by citrate involved formation of soluble metal-citrate chelates rather than displacement of phosphate from adsorption sites.

The influence of Glomus intraradices (BEG87) on Pseudomonas fluorescens DF57 in hyphosphere and rhizosphere soil was examined. Cucumis sativus (Aminex, F1 hybrid) was grown in symbiosis with the arbuscular mycorrhizal fungus G. intraradices in PVC tubes, consisting of a central root compartment and two lateral root-free compartments. Two Tn5-luxAB-marked strains of P. fluorescens DF57 were used. Strain DF57-P2, which has an insertion of Tn5[ratio ][ratio ]luxAB in a phosphate starvation-inducible locus, was used as a phosphate starvation reporter. Another lux-tagged strain DF57-40E7, which carries a constitutively expressed luxAB fusion, was used as control for strain DF57-P2 and for measuring the metabolic activity of P. fluorescens DF57. A strain of P. fluorescens DF57, which carries a constitutively expressed gfp gene, was used in studies of attachment between the bacteria and the hyphae. G. intraradices decreased the culturability of P. fluorescens DF57 significantly, both in rhizosphere and hyphosphere soil, whereas the total number of P. fluorescens DF57 measured by immunofluorescence microscopy was decreased in hyphosphere soil only. G. intraradices did not induce a phosphorus starvation response in P. fluorescens DF57, and the metabolic activity of the bacteria was not affected by the fungus after 48 h. P. fluorescens DF57 did not attach to G. intraradices hyphae and was not able to use the hyphae as carbon substrate. The negative effect of G. intraradices on culturability and on number of P. fluorescens DF57 in hyphosphere soil is discussed.

Despite the usually high abundance of iron (Fe) in soils, the low solubility of Fe-bearing minerals restricts the available Fe pools in most aerobic soils to levels that are far below those required for microbial or plant growth. To acquire the necessary amounts of Fe from the environment, organisms have evolved mechanisms that enhance the solubility and dissolution rate of Fe(iii) oxyhydroxides prevailing in aerobic soils. Chemically, these mechanisms are based on weakening of the Fe–O bond by reduction, chelation and protonation. Physiologically, two distinct and in all known cases mutually exclusive strategies can be distinguished: the excretion of siderophores capable of solubilizing external ferric Fe and subsequent uptake of the ferric siderophore complex; and reduction of Fe(iii) prior to uptake of the more soluble Fe2+ ion. With the exception of graminaceous species, in which Fe uptake is based on the former mechanism, the latter strategy is found in all cormophytes and certain algae, yeast and bacteria. In higher plants, the increase in their capacity to convert extracellular ferric to ferrous Fe is part of a series of physiological and morphological events that act in concert to achieve appropriate internal levels of Fe. It is this amalgam of features that determines the Fe efficiency of a species or cultivar that in turn affects the yield of economically important plants and the natural distribution of species. Adaptive changes to limited Fe availability have been studied at the molecular, physiological and whole-plant level. This review summarises current knowledge of the components of reduction-based Fe uptake in plants and presents an integrated view of the present understanding of mechanisms that control the rate and extent of Fe absorption by roots.

Pathozone behaviour of soil-borne plant pathogenic fungi is characterized by curves for the change in probability of infection with distance of inoculum from a host. We identify three major components that give rise to the pathozone profile for infection efficiency: the germinability of inoculum, given that it occurs in the pathozone (P1), the growth of the resulting fungal colony outwards to make contact with the host (P2), and the infectivity of mycelium once contact is made (P3). The probability of infection (P) is then given by the product, P1 × P2 × P3. Using Raphanus sativus and two contrasting types of inoculum of Rhizoctonia solani as a model experimental system, we measured each of the three components by quantifying germinability, colony architecture (to determine the chance of contact by one or more hyphae) and the change in susceptibility over time as a measure of infectivity as mycelium arrives from different distances away. The germinability of inoculum is uniform across the pathozone whereas the probability of contact declines with distance, and the net effect of host susceptibility and infectivity increases. The characteristics of these components result in pathozone profiles that vary in shape. Infection efficiency can decline in an exponential or sigmoidal fashion with increasing distance from the host or follow a curve that rises close to the host and then falls asymptotically to zero with increasing distance. Colony architecture was summarized by the distribution of the furthest extent of hyphal growth amongst colonies growing out from single inoculum units (described, because of its asymmetrical pattern, by a gamma distribution) and by the radial density of hyphae on concentric circles at different distances from the centre of the colony (described by a negative binomial distribution with parameters changing with distance).

The mechanistic model for the components of pathozone behaviour is tested by comparing the magnitude and shape of pathozone profiles predicted by the model with independent estimates for P obtained by placing inoculum at fixed distances from the host, and measuring the proportion of successful infections. The shape depends on the relative magnitudes and change with distance of the three components, P1, P2 and P3, which differed between the two types of inoculum. The profiles could be reproduced accurately when the probability of contact was based on the distribution and density of hyphae reaching the host rather than on the furthest extent of hyphal growth amongst colonies. The model is used to analyse the effects of replication and stochastic variability in the components of pathozone behaviour on the comparison of treatments for disease control.

This paper presents and tests a method to scale up from the dynamics of infection and disease on single plants in order to predict the behaviour of epidemics in populations of plants, in the presence of a biological control agent. Specifically, we quantify the effect of the antagonistic fungus, Trichoderma viride, Pers ex. Gray, on the pathozone dynamics of the damping-off fungus, Rhizoctonia solani Kühn on radish. The results from these individual-based experiments are used to predict the progress of an epidemic and the results are compared with experimental epidemics in microcosms. The addition of T. viride close to a germinating radish plant reduced the extent of the pathozone influence from 22·6 to 13·8 mm. Trichoderma viride also inhibited the evolution of infection efficiency of R. solani. The evolution of infection efficiency over time is described by a simple non-linear model for the probability of infection with distance, in which certain of the parameters vary with time. By combining this with a model based on conditional probabilities for the location and infectivity of randomly dispersed propagules within the pathozone, we were able to scale up and predict the disease progress of R. solani in a population of radish plants, and the extent of control effected by T. viride. Disease progress rose progressively to a maximum of 42% diseased plants in the unprotected crop compared with a sigmoidal approach to 13% in the protected crop. We show that these properties are consistent with a monomolecular function for primary infection with a temporally-varying rate parameter. We also show that the central region of the pathozone, where the joint probabilities of occurrence of a randomly located propagule and its ability to infect are maximal, has a large influence on the sensitivity of epidemics to pathozone dynamics. This is an important example of interpreting population behaviour of an epidemic from the infection and disease of single plants.

Pathozone behaviour of soil-borne plant pathogenic fungi is characterized by curves for the change in probability of infection with distance of inoculum from a host. We identify three major components that give rise to the pathozone profile for infection efficiency: the germinability of inoculum, given that it occurs in the pathozone (P1), the growth of the resulting fungal colony outwards to make contact with the host (P2), and the infectivity of mycelium once contact is made (P3). The probability of infection (P) is then given by the product, P1 × P2 × P3. Using Raphanus sativus and two contrasting types of inoculum of Rhizoctonia solani as a model experimental system, we measured each of the three components by quantifying germinability, colony architecture (to determine the chance of contact by one or more hyphae) and the change in susceptibility over time as a measure of infectivity as mycelium arrives from different distances away. The germinability of inoculum is uniform across the pathozone whereas the probability of contact declines with distance, and the net effect of host susceptibility and infectivity increases. The characteristics of these components result in pathozone profiles that vary in shape. Infection efficiency can decline in an exponential or sigmoidal fashion with increasing distance from the host or follow a curve that rises close to the host and then falls asymptotically to zero with increasing distance. Colony architecture was summarized by the distribution of the furthest extent of hyphal growth amongst colonies growing out from single inoculum units (described, because of its asymmetrical pattern, by a gamma distribution) and by the radial density of hyphae on concentric circles at different distances from the centre of the colony (described by a negative binomial distribution with parameters changing with distance).

The mechanistic model for the components of pathozone behaviour is tested by comparing the magnitude and shape of pathozone profiles predicted by the model with independent estimates for P obtained by placing inoculum at fixed distances from the host, and measuring the proportion of successful infections. The shape depends on the relative magnitudes and change with distance of the three components, P1, P2 and P3, which differed between the two types of inoculum. The profiles could be reproduced accurately when the probability of contact was based on the distribution and density of hyphae reaching the host rather than on the furthest extent of hyphal growth amongst colonies. The model is used to analyse the effects of replication and stochastic variability in the components of pathozone behaviour on the comparison of treatments for disease control.

Earlier work has shown that rice plants growing in reduced soil are able to solubilize P and thereby increase their P uptake by inducing an acidification in the rhizosphere; the acidification is caused by H+ produced in Fe2+ oxidation by root-released O2, and by the direct release of H+ from the roots to balance cation–anion intake. Here, we report rates of release of O2 and H+ from P-stressed and P-sufficient rice plants into sand cultures continuously perfused with deoxygenated nutrient solution. The P stress was sufficient to reduce plant dry mass by roughly half, but root dry mass increased roughly twofold and root surface area 2·5-fold. The proportion of fine roots increased from 11 to 21% of root length under P deficiency; root porosity, averaged over the whole root system, increased from 0·25 to 0·40. Apparent rates of O2 release were 0·8–3·3 μmol per plant d−1, or 22–87 μmol g−1 (root dry mass) d−1. Assuming that the bulk of the O2 was released from medium and fine roots, the fluxes of O2 were 0·02–0·13 nmol dm−2 (root surface) s−1, which is in the range found for soil-grown plants. The release per plant was twofold greater in the low P treatment, although rates of release per unit root mass were slightly lower. The increased release under P deficiency is consistent with the increased length of fine roots and increased porosity. Rates of H+ release were 0·7–1·2 mmol per plant−1 d−1, or 1·4–6·1 mmol g−1 (root dry mass) d−1. The H+ release per unit plant dry mass was 60% greater in the low P treatment, but the release per unit root mass was 2·5-fold lower. The increased H+ release under P deficiency was associated with increased NH4+ intake and decreased NO3− intake, and a tenfold increase in plant NO3-N. This suggests that P deficiency reduced NO3− assimilation, causing reduced NO3− influx and/or increased efflux.