Selective control of parasitic nematodes using bioactivated nematicides.

Parasitic nematodes are a major threat to global food security, particularly as the world amasses 10 billion people amid limited arable land1-4. Most traditional nematicides have been banned owing to poor nematode selectivity, leaving farmers with inadequate means of pest control4-12. Here we use the model nematode Caenorhabditis elegans to identify a family of selective imidazothiazole nematicides, called selectivins, that undergo cytochrome-p450-mediated bioactivation in nematodes. At low parts-per-million concentrations, selectivins perform comparably well with commercial nematicides to control root infection by Meloidogyne incognita, a highly destructive plant-parasitic nematode. Tests against numerous phylogenetically diverse non-target systems demonstrate that selectivins are more nematode-selective than most marketed nematicides. Selectivins are first-in-class bioactivated nematode controls that provide efficacy and nematode selectivity.

Genome Announcement: Draft Genome Assembly of Heterodera humuli Generated Using Long-Read Sequencing.

The hop cyst nematode, Heterodera humuli, is the most common plant-parasitic nematode associated with hop worldwide. This study reports the draft genome of H. humuli generated on the PacBio Sequel IIe System with the ultra-low DNA input HiFi sequencing method, and the corresponding genome annotation. This genome resource will help further studies on H. humuli and other cyst nematodes.

First report of Meloidogyne hapla on hemp (Cannabis sativa) in Oregon.

Hemp is a crop that has gained interest in Washington and Oregon. As with other crops, hemp production faces challenges due to biotic factors, including plant-parasitic nematodes. During a survey for plant-parasitic nematodes associated with hemp, Meloidogyne sp. was found in a composite root sample collected in Oregon. Morphological characterization of second-stage juveniles identified the nematode as Meloidogyne hapla. Molecular identification confirmed the population as M. hapla. To our knowledge, this is the first report of M. hapla on hemp in the Pacific Northwest of the United States.

Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis.

The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g., citrus, banana). Despite the economic importance of this nematode, little is known about the repertoire of effectors owned by this species. Here we combined spatially and temporally resolved next-generation sequencing datasets of R. similis to select a list of candidates for the identification of effector genes for this species. We confirmed spatial expression of transcripts of 30 new candidate effectors within the esophageal glands of R. similis by in situ hybridization, revealing a large number of pioneer genes specific to this nematode. We identify a gland promoter motif specifically associated with the subventral glands (named Rs-SUG box), a putative hallmark of spatial and concerted regulation of these effectors. Nematode transcriptome analyses confirmed the expression of these effectors during the interaction with the host, with a large number of pioneer genes being especially abundant. Our data revealed that R. similis holds a diverse and emergent repertoire of effectors, which has been shaped by various evolutionary events, including neofunctionalization, horizontal gene transfer, and possibly by de novo gene birth. In addition, we also report the first GH62 gene so far discovered for any metazoan and putatively acquired by lateral gene transfer from a bacterial donor. Considering the economic damage caused by R. similis, this information provides valuable data to elucidate the mode of parasitism of this nematode.

The Hop Cyst Nematode, Heterodera humuli: History, Distribution, and Impact on Global Hop Production.

Humulus lupulus (commonly known as hop) is an herbaceous plant that is used in brewing throughout the world. Hop cones are an essential ingredient in the production of beer, which makes hops of critical importance to global craft beverage industries. The hop cyst nematode, Heterodera humuli, is a plant-parasitic nematode with the potential to substantially limit yields of hop. H. humuli has been detected in many of the most significant regions for hop production worldwide, and infestations of H. humuli can consequently impact hop growth and limit cone production. Despite documented reports on the distribution of and damage caused by H. humuli since its description in 1934, there have been limited studies on the biology, pathogenicity, management, and consequences of infestations on hop production over time. Inconsistencies and gaps in the available information (e.g., the number of H. humuli generations per season, host status of alternate crops), exacerbate difficulties in understanding how H. humuli can be managed. Resolving the existing knowledge gaps identified within this review can lead to determining effective H. humuli management strategies for hop growers.

What is the Optimal Way to Assess Meloidogyne Spp. Reproduction in Greenhouse Pot Experiments?

Often research efforts that address both the practical concerns of managing Meloidogyne spp. and understanding their basic biology involve greenhouse reproduction assays. However, there is little consensus in regards to what parameters should be used to conduct greenhouse assays. The goal of this research was to evaluate how pot size, Meloidogyne spp. inoculation life stage, inoculation density, and time of assay impacted final reproduction factor (RF = initial nematode density/final nematode density) values. In experiments with M. incognita, the factor of the pot size mattered, with higher RF values in pots containing 500 g soil vs. pots with 100 g soil; larger pots containing 3,000 g soil did not have RF values different from the aforementioned sizes. Inoculating with M. incognita J2 resulted in RF values on average of >2 fold higher then when inoculating with eggs at comparable densities. Inoculation density of M. incognita did not have an impact on final M. incognita RF values. In experiments that considered time of assay, three species were evaluated: M. incognita, M. chitwoodi, and M. hapla. There was no difference in M. incognita RF values when assays were conducted for 5 wk, 6 wk, 7 wk, and 8 wk. However, a longer assay time resulted in higher RF values for M. hapla and M. chitwoodi, with at least a 7 week assay required. In conclusion, a moderate pot size (500 g of soil) inoculated with M. incognita J2 resulted in maximum RF values. The length of the assay required will depend on the Meloidogyne spp. in question, with longer duration assays required for M. hapla and M. chitwoodi than for M. incognita.

Genome Announcement: The Draft Genome of the Carrot Cyst Nematode Heterodera Carotae.

Heterodera carotae, the carrot cyst nematode, is a significant pest affecting carrot globally. Here we present the draft genome of H. carotae, which was generated from short read libraries from Illumina HiSeq technology, and the corresponding genome annotation.

Growth, Sporulation, and Pathogenicity of the Raspberry Pathogen Phytophthora rubi Under Different Temperature and Moisture Regimes.

Phytophthora root rot of raspberry, which is mostly caused by Phytophthora rubi, is a significant issue for the Washington State red raspberry industry. Considered a cool weather pathogen, it is often assumed that it is most active and infective during the cool, wet winters of the region when soil temperatures range from 5 to 10°C; however, there are little data to support this view. More recent research has found that symptoms of root disease during late summer were strongly associated with P. rubi. Therefore, experiments were conducted at four temperatures from 5 to 20°C to evaluate the effects of temperature on P. rubi mycelial growth and sporulation and the effects of both temperature and soil moisture on the pathogenicity of P. rubi on red raspberry. At 20°C, P. rubi grew fastest and sporulated the most heavily. However, disease was most severe at both 15 and 20°C. The soil moisture parameters tested did not affect the pathogenicity results. These results show that P. rubi is more likely to infect during the spring and summer months (from May through September), when soil temperatures are consistently in the range of 15 to 20°C.

Differential Response of Meloidogyne, Pratylenchus, Globodera, and Xiphinema Species to the Nematicide Fluazaindolizine.

This research focused on the effects of fluazaindolizine on a diversity of plant-parasitic nematodes. In microwell assays, 24-h dose-response curves were generated for several species and populations of Meloidogyne, Pratylenchus neglectus, P. penetrans, Globodera ellingtonae, and Xiphinema americanum. In a greenhouse study, the impact of fluazaindolizine on fecundity of M. incognita, M. hapla, and M. chitwoodi was tested by exposing nematodes for 24 h in solution and inoculating on tomato. The average 24-h ED50s (dose that resulted in the immobility of 50% of exposed nematodes) for M. hapla, M. chitwoodi, and M. incognita were 325.7, 223.4, and 100.7 ppm, respectively. M. hapla had the most variation among populations, with 24-h ED50s ranging from 72 to 788 ppm. G. ellingtonae had the lowest 24-h ED50 at 30 ppm. Pratylenchus spp. were unaffected by fluazaindolizine. X. americanum was the only species where effects of fluazaindolizine were reversible, but had a 24-h ED50 that fell in the range of the Meloidogyne spp. In the greenhouse study, M. chitwoodi was the least sensitive with reproduction reaching 62% of the untreated control after a pre-exposure to 47 ppm, whereas M. incognita and M. hapla at the same exposure dose had reproduction rates of 27 and 36% of the untreated control, respectively. Despite varying in in vitro responses to fluazaindolizine, reproduction of all Meloidogyne spp. was suppressed after only 24 h of exposure. This study expanded our understanding of how G. ellingtonae, P. thornei, P. penetrans, and X. americanum respond to fluazaindolizine.

First Report of the Hop Cyst Nematode, Heterodera humuli, in Two Counties of the Yakima Valley Region, WA, USA.

Cyst nematodes are ranked as the second most damaging plant-parasitic nematode genus of crops worldwide (Jones et al. 2013). The hop cyst nematode, Heterodera humuli, has been reported to cause up to 38% reduction in dry hops per bine (Hay and Pethybridge 2003). America is the top hop producing country worldwide, with 75% of production occurring in Washington state, with the majority of this production occurring in the Yakima Valley region (USDA, 2019). In late 2019, 30 soil samples from 15 different fields were collected from the hop cvs. HBC 394, HBC 369, and YCR 14. Nematodes were extracted using an adapted centrifugal floatation method (Jenkins 1964) from 100 cc subsamples of soil. Twenty of these samples contained at least one cyst and 23 contained at least one juvenile. Body length of juveniles (n = 5) averaged + standard deviation 377.62 ± 4.76 µm which is consistent with H. humuli juvenile body measurements (Sen 1968). Three samples from Yakima County and two from Benton County were identified to the species level using sequences from the internal transcribed spacer (ITS) region of the 5.8S gene. The sequences (GenBank accession numbers MT840678 to MT840682) were amplified using forward primer 5.8S-F (5'-GTGATTCCATTCACCAHCTACCTG-3'), and reverse primer 5.8S-R (5'-TTCGCACTAATTATCGCAGTTGG-3'). Sequence comparison with available ITS (5.8S) sequences in GenBank using BLAST showed 99.85% identity to H. humuli for all five samples. Because COI sequences of H. humuli are not available, to provide an additional marker for species identification, we amplified the COI sequences by using (forward primer Hete-COI-F (5'-TTTGGDCAYCCHGARGTTTATGTT-3'), and reverse primer Hete-COI-R (5'-AYWGTAAAAAGGRRAATAAAACC-3') for these samples. Four COI sequences (GenBank accession numbers MT840683 to MT840686) were obtained. These COI sequences will be used to identify future H. humuli samples. To confirm pathogenicity, eight 1-gal pots were filled with a 90:10 play sand to potting soil mixture and one hop rhizome cv. 'Centennial' was planted in pots and maintained in a greenhouse. After above ground plant growth was observed, half the pots were inoculated with hand-picked H. humuli cysts from Yakima soil samples at a density of 10 cysts/100 cc of soil. The life cycle of H. humuli in potted experiments is 40 days (McNamara and Mende 1995). Forty-five days after inoculation, plant measurements were recorded and nematodes extracted from five 100 cc soil samples per pot as described above. Soil samples revealed that H. humuli populations had an average Reproductive Factor (RF = final nematode population/initial nematode population) of 2.08. Five cysts were crushed to determine eggs/cyst, which yielded an average of 101 eggs/cyst. Young infected hops lacked vigor, with all replicates stunted both in bine height and leaf length compared to healthy controls. Bine heights were reduced by an average of 40.4% in pots inoculated with H. humuli compared to control plants (P = 0.0016). Distribution of hop cyst within the United States is limited to the top four states for hop production: Washington, Oregon, Idaho and Michigan (Cobb 1962; Sen and Jensen 1967; Hafez et al. 2010, Warner and Bird, 2015). In 1962, Cobb reported H. humuli in Pierce County, Washington, but it had not been reported in Benton County and Yakima County until now. This is a significant finding that has the potential to impact the Washington state hop industry, valued at $475.7 million in 2019 (USDA, 2019). Due to the lack of known effective nematode control measures, the discovery of H. humuli in the major hop-growing region of Washington warrants concern.

New reduced-risk agricultural nematicides - rationale and review.

The last decade has seen a sharp increase in nematicide research in the agricultural industry. As a result, several new synthetic nematicides have become available to growers, and several more are expected in the near future. This new interest in nematicides is directly related to the growing demand for safer and more selective products, and the increasing regulatory pressure on many of the traditional nematicides. This has led to a ban of several widely used fumigant (e.g. methyl bromide) and non-fumigant (e.g. aldicarb) nematicides. The loss of traditional nematicides, combined with a lack of replacement products and awareness of the damage that nematodes can cause, has not only raised concern among growers, but has also created new opportunities for the crop protection industry. Nematicides have become a priority, and many companies are now allocating significant research dollars to discover new nematicides. The new nematicides are very different from previous products: (i) they are more selective, often only targeting nematodes, and (ii) they are less toxic, and safer to use. This review article describes these new developments by discussing the challenges that are associated with finding new nematicides, reviewing the nature, characteristics, and efficacy of new nematicides, and discussing the impact they could have on future nematode management.

Prevalence of the root lesion nematode virus (RLNV1) in populations of Pratylenchus penetrans from North America.

Root lesion nematode virus 1 (RLNV1) was discovered in the migratory endoparasitic nematode species Pratylenchus penetrans. It was found in a P. penetrans population collected from soil samples in Beltsville, Maryland, USA. In this study, the distribution of the RLNV1 in 31 geographically distinct P. penetrans populations obtained from different crops was examined. The results demonstrate that RLNV1 is widespread in North American populations of P. penetrans and exhibits low genetic variability in the helicase and RNA-dependent RNA polymerase regions of the genome.Root lesion nematode virus 1 (RLNV1) was discovered in the migratory endoparasitic nematode species Pratylenchus penetrans. It was found in a P. penetrans population collected from soil samples in Beltsville, Maryland, USA. In this study, the distribution of the RLNV1 in 31 geographically distinct P. penetrans populations obtained from different crops was examined. The results demonstrate that RLNV1 is widespread in North American populations of P. penetrans and exhibits low genetic variability in the helicase and RNA-dependent RNA polymerase regions of the genome.

Short-Term Effects of Sublethal Doses of Nematicides on Meloidogyne incognita.

Meloidogyne species are one of the most important groups of plant-parasitic nematodes globally because of their ability to damage most cultivated plants. Although they are widespread and economically important, there are limited control measures to combat these nematodes. New nonfumigant nematicides have been discovered that have the potential to be widely utilized for the management of plant-parasitic nematodes. Because of the longer half-lives in soil and lower toxicity of new nematicides compared with traditional fumigant and nonfumigant nematicides, understanding how nematodes respond to sublethal doses of nematicides is imperative to understanding whether nematicide resistance has the potential to develop. Characterizing responses of nematodes to sublethal doses will provide the foundation for future work, such as gene expression studies. In this study, the nematicides oxamyl (Vydate), fluazaindolizine (Salibro), fluensulfone (Nimitz), and fluopyram (Velum), were evaluated to understand how sublethal doses affect the fecundity and mobility of Meloidogyne incognita second-stage juveniles (J2). Using a microwell assay system, dose-response curves for each nematicide were established for M. incognita J2. Fluopyram was the most toxic nematicide, with effective doses up to 230 times lower than that of other nematicides. The other nematicides had predicted ED50 values (effective doses that resulted in 50% of the population becoming inactive) of 89.4, 131.7, and 180.6 ppm for oxamyl, fluensulfone, and fluazaindolizine, respectively. The 24-h ED50 of each nematicide was then used in both motility and infectivity assays. The motility and activity of M. incognita J2 exposed to ED50 doses of fluazaindolizine and fluensulfone was significantly reduced, with nematodes initially being motile but eventually becoming inactive. However, the motility of M. incognita J2 exposed to ED50 doses of fluopyram and oxamyl was not different from a water control. In a pot assay, M. incognita J2 exposed to ED50 doses of fluazaindolizine, oxamyl, and fluensulfone were unable to reproduce on tomato, with reproduction factors (RF = final population density/initial population density) of 0 to 0.03. Fluopyram did not reduce reproduction of M. incognita, with a mean RF of 38.7 ± 4.5, which was similar to the RF of 46.3 ± 4.6 for the water control. This study is the first comprehensive evaluation of M. incognita activity, motility, and fecundity after exposure to the traditional nematicide, oxamyl, as well as three new nematicides, fluazaindolizine, fluopyram, and fluensulfone.

Developmental Dynamics of Meloidogyne hapla in Washington Wine Grapes.

Meloidogyne hapla is the most prevalent plant-parasitic nematode in Washington state wine grape vineyards. Understanding the developmental dynamics of M. hapla can improve the timing of diagnostic sampling and nematicide application. Three Vitis vinifera vineyards in Washington were sampled March 2015 to March 2017 to determine the developmental dynamics of M. hapla by measuring second-stage juveniles (J2) in soil, eggs and adult females in roots, and fine root tips. A model of M. hapla J2 development based on soil growing degree days using a base temperature (Tb) of 0°C (GDDsoil) and a start date of 1 March was developed. This model was validated at two additional vineyards in Washington and was robust with R2 values > 0.74. M. hapla has one generation per year and overwinters primarily as the J2 infective stage. Juvenile populations declined after 1 March, reaching their lowest density in early July and reaching a maximum density over the winter. M. hapla egg and root tip densities reached a maximum in early August. The number of females per root tip did not vary throughout the year. A single generation with defined peaks in J2 population densities will allow for specific timing of nematicide interventions.

Impact of Globodera ellingtonae on yield of potato (Solanum tuberosum).

Globodera ellingtonae was described from Oregon and Idaho in 2012. Due to the close phylogenetic relationship of this nematode to the potato cyst nematodes G. pallida and G. rostochiensis, and evidence that G. ellingtonae reproduces on potato (Solanum tuberosum), potential damaging effects to potato by this nematode are of great concern. To evaluate the pathogenic effects of G. ellingtonae on potato, five field and two microplot trials were conducted over a four-year period including comparisons of a range of G. ellingtonae initial population densities (Pi) and potato cultivars. In two field trials, potato 'Russet Burbank' was inoculated with Pi of G. ellingtonae ranging from 0 to 80 eggs/g soil; a similar trial was conducted with potato 'Désirée.' In another field trial, potato cultivars varying in maturity lengths were either inoculated (80 eggs/g soil) or not with G. ellingtonae. In a final field trial, 'Ranger Russet' was inoculated with Pi of G. ellingtonae ranging from 0 to 360 eggs/g soil. Additionally, Russet Burbank was inoculated with G. ellingtonae Pi ranging from 0 to 169 eggs/g soil in microplots. In all trials, data on tuber yield, aboveground biomass, final eggs/cyst, final population densities (Pf), and reproduction factor (RF = Pf/Pi) were collected. In only two of six trials conducted with increasing levels of Pi, was there a significant negative correlation between Pi of G. ellingtonae and yield of potato. Based on the linear regression model of tuber yield on logPi for Russet Burbank, 30.5 to 40.9% yield loss was predicted at a Pi of 40 and 80 eggs/g soil, respectively, and for Ranger Russet, 16.5 and 19.7% yield loss was predicted at a Pi of 40 and 80 eggs/g soil, respectively. None of the potato cultivars inoculated with 80 G. ellingtonae eggs/g soil had significantly reduced yields compared to non-inoculated plants. Reproduction factor values across trials ranged from 4.0 to 8.3 when inoculated with Pi of 40 eggs/g soil, demonstrating that the nematode successfully invaded and reproduced on potato in all trials. Care should be taken in extrapolating the results from these experiments conducted in Oregon to probable effects of G. ellingtonae on potato in other environments.KeywordsPotato, Damage, Globodera, Regression.Globodera ellingtonae was described from Oregon and Idaho in 2012. Due to the close phylogenetic relationship of this nematode to the potato cyst nematodes G. pallida and G. rostochiensis, and evidence that G. ellingtonae reproduces on potato (Solanum tuberosum), potential damaging effects to potato by this nematode are of great concern. To evaluate the pathogenic effects of G. ellingtonae on potato, five field and two microplot trials were conducted over a four-year period including comparisons of a range of G. ellingtonae initial population densities (Pi) and potato cultivars. In two field trials, potato 'Russet Burbank' was inoculated with Pi of G. ellingtonae ranging from 0 to 80 eggs/g soil; a similar trial was conducted with potato 'Désirée.' In another field trial, potato cultivars varying in maturity lengths were either inoculated (80 eggs/g soil) or not with G. ellingtonae. In a final field trial, 'Ranger Russet' was inoculated with Pi of G. ellingtonae ranging from 0 to 360 eggs/g soil. Additionally, Russet Burbank was inoculated with G. ellingtonae Pi ranging from 0 to 169 eggs/g soil in microplots. In all trials, data on tuber yield, aboveground biomass, final eggs/cyst, final population densities (Pf), and reproduction factor (RF = Pf/Pi) were collected. In only two of six trials conducted with increasing levels of Pi, was there a significant negative correlation between Pi of G. ellingtonae and yield of potato. Based on the linear regression model of tuber yield on logPi for Russet Burbank, 30.5 to 40.9% yield loss was predicted at a Pi of 40 and 80 eggs/g soil, respectively, and for Ranger Russet, 16.5 and 19.7% yield loss was predicted at a Pi of 40 and 80 eggs/g soil, respectively. None of the potato cultivars inoculated with 80 G. ellingtonae eggs/g soil had significantly reduced yields compared to non-inoculated plants. Reproduction factor values across trials ranged from 4.0 to 8.3 when inoculated with Pi of 40 eggs/g soil, demonstrating that the nematode successfully invaded and reproduced on potato in all trials. Care should be taken in extrapolating the results from these experiments conducted in Oregon to probable effects of G. ellingtonae on potato in other environments.KeywordsPotato, Damage, Globodera, Regression.

Genome Announcement: The Draft Genomes of Two Radopholus similis populations from Costa Rica.

Radopholus similis is an economically important pest of both banana and citrus in tropical regions. Here we present draft genomes from two populations of R. similis from Costa Rica that were created and assembled using short read libraries from Illumina HiSeq technology.

"Nutrition or no nutrition?": Chylothorax or leakage of total parenteral nutrition?

Total parenteral nutrition (TPN) using a central line is an invasive and widely used procedure associated with several complications. Pleural effusion secondary to the leakage of alimentation into the pleural cavity is a rare but encountered complication of central-line TPN administration. This case study focuses on a postmortem examination of an 84-year-old woman, hospitalized due to malnutrition and dysphagia. The left internal jugular vein was cannulated, with no post-procedural x-ray check-up of the catheter tip position. An autopsy revealed 800 ml of milky-white fluid in the left pleural cavity, raising the issue of whether the pleural effusion was of chylous or TPN origin. The aim of this case study was to describe the postmortem diagnostic approach of the fluid analysis. Suspecting chylothorax, we first analyzed the triglyceride (TG) levels in the fluid, which, according to the literature, is the best parameter to detect chyle when lipoprotein electrophoresis (chylomicron %) is unavailable. Biochemistry showed increased levels of TG, which can be found in both chylous and TPN fluid. We then added glucose and potassium to the biochemical analysis, again showing increased levels at 46 mmol/L and 22 mmol/L, respectively. We had no information about the given TPN, and thus, comparing the final chemical results with the TPN composition was impossible. The presence of increased levels of triglycerides, glucose, and potassium in the white fluid more strongly resembled a standard TPN than chyle. Hence, by using these three measurements, we concluded that the milky-white fluid was a leakage of TPN.

Resistance of Potato Breeding Clones and Cultivars to Three Species of Potato Cyst Nematode.

In the United States, potato cyst nematodes Globodera rostochiensis and G. pallida are quarantined pests. A new cyst nematode species, Globodera ellingtonae, discovered in Oregon and Idaho, reproduces well on potato but is not currently a quarantine pest. Identifying resistance to all three Globodera spp. would provide a valuable management tool. Thirteen breeding clones and nine cultivars were evaluated in Oregon, Idaho, and New York laboratories where the nematode populations are maintained. Minitubers or tissue culture plants were planted into pots and inoculated with eggs in replicated experiments. Results indicated that five entries were partially resistant or resistant to all three species, while another five were resistant or partially resistant to G. rostochiensis and G. ellingtonae. Resistance to G. rostochiensis pathotypes Ro1 and Ro4 is controlled by the H1 gene and this study suggests that H1 may confer resistance to G. ellingtonae as well. Observed resistance to G. pallida was lower relative to the levels of resistance observed for G. rostochiensis and G. ellingtonae. Germplasm with G. pallida or G. ellingtonae resistance will be used in hybridizations to develop russet-skinned cultivars with long tubers which represent the predominant market class in western U.S. production, and to further explore the basis of potato resistance to Globodera spp.

Late-summer Disease Symptoms in Western Washington Red Raspberry Fields Associated with Co-Occurrence of Phytophthora rubi, Verticillium dahliae, and Pratylenchus penetrans, but not Raspberry bushy dwarf virus.

Sixty percent of the $109 million processed red raspberry industry of the United States occurs in northern Washington State. In 2012, late-summer symptoms of vascular wilt and root disease were observed in many raspberry plantings. These symptoms were initially attributed to Verticillium dahliae. However, diagnostic tests for the pathogen were often contradictory and other soilborne pathogens (Phytophthora rubi and Pratylenchus penetrans) or Raspberry bushy dwarf virus (RBDV) might also have been involved. Therefore, a survey was conducted in 2013 and 2014 to (i) establish the incidence and soil population levels of V. dahliae in red raspberry production fields, (ii) compare among diagnostic methods and laboratories for detecting and quantifying V. dahliae from raspberry field soil, and (iii) assess which pathogens are associated with late-summer disease symptoms of raspberry. Plant and soil samples were collected from 51 disease sites and 20 healthy sites located in 24 production fields. Samples were analyzed for the presence and quantity of each pathogen using traditional plating and extraction methods (V. dahliae, P. rubi, and P. penetrans), quantitative polymerase chain reaction (qPCR) (V. dahliae and P. rubi), and enzyme-linked immunosorbent assay (RBDV). Results showed that V. dahliae was present in 88% of the production fields and that detection of the pathogen differed by method and by laboratory: qPCR detected V. dahliae in the soil from approximately three times as many sites (51 of 71 total sites) as by plating on NP10 semi-selective medium (15 of 71 total sites). Soil populations of V. dahliae were slightly greater at disease sites, but the pathogen was detected with similar frequency from healthy sites and it was rarely isolated from diseased plants (4%). P. rubi, P. penetrans, and RBDV were also common in production fields (79, 91, and 53% of fields, respectively). Both P. rubi (soil and root samples) and P. penetrans (root populations only), but not RBDV, were more frequently found at disease sites than healthy sites, and the amount of P. rubi detected by qPCR was greater from disease sites than healthy sites. In addition, P. rubi was isolated from 27% of the symptomatic plants located at disease sites. Regardless of detection method, V. dahliae, P. rubi, and P. penetrans, either with or without RBDV, were more likely to co-occur at disease sites (73%) than healthy sites (35%), suggesting that a soilborne disease complex is present in raspberry production fields. Results indicate that P. rubi is the primary pathogen most strongly associated with late-summer symptoms of disease, but root populations of P. penetrans and higher soil populations of V. dahliae may also be of concern. Therefore, disease control methods should focus on all three soilborne pathogens.

Whole Genome Sequences of the Raspberry and Strawberry Pathogens Phytophthora rubi and P. fragariae.

Phytophthora rubi and P. fragariae are two closely related oomycete plant pathogens that exhibit strong morphological and physiological similarities but are specialized to infect different hosts of economic importance, namely, raspberry and strawberry. Here, we report the draft genome sequences of these two Phytophthora species as a first step toward understanding the genomic processes underlying plant host adaptation in these pathogens.