Species-specific PCR primers for Pythium developed from ribosomal ITS1 region

Chlamydomonas agloeformis from the Ecuadorian Highlands: Nutrients and Bioactive Compounds Profiling and In Vitro Antioxidant Activity

Green microalgae are single-celled eukaryotic organisms that, in recent years, are becoming increasingly important in the nutraceutical, cosmetic, and pharmaceutical fields because of their high content of bioactive compounds. In this study, a particular green microalga was isolated from freshwater highland lakes of Ecuador and morphologically and molecularly identified as Chlamydomonas agloeformis (ChA), and it was studied for nutritional and nutraceutical properties. The phenolic composition and the fatty acids profile of lyophilized cells were determined. The methanolic extract was analyzed for the phenolic compounds profile and the antioxidant capacity by means of in vitro tests. Finally, Human Microvascular Endothelial Cells (HMEC-1) were exploited to explore the capacity of ChA to reduce the endothelial damage induced by oxidized LDL-mediated oxidative stress. The extract showed a good antioxidant ability thanks to the high content in polyphenolic compounds. The observed decrease in HMEC-1 cells endothelial damage also was probably due to the antioxidant compounds present in the extract. Based on the outcomes of our in vitro assays, ChA demonstrated to be a promising source of bioactive compounds possessing exceptional antioxidant capacities which make it a prospective functional food.

Diagnosis of Soybean Diseases Caused by Fungal and Oomycete Pathogens: Existing Methods and New Developments

Soybean (Glycine max) acreage is increasing dramatically, together with the use of soybean as a source of vegetable protein and oil. However, soybean production is affected by several diseases, especially diseases caused by fungal seed-borne pathogens. As infected seeds often appear symptomless, diagnosis by applying accurate detection techniques is essential to prevent propagation of pathogens. Seed incubation on culture media is the traditional method to detect such pathogens. This method is simple, but fungi have to develop axenically and expert mycologists are required for species identification. Even experts may not be able to provide reliable type level identification because of close similarities between species. Other pathogens are soil-borne. Here, traditional methods for detection and identification pose even greater problems. Recently, molecular methods, based on analyzing DNA, have been developed for sensitive and specific identification. Here, we provide an overview of available molecular assays to identify species of the genera Diaporthe, Sclerotinia, Colletotrichum, Fusarium, Cercospora, Septoria, Macrophomina, Phialophora, Rhizoctonia, Phakopsora, Phytophthora, and Pythium, causing soybean diseases. We also describe the basic steps in establishing PCR-based detection methods, and we discuss potentials and challenges in using such assays.

Brassicaceae Fungi and Chromista Diseases: Molecular Detection and Host–Plant Interaction

Brassicaceae plants cover a large number of species with great economic and nutritional importance around the world. The production of Brassica spp. is limited due to phytopathogenic fungal species causing enormous yield losses. In this scenario, precise and rapid detection and identification of plant-infecting fungi are essential to facilitate the effective management of diseases. DNA-based molecular methods have become popular methods for accurate plant disease diagnostics and have been used to detect Brassicaceae fungal pathogens. Polymerase chain reaction (PCR) assays including nested, multiplex, quantitative post, and isothermal amplification methods represent a powerful weapon for early detection of fungal pathogens and preventively counteract diseases on brassicas with the aim to drastically reduce the fungicides as inputs. It is noteworthy also that Brassicaceae plants can establish a wide variety of relationships with fungi, ranging from harmful interactions with pathogens to beneficial associations with endophytic fungi. Thus, understanding host and pathogen interaction in brassica crops prompts better disease management. The present review reports the main fungal diseases of Brassicaceae, molecular methods used for their detection, review studies on the interaction between fungi and brassicas plants, and the various mechanisms involved including the application of omics technologies.

Identification and Characterization of Isolates of Pythium and Phytophthora spp. from Snap Beans with Cottony Leak

Cottony leak is an important disease of snap bean in Oklahoma and nearby states. Oomycete pathogens isolated from diseased pods collected from commercial fields and research plots consisted of both Pythium spp. (n = 131) and Phytophthora spp. (n = 46). Isolates were identified to species by morphological characteristics and by sequencing a portion of the internal transcribed spacer region of representative isolates. The most common Pythium spp. were Pythium ultimum var. ultimum; Pythium 'group HS', a self-sterile form of P. ultimum that produces hyphal swellings in lieu of sporangia (n = 74); and P. aphanidermatum (n = 50). Phytophthora spp. included Phytophthora drechsleri (n = 41) and P. nicotianae (n = 5). Nearly all of the isolates (95%) and all species were pathogenic on detached pods but Pythium ultimum var. ultimum and Pythium 'group HS' were most aggressive. Phytophthora drechsleri was most aggressive on seedlings, causing preemergence damping off and seed rot. Pythium ultimum var. ultimum, Pythium 'group HS', and P. aphanidermatum were intermediate in virulence to seedlings, causing root rot, stunting, and limited postemergence damping off. Phytophthora nicotianae and Pythium diclinum (n = 4) were not pathogenic on seedlings. Most (87%) isolates were sensitive to metalaxyl-M (concentration that caused a 50% reduction in mycelial growth [EC₅₀] < 1 μg/ml) and the rest were intermediate in sensitivity (EC₅₀ > 1 to < 100 μg/ml). Phytophthora drechsleri was the most sensitive species (EC₅₀ = 0.06 μg/ml) compared with Pythium aphanidermatum, which was least sensitive (EC₅₀ = 1.3 μg/ml). Cottony leak is a disease complex caused by several oomycete species that should include Phytophthora drechsleri, a newly reported pathogen of snap bean in the United States.

Systemic acquired resistance in moss: further evidence for conserved defense mechanisms in plants

Vascular plants possess multiple mechanisms for defending themselves against pathogens. One well-characterized defense mechanism is systemic acquired resistance (SAR). In SAR, a plant detects the presence of a pathogen and transmits a signal throughout the plant, inducing changes in the expression of various pathogenesis-related (PR) genes. Once SAR is established, the plant is capable of mounting rapid responses to subsequent pathogen attacks. SAR has been characterized in numerous angiosperm and gymnosperm species; however, despite several pieces of evidence suggesting SAR may also exist in non-vascular plants^6–8, its presence in non-vascular plants has not been conclusively demonstrated, in part due to the lack of an appropriate culture system. Here, we describe and use a novel culture system to demonstrate that the moss species Amblystegium serpens does initiate a SAR-like reaction upon inoculation with Pythium irregulare, a common soil-borne oomycete. Infection of A. serpens gametophores by P. irregulare is characterized by localized cytoplasmic shrinkage within 34 h and chlorosis and necrosis within 7 d of inoculation. Within 24 h of a primary inoculation (induction), moss gametophores grown in culture became highly resistant to infection following subsequent inoculation (challenge) by the same pathogen. This increased resistance was a response to the pathogen itself and not to physical wounding. Treatment with β-1,3 glucan, a structural component of oomycete cell walls, was equally effective at triggering SAR. Our results demonstrate, for the first time, that this important defense mechanism exists in a non-vascular plant, and, together with previous studies, suggest that SAR arose prior to the divergence of vascular and non-vascular plants. In addition, this novel moss – pathogen culture system will be valuable for future characterization of the mechanism of SAR in moss, which is necessary for a better understanding of the evolutionary history of SAR in plants.

Development and application of a loop-mediated isothermal amplification assay for rapid detection of Pythium helicoides

Root rot of poinsettia, caused by Pythium helicoides at high temperatures in hydroponic cultures, has become a serious problem in many parts of the world. We have developed a species-specific, loop-mediated isothermal amplification (LAMP) assay for the rapid diagnosis of this pathogen. The primers were designed using the ribosomal DNA internal transcribed spacer sequence. Primer specificity was established using 40 Pythium species including P. helicoides, 11 Phytophthora species, and eight other soil-borne pathogens. A sensitivity test was carried out using genomic DNA extracted from P. helicoides, and the detection limit was c. 100 fg which is comparable to that of the polymerase chain reaction (PCR). In addition, we tested the ease of pathogen detection in poinsettia roots. The LAMP results were consistent with those from the conventional plating method and showed more sensitivity than the PCR results. Consequently, the LAMP method developed in this study is effective for the rapid and easy detection of P. helicoides.

Development of loop-mediated isothermal amplification assay for the detection of Pythium myriotylum

This study reports the development of a loop-mediated isothermal amplification (LAMP) reaction for the detection of Pythium myriotylum. The primer set targeting the ITS sequence of P. myriotylum worked most efficiently at 60°C and allowed the detection of P. myriotylum DNA within 30 min by fluorescence monitoring using a real-time PCR instrument. The peak denaturing temperature of amplified DNA was about 87·0°C. In specificity tests using eight Pythium myriotylum strains, 59 strains from 39 species of Pythium, 11 Phytophthora strains and eight other soil-borne pathogens, LAMP gave no cross-reactions. The detection limit was 100 fg of genomic DNA, which was as sensitive as PCR. LAMP could detect P. myriotylum in hydroponic solution samples, and the results coincided with those of the conventional plating method in almost all cases. The LAMP method established in this study is a simple and sensitive tool for the detection of P. myriotylum.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows the first LAMP assay for the detection of Pythium myriotylum. The primer set designed from ITS region of P. myriotylum can detect the pathogen in field sample with a fast and convenient method. Analysis of the annealing curve of the LAMP reaction products increases the reliability of the LAMP diagnosis. This study shows that the diagnostic method using the LAMP assay is useful for monitoring P. myriotylum in the field.

Species-specific PCR-DGGE markers to distinguish Pyrenophora species associated to cereal seeds

Pyrenophora species, toxigenic cereal pathogens, and causal agents of leaf and kernel diseases, bring about economic and food safety concerns. Traditionally, Pyrenophora taxa have been identified microscopically after a period of incubation on culture media. In this study, a simple nested PCR-denaturing gel electrophoresis (DGGE) method was developed to detect, differentiate and identify six Pyrenophora species in plant tissues. A primer, specific to Pyrenophora species and able to amplify a fragment of the ribosomal RNA (rRNA), following first round amplification with universal ITS primers, was designed by reviewing Pyrenophora ribosomal DNA sequences deposited in GenBank. The specificity of the primer was assessed by submitting its sequence to the GenBank Basic Local Alignment Search Tool (BLAST) algorithm, and was also tested with DNA extracted from several ascomycetous, basidiomycetous, and zygomycetous taxa. No PCR product was obtained from non-Pyrenophora species. PCR amplification of DNA extracted from pure cultures of the different Pyrenophora species generated amplicons of an approximate 350bp. DGGE effectively separated between all six Pyrenophora amplicons. Subsequently, amplicons of known Pyrenophora species were used as molecular markers when Pyrenophora infected wheat seed was analyzed by PCR-DGGE. The molecular-based approach described herein can be used to identify different Pyrenophora species directly from infected plant material.

Transstadial transmission of Pythium in Bradysia impatiens and lack of adult vectoring capacity

Fungus gnats have been shown to transmit a variety of plant-pathogenic fungi that produce aerial dispersal stages. However, few studies have examined potential interactions between fungus gnats and oomycetes, including Pythium spp. A series of laboratory experiments were conducted to determine whether fungus gnat adults are vectors of several common greenhouse Pythium spp., including Pythium aphanidermatum, P. irregulare, and P. ultimum. An additional objective was to determine whether P. aphanidermatum can be maintained transstadially in the gut of a fungus gnat larva through the pupal stadium to be transmitted by the subsequent adult. Adult fungus gnats did not pick up infectious Pythium propagules from diseased plants and transmit them to healthy plants in any experiment. Species-specific primers and a probe for real-time polymerase chain reaction were developed to detect the presence of P. aphanidermatum DNA in fungus gnat tissue samples. P. aphanidermatum DNA was detectable in the larval and pupal stages; however, none was detected in adult fungus gnats. These results are in agreement with previous studies that have suggested that adult fungus gnats are unlikely vectors of Pythium spp.

Applicability of the 16S-23S rDNA internal spacer for PCR detection of the phytostimulatory PGPR inoculant Azospirillum lipoferum CRT1 in field soil

AIMS

To assess the applicability of the 16S-23S rDNA internal spacer regions (ISR) as targets for PCR detection of Azospirillum ssp. and the phytostimulatory plant growth-promoting rhizobacteria seed inoculant Azospirillum lipoferum CRT1 in soil.

METHODS AND RESULTS

Primer sets were designed after sequence analysis of the ISR of A. lipoferum CRT1 and Azospirillum brasilense Sp245. The primers fAZO/rAZO targeting the Azospirillum genus successfully yielded PCR amplicons (400-550 bp) from Azospirillum strains but also from certain non-Azospirillum strains in vitro, therefore they were not appropriate to monitor indigenous Azospirillum soil populations. The primers fCRT1/rCRT1 targeting A. lipoferum CRT1 generated a single 249-bp PCR product but could also amplify other strains from the same species. However, with DNA extracts from the rhizosphere of field-grown maize, both fAZO/rAZO and fCRT1/rCRT1 primer sets could be used to evidence strain CRT1 in inoculated plants by nested PCR, after a first ISR amplification with universal ribosomal primers. In soil, a 7-log dynamic range of detection (10(2)-10(8) CFU g(-1) soil) was obtained.

CONCLUSIONS

The PCR primers targeting 16S-23S rDNA ISR sequences enabled detection of the inoculant A. lipoferum CRT1 in field soil.

SIGNIFICANCE AND IMPACT OF THE STUDY

Convenient methods to monitor Azospirillum phytostimulators in the soil are lacking. The PCR protocols designed based on ISR sequences will be useful for detection of the crop inoculant A. lipoferum CRT1 under field conditions.

The Pythium - Fusarium root disease complex - an emerging constraint to irrigated maize in southern New South Wales

A pathogen-selective fungicide trial was established at a site with a history of continuous maize cultivation with stubble retention to assess the impacts of Pythium, Fusarium and Rhizoctonia root diseases on maize productivity. High soilborne populations of Pythium and Fusarium were detected at sowing, with no significant differences in their distributions across the site. Significant increases in Fusarium and Pythium isolates were recovered from maize rhizosphere soils after the first 12 weeks of crop growth. While no isolates of phytopathogenic Rhizoctonia were recovered from soil or maize roots, 63 and 100% of roots examined were colonised by Pythium and Fusarium spp., respectively. Fungicides were, therefore, ineffective in suppressing rhizosphere fungal populations and inhibiting root infection and disease development. As a result, there were no significant increases in crop establishment, early crop growth (biomass) or grain yields with any of the pathogen-selective treatments. DNA sequencing identified six Pythium and five Fusarium spp. from infected maize roots (internal transcribed spacer 5.8s rDNA) and rhizosphere soils (rDNA and translation elongation factor-1α). These species have previously been reported as saprophytes on crop residues and as components of a root-disease complex contributing to seedling damping-off and root and stem rots of maize. Growth responses of rotation crops grown in natural and sterilised continuous maize soil indicated that soilborne root pathogens significantly reduced biomass production of maize and wheat, but not Adzuki bean and canola. Fungal isolation frequencies from these crops implied host-mediated selection of Pythium but not Fusarium spp., the former showing a preference for and greater pathogenicity towards maize and wheat.

Identification and Quantification of Pathogenic Pythium spp. from Soils in Eastern Washington Using Real-Time Polymerase Chain Reaction

ABSTRACT Traditional methods of quantifying Pythium spp. rely on the use of selective media and dilution plating. However, high variability is inherent in this type of enumeration and counts may not be representative of the pathogenic population of Pythium spp. Variable regions of the internal transcribed spacer of the rDNA were used to design species-specific primers for detection and quantification of nine Pythium spp. from soils in eastern Washington. Primer pairs were designed for Pythium abappressorium, P. attrantheridium, P. heterothallicum, P. irregulare group I, P. irregulare group IV, P. paroecandrum, P. rostratifingens, P. sylvaticum, and P. ultimum and used with real-time polymerase chain reaction. Standard curves were generated for each of the species using SYBR Green I fluorescent dye for detection of amplification. Seventy-seven isolates of Pythium were screened to confirm specificity of each primer set. DNA was extracted from soil and standard curves were generated for P. irregulare group I, P. irregulare group IV, and P. ultimum to correlate populations of each species in the soil with quantities of DNA amplified from the same soil. Examination of raw field soils revealed results similar to those observed in previous studies. This new technique for the quantification of Pythium spp. is rapid and accurate, and will be a useful tool in the future study of these pathogenic Pythium spp.

Single-strand conformational polymorphism analysis of the ribosomal internal transcribed spacer 1 for rapid species identification within the genus Pythium

Single-strand conformational polymorphism (SSCP) of the ribosomal internal transcribed spacer 1 (ITS-1) was characterized for 58 isolates of Pythium, representing 41 species from the five groups of Plaats-Niterink. Thirty-one species each produced a distinct SSCP pattern. Three species produced more than one unique pattern, corresponding to morphological subgrouping. The remaining seven species produced three distinct patterns with two or three morphologically similar species sharing a pattern. A successful blind test with four samples and the identification of eight previously unknown isolates from irrigation water demonstrated the reliability of this technique for species identification. Each SSCP pattern was defined and described by the positions of the top and bottom bands and the number of bands in between, which allows laboratories to use this technique without need to access the type isolates of Pythium species.

Direct colony PCR-SSCP for detection of multiple pythiaceous oomycetes in environmental samples

Colony PCR was developed for detection of pythiaceous species recovered on selective agar plates without DNA extraction. A minute amount of mycelia from a single colony was picked up with a pipette tip and added directly to the PCR mix as template for DNA amplification. Successful amplification was achieved in over 95% of the colonies recovered from plant tissues, irrigation water and soil with species-specific primers or oomycete ITS-1 primers. PCR was inhibited in the case of colonies emerging from unwashed pine bark potting mix plates. Direct colony PCR with ITS-1 primers combined with single-strand conformation polymorphism analysis (SSCP) was used to determine population levels of single and multiple species in plant and environmental samples. Application of this technique for disease diagnosis and monitoring pathogen sources was explored, and the potential for studying diversity and population dynamics of other cultivated microbial communities in the environment is discussed.

Molecular phylogeny and taxonomy of the genus Pythium

The phylogeny of 116 species and varieties of Pythium was studied using parsimony and phenetic analysis of the ITS region of the nuclear ribosomal DNA. The D1, D2 and D3 regions of the adjacent large subunit nuclear ribosomal DNA of half the Pythium strains were also sequenced and gave a phylogeny congruent with the ITS data. All the 40 presently available ex-type strains were included in this study, as well as 20 sequences of recently described species from GenBank. Species for which no ex-type strains were available were represented by either authentic strains (6), strains used in the 1981 monograph of the genus by van der Plaats-Niterink (33), or strains selected on morphological criteria (17). Parsimony analysis generated two major clades representing the Pythium species with filamentous or globose sporangia. A small clade of species with contiguous sporangia was found in between the two main clades. A total number of 11 smaller clades was recognized, which often correlated with host-type or substrate and in several cases with a subset of morphological characters. Many characters used in species descriptions, such as antheridium position, did not correlate with phylogeny. A comparison of the ex-type and representative strains with all ITS sequences of Pythium in GenBank revealed limited infraspecific variation with the exception of P. rostratum, P. irregulare, P. heterothallicum, and P. ultimum. The total number of species examined was 116 (including 60 ex-type strains). Twenty-six species had ITS sequences identical or nearly identical to formerly described species, suggesting possible conspecificity. The importance of comparing ITS sequences of putative new species to the now available ITS database in order to avoid unwarranted new species names being introduced.