A quantitative real‐time PCR assay for the detection of Ramularia collo‐cygni from barley (Hordeum vulgare)

Aims: The aim of this study was to develop a real‐time quantitative PCR test to recognize and quantify the DNA levels of the increasingly important barley pathogen Ramularia collo‐cygni. Methods and Results: The method described uses specifically designed primers and a molecular beacon probe based on an internal transcribed spacer (ITS) sequence. Pathogen extracted from barley leaves could be quantified to the picogram level in both leaves showing symptoms of infection and symptomless barley leaves. Conclusions: A relationship between R. collo‐cygni DNA levels and disease symptoms was established in spring barley under natural infection conditions. Significance and Impact of the Study: To our knowledge, this is the first report of a test of this type and makes an important contribution to studies into the life cycle of this pathogen.     

Mutual benefit interactions between banded pine weevil Pissodes castaneus and blue‐stain fungus Leptographium serpens in maritime pine

• 1 Ecological interactions between banded pine weevil Pissodes castaneus and blue‐stain fungus Leptographium serpens, when simultaneously sharing the same host plant (maritime pine Pinus pinaster) in winter and spring, were investigated. Temporal components of the interaction were taken into account by either introducing the weevils and the pathogen simultaneously or sequentially, with the weevils being introduced 1 month after the fungal inoculation.
• 2 We measured larval mortality, development time, offspring number, sex ratio and body size of P. castaneus. Phloem phosphorus and nitrogen concentrations were also assessed. Furthermore, we tested whether: (i) emerging offspring transported propagules of the fungus; (ii) artificially‐contaminated weevils may transmit the disease to healthy trees; and (iii) field collected P. castaneus carry the fungus.
• 3 The fungus enhanced weevil colonization and brood production in both seasons. During winter and spring, adults from trees where the pathogen was inoculated prior to weevil introduction emerged earlier than weevils from trees where they had been introduced simultaneously with the fungus. During winter, weevils from pre‐inoculated trees were also larger. Sex ratio and larval mortality were not affected. Leptographium serpens did not affect phloem nitrogen content but phosphorus content was greater in plants inoculated with the pathogen, which may explain the findings on weevil growth.
• 4 Sixty‐five percent of the weevils that emerged from inoculated trees carried spores of L. serpens, although no successful isolation was made from field collected weevils. The fungus was recovered from 25% of the trees infested with artificially‐contaminated weevils.
• 5 These results suggest that P. castaneus benefits from the presence of L. serpens and may contribute to its spread.

     

Fusarium langsethiae – a HT‐2 and T‐2 Toxins Producer that Needs More Attention

Fusarium langsethiae is a toxigenic fungus that was formally described as a new species in 2004. This fungus was first detailed in the 1990s but was initially referred to as ‘powdery Fusarium poae’ having a spore morphology similar to F. poae but a mycotoxin profile like that of Fusarium sporotrichioides. The species has been isolated from infected oat, wheat and barley grains but has been reported as more problematic in the former crop rather than the latter two. Whilst the epidemiology of F. langsethiae remains unclear, the fungus has been shown to produce high levels of type‐A trichothecenes HT‐2 and T‐2 toxins in small‐grain cereals. HT‐2 and T‐2 toxins are two of the most potent trichothecenes capable of inhibiting protein synthesis in eukaryotes. In this regard, mycotoxin contamination caused by F. langsethiae is clearly a food and feed safety hazard. With the European Commission considering legislation of HT‐2 and T‐2 toxins, more information is required not only on the producer and conditions favouring mycotoxin production, but also on reliable methods of pathogen detection and reduction of cereal contamination. This review describes recent research concerning the known epidemiology of F. langsethiae and suggestions of what needs to be known about the fungus in order to be able to understand and employ measures for preventing its infection and contamination of cereals with HT‐2 and T‐2 toxins.     

Surface interactions of Fusarium graminearum on barley

The filamentous fungus Fusarium graminearum, a devastating pathogen of barley (Hordeum vulgare L.), produces mycotoxins that pose a health hazard. To investigate the surface interactions of F. graminearum on barley, we focused on barley florets, as the most important infection site leading to grain contamination. The fungus interacted with silica‐accumulating cells (trichomes and silica/cork cell pairs) on the host surface. We identified variation in trichome‐type cells between two‐row and six‐row barley, and in the role of specific epidermal cells in the ingress of F. graminearum into barley florets. Prickle‐type trichomes functioned to trap conidia and were sites of fungal penetration. Infections of more mature florets supported the spread of hyphae into the vascular bundles, whereas younger florets did not show this spread. These differences related directly to the timing and location of increases in silica content during maturation. Focal accumulation of cellulose in infected paleae of two‐row and six‐row barley indicated that the response is in part linked to trichome type. Overall, silica‐accumulating epidermal cells had an expanded role in barley, serving to trap conidia, provide sites for fungal ingress and initiate resistance responses, suggesting a role for silica in pathogen establishment.     

A TaqMan PCR Method for Routine Diagnosis of the Quarantine Fungus Guignardia citricarpa on Citrus Fruit

With respect to disease risk for the quarantine fungus Guignardia citricarpa on citrus fruit an accurate diagnosis for routine analysis is required. Also, when inspections have to be performed on imported citrus fruits, a fast detection method is urgently needed. A fast automated DNA extraction method based on magnetic beads combined with a real‐time PCR assay was optimized to improve and advance the routine diagnosis of citrus black spot disease. Real‐time PCR was used for detection of the pathogen G. citricarpa in planta. A specific primer/TaqMan probe combination that discriminates between G. citricarpa and the harmless citrus endophyte Guignardia mangiferae, was designed based on the internal transcribed spacer region of the multi‐copy rDNA gene. Co‐amplification of target DNA along with an internal competitor DNA fragment made the diagnostic assay more reliable to check for false negatives. The real‐time PCR was specific, since no cross reaction was observed with a series of citrus pathogens and related species. The diagnostic assay was performed on lesions dissected from imported diseased oranges. Comparison between the conventional PCR and the real‐time PCR methods showed that the TaqMan method was more sensitive.     

Variability of the Ramularia collo‐cygni Population in Central Europe

The genetic structure of the fungal barley pathogen Ramularia collo‐cygni (Rcc) population in Central Europe involving the isolates from the Czech Republic, the Slovak Republic, Germany and Swiss was determined using amplified fragment length polymorphism (AFLP) analysis. One hundred and eighty‐four markers were chosen to determine genetic and genotypic diversity and to test the hypothesis of random mating and population differentiation of Rcc isolates. Among the 337 isolates collected, the overall gene diversity was moderate ( = 0.216). The level of multilocus genotypic diversity was higher within populations than among them. All individuals had unique multilocus genotypes. Genetic differentiation was significant among populations in localities, but at a moderate level (θ = 0.12; P < 0.001), suggesting that gene flow is occurring among populations. The isolates from all twelve clusters produced by Structure were found in all local populations, although at different frequencies. Therefore, the inferred clusters did not represent geographical populations. Although the null hypothesis of random mating in Rcc populations was rejected, the high level of genotypic diversity suggests that the Rcc population structure appears to be generated by a mixed reproductive system including both asexual and sexual reproduction, along with a rather high migration rate.     

Allelic characteristics of the β-amylase gene of barley varieties in Ukraine

Allelic diversity in a set of 99 spring and winter barley varieties intended for different use (malting, cereal, and valuable) was studied. PCR analysis with the use of the β-amylase DNA marker showed that genotypes of different barley varieties may include different alleles of the β-amy1 gene.     

Mapping new EMBL-derived barley microsatellites and their use in differentiating German barley cultivars

By searching the EMBL DNA sequence database, we were able to develop 39 new, database-derived barley microsatellites. Eighteen of these EMBL microsatellites were mapped either to the interspecific barley map Lerche×BGRC41936 (L×41), the Igri×Franka map (I×F, Graner et al. 1991), or to both maps simultaneously. In addition, all 39 EMBL microsatellites were assigned to individual barley chromosomes by PCR screening of wheat barley addition lines. Both studies verified a random distribution of the microsatellites within the barley genome. Subsequently, 22 EMBL microsatellites were used to assess the genetic similarity among a set of 28, mainly German, barley cultivars and two wild form accessions. Spring and winter cultivars could be easily differentiated using the first coordinate of a principal coordinate analysis. Whereas the group of spring barley cultivars appeared rather homogeneous, winter barley cultivars could be divided into three subgroups. Two H. v. ssp. spontaneum accessions were included in the assessment of genetic similarity. They were placed among the winter barley cultivars. Based on the assessment of the 30 barley cultivars and accessions, the polymorphism information content (PIC) of each EMBL microsatellite has been calculated. The average PIC value among the EMBL microsatellites was equal to 0.38, which ascertains the value of these microsatellites as a genetic tool in barley genome research projects. Received: 6 December 1999 / Accepted: 23 February 2000     

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.     

A cAMP‐Dependent Protein Kinase Gene,aapk1, Is Required for Mycelia Growth,Toxicity and Pathogenicity of Alternaria alternata on Tobacco

The fungus Alternaria alternata is a common spot‐producing plant pathogen. During the past decade, tobacco brown spot disease caused by this fungus has became prevalent in China and lead to significant losses. To better understand the molecular pathogenesis of this fungus, the aapk1 gene encoding a cAMP‐dependent protein kinase catalytic subunit was cloned, sequenced and characterized. The aapk1 deletion mutants were identified from hygromycin‐resistant transformants by PCR strategy and confirmed by Southern blot analysis and RT‐PCR. The aapk1 deletion mutant exhibited reduced vegetative growth and was less toxic than the wild‐type strain sd1. Deletion of aapk1 also delayed disease development on detached tobacco leaves. Thus, we propose that the cAMP signalling pathway is involved in mycelia growth and pathogenic phenotype of Alternaria alternata.     

Ramularia collo-cygni: the biology of an emerging pathogen of barley.

Ramularia collo-cygni is now recognized as an important pathogen of barley in Northern Europe and New Zealand. It induces necrotic spotting and premature leaf senescence, leading to loss of green leaf area in crops, and can result in substantial yield losses. The fungus produces a number of anthraquinone toxins called rubellins, which act as host nonspecific toxins with photodynamic activity. These toxins induce lipid peroxidation and are possibly the cause of the chlorosis and necrosis observed in leaves infected with R. collo-cygni. The fact that the fungus can remain latent in barley plants until flowering, coupled with its very slow growth in vitro, makes it difficult to detect in crops. As a result, the epidemiology of this pathogen remains poorly understood. However, the recent development of rapid and reliable PCR methods for specific detection of R. collo-cygni offers the prospect of increased understanding of its epidemiology and improved disease control.     

Contrasting the seasonal and elevational prevalence of generalist avian haemosporidia in co‐occurring host species

Understanding the ecology and evolution of parasites is contingent on identifying the selection pressures they face across their infection landscape. Such a task is made challenging by the fact that these pressures will likely vary across time and space, as a result of seasonal and geographical differences in host susceptibility or transmission opportunities. Avian haemosporidian blood parasites are capable of infecting multiple co‐occurring hosts within their ranges, yet whether their distribution across time and space varies similarly in their different host species remains unclear. Here, we applied a new PCR method to detect avian haemosporidia (genera Haemoproteus, Leucocytozoon, and Plasmodium) and to determine parasite prevalence in two closely related and co‐occurring host species, blue tits (Cyanistes caeruleus, N = 529) and great tits (Parus major, N = 443). Our samples were collected between autumn and spring, along an elevational gradient in the French Pyrenees and over a three‐year period. Most parasites were found to infect both host species, and while these generalist parasites displayed similar elevational patterns of prevalence in the two host species, this was not always the case for seasonal prevalence patterns. For example, Leucocytozoon group A parasites showed inverse seasonal prevalence when comparing between the two host species, being highest in winter and spring in blue tits but higher in autumn in great tits. While Plasmodium relictum prevalence was overall lower in spring relative to winter or autumn in both species, spring prevalence was also lower in blue tits than in great tits. Together, these results reveal how generalist parasites can exhibit host‐specific epidemiology, which is likely to complicate predictions of host–parasite co‐evolution.     

Quantification of Fusarium culmorum in Wheat and Barley Tissues Using Real-Time PCR in Comparison with DON Content

A real‐time polymerase chain reaction (PCR) assay was developed for the specific detection of Fusarium culmorum in infected seeds. Primers and TaqMan minor groove binder probe were derived from the sequences of a F. culmorum specific PCR product. The specificity of the assay was confirmed by test in seven Fusarium species and 21 non‐Fusarium fungal species. With serial dilutions of purified genomic DNA from F. culmorum isolate B as the template, the detection limit of the assay was found to be 0.9 pg of fungal genomic DNA per reaction. A significant correlation ( = 0.982) and collinearity was found between DNA concentration and Ct (cycle threshold) values of real‐time PCR assay with serial diluted DNAs extracted from three seed samples with different deoxynivalenol (DON) content. Eight barley and nine wheat varieties infected by F. culmorum isolate B were evaluated in 1 (barley samples) and in 4 years (wheat samples). The results of real‐time PCR analysis and enzyme‐linked immunosorbent assay testing for DON content were compared and a significant correlation was found for barley samples (r² = 0.935). Concerning wheat we found rather complicated relationship between Ct values and DON contents influenced by environmental conditions of field trials. The real‐time PCR assay was found to be highly specific and sensitive. It could be used in phytopathological studies and praxis.     

Increased Levels of Cytokinins in Barley Leaves Having the Systemic Acquired Resistance to Bipolaris sorokiniana (Sacc.) Shoemaker

The role of endogenously induced higher level of cytokinins and exogenously applied kinetin in relation to the development of barley leaf spot caused by Bipolaris sorokiniana (Sacc.) Shoemaker (syn. Helminthosporium sativum Pammel, King and Bakke) was studied. Spraying barley leaves with kinetin suppressed the number and the size of necrotic spots caused by the fungus. Inoculation of the lower leaves of barley by a spore suspension of the fungus B. sorokiniana induced resistance on the upper leaves against a subsequent challenge inoculation by the same pathogen 10 days later. An increase in the level of cytokinins was observed in these resistant leaves. Elevated levels of cytokinins may cause a type of juvenility in leaf tissues. The juvenile state could be in a causal relationship with the suppression of necrotic spots caused by the fungus.     

The competitive effects of volunteer barley (Hordeum vulgare) on the growth of oilseed rape (Brassica napus)

The effects of competition from volunteer barley (Hordeum vulgare) on the growth and yield of oilseed rape (Brassica napus) were investigated in four experiments over three seasons. The growth of rape in the autumn was reduced by 50 - 91 % by competition from 400 barley plants m^-2. A lower barley density of 200 plants m^-2 had less effect but still reduced growth of rape by 65 - 81% in two of the experiments and 25 - 40% in the other two. During winter and spring the barley decreased in vigour and in the spring the rape started to recover, especially on the early drilled (23 - 30 August) plots. The rape sown in mid-September recovered less quickly. In Experiment 3, herbicides applied in November to control barley did not result in increased growth of rape in winter but led to greater recovery in spring. The barley died during the winter in Experiments 2 and 4, even in the absence of herbicides. Despite the marked effects of barley on the growth of rape in the autumn, yields on plots that had previously contained 200 barley plants m^-2 were reduced by a maximum of only 16% in three of the experiments. In Experiment 3, where the barley was most competitive, this density and 400 plants m^-2 lowered yields by 39% and 78%, respectively. Where a herbicide was used in November to control the barley these yield losses were reduced to 5%. In many rape crops the cost of herbicide treatment would be greater than the financial returns from the expected increase in yield resulting from the control of weeds. Possible reasons for the small loss in yield of rape from barley densities that had substantial effects on the growth of rape in the autumn are discussed.     

Variation in acquisition of soil phosphorus among wheat and barley genotypes

To assess the extent of variation in phosphorus acquisition efficiency of some winter wheat (Triticum aestivum L.), winter and spring barley (Hordeum vulgare L.) genotypes, depletion of inorganic phosphorus (P) extractable with 0.5 M NaHCO₃ (NaHCO₃-P_i) from the rhizosphere soil was studied. Nutrients supply, rhizosphere soil pH and soil water content was kept equal for all the genotypes with the aim to reduce the confounding variation due to these factors. The experimental set up implied that no difference in the relative growth rates, nitrogen, potassium and calcium content of shoot dry matter occurred among the genotypes.The winter wheat, winter barley and spring barley genotypes differed significantly (p>0.05) in their efficiency to acquire NaHCO₃-P_i from the rhizosphere soil. The efficiency of the winter wheat genotypes to acquire NaHCO₃-P_i from rhizosphere soil ranked Kraka > Gawain > Foreman > Sleipner = Obelisk > Kosack > Pepital > Arum. Winter wheat genotypes differed in extent of P depletion profiles in the rhizosphere, indicating variation in root hair length. The winter barley and spring barley genotypes also showed significant differences in their P depletion profiles near roots. The efficiency of the winter barley genotypes to acquire soil P in the rhizosphere ranked Hamu > Frost > Marinka > Astrid > Clarine = Angora. The efficiency of spring barley genotypes to acquire NaHCO₃-P_i in the rhizosphere ranked Canut > Etna Riga > Digger > Peel > Semal > Alexis. The rhizosphere pH remained unchanged, suggesting that additional mechanisms such as root hair formation and root exudates play a significant role in causing variation in P acquisition among the genotypes.