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Research Project: Improved Strategies for Management of Soilborne Diseases of Horticultural Crops

Location: Horticultural Crops Research

2016 Annual Report

Objective 1: Identify and characterize key pathogens to pinpoint critical pathogen vulnerabilities and develop targeted disease management strategies. Objective 2: Identify plant germplasm and cultivars of small fruits resistant to economically-important soilborne diseases. Objective 3: Expand knowledge of genomic features and regulatory mechanisms in biological control strains of Pseudomonas spp. to develop more consistent and effective tools for biologically-based disease management.

Determine the prevalence and characterize the population diversity of important soilborne pathogens affecting horticultural crops. Results from this research will identify specific pathogen populations that constrain production of horticultural crops. These populations can be targeted in the future to develop more effective, economical, and environmentally-acceptable disease management systems. Evaluate germplasm of black raspberry (Rubus occidentalis) for resistance to Verticillium wilt, caused by V. dahliae, and germplasm of red raspberry (Rubus ideaus) for resistance to the root lesion nematode, P. penetrans. Our research will identify Rubus genotypes and raspberry cultivars that are resistant to these soilborne diseases, and can be deployed in horticultural production systems in the future. Develop improved knowledge of the mechanisms by which the biological control agent Pseudomonas fluorescens Pf-5 suppresses disease. Results from this research will enable pathologists, horticulturists, and growers to develop more effective and reliable biological controls for soilborne diseases of horticultural crops.

Progress Report
Towards our first objective to identify key pathogens limiting the production of small fruit or nursery crops, we isolated and identified Phytophthora and Pythium species from rhododendron at several commercial nurseries as part of a ‘Systems Approach’ aimed at improving plant health for nursery production. Isolates of Phytophthora and Pythium from rhododendron were then evaluated in two greenhouse and two field trials to evaluate pathogenicity, effects of irrigation and pathogen population size on disease development, and disease management with fungicides. Results from these studies will provide information on how damaging these pathogens are to rhododendron and whether irrigation and proper use of fungicides can effectively manage Phytophthora root rot of rhododendron. Phytophthora rubi isolates were obtained from 25 commercial red raspberry fields to identify whether fungicide resistance is present in the pathogen population. We tested 90 isolates for sensitivity to mefenoxam, a common fungicide used in the industry to control Phytophthora root rot. Phosphorous acid, dimethomorph, and cyazofamid, three fungicides that have been used to control Phytophthora root rot, are also being evaluated. Results from this study will provide evidence of whether fungicide resistance has developed and whether growers will need to switch fungicide chemistries to obtain disease control. To continue to explore the genetic diversity of the virus transmitting plant-parasitic nematode Xiphinema americanum, the genome of a population was sequenced using MiSeq. The endosymbiont Xiphinematobacter was identified in the nematode. The genome of this organism was assembled; the annotation of the genome suggests that Xiphinematobacter functions as a nutritional mutualist in X. americanum. This data will be used to explore the coevolution of the nematode and endosymbiont. Additionally, the molecular mechanisms of virus vectoring and the development of diagnostic tools continue to be pursued.

1. First report of a bacterial mutualist genome present in dagger nematodes. Dagger nematodes are production limiting plant-parasitic nematodes in small fruit production systems (raspberry, grape, blueberry) because they cause direct damage to the plant and also transmit plant viruses. ARS scientists in Corvallis, Oregon, with collaborators at Oregon State University, found genetic material of a bacterial mutualist in the gut and ovaries of dagger nematodes. They discovered that this bacterium is likely a nutritional mutualist for the nematode supplementing essential nutrients that are not present in the nematodes’ diet. These results are significant because they suggest candidate limiting nutrient pathways in the nematode that may be manipulated. These findings will be used by researchers to develop novel nematode management strategies that target the bacterium associated with this economically-important plant-parasitic nematode.

2. Blueberry cultivars with resistance to Phytophthora cinnamomi. Phytophthora cinnamomi is an important soilborne pathogen of blueberry worldwide, as it causes root rot and limits establishment of new blueberry fields. ARS scientists at Corvallis, Oregon, with collaborators at Oregon State University, evaluated 18 blueberry cultivars for resistance to P. cinnamomi. They discovered six cultivars with resistance towards the pathogen. Results are significant because they provide an alternative disease control method for growers with soil populations of P. cinnamomi and for organic growers who cannot apply fungicides to manage root rot disease.


Review Publications
Song, C., Kidarsa, T., Van De Mortel, J.E., Loper, J.E., Raaijmakers, J.M. 2016. Living on the edge: Emergence of spontaneous gac mutations in Pseudomonas protegens during swarming motility. Environmental Microbiology. 18(10):3453-3465. doi: 10.1111/1462-2920.13288.
Clifford, J.M., Buchanan, A., Vining, O., Kidarsa, T.A., Chang, J.H., Mcphail, K., Loper, J.E. 2015. Phloroglucinol functions as an intracellular and intercellular chemical messenger influencing gene expression in Pseudomonas protegens. Environmental Microbiology. 18(10):3296-3308. doi: 10.1111/1462-2920.13043.
Quecine, M.C., Kidarsa, T.A., Goebel, N.C., Shaffer, B.T., Henkels, M.D., Zabriskie, T.M., Loper, J.E. 2016. An inter-species signaling system mediated by fusaric acid has parallel effects on antifungal metabolite production by Pseudomonas protegens Pf-5 and antibiosis of Fusarium spp. Applied and Environmental Microbiology. 82:1372-1382.
Yeo, J.R., Weiland, G.E., Sullivan, D., Bryla, D.R. 2016. Susceptibility of highbush blueberry cultivars to Phytophthora root rot. HortScience. 51(1):74-78.
Phillips, W.S., Kieren, S.R., Zasada, I.A. 2015. The relationship between temperature and development in Globodera ellingtonae. Journal of Nematology. 47:283-289.
Brown, A.M., Howe, D.K., Wasala, S.K., Peetz, A.B., Phillips, W.S., Zasada, I.A., Denver, D.R. 2015. Comparative genomics of a plant-parasitic nematode endosymbiont suggest a role in nutritional symbiosis. Genome Biology and Evolution. 7:2727-2746.
Araujo, W.L., Creason, A., Mano, E.T., Camargo-Neves, A.A., Minami, S.N., Chang, J.H., Loper, J.E. 2016. Genome sequencing and transposon mutagenesis of Burkholderia seminalis TC3.4.2R3 identify genes contributing to suppression of orchid necrosis caused by B. gladioli. Molecular Plant Microbe International Symposium. 29(6):435-446. doi: 10.1094/MPMI-02-16-0047-R.
Lim, C.K., Penesyan, A., Hassan, K.A., Loper, J.E., Paulsen, I.T. 2016. Disruption of transporters affiliated with enantio-pyochelin biosynthesis gene cluster of Pseudomonas protegens Pf-5 has pleiotropic effects. PLoS One. 11(7):e0159884. doi: 10.1371/journal.pone.0159884.
Loper, J.E., Henkels, M.D., Rangel, L.I., Olcott, M.H., Walker, F.L., Bond, K.L., Kidarsa, T.A., Hesse, C.N., Sneh, B., Stockwell, V.O., Taylor, B.J. 2016. Rhizoxin analogs, orfamide A and chitinase production contribute to the toxicity of Pseudomonas protegens strain Pf-5 to Drosophila melanogaster. Environmental Microbiology. 18(10):3509-3521. doi: 10.1111/1462-2920.13369.
Yan, Q., Philmus, B., Hesse, C.N., Kohen, M., Chang, J.H., Loper, J.E. 2016. The rare codon AGA is involved in regulation of pyoluteorin biosynthesis in Pseudomonas protegens Pf-5. Frontiers in Microbiology. 7:497. doi: 10.3389/fmicb.2016.00497.