Diversity and populations of Phytophthora,Phytopythium and Pythium species recovered from sediments in an agricultural run‐off sedimentation reservoir

Agricultural run‐off sedimentation reservoirs are an emerging aquatic system of critical importance to plant biosecurity, water and environmental sustainability. Oomycete pathogens such as Phytophthora and Pythium species in irrigation water have been demonstrated to pose significant risks to ornamental crops, but little is known about their diversity and populations in sediments of agricultural irrigation systems. This study investigated the oomycete communities including Phytophthora (Ph.), Phytopythium (Pp.) and Pythium (Py.) species in sediments at various depths of an agricultural run‐off sedimentation reservoir in Virginia during the winters of 2011 and 2015. The recovery of these oomycetes declined sharply with sediment depth from surface to 0·8 m and none was recovered from sediments deeper than 1·4 m. A total of 47 oomycete species were recovered, with all four species of Phytophthora and five of Phytopythium exclusively from the surface. Recovered species included many important plant pathogens such as Ph. nicotianae, Ph. pini, Ph. tropicalis, Pp.  vexans, Py. irregulare and Py. monospermum. These results underline the importance of decontaminating sediments excavated from top layers (0–1·4 m) of the sedimentation reservoir before reuse in plant production.     

三类植物卵菌的全基因组比较

为有效防治由不同类型卵菌引起的植物病害,该研究对数据库中的霜霉、疫霉和腐霉3类不同卵菌的全基因组数据进行序列特征分析、同源性分析和共线性分析以及同源差异基因富集通路分析。结果显示,霜霉、疫霉和腐霉来自独立的谱系,且疫霉与霜霉的亲缘关系较近;疫霉的致病相关基因数量最多,主要有RxLR、CRN、NPP、NF和PcF基因家族,霜霉的致病相关基因数量次之,腐霉的致病相关基因数量最少;3类卵菌共确定了13 392个同源基因,其中3类卵菌均共有的同源基因为3 786个,不同菌种的同源基因数量差异较大,整体表现为疫霉>霜霉>腐霉;同源差异基因富集程度最高的前20个通路主要是基础代谢的通路和中间代谢通路,其中抗坏血酸和藻酸盐代谢、ABC转运蛋白和果糖和甘露糖代谢相对富集程度较高,基因数目也较多。     

Pathogenicity and fungicide sensitivity of Pythium and Phytopythium spp. associated with soybean in the Huang-Huai region of China

Pythium and Phytopythium spp. cause seed decay, damping off, and root rot in soybean, wheat, and many other crops. However, their diversity and importance as pathogens, particularly in different crop rotation systems, are largely unknown. A survey was conducted in the Huang-Huai region, one of the main areas of soybean–wheat rotation farming in China. In 2016–2018, we collected 300 soybean seedlings and 150 field soil samples from several representative locations, and identified 26 Pythium and 6 Phytopythium spp. from 212 isolates, based on internal transcribed spacer 2 (ITS2) and cytochrome oxidase subunit 1 sequences. The pathogenicity of these isolates was evaluated by growing soybean and wheat seeds in dishes and pots containing oomycete cultures. We found that 12 Pythium spp. (but no Phytopythium spp.) showed high pathogenicity on soybean and/or wheat, and nine of them (75%) were highly pathogenic on both crops. Among the nine species, Pythium spinosum, Pythium ultimum, Pythium species 1 (tentatively designated as ‘Candidatus Pythium huanghuaiense’), Pythium aphanidermatum, and Pythium myriotylum were highly abundant among all isolates (15%, 10%, 9%, 8%, and 5%, respectively). Nine species were selected for testing of sensitivity to the fungicides metalaxyl and mefenoxam. The EC₅₀ values were all less than 10 μg/ml, indicating little resistance. Minimum inhibitory concentration values indicated isolates were about twice as sensitive to mefenoxam as to metalaxyl. These results provide a systematic understanding of Pythium and Phytopythium species associated with soybean in the Huang-Huai region, which is important for disease management and breeding programmes.     

PCR‐based identification of cacao black pod causal agents and identification of biological factors possibly contributing to Phytophthora megakarya's field dominance in West Africa

Among the Phytophthora species that cause black pod of cacao, P. megakarya is the most virulent, posing a serious threat to cacao production in Africa. Correct identification of the species causing the black pod and understanding the virulence factors involved are important for developing sustainable disease management strategies. A simple PCR‐based species identification method was developed using the species‐specific sequences in the ITS regions of the rRNA gene. A phylogenetic tree generated for 119 Phytophthora isolates, based on the 60S ribosomal protein L10 gene and rDNA sequence, verified the PCR‐based identification assay and showed high interspecific variation among the species causing black pod. Phytophthora megakarya isolates were uniformly virulent in an assay using susceptible cacao pod husks inoculated with zoospores, while the P. palmivora isolates showed greater divergence in virulence. The virulence of P. megakarya was associated with earlier production of sporangia and an accelerated induction of necrosis. While zoospore germ tubes of both species penetrated pods through stomata, only P. megakarya produced significant numbers of appressoria. A hypersensitive‐like response was observed when attached SCA‐6 pods were inoculated with P. palmivora. SCA‐6 pods became vulnerable to P. palmivora when wounded prior to zoospore inoculation. Phytophthora megakarya was more aggressive than P. palmivora on attached SCA‐6 pods, causing expanding necrotic lesions with or without wounding. Phytophthora megakarya is predominant in the Volta region of Ghana and it remains to be seen whether it can displace P. palmivora from cacao plantations of Ghana as it has in Nigeria and Cameroon.     

Plant extracts containing caffeic acid and rosmarinic acid inhibit zoospore germination of Phytophthora spp. pathogenic to Theobroma cacao

The three most important species of Phytophthora worldwide causing black pod disease of cacao are P. palmivora, P. megakarya, and P. capsici. Chemicals are effective in controlling this disease but more natural methods would be preferred. One alternative is to use natural plant extracts. Rosemary and lavender leaf extracts were found to be effective in reducing germination of P. capsici, P. megakarya, and P. palmivora zoospores when supplemented to agar plates at different dilutions. The extracts displayed the biggest impact on P. megakarya zoospores where it completely inhibited germination at a 25% dilution of the prepared extract. When applied to cacao leaf disks, rosemary extract reduced necrosis caused by P. megakarya zoospores. In a bioassay, pears first treated with lavender extract showed no symptoms of P. megakarya infection compared with the non-treated controls. Based upon HPLC analyses, the active compound in these extracts was determined to be caffeic acid, rosmarinic acid or some simple derivative thereof. When added to agar plates, synthetic caffeic acid and rosmarinic acid completely inhibited germination of P. capsici, P. megakarya, and P. palmivora zoospores at concentrations of 3 and 6 g l⁻¹, respectively. In addition, sage and rice bran extracts, which both contain caffeic acid, were also effective in reducing zoospore germination. In contrast, inhibition of Botrytis cinerea or Trichoderma asperellum conidia germination did not occur, displaying some level of specificity. These extracts could provide an economically safe method for reducing damage caused by black pod disease on cacao until resistant varieties are developed and released.     

Prevalence of Phytophthora species in macadamia orchards in Australia and their ability to cause stem canker

In Australia, Phytophthora cinnamomi is the only species reported as the causal agent of stem canker and root rot in macadamia. In other countries, five Phytophthora species have been reported to cause diseases in macadamia, which led us to question if more than one Phytophthora species is responsible for poor tree health in macadamia orchards in Australia. To investigate this, samples were collected from the rhizosphere, stem, and root tissues of trees with and without symptoms, nurseries, and water sources from 70 commercial macadamia orchards in Australia. Phytophthora isolates were identified based on morphological characteristics and DNA sequencing. P. cinnamomi was the most predominant and widely distributed species, and was obtained from the different types of samples including symptomless root tissues. In addition to P. cinnamomi, only P. multivora was isolated from diseased tissue (stem canker) samples. Six other Phytophthora species were obtained from the rhizosphere samples: P. pseudocryptogea, P. citrophthora, P. nicotianae, P. gondwanense, P. sojae, and a new Phytophthora taxon. Only P. cinnamomi was obtained from macadamia nursery samples, while five Phytophthora species were obtained from water sources. Of the heterothallic Phytophthora species, mating type A2 isolates were dominant in P. cinnamomi isolates, whereas only mating type A1 isolates were obtained for P. nicotianae, P. pseudocryptogea, and P. citrophthora. Pathogenicity assays revealed that P. cinnamomi and P. multivora caused significantly larger stem and leaf lesions than P. citrophthora, P. nicotianae, and P. pseudocryptogea. Phytophthora sp. and P. sojae were nonpathogenic towards leaves and stems.     

Isolation of actinomycetes and endospore-forming bacteria from the cacao pod surface and their antagonistic activity against the witches’ broom and black pod pathogens

In this study, actinomycetes and endospore-forming bacteria were isolated from the surface of cacao pods. The activity of these microorganisms againstCrinipellis perniciosa andPhytophthora palmivora, causal agents of witches’ broom and black pod diseases of cacao, respectively, was investigated. A total of 336 isolates of actinomycetes and endosporeforming bacteria were tested on a detached pod assay againstC. perniciosa. The screening procedure used proved to be fast and inexpensive, allowing the selection of five actinomycetes as the most promising isolates for the biocontrol ofC. perniciosa. Under laboratory conditions the actinomycetes were able to inhibit 100% ofC. perniciosa basidiospore germination. However, under field conditions the selected actinomycetes were unable to protect cacao pods against both pathogens. In these experiments, inhibition ofC. perniciosa ranged from 6% to 21% in relation to the control, whereas there was no inhibition of black pod caused byP. palmivora. Formulations need to be improved in order to enhance the activity of the actinomycetes against cacao pathogens in the field. Molecular identification of the selected isolates showed that they are species of the genusStreptomyces.     

<Emphasis Type="Italic">Pythium</Emphasis> and <Emphasis Type="Italic">Phytophthora</Emphasis> species associated with root and stem rots of kalanchoe

Pythium and Phytophthora species were isolated from kalanchoe plants with root and stem rots. Phytophthora isolates were identified as Phytophthora nicotianae on the basis of morphological characteristics and restriction fragment length polymorphism (RFLP) analysis of the rDNA-internal transcribed spacer regions. Similarly, the Pythium isolates were identified as Pythium myriotylum and Pythium helicoides. In pathogenicity tests, isolates of the three species caused root and stem rots. Disease severity caused by the Pythium spp. and Ph. nicotianae was the greatest at 35°–40°C and 30°–40°C, respectively. Ph. nicotianae induced stem rot at two different relative humidities (60% and >95%) at 30°C. P. myriotylum and P. helicoides caused root and stem rots at high humidity (>95%), but only root rot at low humidity (60%).     

Potential of Ypt1 and ITS gene regions for the detection of Phytophthora species in a lab‐on‐a‐chip DNA hybridization array

A novel DNA‐chip hybridization assay that uses the ras‐related GTP‐binding protein 1 gene (Ypt1) was developed for the identification of several devastating Phytophthora species. The hybridization was conducted in a portable microfluidic lab‐on‐a‐chip device for fast and accurate detection of 40 Phytophthora, two Pythium and one Phytopythium species. Moreover, the functionality of the Ypt1 region was examined in comparison to an array for the internal transcribed spacer (ITS) region by in silico modelling. The difference in species‐specific capture probe sequences was lower for the ITS than for the Ypt1 region. While ITS‐probes of Phytophthora ramorum, Phytophthora fragariae and Phytophthora lateralis cross‐reacted with up to 11 non‐target species, Ypt1‐probes were specific except for P. fragariae/Phytophthora rubi. First analyses of artificially inoculated Rhododendron leaves successfully demonstrated the usability of the respective capture probes for the Ypt1 and the ras‐related plant protein Rab1a gene region. The on‐chip hybridization enabled the detection of up to 1 pg μL^?1 target DNA depending on the species examined. Due to the complementarity of ITS and Ypt1 genetic features, the use of multiple loci is recommended to identify targets of different taxonomic rank.     

Characterisation and detection of Pythium and Phytophthora species associated with grapevines in South Africa

Replant and decline diseases of grapevines not only cause quantitative and qualitative yield losses, but also result in extra costs when vineyards have to be replanted. This study investigated the role of Pythium and Phytophthora in the decline syndrome in South Africa by determining (1) the species associated with nursery and established vines, and (2) pathogenicity of Ph. sp. niederhauserii and P. vexans relative to known grapevine pathogens. Quantitative real-time PCR (qPCR) assays were also developed for detection of the most prevalent oomycete groups. In total, 26 Pythium and three Phytophthora species were identified from grapevine nurseries and established vineyards. The most common infections in sampled nursery vines were caused by P. vexans (16.7%), followed by P. ultimum var. ultimum (15.0%) and P. irregulare (11.7%). In established vineyards, P. irregulare (18.0%) and P. vexans (6.2%) were also among the three most prevalent species, along with P. heterothallicum (7.3%). Three Phytophthora species were also identified from the sampled established vines, of which Ph. cinnamomi (5.1%) was predominant, followed by Ph. sp. niederhauserii (1.1%). In established vineyards a higher incidence and more diverse species composition was observed in spring and winter, than in summer. Pathogenicity studies showed that some Ph. sp. niederhauserii and P. vexans isolates were as aggressive as the known grapevine pathogens Ph. cinnamomi and P. irregulare. Sensitive qPCR assays were developed for the detection of P. ultimum var. ultimum, P. irregulare, P. vexans and the genus Phytophthora. These assays will be invaluable in limiting pathogen dispersal through screening of nursery material. This is especially important since pathogenic species were also isolated from healthy looking vines in nurseries.     

Characterization of fungi (Fusarium and Rhizoctonia) and oomycetes (Phytophthora and Pythium) associated with apple orchards in South Africa

Several species of fungi and oomycetes including Fusarium, Rhizoctonia, Phytophthora and Pythium have been reported as root pathogens of apple where they contribute to a phenomenon known as apple replant disease. In South Africa, little is known about specific species in these genera and their pathogenicity toward apple. Therefore, these aspects were investigated along with the development and optimization of qPCR tests for detection and quantification of the most virulent oomycete species. In eight investigated orchards, the oomycete Phythophthora cactorum was widely distributed, while nine Pythium species were differentially distributed among the orchards. Pythium irregulare was the most widely distributed and the most virulent species along with P. sylvaticum, P. vexans and Ph. cactorum. Seven binucleate Rhizoctonia anastomosis groups (AGs) were also differentially distributed among the orchards, with the majority appearing to be non-pathogenic while certain AG-I and AG-F isolates exhibited low virulence on apple. In the genus Fusarium, F. oxysporum was widely distributed, but isolates were non-pathogenic. Fusarium solani and F. avenaceum were less frequently encountered, with only some isolates having low virulence. qPCR data obtained from seedling roots inoculated with the most virulent Pythium species (P. irregulare, P. sylvaticum and P. vexans) and the genus Phytophthora were not always reproducible between trials, or isolates of the same species. In general, seedling growth inhibition was associated with the presence of a low amount of pathogen DNA (±40 fg μl⁻¹ to 2 pg μl⁻¹) in roots. Pythium irregulare, although having the lowest DNA concentrations in roots, was the only species for which a significant negative correlation was found between seedling weight and pathogen DNA concentration.     

Improved assessment of mycelial growth stimulation by low doses of mefenoxam in plant pathogenic <Emphasis Type="Italic">Globisporangium</Emphasis> species

Globisporangium Uzuhashi, Tojo & Kakish. (syn. Pythium Pringsheim) species cause many plant diseases, including Pythium damping-off, leaf and fruit blights, and root rots. Fungicide resistant isolates are selected by repeated use of a single active ingredient on infected crops without rotation. Previous studies demonstrated increased pathogenicity and radial growth in a mefenoxam resistant isolate of Pythium aphanidermatum when exposed to sub-lethal doses of fungicides and ethanol. In those studies, reproducibility of in vitro assays was difficult to achieve due to large variations among trials. This study aimed to examine two protocols for improved reproducibility during the assessment of biphasic dose-responses in mefenoxam-resistant isolates of Globisporangium ultimum and G. irregulare. Two different growth related endpoints, total growth area and total dry mass weight, were assessed. Assays were conducted using ten concentrations of mefenoxam ranging from 0.01 to 1,000 μg/ml. Statistically-significant stimulatory effects were observed in the two Globisporangium species using the two growth related endpoints. Because of its better reproducibility, mycelial growth area is recommended as an endpoint for future studies of chemical hormesis on growth of Globisporangium spp.     

Molecular identification and pathogenicity of Rhizoctonia solani and Pythium spp. associated with damping-off disease on baby leafy vegetables in Greece

In the last years, leafy vegetables cultivated as baby leaves have been established in the market and have attracted the interest of consumers throughout the world. During the growing seasons of 2019 and 2020, 97 isolates of Rhizoctonia solani and 112 isolates of Pythium spp. were obtained from baby leaf vegetables exhibited damping-off symptoms. Representative isolates of R. solani from each surveyed plant species were characterized using sequence analysis of the internal transcribed spacer (rDNA-ITS) region. Isolates were identified as belonging to four anastomosis groups (AGs): AG2-1, AG-IB, AG4-HGI and AG4-HGIII. AG4-HGI was the most prevalent group and phylogenetic analysis showed that the isolates were distinctly separated according to their AGs. Pathogenicity among the four AGs on 23 plant species varied considerably, from not susceptible to highly susceptible, while, in general, AGs did not exhibit host specificity. Furthermore, a total of 112 Pythium spp. isolates were obtained. The ITS region and the cytochrome oxidase II (coxII) gene were amplified, and three Pythium spp. were identified (P. ultimum, P. aphanidermatum and P. sylvaticum), which were used further for maximum-likelihood phylogenetic analysis. The pathogenicity of representative isolates was assessed in vitro and in vivo on 10 plant species. In general, all three tested Pythium spp. were virulent when used in vitro, while P. ultimum was the most virulent in vivo. This is the first comprehensive study aimed at determining the occurrence of specific R. solani AGs and Pythium spp. derived from baby leafy vegetables exhibiting damping-off symptoms in Greece.     

Identification and differentiation of Phytophthora by electrophoresis of mycelial proteins and isoenzymes1

Total proteins (both native and denatured) and three isoenzyme systems (esterases, malate dehydrogenases, superoxide dismutases) were analysed for eight Phytophthora species and for eight strains of P. nicotianae. The results obtained showed low intraspecific variability (62-100% of similarity index) for P. nicotianae and allowed the characterization of P. capsici, cinnamomi, cryptogea, megakarya, megasperma, nicotianae, palmivora and citrophthora by the polyacrylamide gel electrophoretic profiles of native proteins and isoenzymes. The interspecific variability between these eight species is high (27-49% of similarity index). The results obtained support the use of these macromolecular criteria as an aid to the identification of Phytophthora spp.     

Diversity of Phytophthora species in natural ecosystems of Taiwan and association with disease symptoms

In 2013 a survey of Phytophthora diversity was performed in 25 natural and seminatural forest stands and 25 rivers in temperate montane and subtropical lowland regions of Taiwan. Using baiting assays, 10 described species and 17 previously unknown taxa of Phytophthora were isolated from 71.5% of the 144 rhizosphere soil samples from 33 of 40 tree species sampled in 24 forest stands, and from 19 rivers: P. capensis, P. citrophthora, P. plurivora, P. tropicalis, P. citricola VII, P. sp. × botryosa‐like, P. sp. × meadii‐like and P. sp. occultans‐like from Clade 2; P. palmivora from Clade 4; P. castaneae and P. heveae from Clade 5; P. chlamydospora and P. sp. forestsoil‐like from Clade 6; P. cinnamomi (Pc), P. parvispora, P. attenuata nom. prov., P. flexuosa nom. prov., P. formosa nom. prov., P. intricata nom. prov., P. × incrassata nom. prov. and P. × heterohybrida nom. prov. from Clade 7; P. sp. palustris and five new hybrid species from Clade 9. The A1 mating type of Pc was widespread in both montane and lowland forests and rarely associated with disease, whereas the A2 mating type was limited to lowland forests and in some cases causing severe dieback. Most other Phytophthora species were not associated with obvious disease symptoms. It is concluded that (i) Taiwan is within the centre of origin of most Phytophthora taxa found, (ii) Pc A2 is an introduced invasive pathogen, and (iii) interspecific hybridizations play a major role in speciation and species radiations in diverse natural ecosystems.     

Identification and pathogenicity of Pythium species causing damping-off of kidney bean

Five Pythium species (Pythium irregulare, P. mamillatum, P. myriotylum, P. spinosum and P. ultimum var. ultimum) were isolated from the hypocotyls and roots of kidney bean plants with damping-off from a commercial field and from experimental plots that have undergone either continuous cropping with kidney bean or rotational cropping with arable crops. In inoculation tests, all five Pythium species were pathogenic to kidney bean. This is the first report of damping-off of kidney bean caused by Pythium species; we named this disease damping-off of kidney bean. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under accession numbers AB291811, AB291944 and AB291945.     

Fungicide resistance in soil-borne Phytophthora species1

Systemic fungicides such as the phenylamides and phosphonates have provided new opportunities for chemical control of soil-borne Phytophthora species. Potential problems in their use include biodegradation in soils, and the emergence of pathogen isolates resistant to these compounds. Resistance to phenylamides is well known in leaf-infecting Oomycetes, but less is known about the development and relative fitness of resistant isolates among populations of soil-borne Phytophthora species. Experiments with P. capsici and P. palmivora have shown that stable resistant and virulent isolates can be selected under laboratory conditions. Some mutants resistant to both metalaxyl and fosetyl-A1 have been recovered, with growth rates and sporulation equivalent to parental wild types. Selected mutants proved able to compete in vivo with fungicide-sensitive wild types in the absence of the compounds. More information is required to fully evaluate the implications of these results for chemical control of soil-borne Phytophthora species in the field. Résistance des Phytophthora du sol aux fongicides     

Damping-off of soybean in southern Brazil can be associated with different species of Globisporangium spp. and Pythium spp.

Damping-off of soybean is a common problem in some fields in southern Brazil. Frequently, Phytophthora sojae has been pointed out as the main causal agent. However, questions were raised as to whether other oomycetes could also be present. Hence, the objectives of this study were to isolate, identify, and determine the pathogenicity and aggressiveness of oomycetes isolated from soybean seedlings. Thirty-three isolates were obtained from 13 fields. Isolates were identified based on morphology and molecular methods. Nine species were recovered: Pythium conidiophorum (n = 14, 42.4%), Globisporangium rostratifingens (n = 7, 21.2%), G. irregulare (n = 2, 6.1%), G. spinosum (n = 1, 3.0%), G. ultimum var. sporangiiferum (n = 2, 6.1%), Pythium acanthicum (n = 2, 6.1%), P. deliense (n = 1, 3.0%), P. inflatum (n = 1, 3.0%), and P. torulosum (n = 3, 9.1%). Pathogenicity and aggressiveness were determined with two soybean cultivars (DM57i52 and NEO530) in a seed rot assay and a root rot assay. All isolates were pathogenic to soybean with variable levels of aggressiveness in both assays. The range of seed disease severity index varied from 7.5 to 100 for DM57i52 and from 23.1 to 100 for NEO530. The mean root disease severity index of the soybean cultivars ranged from 29.4 to 92.8. This is the first official report of G. irregulare, G. rostratifingens, G. spinosum, G. ultimum var. sporangiiferum, P. acanthicum, P. conidiophorum, P. deliense, P. inflatum, and P. torulosum causing damping-off of soybean in the state of Rio Grande do Sul in southern Brazil.     

First report of Phytophthora palmivora as a causal pathogen of citrus brown rot in Japan

A fruit rot, similar to brown rot, occurred on extremely early ripening Satsumas in Saga Prefecture in the early autumn of 1999. A single species of Phytophthora was isolated from the affected fruit. After nonwounding inoculation of healthy fruits of Citrus spp. including Satsuma with the isolated fungus, the fungus was reisolated from fruit with symptoms similar to those in nature. On the basis of its morphology and molecular analysis of the rDNA-internal transcribed spacer regions, the pathogen was identified as P. palmivora. This is the first report of P. palmivora as a causal pathogen of citrus brown rot in Japan.