Phytopythium: molecular phylogeny and systematics

Synchrospora gen. nov., a New Peronosporaceae Genus with Aerial Lifestyle from a Natural Cloud Forest in Panama

During a survey of Phytophthora diversity in Panama, fast-growing oomycete isolates were obtained from naturally fallen leaves of an unidentified tree species in a tropical cloud forest. Phylogenetic analyses of sequences from the nuclear ITS, LSU and ßtub loci and the mitochondrial cox1 and cox2 genes revealed that they belong to a new species of a new genus, officially described here as Synchrospora gen. nov., which resided as a basal genus within the Peronosporaceae. The type species S. medusiformis has unique morphological characteristics. The sporangiophores show determinate growth, multifurcating at the end, forming a stunted, candelabra-like apex from which multiple (8 to >100) long, curved pedicels are growing simultaneously in a medusa-like way. The caducous papillate sporangia mature and are shed synchronously. The breeding system is homothallic, hence more inbreeding than outcrossing, with smooth-walled oogonia, plerotic oospores and paragynous antheridia. Optimum and maximum temperatures for growth are 22.5 and 25-27.5 °C, consistent with its natural cloud forest habitat. It is concluded that S. medusiformis as adapted to a lifestyle as a canopy-dwelling leaf pathogen in tropical cloud forests. More oomycete explorations in the canopies of tropical rainforests and cloud forests are needed to elucidate the diversity, host associations and ecological roles of oomycetes and, in particular, S. medusiformis and possibly other Synchrospora taxa in this as yet under-explored habitat.

Globisporangium and Pythium Species Associated with Yield Decline of Pyrethrum (Tanacetum cinerariifolium) in Australia

Pyrethrum (Tanacetum cinerariifolium) cultivation in Australia, which accounts for the majority of global production of natural insecticidal pyrethrins, is affected by a persistent yield decline which in part is caused by a complex of pathogens. Globisporangium and Pythium species were isolated from crown and roots of pyrethrum plants showing stunting and brown discoloration of crown tissue, and from soil adjacent to diseased plants from yield-decline-affected sites in Tasmania and Victoria, Australia. Ten known Globisporangium species (Globisporangium attrantheridium, G. erinaceum, G. intermedium, G. irregulare, G. macrosporum, G. recalcitrans, G. rostratifingens, G. sylvaticum, G. terrestris and G. ultimum var. ultimum), two new Globisporangium species (Globisporangium capense sp. nov. and Globisporangium commune sp. nov.) and three Pythium species (Pythium diclinum/lutarium, P. tracheiphilum and P. vanterpoolii) were identified through morphological studies and multigene phylogenetic analyses using ITS and Cox1 sequences. Globisporangium ultimum var. ultimum, G. sylvaticum, G. commune sp. nov. and G. irregulare were most abundant. Globisporangium attrantheridium, G. macrosporum and G. terrestris were reported for the first time in Australia. Seven Globisporangium species were pathogenic on both pyrethrum seeds (in vitro assays) and seedlings (glasshouse bioassays), while two Globisporangium species and three Pythium species only caused significant symptoms on pyrethrum seeds. Globisporangium irregulare and G. ultimum var. ultimum were the most aggressive species, causing pyrethrum seed rot, seedling damping-off and significant plant biomass reduction. This is the first report of Globisporangium and Pythium species causing disease in pyrethrum globally and suggests that oomycete species in the family Pythiaceae may have an important role in the yield decline of pyrethrum in Australia.

Biocontrol of Diseases Caused by Phytophthora capsici and P. parasitica in Pepper Plants

The main objective of this study was to evaluate the ability of Trichoderma aggressivum f. europaeum, T. longibrachiatum, Paecilomyces variotii, and T. saturnisporum as biological control agents (BCAs) against diseases caused by P. capsici and P. parasitica in pepper. For this purpose, their antagonistic activities were evaluated both in vitro and in vivo. We analysed the expression patterns of five defence related genes, CaBGLU, CaRGA1, CaBPR1, CaPTI1, and CaSAR8.2, in leaves. All BCAs showed a high in vitro antagonistic activity, significantly reducing the mycelial growth of P. capsici and P. parasitica. The treatments with T. aggressivum f. europaeum, T. longibrachiatum, and P. variotii substantially reduced the severity of the disease caused by P. capsici by 54, 76, and 70%, respectively, and of the disease caused by P. parasitica by 66, 55, and 64%, respectively. T. saturnisporum had the lowest values of disease reduction. Reinoculation with the four BCAs increased the control of both plant pathogens. Markedly different expression patterns were observed in the genes CaBGLU, CaRGA1, and CaSAR8.2. Based on the results, all four BCAs under study could be used as a biological alternative to chemicals for the control of P. capsici and P. parasitica in pepper with a high success rate.

Characterization of Phytopythium Species Involved in the Establishment and Development of Kiwifruit Vine Decline Syndrome

Since 2012, the kiwifruit vine decline syndrome (KVDS) has progressively compromised Italian kiwifruit orchards. Different abiotic and biotic factors have been associated with the establishment and development of KVDS. During monitoring of orchards affected by KVDS in north-western Italy during 2016-2019, 71 Phytopythium spp. were isolated. Based on maximum likelihood concatenated phylogeny on the ITS1-5.8S-ITS2 region of the rDNA, large subunit rDNA, and cytochrome oxidase I, isolates were identified as P. vexans (52), P. litorale (10), P. chamaehyphon (7) and P. helicoides (2). Phytopythium litorale and P. helicoides are reported for the first time as agents of KVDS in Italy. To demonstrate pathogenicity and fulfil Koch's postulates, representative isolates of P. vexans, P. litorale, P. chamaehyphon and P. helicoides were inoculated in potted plants. In these trials, waterlogging was applied to stress plant with a temporary anoxia and to favour the production of infective zoospores by the oomycetes. In experiments in vitro, the four species showed the highest growth at 25-30 °C, depending on the media used. P. helicoides was able to grow also at 40 °C. The four species were able to grow in vitro at a pH ranging from 5.0 to 8.0, showing that pH had less effect on growth than temperature. The present study suggests a strong role of different species of Phytopythium in the establishment and development of KVDS. Phytopythium spp. could be favoured by the average increase in soil temperatures during summer, associated with global warming.

Globisporangium coniferarum sp. nov., associated with conifers and Quercus spp

During a survey of gardens in Shiraz County, Iran, aimed at identifying oomycetes associated with roots of ornamental trees, a species of Globisporangium with distinctive morphological characters separating it from other known species in this genus was recovered from conifers and occasionally from a Quercus sp. Five isolates of this species were characterised. Phylogenetic analyses of nuclear (ITS and βtub) and mitochondrial (cox1 and cox2) loci using Bayesian inference and maximum likelihood analyses as well as their distinct morphological and cultural characteristics (e.g., abundant production of chlamydospores; globose, ellipsoid to ovoid sporangia; amorphous oogonia with a smooth wall; paragynous to rarely hypogynous antheridia and 1-5 antheridia per oogonium; mostly plerotic oospores) revealed that these isolates belong to a new Globisporangium species grouping in the phylogenetic clade G of Pythium sensu lato. This paper formally describes Globisporangium coniferarum sp. nov. as a new species and compares it with other phylogenetically related and already known Globisporangium species, including G. nagaii, G. violae, G. paddicum, G. okanoganense, G. iwayamae and G. canariense. Citation: Salmaninezhad F, Aloi F, Pane A, Mostowfizadeh-Ghalamfarsa R, Cacciola SO (2022). Globisporangium coniferarum sp. nov., associated with conifers and Quercus spp. Fungal Systematics and Evolution 10: 127-137. doi: 10.3114/fuse.2022.10.05.

Influence of Culture Media and Environmental Factors (Water Potential and Temperature) on Mycelial Growth of Phytopythium vexans (de Bary), the Causal Agent of Dieback Disease in Apple Trees

This study aimed at evaluating the effects of culture media and environmental factors (temperature and water potential (Ψw)) on the growth of the pathogenic fungus Phytopythium vexans (de Bary) associated with root rot and dieback disease in apple trees. Tomato agar, potato dextrose agar (PDA), and soybean agar were the most favourable for rapid mycelial growth, with optimum growth recorded for PDA medium. To determine the environmental conditions that promoted the development of this phytopathogen, the effects of temperature (5–30 °C), water potential (Ψw) (−15.54; −0.67 MPa) (0.89–0.995 aw), and their interaction were evaluated on the in vitro radial growth rates of the five isolates of P. vexans and on their latency phase (time period prior to growth). The results of this study showed that temperature, water potential, and their interaction had significant effects (p < 0.001) on the radial growth rates and latency phases of all tested P. vexans isolates. All isolates were able to grow throughout the temperature range (5 to 30 °C), with the maximum radial growth rate being observed at the highest temperatures, 25–30 °C. Growth was seen to be faster at −0.67 MPa (0.995 aw) at 25 °C and 30 °C. No growth was observed at Ψw < −5.44 MPa (0.96 aw), regardless of the temperature. It was found that the length of the latency phase depended significantly on both environmental factors. The longest latency phases (5 days on average) were recorded at a temperature of 5 °C and Ψw of −0.67 MPa (0.995 aw) and −2.69 MPa (0.98 aw), while the shortest latency phases were observed at a temperature of 30 °C and a Ψw of −0.67 MPa (0.995 aw), with an average of 0.2 days. The findings from this study could help to understand the impact of these environmental factors on the occurrence of diseases caused by P. vexans and more likely to design a reliable preventive control strategy based on the avoidance of conditions that play in favour of the phytopathogen.

Rapid detection of Phytophthora cinnamomi based on a new target gene Pcinn13739

Phytophthora cinnamomi causes crown and root wilting in more than 5,000 plant species and represents a significant threat to the health of natural ecosystems and horticultural crops. The early and accurate detection of P. cinnamomi is a fundamental step in disease prevention and appropriate management. In this study, based on public genomic sequence data and bioinformatic analysis of several Phytophthora, Phytopythium, and Pythium species, we have identified a new target gene, Pcinn13739; this allowed us to establish a recombinase polymerase amplification–lateral flow dipstick (RPA-LFD) assay for the detection of P. cinnamomi. Pcinn13739-RPA-LFD assay was highly specific to P. cinnamomi. Test results for 12 isolates of P. cinnamomi were positive, but negative for 50 isolates of 25 kinds of Phytophthora species, 13 isolates of 10 kinds of Phytopythium and Pythium species, 32 isolates of 26 kinds of fungi species, and 11 isolates of two kinds of Bursaphelenchus species. By detecting as little as 10 pg.µl−1 of genomic DNA from P. cinnamomi in a 50-µl reaction, the RPA-LFD assay was 100 times more sensitive than conventional PCR assays. By using RPA-LFD assay, P. cinnamomi was also detected on artificially inoculated fruit from Malus pumila, the leaves of Rhododendron pulchrum, the roots of sterile Lupinus polyphyllus, and the artificially inoculated soil. Results in this study indicated that this sensitive, specific, and rapid RPA-LFD assay has potentially significant applications to diagnosing P. cinnamomi, especially under time- and resource-limited conditions.

Oxathiapiprolin Alone or Mixed with Metalaxyl Seed Treatment for Management of Soybean Seedling Diseases Caused by Species of Phytophthora, Phytopythium, and Pythium

Species of Phytophthora, Phytopythium, and Pythium affect soybean seed and seedlings each year, primarily through reduced plant populations and yield. Oxathiapiprolin is effective at managing several foliar diseases caused by some oomycetes. The objectives of these studies were to evaluate oxathiapiprolin in a discriminatory dose assay in vitro; evaluate oxathiapiprolin as a soybean seed treatment on a moderately susceptible cultivar in 10 environments; compare the impact of seed treatment on plant populations and yields in environments with low and high precipitation; and compare a seed treatment mixture on cultivars with different levels of resistance in four environments. There was no reduction in growth in vitro among 13 species of Pythium at 0.1 µg ml-1. Soybean seed treated with the base fungicide plus oxathiapiprolin (12 and 24 µg a.i. seed-1) alone, oxathiapiprolin (12 µg a.i. seed-1) plus mefenoxam (6 µg a.i. seed-1), or oxathiapiprolin (24 µg a.i. seed-1) plus ethaboxam (12.1 µg a.i. seed-1) had greater yields in environments that received ≥50 mm of precipitation within 14 days after planting compared with those that received less. Early plant population and yield were significantly higher for seed treated with oxathiapiprolin (24 µg a.i. seed-1) + metalaxyl (13.2 µg a.i. seed-1) compared with nontreated for six of seven cultivars in at least one of four environments. Oxathiapiprolin combined with another Oomycota fungicide applied to seed has the potential to be used to protect soybean plant establishment and yield in regions prone to poor drainage after high levels of precipitation.

Phytophthora: an ancient, historic, biologically and structurally cohesive and evolutionarily successful generic concept in need of preservation

The considerable economic and social impact of the oomycete genus Phytophthora is well known. In response to evidence that all downy mildews (DMs) reside phylogenetically within Phytophthora, rendering Phytophthora paraphyletic, a proposal has been made to split the genus into multiple new genera. We have reviewed the status of the genus and its relationship to the DMs. Despite a substantial increase in the number of described species and improvements in molecular phylogeny the Phytophthora clade structure has remained stable since first demonstrated in 2000. Currently some 200 species are distributed across twelve major clades in a relatively tight monophyletic cluster. In our assessment of 196 species for twenty morphological and behavioural criteria the clades show good biological cohesion. Saprotrophy, necrotrophy and hemi-biotrophy of woody and non-woody roots, stems and foliage occurs across the clades. Phylogenetically less related clades often show strong phenotypic and behavioural similarities and no one clade or group of clades shows the synapomorphies that might justify a unique generic status. We propose the clades arose from the migration and worldwide radiation ~ 140 Mya (million years ago) of an ancestral Gondwanan Phytophthora population, resulting in geographic isolation and clade divergence through drift on the diverging continents combined with adaptation to local hosts, climatic zones and habitats. The extraordinary flexibility of the genus may account for its global 'success'. The 20 genera of the obligately biotrophic, angiosperm-foliage specialised DMs evolved from Phytophthora at least twice via convergent evolution, making the DMs as a group polyphyletic and Phytophthora paraphyletic in cladistic terms. The long phylogenetic branches of the DMs indicate this occurred rather rapidly, via paraphyletic evolutionary 'jumps'. Such paraphyly is common in successful organisms. The proposal to divide Phytophthora appears more a device to address the issue of the convergent evolution of the DMs than the structure of Phytophthora per se. We consider it non-Darwinian, putting the emphasis on the emergent groups (the DMs) rather than the progenitor (Phytophthora) and ignoring the evolutionary processes that gave rise to the divergence. Further, the generic concept currently applied to the DMs is narrower than that between some closely related Phytophthora species. Considering the biological and structural cohesion of Phytophthora, its historic and social impacts and its importance in scientific communication and biosecurity protocol, we recommend that the current broad generic concept is retained by the scientific community.

Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium

The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1-D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of Pythium and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of Pythium s.l. The status of alternative generic names that have been used for species of Pythium in the past (e.g., Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium) was investigated. Based on our molecular analyses and review of the Pythium generic concepts, we urge the scientific community to adopt the generic names Pythium, Elongisporangium, Globisporangium, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described Pythium spp. are transferred to Elongisporangium and Globisporangium.

Peronosporales Species Associated with Strawberry Crown Rot in the Czech Republic

The symptoms of crown rot on strawberry plants are considered typical for the pathogen Phytophthora cactorum, which causes high losses of this crop. However, an unknown number of related species of pathogens of Peronosporales cause symptoms quite similar to those caused by P. cactorum. To determine their spectrum and importance, strawberry plants were sampled from 41 farms in the Czech Republic. The cultures were isolated from the symptomatic plants using the baiting method, with subsequent cultivation on a semiselective medium. Isolates were identified to the species level using nuclear ribosomal internal transcribed spacer (ITS) barcoding after preliminary morphological determination. In total, 175 isolates of 24 species of Phytophthora, Phytopythium, Pythium, and Globisporangium were detected. The most represented was Phytophthora cactorum, with 113 (65%) isolates, which was recorded in 61% of farms, and the Pythium dissotocum complex with 20 (11%) isolates, which was recorded in 27% of farms. Other species were represented in units of percent. Large differences between farms in the species spectra were ascertained. The differences between species in cardinal growth temperatures and different management of the farms are discussed as a main reason for such a diversification. Regarding the dissimilar sensitivity of various species of Peronosporales against fungicides, the proper determination of the cause of disease is of crucial significance in plant protection.

Characterization and Pathogenicity of Pythium-Like Species Associated with Root and Collar Rot of Kiwifruit in Turkey

During the period of June to October in 2018, a widespread decline was observed on kiwifruit vines in the vineyards located in the Altınordu, Fatsa, and Perşembe districts of Ordu province in Turkey. The symptoms were associated with reddish-brown rots expanding from the root to the collar with sparse off-color foliage. Based on the percentage of the total infected samples across 18 vineyards, the most common oomycete species were Globisporangium intermedium (37.1%), Phytopythium vexans (34.3%), Globisporangium sylvaticum (14.3%), Globisporangium heterothallicum (11.4%), and Pythium dissotocum (2.9%). The morphological identification of isolates was confirmed based on partial DNA sequences containing the nuclear rDNA internal transcribed spacer region gene and the mitochondrial cytochrome c oxidase subunit II gene. The optimum growth temperature and the optimum pH values of the five species ranged from 22.98 to 28.25°C and 5.67 to 8.51, respectively. Pathogenicity tests on the seedlings of kiwifruit cv. Hayward revealed significant differences in virulence among isolates. Phytopythium vexans and Globisporangium sylvaticum isolates caused severe root and collar rot resulting in seedling death, while Globisporangium heterothallicum and Globisporangium intermedium isolates had relatively lower virulence. All Globisporangium spp. and Phytopythium vexans isolates significantly decreased plant growth parameters (plant height, shoot and root dry weights, and root length); however, Pythium dissotocum caused very mild symptoms and did not affect these parameters of growth. To our knowledge, this is the first study reporting Globisporangium sylvaticum, Globisporangium heterothallicum, and Globisporangium intermedium causing root and collar rot on kiwifruit not only in Turkey but also in the world.

Neofunctionalization of Glycolytic Enzymes: An Evolutionary Route to Plant Parasitism in the Oomycete Phytophthora nicotianae

Oomycetes, of the genus Phytophthora, comprise of some of the most devastating plant pathogens. Parasitism of Phytophthora results from evolution from an autotrophic ancestor and adaptation to a wide range of environments, involving metabolic adaptation. Sequence mining showed that Phytophthora spp. display an unusual repertoire of glycolytic enzymes, made of multigene families and enzyme replacements. To investigate the impact of these gene duplications on the biology of Phytophthora and, eventually, identify novel functions associated to gene expansion, we focused our study on the first glycolytic step on P. nicotianae, a broad host range pathogen. We reveal that this step is committed by a set of three glucokinase types that differ by their structure, enzymatic properties, and evolutionary histories. In addition, they are expressed differentially during the P. nicotianae life cycle, including plant infection. Last, we show that there is a strong association between the expression of a glucokinase member in planta and extent of plant infection. Together, these results suggest that metabolic adaptation is a component of the processes underlying evolution of parasitism in Phytophthora, which may possibly involve the neofunctionalization of metabolic enzymes.

Eight new Halophytophthora species from marine and brackish-water ecosystems in Portugal and an updated phylogeny for the genus

During an oomycete survey in December 2015, 10 previously unknown Halophytophthora taxa were isolated from marine and brackish water of tidal ponds and channels in saltmarshes, lagoon ecosystems and river estuaries at seven sites along the Algarve coast in the South of Portugal. Phylogenetic analyses of LSU and ITS datasets, comprising all described Halophytophthora species, the 10 new Halophytophthora taxa and all relevant and distinctive sequences available from GenBank, provided an updated phylogeny of the genus Halophytophthora s.str. showing for the first time a structure of 10 clades designated as Clades 1–10. Nine of the 10 new Halophytophthora taxa resided in Clade 6 together with H. polymorphica and H. vesicula. Based on differences in morphology and temperature-growth relations and a multigene (LSU, ITS, Btub, hsp90, rpl10, tigA, cox1, nadh1, rps10) phylogeny, eight new Halophytophthora taxa from Portugal are described here as H. brevisporangia, H. cele­ris, H. frigida, H. lateralis, H. lusitanica, H. macrosporangia, H. sinuata and H. thermoambigua. Three species, H. frigida, H. macrosporangia and H. sinuata, have a homothallic breeding system while the remaining five species are sterile. Pathogenicity and litter decomposition tests are underway to clarify their pathological and ecological role in the marine and brackish-water ecosystems. More oomycete surveys in yet undersurveyed regions of the world and population genetic or phylogenomic analyses of global populations are needed to clarify the origin of the new Halophytophthora species.

Pythium intermedium, a species complex consisting of three phylogenetic species found in cool-temperate forest ecosystems

Pythium intermedium plays a vital role in the carbon cycle of cool-temperate forests and is widely distributed in Japan's forest soils. In this study, we performed a phylogenetic analysis of the P. intermedium species complex using DNA sequences from multiple loci. The study included 35 isolates from cool-temperate forest soils, seven known P. intermedium isolates, and six known Pythium attrantheridium isolates. We also performed morphological observations and mating tests. Our results showed that all the isolates formed one large clade but were divided into three subclades. Furthermore, we observed many mating reactions between isolates from different subclades, including between P. attrantheridium and P. intermedium. Therefore, we suggest that P. intermedium, P. attrantheridium, and another phylogenetic species belong to one species complex. This is the first report of a species complex within P. intermedium and will be helpful in understanding the evolution of Pythium species in natural ecosystems.

Pathogenicity of Phytopythium chamaehyphon: A New Player in Kiwifruit Vine Decline Syndrome of Actinidia chinensis var. deliciosa 'Hayward' in Italy

Kiwifruit vine decline syndrome (KVDS) is a serious soil-borne disease that degrades the fine roots of both Actinidia chinensis var. deliciosa and var. chinensis. The disease seems to be the result of an interaction between several soil-borne pathogens, mostly oomycetes, and waterlogging. This work investigates the pathogenicity of the oomycete Phytopythium chamaehyphon recently isolated from roots of diseased plants. Pathogenicity was tested in 6-month-old and 1-year-old plants that, after inoculation, were flooded up to three times to induce symptom appearance. Leaf wilting and root rot typical of KVDS was observed in all the plants inoculated with P. chamaehyphon strain KD-15 (PCHA) and in all the positive controls potted in a mix of peat and soils collected in KVDS-affected orchards, while negative controls remained symptomless. Disease development on 6-month-old plants was characterized by unusual degradation of the not-lignified collar, occurring even in absence of flooding. Conversely, on 1-year-old plants, symptoms faithfully reproduced KVDS dynamics observed in orchard. This work confirmed the pathogenicity of P. chamaehyphon and raised new questions about the actual role of waterlogging in KVDS etiology.

Development of a Loop-Mediated Isothermal Amplification Method for the Rapid Detection of Phytopythium vexans

Brown root rot caused by Phytopythium vexans is a new destructive root disease on many plants such as Gingko, Citrus, kiwifruit, and ramie. The establishment of loop-mediated isothermal amplification (LAMP) technology for detecting P. vexans can help monitor and control brown root rot quickly, efficiently, and accurately. LAMP technology is known for its simplicity, sensitivity, and speed; and it does not require any specialized equipment – a water bath or a thermoblock is sufficient for isothermal amplifications. LAMP products can be visualized by using hydroxy naphthol blue (HNB) dye or agarose gel electrophoresis. In this study, by searching and comparing the internal transcribed spacer (ITS) sequences of P. vexans and the related species in oomycete genera Pythium, Phytopythium, and Phytophthora, we designed specific primers targeting the ITS gene region of P. vexans. Using HNB dye, we established a LAMP technique for rapid detection of P. vexans by visible color change. In addition, we optimized the protocol to enhance both sensitivity and specificity for P. vexans detection. Under the optimized condition, our protocol based on LAMP technology could detect as low as 24 copies of the P. vexans genomic DNA, which is ∼100 times more sensitive than conventional PCR. This method can successfully detect P. vexans using cell suspensions from P. vexans – infected ramie root tissues.

Phytopythium vexans Associated with Apple and Pear Decline in the Saïss Plain of Morocco

An extensive survey conducted in the Saïss plain of Morocco during the 2017-2018 growing season revealed that 35 out of 50 apple and pear orchards were infested with a pathogen that causes the decline disease. Morphological and phylogenetic tree analyses using the cox II gene allowed us to identify the pathogen as Phytopythium vexans. Interestingly, no Phytophthora and Pythium species were isolated. The occurrence and prevalence of the disease varied between locations; the most infested locations were Meknes (100%), Imouzzer (83%), and Sefrou (80%). To fulfill Koch's postulate, a greenhouse pathogenicity test was performed on the stem and collar of one-year-old healthy seedlings of apple rootstock M115. Symptoms similar to those observed in the field were reproduced in less than 4 months post-inoculation with root rot disease severity ranging from 70 to 100%. The survey results evidenced that apple rootstocks, soil type, and irrigation procedure may contribute significantly to the occurrence of the disease. The disease was most prevalent in drip water irrigation and sandy-clay soil on wild apple rootstock. Accordingly, a rational drip advanced watering system and good sanitation practices could eliminate water stagnation and help prevent the onset of this disease. It was concluded that Pp. vexans occurrence may be strongly influenced by irrigation mode and type of soil. Therefore, the obtained findings of this study could help to better understand the recurrence of this disease and to develop a reliable integrated strategy for its management.

Insights into the Host Specificity of a New Oomycete Root Pathogen, Pythium brassicum P1: Whole Genome Sequencing and Comparative Analysis Reveals Contracted Regulation of Metabolism, Protein Families, and Distinct Pathogenicity Repertoire

Pythium brassicum P1 Stanghellini, Mohammadi, Förster, and Adaskaveg is an oomycete root pathogen that has recently been characterized. It only attacks plant species belonging to Brassicaceae family, causing root necrosis, stunting, and yield loss. Since P. brassicum P1 is limited in its host range, this prompted us to sequence its whole genome and compare it to those of broad host range Pythium spp. such as P. aphanidermatum and P. ultimum var. ultimum. A genomic DNA library was constructed with a total of 374 million reads. The sequencing data were assembled using SOAPdenovo2, yielding a total genome size of 50.3 Mb contained in 5434 scaffolds, N50 of 30.2 Kb, 61.2% G+C content, and 13,232 putative protein-coding genes. Pythium brassicum P1 had 175 species-specific gene families, which is slightly below the normal average. Like P. ultimum, P. brassicum P1 genome did not encode any classical RxLR effectors or cutinases, suggesting a significant difference in virulence mechanisms compared to other oomycetes. Pythium brassicum P1 had a much smaller proportions of the YxSL sequence motif in both secreted and non-secreted proteins, relative to other Pythium species. Similarly, P. brassicum P1 had the fewest Crinkler (CRN) effectors of all the Pythium species. There were 633 proteins predicted to be secreted in the P. brassicum P1 genome, which is, again, slightly below average among Pythium genomes. Pythium brassicum P1 had only one cadherin gene with calcium ion-binding LDRE and DxND motifs, compared to Pythium ultimum having four copies. Pythium brassicum P1 had a reduced number of proteins falling under carbohydrate binding module and hydrolytic enzymes. Pythium brassicum P1 had a reduced complement of cellulase and pectinase genes in contrast to P. ultimum and was deficient in xylan degrading enzymes. The contraction in ABC transporter families in P. brassicum P1 is suggested to be the result of a lack of diversity in nutrient uptake and therefore host range.

Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes

As evidenced in parasitism, host and niche shifts are a source of genomic and phenotypic diversification. Exemplary is a reduction in the core metabolism as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone recent lifestyle or host changes have not been fully investigated. Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a wide and diverse range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyles. Moreover, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaptation in oomycetes. Given the high correlation between lifestyle and genome properties in our oomycete dataset, together with the known convergent evolution of fungal and oomycete genomes, we developed a model that predicts plant pathogenic lifestyles with high accuracy based on functional annotations. These insights into how selective pressures correlate with lifestyle may be crucial to better understand host/lifestyle shifts and their impact on the genome.

Identification and Chemical and Biological Management of Phytopythium vexans, the Causal Agent of Phytopythium Root and Crown Rot of Woody Ornamentals

Soilborne diseases caused by pathogens such as Phytophthora, Rhizoctonia, Fusarium, Verticillium, and Pythium species are the most important diseases of woody ornamentals. Ginkgo (Ginkgo biloba) and red maple (Acer rubrum 'October Glory') plants grown in containers and fields in Tennessee showed root and crown rot symptoms with dark brown to black lesions in 2017 and 2018. The objective of this research was to isolate and identify pathogens affecting ginkgo and red maple plants in Tennessee nurseries and to develop fungicide/biofungicide management recommendations for nursery producers. Isolations were made from the infected roots. Several Phytophthora-like colonies with spherical zoospores, filamentous to globose oogoni, and whitish mycelium were isolated on V8-PARPH medium. To confirm identity, total genomic DNA was extracted, followed by sequence analysis of the internal transcribed spacer regions, large subunit of nuclear rRNA, and cytochrome c oxidase subunits I and II of mitochondrial DNA. Based on morphological and molecular analysis, Phytopythium vexans was described as a causal agent of crown and root rot from the infected ginkgo and red maple plants. To complete Koch's postulates, a pathogenicity test was performed by drenching 100 ml of V8 agar medium slurry of Phytopythium vexans inoculum on 1-year-old potted ginkgo plant root systems as well as red maple October Glory. Necrotic lesion development was observed in the root system 45 days after inoculation and Phytopythium vexans was reisolated from the roots of both ginkgo and red maple. All control ginkgo and red maple plants remained disease free and no pathogen was reisolated. In addition, the efficacy of fungicides, biofungicides, fertilizer, and host plant defense inducers (traditionally recommended for management of oomycete diseases) for control of Phytopythium crown and root rot was evaluated on ginkgo and red maple October Glory seedlings in greenhouse and field trials. Fungicides such as Empress Intrinsic, Pageant Intrinsic, Segovis, and Subdue MAXX were effective in both greenhouse and field trials, and the biofungicide Stargus reduced disease severity caused by pathogen Phytopythium vexans on ginkgo and red maple plants in greenhouse trials. These results will help nursery producers make proper management decisions for newly reported Phytopythium crown and root rot disease of ginkgo and red maple plants.

Taxonomic and pathogenic characterization of Phytopythium species from West Azarbaijan, Iran, and description of two new species

Phytopythium is a globally distributed genus, species of which occur in various ecological niches. Despite their importance as plant pathogens, information on species diversity and their distribution in West Azarbaijan Province of Iran is limited. This study aimed to investigate the taxonomy and plant pathogenicity of Phytopythium isolates recovered from soils in the province. A polyphasic taxonomy based on morphological, cultural, and multilocus sequence data revealed two new species, described here as P. babaiaharii and P. longitubum. In addition, a putatively new species and five known species, P. boreale, P. carbonicum, P. mercuriale, P. ostracodes, and P. vexans, were found in the studied region. Phytopythium ostracodes, P. mercuriale, and P. boreale were the three most frequent species isolated from soil, although P. mercuriale was only found in one field. Among the studied species, P. mercuriale, P. ostracodes, and P. vexans exhibited various levels of pathogenicity on sugar beet, sunflower, and tomato, and P. boreale was documented for first time as a plant pathogen. Phytopythium ostracodes was highly aggressive on sugar beet and sunflower but lowly aggressive on tomato, whereas P. vexans exhibited high aggressiveness toward the three crop plants. Both P. boreale and P. mercuriale were found to be lowly aggressive on the host plants. The results indicated that members of Phytopythium, particularly plant-pathogenic species, are common in arable soils of West Azarbaijan Province and can pose a threat to agricultural crops in the region.

Observations on early fungal infections with relevance for replant disease in fine roots of the rose rootstock Rosa corymbifera 'Laxa'

Replant disease is a worldwide phenomenon affecting various woody plant genera and species, especially within the Rosaceae. Compared to decades of intensive studies regarding replant disease of apple (ARD), the replant disease of roses (RRD) has hardly been investigated. The etiology of RRD is also still unclear and a remedy desperately needed. In greenhouse pot trials with seedlings of the RRD-sensitive rootstock Rosa corymbifera ‘Laxa’ cultured in replant disease affected soils from two different locations, early RRD symptom development was studied in fine roots. In microscopic analyses we found similarities to ARD symptoms with regards to structural damages, impairment in the root hair status, and necroses and blackening in the cortex tissue. Examinations of both whole mounts and thin sections of fine root segments revealed frequent conspicuous fungal infections in association with the cellular disorders. Particularly striking were fungal intracellular structures with pathogenic characteristics that are described for the first time. Isolated fungi from these tissue areas were identified by means of ITS primers, and many of them were members of the Nectriaceae. In a next step, 35 of these isolates were subjected to a multi-locus sequence analysis and the results revealed that several genera and species were involved in the development of RRD within a single rose plant. Inoculations with selected single isolates (Rugonectria rugulosa and Ilyonectria robusta) in a Perlite assay confirmed their pathogenic relationship to early necrotic host plant reactions, and symptoms were similar to those exhibited in ARD.

Sensitivity of Pythium spp. and Phytopythium spp. and tolerance mechanism of Pythium spp. to oxathiapiprolin

BACKGROUND

Oxathiapiprolin, developed by DuPont, is the only commercial oxysterol-binding protein inhibitor (OSBPI) of oomycete pathogens. Although the activity of oxathiapiprolin on some Pythium spp. and Phytopythium spp. has been reported, it has not been tested on many other species, and little is known about the mechanisms of Pythium spp. that are tolerant to it.

RESULTS

Oxathiapiprolin exhibited a strong inhibitory effect on mycelial growth of Phy. litorale, Phy. helicoides and Phy. chamaehyphon, with EC₅₀ values ranging from 0.002 to 0.013 μg mL^-1 . It also showed good effectiveness against Py. splendens and two Py. ultimum isolates, with EC₅₀ values ranging from 0.167 to 0.706 μg mL^-1 , but showed no activity against 14 other Pythium spp. Oxathiapiprolin provoked a slight upregulation of PuORP1 in Py. ultimum, but it did not lead to PaORP1-1 or PaORP1-2 overexpression in Py. aphanidermatum. Transformation and expression of PuORP1, PaORP1-1 or PaORP1-2 in the sensitive wild-type Phytophthora sojae isolate P6497 confirmed that either the PuORP1, PaORP1-1 or PaORP1-2 was responsible for the observed oxathiapiprolin tolerance.

CONCLUSION

This study showed that oxathiapiprolin had excellent activity against Phytopythium spp. but displayed a differentiated activity against different Pythium spp. ORP1s in Pythium spp. are positively related to the tolerance of Pythium species to oxathiapiprolin. © 2020 Society of Chemical Industry.

Characterization of Pythium Species Collected from a Multiple Time-Point Sampling of Cucurbits in South Carolina

Species of Pythium cause root and stem rot in cucurbits, but no formal surveys have been conducted in the United States to identify which species are responsible. The cucurbit hosts bottle gourd, cucumber, Hubbard squash, and watermelon were transplanted in May, July, September, and November into sentinel plots in four and five different fields in 2017 and 2018, respectively, in South Carolina. Eight of the nine fields were replanted in March 2019. Isolates (600) were collected and identified by sequencing DNA of the mitochondrial cytochrome oxidase I region. The four most common species were P. spinosum (45.6% of all isolates), P. myriotylum (20.0%), P. irregulare (15.3%), and P. aphanidermatum (12.8%). P. myriotylum and P. aphanidermatum were predominantly isolated in May, July, and September, whereas P. spinosum and P. irregulare were predominantly isolated in November and March. Isolates of P. ultimum, P. irregulare, and P. spinosum were more virulent than isolates of P. myriotylum and P. aphanidermatum at 25°C. Representative isolates were screened in vitro for sensitivity to three fungicides: mefenoxam, propamocarb, and oxathiapiprolin. All isolates were sensitive to mefenoxam and propamocarb, but these same isolates were insensitive to oxathiapiprolin, except those classified taxonomically in Pythium clade I.

Genome Sequence Resource for the Ramie Oomycete Pathogen Phytopythium vexans HF1

The oomycete Phytopythium vexans is a causative agent of patch canker, damping-off, and crown, stem, and root rot in many economically important plants. P. vexans HF1 was isolated in China, where it caused brown root rot of ramie, a fiber crop broadly cultivated in Asia. The genome of HF1 was sequenced by a combination of technologies producing short (Illumina HiSeq X) and long (PacBio RS) reads. The genome is 41.73 Mbp long, assembled into 44 contigs. It has a GC content of 58.17% and contains 13,051 predicted coding genes, including 1,461 putative virulence genes and 220 putative antimicrobial resistance genes. This genome sequence provides a resource for determining the molecular mechanisms of disease development in this pathosystem.

Phytopythium litorale: A Novel Killer Pathogen of Plane (Platanus orientalis) Causing Canker Stain and Root and Collar Rot

Decline symptoms associated with lethal stem and branch canker stain along with root and collar rots were observed on 5- to 7-year-old roadside oriental plane trees (Platanus orientalis) in Diyarbakır, Turkey. Above-ground symptoms included leaf necrosis, leaf curling, extensive bluish or blackish staining of shoots, branches, stem bark, and wood surfaces, as well as stem cankers and exfoliation of branch bark scales. A general decline of the trees was distinctly visible from a distance. A Phytophthora/Pythium-like oomycete species with globose to ovoid, often papillate and internally proliferating sporangia was consistently isolated from the fine and coarse roots and stained branch parts and shoots. The pathogen was identified as Phytopythium litorale based on several morphological features. Partial DNA sequences of three loci, including nuclear rDNA internal transcribed spacer (ITS) and the large ribosomal subunit (LSU), and mitochondrial cytochrome c oxidase subunit II (coxII) confirmed the morphological identification. All P. litorale isolates were homothallic, developing gametangia, ornamented oogonia with elongate to lobate antheridia. Pathogenicity of P. litorale was tested by inoculation on excised shoots and by root inoculation on seedlings. P. litorale produced large lesions and blights on shoots in just 5 days and killed 100% of the seedlings in a month. This paper presents the first confirmed report of P. litorale as an important pathogen on a plant species causing branch and stem cankers, and root and collar rot, in and on P. orientalis, resulting in a rapid decline of trees and suggesting a threat to plane.

First Report of Phytopythium vexans Causing Root and Crown Rot on Flowering Cherry in Tennessee

Flowering cherry (Prunus serrulata Lindl. 'Kwanzan') rooted cuttings grown in propagation beds containing 40% coarse sand and 60% ground pine bark in a commercial propagation nursery in Warren County, Tennessee were exhibiting root and crown rot in December 2016. Dark brown to black soft lesions were observed in the roots as well as the crown region of flowering cherry rooted cuttings and those rooted cuttings were non-marketable due to lesions. Disease incidence was approximately 60% of 10,000 plants. Phytophthora ImmunoStrip test (Agdia Inc., Elkhart, IN, USA) was performed and the test result was positive. Diseased plant tissues were surface sterilized with 70% ethanol and washed twice with distilled water. Culturing the affected root and crown parts (1 cm pieces) on V8-PARPH, an oomycete-selective medium consistently yielded whitish radiate mycelial growth pattern with spherical zoospores, filamentous to globose oogoni, elongated, and cylindrical antheridia with constrictions (De Cock et al., 2015) after 7 days of incubation at 25°C in a 12-h fluorescent light and dark cycle, which is the typical morphology of Phytopythium vexans (de Bary) Abad, de Cock, Bala, Robideau, Lodhi & Lévesque. To confirm pathogen identity, total DNA was extracted using the UltraClean Microbial DNA Isolation Kit (MO BIO Laboratories, Inc., Carlsbad, CA, USA) directly from a 3-day old culture of isolate (FBG2017010) on V8 medium. The internal transcribed spacer (ITS) and 28S large subunit of ribosomal RNA, and cytochrome c oxidase subunit I (CoxI) of mitochondrial DNA (mtDNA) genes/ region were amplified by PCR using the primer pairs ITS1/ ITS4 (White et al., 1990), NL1/ NL4 (Baten et al., 2014), and Levup and Fm85mod (Robideau et al., 2011), respectively. The PCR products were sequenced and the sequences (GenBank accession nos. MT533275, MT533451, and MT547980) were compared to the voucher specimens. They were 99.23, 99.60, and 98.92% similar to those of P. vexans isolates in the NCBI database (HQ643400, KR092144, and HQ708996, respectively). To complete Koch's postulates, 'Kwanzan' flowering cherry rooted cuttings grown on propagation substrate (10 cm pot containing 1 kg sterilized 40% coarse sand and 60% ground pine bark) were inoculated with identified pathogen and observations were taken on root rot disease symptoms. Five plants were inoculated with 100 ml of pathogen agar-slurry (1 plate of a 7-day old culture of isolate FBG2017010/1 L of sterilized water), and five control plants were drenched with agar slurry. The plants were maintained in the greenhouse condition (day/night temperature of 26/24°C), and irrigated twice a day for 2 min by overhead irrigation system. After 2 weeks, dark brown to black necrotic root lesions developed on all inoculated cuttings and P. vexans was consistently re-isolated from the inoculated plants. The morphology of the pathogen isolated on the V8-PARPH medium was identical to the original isolate. All control plants remained symptom-free and P. vexans was not isolated from the root tissue. To our knowledge, this is the first report of P. vexans causing root and crown rot in 'Kwanzan' flowering cherry in Tennessee, which can be a potential threat for the nursery crop production. The identification of P. vexans, the causal agent of Phytopythium root and crown rot is important in determination and implementation of effective management strategies.

Recent advances in oomycete genomics

The oomycetes are a class of ubiquitous, filamentous microorganisms that include some of the biggest threats to global food security and natural ecosystems. Within the oomycete class are highly diverse species that infect a broad range of animals and plants. Some of the most destructive plant pathogens are oomycetes, such as Phytophthora infestans, the agent of potato late blight and the cause of the Irish famine. Recent years have seen a dramatic increase in the number of sequenced oomycete genomes. Here we review the latest developments in oomycete genomics and some of the important insights that have been gained. Coupled with proteomic and transcriptomic analyses, oomycete genome sequences have revealed tremendous insights into oomycete biology, evolution, genome organization, mechanisms of infection, and metabolism. We also present an updated phylogeny of the oomycete class using a phylogenomic approach based on the 65 oomycete genomes that are currently available.

New insights on evolutionary aspects of Pythium insidiosum and other peronosporaleans

BACKGROUND

The evolution of pathogenic mechanisms is a major challenge, which requires a thorough comprehension of the phylogenetic relationships of pathogens. Peronosporaleans encompasses a heterogeneous group of oomycetes that includes some animal/human pathogens, like Pythium insidiosum.

OBJECTIVE

We analysed here the phylogenetic positioning and other evolutionary aspects related to this species and other peronosporaleans, using a multi-locus approach with one mitochondrial and three nuclear genes.

METHODOLOGY

Phylogenetic patterns of 55 oomycetes were inferred by maximum likelihood and Bayesian analysis, and a relaxed molecular clock method was applied to infer the divergence time of some peronosporaleans branches.

RESULTS

Pythium insidiosum was monophyletic with a major and polytomous clade of American isolates; however, Pythium spp. was found to be paraphyletic with Phytopythium sp. and Phytophthora spp. In general, peronosporaleans subdivided into four lineages, one of which evidenced a close relationship of P insidiosum, P aphanidermatum and P arrhenomanes. This lineage diverged about 63 million years ago (Mya), whereas P insidiosum diversified at approximately 24 Mya. The divergence of American and Thai isolates seems to have occurred at approximately 17 Mya, with further American diversification at 2.4 Mya.

CONCLUSION

Overall, this study clarifies the phylogenetic relationships of P insidiosum regarding other peronosporaleans in a multi-locus perspective, despite previous claims that phylogenomic analyses are needed to accurately infer the patterns and processes related to the evolution of different lineages in this group. Additionally, this is the first time that a molecular clock was applied to study the evolution of P insidiosum.

Phytopythium and Pythium Species (Oomycota) Isolated from Freshwater Environments of Korea

Oomycetes are widely distributed in various environments, including desert and polar regions. Depending upon different habits and hosts, they have evolved with both saprophytic and pathogenic nutritional modes. Freshwater ecosystem is one of the most important habitats for members of oomycetes. Most studies on oomycete diversity, however, have been biased mostly towards terrestrial phytopathogenic species, rather than aquatic species, although their roles as saprophytes and parasites are essential for freshwater ecosystems. In this study, we isolated oomycete strains from soil sediment, algae, and decaying plant debris in freshwater streams of Korea. The strains were identified based on cultural and morphological characteristics, as well as molecular phylogenetic analyses of ITS rDNA, cox1, and cox2 mtDNA sequences. As a result, we discovered eight oomycete species previously unknown in Korea, namely Phytopythium chamaehyphon, Phytopythium litorale, Phytopythium vexans, Pythium diclinum, Pythium heterothallicum, Pythium inflatum, Pythium intermedium, and Pythium oopapillum. Diversity and ecology of freshwater oomycetes in Korea are poorly understood. This study could contribute to understand their distribution and ecological function in freshwater ecosystem.

Survey in Nurseries and Irrigation Water Reservoirs as Sources of Oomycetes Found in Avocado Orchards in the Canary Islands

Nursery stocks and irrigation water are important sources of Phytophthora spp. In this study, 20 irrigation water reservoirs and 10 avocado nurseries were surveyed in the Canary Islands between 2013 and 2015 to investigate their potential role in disseminating pathogenic species in avocado orchards. Phytophthora multivora was isolated from one of the irrigation reservoirs, whereas, in two surveys conducted in nurseries, Phytophthora cinnamomi, the primary pathogen in avocado, was detected in addition to other Phytophthora species (P. lacustris, P. multivora, P. nicotianae, P. niederhauserii, and P. palmivora) and Phytopythium vexans. The species recovered from nurseries were isolated mostly from propagated plants but also from nursery irrigation water, soil used for substrate preparation, and soil samples collected in orchards that supply seeds for seedling propagation. Species recovered from nurseries correlated with those found in avocado orchards in a previous study, except for P. lacustris, suggesting that nurseries could be involved in their dissemination in avocado orchards. The improved sanitary status of nurseries resulted in reduced incidence in the second survey, indicating the importance of nursery monitoring to reduce infestations.

Revisiting Salisapiliaceae

Of the diverse lineages of the Phylum Oomycota, saprotrophic oomycetes from the salt marsh and mangrove habitats are still understudied, despite their ecological importance. Salisapiliaceae, a monophyletic and monogeneric taxon of the marine and estuarine oomycetes, was introduced to accommodate species with a protruding hyaline apical plug, small hyphal diameter and lack of vesicle formation during zoospore release. At the time of description of Salisapilia, only few species of Halophytophthora, an ecologically similar, phylogenetically heterogeneous genus from which Salisapilia was segregated, were included. In this study, a revision of the genus Salisapilia is presented, and five new combinations (S. bahamensis, S. elongata, S. epistomia, S. masteri, and S. mycoparasitica) and one new species (S. coffeyi) are proposed. Further, the species description of S. nakagirii is emended for some exceptional morphological and developmental characteristics. A key to the genus Salisapilia is provided and its generic circumscription and character evolution in cultivable Peronosporales are discussed.

Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution

The use of host nutrients to support pathogen growth is central to disease. We addressed the relationship between metabolism and trophic behavior by comparing metabolic gene expression during potato tuber colonization by two oomycetes, the hemibiotroph Phytophthora infestans and the necrotroph Pythium ultimum. Genes for several pathways including amino acid, nucleotide, and cofactor biosynthesis were expressed more by Ph. infestans during its biotrophic stage compared to Py. ultimum. In contrast, Py. ultimum had higher expression of genes for metabolizing compounds that are normally sequestered within plant cells but released to the pathogen upon plant cell lysis, such as starch and triacylglycerides. The transcription pattern of metabolic genes in Ph. infestans during late infection became more like that of Py. ultimum, consistent with the former's transition to necrotrophy. Interspecific variation in metabolic gene content was limited but included the presence of γ-amylase only in Py. ultimum. The pathogens were also found to employ strikingly distinct strategies for using nitrate. Measurements of mRNA, ¹⁵N labeling studies, enzyme assays, and immunoblotting indicated that the assimilation pathway in Ph. infestans was nitrate-insensitive but induced during amino acid and ammonium starvation. In contrast, the pathway was nitrate-induced but not amino acid-repressed in Py. ultimum. The lack of amino acid repression in Py. ultimum appears due to the absence of a transcription factor common to fungi and Phytophthora that acts as a nitrogen metabolite repressor. Evidence for functional diversification in nitrate reductase protein was also observed. Its temperature optimum was adapted to each organism's growth range, and its K_m was much lower in Py. ultimum. In summary, we observed divergence in patterns of gene expression, gene content, and enzyme function which contribute to the fitness of each species in its niche.

A key feature of disease is the pathogen's consumption of host metabolites to support its growth and multiplication. Understanding how host nutrients are used by pathogens may lead to strategies for limiting disease, for example by developing inhibitors of metabolic pathways needed for pathogen growth. Feeding strategies of plant pathogens range between two extremes: necrotrophs kill host cells and consume the released nutrients, while biotrophs do not injure host cells but instead acquire nutrients from extracellular spaces in the plant. In this study, a comparison was made between the metabolism of Phytophthora infestans (the infamous Irish Famine pathogen) and Pythium ultimum during potato tuber colonization. These microbes have close evolutionary histories, but while Py. ultimum is a necrotroph, Ph. infestans is a biotroph for most of the disease cycle. It was discovered that distinct patterns of metabolic gene expression, gene content, and enzyme behavior underlie these lifestyles. For example, genes for utilizing compounds that are normally stored within plant cells were expressed more by Py. ultimum, while Ph. infestans appeared to synthesize more biosubstances from precursors. Several differences in carbon and nitrogen metabolism were linked to variation in enzyme content and gene expression regulators in the two species.

Characterization of Oomycete Species Associated With Root and Crown Rot of English Walnut in Chile

English (Persian) walnut (Juglans regia) trees affected by root and crown rot were surveyed in five regions of central Chile between 2015 and 2017. In each region, nine orchards, ranging from 1 to 21 years old, were randomly selected and inspected for incidence and severity of tree decline associated with crown and root rot. Soil and symptomatic crown and root tissues were collected and cultured in P₅ARP semiselective medium to isolate potential oomycete pathogens, which were identified through morphology and molecularly using ITS sequences in the rDNA gene and beta tubulin gene. The most frequently isolated species was Phytophthora cinnamomi. Pathogenicity tests were conducted with representative oomycete isolates. P. cinnamomi, P. citrophthora, and Pythium ultimum were all pathogenic in J. regia. Nevertheless, only P. cinnamomi and P. citrophthora were pathogenic to English walnut. Py. ultimum caused limited levels of root damage to English walnut seedlings. Our research indicates that as the Chilean walnut industry has expanded, so have walnut crown and root rots induced by oomycetes.

Three new Pythium species from rice paddy fields

In an investigation of the oomyceteous flora in rice paddy fields of Fars Province, Iran, three new Pythium species were isolated and identified on the basis of morphological features and molecular phylogenetic characteristics. Their unique morphological traits, including sexual and asexual structural characteristics (i.e., sporangial type; oogonial type and ornamentations; type and the number of antheridia per oogonium; and oospore type), cardinal temperatures, and colony morphology on various media, separated them from other known species. Using nuclear and mitochondrial genes, each species formed discrete lineages in phylogenetic analyses based on Bayesian inference and maximum likelihood methods. This paper describes these three new Pythium species, P. heteroogonium, P. longipapillum, and P. oryzicollum, and compares them with their related taxa via morphological features and molecular characteristics. Pathogenicity tests revealed the ability of P. oryzicollum to cause pre- and post-emergence damping-off, seed rot, crown rot, and reduced growth rate on rice.

Population structures of the water-borne plant pathogen Phytopythium helicoides reveal its possible origins and transmission modes in Japan

The purpose of this study was to clarify the genetic diversity of Phytopythium helicoides and to understand the transmission mode of the pathogen in Japan. In total, 232 P. helicoides isolates were collected from various host plants and geographic origins, including farms and natural environments. We developed 6 novel microsatellite markers for use in the study and found 90 alleles among the 6 markers in the 232 isolates. The analysis of molecular variance suggested that P. helicoides has high variance within individuals and low fixation indices between populations. A phylogenetic analysis revealed that isolates collected from the same hosts and/or geographic origins were often grouped together. For example, several isolates from natural environments were grouped with isolates from nearby agricultural areas. On the other hand, 2 geographically distant populations collected from the same host plant had similar genotypes. Our results suggested that migration of the pathogen could be facilitated naturally via drainage systems or by human activity in the transport of agricultural materials.

Canker and decline diseases caused by soil- and airborne Phytophthora species in forests and woodlands

Most members of the oomycete genus Phytophthora are primary plant pathogens. Both soil- and airborne Phytophthora species are able to survive adverse environmental conditions with enduring resting structures, mainly sexual oospores, vegetative chlamydospores and hyphal aggregations. Soilborne Phytophthora species infect fine roots and the bark of suberized roots and the collar region with motile biflagellate zoospores released from sporangia during wet soil conditions. Airborne Phytophthora species infect leaves, shoots, fruits and bark of branches and stems with caducous sporangia produced during humid conditions on infected plant tissues and dispersed by rain and wind splash. During the past six decades, the number of previously unknown Phytophthora declines and diebacks of natural and semi-natural forests and woodlands has increased exponentially, and the vast majority of them are driven by introduced invasive Phytophthora species. Nurseries in Europe, North America and Australia show high infestation rates with a wide range of mostly exotic Phytophthora species. Planting of infested nursery stock has proven to be the main pathway of Phytophthora species between and within continents. This review provides insights into the history, distribution, aetiology, symptomatology, dynamics and impact of the most important canker, decline and dieback diseases caused by soil- and airborne Phytophthora species in forests and natural ecosystems of Europe, Australia and the Americas.

Probing the Phylogenomics and Putative Pathogenicity Genes of Pythium insidiosum by Oomycete Genome Analyses

Pythium insidiosum is a human-pathogenic oomycete. Many patients infected with it lose organs or die. Toward the goal of developing improved treatment options, we want to understand how Py. insidiosum has evolved to become a successful human pathogen. Our approach here involved the use of comparative genomic and other analyses to identify genes with possible functions in the pathogenicity of Py. insidiosum. We generated an Oomycete Gene Table and used it to explore the genome contents and phylogenomic relationships of Py. insidiosum and 19 other oomycetes. Initial sequence analyses showed that Py. insidiosum is closely related to Pythium species that are not pathogenic to humans. Our analyses also indicated that the organism harbours secreted and adhesin-like proteins, which are absent from related species. Putative virulence proteins were identified by comparison to a set of known virulence genes. Among them is the urease Ure1, which is absent from humans and thus a potential diagnostic and therapeutic target. We used mass spectrometric data to successfully validate the expression of 30% of 14,962 predicted proteins and identify 15 body temperature (37 °C)-dependent proteins of Py. insidiosum. This work begins to unravel the determinants of pathogenicity of Py. insidiosum.

An expanded phylogeny for the genus Phytophthora

A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P. asparagi to clade 6 and P. intercalaris to clade 10. On the basis of this phylogeny and ancestral state reconstructions, new hypotheses were proposed for the evolutionary history of sporangial papillation of Phytophthora species. Non-papillate ancestral Phytophthora species were inferred to evolve through separate evolutionary paths to either papillate or semi-papillate species.

Nothophytophthora gen. nov., a new sister genus of Phytophthora from natural and semi-natural ecosystems

During various surveys of Phytophthora diversity in Europe, Chile and Vietnam slow growing oomycete isolates were obtained from rhizosphere soil samples and small streams in natural and planted forest stands. Phylogenetic analyses of sequences from the nuclear ITS, LSU, β-tubulin and HSP90 loci and the mitochondrial cox1 and NADH1 genes revealed they belong to six new species of a new genus, officially described here as Nothophytophthora gen. nov., which clustered as sister group to Phytophthora. Nothophytophthora species share numerous morphological characters with Phytophthora: persistent (all Nothophytophthora spp.) and caducous (N. caduca, N. chlamydospora, N. valdiviana, N. vietnamensis) sporangia with variable shapes, internal differentiation of zoospores and internal, nested and extended (N. caduca, N. chlamydospora) and external (all Nothophytophthora spp.) sporangial proliferation; smooth-walled oogonia with amphigynous (N. amphigynosa) and paragynous (N. amphigynosa, N. intricata, N. vietnamensis) attachment of the antheridia; chlamydospores (N. chlamydospora) and hyphal swellings. Main differing features of the new genus are the presence of a conspicuous, opaque plug inside the sporangiophore close to the base of most mature sporangia in all known Nothophytophthora species and intraspecific co-occurrence of caducity and non-papillate sporangia with internal nested and extended proliferation in several Nothophytophthora species. Comparisons of morphological structures of both genera allow hypotheses about the morphology and ecology of their common ancestor which are discussed. Production of caducous sporangia by N. caduca, N. chlamydospora and N. valdiviana from Valdivian rainforests and N. vietnamensis from a mountain forest in Vietnam suggests a partially aerial lifestyle as adaptation to these humid habitats. Presence of tree dieback in all forests from which Nothophytophthora spp. were recovered and partial sporangial caducity of several Nothophytophthora species indicate a pathogenic rather than a saprophytic lifestyle. Isolation tests from symptomatic plant tissues in these forests and pathogenicity tests are urgently required to clarify the lifestyle of the six Nothophytophthora species.

Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal

The oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely sequenced. Large expansions of effector protein families in Phytophthora species, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, were observed. Species-specific expansions were detected, including chitinases in Aphanomyces astaci and Pythium oligandrum. Novel effectors which may be involved in suppressing animal immune responses were identified in Ap. astaci and Py. oligandrum. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available.

The oomycetes are a class of microscopic, filamentous eukaryotes within the stramenopiles-alveolate-Rhizaria (SAR) supergroup and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. This study investigated the expansion and evolution of effectors in 37 oomycete species in 4 oomycete orders, including Albuginales, Peronosporales, Pythiales, and Saprolegniales species. Our results highlight the large expansions of effector protein families, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, in Phytophthora species. Species-specific expansions, including expansions of chitinases in Aphanomyces astaci and Pythium oligandrum, were detected. Novel effectors which may be involved in suppressing animal immune responses in Ap. astaci and Py. insidiosum were also identified. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located in a number of oomycete species. We also investigated the "RxLR" effector complement of all 37 species and, as expected, observed large expansions in Phytophthora species numbers. Our results provide in-depth sequence information on all putative RxLR effectors from all 37 species. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available.

IMPORTANCE The oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely sequenced. Large expansions of effector protein families in Phytophthora species, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, were observed. Species-specific expansions were detected, including chitinases in Aphanomyces astaci and Pythium oligandrum. Novel effectors which may be involved in suppressing animal immune responses were identified in Ap. astaci and Py. oligandrum. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available.

Pathogenicity and Virulence of Soilborne Oomycetes on Phaseolus vulgaris

Dry bean (Phaseolus vulgaris L.) is a globally important leguminous food crop. Yields can be reduced by high incidence of soilborne oomycetes that cause seedling disease. Breeders have attempted to develop Pythium root rot-resistant bean varieties; however, relationships between dry bean and most soilborne oomycete species remain uncharacterized. Oomycete species (n = 28), including Pythium spp. and Phytopythium spp., were tested in a growth chamber seedling assay at 20°C and an in vitro seed assay at 20°C and 26°C to evaluate their pathogenicity and virulence on 'Red Hawk' dark red kidney bean and 'Zorro' black bean. Root size or disease severity was significantly impacted by 14 oomycete species, though results varied by bean variety, temperature, and assay. Of these 14 pathogenic oomycete species, 11 species exhibited significant differences in DSI due to temperature on at least one bean variety. Pythium aphanidermatum, P. myriotylum, P. ultimum, P. ultimum var. sporangiiferium, and P. ultimum var. ultimum were the most virulent species in both assays, causing seed rot and pre-emergence damping-off of dry bean. Oomycete species were clustered into three groups based on symptom development: seed rot pathogens, root rot pathogens, or nonpathogens. Intraspecific variability in virulence was observed for eight of the 14 pathogenic oomycete species. Improved understanding of Pythium and Phytopythium interactions with dry bean may enable breeders and pathologists to more effectively evaluate strategies for oomycete seedling disease management.