Location: Mycology and Nematology Genetic Diversity and Biology Laboratory
2021 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
The work in this project falls under National Program 303, C1, PS1; C2, PS2A; and C3, PS3B. No progress was recorded under Objective 1 due to the retirement of the two scientists associated with this objective.
As part of Objective 2, winter pea cultivars were tested for host status to root-knot nematodes. The research on winter pea demonstrated that the cultivars were susceptible to this nematode. This information is important because it demonstrates that winter pea cultivar selection will likely not be a factor in suppression of phytoparasitic nematodes in agricultural fields. A study on a bacterium isolated from soybean cyst nematode showed that the microbe was active against root-knot and soybean cyst nematodes, and that it produced nematotoxic metabolites. Research on nematode-antagonistic microbes will lead to identification of strains or metabolites that may be utilized for managing these nematodes.
For Objectives 3-6, many new locations and new host associations for nematode species were recorded from the United States. The cyst nematode Cactodera torreyanae was detected for the first time on potato from Minnesota. New records of two new sheath nematodes, one new pin nematode, and one new stubby-root nematode in Maryland were characterized by both morphological and molecular means. Progress included molecular identification and characterization of barley root-knot nematode from turfgrass in Idaho, and Seville root-knot nematode on corn from South Carolina. These discoveries provided new molecular and morphological information on these new species and new records facilitating future identifications of cyst, lesion, and other nematodes.
As part of the service component of Objective 4, ARS scientists provided nematode identifications and expertise during the last year for over 348 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 213 valuable slides and vials, bringing the total number including museum jars to 61,441. Thirteen slides and 13 samples (about 171 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 232 specimen records were entered in the database for a total of 50,495 current records. During FY 2021 accurate nematode identifications and related expertise were provided for 313 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. Movement and tracking of invasive, disease-vectoring nematode of beech trees. Beech Leaf Disease is caused by a newly identified nematode, Litylenchus crenatae mccannii, and can kill both saplings and mature beech trees. ARS scientists from Beltsville, Maryland, in collaboration with scientists from Ontario, Canada, and the state of Rhode Island, generated DNA marker sequences of Litylenchus crenatae mccannii from Beech Leaf Disease samples in the United States and Canada. In addition, microsatellite markers were generated to assist with tracking genetic subpopulations for insight into the spread of the disease in North America. Litylenchus crenatae mccannii has moved from the Great Lakes to the Atlantic Ocean since its emergence. This research will be used by scientists, growers, action agencies, and extension agencies to monitor and control the spread of this emerging nematode more effectively.
2. A patent application and a provisional patent were filed for nematode management agents. Plant-parasitic nematodes cause annual crop losses of $150 billion worldwide. Due to the deregistration of commonly used synthetic chemical nematicides, novel methods are needed to suppress these plant pathogens. A patent application, 0128.18 (Methods of Killing Nematodes), was filed to use complexes to manage phytoparasitic nematodes. In a separate project, a provisional patent application (No. 63/123,615- DN. 76.20) was filed for the use of natural product analogs and combinations for nematode management. These are significant because they have resulted in the identification of compounds and complexes with efficacy against soilborne phytoparasitic nematodes. The proposed technologies will be safer than currently used synthetic chemicals, providing growers worldwide with eco-friendly products for managing plant-parasitic nematodes.
3. New lesion nematode identified from North Dakota. Lesion nematodes are the third most important group of plant-parasitic nematodes after root-knot and cyst nematodes and cause damage to the roots of many kinds of plants worldwide, including soybeans. Management is often hampered by a lack of species identification for the offending pest. In this study, a team of ARS scientists from Beltsville, Maryland, and colleagues from North Dakota State University identified a new species of lesion nematode, Pratylenchus dakotiensis, from a soybean field in North Dakota by both morphological and molecular means. This discovery is significant because information obtained for this new species will facilitate future identifications of this lesion nematode and the management of this emerging soybean pest.
4. Lesion nematode detected in a California vineyard. Lesion nematodes are an important problem damaging the roots of many kinds of plants worldwide. Emerging new species that appear on new hosts or in new locations create significant challenges for crop management. ARS scientists from Beltsville, Maryland, and researchers at the University of Idaho identified a lesion nematode species called Pratylenchus hippeastri from a vineyard in California, using morphological and molecular approaches. The information obtained will allow this nematode to be more easily distinguished from morphologically similar lesion nematodes. This research will be used by scientists, growers, action agencies, and extension agencies to monitor and control the spread of this emerging nematode, which could threaten the $70 billion California wine industry.
5. New reference guides published for nematode genera. Spiral, lesion, ring, and other nematodes are economically important groups of plant-parasitic nematodes that damage the roots of many kinds of plants worldwide. In this study, a team of ARS scientists from Beltsville, Maryland, in collaboration with the Indian Agricultural Research Institute in New Delhi analyzed anatomical traits to identify various plant-parasitic nematodes isolated from vegetable and fruit crops of the Jammu and Kashmir states in India. New morphological information obtained from these new species will facilitate future identifications of these plant-parasitic nematodes and serve as a useful guide to researchers and diagnosticians.
6. A new species of cyst nematode identified from turfgrass in Oregon. Cyst nematodes are an important group of plant-parasitic nematodes that damage the roots of many kinds of plants worldwide, including Poa annua on golf courses. In this study, a team of ARS scientists from Beltsville, Maryland, and colleagues from Oregon State University analyzed anatomical and molecular traits to describe a new species of cyst nematode (Punctodera mulveyi) isolated from turfgrass in Oregon. This discovery is significant because new information obtained will facilitate the identification of this cyst nematode for enhanced disease management strategies. This report will serve as a useful guide to researchers and diagnosticians to help track this potential new threat to the $40-billion recreational turfgrass industry.
7. Detection and identification of pin nematodes in the United States. Pin nematodes (Paratylenchus spp.) are an important group of plant-parasitic nematodes that damage the roots of many kinds of plants worldwide, including grasses. In this study, scientists from the California Department of Food and Agriculture, Sacramento, California, and North Dakota State University and ARS scientists in Beltsville, Maryland, analyzed anatomical and molecular traits to identify the pin nematodes isolated from grasses in Virginia and North Dakota. Information on how to distinguish molecularly among closely related species of nematodes is also included, along with anatomical illustrations. This discovery is significant because new molecular and morphological information obtained from these species will facilitate future identifications of the pin nematodes. This research will be used by scientists, action agencies, and extension agencies involved in nematode identification and control.
Review Publications
Handoo, Z.A., Kantor, M.A., Khan, E. 2020. Description of seven new species and one new record of plant-parasitic nematodes (Nematoda: Tylenchida) associated with economically important crops of Kashmir Valley, Jammu and Kashmir (Part-1 of the series). Pakistan Journal of Nematology. 38(2):110-123.
Kantor, M.A., Handoo, Z.A., Skantar, A.M., Hult, M.N., Ingham, R., Wade, N., Ye, W., Bauchan, G.R., Mowery, J.D. 2020. Morphological and molecular characterisation of Punctodera mulveyi n. sp. (Nematoda: Punctoderidae) from a golf course green in Oregon, USA, with a key to species of the Punctodera. Nematology. https://doi.org/10.1163/15685411-bja10068.
Subbotin, S.A., Yan, G.P., Kantor, M.R., Handoo, Z.A. 2020. On the molecular identity of Paratylenchus nanus Cobb, 1923 (Nematoda: Tylenchida). Journal of Nematology. 52:1-7. doi:10.21307/jofnem-2020-127.
Meyer, S.L.F., MacDonald, M.H., Reetz, N.D., Kantor, M.R., Carta, L.K., Handoo, Z.A., Camp, M.J., Phillips, T.D. 2020. Chia: Host status for Meloidogyne incognita and activity of plant extracts. Plant Disease. 104:2979–2985. https://doi.org/10.1094/PDIS-10-19-2171-RE.
Meyer, S.L., Patchett, B.J., Gillanders, T., Kantor, M., Timper, P., MacDonald, M.H. 2020. Festulolium and fungal endophyte associations: host status for Meloidogyne incognita and nematotoxic plant extracts. Journal of Nematology. 52:1-16. https://doi.org/10.21307/jofnem-2020-076.
Handoo, Z.A., Kantor, M.A., Khan, E. 2021. Description of ten new species including two new genera of nematodes (Nematoda) associated with economically important crops of Kashmir Valley, Jammu and Kashmir. Pakistan Journal of Nematology. 39(1):24-40. https://doi.org/10.17582/journal.pjn/2021/39.1.24.40.
Skantar, A.M., Handoo, Z.A., Kantor, M.R., Hult, M.N., Hafez, S.A., Komroy, K., Sigurdson, K., Grabowski, M. 2021. First report of Cactodera milleri Graney & Bird, 1990 from Colorado and Minnesota. Journal of Nematology. 53:1-7. https://doi.org/10.21307/jofnem-2021-017.
Baldwin, J.G., Handoo, Z.A. 2018. General Morphology. In: Perry, R.N., Moens, M. and Jones, J.T. editors: Cyst Nematodes. Wallingford, Oxfordshire, UK: CABI. p. 337-364.
Handoo, Z.A., Kantor, M.A., Mostafa, H.M., Moawad, M.M., Mahfouz, A.M. 2020. First report of Mesocriconema sphaerocephalum (Taylor, 1936) Loof, 1989 associated with bell pepper (Capsicum annuum) in Egypt. Egyptian Journal of Entomology. 19(1):19-28. https://doi.org/10.21608/ejaj.2020.105860.
Handoo, Z.A., Skantar, A.M., Kantor, M.R., Hafez, S.L., Hult, M.N. 2020. Molecular and morphological characterization of the amaryllis lesion nematode, Pratylenchus hippeastri (Inserra et al., 2007), from California. Journal of Nematology. 52(1):1-5. https://doi.org/10.21307/jofnem-2020-058.
Handoo, Z.A., Subbotin, S.A. 2018. Taxonomy, identification and principal species. In: Perry, R.N., Moens, M. and Jones, J.T. editors. Cyst Nematodes. Wallingsford, Oxfordshire, UK: CABI. p. 365-398.
Handoo, Z.A., Yan, G., Kantor, M., Huang, D., Chowdhury, I.A., Plaisance, A., Bauchan, G.R., Mowery, J.D. 2021. Morphological and molecular characterization of Pratylenchus dakotiensis n. sp. (Nematoda: Pratylenchidae), a new root-lesion nematode species on soybean in North Dakota, USA. Plants. 10(168):1-13. https://doi:10.3390/plants10010168.
Handoo, Z.A., Kantor, M.A., Carta, L.K. 2020. Taxonomy identification of principal foliar nematode species (Aphelenchoides and Litylenchus). Plants. 9(1490):1-31. https://doi.org/10.3390/plants9111490.
