Modern approaches to species concepts in downy mildews

Inadequate species definitions present a serious problem to the pathologist working in plant hygiene or quarantine which demands urgent attention. Species concepts in the downy mildews have not kept pace with developments in evolutionary and molecular biology, or with advances in ecological genetics, because the downy mildews are obligate biotrophs that are not easily cultured in the laboratory. Existing approaches to species concepts in this group (morphometric, Ga¨umann's 'biological species' and Skalicý's 'eco–physio–phentic' concepts) are examined and found to be inadequate and potentially misleading. The systematic treatment of the downy mildews is beginning to benefit from the application of modern methods of systematic analysis. The contribution and potential of ultrastructure, karyotyping, sterol and fatty acid composition, isoenzyme patterns, molecular biology, numerical methods, immunoassay and hypotheses of coevolution to the development of species concepts are reviewed and their wider application is seen as a priority. The application to the downy mildews of two widespread species concepts, the biological and phylogenetic concepts, is examined in the light of the information gained from modern methods of analysis, but neither is found adequate to describe species of downy mildews as they occur in nature. Modern methods can suggest phylogenetic relationships on the basis of statistical probabilities and may also detect microevolutionary change, but it is concluded that much more information is required about individual breeding systems, gene flow, ecology, phylogeny and distribution before informed decisions about the delimitation of most species can be made. Until patterns of genetic diversity can be established, a modified phylogenetic species concept may offer one interim solution to the problem of species definition in the downy mildews.     

Molecular phylogenetic analysis of <Emphasis Type="Italic">Peronosclerospora</Emphasis> (Oomycetes) reveals cryptic species and genetically distinct species parasitic to maize

Downy mildews are amongst the most widespread and economically important pathogens of cultivated grasses in the tropics and subtropics. Despite their importance, molecular methods, particularly DNA sequence analysis, have rarely been applied to either species identification or to the determination of phylogenetic relationships between species. Here we report the presence of several cryptic species in the genus Peronosclerospora. Further we confirm that maize can be parasitised by several species of Peronosclerospora, including P. eriochloae, which has not been reported previously as a pathogen of maize. The presence of 14 distinct phylogenetic lineages, including three that are parasitic to maize, highlights the current fragmentary knowledge on the diversity and classification of species within Peronosclerospora. Species identification in Peronosclerospora has been traditionally based on the host genus and a set of variable morphological characteristics, which has meant that the identification of species is often unreliable. This situation is primed for the application of molecular techniques for the identification of species. One of the lineages parasitic to maize in Australia has not yet been formally described and its distribution is not known. Future investigation including a broad sampling of downy mildews from maize and other cultivated and native grasses on a world-wide basis is a prerequisite to a re-evaluation of quarantine regulations aimed at restricting or limiting their spread.     

Host matrix has major impact on the morphology of <Emphasis Type="Italic">Pseudoperonospora cubensis</Emphasis>

Oomycetes contain some of the economically most important pathogens of flowering plants. Most have a rather narrow host range, often being restricted to single host species. In downy mildews and other obligate biotrophic plant parasites, like powdery mildews and rusts, delimitating species on grounds of morphological characteristics is often hardly possible and thus often based on only subtle differences. This has led to the widespread application of a broad species concept for these organisms. Consequently, despite the fact that morphological differences were reported for Pseudoperonospora cubensis from different host species, the corresponding new pathogen species were not accepted as being independent, and the host range of Pseudoperonospora cubensis is reported to encompass more than 50 host species in the Cucurbitaceae in temperate to tropical climates. However, recent studies have reported narrow host ranges for other downy mildew genera and advocated a narrow species concept. Here, we report successful colonisation of five different tribes of the Cucurbitaceae by a strain of Pseudoperonospora cubensis and demonstrate that the host matrix has a major impact on the morphology of the pathogen. On the basis of five morphological criteria significant differences could be found for all hosts. These differences were more pronounced in phylogenetically unrelated than in related hosts. Our results provide evidence for a broad host range of Pseudoperonospora cubensis and demonstrate that species delimitation based on morphological characters is not feasible in Pseudoperonospora on Cucurbitaceae. Also in other biotrophic plant pathogens, the situation could be similar, thus necessitating thorough morphological, molecular phylogenetic and cross inoculation experiments for species recognition.     

A potential perennial host for <Emphasis Type="Italic">Pseudoperonospora cubensis</Emphasis> in temperate regions

Pseudoperonospora cubensis causes great losses in cucurbitaceous crops worldwide. In cool temperate climates of northern Europe or North America overwintering as active mycelium is not possible, because all hosts so far reported there are summer annuals. Oospores have not yet been found in these regions under field conditions. The only perennial member of the Cucurbitaceae found naturally in central and northern Europe is Bryonia dioica. To date this plant has not been recorded as a host for downy mildews, but our infection trials demonstrate that P. cubensis is able to infest this plant. Amplification and sequencing of the ITS rDNA confirmed the observed downy mildew disease on B. dioica as P. cubensis. From these findings, the possibility that P. cubensis may be able to overwinter on this perennial host cannot be excluded. Whether or not B. dioica plays a part in the epidemology of P. cubensis in Europe requires evaluation by further studies.     

Evaluation of the API 50CH and API ZYM systems for rapid characterization of Clavibacter michiganensis subsp. sepedonicus, causal agent of potato ring rot

API 50CH and API ZYM systems were used to characterize fifty-three strains of Clavibacter michiganensis subsp. sepedonicus from different geographic locations and several reference strains of the same and different species, including other potato pathogens. Clavibacter michiganensis subsp. sepedonicus strains displayed a high level of homogeneity, both in carbohydrate utilization and in enzymatic activity. Using API 50CH and API ZYM it was possible to differentiate C. michiganensis subsp. sepedonicus strains from the remaining taxa analysed in this study, which included representative strains of the other subspecies of C. michiganensis as well as other bacterial pathogens affecting potatoes. Therefore, these systems could be used as an effective method to characterize C. michiganensis subsp. sepedonicus. Such a procedure would constitute an alternative system to the conventional nutritional and physiological identification tests currently included in the official methods employed in the European Union to detect and identify this bacterium. The results obtained with the API systems agreed with the current taxonomic classification of C. michiganensis, clearly separating sepedonicus from the other subspecies belonging to this species.     

The epidemiology, variability and control of the downy mildews of pearl millet and sorghum, with particular reference to Africa

Sorghum downy mildew ( Peronosclerospora sorghi ) infecting sorghum and maize, and pearl millet downy mildew ( Sclerospora graminicola ) infecting pearl millet can cause considerable yield loss in Africa. The last 15 years have witnessed an increase in knowledge of the biology, epidemiology and control of these two pathogens. Much information has been obtained on the effect of environmental factors on disease epidemiology, spore production and dispersal. Molecular techniques applied to study pathogenic variability have aided in defining relationships among these pathogens, although scope of the work is limited. Knowledge of the genetics and inheritance of resistance, and of resistance mechanisms, has also increased. This review presents the current state of knowledge of both downy mildew pathogens, with focus on their status on sorghum and pearl millet in Africa. Despite the advances in knowledge over the last 15 years, these downy mildews remain important constraints to sustainable crop production in the semi-arid regions of Africa. In some cases information obtained in Asia and the Americas can be extrapolated to Africa but care must be taken in ensuring its applicability. Priorities for future research relevant for Africa are proposed and discussed.     

Advances in research on oomycete root pathogens

This review discusses recent advances in research into plant pathogenic oomycetes with an emphasis on root-infecting species. We focus on aspects of host targeting, mycoparasitism, and the development of molecular techniques that enable functional dissection of key genes of this economically important group of pathogens, including genomics, proteomics and gene silencing. We have not incorporated aspects relating to host resistance, research carried out into downy mildews, and other phyloplane oomycetes, unless there is also a specific relevance to the root-oomycete research community. The analysis of the asexual life stages of these organisms from zoosporogenesis through zoospore liberation, host targeting, encystment, germination, and the formation of appressoria-like structures in the rhizosphere offer significant potential in the establishment of new approaches for the treatment of disease in these organisms. The advent of appropriate molecular tools is now enabling the molecular analysis of these developmental stages to begin in earnest and will stimulate research into an economically important but scientifically neglected group of organisms.     

Identification and Characterisation of Xanthomonas campestris pv. campestris Strains from Tanzania by Pathogenicity Tests, Biolog, rep-PCR and Fatty Acid Methyl Ester Analysis

Black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is a major disease constraint to cabbage production by smallholder farmers in Africa. Variability exists within the pathogen, and yet differentiation of Xcc strains from other closely-related xanthomonads attacking crucifers is often difficult. The Biolog system, fatty acid methyl ester analysis using microbial identification system (MIS), rep-PCR and pathogenicity tests were used to identify and characterise Xcc strains from Tanzania. Great diversity was observed among Xcc strains in their Biolog and rep-PCR profiles. Specific rep-PCR genomic fingerprints were linked to some geographical areas in the country. Most of the Xcc strains were clustered in two groups based on their fatty acid profiles and symptom expression in cabbage although some deviant strains were found. Each of the methods allowed a degree of identification from species, pathovar to the strain level. Biolog and MIS identified all Xcc strains at least to the genus level. Additionally, Biolog identified 47% of Xcc strains to the pathovar and 43% to strain level, whereas MIS identified 43% of the strains to pathovar level. In the absence of a database, the utility of rep-PCR for routine diagnosis of strains was limited, although the procedure was good for delineation of Xcc to the strain level. These findings indicate the existence of Xcc strains in Tanzania that are distinct from those included in Biolog and MIS databases. The limitations noticed warrant continued improvement of databases and inclusion of pathogenicity testing, using universally susceptible cultivars, as an integral part of strain identification.     

Tracking host infection and reproduction of Peronospora salviae-officinalis using an improved method for confocal laser scanning microscopy

Peronospora salviae-officinalis, the causal agent of downy mildew on common sage, is an obligate biotrophic pathogen. It grows in the intercellular spaces of the leaf tissue of sage and forms intracellular haustoria to interface with host cells. Although P. salviae-officinalis was described as a species of its own 10 years ago, the infection process remains obscure. To address this, a histological study of various infection events, from the adhesion of conidia on the leaf surface to de novo sporulation is presented here. As histological studies of oomycetes are challenging due to the lack of chitin in their cell wall, we also present an improved method for staining downy mildews for confocal laser scanning microscopy as well as evaluating the potential of autofluorescence of fixed nonstained samples. For staining, a 1:1 mixture of aniline blue and trypan blue was found most suitable and was used for staining of oomycete and plant structures, allowing discrimination between them as well as the visualization of plant immune responses. The method was also used to examine samples of Peronospora lamii on Lamium purpureum and Peronospora belbahrii on Ocimum basilicum, demonstrating the potential of the presented histological method for studying the infection processes of downy mildews in general.     

Confirmation of <Emphasis Type="Italic">Peronospora agrimoniae</Emphasis> as a distinct species

Leaves with typical symptoms of downy mildew were found on common agrimony in the Czech Republic in 2014 and 2015 and at several locations in Germany from 2010 to 2014. The causal agent of downy mildew of agrimony was often reported as Peronospora agrimoniae, but sometimes also as P. sparsa. Morphological characteristics of the pathogens found in both countries are in the range of previous works for P. agrimoniae, but also other downy mildews parasitic on Rosaceae, rendering their discrimination based on published observations difficult. For molecular identification sequencing of several loci (nrITS rDNA, cox1 and cox2) was performed. Phylogenetic analyses based on nrITS rDNA clearly separated P. agrimoniae from other Peronospora species infecting Rosaceae. Thus, considering P. agrimoniae as separate species seems justified. Two German specimens were identical to two Czech samples in both nrITS rDNA and cox1 mtDNA sequences, but differed in a single nucleotide substitution in cox2 region. To our knowledge, this is the first verified record of P. agrimoniae on common agrimony in the Czech Republic.     

A review of fungal antagonists of powdery mildews and their potential as biocontrol agents

There are approximately 40 fungal species that have so far been reported as natural antagonists of powdery mildews or have been tested as their potential biocontrol agents. This review summarizes the published data on their identification, taxonomy, ecology, modes of action and biocontrol efficacy. The results obtained with the two products already registered, AQ10 Biofungicide and Sporodex, are also discussed.     

Monitoring physiological races of<Emphasis Type="Italic">Podosphaera xanthii</Emphasis> (syn.<Emphasis Type="Italic">Sphaerotheca fuliginea</Emphasis>), the causal agent of powdery mildew in cucurbits: Factors affecting race identification and the importance for research and commerce

Identification of the physiological races ofPodosphaera xanthii (syn.Sphaerotheca fuliginea), the causal agent of powdery mildew in cucurbits, is based upon the differing responses of various melon cultigens to the pathogen. Eight races of the pathogen have been identified to date in the USA, Africa, Europe and around the Mediterranean Sea, and four new races were reported from greenhouse melons in the major growing area of Japan. Plant responses to powdery mildew may be affected by environmental factors such as light intensity, temperature and humidity, as well as by age and nutritional status of the plants. The same factors affect the accuracy and reliability of race identification. In an attempt to overcome those obstacles, the genetic diversity ofP. xanthii was studied using molecular markers. Unfortunately, no correlation was found between DNA polymorphism and the race of the pathogen as identified by biological tests. The usefulness of race identification as a guide for the grower in selecting appropriate cultivars is limited because changes or shifts in the pathogen population are common. Such changes may be found among growing seasons, geographic regions and hosts, and also within a single greenhouse during a single season. On the other hand, race identification is important for basic research and is especially important for the commercial seed industry, which requires accuracy in declaring the type and level of resistance to powdery mildew in its products. http://www.phytoparasitica.org posting March 2, 2004. Contribution from the Agricultural Research Organization. No. 501/04.     

Note: Molecular identification of three entomopathogenic nematodes from turkey by PCR-RFLP of the ITS regions

Molecular identification methods are widely used for the classification of organisms worldwide. Entomopathogenic nematodes are the most often isolated insect parasitic nematodes in the tropical and subtropical regions. In our investigation, PCR-RFLP (Polymerase Chain Reaction — Restriction Fragment Length Polymorphism) of the ITS region (Internal Transcribed Spacer) on the ribosomal (r) DNA of three entomopathogenic nematodes isolated from Ankara, Turkey, was analyzed for identification. The ITS region of rDNA was amplified by PCR and then digested with the following nine restriction enzymes: Alu I, Dde I, Hae III, Hha I, Hind III, Hinf I, Hpa II, Rsa I and Sau 3AI. The amplified and restricted sequences of the ITS regions were separated by agarose gel electrophoresis and the RFLP patterns of these three species were shown in this study. According to our results, these species were identified asSteinernema feltiae, Steinernema carpocapsae andHeterorhabditis bacteriophora. http://www.phytoparasitica.org posting Nov. 4, 2005.     

Microscopical studies of the effect of metalaxyl on the interaction between sunflower,Helianthus annuus L. and downy mildew,Plasmopara halstedii

The mode of action of the fungicide metalaxyl againstPlasmopara halstedii, the causal agent of sunflower downy mildew, was studied following its application before, during and after artificial contamination of seedlings. The development of the fungus within the treated seedlings was examined microscopically and compared to that occuring in untreated genetically susceptible or resistant genotypes. Hypersensitive-like reactions and necrotic zones leading to the inhibition of fungus growth within the hypocotyl were observed for the three modes of application. This suggests that sunflower defence mechanisms activated by genetical resistance are also involved in the control of downy mildew by metalaxyl.     

An Aqueous Extract of the Dry Mycelium of Penicillium chrysogenum Induces Resistance in Several Crops under Controlled and Field Conditions

We have examined the effect of Pen, an aqueous extract of the dry mycelium of Penicillium chrysogenum, on plant–pathogen interactions. Pen controlled a broad range of pathogens on several crop plants under greenhouse and field conditions. Pen protected grapevine from downy and powdery mildew (caused by Plasmopara viticola and Uncinula necator), tomato from early blight (caused by Phytophthora infestans), onion from downy mildew (Peronospora destructor) and apple trees from apple scab (caused by Venturia inaequalis) to a similar extent as fungicides such as copper and sulphur or well-known inducers such as benzothiadiazole or β-aminobutyric acid. Pen had no major direct fungicidal effect and is thus supposed to protect plants by activating their defense mechanisms. The raw material for extraction of Pen was available in constant quality, a prerequisite for commercial application. Under certain conditions, Pen caused phytotoxic side effects. The symptoms mostly consisted of small necrotic spots or, more rarely, of larger necrotic areas. The development of the symptoms was dependent on several parameters, including concentration of Pen, the number of applications, the persistence on the plant tissue, the plant species and variety and environmental conditions. In grapevine, a partially purified fraction of Pen was much less toxic than the crude Pen extract, but protected the plants to a similar extent against P. viticola. Our data show that Pen has interesting and unique properties as a plant protection agent, but more research is needed to further reduce its phytotoxic side effects.     

Pathotypic diversity of Hyaloperonospora brassicae collected from Brassica oleracea

Downy mildew caused by Hyaloperonospora brassicae is an economically destructive disease of brassica crops in many growing regions throughout the world. Specialised pathogenicity of downy mildews from different Brassica species and closely related ornamental or wild relatives has been described from host range studies. Pathotypic variation amongst Hyaloperonospora brassicae isolates from Brassica oleracea has also been described; however, a standard set of B. oleracea lines that could enable reproducible classification of H. brassicae pathotypes was poorly developed. For this purpose, we examined the use of eight genetically refined host lines derived from our previous collaborative work on downy mildew resistance as a differential set to characterise pathotypes in the European population of H. brassicae. Interaction phenotypes for each combination of isolate and host line were assessed following drop inoculation of cotyledons and a spectrum of seven phenotypes was observed based on the level of sporulation on cotyledons and visible host responses. Two host lines were resistant or moderately resistant to the entire collection of isolates, and another was universally susceptible. Five lines showed differential responses to the H. brassicae isolates. A minimum of six pathotypes and five major effect resistance genes are proposed to explain all of the observed interaction phenotypes. The B. oleracea lines from this study can be useful for monitoring pathotype frequencies in H. brassicae populations in the same or other vegetable growing regions, and to assess the potential durability of disease control from different combinations of the predicted downy mildew resistance genes.     

Variation in the nrDNA ITS sequences of some powdery mildew species: do routine molecular identification procedures hide valuable information?

During the past years, nrDNA ITS sequences have supported the identification of many powdery mildew fungi because comprehensive analyses showed that differences in these sequences have always correlated with the delimitation of different species and formae speciales of the Erysiphales. Published data, obtained using direct sequencing of the PCR products, suggested that even one to five nucleotide differences in the ITS sequences delimit different, albeit closely related, species, and/or indicate differences in host range patterns. Here we show that such differences in the ITS sequences can be detected even in a single sample of a powdery mildew fungus. We sequenced the ITS region in 17 samples, representing six powdery mildew species, both directly and after cloning the PCR products. Among these, samples of O. longipes exhibited two or three, samples of O. neolycopersici three or four, those of an Oidium sp. from Chelidonium majus up to seven, and a sample of another Oidium sp. from Passiflora caerulea two different ITS types determined after cloning. No ITS nucleotide polymorphisms were found in samples of O. lycopersici and Erysiphe aquilegiae. This suggests that some powdery mildew taxa are more variable at the ITS level than others. Thus, although the ITS sequences determined by direct sequencing represent robust data useful in delimitation and phylogenetic analysis of distinct species of the Erysiphales, these need to be used with precaution, and preferably determined after cloning, especially when dealing with closely related taxa at species and sub-species levels. With this method a hitherto undetected genetic diversity of powdery mildews can be revealed.     

北京市生菜链格孢根腐病病原菌鉴定

为明确北京市生菜链格孢根腐病的病原菌种类,采用常规组织分离法分离获得病原菌,依据柯赫氏法则对病原菌进行致病力检测,并利用分子生物学技术结合形态学鉴定确定病原菌分类地位。结果显示,从生菜病样组织中分离到2种病原菌共18株,形态学鉴定结果为芸薹链格孢Alternaria brassicae和万寿菊链格孢A. tagetica,分离比例分别为55.6%和44.4%,且二者均能单独侵染生菜根部,前者致病力较后者强,亦能复合侵染。对致病菌株进行GAPDH基因的PCR扩增和测序,并建立了基于GAPDH基因序列的系统发育树,聚类分析结果与形态学鉴定结果一致,因此证实北京市生菜链格孢根腐病是由芸薹链格孢和万寿菊链格孢复合侵染所致。     

Molecular approaches for characterization and use of natural disease resistance in wheat

Wheat production is threatened by a constantly changing population of pathogen species and races. Given the rapid ability of many pathogens to overcome genetic resistance, the identification and practical implementation of new sources of resistance is essential. Landraces and wild relatives of wheat have played an important role as genetic resources for the improvement of disease resistance. The use of molecular approaches, particularly molecular markers, has allowed better characterization of the genetic diversity in wheat germplasm. In addition, the molecular cloning of major resistance (R) genes has recently been achieved in the large, polyploid wheat genome. For the first time this allows the study and analysis of the genetic variability of wheat R loci at the molecular level and therefore, to screen for allelic variation at such loci in the gene pool. Thus, strategies such as allele mining and ecotilling are now possible for characterization of wheat disease resistance. Here, we discuss the approaches, resources and potential tools to characterize and utilize the naturally occurring resistance diversity in wheat. We also report a first step in allele mining, where we characterize the occurrence of known resistance alleles at the wheat Pm3 powdery mildew resistance locus in a set of 1,320 landraces assembled on the basis of eco-geographical criteria. From known Pm3 R alleles, only Pm3b was frequently identified (3% of the tested accessions). In the same set of landraces, we found a high frequency of a Pm3 haplotype carrying a susceptible allele of Pm3. This analysis allowed the identification of a set of resistant lines where new potentially functional alleles would be present. Newly identified resistance alleles will enrich the genetic basis of resistance in breeding programmes and contribute to wheat improvement.