Effects of Crop Rotations and Tillage on Pratylenchus spp. in the Semiarid Pacific Northwest United States

DNA-based assessment of root lesion nematode infections in cereal roots

Root lesion nematodes (RLN) of the genus Pratylenchus are causing significant damage in cereal production worldwide. Due to climate change and without efficient and environment-friendly treatments, the damages through RLNs are predicted to increase. Microscopic assessments of RLNs in the field and the greenhouses are time-consuming and laborious. As a result, cereal breeders have mostly ignored this pest. We present a method measuring RLN in infected cereal roots using a standardized PCR approach. Publicly available Pratylenchus neglectus primer combinations were evaluated. An optimal primer combination for RT-qPCR assay was identified to detect and quantify P. neglectus within infected cereal roots. Using the RT-qPCR detection assay, P. neglectus could be clearly distinguished from other plant parasitic nematodes. We could identify P. neglectus DNA in barley and wheat roots as low as 0.863 and 0.916 ng/µl of total DNA, respectively. A single P. neglectus individual was detected in water suspension and within barley and wheat roots. The RT-qPCR detection assay provides a robust and accurate alternative to microscopic nematode identification and quantification. It could be of interest for resistance breeding, where large populations must be screened to detect and quantify P. neglectus in farmer's fields.

Root-Lesion Nematodes Affecting Dryland Cereals in the Semiarid Pacific Northwest U.S.A

Root-lesion nematodes (Pratylenchus spp.) are parasites that invade and deteriorate roots, thereby reducing the efficiency of water and nutrient uptake. Pratylenchus neglectus and P. thornei are the two species that are most prevalent and cause reduced yields of rainfed wheat and barley in semiarid regions of the Pacific Northwest. They are particularly damaging where wheat and barley are produced without irrigation in areas receiving less than 450 mm (18 in.) of precipitation annually. This review is focused on the biology and management of P. neglectus and P. thornei in semiarid rainfed agriculture. Characteristics of climates, soils, and crop production systems are described as a preface to constraints placed upon management options. Discussions include the economic importance, host ranges, and protocols for sampling and species identification. Discussion of disease management options include crop rotation, genetic resistance and tolerance, planting date, trap and biofumigant crops, crop nutrition, chemical and biological nematicides, and tillage. Predictions for rainfed agriculture in a period of changing climate are presented, as are suggestions for important areas of research including crop genetics, nematode testing, and communication of results, Pratylenchus biology, mechanisms of resistance, the phytobiome, and closing the "yield gap" between actual and attainable yields.

Assessment of Factors Associated with Molecular Quantification of Stubby Root Nematode Paratrichodorus allius from Field Soil DNA

Factors relating to SYBR Green-based quantitative real-time PCR (qPCR) quantification of stubby root nematode Paratrichodorus allius using soil DNA were evaluated in this study. Soils used were loamy sand from potato fields in North Dakota and Idaho. Results showed that the largest nematode individuals (body length >720 µm) produced significant lower Cq values than the smallest individuals (<359 µm), indicating more total DNA amount in the largest nematodes. Soil pre-treatments showed that autoclaved field soil had significantly reduced DNA amount and quality. The air- or oven-dried soil yielded a lower amount of DNA with similar purity, compared with natural field soil. PCR inhibitors were detected in soil DNA substrates targeting pBluescript II SK(+)-plasmid DNA. Al(NH₄)(SO₄)₂ treatment during DNA preparation significantly reduced the inhibitors compared with post-treatment of soil DNA with polyvinylpolypyrrolidone column. The effect of PCR inhibitors on qPCR was suppressed by bovine serum albumin. Quantification results did not significantly change when increasing the number of DNA extractions from three to six per soil sample when soil grinding and grid sampling strategies were used. Two standard curves, generated from serial dilutions of plasmid DNA containing P. allius ITS1 rDNA and soil DNA containing known nematode numbers, produced similar correlations between Cq values and amount of targets. The targets in soil DNA quantified by qPCR using either standard curve correlated well with microscopic observations using both artificially and naturally infested field soils. This is the first study for assessing various factors that may affect qPCR quantification of stubby root nematodes. Results will be useful during the setup or optimization of qPCR-based quantification of plant-parasitic nematodes from soil DNA.

Pathotypes Detected Among Populations of Pratylenchus neglectus Collected From Montana

The root lesion nematode, Pratylenchus neglectus, is one of the most damaging nematodes to affect wheat worldwide. The nematode is widely distributed in Montana, primarily affecting winter wheat within the state. Managing the nematode primarily involves rotation to resistant and moderately resistant crops (peas, lentils, and barley). A nematode survey was conducted across the state nearly 10 years after an initial survey, to reassess the nematode threat and assess the impact of changing trends in crop rotations. To assess the broad applicability of rotation crops to control P. neglectus across Montana, greenhouse trials were conducted to challenge rotational crops using eight populations of P. neglectus collected from geographically diverse locations across the state. In the trials, conducted with four Montana crops, a significant interaction was detected between crop and nematode population (analysis of variance P < 0.001). Populations from Hill, Dawson, and Chouteau counties were found to be pathogenic on barley. Male nematodes were detected in seven of the eight pot culture populations, and these were confirmed to be P. neglectus by morphological and molecular methods. These results suggest a re-evaluation of barley and lentils as a management option for P. neglectus in Montana, as pathotypes for each exist within the state.

Impact of agricultural practices and environmental variables on plant-parasitic nematode communities in fields at a landscape scale

Agricultural practices shaping plant-parasitic nematode (PPN) assembly are still unclear, and this limits our understanding of the impact of anthropic disturbances on the resilience of PPN communities and the emergence of agronomic problems. Here the abundance and diversity of PPN in France’s oilseed rape production area was determined by sampling 72 fields over two consecutive years. We identified and counted PPN taxa and collected anthropic and environmental variables for the past 5 years. PPN were assigned to seven genera and one family including PPN that have not been identified to genus level. Using multiple correspondence analyses, we selected the main variables and tested their effect on the abundance of each taxon with mixed generalised linear models. We emphasise that at the landscape scale investigated, crop rotations were no longer a major factor impacting the PPN communities. However, we observed that tillage and pesticides had a significant impact on several taxa.

Assessment and Management of Root Lesion Nematodes in Montana Wheat Production

Root lesion nematodes (Pratylenchus spp.) hinder dryland wheat production worldwide. Montana, a leading U.S. wheat production region, has climatic conditions favorable for Pratylenchus spp. A 2006-2007 statewide soil survey revealed damaging populations of Pratylenchus neglectus, primarily in winter wheat production areas of Montana, whereas P. thornei was not found. Analyses of wheat yields in infested fields revealed negative correlations between yields and spring nematode populations (all P < 0.05 and all R² > 0.2). Statewide yield losses due to root lesion nematodes were an estimated 12 and 15% for winter wheat in 2006 and 2007, respectively. A subsequent study conducted in 2008 to 2009 revealed significant differences in reproductive success of P. neglectus among seven rotation treatments (P < 0.001). Nematode populations persisted from spring to fall under fallow, barley, pea, and camelina; increased under winter wheat and canola; and decreased under lentil. Populations were sustained through winter following winter wheat and barley but declined following canola, camelina, pea, lentil, and fallow. A screening of 19 barley lines for resistance to P. neglectus revealed significant variation in resistance among entries (P < 0.001), with 'Harrington' barley displaying promising levels of resistance. Development of resistant wheat cultivars remains a principal goal in managing this nematode.

Rapid Quantification of Soilborne Pathogen Communities in Wheat-Based Long-Term Field Experiments

Rainfed experiments operated continuously for up to 84 years in semiarid eastern Oregon are among the oldest agronomic trials in North America. Disease incidence and severity had been quantified visually but quantification of inoculum density had not been attempted. Natural inoculum of 17 fungal and nematode pathogens were quantified for each of 2 years on eight trials using DNA extracts from soil. Crop type, tillage, rotation, soil fertility, year, and their interactions had large effects on the pathogens. Fusarium culmorum and Pratylenchus thornei were more dominant than F. pseudograminearum and P. neglectus where spring crops were grown, and the opposite species dominances occurred where winter wheat was the only crop. Bipolaris sorokiniana and Phoma pinodella were restricted to the presence of spring cereals and pulse crops, respectively. Helgardia spp. occurred in winter wheat-fallow rotations but not in annual winter wheat. Gaeumannomyces graminis var. tritici was more prevalent in cultivated than noncultivated soils and the opposite generally occurred for Rhizoctonia solani AG-8. Densities of Pythium spp. clade F were high but were also influenced by treatments. Significant treatment effects and interactions were more prevalent in two long-standing (>50-year) annually cropped experiments (29%) than two long-standing 2-year wheat-fallow rotations (14%). Associations among pathogens occurred mostly in an 84-year-old annual cereals experiment. This survey provided guidance for research on dynamics of root-infecting pathogens of rainfed field crops and identified two pathogens (Drechslera tritici-repentis and P. pinodella) not previously identified at the location.

Predicting Cereal Root Disease in Western Australia Using Soil DNA and Environmental Parameters

Root diseases have long been prevalent in Australian grain-growing regions, and most management decisions to reduce the risk of yield loss need to be implemented before the crop is sown. The levels of pathogens that cause the major root diseases can be measured using DNA-based services such as PreDicta B. Although these pathogens are often studied individually, in the field they often occur as mixed populations and their combined effect on crop production is likely to vary across diverse cropping environments. A 3-year survey was conducted covering most cropping regions in Western Australia, utilizing PreDicta B to determine soilborne pathogen levels and visual assessments to score root health and incidence of individual crop root diseases caused by the major root pathogens, including Rhizoctonia solani (anastomosis group [AG]-8), Gaeumannomyces graminis var. tritici (take-all), Fusarium pseudograminearum, and Pratylenchus spp. (root-lesion nematodes) on wheat roots for 115, 50, and 94 fields during 2010, 2011, and 2012, respectively. A predictive model was developed for root health utilizing autumn and summer rainfall and soil temperature parameters. The model showed that pathogen DNA explained 16, 5, and 2% of the variation in root health whereas environmental parameters explained 22, 11, and 1% of the variation in 2010, 2011, and 2012, respectively. Results showed that R. solani AG-8 soil pathogen DNA, environmental soil temperature, and rainfall parameters explained most of the variation in the root health. This research shows that interactions between environment and pathogen levels before seeding can be utilized in predictive models to improve assessment of risk from root diseases to assist growers to plan more profitable cropping programs.

Selected Pacific Northwest Crops as Hosts of Pratylenchus neglectus and P. thornei

Thirty crop species and cultivars were assayed in the greenhouse for efficiency as hosts of Pratylenchus neglectus and P. thornei. Hosting ability ratings were assigned using the ratio of final versus initial nematode density and also by comparing the final nematode density to that of a susceptible wheat control. Good hosts of both Pratylenchus spp. included oat 'Monida', chickpea 'Myles', and lentil 'Athena' and 'Morton'. Good hosts of P. neglectus but not of P. thornei included 10 Brassica spp. (5 canola, 2 mustard, and 3 camelina cultivars), chickpea 'Sierra', sudangrass 'Piper', and sorghum/sudangrass hybrid 'Greentreat Plus'. Good hosts of P. thornei but not of P. neglectus included lentil 'Skyline' and pea 'Granger', 'Journey', and 'Universal'. Poor or minor hosts of both Pratylenchus spp. included chickpea 'Dwelley', pea 'Badminton', safflower 'Gila', 'Girard', and 'KN 144', sunflower '2PD08', flax 'Pembina', eastern gamagrass 'Pete', and switchgrass 'Blackwell'. Results of these assays will provide guidance for improving crop rotation and cultivar selection efficiencies.

Selected Pacific Northwest Rangeland and Weed Plants as Hosts of Pratylenchus neglectus and P. thornei

Eighteen rangeland plants and 16 weed species were assayed in the greenhouse for efficiency as hosts of Pratylenchus neglectus and P. thornei. Hosting ability ratings were assigned using the ratio of final versus initial nematode density and by comparing the final nematode density to that of susceptible wheat controls. Good hosts of both Pratylenchus spp. included thickspike bluegrass 'Critana', smooth brome 'Manchar', seven wheatgrasses, and jointed goatgrass. Good hosts of P. neglectus but not P. thornei included two hairy vetches, western wheatgrass 'Rosana', big bluegrass 'Sherman', tall wheatgrass 'Alkar', green foxtail, kochia, large crabgrass, palmer amaranth, redroot pigweed, tumble mustard, and wild oat. Good hosts of P. thornei but not P. neglectus included hard fescue 'Durar', sheep fescue 'Blacksheep', downy brome, and rattail fescue. Poor or minor hosts of both Pratylenchus spp. included two alfalfas, dandelion, horseweed, lambsquarters, prostrate spurge, and Russian thistle. These assays will provide guidance for transitioning rangeland into crop production and for understanding the role of weeds on densities of Pratylenchus spp. in wheat-production systems.

Resistance and Tolerance of Landrace Wheat in Fields Infested with Pratylenchus neglectus and P. thornei

Pratylenchus neglectus and P. thornei reduce wheat yields in the Pacific Northwest of the United States. Resistant landrace cultivars have been identified using controlled environments. Field resistance and tolerance characteristics were compared over 3 years and two locations for four spring wheat cultivars: the susceptible 'Alpowa' and 'Louise' and the resistant landraces AUS28451 and Persia 20. Proportions and densities of P. neglectus and P. thornei differed across seasons and locations. Resistance was evaluated by comparing preplant and postharvest densities of nematodes in soil. Tolerance was evaluated by comparing grain yield and grain quality in plots treated or untreated by the nematicide aldicarb. Alpowa was susceptible and intolerant, Louise was susceptible and moderately tolerant, AUS28451 was resistant and intolerant, and Persia 20 was moderately susceptible and moderately intolerant. The species dominance shifted from P. neglectus to P. thornei in one field over a period of 3 years in apparent response to cultivars and crops planted. Estimates of economic loss caused by Pratylenchus spp. ranged from $8 to $20/ha. Economic benefits appear to be achievable by developing a spring wheat genotype with tolerance plus resistance, such as with a cross between AUS28451 and Louise.

Natural Suppression of Rhizoctonia Bare Patch in a Long-Term No-Till Cropping Systems Experiment

The soilborne fungus Rhizoctonia solani AG-8 is a major concern for farmers who practice no-till in the inland Pacific Northwest of the United States. Bare patches caused by Rhizoctonia spp. first appeared in 1999 during year 3 of a 15-year no-till cropping systems experiment near Ritzville, WA (269 mm of annual precipitation). The extent and pattern of patches were mapped each year from 1999 to 2012 at the 8-ha study site with a backpack-mounted global positioning system equipped with mapping software. Bare patches appeared in winter and spring wheat (SW; Triticum aestivum), spring barley (SB; Hordeum vulgare), yellow mustard (Brassica hirta), and safflower (Carthamus tinctorius). At its peak in years 5 to 7, bare patches occupied as much as 18% of total plot area in continuous annual monoculture SW. The area of bare patches began to decline in year 8 and reached near zero levels by year 11. No measurable patches were present in years 12 to 15. Patch area was significantly greater in continuous SW compared with SW grown in a 2-year rotation with SB. Additionally, the 15-year average grain yield for SW in rotation with SB was significantly greater than for continuous SW. Russian thistle (Salsola tragus), a troublesome broadleaf weed with a fast-growing tap root, was the only plant that grew within patches. This article reports the first direct evidence of natural suppression of Rhizoctonia bare patch with long-term no-till in North America. This suppression also developed in a rotation that contained broadleaf crops (yellow mustard and safflower) in all but 5 years of the study, and the suppression was maintained when safflower was added back to the rotation.

Developing a Real-Time PCR Assay for Detection and Quantification of Pratylenchus neglectus in Soil

Pratylenchus neglectus is one of the most widespread and economically important nematodes that invades plant roots and restricts wheat productivity in the Pacific Northwest. It is challenging to quantify P. neglectus using microscopic methods for studies that require large-scale sampling, such as assessment of rotation crops, wheat cultivars, and other management practices. A real-time quantitative polymerase chain reaction (qPCR) assay was developed to detect and quantify P. neglectus from DNA extracts of soil. The primers, designed from the internal transcribed spacer region of rDNA, showed high specificity with a single melt curve peak to DNA from eight isolates of P. neglectus but did not amplify DNA from 28 isolates of other plant-parasitic and non-plant-parasitic nematodes. A standard curve (R² = 0.96; P < 0.001) was generated by amplifying DNA extracted from soil to which nematodes were added. The soil standard curve was validated using sterilized soil inoculated with lower numbers of P. neglectus. A significant positive relationship (R² = 0.66; P < 0.001) was observed for nematode numbers quantified from 15 field soils using qPCR and the Whitehead tray and microscopic method but the qPCR generally tended to provide higher estimates. Real-time PCR potentially provides a useful platform for efficient detection and quantification of P. neglectus directly from field soils.

Influence of Semiarid Cropping Systems on Root Diseases and Inoculum Density of Soilborne Pathogens

There is interest in converting the 2-year rotation of rainfed winter wheat with cultivated fallow in the Pacific Northwest of the United States into direct-seed (no-till) systems that include chemical fallow, spring cereals, and food-legume and brassica crops. Eight cropping systems in a low-precipitation region (<330 mm) were compared over 9 years to determine effects of changes on diseases. Fusarium crown rot was more prevalent in wheat following cultivated than chemical fallow, and Rhizoctonia root rot was more severe when winter wheat was rotated with chemical fallow than with no-till winter pea. Take-all occurred even during the driest years and was more severe on annual spring wheat than on annual spring barley. Inoculum density (picograms of DNA per gram of soil) differed (α < 0.05) among cropping systems for Fusarium culmorum, F. pseudograminearum, Gaeumannomyces graminis var. tritici, and Pythium spp. but not for Rhizoctonia solani AG-8. Phoma medicaginis var. pinodella was detected only where winter pea was planted frequently. This is the first report of P. medicaginis as a component of the dryland stem rot complex of pea in north-central Oregon. Results of this investigation will provide guidance for developing crop species with resistance to Fusarium crown rot and black stem of pea.