Taxonomy, DNA barcoding and phylogeny of three new species of Pythium from Canada

An assessment of the species diversity and disease potential of Pythium communities in Europe

Pythium sensu lato (s.l.) is a genus of parasitic oomycetes that poses a serious threat to agricultural production worldwide, but their severity is often neglected because little knowledge about them is available. Using an internal transcribed spacer (ITS) amplicon-based-metagenomics approach, we investigate the occurrence, abundance, and diversity of Pythium spp. s.l. in 127 corn fields of 11 European countries from the years 2019 to 2021. We also identify 73 species, with up to 20 species in a single soil sample, and the prevalent species, which show high species diversity, varying disease potential, and are widespread in most countries. Further, we show species-species co-occurrence patterns considering all detected species and link species abundance to soil parameter using the LUCAS topsoil dataset. Infection experiments with recovered isolates show that Pythium s.l. differ in disease potential, and that effective interference with plant hormone networks suppressing JA (jasmonate)-mediated defenses is an essential component of the virulence mechanism of Pythium s.l. species. This study provides a valuable dataset that enables deep insights into the structure and species diversity of Pythium s.l. communities in European corn fields and knowledge for better understanding plant-Pythium interactions, facilitating the development of an effective strategy to cope with this pathogen.

Pythium banihashemianum sp. nov. and Globisporangium izadpanahii sp. nov.: Two New Oomycete Species from Rice Paddies in Iran

An investigation into oomycete diversity in rice paddies of Fars Province in Iran led to the identification of two new Pythium sensu lato (s.l.) species as Globisporangium izadpanahii sp. nov. and Pythium banihashemianum sp. nov. The identification was based on morphological and physiological features as well as on the phylogenetic analysis of nuclear (ITS and βtub) and mitochondrial (cox1 and cox2) loci using Bayesian inference and Maximum Likelihood. The present paper formally describes these two new species and defines their phylogenetic relationships with other congeneric species. According to multiple gene genealogy analysis, G. izadpanahii sp. nov. was grouped with other species of Globisporangium (formerly, clade G of Pythium s.l.) and was closely related to both G. nagaii and the recently described G. coniferarum. The second species, designated P. banihashemianum sp. nov., was grouped with other species of Pythium sensu stricto (formerly, clade B of Pythium s.l.) and, according to the phylogenetic analysis, shared an ancestor with P. plurisporium. The production of globose hyphal swellings was a major characteristic of G. izadpanahii sp. nov., which did not produce vesicles and zoospores. In pathogenicity tests on rice seedlings, P. banihashemianum sp. nov. isolates were highly pathogenic and caused severe root and crown rot, while G. izadpanahii sp. nov. isolates were not pathogenic.

Grapevine Trunk Diseases in Greece: Disease Incidence and Fungi Involved in Discrete Geographical Zones and Varieties

A three-year survey was conducted to estimate the incidence of grapevine trunk diseases (GTDs) in Greece and identify fungi associated with the disease complex. In total, 310 vineyards in different geographical regions in northern, central, and southern Greece were surveyed, and 533 fungal strains were isolated from diseased vines. Morphological, physiological and molecular (5.8S rRNA gene-ITS sequencing) analyses revealed that isolates belonged to 35 distinct fungal genera, including well-known (e.g., Botryosphaeria sp., Diaporthe spp., Eutypa sp., Diplodia sp., Fomitiporia sp., Phaeoacremonium spp., Phaeomoniella sp.) and lesser-known (e.g., Neosetophoma sp., Seimatosporium sp., Didymosphaeria sp., Kalmusia sp.) grapevine wood inhabitants. The GTDs-inducing population structure differed significantly among the discrete geographical zones. Phaeomoniella chlamydospora (26.62%, n = 70), Diaporthe spp. (18.25%, n = 48) and F. mediterranea (10.27%, n = 27) were the most prevalent in Heraklion, whereas D. seriata, Alternaria spp., P. chlamydospora and Fusarium spp. were predominant in Nemea (central Greece). In Amyntaio and Kavala (northern Greece), D. seriata was the most frequently isolated species (>50% frequency). Multi-genes (rDNA-ITS, LSU, tef1-α, tub2, act) sequencing of selected isolates, followed by pathogenicity tests, revealed that Neosetophoma italica, Seimatosporium vitis, Didymosphaeria variabile and Kalmusia variispora caused wood infection, with the former being the most virulent. To the best of our knowledge, this is the first report of N. italica associated with GTDs worldwide. This is also the first record of K. variispora, S. vitis and D. variabile associated with wood infection of grapevine in Greece. The potential associations of disease indices with vine age, cultivar, GTD-associated population structure and the prevailing meteorological conditions in different viticultural zones in Greece are presented and discussed.

Effect of Infection Timing by Four Pythium spp. on Soybean Damping-Off Symptoms with and Without Cold Stress

Pythium spp. cause damping-off of soybean, especially when soil conditions at or shortly after planting are cool and wet. Soybean planting dates continue to shift to earlier dates, so germinating seed and seedlings are exposed to periods of cold stress at a time which favors infection by Pythium, and seedling disease occurs. The objective of this study was to assess infection timing and cold stress on soybean seedling disease severity caused by four Pythium spp. prevalent in Iowa, namely P. lutarium, P. oopapillum, P. sylvaticum, and P. torulosum. Each species was used individually to inoculate soybean cultivar 'Sloan' using a rolled towel assay. Two temperature treatments (continuous 18°C [C18]; a 48-h cold stress period at 10°C [CS]) were applied. Soybean seedling age was divided into five growth stages (GS1 to GS5). Root rot severity and root length were assessed at 2, 4, 7, and 10 days after inoculation (DAI). At C18, root rot was greatest when soybean was inoculated with P. lutarium or P. sylvaticum at GS1 (seed imbibes water) and with P. oopapillum or P. torulosum at GS1, GS2 (radicle elongation), and GS3 (hypocotyl emergence). After CS, soybean susceptibility to P. lutarium and P. sylvaticum was reduced compared to C18 for inoculation at all GSs except GS5 (unifoliate leaf emergence). Conversely, root rot by P. oopapillum and P. torulosum was greater after CS compared to C18. Data from this study demonstrate that greater root rot, and consequently more damping-off, is likely if infection occurs at early germination stages before seedling emergence.

Diversity of Pythium Species Recovered from Float-Bed Tobacco Transplant Production Greenhouses

Pythium diseases are common in hydroponic crop production and often threaten the greenhouse production of cucumber, tomato, lettuce, and other crops. In tobacco transplant production, where float-bed hydroponic greenhouses are commonly used, Pythium diseases can cause up to 70% seedling loss. However, there have been few comprehensive studies on the composition and diversity of Pythium communities in tobacco greenhouses. In a 2017 survey, 360 Pythium isolates were collected from 41 tobacco greenhouses across four states (VA, MD, GA, and PA). Samples were collected from one to seven sites within each greenhouse. Twelve described Pythium species were identified (P. adhaerens, P. aristosporum, P. attrantheridium, P. catenulatum, P. coloratum, P. dissotocum, P. inflatum, P. irregulare, P. myriotylum, P. pectinolyticum, P. porphyrae, and P. torulosum) among the isolates obtained. Approximately 80% of the surveyed greenhouses harbored Pythium in at least one of four sites (bay water, tobacco seedlings, weeds, and center walkways) within the greenhouse. The structure of Pythium communities was diverse among the surveyed greenhouses: multiple Pythium species coexisted in the same sample, and multiple species were present within the same greenhouse at different sites. This diversity appeared to be influenced by the sampling sites within the surveyed tobacco greenhouses, sample type, and sampling time. Intraspecific variation may also exist among the P. dissotocum populations found in this study. These results uncovered the complexity and diversity of the Pythium communities within float tobacco transplant greenhouses, which could play a role in the variation in Pythium diseases observed in these production systems.

Molecular Characterization of Peronospora variabilis Isolates Infecting Chenopodium quinoa and Chenopodium album in Spain

Quinoa is an expanding crop in southern Spain. Downy mildew, caused by Peronospora variabilis, is the most important quinoa disease in Spain and worldwide. In Spain, this disease has also been observed on the weed Chenopodium album. The objectives of this study were to unravel the origin of the P. variabilis isolates currently infecting quinoa in southern Spain and to study their genetic diversity. We hypothesized that P. variabilis isolates infecting quinoa in Spain could have been introduced through the seeds of the quinoa varieties currently grown in the country or, alternatively, that these isolates are endemic isolates, originally infecting C. album, that jumped to quinoa. In order to test these hypotheses, we sequenced the internal transcribed spacer (ITS), cytochrome c oxidase subunit 1 (cox1), and cox2 regions of 33 P. variabilis isolates infecting C. quinoa and C. album in southern Spain and analyzed their phylogenetic relationship with isolates present in other countries infecting Chenopodium spp. cox1 gene sequences from all of the Spanish P. variabilis isolates were identical and exhibited nine single-nucleotide polymorphisms (SNPs) compared with a single P. variabilis cox1 sequence found at GenBank. Phylogenetic analyses based on the ITS ribosomal DNA region were not suitable to differentiate isolates according to their geographical origin or host. The cox2 sequences from P. variabilis Spanish isolates collected from C. quinoa and C. album were all identical and had a distinctive SNP in the last of four polymorphic sites that distinguished Spanish isolates from isolates from other countries. These results suggest that P. variabilis infecting quinoa in southern Spain could be native isolates that originally infected C. album.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Root Rot of Cinnamomum camphora (Linn) Presl Caused by Phytopythium vexans in China

As a famous street tree, camphor (Cinnamomum camphora) is widely planted worldwide. However, in recent years, camphor with root rot was observed in Anhui Province, China. Based on morphological characterization, thirty virulent isolates were identified as Phytopythium species. Phylogenetic analysis of combined ITS, LSU rDNA, β-tubulin, coxI, and coxII sequences assigned the isolates to Phytopythium vexans. Koch's postulates were fulfilled in the greenhouse, and the pathogenicity of P. vexans was determined by root inoculation tests on 2-year-old camphor seedlings; the symptoms of indoor inoculation were consistent with those in the field. P. vexans can grow at 15-30 °C, with an optimal growth temperature of 25-30 °C. The results of fungicide sensitivity experiments indicated that P. vexans was the most sensitive to metalaxyl hymexazol, which may be a useful idea for the future prevention and control management of P.vexans. This study provided the first step for further research on P. vexans as a pathogen of camphor, and provided a theoretical basis for future control strategies.

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.

A Novel Seimatosporium and Other Sporocadaceae Species Associated with Grapevine Trunk Diseases in Cyprus

Besides well-known grapevine trunk disease (GTD)-related pathogens, there is an increased interest in wood-colonizing fungi that infect grapevines. During 2017-2018, a survey was conducted in Cyprus and wood samples were collected from vines exhibiting typical GTD symptoms. Based on morphological and multilocus phylogenetic analyses (ITS, LSU, bt2, tef1-a), four species in the Sporocadaceae family were described and typified; two in the genus of Seimatosporium: Seim. cyprium sp. nov. and Seim. vitis-viniferae and two in Sporocadus: Spo. kurdistanicus and Spo. rosigena. The teleomorph of Seim. cyprium sp. nov. was also described. Pathogenicity trials with representative isolates of each species were performed on woody stems of two-year-old potted grapevines for 12 months under field conditions. All isolates were pathogenic, causing dark brown to black vascular discoloration, extending upward and downward from the inoculation point. Sporocadus isolates were significantly more aggressive than Seimatosporium with lesion lengths ranging from 9.24 to 6.90 and 4.13 to 4.00 cm, respectively. Successful re-isolations were also evident for all species and isolates. Seim. cyprium sp. nov. is a newly described species, while Spo. kurdistanicus and Spo. rosigena are reported for the first time in Europe on Vitis vinifera, suggesting the potential role of Sporocadaceae in the GTDs complex.

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.

Development and comparison of loop-mediated isothermal amplification with quantitative PCR for the specific detection of Saprolegnia spp

Saprolegniasis is an important disease in freshwater aquaculture, and is associated with oomycete pathogens in the genus Saprolegnia. Early detection of significant levels of Saprolegnia spp. pathogens would allow informed decisions for treatment which could significantly reduce losses. This study is the first to report the development of loop-mediated isothermal amplification (LAMP) for the detection of Saprolegnia spp. and compares it with quantitative PCR (qPCR). The developed protocols targeted the internal transcribed spacer (ITS) region of ribosomal DNA and the cytochrome C oxidase subunit 1 (CoxI) gene and was shown to be specific only to Saprolegnia genus. This LAMP method can detect as low as 10 fg of S. salmonis DNA while the qPCR method has a detection limit of 2 pg of S. salmonis DNA, indicating the superior sensitivity of LAMP compared to qPCR. When applied to detect the pathogen in water samples, both methods could detect the pathogen when only one zoospore of Saprolegnia was present. We propose LAMP as a quick (about 20–60 minutes) and sensitive molecular diagnostic tool for the detection of Saprolegnia spp. suitable for on-site applications.

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.

High-Temperature-Tolerant Fungus and Oomycetes in Korea, Including Saksenaea longicolla sp. nov

Global temperatures are steadily increasing, leading to significant changes in microbial diversity and ecology. In the present study, we isolated high-temperature-growing fungi and fungi-like group (Oomycota) strains from freshwater environments of Korea and identified them based on cultural, morphological, and multilocus phylogenetic analyses. As a result, we introduce Saksenaea (Fungi) isolates as a new species, Saksenaea longicolla sp. nov. and record Phytophthora chlamydospora and P. lagoariana (Oomycota) new to Korea. In the growth experiments, they exhibited high-temperature tolerance, which can grow at 35-40 °C but become inactive at 4 °C and below. This study confirms the presence of high-temperature-tolerant fungi and oomycetes in Korea and suggests that the Korean climate conditions are changing in favor of these species. This indicates that climate warming is altering microbial distributions in freshwater environments.

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.

Cox2 community barcoding at Prince Edward Island reveals long-distance dispersal of a downy mildew species and potentially marine members of the Saprolegniaceae

Marine oomycetes are highly diverse, globally distributed, and play key roles in marine food webs as decomposers, food source, and parasites. Despite their potential importance in global ocean ecosystems, marine oomycetes are comparatively little studied. Here, we tested if the primer pair cox2F_Hud and cox2-RC4, which is already well-established for phylogenetic investigations of terrestrial oomycetes, can also be used for high-throughput community barcoding. Community barcoding of a plankton sample from Brudenell River (Prince Edward Island, Canada), revealed six distinct oomycete OTU clusters. Two of these clusters corresponded to members of the Peronosporaceae—one could be assigned to Peronospora verna, an obligate biotrophic pathogen of the terrestrial plant Veronica serpyllifolia and related species, the other was closely related to Globisporangium rostratum. While the detection of the former in the sample is likely due to long-distance dispersal from the island, the latter might be a bona fide marine species, as several cultivable species of the Peronosporaceae are known to withstand high salt concentrations. Two OTU lineages could be assigned to the Saprolegniaceae. While these might represent marine species of the otherwise terrestrial genus, it is also conceivable that they were introduced on detritus from the island. Two additional OTU clusters were grouped with the early-diverging oomycete lineages but could not be assigned to a specific family. This reflects the current underrepresentation of cox2 sequence data which will hopefully improve with the increasing interest in marine oomycetes.

An expanded diversity of oomycetes in Carboniferous forests: Reinterpretation of Oochytrium lepidodendri (Renault 1894) from the Esnost chert, Massif Central, France

335-330 million-year-old cherts from the Massif Central, France, contain exceptionally well-preserved remains of an early forest ecosystem, including plants, fungi and other microorganisms. Here we reinvestigate the original material prepared by Renault and Roche from collections of the Muséum National d'Histoire Naturelle, Paris, and present a re-evaluation of Oochytrium lepidodendri (Renault 1894), originally described as a zoosporic fungus. Confocal laser scanning microscopy (CLSM) was used to study the microfossils, enabling us in software to digitally reconstruct them in three-dimensional detail. We reinterpret O. lepidodendri as a pseudofungus and favour placement within the oomycetes, a diverse clade of saprotrophs and both animal and plant parasites. Phylogenetically, O. lepidodendri appears to belong to a group of oomycetes distinct from those previously described from Paleozoic rocks and most likely related to the Peronosporales s.l. This study adds to our knowledge of Paleozoic eukaryotic diversity and reinforces the view that oomycetes were early and diverse constituents of terrestrial biotas, playing similar ecological roles to those they perform in modern ecosystems.

Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina

Fungi in the marine environment are often neglected as a research topic, despite that fungi having critical roles on land as decomposers, pathogens or endophytes. Here we used culture-dependent methods to survey the fungi associated with the seagrass, Zostera marina, also obtaining bacteria and oomycete isolates in the process. A total of 108 fungi, 40 bacteria and 2 oomycetes were isolated. These isolates were then taxonomically identified using a combination of molecular and phylogenetic methods. The majority of the fungal isolates were classified as belonging to the classes Eurotiomycetes, Dothideomycetes, and Sordariomycetes. Most fungal isolates were habitat generalists like Penicillium sp. and Cladosporium sp., but we also cultured a diverse set of rare taxa including possible habitat specialists like Colletotrichum sp. which may preferentially associate with Z. marina leaf tissue. Although the bulk of bacterial isolates were identified as being from known ubiquitous marine lineages, we also obtained several Actinomycetes isolates and a Phyllobacterium sp. We identified two oomycetes, another understudied group of marine microbial eukaryotes, as Halophytophthora sp. which may be opportunistic pathogens or saprophytes of Z. marina. Overall, this study generates a culture collection of fungi which adds to knowledge of Z. marina associated fungi and highlights a need for more investigation into the functional and evolutionary roles of microbial eukaryotes associated with seagrasses.

Phylogeny and morphology of new species of Globisporangium

An isolate originally obtained from pond water in Osaka in 1992 and identified as Pythium marsipium, was subsequently classified as Globisporangium marsipium. According to molecular phylogenetic analyses based on the internal transcribed spacer regions of the nuclear ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 genes, this isolate was shown to represent a new species, described here as G. lacustre sp. nov. In addition, two further new combinations are introduced in Globisporangium as G. camurandrum and G. takayamanum based on their DNA phylogeny.

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.

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.

Novel Seimatosporium Species from Grapevine in Northern California and Their Interactions with Fungal Pathogens Involved in the Trunk-Disease Complex

Seimatosporium spp. and closely related "pestalotioid fungi" have been isolated from vineyards worldwide, but their ecological status in grapevine wood is unclear. To determine their involvement in the grapevine trunk-disease complex, we tested the pathogenicity of Californian isolates obtained from vines with general symptoms of Botryosphaeria, Eutypa, and Phomopsis diebacks. Multilocus phylogenetic analyses revealed three species: Seimatosporium vitis and two newly described and typified species, S. luteosporum sp. nov. and S. vitifusiforme sp. nov. Inoculations to woody stems of potted grapevines of both isolates of S. vitis and one isolate of S. vitifusiforme, but not S. luteosporum, were associated with significantly larger lesions than those of noninoculated controls. Coinoculations with trunk pathogens (Cryptovalsa ampelina, Diaporthe ambigua, Diatrypella verruciformis, Diplodia seriata, and Eutypa lata), coisolated from the same wood cankers in the field, brought about increased lesion lengths for S. vitifusiforme paired with D. seriata, and S. luteosporum paired with Diaporthe ambigua. In contrast, there were no differences in lesion lengths of S. vitis and Diatrypella verruciformis or S. vitis and E. lata, inoculated alone or together. Our findings suggest that Seimatosporium spp. are involved in the grapevine trunk-disease complex, and their virulence may depend on or affect that of trunk pathogens.

Modeling Effects of Temperature, Soil, Moisture, Nutrition and Variety As Determinants of Severity of Pythium Damping-Off and Root Disease in Subterranean Clover

Subterranean clover (Trifolium subterraneum) is a critical pasture legume in Mediterranean regions of southern Australia and elsewhere, including Mediterranean-type climatic regions in Africa, Asia, Australia, Europe, North America, and South America. Pythium damping-off and root disease caused by Pythium irregulare is a significant threat to subterranean clover in Australia and a study was conducted to define how environmental factors (viz. temperature, soil type, moisture and nutrition) as well as variety, influence the extent of damping-off and root disease as well as subterranean clover productivity under challenge by this pathogen. Relationships were statistically modeled using linear and generalized linear models and boosted regression trees. Modeling found complex relationships between explanatory variables and the extent of Pythium damping-off and root rot. Linear modeling identified high-level (4 or 5-way) significant interactions for each dependent variable (dry shoot and root weight, emergence, tap and lateral root disease index). Furthermore, all explanatory variables (temperature, soil, moisture, nutrition, variety) were found significant as part of some interaction within these models. A significant five-way interaction between all explanatory variables was found for both dry shoot and root dry weights, and a four way interaction between temperature, soil, moisture, and nutrition was found for both tap and lateral root disease index. A second approach to modeling using boosted regression trees provided support for and helped clarify the complex nature of the relationships found in linear models. All explanatory variables showed at least 5% relative influence on each of the five dependent variables. All models indicated differences due to soil type, with the sand-based soil having either higher weights, greater emergence, or lower disease indices; while lowest weights and less emergence, as well as higher disease indices, were found for loam soil and low temperature. There was more severe tap and lateral root rot disease in higher moisture situations.

Temperature Affects Aggressiveness and Fungicide Sensitivity of Four Pythium spp. that Cause Soybean and Corn Damping Off in Iowa

Damping off of soybean and corn, caused by Pythium spp., is favored by cool temperatures and wet soil conditions and is primarily managed using fungicide seed treatments. The goal of this research was to determine the effect of temperature on aggressiveness and fungicide sensitivity of Pythium spp. recovered from soybean and corn in Iowa. A total of 21 isolates of four of the most prevalent Pythium spp. in Iowa were screened. Seed and seedling assays were used to quantify the aggressiveness of P. lutarium, P. oopapillum, P. sylvaticum, and P. torulosum on soybean and corn at 13, 18, and 23°C. Isolates recovered from soybean or corn were equally pathogenic on both hosts. P. torulosum was more aggressive at 13°C compared with 18 and 23°C. Conversely, P. sylvaticum was more aggressive at 18 and 23°C than at 13°C. A plate assay was used to assess fungicide sensitivity to seven fungicides that are commonly used as seed treatments, and EC₅₀ values at each of the three temperatures were determined and compared. EC₅₀ values for P. torulosum were higher for all fungicides tested at 13°C, compared with 18 or 23°C, whereas EC₅₀ values for P. sylvaticum were higher for all fungicides at 18 and 23°C compared with 13°C. These data contribute to our understanding of the effect of soil temperature on the risk of soybean and corn damping off, which may aid in the development of more effective management practices.

Towards a universal barcode of oomycetes--a comparison of the cox1 and cox2 loci

Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.

Pythium rishiriense sp. nov. from water and P. alternatum sp. nov. from soil, two new species from Japan

In an investigation of Pythium species in natural ecosystems of Rishiri Island in Northern Japan, two new species, Pythium rishiriense and P. alternatum, were identified based on morphological and molecular analyses. Pythium rishiriense differed morphologically from other Pythium species by its characteristic oogonial formation which occasionally arranged in chains. Pythium alternatum differed morphologically from other Pythium species by its distinguishing sexual organs where oogonia occasionally arranged alternately with antheridia in chains. Pythium rishiriense is a fast growing, high-temperature loving species, while P. alternatum is a slow growing species. Phylogenetic analyses based on the internal transcribed spacer region and cytochrome c oxidase 1 gene sequences showed that these two species are clearly separate from morphologically similar species.

Phytopythium: molecular phylogeny and systematics

The genus Phytopythium (Peronosporales) has been described, but a complete circumscription has not yet been presented. In the present paper we provide molecular-based evidence that members of Pythium clade K as described by Lévesque & de Cock (2004) belong to Phytopythium. Maximum likelihood and Bayesian phylogenetic analysis of the nuclear ribosomal DNA (LSU and SSU) and mitochondrial DNA cytochrome oxidase subunit 1 (COI) as well as statistical analyses of pairwise distances strongly support the status of Phytopythium as a separate phylogenetic entity. Phytopythium is morphologically intermediate between the genera Phytophthora and Pythium. It is unique in having papillate, internally proliferating sporangia and cylindrical or lobate antheridia. The formal transfer of clade K species to Phytopythium and a comparison with morphologically similar species of the genera Pythium and Phytophthora is presented. A new species is described, Phytopythium mirpurense.

Identification and Pathogenicity of Pythium on Soybean in North Dakota

The oomycete Pythium comprises one of the most important groups of seedling pathogens affecting soybean. There has been limited research on Pythium spp. pathogenic on soybean in the northern Great Plains. The objectives of this research were to isolate and identify Pythium spp. infecting soybean in North Dakota and to test their pathogenicity. Identification of Pythium spp. was achieved using molecular techniques and morphological features. A total of 26 known Pythium spp. and three unknown species were recovered from soybean seedling roots collected from 125 fields between 2011 and 2012. In 2011, the three most abundant species isolated were P. ultimum, Pythium sp. (unknown; GenBank HQ643777.1), and P. heterothallicum, representing 21, 16, and 12% of 2,675 isolates, respectively. More species and isolates were obtained in 2011, a wet and cool year, compared with 2012, which was dry and warm. The majority of Pythium spp. caused pre-emergence damping-off on soybean with less than 50% emergence in a 2-week test using infested soil at 23°C. In contrast, in the presence of P. orthogonon, P. nunn, or P. rostratifingens there was approximately 80% or greater emergence and most plants survived for several weeks, although lesions were observed on roots. Mortierella spp., a zygomycete, was commonly isolated along with Pythium spp. in 2012, but not in 2011. This is the first report of P. kashmirense, P. minus, P. periilum, P. rostratifingens, P. terrestris, P. viniferum, and P. violae as pathogens of soybean seedlings. In addition, this is the first report of P. kashmirense, P. viniferum, and P. terrestris in the United States.

Species of Pythium Associated with Seedling Root and Hypocotyl Disease on Common Bean (Phaseolus vulgaris) in Western Australia

The occurrence and distribution of Pythium spp. were determined by collecting isolates of Pythium from common bean (Phaseolus vulgaris) plants showing root or hypocotyl disease symptoms from different areas of Western Australia in 2012. Eight different Pythium species (Pythium conidiophorum, P. diclinum, P. intermedium, P. irregulare, P. lutarium, P. mamillatum, P. pachycaule, and P. perplexum) were isolated and identified according to molecular sequences. P. irregulare was the most widespread Pythium sp. All species, except P. perplexum, were pathogenic to the hypocotyl and root of common bean. We believe this is the first report of P. intermedium as a pathogen on common bean worldwide. This is also the first report of P. conidiophorum, P. intermedium, P. lutarium, P. mamillatum, P. pachycaule, and P. diclinum as pathogens on common bean in Australia and the first report of P. irregulare as a pathogen on common bean in Western Australia. P. intermedium was the most pathogenic species, causing the most severe disease on 'Gourmet Delight' (percent root disease index [%RDI] 75 ± 2.9 and percent hypocotyl disease index [%HDI] 59.2 ± 3.2) and 'Pioneer' (%RDI 75 ± 2.9 and %HDI 65.8 ± 3.2). That the relative susceptibility or resistance (the ability of a plant to reduce the extent of invasion by the pathogen) of a given bean variety to one Pythium sp. was, in general, similar across the other Pythium spp. was an important finding, because this opens up opportunities to utilize a single virulent isolate of one Pythium sp. to identify general resistance to a wider spectrum of Pythium spp.

Characterization of Pythium oligandrum populations that colonize the rhizosphere of vines from the Bordeaux region

This study focused on one oomycete, Pythium oligandrum, well-known for its plant protection abilities, which thrives in microbial environment where bacteria and fungal communities are also present. The genetic structures and dynamics of fungal and bacterial communities were studied in three Bordeaux subregions with various types of soil, using single-strand conformation polymorphism. The structure of the fungal communities colonizing the rhizosphere of vines planted in sandy-stony soils was markedly different from that those planted in silty and sandy soils; such differences were not observed for bacteria. In our 2-year experiment, the roots of all the vine samples were also colonized by echinulated oospore Pythium species, with P. oligandrum predominating. Cytochrome oxidase I and tubulin gene sequencings showed that P. oligandrum strains clustered into three groups. Based on elicitin-like genes coding for proteins able to induce plant resistance, six populations were identified. However, none of these groups was assigned to a particular subregion of Bordeaux vineyards, suggesting that these factors do not shape the genetic structure of P. oligandrum populations. Results showed that different types of rootstock and weeding management both influence root colonization by P. oligandrum. These results should prove particularly useful in improving the management of potentially plant-protective microorganisms.

Host adaptation and speciation through hybridization and polyploidy in Phytophthora

It is becoming increasingly evident that interspecific hybridization is a common event in phytophthora evolution. Yet, the fundamental processes underlying interspecific hybridization and the consequences for its ecological fitness and distribution are not well understood. We studied hybridization events in phytophthora clade 8b. This is a cold-tolerant group of plant pathogenic oomycetes in which six host-specific species have been described that mostly attack winter-grown vegetables. Hybrid characterization was done by sequencing and cloning of two nuclear (ITS and Ypt1) and two mitochondrial loci (Cox1 and Nadh1) combined with DNA content estimation using flow cytometry. Three different mtDNA haplotypes were recovered among the presumed hybrid isolates, dividing the hybrids into three types, with different parental species involved. In the nuclear genes, additivity, i.e. the presence of two alleles coming from different parents, was detected. Hybrid isolates showed large variations in DNA content, which was positively correlated with the additivity in nuclear loci, indicating allopolyploid hybridization followed by a process of diploidization. Moreover, indications of homeologous recombination were found in the hybrids by cloning ITS products. The hybrid isolates have been isolated from a range of hosts that have not been reported previously for clade 8b species, indicating that they have novel pathogenic potential. Next to this, DNA content measurements of the non-hybrid clade 8b species suggest that polyploidy is a common feature of this clade. We hypothesize that interspecific hybridization and polyploidy are two linked phenomena in phytophthora, and that these processes might play an important and ongoing role in the evolution of this genus.

Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes

The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including Phytophthora, Pythium and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six Pythium genomes and comparison with other stramenopiles including photosynthetic diatoms, and other plant pathogenic oomycetes such as Phytophthora species, Hyaloperonospora arabidopsidis, and Pythium ultimum var. ultimum. Novel features of the oomycete genomes include an expansion of genes encoding secreted effectors and plant cell wall degrading enzymes in Phytophthora species and an over-representation of genes involved in proteolytic degradation and signal transduction in Pythium species. A complete lack of classical RxLR effectors was observed in the seven surveyed Pythium genomes along with an overall reduction of pathogenesis-related gene families in H. arabidopsidis. Comparative analyses revealed fewer genes encoding enzymes involved in carbohydrate metabolism in Pythium species and H. arabidopsidis as compared to Phytophthora species, suggesting variation in virulence mechanisms within plant pathogenic oomycete species. Shared features between the oomycetes and diatoms revealed common mechanisms of intracellular signaling and transportation. Our analyses demonstrate the value of comparative genome analyses for exploring the evolution of pathogenesis and survival mechanisms in the oomycetes. The comparative analyses of seven Pythium species with the closely related oomycetes, Phytophthora species and H. arabidopsidis, and distantly related diatoms provide insight into genes that underlie virulence.

Carbohydrate-active enzymes in pythium and their role in plant cell wall and storage polysaccharide degradation

Carbohydrate-active enzymes (CAZymes) are involved in the metabolism of glycoconjugates, oligosaccharides, and polysaccharides and, in the case of plant pathogens, in the degradation of the host cell wall and storage compounds. We performed an in silico analysis of CAZymes predicted from the genomes of seven Pythium species (Py. aphanidermatum, Py. arrhenomanes, Py. irregulare, Py. iwayamai, Py. ultimum var. ultimum, Py. ultimum var. sporangiiferum and Py. vexans) using the "CAZymes Analysis Toolkit" and "Database for Automated Carbohydrate-active Enzyme Annotation" and compared them to previously published oomycete genomes. Growth of Pythium spp. was assessed in a minimal medium containing selected carbon sources that are usually present in plants. The in silico analyses, coupled with our in vitro growth assays, suggest that most of the predicted CAZymes are involved in the metabolism of the oomycete cell wall with starch and sucrose serving as the main carbohydrate sources for growth of these plant pathogens. The genomes of Pythium spp. also encode pectinases and cellulases that facilitate degradation of the plant cell wall and are important in hyphal penetration; however, the species examined in this study lack the requisite genes for the complete saccharification of these carbohydrates for use as a carbon source. Genes encoding for xylan, xyloglucan, (galacto)(gluco)mannan and cutin degradation were absent or infrequent in Pythium spp.. Comparative analyses of predicted CAZymes in oomycetes indicated distinct evolutionary histories. Furthermore, CAZyme gene families among Pythium spp. were not uniformly distributed in the genomes, suggesting independent gene loss events, reflective of the polyphyletic relationships among some of the species.

The safety assessment of Pythium irregulare as a producer of biomass and eicosapentaenoic acid for use in dietary supplements and food ingredients

Polyunsaturated fatty acids, docosahexaenoic acid (DHA, 22:6, n-3), eicosapentaenoic acid (EPA, 20:5, n-3), and arachidonic acid (ARA, 20:4 n-6), have multiple beneficial effects on human health and can be used as an important ingredient in dietary supplements, food, feed and pharmaceuticals. A variety of microorganisms has been used for commercial production of these fatty acids. The microorganisms in the Pythium family, particularly Pythium irregulare, are potential EPA producers. The aim of this work is to provide a safety assessment of P. irregulare so that the EPA derived from this species can be potentially used in various commercial applications. The genus Pythium has been widely recognized as a plant pathogen by infecting roots and colonizing the vascular tissues of various plants such as soybeans, corn and various vegetables. However, the majority of the Pythium species (including P. irregulare) have not been reported to infect mammals including humans. The only species among the Pythium family that infects mammals is P. insidiosum. There also have been no reports showing P. irregulare to contain mycotoxins or cause potentially allergenic responses in humans. Based on the safety assessment, we conclude that P. irregulare can be considered a safe source of biomass and EPA-containing oil for use as ingredients in dietary supplements, food, feed and pharmaceuticals.

The expansion of Phytophthora clade 8b: three new species associated with winter grown vegetable crops

Despite its association with important agricultural crops, Phytophthora clade 8b is a poorly studied group of species. The clade currently consists of three officially described species (Phytophthora porri, P. brassicae and P. primulae) that are host-specific pathogens of leek, cabbages and Primula spp., respectively. However, over the past few decades, several other clade 8b-like Phytophthoras have been found on a variety of different host plants that were all grown at low temperatures in winter seasons. In this study, a collection of 30 of these isolates was subjected to a phylogenetic study using two loci (the rDNA ITS region and the mitochondrial cox1 gene). This analysis revealed a clear clustering of isolates according to their host plants. To verify whether these isolates belong to separate species, a detailed morphological study was conducted. On the basis of genetic and morphological differences and host specificity, we now present the official description of three new species in clade 8b: Phytophthora cichorii sp. nov., P. dauci sp. nov. and P. lactucae sp. nov. Two other groups of isolates (Phytophthora taxon castitis and Phytophthora taxon parsley) might also represent new species but the data available at this time are insufficient for an official description. This brings Phytophthora clade 8b to a group of six species that are all host-specific, slow-growing and specifically infect herbaceous crops at low temperatures.

DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer

Oomycete species occupy many different environments and many ecological niches. The genera Phytophthora and Pythium for example, contain many plant pathogens which cause enormous damage to a wide range of plant species. Proper identification to the species level is a critical first step in any investigation of oomycetes, whether it is research driven or compelled by the need for rapid and accurate diagnostics during a pathogen outbreak. The use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase subunit I (COI) is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. In this study we have sequenced COI, from 1205 isolates representing 23 genera. A comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI identification is a practical option; complementary because it uses the mitochondrial genome instead of nuclear DNA. In some cases COI was more discriminative than ITS at the species level. This is in contrast to the large ribosomal subunit, which showed poor species resolution when sequenced from a subset of the isolates used in this study. The results described in this paper indicate that COI sequencing and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources, and that both COI, the default DNA barcode supported by GenBank, and ITS, the de facto barcode accepted by the oomycete and mycology community, are acceptable and complementary DNA barcodes to be used for identification of oomycetes.