The 18S rDNA sequence of Synchytrium endobioticum and its utility in microarrays for the simultaneous detection of fungal and viral pathogens of potato

Chitosan induces resistance to tuber rot in stored potato caused by Alternaria tenuissima

Alternaria tenuissima infects stored potatoes, and causes tuber rot, resulting in significant economic losses. As a naturally-occurring polysaccharide (poly-β-(1 → 4) N-acetyl-D-glucosamine), chitosan has been reported to be an eco-friendly alternative to synthetic fungicides for the control of postharvest diseases on agricultural commodities. In this study, application of 0.25-1.25 g/L chitosan significantly inhibited spore germination and mycelial growth of A. tenuissima in vitro, with the greatest inhibitory effect observed at the highest concentration. Cytological and biochemical analysis of A. tenuissima spores indicated that exposure to 1.25 g/L chitosan significantly damaged the plasma membrane and increased the level of lipid oxidation. Gene expression analysis in potato tuber revealed that an application of 1.25 g/L chitosan induced the expression of defense-related genes, including catalase, peroxidase, polyphenol oxidase, chitinase and β-1,3-glucanase, and the level of flavonoids and lignin. Chitosan effectively controlled tuber rot caused by A. tenuissima. Collectively, results of the current study indicate that the ability of chitosan to reduce Alternaria rot in stored potato tubers is due to its direct antifungal activity and its ability to induce defense responses in potato tuber tissues. Chitosan may have the potential as a substitute for synthetic fungicides to reduce postharvest losses in potato.

Genomic and Transcriptomic Resources for Marker Development in Synchytrium endobioticum, an Elusive but Severe Potato Pathogen

Synchytrium endobioticum is an obligate biotrophic fungus that causes wart diseases in potato. Like other species of the class Chytridiomycetes, it does not form mycelia and its zoospores are small, approximately 3 μm in diameter, which complicates the detection of early stages of infection. Furthermore, potato wart disease is difficult to control because belowground organs are infected and resting spores of the fungus are extremely durable. Thus, S. endobioticum is classified as a quarantine organism. More than 40 S. endobioticum pathotypes have been reported, of which pathotypes 1(D1), 2(G1), 6(O1), 8(F1), and 18(T1) are the most important in Germany. No molecular methods for the differentiation of pathotypes are available to date. In this work, we sequenced both genomic DNA and cDNA of the German pathotype 18(T1) from infected potato tissue and generated 5,422 expressed sequence tags (EST) and 423 genomic contigs. Comparative sequencing of 33 genes, single-stranded confirmation polymorphism (SSCP) analysis with polymerase chain reaction fragments of 27 additional genes, as well as the analysis of 41 simple sequence repeat (SSR) loci revealed extremely low levels of variation among five German pathotypes. From these markers, one sequence-characterized amplified region marker and five SSR markers revealed polymorphisms among the German pathotypes and an extended set of 11 additional European isolates. Pathotypes 8(F1) and 18(T1) displayed discrete polymorphisms which allow their differentiation from other pathotypes. Overall, using the information of the six markers, the 16 isolates could be differentiated into three distinct genotype groups. In addition to the presented markers, the new collection of EST from genus Synchytrium might serve in the future for molecular taxonomic studies as well as for analyses of the host-pathogen interactions in this difficult pathosystem. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Development of Polymorphic Microsatellite Loci for Potato Wart from Next-Generation Sequence Data

Synchytrium endobioticum is the fungal agent causing potato wart disease. Because of its severity and persistence, quarantine measures are enforced worldwide to avoid the spread of this disease. Molecular markers exist for species-specific detection of this pathogen, yet markers to study the intraspecific genetic diversity of S. endobioticum were not available. Whole-genome sequence data from Dutch pathotype 1 isolate MB42 of S. endobioticum were mined for perfect microsatellite motifs. Of the 62 selected microsatellites, 21 could be amplified successfully and displayed moderate levels of polymorphism in 22 S. endobioticum isolates from different countries. Nineteen multilocus genotypes were observed, with only three isolates from Canada displaying identical profiles. The majority of isolates from Canada clustered genetically. In contrast, most isolates collected in Europe show no genetic clustering associated with their geographic origin. S. endobioticum isolates with the same pathotype displayed highly variable genotypes and none of the microsatellite markers correlated with a specific pathotype. The markers developed in this study can be used to assess intraspecific genetic diversity of S. endobioticum and allow track and trace of genotypes that will generate a better understanding of the migration and spread of this important fungal pathogen and support management of this disease.

Phylogeny of the genus Synchytrium and the development of TaqMan PCR assay for sensitive detection of Synchytrium endobioticum in soil

Potato wart, caused by the fungal pathogen Synchytrium endobioticum, is a serious disease with the potential to cause significant economic damage. The small subunit (SSU) and internal transcribed spacer (ITS) ribosomal DNA (rDNA) were sequenced for several Synchytrium spp., showing a high rate of variability for both of these markers among the different species and monophyly of the genus within phylum Chytridiomycota. The intergenic nontranscribed spacer (IGS) of rDNA was sequenced for different pathotypes and showed no intraspecific variation within S. endobioticum, similar to the other rDNA markers from this study. To facilitate screening for the pathogen in soil, three TaqMan polymerase chain reaction (PCR) assays were developed from SSU, ITS, and IGS rDNA sequences to detect S. endobioticum sporangia in the chloroform-flotation fraction of sieved soil extracts. In the screening portion of the method, a first TaqMan assay targeting the SSU rDNA was developed with positive results that were further confirmed with amplicon melt analysis. A synthetic reaction control cloned into a plasmid was incorporated into the procedure, facilitating the validation of negative results. The presence of the reaction control did not adversely affect the efficiency of the SSU target amplification. A second TaqMan assay targeting the ITS-1 region was developed as a confirmatory test. There was 100% accordance between the SSU and ITS-1 TaqMan assays. Utilizing these two assays in tandem achieved good specificity for S. endobioticum, generating negative results with the cloned SSU and ITS-1 regions from all 14 other Synchytrium spp. considered. Spike recovery experiments indicated that these assays, targeting the SSU and ITS-1 rDNA regions, developed from a phylogeny dataset of the genus, could reliably detect a single sporangium in the chloroform flotation fraction of a soil extract. Good correlation between microscopic detection of sporangia and PCR results in both positive and negative soil samples was dually demonstrated for both the SSU and ITS-1 assays.

Managing potato wart: a review of present research status and future perspective

Identification of resistance genes to potato wart disease caused by Synchytrium endobioticum is the key for developing diagnostic markers for breeding resistant cultivars. We present an overview on the current knowledge of this host-pathogen system and molecular advances while highlighting future research focus. Potato wart is a quarantined disease of cultivated potato (Solanum tuberosum L.) caused by the obligate biotrophic, soil-borne fungus Synchytrium endobioticum (Schilb.) Perc. Since its discovery by Schilberszky in 1896, the management of wart disease was enabled by research efforts focusing on understanding and classifying the causative agent, its mode of infection, pathogenesis, geographical distribution, detection and chemical control, on developing screening methods for host resistance and on genetic analyses, which led to the development of resistant cultivars. These early successes are currently challenged by new S. endobioticum pathotypes evolving and the increased risk of dissemination by potato tuber trade. New research efforts are therefore required to ensure continuation of effective and sustainable management of the potato wart disease. Advances in molecular biology and genomic tools offer potential for innovations. This review presents an overview on what we know about this complex host-pathogen interaction, highlights recent molecular work and embarks on an outlook towards future research directions.

A universal oligonucleotide microarray with a minimal number of probes for the detection and identification of viroids at the genus level

A major challenge in the agricultural industry is the development of techniques that can screen plant samples for viroid infection. Microarrays are promising in this regard, as their high throughput nature can potentially allow for the detection of a range of viroids in a single test. In this paper we present a microarray that can detect a wide spectrum of all 8 reported viroid genera including 37 known plant viroid species. The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viroids at the genus level. The designed microarray showed a high specificity and sensitivity when tested with a set of standard virus samples. Finally, the microarray was applied to screen infected field samples, with Hop stunt viroid infection identified as the major disease causing pathogen for an infected citrus sample.

Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations

BACKGROUND

Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient.

METHODOLOGY/PRINCIPAL FINDINGS

A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS) and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp.) species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta). Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda) are used as medicinal plants.

CONCLUSIONS/SIGNIFICANCE

Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health.

Optimization and improvement of oligonucleotide microarray-based detection of tomato viruses and pospiviroids

Tomato (Solanum lycopersicum L.) is a vegetable crop which is affected by many viruses and several viroids, causing significant economic loss. Their detection and identification is of critical importance for plant protection and quarantine and certification programs. The potential was examined of an array based on the Combimatrix platform for the detection of 37 viruses belonging to 13 families, one of which is unassigned, together with six pospiviroid species, genus Pospiviroid, family Pospiviroidae. More than 470 oligonucleotide probes (40-mer) were selected for the microarray diagnostic technique developed in this investigation. Most of the virus probes were highly specific and were able to identify tomato viruses. Most pospiviroid probes, however, were non-specific in terms of species, but were specific at the genus level as they hybridized to members of the genus Pospiviroid. Only one probe of the Tomato apical stem viroid was species specific. The repeatability and specificity of the Combimatrix method showed that it can be considered for routine diagnostic use in suspected tomato germplasm since it detected 37 viruses and one pospiviroid at the species level and 5-6 pospiviroids at the genus level. The estimated cost for testing of a single tomato virus is similar to or less than the cost of using ELISA.

Amplification-free detection of grapevine viruses using an oligonucleotide microarray

A single-colour microarray hybridization system was designed and evaluated for the detection of viruses infecting grapevine. Total RNA (≥0.5μg) from infected plants was converted to cDNA and labelled with Cy3 using two different strategies. While amine-modified and labelled cDNA was adequate for the detection of nepoviruses, the 3DNA technique, a post-hybridization detection method that uses intensely fluorescent dendrimer reagents, was required for the detection of closteroviruses in infected plants. Threshold detection levels were based on the ratio between viral specific and 18S rRNA positive control signal intensities. Oligonucleotides between 27 and 75 nucleotides in length were evaluated and compared. Viruses detected include eight nepoviruses, two vitiviruses, and one each of closterovirus, foveavirus, ampelovirus, maculavirus and sadwavirus. Results of this work demonstrate the potential of microarray technique to detect viral pathogens without sequence bias amplification of template RNA.

Oligonucleotide microarray with a minimal number of probes for the detection and identification of thirteen genera of plant viruses

A major challenge facing agriculture at present is the development of techniques that can screen field samples and other plant materials simultaneously for the presence of many viruses. Microarray techniques show promise in this regard, as their high throughput nature can potentially detect a range of viruses using a single test. In this paper we present an array that can detect a wide spectrum of 169 plant virus species from 13 different genera. The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viruses at the genus level. The designed arrays showed a high specificity and sensitivity when tested with a set of standard virus samples. Field samples collected from a severe disease outbreak of Panax notoginseng farms in Yunnan, China, in 2001 were screened, where a potyvirus infection was identified associated with the disease.

Rapid and reliable detection of 11 food-borne pathogens using thin-film biosensor chips

Traditional methods for identifying food-borne pathogens are time-consuming and laborious, so it is necessary to develop innovative methods for the rapid identification of food-borne pathogens. Here, we report the development of silicon-based optical thin-film biosensor chips for sensitive detection of 11 food-borne pathogens. Briefly, aldehyde-labeled probes were arrayed and covalently attached to a hydrazine-derivatized chip surface, and then, biotinylated polymerase chain reaction (PCR) amplicons were hybridized with the probes. After washing and brief incubation with an antibiotin immunoglobulin G-horseradish peroxidase conjugate and a precipitable horseradish peroxidase substrate, biotinylated chains bound to the probes were visualized as a color change on the chip surface (gold to blue/purple). Highly sensitive and accurate examination of PCR fragment targets can be completed within 30 min. This assay is extremely robust, sensitive, specific, and economical and can be adapted to different throughputs. Thus, a rapid, sensitive, and reliable technique for detecting 11 food-borne pathogens was successfully developed.

Distinguishing bacterial pathogens of potato using a genome-wide microarray approach

A set of 9676 probes was designed for the most harmful bacterial pathogens of potato and tested in a microarray format. Gene-specific probes could be designed for all genes of Pectobacterium atrosepticum, c. 50% of the genes of Streptomyces scabies and c. 30% of the genes of Clavibacter michiganensis ssp. sepedonicus utilizing the whole-genome sequence information available. For Streptomyces turgidiscabies, 226 probes were designed according to the sequences of a pathogenicity island containing important virulence genes. In addition, probes were designed for the virulence-associated nip (necrosis-inducing protein) genes of P. atrosepticum, P. carotovorum and Dickeya dadantii and for the intergenic spacer (IGS) sequences of the 16S-23S rRNA gene region. Ralstonia solanacearum was not included in the study, because it is a quarantine organism and is not presently found in Finland, but a few probes were also designed for this species. The probes contained on average 40 target-specific nucleotides and were synthesized on the array in situ, organized as eight sub-arrays with an identical set of probes which could be used for hybridization with different samples. All bacteria were readily distinguished using a single channel system for signal detection. Nearly all of the c. 1000 probes designed for C. michiganensis ssp. sepedonicus, c. 50% and 40% of the c. 4000 probes designed for the genes of S. scabies and P. atrosepticum, respectively, and over 100 probes for S. turgidiscabies showed significant signals only with the respective species. P. atrosepticum, P. carotovorum and Dickeya strains were all detected with 110 common probes. By contrast, the strains of these species were found to differ in their signal profiles. Probes targeting the IGS region and nip genes could be used to place strains of Dickeya to two groups, which correlated with differences in virulence. Taken together, the approach of using a custom-designed, genome-wide microarray provided a robust means for distinguishing the bacterial pathogens of potato.

Macroarray Detection of Eleven Potato-Infecting Viruses and Potato spindle tuber viroid

A macroarray was developed for the detection of 11 potato viruses and Potato spindle tuber viroid. The 11 viruses detected included those commonly found or tested for in North American potato seed certification programs: Alfalfa mosaic virus, Cucumber mosaic virus, Potato mop top virus, Potato leafroll virus, Potato latent virus, Potato virus A, Potato virus M, Potato virus S, Potato virus X, Potato virus Y, and Tobacco rattle virus. These viruses were detected using oligonucleotide 70-mer probes and labeled targets prepared by a random primed amplification procedure. Potato plants analyzed included those infected with 12 reference virus stocks and 36 field isolates. Results from the macroarray were entirely consistent with those obtained using a standard serological assay (enzyme-linked immunosorbent assay). Four isolates of Potato spindle tuber viroid, in mixed infection with one or more viruses, also were detected in the array, although strong hybridization signals required amplification with viroid-specific primers in combination with anchored-random primers. In individual plants, up to four viruses, or a viroid plus two viruses, were detected, with no apparent competition or inhibition. Macroarrays are a cost-effective approach to the simultaneous diagnostic detection of multiple pathogens from infected plants.

Simultaneous detection of potato viruses, PLRV, PVA, PVX and PVY from dormant potato tubers by TaqMan real-time RT-PCR

The requirements of sprouting dormant potato tubers for biological or serological assays or RNA extraction for nucleic acid and PCR assays add to the cost of virus screening. Recently, cheaper, reliable and more rapid methods for the screening of potato tuber-seed pieces for viruses have been developed that do not require sprouted tubers for indexing, including TaqMan real-time RT-PCR. Although the assays are often designed for minimal time and reagent use, they still require a time-consuming and laborious RNA extraction step. This paper describes an assay where four common potato-infecting viruses, Potato leafroll virus, Potato virus A, Potato virus X and Potato virus Y, were detected simultaneously from total RNA and saps of dormant potato tubers in a quadruplex real-time RT-PCR. Factors critical for the detection of these viruses in saps of dormant potato tubers included: optimum dilution and inhibition of RNAses, and the optimization of the reverse transcription and PCR steps. Potato virus detection directly from tuber saps was comparable to that from purified total plant RNA, and this represents significant savings of time and expense. The TaqMan system developed in this study detected between 200 and 400 copies of potato virus RNA.

Macroarray Detection of Plant RNA Viruses Using Randomly Primed and Amplified Complementary DNAs from Infected Plants

ABSTRACT Membrane-based macroarrays provide a relatively inexpensive technology with the potential to detect hundreds of pathogens in a single assay. For the simultaneous detection of a large number of pathogens, it is necessary to obtain sufficient nucleic acids for labeling, and any amplification reactions need to be performed using unbiased, pathogen-non-specific primers. A nonradioactive macroarray system is described to test for plant RNA viruses using 70-mer oligonucleotide probes immobilized on nylon membranes. Starting with a total plant RNA extract, complementary DNA (cDNA) and second-strand syntheses were carried out using an anchor primer sequence with random pentamers coupled at the 3' end. Subsequent synthesis by polymerase chain reaction using the anchor primer alone resulted in a relatively unbiased amplification of plant and viral RNAs. These cDNAs were chemically labeled and the product used as a target in hybridization analyses. The system was validated using RNA extracts from plants infected with Cucumber mosaic virus, Potato virus Y, and Potato leaf roll virus (PLRV). Despite the relative excess of host-derived nonviral sequences, viral RNAs were amplified between 100- and 1,000-fold and were detected in single and mixed infections. The macroarray sensitivity was comparable to that of double-antibody sandwich enzyme-linked immunosorbent assay, with PLRV being detected in sap dilutions of 1:100. The potential for the development of a relatively inexpensive multipathogen detection system is discussed.