Detection and Measurement of <Emphasis Type="Italic">Plasmodiophora brassicae</Emphasis>

Clubroot, caused by Plasmodiophora brassicae, is one of the most important diseases of brassicas. Management of clubroot is difficult, and the best means of avoiding the disease include planting in areas where P. brassicae is not present and using plants and growing media free from pathogen inoculum. As P. brassicae is not culturable, its detection has traditionally relied on plant bioassays, which are time-consuming and require large amounts of glasshouse space. More recently, fluorescence microscopy, serology, and DNA-based methods have all been used to test soil, water, or plant samples for clubroot. The use of fluorescence microscopy to detect and count pathogen spores in the soil requires significant operator skill and is unlikely to serve as the basis for a routine diagnostic test. By contrast, serologic assays are inexpensive and amenable to high-throughput screening but need to be based on monoclonal antibodies because polyclonal antisera cannot be reproduced and are therefore of limited quantity. Several polymerase chain reaction (PCR)-based assays have also been developed; these are highly specific for P. brassicae and have been well-correlated with disease severity. As such, PCR-based diagnostic tests have been adopted to varying extents in Canada and Australia, but wide implementation has been restricted by sample processing costs. Efforts are underway to develop inexpensive serologic on-farm diagnostic kits and to improve quantification of pathogen inoculum levels through real-time PCR. Proper detection and quantification of P. brassicae will likely play an increasingly important role in the development of effective clubroot management strategies.     

Mechanisms of the biofungicide Serenade (Bacillus subtilis QST713) in suppressing clubroot

Clubroot is a serious threat to canola production in western Canada. The biofungicide Serenade® (Bacillus subtilis QST713) reduced the disease substantially in controlled environment, but showed variable efficacy in field trials. To better understand how this biofungicide works, two of the product components, i.e., B. subtilis and its metabolites (product filtrate), were assessed under controlled conditions for their relative contribution to clubroot control. The information may be used to optimize the product formulation. The bacterium or product filtrate alone was only partially effective against clubroot, reducing disease severity by about 60% relative to untreated controls. In contrast, Serenade controlled the disease by over 90%. This pattern of response was mirrored in quantitative PCR assessment on P. brassicae DNA within canola roots; the lowest and highest amounts of pathogen DNA were found in roots of Serenade treatment (0.02 and 0.01 ng/g) and controls (0.52 and 13.35 ng/g), respectively, at 2 and 3 weeks after treatment. During this period, the amount of DNA changed little in Serenade-treated roots but increased by almost 30-fold in the control. The product filtrate or B. subtilis also reduced the pathogen DNA substantially (0.03–1.16 ng/g). Serenade decreased the germination and viability of P. brassicae resting spores only marginally. It is suggested that biofungicide Serenade controls clubroot largely via suppressing root-hair and cortical infection by P. brassicae zoospores. The bacterial metabolites in the product formulation possibly assist B. subtilis in rhizosphere colonization and clubroot control by minimizing the competition from other soil microbes.     

Detection and quantification of Entomophaga maimaiga resting spores in forest soil using real-time PCR

Environmental sampling to monitor entomopathogen titre in forest soil, a known reservoir of insect pathogens such as fungi and viruses, is important in the evaluation of conditions that could trigger epizootics and in the development of strategies for insect pest management. Molecular or PCR-based analysis of environmental samples provides a sensitive method for strain- or species-based detection, and real-time PCR, in particular, allows quantification of the organism of interest. In this study we developed a DNA extraction method and a real-time PCR assay for detection and quantification of Entomophaga maimaiga (Zygomycetes: Entomophthorales), a fungal pathogen of the gypsy moth, in the organic layer of forest soil. DNA from fungal resting spores (azygospores) in soil was extracted using a detergent and bead mill homogenization treatment followed by purification of the crude DNA extract using Sephadex–polyvinylpolypyrrolidone microcolumns. The purification step eliminated most of the environmental contaminants commonly co-extracted with genomic DNA from soil samples but detection assays still required the addition of bovine serum albumin to relieve PCR inhibition. The real-time PCR assay used primers and probe based on sequence analysis of the nuclear ribosomal ITS region of several E. maimaiga and two E. aulicae strains. Comparison of threshold cycle values from different soil samples spiked with E. maimaiga DNA showed that soil background DNA and remaining co-extracted contaminants are critical factors determining detection sensitivity. Based on our results from comparisons of resting spore titres among different forest soils, estimates were best for organic soils with comparatively high densities of resting spores.     

A method for the extraction and enumeration of resting spores of Plasmodiophora brassicae from infested soil

A technique is described for the extraction of the resting spores of Plasmodiophora brassicae from soil. After deflocculation, coarse mineral matter was filtered from soil samples and the remainder mixed with 40% sucrose. The mixture was allowed to stand for 2–5 days; this enabled most mineral particles to settle out leaving the spores in suspension. The spores were counted optically on a microscope using Nomarski interference contrast optics, although preliminary studies had indicated that electronic image analysis was a more satisfactory method. Good recovery of spores was achieved from artificially infested soils containing 10⁶ spores/g but the technique can be satisfactorily applied to less heavily infested soils. Clubroot symptoms developed on seedlings dipped in suspensions of spores recovered in this way.     

Real-time polymerase chain reaction assay for rapid and sensitive detection of anthrax spores in spiked soil and talcum powder

Real-time polymerase chain reaction (real-time PCR) is a laboratory technique based on PCR. This technique is able to detect sequence-specific PCR products as they accumulate in “real time” during the PCR amplification, and also to quantify the number of substrates present in the initial PCR mixture before amplification begins. In the present study, real-time PCR assay was employed for rapid and real-time detection of Bacillus anthracis spores spiked in 0.1 g of soil and talcum powder ranging from 5 to 10⁷ spores. DNA was isolated from spiked soil and talcum powder, using PBS containing 1 % Triton-X-100, followed by heat treatment. The isolated DNA was used as template for real-time PCR and PCR. Real-time PCR amplification was obtained in 60 min under the annealing condition at 60°C by employing primers targeting the pag gene of B. anthracis. In the present study, the detection limit of real-time PCR assay in soil was 10³ spores and10² spores in talcum powder, respectively, whereas PCR could detect 10⁴ spores in soil and 10³ spores in talcum powder, respectively.     

Life Cycle of <Emphasis Type="Italic">Plasmodiophora brassicae</Emphasis>

Plasmodiphora brassicae is a soil-borne obligate parasite. The pathogen has three stages in its life cycle: survival in soil, root hair infection, and cortical infection. Resting spores of P. brassicae have a great ability to survive in soil. These resting spores release primary zoospores. When a zoospore reaches the surface of a root hair, it penetrates through the cell wall. This stage is termed the root hair infection stage. Inside root hairs the pathogen forms primary plasmodia. A number of nuclear divisions occur synchronously in the plasmodia, followed by cleavage into zoosporangia. Later, 4–16 secondary zoospores are formed in each zoosporangium and released into the soil. Secondary zoospores penetrate the cortical tissues of the main roots, a process called cortical infection. Inside invaded roots cells, the pathogen develops into secondary plasmodia which are associated with cellular hypertrophy, followed by gall formation in the tissues. The plasmodia finally develop into a new generation of resting spores, followed by their release back into soil as survival structures. In vitro dual cultures of P. brassicae with hairy root culture and suspension cultures have been developed to provide a way to nondestructively observe the growth of this pathogen within host cells. The development of P. brassicae in the hairy roots was similar to that found in intact plants. The observations of the cortical infection stage suggest that swelling of P. brassicae-infected cells and abnormal cell division of P. brassicae-infected and adjacent cells will induce hypertrophy and that movement of plasmodia by cytoplasmic streaming increases the number of P. brassicae-infected cells during cell division.     

Aboveground herbivory affects indirect defences of brassicaceous plants against the root feeder Delia radicum Linnaeus: laboratory and field evidence

1. Belowground herbivory has recently been shown to disrupt the host location behaviour of aboveground parasitoids and thereby impact plants indirect defences. Reverse interactions, on the other hand, have received little attention so far. 2. Lab and field studies were conducted to examine whether the presence of the leaf herbivore Pieris brassicae Linnaeus on brassicaceous plants influences the response of Trybliographa rapae Westwood, a specialist parasitoid of the root feeder Delia radicum Linnaeus. 3. The present results show that the attraction of the parasitoid towards host‐infested plants disappeared when these plants were also infested by P. brassicae. This absence of attraction was observed both when the complete odour blend or only undamaged leaves from damaged plants were offered, emphasising the role of systemically induced volatiles for host location in T. rapae. 4. Furthermore, the field study revealed that parasitism levels dropped from 30% on root‐infested plants to 4% on double‐infested plants. 5. The present study is the first to confirm that reduced attraction to host‐infested plants as a result of simultaneous attack by below‐ and aboveground herbivores translates into lower levels of parasitism in the field.     

Analysing spatial patterns of spread of Lettuce necrotic yellows virus and lettuce big-vein disease in lettuce field plantings

Spatial patterns of spread of lettuce big‐vein disease (LBVD) and Lettuce necrotic yellows virus (LNYV) were examined in two plantings each consisting of two blocks of lettuce. LBVD came from planting land infested with viruliferous Olpidium brassicae resting spores, while LNYV was introduced by aphid vectors from external sources consisting of LNYV‐infected sowthistle (Sonchus oleraceus) weeds. Clustering of LBVD was obvious in an area where the soil was heavily infested with only sporadic occurrence elsewhere. There was a steep decline in LNYV incidence over distance from a concentrated external weed source, with clustering of LNYV‐infected plants at the crop edge closest to it. There was no evidence of secondary spread with LBVD or LNYV.     

Assessment of Predacity and Efficacy of Arthrobotrys dactyloides for Biological Control of Root Knot Disease of Tomato

Five isolates of Arthrobotrys dactyloides were isolated from different locations of India and their in vitro predacity was tested against Meloidogyne incognita (J₂), Tylenchorhynchus brassicae and Hoplolaimus indicus. All isolates of A. dactyloides captured and killed M. incognita and T. brassicae but not H. indicus. The isolates also differed in their predacity of the first two nematode species. The application of mass culture of A. dactyloides in soil infested with 2000 juveniles of M. incognita per ‘kg’ before planting of tomato seedlings reduced the number of root knots by 5.6–45.6%, of females by 44.7–72.9%, of egg masses by 44.5–51.3% and of juveniles by 37.9–81.8% and increased the plant growth in a pot experiment. The effect of this fungus as biocontrol agent was enhanced when its mass culture was applied with cow dung manure, which reduced the number of root knots by 61.7–66.6%, of females by 80.6–94.7%, of egg masses by 80.3–89.6% and of juveniles by 68.1–88.0%.     

Application of PCR based diagnostics in the exploration of Parastagonospora nodorum prevalence in wheat growing regions of Himachal Pradesh

Stagonospora leaf and glume blotch (SLGB) of wheat caused by Parastagonospora nodorum (formerly Stagonospora nodorum) has recently emerged as a major problem in changing climatic conditions of Himachal Pradesh (HP), especially during delayed winter rains. In the present studies symptomatology, morpho-cultural as well as molecular marker based identification showed the prevalence of disease in the state and conclusively proved that leaf and glume blotch of wheat is caused by P. nodorum. The test pathogen showed 100% homology with other reported P. nodorum isolates by rDNA (ribosomal DNA) analysis. In addition, the amplification of rDNA region of 36 P. nodorum isolates representing various agro-ecological areas of HP and one infected wheat leaf sample generated an amplicon of ~ 449-bp with JB433 (5′-ACACTCAGTAGTTTACTACT-3′) and JB434 (5′-TGTGCTGCGCTTCAATA-3′) P. nodorum specific primer pair whereas no amplification was observed with the genomic DNA of Septoria titici, Stemphylium vesicarium and healthy wheat leaf sample. This study on integration of morpho-cultural and microscopic methods along with PCR based technique could form basis for routine diagnosis of the SLGB in wheat samples during early growth stages of crop in the seed production fields.

     

Powdery mildew suppresses herbivore‐induced plant volatiles and interferes with parasitoid attraction in Brassica rapa

The co‐occurrence of different antagonists on a plant can greatly affect infochemicals with ecological consequences for higher trophic levels. Here we investigated how the presence of a plant pathogen, the powdery mildew Erysiphe cruciferarum, on Brassica rapa affects (1) plant volatiles emitted in response to damage by a specialist herbivore, Pieris brassicae; (2) the attraction of the parasitic wasp Cotesia glomerata and (3) the performance of P. brassicae and C. glomerata. Plant volatiles were significantly induced by herbivory in both healthy and mildew‐infected plants, but were quantitatively 41% lower for mildew‐infected plants compared to healthy plants. Parasitoids strongly preferred Pieris‐infested plants to dually‐infested (Pieris + mildew) plants, and preferred dually infested plants over only mildew‐infected plants. The performance of P. brassicae was unaffected by powdery mildew, but C. glomerata cocoon mass was reduced when parasitized caterpillars developed on mildew‐infected plants. Thus, avoidance of mildew‐infested plants may be adaptive for C. glomerata parasitoids, whereas P. brassicae caterpillars may suffer less parasitism on mildew‐infected plants in nature. From a pest management standpoint, the concurrent presence of multiple plant antagonists can affect the efficiency of specific natural enemies, which may in turn have a negative impact on the regulation of pest populations.     

The A and B conformations of DNA and RNA subunits. Potential energy calculations for dGpdC

In order to obtain a molecular picture of the A and B forms of a DNA subunit, potential energy calculations have been made for dGpdC with C(3′)-endo and C(2′)-endo [or C(3′)-exo] sugar puckerings. These are compared with results for GpC. The global minima for dGpdC and GpC are almost identical. They are like A-form duplex DNA and RNA, respectively, with bases anti, the ω′, ω angle pair near 300°, 280°, and sugar pucker C(3′)-endo. For dGpdC, a B-form helical conformer, with sugar pucker C(2′)-endo and ω′ = 257°, ω = 298°, is found only 0.4 kcal/mol above the global minimum. A second low-energy conformation (2.3 kcal/mol) has ω′ = 263°, ω = 158° and ψ near 180°. This has dihedral angles like the original Watson–Crick model of the double helix. In contrast, for GpC, the C(2′)-endo B form is 6.9 kcal/mol above the global minimum. These theoretical results are consistent with experimental studies on DNA and RNA fibers. DNA fibers exist in both A and B forms, while RNA fibers generally assume only the A form. A low-energy conformation unlike the A or B forms was found for both dGpdC and GpC when the sugars were C(3′)-endo. This conformation—ω′,ω near 20°,80°—was not observed for C(2′)-endo dGpdC. Energy surface maps in the ω′,ω plane showed that C(2′)-endo dGpdC has one low-energy valley. It is in the B-form helical region (ω′ ～ 260°, ω ～ 300). When the sugar pucker is C(3′)-endo, dGpdC has two low-energy regions: the A-form helical region and the region with the minimum at ω′ = 16°, ω = 85°.     

Conformational features of 2′-O-methyl-adenosylyl-adenosine

In order to obtain information about the conformational features of a 2′-O-methylated polyribonucleotide at the nearest neighbor level, a detailed nuclear magnetic resonance study of AmpA was undertaken. AmpA was isolated from alkali hydrolysates of yeast RNA, and proton spectra were recorded at 100 MHz in the Fourier transform mode in D₂O solutions, 0.01 M, pH 5.4 and 1.5 at 25°C. ³¹P spectra were recorded at 40.48 MHz. Complete, accurate sets of nmr parameters derived for each nucleotidyl unit by simulation iteration methods. The nmr data were translated into conformational parameters for all the bonds using procedures developed in earlier studies from these laboratories. It is shown that AmpA exists in aqueous solution with a flexible molecular framework, which shows preferences for certain orientations. The ribose rings exist as a ²E ? ³E equilibrium with the —pA ribose showing a bias for the ³E pucker. The C(4′)—C(5′) bonds of both nucleotidyl units show significant preference (75–80%) to exist in gg conformation. The dominant conformer (80%) about C(5′)—O(5′) of the 5′-nucleotidyl unit is g′g′. Even though an unambiguous determination of the orientation of the 3′-phosphate group cannot be made, tentative evidence shows that it preferentially occupies g⁺ domains [O(3′)—P trans to C(3′)—C(2′)] in which the H(3′) —C(3′)—O(3′)—P(3′) dihedral angle is about 31°. There is reasonable evidence that the 2′-O-methyl preferentially occupies the domain in which the O(2′)—CH₃ bond is trans to C(2′)—C(1′). Lowering of pH to 1.5, which results in protonation of both the adenine moieties, causes destacking of AmpA. Such destacking is accompanied by small, but real, perturbations in the conformations about most of the bonds in the backbone. A detailed comparison of the solution conformations of ApA and AmpA clearly shows that 2′-O-methylation strongly influences the conformational preference about the C(3′)—O(3′) bond of the 3′-nucleotidyl unit, in addition to inducing small changes in the overall ribophosphate backbone conformational equilibria. The effect of 2′-O-methylation is such that the C(3′)—O(3′) is forced to occupy preferentially the g⁺ domain rather than the normally preferred g^? domain [O(3′)—P trans to C(3′)—C(4′)] in ApA. The data on ApA and AmpA further reveal that the extent of stacking interaction is less in AmpA compared to ApA. It is suggested that stacked species of AmpA exist as right-handed stacks where the magnitude of ω and ω′ about O(5′)—P and P—O(3′) is about 290°. The reason for the lesser degree of stacking in AmpA compared to ApA is intramolecular interaction between 2′-O-methyl and the flexible O(3′)—P—O(5′) bridge, the interaction causing some perturbation in the magnitudes of ω/ω′, causing destacking. The destacking will lead to an increase in _χCN by a few degrees, causing an increase in ²E populations; the latter in turn will shift the 3′ phosphate group from g^? to g⁺ domains. In short, a coupled series of conformational events is envisioned at the onset of destacking, made feasible by the interaction between the 2′-O-methyl group and the swivel O(3′)—P—O(5′) bridge.     

Comparative headspace analysis of cabbage plants damaged by two species ofPieris caterpillars: consequences for in-flight host location byCotesia parasitoids

Headspace composition, collected from intact cabbage plants and cabbage plants infested with eitherPieris brassicae L. orP. rapae L. (Lepidoptera: Pieridae) first instar larvae, was determined by GC-MS. Twenty-one volatiles were identified in the headspace of intact plants. Twenty-two volatiles were identified in the headspace of plants infested byP. brassicae larvae, 2 of which, Z-3-hexenyl butyrate and Z-3-hexenyl isovalerate, were not detected in the headspace of either intact orP. rapae damaged plants. In the headspace of the latter, 21 compounds were identified, all of which which were also produced by intact plants. No significant quantitative differences were found between headspace composition of the plants damaged by one or the other caterpillar species. Major differences between intact and caterpillar-damaged plants in contribution to the headspace profile were revealed for hexyl acetate, Z-3-hexenyl acetate, myrcene, sabinene and 1,8-cineole. The larval endoparasitoidCotesia glomerata L. was attracted by the volatiles emanating fromB. oleracea damaged byP. brassicae first instar larvae.C. rubecula L., a specialized larval endoparasitoids ofP. rapae, was attracted by the volatiles released from theB. oleracea-P. rapae plant-host complex. This shows that cabbage plants kept under the conditions of headspace collection produce attractive volatiles for both parasitoids.     

An evaluation of commercial DNA extraction kits for the isolation of bacterial spore DNA from soil

Aims: To evaluate six commercial DNA extraction kits for their ability to isolate PCR‐quality DNA from Bacillus spores in various soil samples. Methods and Results: Three soils were inoculated with various amounts of Bacillus cereus spores to simulate an outbreak or intentional release of the threat agent Bacillus anthracis. DNA was isolated from soil samples using six commercial DNA extraction kits. Extraction and purification efficiencies were assessed using a duplex real‐time PCR assay that included an internal positive control. The FastDNA^® SPIN kit for Soil showed the highest DNA extraction yield, while the E.Z.N.A.^® Soil DNA and PowerSoil^® DNA Isolation kits showed the highest efficiencies in removing PCR inhibitors from loam soil extracts. Conclusions: The results of this study suggest that commercially available extraction kits can be used to extract PCR‐quality DNA from bacterial spores in soil. The selection of an appropriate extraction kit should depend on the characteristics of the soil sample and the intended downstream application. Significance and Impact of the Study: The results of this study aid in the selection of an appropriate DNA extraction kit for a given soil sample. Its application could expedite sample processing for real‐time PCR detection of a pathogen in soil.     

The Response Specificity of <Emphasis Type="Italic">Trichogramma</Emphasis> Egg Parasitoids towards Infochemicals during Host Location

Parasitoids are confronted with many different infochemicals of their hosts and food plants during host selection. Here, we investigated the effect of kairomones from the adult host Pieris brassicae and of cues present on Brussels sprout plants infested by P. brassicae eggs on the behavioral response of the egg parasitoid Trichogramma evanescens. Additionally, we tested whether the parasitoid’s acceptance of P. brassicae eggs changes with different host ages. The wasps did not discriminate between olfactory cues from mated and virgin females or between mated females and males of P. brassicae. T. evanescens randomly climbed on the butterflies, showing a phoretic behavior without any preference for a certain sex. The parasitoid was arrested on leaf parts next to 1-day-old host egg masses. This arrestment might be due to cues deposited during oviposition. The wasps parasitized host eggs up to 3 days old equally well. Our results were compared with former studies on responses by T .brassicae showing that T. evanescens makes less use of infochemicals from P. brassicae than T. brassicae.     

A real‐time PCR method to quantify spores carrying the Bacillus thuringiensis var. israelensis cry4Aa and cry4Ba genes in soil

Aim: To develop a rapid real‐time PCR method for the specific detection and quantification of Bacillus thuringiensis var. israelensis (Bti) spores present in the environment. Methods and Results: Seven soil samples as well as one sediment sample obtained from various regions of Switzerland and characterized by different granulometry, pH values, organic matter and carbonate content were artificially inoculated with known amounts of Bti spores. After DNA extraction, DNA templates were amplified using TaqMan real‐time PCR targeting the cry4Aa and cry4Ba plasmid genes encoding two insecticidal toxins (δ‐endotoxins), and quantitative standard curves were created for each sample. Physicochemical characteristics of the samples tested did not influence DNA extraction efficiency. Real‐time PCR inhibition because of the presence of co‐extracted humic substances from the soil was observed only for undiluted DNA extracts from samples with very high organic matter content (68%). The developed real‐time PCR system proved to be sensitive, detecting down to 1 × 10³ Bti spores per g soil. One‐way analysis of variance confirmed the accuracy of the method. Conclusions: Direct extraction of DNA from environmental samples without culturing, followed by a specific real‐time PCR allowed for a fast and reliable identification and quantification of Bti spores in soil and sediment. Significance and Impact of the Study: The developed real‐time PCR system can be used as a tool for ecological surveys of areas where treatments with Bti are carried out.     

Detection of the defoliating and nondefoliating pathotypes of <Emphasis Type="Italic">Verticillium dahliae</Emphasis> in artificial and natural soils by nested PCR

In Spain, Verticillium wilt, caused by Verticillium dahliae, is the most important disease of cotton and olive. Isolates of V. dahliae infecting these crops can be classified into highly virulent, defoliating (D), and mildly virulent, nondefoliating (ND), pathotypes. Infested soil is the primary source of inoculum for Verticillium wilt epidemics in cotton and olive, and severity of disease relates to the prevailing V.dahliae pathotype. In this work we have adapted the use of previously developed primer pairs specific for D and ND V. dahliae for the detection of these pathotypes by nested PCR in artificial and natural soils. Success in the detection procedure depends upon efficiency in extracting PCR-quality DNA from soil samples. We developed an efficient DNA extraction method from microsclerotia infesting the soil that includes the use of acid washed sand during the grinding process and skimmed milk to avoid co-purification of Taq-polymerase inhibitors with DNA. The specific nested-PCR procedure effectively detected 10 or more microsclerotia per gram of soil. The detection procedure has proven efficient when used with a naturally infested soil, thus demonstrating usefullness of the diagnostic method for rapid and accurate assessment of soil contamination by V. dahliae pathotypes.