Phytophthora

The genus Phytopythium is a relatively new group of organisms distinguished from the Pythium genus. These are organisms closely related to Pythium and Phytophthora, with similar structure and biology. Despite many similarities, this genus is characterised by several morphological features that allow it to be easily identified. Until now, more than 20 species belong to this genus, most of which are saprophytic organisms. However, there is also a group of species particularly dangerous to plants. These species include, among others, Pp. litorale, Pp. helicoides and Pp. vexans. The purpose of this work was to collect information about these organisms and present them in a condensed form. The study contains basic information about the history of the type of separation, differences in morphology distinctive genus of Phytopythium, Phytophthora and Pythium and information about diseases and host plants. Information is also provided on the potential threat posed by these organisms to forest ecosystems.

Excess copper in plants causes physiological alterations that lead to crop productivity losses. However, cupric fungicides have been utilized in the control of Alternaria solani and Phytophtora infestans fungi, which cause early blight and late blight in potato, respectively. Thus, this study aimed to investigate the effect of different copper oxychloride levels on potato plants through some biochemical and physiological parameters. The fungicide was applied at the recommended level (2.50 g L À1 ), at a reduced level (1.25 g L À1 ), and at 5.00 g L À1 , to simulate spraying in the field twice during the same period with the recommended level. The results revealed that superoxide dismutase (SOD, EC 1.15.1.1) protected plants against oxidative stress at the beginning of the cycle since lipoperoxide levels were low in that period. In addition, increased SOD activity positively correlated with increased usable leaf area for photosynthesis (leaf area ratio, LAR), photosynthetic effectiveness (net assimilation rate, NAR), and growth relative to pre-existing dry matter (relative growth rate, RGR). Concomitantly, there was a negative correlation between lipoperoxide levels and LAR and RGR. Plants randomly sprayed twice in the same period with the level recommended for potato crop protection in the field do not present damage regarding their development. However, additional studies are needed in order to reduce the use of copper fungicides in the control of early and late blight in potato crop production, then decreasing the release of copper in the environment.

Potato (Solanum tuberosum) is the world's third-largest food crop. It severely suffers from late blight, a devastating disease caused by Phytophthora infestans. This oomycete pathogen secretes host-translocated RXLR effectors that include avirulence (AVR) proteins, which are targeted by resistance (R) proteins from wild Solanum species. Most Solanum R genes appear to have coevolved with P. infestans at its center of origin in central Mexico. Various R and Avr genes were recently cloned, and here we catalog characterized R-AVR pairs. We describe the mechanisms that P. infestans employs for evading R protein recognition and discuss partial resistance and partial virulence phenotypes in the context of our knowledge of effector diversity and activity. Genome-wide catalogs of P. infestans effectors are available, enabling effectoromics approaches that accelerate R gene cloning and specificity profiling. Engineering R genes with expanded pathogen recognition has also become possible. Importantly, monitoring effector allelic diversity in pathogen populations can assist in R gene deployment in agriculture.

Phytophthora capsici is an important, destructive, broad-host range pathogens of Chilli (Capsicum annum L.) leading to high economic losses worldwide. Currently available control measures rely on excessive use of chemicals harmful to humans and the environment. Thus use of biocontrol agents can be considered as a safe and ecofriendly alternative to disease control. Pre-treatment with Pseudomonas aeruginosa KUCd1 strain reduced Phytophthora infection in chilli plants (62.5%). There was also considerable enhancement of various plant growth parameters such as root length (RL), root fresh weight (RFW), root dry weight (RDW), shoot length (SL), shoot fresh (SFW) and shoot dry weight (SDW) of the chilli plants in both winter and wet season trials. Increases were as follows: RL (27.3% in wet & 56.1 % in winter); RFW (42.6 % in wet & 29.8% in winter); RDW (39.6% in wet & 24% in winter); SL (18.3 % in wet & 16.3% in winter); SFW (3.8% in wet & 13.8% in winter) and SDW (5.5 % in wet &11.4% in winter,). KUCd1 was also a competent colonizer of the rhizosphere (6.32 log CFU g -1 ) and rhizoplane (6.20 log CFU g -1 ) in challenge inoculated chilli plants. Pretreatment of plants with plant growth promoting KUCd1 induced systemic resistance against Phytophthora capsici and elicitated rapid defence response (as evident from the increased activity of various defense-related enzymes; PAL, POD, PPO and catalases) protecting the plant from pathogen ingress and hence protection from disease. In conclusion KUCd1for its aggressive root colonization, plant growth promotion and biocontrol properties can be further explored as biofertizer/ biopesticide.

The paper treats alien and invasive fungi reported from Poland. Invasive fungi are discussed generally, and 86 species included in four groups are enumerated: Peronosporales and Saprolegniales, Chytridiales, Erysiphales and other Ascomycetes, and Pucciniales and other Basidiomycetes. The species within these four groups are briefly discussed.

Phytophthora nicotianae was first isolated from tobacco at the end of the 19th century. This organism is now considered as one of the most devastating oomycete plant pathogens, with a recognized host range of more than 255 species over five continents and a wide diversity of climates. The economic losses caused by P. nicotianae are difficult to estimate, because of the diversity of its hosts and ecological niches. For these reasons, this pathogen represents a continuous challenge to plant disease management programmes, which frequently rely solely on the use of chemicals. Phytophthora nicotianae is better adapted than its competitors to abiotic stresses, especially to climate warming. As a result, its importance is increasing. This review illustrates, with some examples, how P. nicotianae currently impacts plant economies worldwide, and how it may constitute more severe threats to agriculture and natural ecosystems in the context of global climate change.

Biosurfactants containing rhamnose and β-hydroxydecanoic acid and called rhamnolipids are reviewed with respect to microbial producers, their physiological role, biosynthesis and genetics, and especially their microbial overproduction, physicochemical properties and potential applications. With Pseudomonas species, more than 100 g l−1 rhamnolipids were produced from 160 g l−1 soybean oil at a volumetric productivity of 0.4 g l−1 h−1. The individual rhamnolipids are able to lower the surface tension of water from 72 mN m−1 to 25–30 mN m−1 at concentrations of 10–200 mg l−1. After initial testing, rhamnolipids seem to have potential applications in combating marine oil pollution, removing oil from sand and in combating zoosporic phytopathogens. Rhamnolipids are also a source of l-rhamnose, which is already used for the industrial production of high-quality flavor components.

Two distinct subgroups (L2 and A 22 ) were recovered from irrigation reservoirs and a stream in Virginia, USA. After molecular, morphological and physiological examinations, the L2 subgroup was named Phytophthora aquimorbida and the A 22 designated as Phytophthora taxon 'aquatilis'. Both taxa are homothallic. P. aquimorbida is characterized by its noncaducous and nonpapillate sporangia, catenulate and radiating hyphal swellings and thick-walled plerotic oospores formed in globose oogonia mostly in the absence of an antheridium. P. taxon 'aquatilis' produces plerotic oospores in globose oogonia mostly with a paragynous antheridium. It has semi-papillate, caducous sporangia with variable pedicels, but it does not have hyphal swelling. Analyses of ITS, CO1, b-tubulin and NADH1 sequences revealed that P. aquimorbida is closely related to P. hydropathica, P. irrigata and P. parsiana, and P. taxon 'aquatilis' is related to P. multivesiculata. The optimum temperature for culture growth is 30 and 20 C for P. aquimorbida and P. taxon 'aquatilis' respectively. Both taxa were pathogenic to rhododendron plants and caused root discoloration, pale leaves, wilting, tip necrosis and dieback. Their plant biosecurity risk also is discussed.

Phytophthora nicotianae was first isolated from tobacco at the end of the 19th century. This organism is now considered as one of the most devastating oomycete plant pathogens, with a recognized host range of more than 255 species over five continents and a wide diversity of climates. The economic losses caused by P. nicotianae are difficult to estimate, because of the diversity of its hosts and ecological niches. For these reasons, this pathogen represents a continuous challenge to plant disease management programmes, which frequently rely solely on the use of chemicals. Phytophthora nicotianae is better adapted than its competitors to abiotic stresses, especially to climate warming. As a result, its importance is increasing. This review illustrates, with some examples, how P. nico-tianae currently impacts plant economies worldwide, and how it may constitute more severe threats to agriculture and natural ecosystems in the context of global climate change.

A 3,5-disubstituted furan, named flufuran, was isolated from a culture filtrate of a strain of Aspergillus flavus obtained from a chestnut compost created in the same orchard. Flufuran was identified by spectroscopic methods, and its structure was confirmed through the preparation of some key derivatives, also used to test the antifungal activity. At a concentration of 0.2 mg/ml, assayed against three Phytophthora species, pathogenic of some forest and agrarian plants, flufuran and especially its acetyl derivative showed significant antifungal activity. Although flufuran appears to be identical to a fungal metabolite isolated previously from some Polyporus spp., its interesting antifungal activity has never been reported before.

Three-year-old Alnus glutinosa (L.) Gaertn. (alder) saplings were single or double inoculated at the stem base with Phytophthora alni subsp. alni Brasier & S.A. Kirk under natural climatic conditions. Lesion formation on the bark showed a biphasic pattern of development, with extension occurring at a moderate rate in spring, and more rapidly during late summer. However, large variability was encountered in pathogen development within the population of infected saplings, ranging from high susceptibility to almost complete resistance. Infection resulted in severe growth retardation, and death within two years of inoculation in 75% of the saplings. During disease development, rates of transpiration and CO 2 uptake were significantly reduced. Consequently, minimum leaf water potentials were less negative in infected saplings than in control saplings. Surviving saplings matched control trees in photosynthetic capacity, transpiration rate and water potential during the second year of infection. Leaf starch concentration of infected saplings was significantly higher than in control saplings, possibly indicating that the destruction of bark tissue by the pathogen impaired phloem transport from leaves to roots.

Background: Phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The P. infestans genome experienced a repeat-driven expansion relative to the genomes of Phytophthora sojae and Phytophthora ramorum and shows a discontinuous distribution of gene density. Effector genes, such as members of the RXLR and Crinkler (CRN) families, localize to expanded, repeat-rich and gene-sparse regions of the genome. This distinct genomic environment is thought to contribute to genome plasticity and host adaptation. Results: We used in silico approaches to predict and describe the repertoire of P. infestans secreted proteins (the secretome). We defined the "plastic secretome" as a subset of the genome that (i) encodes predicted secreted proteins, (ii) is excluded from genome segments orthologous to the P. sojae and P. ramorum genomes and (iii) is encoded by genes residing in gene sparse regions of P. infestans genome. Although including only~3% of P. infestans genes, the plastic secretome contains~62% of known effector genes and shows >2 fold enrichment in genes induced in planta. We highlight 19 plastic secretome genes induced in planta but distinct from previously described effectors. This list includes a trypsin-like serine protease, secreted oxidoreductases, small cysteine-rich proteins and repeat containing proteins that we propose to be novel candidate virulence factors.

Phytophthora nicotianae Breda de Haan (syn P. parasitica Dastur) is an important broad-host range pathogen of brinjal (Solanum melongena L.). Currently available cultural practices and chemical control measures are often limited, ineffective and hazardous to human health and environment. On the other hand, biological control with microbial agents can be a safer, environment-friendly disease management alternative.

In this study, treatment with bacterial agent Pseudomonas aeruginosa KUCd1strain- a competent colonizer of the rhizosphere and rhizoplane of brinjal plants, could significantly improve plant growth as well as reduce Phytophthora infection in brinjal under in vivo conditions. It also induced systemic resistance against Phytophthora nicotianae and elicitated rapid defence response (as evident from the several fold increased activity of various defense-related enzymes; PAL, POD, PPO and CAT) protecting
the plant from pathogen ingress and hence protection from disease. The present study thus explores its potential for use as biocontrol agent against P. nicotianae or as biofertilzer or both in future which requires further investigation.

Phytophthora nicotianae was first isolated from tobacco at the end of the 19th century. This organism is now considered as one of the most devastating oomycete plant pathogens, with a recognized host range of more than 255 species over five continents and a wide diversity of climates. The economic losses caused by P. nicotianae are difficult to estimate, because of the diversity of its hosts and ecological niches. For these reasons, this pathogen represents a continuous challenge to plant disease management programmes, which frequently rely solely on the use of chemicals. Phytophthora nicotianae is better adapted than its competitors to abiotic stresses, especially to climate warming. As a result, its importance is increasing. This review illustrates, with some examples, how P. nico-tianae currently impacts plant economies worldwide, and how it may constitute more severe threats to agriculture and natural ecosystems in the context of global climate change.

Eighteen Phytophthora species and one species of Halophytophthora were identified in 113 forest streams in Alaska, western Oregon and southwestern Oregon that were sampled by baiting or filtration of stream water with isolation on selective media. Species were identified by morphology and DNA characterization with single strand conformational polymorphism, COX spacer sequence and ITS sequence. ITS Clade 6 species were most abundant overall, but only four species, P. gonapodyides (37% of all isolates), P. taxon Salixsoil, P. taxon Oaksoil and P. pseudosyringae, were found in all three regions. The species assemblages were similar in the two Oregon regions, but P. taxon Pgchlamydo was absent in Alaska and one new species present in Alaska was absent in Oregon streams. The number of Phytophthora propagules in Oregon streams varied by season and in SW Oregon, where sampling continued year round, P. taxon Salixsoil, P. nemorosa and P. siskiyouensis were recovered only in some seasons.

Phytophthora palmivora causes pod rot, a serious disease on cocoa widespread throughout the producing regions. In order to ascertain the genetic determination of cocoa resistance to P. palmivora, a study was carried out on two progenies derived from crosses between a heterozygous, moderately resistant Forastero clone, T60/887, and two closely related and highly susceptible Forastero clones, one completely homozygous, IFC2, and one partially heterozygous, IFC5. The cumulative size of both progenies was 112 individuals. Plants were subjected to natural and artificial inoculation of P. palmivora in Côte d'Ivoire. The genetic maps of T60/887 and of IFC5 were constructed using amplified fragment length polymorphism (AFLP) markers and microsatellites. The map of T60/887 comprised 198 markers assembled in 11 linkage groups and representing a total length of 793 cM. The map of IFC5 comprised 55 AFLP markers that were assembled into six linkage groups for a total length of 244 cM. Ratio of rotten over total number of fruit under natural infection was measured for each tree over two harvests. Artificial inoculations were performed on leaves and pods. These tests were weakly correlated with the pod rot rate in the field. Five quantitative trait loci (QTLs) of resistance were detected for T60/887 but none were common between the three traits measured. Stability and reliability of the experimental procedures are discussed and revealed the difficult use of these artificial tests on adult trees for a good prediction of field resistance.

Background: How photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. The history of plastid endosymbioses commonly is interpreted under the "chromalveolate" hypothesis, which requires numerous plastid losses from certain heterotrophic groups that now are entirely aplastidic. In this context, discoveries of putatively algal genes in plastid-lacking protists have been cited as evidence of gene transfer from a photosynthetic endosymbiont that subsequently was lost completely. Here we examine this evidence, as it pertains to the chromalveolate hypothesis, through genome-level statistical analyses of similarity scores from queries with two diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana, and two aplastidic sister taxa, Phytophthora ramorum and P. sojae. Results: Contingency tests of specific predictions of the chromalveolate model find no evidence for an unusual red algal contribution to Phytophthora genomes, nor that putative cyanobacterial sequences that are present entered these genomes through a red algal endosymbiosis. Examination of genes unrelated to plastid function provide extraordinarily significant support for both of these predictions in diatoms, the control group where a red endosymbiosis is known to have occurred, but none of that support is present in genes specifically conserved between diatoms and oomycetes. In addition, we uncovered a strong association between overall sequence similarities among taxa and relative sizes of genomic data sets in numbers of genes. Conclusion: Signal from "algal" genes in oomycete genomes is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution. Combined with the numerous sources of intragenomic phylogenetic conflict characterized previously, our results underscore the potential to be mislead by a posteriori interpretations of variable phylogenetic signals contained in complex genome-level data. They argue strongly for explicit testing of the different a priori assumptions inherent in competing evolutionary hypotheses.

Single-strand-conformation polymorphism (SSCP) of ribosomal DNA of 29 species (282 isolates) of Phytophthora was characterized in this study. megasperma each had more than one distinct pattern. A single-stranded DNA ladder also was developed, which facilitates comparison of SSCP patterns within and between gels. With a single DNA fingerprint, 277 isolates of Phytophthora recovered from irrigation water and plant tissues in Virginia were all correctly identified into eight species at substantially reduced time, labor, and cost. The SSCP analysis presented in this work will aid in studies on taxonomy, genetics, and ecology of the genus Phytophthora.

A new species of Phytophthora, previously referred to as the 'Dre I' taxon, is named Phytophthora irrigata. Isolates of P. irrigata morphologically and physiologically resemble Phytophthora drechsleri. They are heterothallic, produce nonpapillate sporangia, and grow well at 35 1C. The above two species differ significantly in uniformity of mycelium, presence of chlamydospores, DNA fingerprint, and sequences of multiple nuclear and mtDNA regions. Phytophthora irrigata produces smaller sporangia and a distinct DNA fingerprint. Sequence alignments in the ribosomal DNA internal transcribed spacer regions place Phytophthora fallax and Phytophthora captisoa as its closest relatives. The optimal temperature for culture growth is above 30 1C and the maximum temperature is 40 1C. This new species is abundant in irrigation reservoirs and natural waterways in Virginia and was also isolated in Pennsylvania.

Elicitins form a family of structurally related proteins that induce the hypersensitive response (HR) in plants, particularly Nicotiana spp. The elicitin family is composed of several classes. Most species of the plant-pathogenic oomycete genus Phytophthora produce the well-characterized 10-kDa canonical elicitins (class I), such as INF1 of the potato and tomato pathogen Phytophthora infestans. Two genes, inf2A and inf2B, encoding a distinct class (class III) of elicitinlike proteins, also occur in P. infestans. Unlike secreted class I elicitins, class III elicitins are thought to be cell-surface-anchored polypeptides. Molecular characterization of the inf2 genes indicated that they are widespread in Phytophthora spp. and occur as a small gene family. In addition, Southern blot and Northern blot hybridizations using gene-specific probes showed that inf2A and inf2B genes and transcripts can be detected in 17 different P. infestans isolates. Functional secreted expression in plant cells of the elicitin domain of the inf1 and inf2 genes was conducted using a binary Potato virus X (PVX) vector (agroinfection) and Agrobacterium tumefaciens transient transformation assays (agroinfiltration), and resulted in HR-like necrotic symptoms and induction of defense response genes in tobacco. However, comparative analyses of elicitor activity of INF1, INF2A, and INF2B revealed significant differences in intensity, specificity, and consistency of HR induction. Whereas INF1 induced the HR in Nicotiana benthamiana, INF2A induced weak symptoms and INF2B induced no symptoms on this plant. Nonetheless, similar to INF1, HR induction by INF2A in benthamiana required the ubiquitin ligase-associated protein SGT1. Overall, these results suggest that variation in the resistance of Nicotiana spp. to P. infestans is shadowed by variation in the response to INF elicitins. The ability of tobacco, but not N. benthamiana, to respond to INF2B could explain differences in resistance to P. infestans observed for these two species.

In several studies of oak decline in Europe, a semi-papillate homothallic Phytophthora taxon was consistently isolated, together with other Phytophthora species, from rhizosphere soil samples. It was also found associated with necrotic fine roots and stem necroses of Fagus sylvatica and Alnus glutinosa. Due to morphological and physiological similarities, the semi-papillate isolates were previously identified as P. syringae by various authors. The morphology, physiology and pathogenicity against fine roots of Quercus robur, Q. petraea and F. sylvatica, bark of A. glutinosa, leaves of Ilex aquifolium and apple fruits of this Phytophthora species are described and compared with those of related and similar Phytophthora species, namely P. ilicis, P. psychrophila, P. quercina, P. citricola and P. syringae. The phylogenetic placement on the basis of ITS and mtDNA sequence data was also examined. Isolates of this taxon produce colonies with stellate to rosaceous growth patterns and limited aerial mycelium on various agar media. Antheridia are predominantly paragynous. In water culture catenulate hyphal swellings and semi-papillate caducous sporangia, that are usually limoniform, ellipsoid or ovoid, are formed abundandly, mostly in lax or dense sympodia. This taxon is a moderately slow growing, low temperature species with optimum and maximum temperatures around 20 and 25 xC, respectively. Tested isolates are moderately aggressive to fine roots of oaks and beech, highly aggressive to holly leaves and apple fruits, and slightly pathogenic to alder bark. Thirteen tested isolates had an identical and distinct ITS sequence which was more similar to that of P. ilicis and P. psychrophila than any other known taxa. On the basis of their unique combination of morphological characters, colony growth patterns, cardinal temperatures for growth, growth rates, pathogenicity to oaks, beech, alder, apple and holly, their host range, and ITS and mtDNA sequences the semi-papillate caducous Phytophthora isolates from oaks, beech and alder are clearly separated from related and similar Phytophthora spp., and described as a new species, P. pseudosyringae sp. nov.

Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating disease for potato cultivation. Here, we describe the positional cloning of the Rpi-blb1 gene from the wild potato species Solanum bulbocastanum known for its high levels of resistance to late blight. The Rpi-blb1 locus, which confers full resistance to complex isolates of P. infestans and for which race speci®city has not yet been demonstrated, was mapped in an intraspeci®c S. bulbocastanum population on chromosome 8, 0.3 cM from marker CT88. Molecular analysis of a bacterial arti®cial chromosome (BAC) clone spanning the Rpi-blb1 locus identi®ed a cluster of four candidate resistance gene analogues of the coiled coil, nucleotide-binding site, leucine-rich repeat (CC-NBS-LRR) class of plant resistance (R ) genes. One of these candidate genes, designated the Rpi-blb1 gene, was able to complement the susceptible phenotype in a S. tuberosum and tomato background, demonstrating the potential of interspeci®c transfer of broad-spectrum late blight resistance to cultivated Solanaceae from sexually incompatible host species. Paired comparisons of synonymous and non-synonymous nucleotide substitutions between different regions of Rpi-blb1 paralogues revealed high levels of synonymous divergence, also in the LRR region. Although amino acid diversity between Rpi-blb1 homologues is centred on the putative solvent exposed residues of the LRRs, the majority of nucleotide differences in this region have not resulted in an amino acid change, suggesting conservation of function. These data suggest that Rpi-blb1 is relatively old and may be subject to balancing selection.

Aspartic proteinases (EC 3.4.23) are widely distributed in the plant kingdom, and a number of cDNAs have been isolated from different plants. Here we report the isolation an expression analysis of a cDNA from Solanum tuberosum L. (cv. Pampeana) named StAsp. The StAsp cDNA ...

Cell death plays a ubiquitous role in plant-microbe interactions, given that it is associated with both susceptible and resistance interactions. A class of cell death-inducing proteins, termed Nep1-like proteins (NLPs), has been reported in bacteria, fungi, and oomycetes. These proteins induce nonspecific necrosis in a variety of dicotyledonous plants. Here, we describe three members of the NLP family from the oomycete Phytophthora infestans (PiNPP1.1, PiNPP1.2, and PiNPP1.3). Using agroinfection with a binary Potato virus X vector, we showed that PiNPP1.1 induces cell death in Nicotiana benthamiana and the host plant tomato. Expression analyses indicated that PiNPP1.1 is up-regulated during late stages of infection of tomato by P. infestans. We compared PiNPP1.1 necrosis-inducing activity to INF1 elicitin, a wellstudied protein that triggers the hypersensitive response in Nicotiana spp. Using virus-induced gene silencing, we showed that the cell death induced by PiNPP1.1 is dependent on the ubiquitin ligase-associated protein SGT1 and the heat-shock protein HSP90. In addition, cell death triggered by PiNPP1.1 but not that by INF1 was dependent on the defense-signaling proteins COI1, MEK2, NPR1, and TGA2.2, suggesting distinct signaling requirements. Combined expression of PiNPP1.1 and INF1 in N. benthamiana resulted in enhanced cell death, suggesting synergistic interplay between the two cell-death responses. Altogether, these results point to potentially distinct but interacting cell-death pathways induced by PiNPP1.1 and INF1 in plants.

Phytophthora capsici is a highly dynamic and destructive pathogen of vegetables. It attacks all cucurbits, pepper, tomato and eggplant, and, more recently, snap and lima beans. The disease incidence and severity have increased significantly in recent decades and the molecular resources to study this pathogen are growing and now include a reference genome. At the population level, the epidemiology varies according to the geographical location, with populations in South America dominated by clonal reproduction, and populations in the USA and South Africa composed of many unique genotypes in which sexual reproduction is common. Just as the impact of crop loss as a result of P. capsici has increased in recent decades, there has been a similar increase in the development of new tools and resources to study this devastating pathogen. Phytophthora capsici presents an attractive model for understanding broad-host-range oomycetes, the impact of sexual recombination in field populations and the basic mechanisms of Phytophthora virulence.

Phytophthora species are devastating plant pathogens in both agricultural and natural environments. Due to their significant economic and environmental impact, there has been increasing interest in Phytophthora genetics and genomics, culminating in the recent release of three complete genome sequences (P. ramorum, P. sojae, and P. infestans). In this study, genome and other large sequence databases were used to identify over 225 potential genetic markers for phylogenetic analyses. Here, we present a genus-wide phylogeny for 82 Phytophthora species using seven of the most informative loci (approximately 8700 nucleotide sites). Our results support the division of the genus into 10 well-supported clades. The relationships among these clades were rigorously evaluated using a number of phylogenetic methods. This is the most comprehensive study of Phytophthora relationships to date, and many newly discovered species have been included. A more resolved phylogeny of Phytophthora species will allow for better interpretations of the overall evolutionary history of the genus.

Seven plant species (lucerne, maize, oat, sugarbeet, sorghum, tomato, wheat) and 12 Pythium and Phytophthora species were used in a comparative study designed to investigate the effects of plant and oomycete inter-specific variation on zoospore encystment density and pathogenicity. Zoospores showed differential encystment behaviour and they encysted more on dicotyledonous than on monocotyledonous plants. Pythium aphanidermatum, P. deliense, and Phytophthora nicotianae were the most aggressive species. Sugarbeet was the most severely attacked plant species followed by tomato while oat plants were relatively unaffected. The relationship between zoospore encystment on roots and disease severity depended on the oomycete-plant combination. Correlation analysis between zoospore encystment density and disease severity indicated low and no significant levels (pp:05) of association for most plantoomycete combinations.

The mitochondrial genomes of haplotypes of the Irish potato famine pathogen, Phytophthora infestans, were sequenced. The genome sizes were 37,922, 39,870 and 39,840 bp for the type Ia, IIa and IIb mitochondrial DNA (mtDNA) haplotypes, respectively. The mitochondrial genome size for the type Ib haplotype, previously sequenced by others, was 37,957 bp. More than 90% of the genome contained coding regions. The GC content was 22.3%. A total of 18 genes involved in electron transport, 2 RNAencoding genes, 16 ribosomal protein genes and 25 transfer RNA genes were coded on both strands with a conserved arrangement among the haplotypes. The type I haplotypes contained six unique open reading frames (ORFs) of unknown function while the type II haplotypes contained 13 ORFs of unknown function. Polymorphisms were observed in both coding and noncoding regions although the highest variation was in non-coding regions. The type I haplotypes (Ia and Ib) differed by only 14 polymorphic sites, whereas the type II haplotypes (IIa and IIb) differed by 50 polymorphic sites. The largest number (152) of polymorphic sites was found between the type IIb and Ia haplotypes. A large spacer flanked by the genes coding for tRNA-Tyr (trnY) and the small subunit RNA (rns) contained the largest number of polymorphic sites and corresponds to the region where a large indel that differentiates type II from type I haplotypes is located. The size of this region was 785, 2,666 and 2,670 bp in type Ia, IIa and IIb haplotypes, respectively. Among the four haplotypes, 81 mutations were identified. Phylogenetic and coalescent analysis revealed that although the type I and II haplotypes shared a common ancestor, they clearly formed two independent lineages that evolved independently. The type II haplotypes diverged earlier than the type I haplotypes. Thus our data do not support the previous hypothesis that the type II lineages evolved from the type I lineages. The type I haplotypes diverged more recently and the mutations associated with the evolution of the Ia and Ib types were identified.

Phytophthora capsici, a pathogen of a range of tropical crops, such as black pepper, betel, cacao and rubber, is not managed effectively in developing countries due to lack of knowledge on the interactions between the pathogen and its many hosts (Drenth and Guest 2004). Although diseases of crops caused by P. capsici in temperate regions have been investigated in great detail, a lot less is known about this species in the South East Asian region. P. capsici is the causal agent of black pepper foot rot. With the need for integrated disease management in mind, questions arise as to the cross-infectivity of the pathogen from different hosts and whether chilli could be an alternative host harbouring the black pepper pathogen. In light of the finding that the genetic diversity of P. capsici from black pepper was relatively low, the level of diversity among isolates from chilli needed to be investigated. This study described the testing of three hypotheses. The first was that P. capsici isolates from chilli were pathogenic on black pepper and conversely black pepper isolates on chilli. The second was that chilli isolates were genetically different from black pepper isolates. The third was that there was genetic diversity among P. capsici isolates from chilli.

In the present study, antibacterial and antifungal activities of essential oils of four Salvia species against five bacteria and one fungus were evaluated at concentrations of 1/10, 1/20 and 1/30 and incubated for 24 h. Aqueous and hexane extracts of each plant were tested for their antibacterial and antifungal activity by using agar disc diffusion method. The result indicated that all essential oils exhibit antibacterial activity against Bacillus subtilis, Escherichia coli and Staphylococcus aureus. In addition, essential oils of Salvia multicaulis exhibit the antibacterial activity against Pseudomonas aeruginosa. Essential oils of Salvia syriaca exhibit antibacterial and antifungal activities against all micro-organisms.

Production of 2,4-diacetylphloroglucinol (2,4-DAPG) and hydrogen cyanide (HCN) by Pseudomonas spp. shows great potential for controlling soilborne plant pathogens. However, little is known about the transcriptional activity of phl and hcn genes encoding 2,4-DAPG and HCN, respectively. To progress toward a better understanding of what triggers phl and hcn expression under rhizosphere conditions, novel PCR primers and TaqMan probes were designed to monitor relative phlD and hcnBC expression in quantitative real time-PCR assays. Transcriptional activity of phlD and hcnBC was studied in time-course confrontational assays using combinations of Pseudomonas spp. isolated in this study: LBUM300 (producing 2,4-DAPG and HCN) and LBUM647 (producing HCN only); pathogens Phytophthora cactorum and Verticillium dahliae; and solid growth media King's B medium and potato dextrose agar. In correlation with the antagonistic activity observed, expression of phlD and hcnBC and production of 2,4-DAPG was detected throughout the 14-day course of the experiment in LBUM300 on both media, while hcnBC expression diminished to undetectable levels in LBUM647. In LBUM300 expression of phlD and hcnBC significantly changed over time and was also influenced by the presence of pathogen and growth media following time-dependent responses.

Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is controlled by Rps genes. However, little is known regarding the Rps-induced molecular responses to P. sojae and how they actually overlap. We thus sequenced, analyzed, and compared the transcriptomes of 10 near isogenic lines (NILs), each with a unique Rps gene/allele, and the susceptible parent Williams, pre-and post-inoculation with the pathogen.

Phytophthora lateralis is a fungus-like (oomycete) pathogen of trees in the family Cupressaceae, including Chamaecyparis lawsoniana (Lawson cypress or Port Orford cedar). Known in North America since the 1920s, presumably having been accidentally introduced from its assumed East Asian centre of origin, until recently, this pathogen has not been identified causing disease in Europe except for a few isolated outbreaks. However, since 2010, there have been several reports of infection of C. lawsoniana by P. lateralis in the United Kingdom, including Northern Ireland. We sequenced the genomes of four isolates of P. lateralis from two sites in Northern Ireland in 2011. Comparison with the closely related tree and shrub pathogen P. ramorum (cause of ramorum disease of larch and other species in the UK) shows that P. lateralis shares 91.47% nucleotide sequence identity over the core conserved compartments of the genome. The genomes of the four Northern Ireland isolates are almost identical, but we identified several single-nucleotide polymorphisms (SNPs) that distinguish between isolates, thereby presenting potential molecular markers of use for tracking routes of spread and in epidemiological studies. Our data reveal very low rates of heterozygosity (compared with P. ramorum), consistent with inbreeding within this P. lateralis population.

Soil borne Phytophthora cinnamomi and Phytophthora cambivora are considered the most pathogenic species associated with chestnut (Castanea sativa) decline in Europe. Mapping their incidence and distribution from nursery and plantation soils may offer valuable information for limiting spread. As conventional biological baiting and taxonomic confirmation is generally time consuming, labour, logistically and space intensive, we have focused on the development of a specific touchdown nested multiplex Polymerase Chain Reaction (PCR) approach for the simultaneous detection of both species direct from soil. Pre-existing and novel primers, based on Internal Transcribed Spacer (ITS) sequences, have been evaluated for their specificity and use in a multiplex capacity in various combinations. Coupled to this we have modified a mechanical lysis procedure for DNA extraction from up to 10 g of chestnut under storey soils (ranging from 0.5 to 25 mg DNA g À1 fresh soil). Using serial dilutions and/or polyvinylpolypyrrolidone chromatography purification, both species have been successfully detected, in artificially and naturally infected soils. Levels of assay detection are comparable to other Phytophthora species where PCR based diagnostic systems have been reported. A qualitative evaluation of this approach against conventional baiting is presented.

There is emerging evidence that the proteolytic machinery of plants plays important roles in defense against pathogens. The oomycete pathogen Phytophthora infestans, the agent of the devastating late blight disease of tomato (Lycopersicon esculentum) and potato (Solanum tuberosum), has evolved an arsenal of protease inhibitors to overcome the action of host proteases. Previously, we described a family of 14 Kazal-like extracellular serine protease inhibitors from P. infestans. Among these, EPI1 and EPI10 bind and inhibit the pathogenesis-related (PR) P69B subtilisin-like serine protease of tomato. Here, we describe EPIC1 to EPIC4, a new family of P. infestans secreted proteins with similarity to cystatin-like protease inhibitor domains. Among these, the epiC1 and epiC2 genes lacked orthologs in Phytophthora sojae and Phytophthora ramorum, were relatively fastevolving within P. infestans, and were up-regulated during infection of tomato, suggesting a role during P. infestans-host interactions. Biochemical functional analyses revealed that EPIC2B interacts with and inhibits a novel papain-like extracellular cysteine protease, termed Phytophthora Inhibited Protease 1 (PIP1). Characterization of PIP1 revealed that it is a PR protein closely related to Rcr3, a tomato apoplastic cysteine protease that functions in fungal resistance. Altogether, this and earlier studies suggest that interplay between host proteases of diverse catalytic families and pathogen inhibitors is a general defensecounterdefense process in plant-pathogen interactions.

Phytophthora species secrete a large array of effectors during infection of their host plants. The Crinkler (CRN) gene family encodes a ubiquitous but understudied class of effectors with possible but as of yet unknown roles in infection. To appreciate CRN effector function in Phytophthora, we devised a simple Crn gene identification and annotation pipeline to improve effector prediction rates. We predicted 84 full-length CRN coding genes and assessed CRN effector domain diversity in sequenced Oomycete genomes. These analyses revealed evidence of CRN domain innovation in Phytophthora and expansion in the Peronosporales. We performed gene expression analyses to validate and define two classes of CRN effectors, each possibly contributing to infection at different stages. CRN localisation studies revealed that P. capsici CRN effector domains target the nucleus and accumulate in specific sub-nuclear compartments. Phenotypic analyses showed that few CRN domains induce necrosis when expressed in planta and that one cell death inducing effector, enhances P. capsici virulence on Nicotiana benthamiana. These results suggest that the CRN protein family form an important class of intracellular effectors that target the host nucleus during infection. These results combined with domain expansion in hemibiotrophic and necrotrophic pathogens, suggests specific contributions to pathogen lifestyles. This work will bolster CRN identification efforts in other sequenced oomycete species and set the stage for future functional studies towards understanding CRN effector functions. Citation: Stam R, Jupe J, Howden AJM, Morris JA, Boevink PC, et al. (2013) Identification and Characterisation CRN Effectors in Phytophthora capsici Shows Modularity and Functional Diversity. PLoS ONE 8(3): e59517.