Location: Mycology and Nematology Genetic Diversity and Biology Laboratory
2020 Annual Report
Objectives
Objective 1: Identify and characterize nematode proteins and lipids that inhibit the metabolic pathways critical to fundamental processes in plant-parasitic nematodes.
Sub-objective 1A: Discover and characterize endogenous nematode agonists or antagonists, including bioactive peptides, which affect metabolism and behavior.
Sub-objective 1B: Characterize protease and other enzyme profiles in plant-parasitic nematodes, and determine their roles and modes of action in regulating development and hatching.
Sub-objective 1C. Identify lipids and steroids with likely regulatory roles in plant-parasitic nematodes and design methods to disrupt this regulation.
Objective 2: Improve the effectiveness of nematode management based on amendments and beneficial organisms, and by identifying and characterizing plant, microbe or nematode products antagonistic to nematodes.
Sub-objective 2A: Evaluate cover crops, soil amendments and microbes for suppressing plant-parasitic nematode populations on agricultural crops.
Sub-objective 2B: Determine effects of natural products from plants, microbes, and nematodes on plant-parasitic nematodes, and evaluate selected nematode-antagonistic products as potential nematotoxins.
Objective 3: Assay and analyze the variability in DNA genetic markers across nematode taxa to ascertain those markers optimal for identifying priority crop parasitic nematodes and for refining their phylogenies. [NP303, C1, PS1]
Objective 4: Apply microscopic and DNA genetic marker methods to a diversity of crop parasitic nematode taxa and specimens to identify unknown specimens and to improve diagnostic approaches.
[NP303, C1, PS1]
Objective 5: Identify and describe invasive and emerging plant-parasitic nematodes from forage and biomass legumes, turf, grasses, and associated rotation crops - including species of quarantine significance - to enable specific and timely management of these pests. [NP303, C1, PS1]
Objective 6: Improve molecular methodologies for the identification and classification of nematodes from forage legumes and grasses in order to better predict and respond to nematode outbreaks and to improve detection and diagnostic methodologies to distinguish closely related or morphologically similar species. [NP303, C1, PS1]
Approach
1. Discovering and characterizing internal plant parasitic nematode regulatory molecules, including peptides, proteases, inhibitors, and nematode-unique lipids and steroids, that act as effectors of behavior, development, hatching and metabolism, will provide novel targets for disruption of nematode life processes. Analyzing external signals, including plant chemicals, and their interactions with internal nematode pathways, will expand the number of molecular targets for nematode control. 2. Evaluating cover crops, soil amendments, microbes, and other beneficial agents, and improving strategies for their application, will lead to enhanced plant-parasitic nematode suppression and improved plant yields. Assessing the biological effects of selected beneficial organisms, and the analysis of natural products from plant, microbial and nematode origins, will reveal novel nematotoxins and other suppressive agents for plant-parasitic nematode control and agricultural crop protection. 3. Expanding ribosomal and nuclear gene sequences to more nematode species beyond the relatively few in GenBank will produce more informative family trees demonstrating the distribution of plant parasitism for improved pathology prediction. 4. Advanced microscopy techniques and appropriately selected and designed DNA genetic markers will reveal more detailed features and increase consistency of nematode description for improved diagnosis of nematodes that may damage agriculturally important plants.
Progress Report
This report is for Project 8042-22000-300-00D “Molecular Systematics, Identification, Biology, and Management of Crop-Parasitic Nematodes.” Progress was made under Objectives 2, 3, and 4. No progress was recorded under Objective 1 due to the retirement of the two scientists associated with this objective. The work in this project falls under National Program 303, C1, PS1; C2, PS2A; and C3, PS3B.
As part of Objective 2, research was conducted on winter pea cover crops to determine host status of selected cultivars to root-knot nematodes, and effects of these cover crops on root-knot nematode populations on a succeeding vegetable crop. Microbes were studied as potential biological control agents and as sources of compounds active against nematodes. Research was also conducted to determine nematotoxicity of natural products. These investigations are important for enhancing or developing methods for managing plant-parasitic nematodes and improving crop yields.
As part of Objective 3, multiple molecular markers were developed and used for parasitic and other nematodes, thereby improving identification and construction of comprehensive phylogenetic trees. New primers were adapted to more reliably generate 18S ribosomal DNA markers for nematodes previously difficult to amplify. Primers were also produced to generate a much longer ribosomal DNA sequence spanning three regions for more accurate and rapid molecular diagnoses. In collaboration with scientists from University of Alexandria, Egypt, research was completed that provided the first evidence for resistance and susceptibility in specific cultivars of oats and wheat and five weedy grasses to the cyst nematode Heterodera goldeni in the greenhouse. A second study involved the reactions of four cotton, two sesame, and six flax cultivars to the root-knot nematodes Meloidogyne arenaria, M. incognita race 1 and/or M. javanica in the greenhouse. The results showed all three tested root-knot nematode species reproduced successfully on some of the tested cultivars but not others. For Objective 3B nematodes from long-term agricultural research farming system plots in Beltsville, Maryland, were enumerated, imaged, described and DNA sequences generated.
For Objectives 3 and 4, two new species and one new subspecies of plant-parasitic nematodes were identified and/or described using microscopic and SEM techniques to detail anatomical features as well as molecular and phylogenetic details. A potentially lethal, invasive beech leaf disease nematode (BLD) subspecies Litylenchus crenatae mccannii was described as transmitting to beech buds and leaves, generating international concerns. This discovery in Ohio woodland has turned into a multidisciplinary and multinational effort to piece together a puzzle and understand a scourge that is killing trees by the thousands in northern states east of the Great Plains (ARS Tellus 2019 Cover story). One new lesion nematode and one new cyst nematode, parasitizing soybean in North Dakota and on golf courses in Southern Oregon, respectively, were discovered and characterized; four new country records of nematodes were discovered including three from the USA and one from Rwanda as follows: Boleodorus volutus on Hemp in Maryland, root-knot nematode (Meloidogyne hispanica) and Tylenchus rex on corn in South Carolina, and reniform nematode (Rotylenchulus parvus) on soybean from Rwanda. New records of two cyst nematodes (Heterodera medicaginis and Vittatidera zeaphila) from alfalfa fields in Utah and corn in Indiana (respectively), and one lesion nematode (Pratylenchus fallax) on soybean in Wisconsin were characterized and published. In addition, six new records were made of economically important nematodes: one lesion (Pratylenchus hipeastri on grapevine in California), one root-knot (Meloidogyne naasi from a golf course in Idaho), and one cyst (Cactodera milleri on quinoa: Chenopodium quinoa, in Idaho and Minnesota), and three new records of invasive beech leaf disease nematode (BLD; subspecies Litylenchus crenatae mccannii) parasitizing beech leaf in Connecticut, New York and Pennsylvania. Aphelenchoides fragariae associated with Bursaphelenchus antoniae found in the U.S. on white pine in Massachusetts was characterized.
As part of the service component of Objective 4, ARS scientists provided nematode identifications and expertise during the last year for over 385 samples submitted by various customers for research, regulation and control purposes. The USDA Nematode Collection, one of the largest in existence, was curated, managed and expanded with the addition of 377 valuable slides and vials, bringing the total number including museum jars to 61,228. Three slides and 34 samples (about 750 specimens) were either loaned to scientists or sent for molecular analysis for research purposes and a computerized internet-accessible database was updated for the Collection with thousands of sample records on hosts, occurrence and distribution. Over 150 specimen records were entered in the database for a total of 50,265 current records. During FY 2020 accurate nematode identifications and related expertise were provided for 175 urgent plant and soil samples intercepted by APHIS at ports-of-entry or during domestic surveys. Domestic surveys included national surveys for the presence of potato pale cyst nematodes and surveys in New York and Idaho to delineate the distribution of golden and pale cyst nematodes and the viability of cysts following soil fumigation. Nematodes identified from plant materials intercepted at ports of entry included a variety of cyst, root-knot, lesion, foliar, dagger, stunt, ring, spiral, and burrowing nematodes. Related expertise provided to APHIS included information about the distribution and pathogenicity of many of these nematodes as well as potentially invasive nematode species, information on morphological and molecular protocols useful for identification, and information about which nematode species pose threats to agriculture. The results of these identifications were used by APHIS for taking appropriate regulatory actions beneficial to growers and the public. These taxonomic reports and resources are used by research scientists, extension agencies and regulatory action agencies involved in nematode research and control.
Accomplishments
1. Invading nematode discovered on beech trees. The American beech tree represents a major component in North American deciduous forests. The green and yellow stripes of beech leaf disease (BLD) were first discovered near Cleveland, Ohio, in 2012. ARS scientists from Beltsville, Maryland, in collaboration with the Forest Service, Ohio’s Department of Agriculture and Holden Arboretum, and Canadian researchers discovered and described a new subspecies of the foliar plant-parasitic nematode causing this disease. This potentially lethal (BLD) nematode subspecies Litylenchus crenatae mccannii is of international concern because it is believed to be an invasive species from Asia and that North American native trees have little to no resistance. This work is of critical importance to domestic and international regulatory officials and forest health professionals in the control and management of this disease.
2. Chia plants host and produces compounds active against nematodes. Chia (Salvia hispanica L.) seeds have a market size of over $1 billion globally and are one of the fastest-growing commodity markets, with an increasing demand for use in food, drinks, oil, cosmetics, pharmaceuticals, and animal feed. ARS researchers in Beltsville, Maryland, and a University of Kentucky collaborator discovered that chia plants could host the root-knot nematode Meloidogyne incognita and produce compounds active against nematodes. This research will assist growers and plant disease management professionals by demonstrating that nematode pathogens should be considered when planning management strategies for chia crops and chia might be a source of natural chemicals useful in the control of nematodes.
3. Fiber and grain crops are infected by root-knot and cyst nematodes. Plant-parasitic nematodes cause an estimated ten billion dollars of crop losses each year in the United States and 100 billion dollars globally, but little is known of their host ranges. ARS scientists at Beltsville, Maryland, in collaboration with Egyptian scientists discovered that root-knot nematodes could infect specific cotton, sesame, and flax cultivars and a cyst nematode could infect oat and wheat cultivars as well as five weedy grasses in greenhouse trials. These results are significant because they provide the first evidence that tested cultivars are susceptible to the nematode species examined. This research will be used by scientists, growers and extension personnel involved in root-knot and cyst nematode research and control.
Review Publications
Jindapunnapat, K., Meyer, S.L., Macdonald, M.H., Reetz, N.D., Chitwood, D.J., Masler, E.P., Soonthornchareonnon, N., Camp, M.J., Sasnarukkit, A., Chinnasri, B. 2019. Vegetable plant vigor and suppression of Meloidogyne incognita with vetiver shoot amendments in soil. Nematropica. 49:208-219.
Ibrahim, I.K., Handoo, Z.A., Zid, A.M., Kantor, M.R. 2019. Evaluation of some plant species for their resistance against root-knot nematode Meloidogyne spp. Pakistan Journal of Nematology. 37(2):135-140. https://doi.org/10.18681/pjn.v37.i02.p135-140.
Carta, L.K., Handoo, Z.A., Li, S., Kantor, M., Bauchan, G.R., Mccann, D., Gabriel, C.K., Yu, Q., Reed, S., Koch, J., Martin, D., Burke, D.J. 2020. Beech leaf disease symptoms caused by newly recognized nematode subspecies Litylenchus crenatae mccannii (Anguinata) described from Fagus grandifolia in North America. Forest Pathology. 50(2):e12580. https://doi.org/10.1111/efp.12580.
Ibrahim, I.K., Awd-Allah Sherin, F., Handoo, Z.A., Khalil, A.E., Kantor, M. 2019. Reaction of oat and wheat cultivars and Poaceous grasses to the cyst Nematode Heterodera goldeni. Nematropica. 49:189-193.
Handoo, Z.A., Skantar, A.M., Hafez, S.A., Kantor, M.R., Hult, M.N., Rogers, S.T. 2020. Molecular and morphological characterization of the alfalfa cyst nematode, Heterodera medicaginis, from Utah. Journal of Nematology. 19(52):1065-1081.
Azevedo, L.H., Moreira, M.F., Grilli, G., Borges, V., De Moraes, G.J., Inomoto, M.M., Vicente, M., Desiqueira, M., Peres, L.P., Rueda-Ramirez, D., Carta, L.K., Meyer, S.L., Mowery, J.D., Bauchan, G.R., Ochoa, R., Palevsky, E. 2020. Combined releases of predatory mites and provisioning of free-living nematodes for the biological control of root-knot nematodes on `Micro Tom tomato'. Biological Control. https://doi.org/10.1016/j.biocontrol.2020.104280.
Wen, Y., Meyer, S.L., MacDonald, M.H., Zheng, L., Jing, C., Chitwood, D.J. 2019. Nematotoxicity of Paeonia spp. extracts and Camellia oleifera tea seed cake and extracts to Heterodera glycines and Meloidogyne incognita. Plant Disease. 103:2191-2198. https://doi.org/10.1094/PDIS-09-18-1663-RE.
Skantar, A.M., Handoo, Z.A., Kantor, M.R., Carta, L.K., Faghihi, J., Ferris, V. 2020. Characterization of Vittatidera zeaphila (Nematoda: Heteroderidae) from Indiana with molecular phylogenetic analysis of the genus. Journal of Nematology. 52:1-8. https:/doi:10.21307/jofnem-2020-024.
García De La Cruz, R., Knudsen, G.R., Dandurand, L.C., Carta, L.K., Newcombe, G. 2020. Nematodes associated with invasive spotted knapweed. Nematropica. 49(2):200-207.
Saikai, K.K., Handoo, Z.A., MacGuidwin, A.E. 2019. First report of the root-lesion Nematode, Pratylenchus fallax, on soybean in Wisconsin, USA. Plant Disease. 103(8):1555. https://doi.org/10.1094/PDIS-02-19-0288-PDN.
Carta, L.K., Li, S. 2020. Improvement of long segment ribosomal PCR amplification for the molecular taxonomic identification of Litylenchus crenatae mccannii in beech trees with beech leaf disease. Journal of Nematology. 52:e2020-016. https://doi.org/10.21307/jofnem-2020-016.
Reed, S., Greifenhagen, S., Yu, Q., Burke, D., Carta, L.K., Handoo, Z.A., Kantor, M., Koch, J. 2020. Foliar nematode, Litylenchus crenatae ssp. mccannii, population dynamics in leaves and buds of beech leaf disease affected trees in Canada and the US. Forest Pathology. https://doi.org/10.1111/efp.12599.
Skantar, A.M., Handoo, Z.A., Kantor, M.R., Hult, M.N., Hafez, S.A. 2019. First report of the cactus cyst nematode, Cactodera cacti, from a cactus garden in Idaho. Journal of Nematology. 51:1-6. https://doi.org/10.21307/jofnem-2019-044.
