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Number of nucleotide differences in the internal transcribed spacer (ITS) and cytochrome oxidase (cox) DNA regions of Pythium and Phyto- pythium isolates from recycling ebb-and-flood irrigation water in two com- mercial greenhouses as compared with their closest relative in The Barcode of Life Data System (Ratnasingham and Hebert 2007)
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Two commercial greenhouses producing potted plants in Pennsylvania using recycled irrigation water in an ebb-and-flood system have incurred significant crop losses due to Pythium aphanidermatum. In cooperation with the greenhouses, one or more of their water tanks was monitored continuously (128 tank samplings) for Pythium spp. by baiting. Nine spe...
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Context 1
... total, nine Pythium and three Phytopythium spp. representing clades A, B, E, and K (Table 2) were discovered, but P. aphanidermatum was not found in any tank. The Pythium spp. ...Context 2
... number of nucleotide differences in the ITS and cox DNA regions from their closest match on BOLD is shown in Table 2. It is apparent that the species we confidently identified had few nucleotide differences and that the putative new species have a greater number of nucleotide differences from their closest relative. ...Similar publications
Pythium s.l. is an ecologically important taxon of the phylum Oomycota that lives in
terrestrial and aquatic ecosystems as saprobes. Many species are facultative parasites of plants, causing losses worldwide. Thirty-six putative isolates of the genus from the District Bajaur were characterised morphologically and molecularly during the present stu...
Citations
... Oomycetes are also called "water molds," and most of the species in this group are found in aquatic habitats (Li et al. 2014;Link et al. 2002). These two species of Phytopythium are abundantly found in greenhouse irrigation water tanks (Choudhary et al. 2016;Parke et al. 2019), hydroponic systems (Gonçalves et al. 2016;Kanjanamaneesathian et al. 2013;Teixeira et al. 2006), ebb and flow irrigation systems , and natural rivers and reservoirs used as a source of agricultural irrigation (Hon-Hing et al. 2012;Nam and Choi 2019). ...
... P. helicoides was first documented to be present in natural forest soils of the Southeastern United States in 1968 (Hendrix and Campbell 1968). Diseases caused by P. helicoides were reported on cultivated plants in Asia (Japan Kageyama et al. 2002;Kato et al. 2013;Miyake et al. 2014;Miyazaki et al. 2009;Tsukiboshi et al. 2007;Watanabe et al. 2007], India [Roy and Hong 2008], Taiwan [Huang 2009], Korea [Han et al. 2010], China Wang et al. 2015], Turkey [Avan et al. 2020], and Iran [Azizi et al. 2013]), South America (Brazil [Gonçalves et al. 2016;Teixeira et al. 2006]), Oceania (New Zealand [Kanjanamaneesathian et al. 2013]), and North America (various states of the United States, including Florida [Chellemi et al. 2000;Marin et al. 2019;Rosskopf et al. 2005], Virginia [Yang et al. 2013], California [Fichtner et al. 2016], Pennsylvania [Choudhary et al. 2016], and South Carolina [Toporek and Keinath 2020]) (Fig. 2). ...
Phytopythium vexans and Phytopythium helicoides are important waterborne plant pathogens causing root and crown rot disease in plants from different families ( P. vexans = 19 and P. helicoides = 18) worldwide. The main objective of this diagnostic guide is to provide detailed information about symptoms and signs of root and crown rot disease, host range, geographic distribution, pathogen isolation, conventional and molecular identification, storage, and pathogenicity testing, and present a reliable zoospore production procedure for these pathogens. This guide is aimed at facilitating the detection and identification of these pathogens in the field and laboratory, and the zoospore production procedure is anticipated to help in further investigations and development of different management strategies.
[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
... The oomycete P. chamaehyphon (previously known as Pythium chamaehyphon and Ovatisporangium chamaehyphon) has been reported to cause damping-off on seedlings of Anacardium excelsum (wild cashew), and Tetragastris panamensis (kerosin) (Davidson et al., 2000). Recent reports indicate that P. chamaehyphon is associated with potted floricultural crop losses ocurring in commercial greenhouses in Pennsylvania, USA and with the Kiwifruit Vine Decline Syndrome (KVDS) in Italy (Choudhary et al., 2016;Savian et al., 2021). Based on molecular and phylogenetic analyses, the isolated oomycetes were identified as P. chamaehyphon. ...
Taro (Colocasia esculenta) is a food cropcultivated in tropical areas of the world. However, whenuncultivated, taro is considered an invasive plant speciesdue to its ability to colonize aquatic and semi-aquaticareas and replace native plants. Disease symptoms wereobserved on uncultivated taro growing in water-saturated soil at the Bluebonnet Swamp Nature Center,Baton Rouge, Louisiana, USA. Symptoms consisted ofcorm and root rot, dead leaves, and wilting petioles.Roots samples from affected plants were collected andplated on corn meal agar amended with antibiotics.Mycelium growing on the plates were transferred toplates containing V8 juice agar. Examinations of themycelia revealed ovoid sporangia, and coenocytic hy-phae which suggested an oomycete. To determine theidentity of the putative oomycete, DNA was extractedand used in PCR reactions. PCR products were se-quenced and compared with sequences in the GenBankdatabase using BLASTn. Based on results of molecularand phylogenetic analyses, the isolated oomycete wasidentified asPhytopythium chamaehyphon.
... helicoides, and Phy. chamaehyphon (Choudhary et al. 2016), but the full list is undoubtedly much longer. In many species, resistance was repeatedly documented and in different parts of the world as well. ...
Upon its discovery and implementation in plant protection, metalaxyl became one of the most important fungicides against Phytophthora infestans, but its efficiency has also been proven against other soil pathogens of the class Peronosporomycetes. The most important genus – Phytophthora comprises more than 150 plant pathogens, which cause significant losses in crop production or damage to natural plant associations. Many species of related genera Pythium, Phytopythium and Globisporangium have a similar ability as the species of Phytophthora. Those pathogens are able to quickly spread in wet soils by actively movable zoospores or in the air by means of zoosporangia; they are able to persist in an environment for long periods once they are introduced into the locality, having durability from their resting structures (chlamydospores, hyphal swelling and oospores). Metalaxyl has proven to be very efficient against these pathogens. However, shortly after its release, the rapid development of resistance against this compound was recorded in many species of the class Peronosporomycetes. Such easily developed resistance is due to the monogenic nature of the resistance, which also determines any anti-resistant strategies. The solution of this issue rests in the cautious use of metalaxyl, with consideration given to these strategies, and should be based also on precise information about the environment and the present pathogenic agents.
... significant, causing up to 60%-100% of yield losses depending on the environmental conditions (Adeniyi, 2019). However, other oomycetes remain under-studied, even though different genera have been frequently found in other crops causing damping-off, root damage, and other diseases (Choudhary et al., 2016). Thus, it is very possible that they are also present in cacao crops, possibly affecting them. ...
... The genus Phytopythium was present not only in soil and roots, where it is typically found (Choudhary et al., 2016), but was also isolated from samples of necrotic leaves and vascular section of stems with canker. This is an interesting result because it indicates this species has a role in diseases commonly associated with Phytophthora spp. ...
The study of oomycetes associated with crops is highly important due to the economic losses they might cause. In cacao, the genus Phytophthora has been extensively studied, but little is known about other genera and species of oomycetes associated with this plant. This study aimed to determine the oomycetes’ diversity present in Colombian cacao crops. A total of 146 isolates were obtained from diseased plants and soil in 11 departments. Analysis of ITS and coxI sequences was performed along with the assessment of morphological characteristics. Nine species were identified distributed in four genera: Phytophthora (P. palmivora (54%), P. nicotianae (1%)), Phytopythium (Phy. chamaehyphon (15%), Phy. cucurbitacearum (9%), Phy. vexans (7%), Phy. helicoides (1%)), Globisporangium (G. splendens (3%)), and Pythium (Py. deliense (1%), Py. inflatum (1%)). Additionally, an unidentified and possibly new species of Phytophthora (5%) and three unidentified species of Phytopythium (3%) were found. This is the first report of Globisporangium, Phytopythium, and Pythium, in cacao crops of Colombia and the first report of the species Phytopythium chamaehyphon in the country. Interestingly, some isolates of Phytopythium sp. were isolated from necrotic leaves and vascular section of stems which may suggest a role in cacao diseases traditionally associated with Phytophthora. Also, it is proposed that the new species of Phytophthora may be contributing significantly to black pod disease in Colombian cacao crops, and we highlight that the study of P. palmivora is urgent because of its distribution all over the country.
... The latter demonstrates that the heterogeneity of environmental conditions has likely contributed to the observed differences in richness and composition of fungal communities in different forest nurseries (Figures 1 and 2; Tables 2 and 3). This is in agreement with similar studies on aquatic fungi for which the diversity and composition may change depending on the source, location, and time of the year [52][53][54][55]. Indeed, as the sampling at different sites was carried out both in the autumn (Anykščiai, Kretinga and Dubrava) and in the spring (Trakai) ( Table 1), the possibility should not be excluded that this has also contributed to the observed variation in richness and the composition of fungal communities among different forest nurseries. ...
... Alternatively, this can partly be due to PCR biases that selected for shorter fragments of fungal DNA. Nevertheless, the oomycete diversity in the irrigation water may change depending on environmental conditions and the time of the year, as these factors may affect the survival and activity of individual taxa, and thus, may affect the degree of plant infections [6,16,[52][53][54][55]75,76]. ...
The aim of the present study was to assess fungal and oomycete communities in the irrigation water of forest nurseries, focusing on plant pathogens in the hope of getting a better understanding of potential pathogenic microorganisms and spreading routes in forest nurseries. The study sites were at Anykščiai, Dubrava, Kretinga and Trakai state forest nurseries in Lithuania. For the collection of microbial samples, at each nursery five 100-L water samples were collected from the irrigation ponds and filtered. Following DNA isolation from the irrigation water filtrate samples, these were individually amplified using ITS rDNA as a marker and subjected to PacBio high-throughput sequencing. Clustering in the SCATA pipeline and the taxonomic classification of 24,006 high-quality reads showed the presence of 1286 non-singleton taxa. Among those, 895 were representing fungi and oomycetes. The detected fungi were 57.3% Ascomycota, 38.1% Basidiomycota, 3.1% Chytridiomycota, 0.8% Mucoromycota and 0.7% Oomycota. The most common fungi were Malassezia restricta E. Guého, J. Guillot & Midgley (20.1% of all high-quality fungal sequences), Pezizella discreta (P. Karst.) Dennis (10.8%) and Epicoccum nigrum Link (4.9%). The most common oomycetes were Phytopythium cf. citrinum (B. Paul) Abad, de Cock, Bala, Robideau, Lodhi & Lévesque (0.4%), Phytophthora gallica T. Jung & J. Nechwatal (0.05%) and Peronospora sp. 4248_322 (0.05%). The results demonstrated that the irrigation water used by forest nurseries was inhabited by a species-rich but largely site-specific communities of fungi. Plant pathogens were relatively rare, but, under suitable conditions, these can develop rapidly, spread efficiently through the irrigation system and be a threat to the production of high-quality tree seedlings.
... Evidence for plant pathogenicity of P. litorale is mixed. Phytopythium litorale is commonly isolated from irrigation ponds in Georgia where it was shown to cause seedling damping-off and fruit rot of squash (Cucurbita pepo) (Parkunan and Ji, 2013), but isolates from greenhouse water tanks in Pennsylvania were not pathogenic in assays with geranium (Pelargonium ·hortorum) seedlings (Choudhary et al., 2016). It is not known if P. litorale is causing disease in Nursery B. ...
Phytophthora species cause crop losses and reduce the quality of greenhouse and nursery plants. Phytophthora species can also be moved long distances by the plant trade, potentially spreading diseases to new hosts and habitats. Phytosanitary approaches based on quarantines and endpoint inspections have reduced, but not eliminated, the spread of Phytophthora species from nurseries. It is therefore important for plant production facilities to identify potential sources of contamination and to take corrective measures to prevent disease. We applied a systems approach to identify sources of contamination in three container nurseries in Oregon, California, and South Carolina. Surface water sources and recaptured runoff water were contaminated with plant pathogenic species at all three nurseries, but one nursery implemented an effective disinfestation treatment for recycled irrigation water. Other sources of contamination included cull piles and compost that were incorporated into potting media, infested soil and gravel beds, used containers, and plant returns. Management recommendations include preventing contact between containers and contaminated ground, improving drainage, pasteurizing potting media ingredients, steaming used containers, and quarantine and testing of incoming plants for Phytophthora species. These case studies illustrate how recycled irrigation water can contribute to the spread of waterborne pathogens and highlight the need to implement nursery management practices to reduce disease risk.
... Therefore, knowing about their response to fungicides is important. Phytopythium sp. is commonly found in water tanks and areas with irrigation of water (Choudhary et al. 2016). Isolates of Phytopythium sp. ...
... Isolates of Phytopythium sp. highly sensitive (Choudhary et al. 2016;Radmer et al. 2017), intermediate (Choudhary et al. 2016), and insensitive to mefenoxam (Demott 2015) have been reported. Thus, knowledge on the sensitivity of this species to this fungicide is relevant. ...
... Isolates of Phytopythium sp. highly sensitive (Choudhary et al. 2016;Radmer et al. 2017), intermediate (Choudhary et al. 2016), and insensitive to mefenoxam (Demott 2015) have been reported. Thus, knowledge on the sensitivity of this species to this fungicide is relevant. ...
Phytophthora infestans is the causal agent of late blight disease of potatoes and tomatoes. This disease causes devastating economic losses each year, and control is mainly achieved by the use of fungicides. Unfortunately, populations of P. infestans resistant to fungicides have been documented. Furthermore, studies have reported that sensitive isolates to the phenylamide fungicide, mefenoxam, become less sensitive in vitro after a single passage through sublethal concentrations of fungicide-amended medium. The first objective of this study was to investigate if isolates of P. infestans are capable of acquiring resistance to two additional systemic fungicides, fluopicolide (benzamide) and cymoxanil (cyanoacetamide-oxime). In contrast to the situation with mefenoxam, exposure of isolates to sublethal concentrations of fluopicolide and cymoxanil did not induce reduced sensitivity to these two fungicides. The second objective was to assess if reduced sensitivity to mefenoxam could occur in naturally sensitive isolates of other Phytophthora species and of Phytopythium sp., another oomycete plant pathogen. All Phytophthora spp. assessed (P. infestans, P. betacei, and P. pseudocryptogea) as well as Phytopythium sp. acquired resistance to mefenoxam after previous exposure through medium containing 1 µg ml-1 of mefenoxam. Interestingly, isolate 66 of Phytopythium sp. and the isolate of P. pseudocryptogea tested do not seem to be acquiring resistance to mefenoxam after exposure to medium containing 5 µg ml-1 of this fungicide. The tested isolates of P. palmivora and P. cinnamomi were extremely sensitive to mefenoxam, and thus it was not possible to perform a second transfer to access acquisition of resistance to this fungicide.
... [22], and this fast growth pattern was proved in the present study. Clade A with mainly aquatic species [40,41] was not found in the present study. ...
... cucurbitacearum, but distinguished from Phy. vexans by having larger oogonia and from Phy. cucurbitacearum by having non-papillate sporangia [21]. This species was previously isolated from irrigation water tanks in a greenhouse, with a pathogenicity on greenhouse crops [41]. Note: Isolates W630 and W595 are morphologically similar and phylogenetically close to ex-type strain CBS118360 "Phy. ...
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.
... Some species found in aquatic habitats, especially Phytophthora Clade 6 species, appear to be facultative pathogens or aquatic opportunists that have not been associated with plant disease (Hansen et al. 2012;Jung et al. 2011;Marano et al. 2016;van der Plaats-Niterink 1981). Phytopathogens appear to constitute only a small portion of the total species recovered from streams, rivers, and irrigation water reservoirs (Brazee et al. 2017;Choudhary et al. 2016;Copes et al. 2015;Hong et al. 2012Hong et al. , 2008Loyd et al. 2014;MacDonald et al. 1994;Parke et al. 2014;Yang 2013;Yang and Hong 2013;Yang et al. 2012Yang et al. , 2014Yang et al. , 2016. Genus-level identification of Phytophthora, Pythium, and Phytopythium is therefore insufficient to assess the risks posed to plants. ...
... There are indications that oomycete species diversity in irrigation water may change with source, location, and time of the year, influencing the survival of individual species, and the risk of plant disease Choudhary et al. 2016;Copes et al. 2015;Hong and Moorman 2005;Hong et al. 2008;Loyd et al. 2014;MacDonald et al. 1994;Parke et al. 2014), but the biases of culturebased methods have limited our understanding of how pathogen communities vary in time and space within the nursery irrigation system. ...
Recycling of irrigation water increases disease risks due to spread of waterborne oomycete plant pathogens such as Phytophthora, Pythium and Phytopythium. A comprehensive metabarcoding study was conducted to determine spatial and temporal dynamics of oomycete communities present in irrigation water collected from a creek (main water source), a pond, retention reservoirs, a chlorinated water reservoir, and runoff channels within a commercial container nursery in Oregon over the course of one year. Two methods, filtration and leaf baiting, were compared for the detection of oomycete communities. Oomycete communities in recycled irrigation water were less diverse but highly enriched with biologically active plant pathogens as compared to the creek water. The filtration method captured a larger portion of oomycete diversity, while leaf baiting was more selective for plant-associated oomycete species of Phytophthora and a few Pythium and Phytopythium species. Seasonality strongly influenced oomycete diversity in irrigation water and detection with leaf baiting. Phytophthora was the major colonizer of leaf baits in winter, while all three genera were equally abundant on leaf baits in summer. The metabarcoding approach was highly effective in studying oomycete ecology, however, it failed to distinguish some closely related species. We developed a custom oomycete ITS1 reference database containing shorter sequences flanked by ITS6 and ITS7 primers used in metabarcoding and used it to assemble a list of indistinguishable species complexes and clusters to improve identification. The predominant bait-colonizing species detected in recycled irrigation water were the Phytophthora citricola-complex, P. syringae, P. parsiana-cluster, P. chlamydospora, P. gonapodyides, P. irrigata, P. taxon Oaksoil-cluster, P. citrophthora-cluster, P. megasperma-cluster, Pythium chondricola-complex, Py. dissotocum-cluster, and Phytopythium litorale.
... For example, a plant-indexing propagation operation found municipal water to be the source of Pythium spp. at the facility. Irrigation water drawn from natural water ways and from recycling water basins potentially contain plant pathogens, such as plant pathogenic Erwinia spp., Fusarium spp., Pythium spp., Phytopythium spp., and Phytophthora spp., that may require treatment Del Castillo Múnera and Hausbeck 2015;Elmer 2008;Ghimire et al. 2011;Choudhary et al. 2016;Moorman et al. 2002;Parke and Grunwald 2012). Even with these seemingly risky water sources, water treatment is only required when pathogens capable of causing crop loss are being dispersed in irrigation water. ...
... Recent research results have shown that detection of Pythium spp., Phytopythium spp., and Phytophthora spp. in irrigation water does not confirm a plant pathogen problem Hong and Moorman 2005;Choudhary et al. 2016;Loyd et al. 2014;Parke et al. 2014;Zappia et al. 2014). Unfortunately, these results provide an additional burden for plant producers, because isolates need to be identified to species by qualified plant disease clinics and associated with past or current plant disease problems, or a high potential for disease to determine whether water treatment is required. ...
Sanitation involves efforts aimed to prevent introduction of pathogen propagules into a production facility, remove sources of propagules from active production areas to substantially slow disease development, and eliminate pathogen propagules from future production areas. Sanitation includes many practices such as using disease-free certified seed and propagative material, maintaining weed-free zones around production areas, use of screens to block entry of insects, use of double doors and foot paths, cleaning and sanitizing production areas between crops, sanitizing tools and equipment, and early removal of diseased plant material. General sanitation should be a matter of routine good agricultural practices. Because it is so important to do a thorough job, key sanitation practices should be selected that control the pathogens that routinely affect plants at a facility and those that are prevalent and would severely impact production if introduced. Good records are an important tool to select which pathosystems are problems, to determine cost benefit decisions, and to select subject matter for worker training modules. The information in this chapter represents an overview of methods known to be effective.
