PCR Amplification of Ribosomal DNA for Species Identification in the Plant Pathogen Genus Phytophthora

We have developed a PCR procedure to amplify DNA for quick identification of the economically important species from each of the six taxonomic groups in the plant pathogen genus Phytophthora. This procedure involves amplification of the 5.8S ribosomal DNA gene and internal transcribed spacers (ITS) with the ITS primers ITS 5 and ITS 4. Restriction digests of the amplified DNA products were conducted with the restriction enzymes RsaI, MspI, and HaeIII. Restriction fragment patterns were similar after digestions with RsaI for the following species: P. capsici and P. citricola; P. infestans, P. cactorum, and P. mirabilis; P. fragariae, P. cinnamomi, and P. megasperma from peach; P. palmivora, P. citrophthora, P. erythroseptica, and P. cryptogea; and P. megasperma from raspberry and P. sojae. Restriction digests with MspI separated P. capsici from P. citricola and separated P. cactorum from P. infestans and P. mirabilis. Restriction digests with HaeIII separated P. citrophthora from P. cryptogea, P. cinnamomi from P. fragariae and P. megasperma on peach, P. palmivora from P. citrophthora, and P. megasperma on raspberry from P. sojae. P. infestans and P. mirabilis digests were identical and P. cryptogea and P. erythroseptica digests were identical with all restriction enzymes tested. A unique DNA sequence from the ITS region I in P. capsici was used to develop a primer called PCAP. The PCAP primer was used in PCRs with ITS 1 and amplified only isolates of P. capsici, P. citricola, and P. citrophthora and not 13 other species in the genus. Restriction digests with MspI separated P. capsici from the other two species. PCR was superior to traditional isolation methods for detection of P. capsici in infected bell pepper tissue in field samples. The techniques described will provide a powerful tool for identification of the major species in the genus Phytophthora.     

Isolation and Partial Characterization of Bacteriophages of the Phytopathogen Pseudomonas syringae

Bacteriophages isolated from culture supernatants of Pseudomonas syringae pv. syringae and from sewage were identified. The DNA from each phage was isolated and digested with the restriction endonuclease EcoRI. Eight isolates were determined to be different, with two phage isolates from sewage having restriction patterns identical to two phages from culture supernatants. The sizes of the phage DNA ranged from 24 to49 kilobases for isolates from sewage and from 39 to 52.5 kilobases for the isolates from culture supernatants. Buoyant densities of phage particles in CsCl varied from 1.498 to 1.507 g/cm³ for isolates from sewage and from 1.506 to 1.516 g/cm³ for isolates from culture supernatants. Electron microscopy revealed four morphological types. Based on plaque-forming ability of culture supernatants, 31 out of 47 strains of P. syringae are probably lysogenic.     

Distribution of Phytophthora citrophthora R.E. Sm. and E.H. Sm. and P. parasitica Dastur within citrus orchards in Kerman province,Iran

In this research, distribution of Phytophthora species were determined in Kerman Province (Bam, Shahdad and Arzuiyeh) during 2004–2007. The Phytophthora species were isolated from infected root, crown and soil. Root and crown pieces were washed and cultured on a CMA-PARPH medium. The isolation from infected soil was performed by bating method using citrus leaves. It was identified by morphological and several physiological characteristics. Distribution of species was determined by recording the number of isolates recovered from samples from each city. In this study, from 220 soil samples collected from 52 citrus orchards, 80 isolates of Phytophthora were recovered. Among of all isolates of Phytophthora, P. parasitica and P. citrophthora were the most important species of causal agent of gummosis on Citrus sp. Distribution of P. citrophthora was highest in Arzuiyeh and lowest in Bam and Shahdad cities, while distribution of P. parasitica was highest in Bam and Shahdad cities. The majority of soil samples contained only P. parasitica, but a few of percentage samples containing P. citrophthora alone and both of fungi in cites samples.     

Behaviour of Phytophthora citrophthora and P. nicotianae var. in soil, and Differences in Their Tolerance to Antimicrobial Components of Selective Media Used for Isolation of Phytophthora spp.

Phytophthora citrophthora was inhibited to a greater extent than P. nicotianac var. parasitica by chloramphenicol, hymexazol, PCNB and pimaricin at concentrations used in selective media for the isolation of Phytophthora spp. Reduced concentrations of the antimicrobial components of the selective media to tolerant levels for P. citrophthora markedly increased the recovery of the two brown rot pathogens from soil. Mycelium of both Phytophthora spp. survived in air-dried soil for at least 5 months while mycelium of most Phytophthora spp. do not survive in dry soil. In moist soil, P. nicotianae var. parasitica produced hyphal swellings, sporangia and chlamydospores. P. citrophthora produced hyphal swellings and sporangia, but no chlamydospores. No oospores were produced, even in pairing cultures on agar plates with isolates obtained from several locations of citrus groves andfruits by both species. Sporania were obtained in both species in citrus groves on mycelium mats, in the rhizosphere, in infected leaves and fruits buried at soil depths of 5–35 cm. Numbers of propagules declined during the incubation period, but conside, rable numbers survived throughout the experimental period (6 months). Although P. nicotianae var. parasitica produced chlamydospores while P. citrophthora did not, numbers of surviving propagules recovered from soil after 6 months were comparable with both species. The brown rot pathogens survived in soil both as colonizers of detached leaves and fruits and as parasites in living root tissues.     

Influence of Fusarium solani on citrus root rot caused by Phytophthora parasitica and Phytophthora citrophthora

Interactions between Fusarium solani and Phytophthora parasitica or F. solani and P. citrophthora influenced the development of root rot of citrus but depended on the temporal order of inoculation with F. solani or the two Phytophthora spp. Inoculation of citrus with either Fusarium solani and Phytophthora parasitica or Phytophthora citrophthora increased root rot compared to inoculation with P. parasitica or P. citrophthora alone when plants were inoculated with Phytophthora by dipping their roots in zoospore suspensions and subsequently transplanted into soil infested with F. solani. However, root rot was not increased by simultaneous co-inoculation of P. parasitica and F. solani or when plants were inoculated with F. solani first. Root rot was not increased when heat-stressed or non-stressed plants were inoculated with P. parasitica 30 days after transplanting into soil infested with F. solani. In most but not all experiments, F. solani alone reduced growth of tops or roots a small but significant amount.Co-inoculation of citrus by root-dipping into zoospore suspensions of P. parasitica and transplanting into soil infested with F. solani reduced feeder root length by 62% and root weight by 61% but did not significantly reduce the percentage of living roots when compared to inoculation with P. parasitica alone. When citrus roots were immersed in zoospore suspensions of P. citrophthora and transplanted into soil infested with F. solani, feeder root length was reduced by 68%, but feeder root weight and the percentage of living roots were not significantly reduced when compared to plants inoculated with P. citrophthora alone.Propagule densities of both P. parasitica and P. citrophthora in the rhizosphere of plants inoculated by root-immersion and then transplanting into soil infested with F. solani were not significantly different than propagule densities from plants transplanted into non-infested soil. Propagule densities of P. parasitica were suppressed an average of 41% when citrus was inoculated with P. parasitica 30 days after transplanting into soil infested with F. solani and by 41% when citrus was co-inoculated by transplanting into soil infested with both F. solani and P. parasitica.     

High temperatures are not responsible for lack of infection of citrus roots by Phytophthora citrophthora during the summer,but suppressive soil microorganisms may inhibit infection by P. citrophthora

In regions with a mediterranean climate such as southern California, P. citrophthora infection of citrus does not normally occur during the summer. However, in this study, P. citrophthora was isolated abundantly from alternative hosts planted in an infested citrus grove, in the middle of the summer. Citrus root infection from P. citrophthora did occur in this study but it was extremely low. Citrus seedlings grown in autoclaved soil from Pauma Valley, artificially infested with P. citrophthora, contained significantly higher levels of infection than seedlings grown in infested, non-autoclaved, soil or in part autoclaved, part non-autoclaved, infested soil. This suggests that the Pauma Valley soil contains microorganisms naturally suppressive to P. citrophthora.The low occurrence of P. citrophthora infection of citrus roots during the summer may be partially due to soil microorganisms associated with the citrus host and not the inability of P. citrophthora to grow well at the soil temperatures found during the summer in southern California.     

Mitochondrial and nuclear DNA diversity within six species ofPhytophthora

The extent of intraspecific mitochondrial DNA (mtDNA) diversity was investigated in isolates ofPhytophthora capsici,P. citricola, P. citrophthora, P. megakarya, P. palmivora, andP. parasitica that represented a wide range of host plants and geographic origins. Phenograms were constructed following the analysis of restriction fragment patterns that were generated by several endonucleases. The six species showed different degrees of mtDNA diversity. Restriction fragment patterns inP. palmivora andP. parasitica were very uniform. Distinct subgroups could be distinguished inP. megakarya andP. citrophthora that correlated with the geographic origin or the host plant, respectively. These subgroups did not seem to be closely related to each other. High degrees of diversity were also evident inP. citricola andP. capsici. Although some isolates ofP. capsici had identical mtDNA patterns, no distinct subgroups were found that could be correlated with either a specific host plant or geographic origin. InP. capsici andP. parasitica variation in nuclear DNA was much more pronounced as compared to mtDNA. InP. capsici both types of analysis correlated well. Because of very limited variation of mtDNA inP. parasitica a comparison between the two phenograms was difficult.     

DNA Probes Show Genetic Variation in Cyanobacterial Symbionts of the Azolla Fern and a Closer Relationship to Free-Living Nostoc Strains than to Free-Living Anabaena Strains

Twenty-two isolates of Anabaena azollae derived from seven Azolla species from various geographic and ecological sources were characterized by DNA-DNA hybridization. Cloned DNA fragments derived from the genomic sequences of three different A. azollae isolates were used to detect restriction fragment length polymorphism among all symbiotic anabaenas. DNA clones were radiolabeled and hybridized against southern blot transfers of genomic DNAs of different isolates of A. azollae digested with restriction endonucleases. Eight DNA probes were selected to identify the Anabaena strains tested. Two were strain specific and hybridized only to A. azollae strains isolated from Azolla microphylla or Azolla caroliniana. One DNA probe was section specific (hybridized only to anabaenas isolated from Azolla ferns representing the section Euazolla), and five other probes gave finer discrimination among anabaenas representing various ecotypes of Azolla species. These cloned genomic DNA probes identified 11 different genotypes of A. azollae isolates. These included three endosymbiotic genotypes within Azolla filiculoides species and two genotypes within both A. caroliniana and Azolla pinnata endosymbionts. Although we were not able to discriminate among anabaenas extracted from different ecotypes of Azolla nilotica, Azolla mexicina, Azolla rubra and Azolla microphylla species, each of the endosymbionts was easily identified as a unique genotype. When total DNA isolated from free-living Anabaena sp. strain PCC7120 was screened, none of the genomic DNA probes gave detectable positive hybridization. Total DNA of Nostoc cycas PCC7422 hybridized with six of eight genomic DNA fragments. These data imply that the dominant symbiotic organism in association with Azolla spp. is more closely related to Nostoc spp. than to free-living Anabaena spp.     

Detection of simple mutations and polymorphisms in large genomic regions

We have developed a novel technology that makes it possible to detect simple nucleotide polymorphisms directly within a sample of total genomic DNA. It allows, in a single Southern blot experiment, the determination of sequence identity of genomic regions with a combined length of hundreds of kilobases. This technology does not require PCR amplification of the target DNA regions, but exploits preparative size-fractionation of restriction-digested genomic DNA and a newly discovered property of the mismatch-specific endonuclease CEL I to cleave heteroduplex DNA with a very high specificity and sensitivity. We have used this technique to detect various simple mutations directly in the genomic DNA of isogenic pairs of recombinant Pseudomonas aeruginosa, Escherichia coli and Salmonella isolates. Also, by using a cosmid DNA library and genomic fractions as hybridization probes, we have compared total genomic DNA of two clinical P.aeruginosa clones isolated from the same patient, but exhibiting divergent phenotypes. The mutation scan correctly detected a GA insertion in the quorum-sensing regulator gene rhlR and, in addition, identified a novel intragenomic polymorphism in rrn operons, indicating very high stability of the bacterial genomes under natural non-mutator conditions.     

Evaluation of fatty acid methyl ester profile and amplified fragment length polymorphism analyses to distinguish five species of Phytophthora associated with ornamental plants

Fatty acid methyl ester (FAME) profiles and amplified fragment length polymorphisms (AFLPs) were evaluated as tools for identifying species of Phytophthora. Five isolates of each of Phytophthora cactorum, Phytophthora citrophthora, Phytophthora cinnamomi, Phytophthora nicotianae and Phytophthora cryptogea were subjected to both analyses to examine variation among and within species. In FAME analysis, isolates of P. cactorum, P. cinnamomi and P.nicotianae were clustered by species, but isolates of P. citrophthora and P.cryptogea were divided into multiple clusters based on greater variations within these two species. The AFLP analysis differentiated all five species of Phytophthora. The five isolates of each species were grouped in a separate terminal cluster, but diversity within a species cluster varied considerably with variation greater in P. cryptogea and P. citrophthora. Comparing the dendrograms based on FAME and AFLP analyses, the overall patterns of both were similar. The P. cactorum cluster was distinct from clusters of the other four species, which formed one large cluster. The higher values of percentages of polymorphic loci and gene diversity in AFLP analysis substantiated diversity observed among isolates of P. citrophthora and P. cryptogea in FAME and AFLP dendrograms. Both FAME and AFLP appear to be useful tools for identifying species of Phytophthora, but only AFLP analysis has potential to study genetic and phylogenetic relationships within and among species in this genus.     

Large-Restriction-Fragment Polymorphism Analysis of Mycobacterium chelonae and Mycobacterium terrae Isolates

Mycobacterium chelonae and Mycobacterium terrae were reported to be frequently present in the environment of the Mycobacterium bovis BCG trial area in south India. Six isolates of M. chelonae and four isolates of M. terrae obtained from different sources in this area were analyzed by pulsed-field gel electrophoresis (PFGE) to examine large-restriction-fragment (LRF) polymorphism using the chromosomal DNA digested with DraI and XbaI restriction enzymes. With the exception of one isolate of M. terrae, DNA from all other isolates could be digested with DraI and XbaI and resulted in separable fragments. Visual comparison of the LRFs showed a unique pattern for each of the isolates tested. A computer-assisted dendrogram of the percent similarity demonstrated a high degree of genetic diversity in this group of isolates. This study demonstrates that species of nontuberculous mycobacteria, particularly M. chelonae and M. terrae, can be successfully typed by their LRF pattern using PFGE, which does not require species-specific DNA probes.     

Experimental Evidence of Biological Interactions among Different Isolates of Trypanosoma cruzi from the Chaco Region

Many infectious diseases arise from co-infections or re-infections with more than one genotype of the same pathogen. These mixed infections could alter host fitness, the severity of symptoms, success in pathogen transmission and the epidemiology of the disease. Trypanosoma cruzi, the etiological agent of Chagas disease, exhibits a high biological variability often correlated with its genetic diversity. Here, we developed an experimental approach in order to evaluate biological interaction between three T. cruzi isolates belonging to different Discrete Typing Units (DTUs TcIII, TcV and TcVI). These isolates were obtained from a restricted geographical area in the Chaco Region. Different mixed infections involving combinations of two isolates (TcIII + TcV, TcIII + TcVI and TcV + TcVI) were studied in a mouse model. The parameters evaluated were number of parasites circulating in peripheral blood, histopathology and genetic characterization of each DTU in different tissues by DNA hybridization probes. We found a predominance of TcVI isolate in blood and tissues respect to TcIII and TcV; and a decrease of the inflammatory response in heart when the damage of mice infected with TcVI and TcIII + TcVI mixture were compared. In addition, simultaneous presence of two isolates in the same tissue was not detected. Our results show that biological interactions between isolates with different biological behaviors lead to changes in their biological properties. The occurrence of interactions among different genotypes of T. cruzi observed in our mouse model suggests that these phenomena could also occur in natural cycles in the Chaco Region.     

<Emphasis Type="Italic">Pythium apinafurcum</Emphasis>: its morphology,molecular phylogeny,and infectivity for plants

During a survey of Pythium species in soils of Japan, Pythium isolates growing at high temperatures were obtained from an uncultivated field soil in Wakayama Prefecture. All six isolates showed similar morphology to each other and had complexly branched secondary hyphae, globose nonproliferating sporangia, and smooth-surfaced oogonia that have one or two oospores per oogonium. The combination of these characteristics differentiated these isolates from other Pythium species reported. Phylogenetic analyses based on sequences of the ribosomal DNA ITS and D1/D2 region of the large subunit showed that all Pythium isolates were clustered in a single clade that was distantly related to other known clades of the genus. We described these isolates as a new Pythium species, Pythium apinafurcum, based on morphology and molecular phylogeny. The P. apinafurcum isolates nonsymptomatically infected the roots of seedlings of bermudagrass, cabbage, and cucumber in a pot inoculation test.     

Development of Goose- and Duck-Specific DNA Markers To Determine Sources of Escherichia coli in Waterways

The contamination of waterways with fecal material is a persistent threat to public health. Identification of the sources of fecal contamination is a vital component for abatement strategies and for determination of total maximum daily loads. While phenotypic and genotypic techniques have been used to determine potential sources of fecal bacteria in surface waters, most methods require construction of large known-source libraries, and they often fail to adequately differentiate among environmental isolates originating from different animal sources. In this study, we used pooled genomic tester and driver DNAs in suppression subtractive hybridizations to enrich for host source-specific DNA markers for Escherichia coli originating from locally isolated geese. Seven markers were identified. When used as probes in colony hybridization studies, the combined marker DNAs identified 76% of the goose isolates tested and cross-hybridized, on average, with 5% of the human E. coli strains and with less than 10% of the strains obtained from other animal hosts. In addition, the combined probes identified 73% of the duck isolates examined, suggesting that they may be useful for determining the contribution of waterfowl to fecal contamination. However, the hybridization probes reacted mainly with E. coli isolates obtained from geese in the upper midwestern United States, indicating that there is regional specificity of the markers identified. Coupled with high-throughput, automated macro- and microarray screening, these markers may provide a quantitative, cost-effective, and accurate library-independent method for determining the sources of genetically diverse E. coli strains for use in source-tracking studies. However, future efforts to generate DNA markers specific for E. coli must include isolates obtained from geographically diverse animal hosts.     

Characterization of a Single-Spore Isolate Population of Plasmodiophora brassicae Resulting from a Single Club

The single‐spore isolates ‘e₃’ and ‘e₆’ of Plasmodiophora brassicae with different virulence patterns were distinguished by restriction fragment length polymorphisms in fingerprint‐like patterns and by electrophoretic karyotypes using repetitive fragments as hybridization probes. These molecular tools were used to characterize a set of isolates originated from an infected root, which was inoculated with a mixture of the two single‐spore isolates (e₃ and e₆). Spores harvested from mixed‐infected roots were used to establish 53 new single‐spore isolates. All these single‐spore isolates revealed parental patterns according to their molecular fingerprints and their virulence pattern. No sexual recombination could be detected with repetitive molecular probes. However, one isolate (M₃₆ES49) showed the same fingerprint pattern and virulence pattern but different sizes of small chromosomes than the parental type ‘e₆’, which is taken as an indication of chromosome rearrangement during the infection cycle.     

PCR-linked reverse DNA hybridization using oligonucleotide-specific probes of rpoB for identification of Mycobacterium avium and Mycobacterium intracellulare

A PCR-linked reverse DNA hybridization method using two different specific rpoB DNA probes (Avp and Intp) of Mycobacterium avium and Mycobacterium intracellulare, respectively, were evaluated for the differentiation and identification of M. avium and M. intracellulare culture isolates. Among the 504 culture isolates tested by this method, 48 strains showed positive results for M. avium and 60 strains showed positive results for M. intracellulare. The other 396 culture isolates showed negative results for both M. avium and M. intracellulare. These results were consistent with those obtained from partial rpoB (306 bp) sequence analysis and biochemical tests. The negative strains obtained by this DNA hybridization method were identified as M. tuberculosis (366 strains), M. peregrinum (11 strains), M. abscessus (9 strains), M. fortuitum (8 strains), and M. flavescens (2 strains) by rpoB DNA sequence analysis. Due to the high sensitive and specific result obtained by this assay, we suggest that this PCR-linked reverse DNA hybridization method using two different specific rpoB DNA probes of M. avium and M. intracellulare would be used for the rapid and precise method for differentiation and identification of M. avium and M. intracellulare.     

Detection of Pseudomonas savastanoi pv. savastanoi in Olive Plants by Enrichment and PCR

The sequence of the gene iaaL of Pseudomonas savastanoi EW2009 was used to design primers for PCR amplification. The iaaL-derived primers directed the amplification of a 454-bp fragment from genomic DNA isolated from 70 strains of P. savastanoi, whereas genomic DNA from 93 non-P. savastanoi isolates did not yield this amplified product. A previous bacterial enrichment in the semiselective liquid medium PVF-1 improved the PCR sensitivity level, allowing detection of 10 to 100 CFU/ml of plant extract. P. savastanoi was detected by the developed enrichment-PCR method in knots from different varieties of inoculated and naturally infected olive trees. Moreover, P. savastanoi was detected in symptomless stem tissues from naturally infected olive plants. This enrichment-PCR method is more sensitive and less cumbersome than the conventional isolation methods for detection of P. savastanoi.     

Detection and Identification of Bacterial Endosymbionts in Arbuscular Mycorrhizal Fungi Belonging to the Family Gigasporaceae

Intracellular bacteria have been found previously in one isolate of the arbuscular mycorrhizal (AM) fungus Gigaspora margarita BEG 34. In this study, we extended our investigation to 11 fungal isolates obtained from different geographic areas and belonging to six different species of the family Gigasporaceae. With the exception of Gigaspora rosea, isolates of all of the AM species harbored bacteria, and their DNA could be PCR amplified with universal bacterial primers. Primers specific for the endosymbiotic bacteria of BEG 34 could also amplify spore DNA from four species. These specific primers were successfully used as probes for in situ hybridization of endobacteria in G. margarita spores. Neighbor-joining analysis of the 16S ribosomal DNA sequences obtained from isolates of Scutellospora persica, Scutellospora castanea, and G. margarita revealed a single, strongly supported branch nested in the genus Burkholderia.     

Effects of mycorrhizal fungi on symbiotic seed germination of Pecteilis susannae (L.) Rafin (Orchidaceae), a terrestrial orchid in Thailand

Symbiotic seed germination of Pecteilis susannae (L.) Rafin was investigated using 11 fungal isolates recovered from roots of four Thai terrestrial orchids (P. susannae, Eulophia spectabilis, Paphiopedilum bellatulum and Spathoglottis affinis). Seed germination and protocorm development were evaluated up to 133 days after sowing. Protocorm development was most advanced, up to stage 5 (elongation of the first leaf), when seeds were cultured with 4 Epulorhiza isolates obtained from roots of P. susannae (CMU-Aug 028, 4.3%, CMU-Aug 007, 4.2%, and CMU-Aug 013, 2.2%) and E. spectabilis (CMU-STE 014, 3.9%). Moreover, stage 4 protocorm development (emergence of the first leaf) occurred with fungal isolates CMU-STE 011, 5.7%, (Epulorhiza sp.) and CMU-AU 212, 4.3%, (Tulasnella sp.) obtained from roots of E. spectabilis and S. affinis respectively. When seed was incubated without fungi (control), development was limited to stage 3 of protocorm development (appearance of promeristem). This is the first report of protocorm stage 5 development in P. susannae using compatible fungal symbionts. Optimization of seed germination and seedling fitness will assist the conservation and propagation of this orchid species and other terrestrial orchids in Thailand.     

Electrophoretic protein patterns of three species ofPhytophthora associated with black pod disease of cocoa (Theobroma cacao L.)

When electrophoretic profiles of native proteins from vegetative mycelia ofPhytophthora palmivora, Phytophthora capsici and Phytophthora citrophthora causing black pod disease of cocoa in India were compared on a single Polyacrylamide gel, the isolates of same species were readily distinguished both qualitatively by visual similarity in banding patterns and quantitatively by calculating similarity coefficients. Similarity coefficients were generally much higher between isolates within a species than between isolates of different species. The dendrograms obtained after unweighted pair grouping with arithmetic averaging cluster analysis, revealed that all the isolates ofPhytophthora capsici were highly homogenous and formed a single cluster. The isolates ofPhytophthora citrophthora were resolved into two electrophoretic types which were clustered into two distinct sub groups.Phytophthora palmivora formed a separate group. Thus, the results reveal that polyacrylamide gel electrophoresis can be used successfully in distinguishing species and sub groups within a species ofPhytophthora encountered on cocoa. CPCRl contribution No. 914.