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United States Department of Agriculture

Agricultural Research Service

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

Location: Horticultural Crops Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Characterization of toxin complex gene clusters and insect toxicity of bacteria representing four sub-groups of Pseudomonas fluorescens - (Peer Reviewed Journal)
(15-Aug-16)
Effect of application timing of oxamyl in non-bearing raspberry for Pratylenchus penetrans management - (Peer Reviewed Journal)
(24-Jul-16)
Genome skimming: A rapid approach to gaining diverse biological insights into multicellular pathogens - (Peer Reviewed Journal)
Denver, D., Brown, A.M., Howe, D.K., Peetz, A.B., Phillips, W.S., Zasada, I.A. 2016. Genome skimming: A rapid approach to gaining diverse biological insights into multicellular pathogens. PLoS Pathogens. 12(8):e1005713. doi: 10.1371/journal.ppat.1005713.
Disruption of transporters affiliated with enantio-pyochelin biosynthesis gene cluster of Pseudomonas protegens Pf-5 has pleiotropic effects - (Peer Reviewed Journal)
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.
Rhizoxin, orfamide A, and chitinase production contribute to the toxicity of Pseudomonas protegens strain Pf-5 to Drosophila melanogaster - (Peer Reviewed Journal)
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, orfamide A, and chitinase production contribute to the toxicity of Pseudomonas protegens strain Pf-5 to Drosophila melanogaster. Environmental Microbiology. doi:10.1111/1462-2920.13369.
First report of Phaeobotryon cupressi causing canker of Calocedrus decurrens in Oregon. - (Peer Reviewed Journal)
(01-Apr-16)
The rare codon AGA is involved in regulation of pyoluteorin biosynthesis in Pseudomonas protegens Pf-5 - (Peer Reviewed Journal)
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.
New canker disease of Incense-cedar in Oregon caused by Phaeobotryon cupressi. - (Abstract Only)
(18-Mar-16)
Living on the edge: Emergence of spontaneous gac mutations in Pseudomonas protegens during swarming motility - (Peer Reviewed Journal)
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. doi: 10.1111/1462-2920.13288.
Genome sequencing and transposon mutagenesis of Burkholderia seminalis TC3.4.2R3 identify genes contributing to suppression of orchid necrosis caused by B. gladioli - (Peer Reviewed Journal)
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.
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. - (Peer Reviewed Journal)
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.
Susceptibility of highbush blueberry cultivars to Phytophthora root rot - (Peer Reviewed Journal)
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.
The relationship between temperature and development in Globodera ellingtonae - (Peer Reviewed Journal)
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.
Phloroglucinol functions as an intracellular and intercellular chemical messenger influencing gene expression in Pseudomonas protegens - (Peer Reviewed Journal)
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. doi: 10.1111/1462-2920.13043.
Comparative genomics of a plant-parasitic nematode endosymbiont suggest a role in nutritional symbiosis - (Peer Reviewed Journal)
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.
Identification of a Signal That Mediates the Crosstalk Between Biosynthetic Gene Clusters for the Antibiotics 2,4-diacetylphloroglucinol and Pyoluteorin in Pseudomonas protegens Pf-5 - (Abstract Only)
Yan, Q., Philmus, B., Chang, J.H., Loper, J.E. 2015. Identification of a Signal That Mediates the Crosstalk Between Biosynthetic Gene Clusters for the Antibiotics 2,4-diacetylphloroglucinol and Pyoluteorin in Pseudomonas protegens Pf-5 [abstract]. American Society for Microbiology Conference on Pseudomonas 2015.
Genes expressed by the biological control bacterium Pseudomonas protegens Pf-5 on seed surfaces - (Abstract Only)
Kidarsa, T.A., Loper, J.E. 2015. Genes expressed by the biological control bacterium Pseudomonas protegens Pf-5 on seed surfaces [abstract]. 10th International PGPR Workshop.
Investigations into the biosynthesis, regulation and self-resistance of toxoflavin in Pseudomonas protegens Pf-5 - (Peer Reviewed Journal)
Philmus, B.J., Shaffer, B.T., Kidarsa, T.A., Yan, Q., Raaijmakers, J.M., Begley, T.P., Loper, J.E. 2015. Investigations into the biosynthesis, regulation and self-resistance of toxoflavin in Pseudomonas protegens Pf-5. ChemBioChem. doi: 10.1002/cbic.201500247.
Influence of native plasmids to fitness of Pantoea vagans strain C9-1 - (Abstract Only)
Klein, J.M., Stockwell, V.O., Loper, J.E. 2015. Influence of native plasmids to fitness of Pantoea vagans strain C9-1 [abstract]. Phytopathology. 105:54-73.
Influence of native plasmids to fitness of Pantoea vagans strain C9-1 - (Abstract Only)
Klein, J.M., Stockwell, V.O., Loper, J.E. 2015. Influence of native plasmids to fitness of Pantoea vagans strain C9-1 A functional gene cluster for toxoflavin biosynthesis in the genome of the soil bacterium Pseudomonas protegens Pf-5 [abstract]. Phytopathology. 105. Phytopathology. 105:54.73.
A functional gene cluster for toxoflavin biosynthesis in the genome of the soil bacterium Pseudomonas protegens Pf-5 - (Abstract Only)
Philmus, B., Shaffer, B.T., Yan, Q., Loper, J.E. 2015. A functional gene cluster for toxoflavin biosynthesis in the genome of the soil bacterium Pseudomonas protegens Pf-5 [abstract]. Phytopathology. 105:54.
Characterization of Pseudomonas syringae from blueberry fields in Oregon and Washington - (Abstract Only)
Stockwell, V.O., Shaffer, B.T., Bennett, R., Lee, J., Loper, J.E. 2015. Characterization of Pseudomonas syringae from blueberry fields in Oregon and Washington [abstract]. Phytopathology. 105:54.132.
Identification of a signal that mediates the crosstalk between biosynthetic gene clusters for the antibiotics 2,4-diacetylphloroglucinol and pyoluteorin in Pseudomonas protegens Pf-5 - (Abstract Only)
Yan, Q., Clifford, J.M., Philmus, B., Chang, J.H., Loper, J.E. 2015. Identification of a signal that mediates the crosstalk between biosynthetic gene clusters for the antibiotics 2,4-diacetylphloroglucinol and pyoluteorin in Pseudomonas protegens Pf-5 [abstract]. 10th International PGPR Workshop.
First description of necrosis in leaves and pseudo-bulbs of Oncidium orchids caused by Burkholderia gladioli in São Paulo State, Brazil - (Peer Reviewed Journal)
Mano, E.T., Minami, S.N., Loper, J.E., Araujo, W.L. 2015. First description of necrosis in leaves and pseudo-bulbs of Oncidium orchids caused by Burkholderia gladioli in São Paulo State, Brazil. Plant Disease. doi: 10.1094/PDIS-03-15-0297-PDN.
pltM is important in the phloroglucinol-mediated crosstalk between biosynthetic gene clusters for the antibiotics 2,4-diacetylphloroglucinol and pyoluteorin in Pseudomonas protegens Pf-5 - (Abstract Only)
Yan, Q., Chang, J.H., Loper, J.E., Clifford, J.M. 2015. pltM is important in the phloroglucinol-mediated crosstalk between biosynthetic gene clusters for the antibiotics 2,4-diacetylphloroglucinol and pyoluteorin in Pseudomonas protegens Pf-5 A functional gene cluster for toxoflavin biosynthesis in the genome of the soil bacterium Pseudomonas protegens Pf-5 [abstract]. Phytobiomes 2015: Designing a New Paradigm for Crop Improvement.
Soilborne Diseases of the Nursery Industry: USDA-ARS and OSU Team Up to Tackle this Pernicious Problem - (Trade Journal)
Weiland, G.E., Scagel, C.F., Grunwald, N.J., Foster, Z., Santamaria, L. 2015. Soilborne Diseases of the Nursery Industry: USDA-ARS and OSU Team Up to Tackle this Pernicious Problem. Digger. 59(7):33-36.
Host status of own-rooted Vitis vinifera varieties to Meloidogyne hapla - (Peer Reviewed Journal)
Howland, A., Skinkis, P.A., Wilson, J.H., Riga, E., Pinkerton, J.N., Schreiner, R.P., Zasada, I.A. 2015. Host status of own-rooted Vitis vinifera varieties to Meloidogyne hapla. Journal of Nematology. 47:141-147.
Root removal to improve disease management in replanted Washington red raspberry fields - (Abstract Only)
Weiland, G.E., Zasada, I.A., Devetter, L.W., Walters, T., Rudolph, R., Watkinson, S. 2015. Root removal to improve disease management in replanted Washington red raspberry fields. American Phytopathological Society Annual Meeting, August 1-5, 2015, Pasadena, California.
Impact of grapevine (Vitis vinifera) varieties on reproduction of the northern root-knot nematode (Meloidogyne hapla) - (Peer Reviewed Journal)
Howland, A.D., Skinkis, P.A., Wilson, J.H., Riga, E., Pinkerton, J.N., Schreiner, R.P., Zasada, I.A. 2015. Impact of grapevine (Vitis vinifera) varieties on reproduction of the northern root-knot nematode (Meloidogyne hapla). Journal of Nematology. 47(2):141–147.
Genomics-guided discovery of secondary metabolites and their regulation in Pseudomonas protegens Pf-5 - (Abstract Only)
Yan, Q., Paulsen, I., Gross, H., Clifford, J.M., Loper, J.E. 2015. Genomics-guided discovery of secondary metabolites and their regulation in Pseudomonas protegens Pf-5 [abstract]. 11th Annual Genomics of Energy & Environmental Meeting.
Phloroglucinol functions as an intercellular chemical messenger with broad transcriptional effects in Pseudomonas protegens Pf-5 - (Abstract Only)
Clifford, J.M., Buchanan, A., Yan, Q., Chang, J.H., Loper, J.E. 2015. Phloroglucinol functions as an intercellular chemical messenger with broad transcriptional effects in Pseudomonas protegens Pf-5 [abstract]. Rhizosphere4.
Greenhouse plants, ornamental – Pythium seed rot, damping-off, and root rot - (Review Article)
Weiland, G.E., Santamaria, L. 2015. Greenhouse plants, ornamental – Pythium seed rot, damping-off, and root rot. Pacific Northwest Plant Disease Control Handbook. p. 4G-47-4G-48.
Population structure of Pythium irregulare, P. sylvaticum, and P. ultimum in forest nursery soils of Oregon and Washington - (Peer Reviewed Journal)
Weiland, G.E., Garrido, P., Kamvar, Z.N., Marek, S.M., Grunwald, N.J., Garzon, C.D. 2015. Population structure of Pythium irregulare, P. sylvaticum, and P. ultimum in forest nursery soils of Oregon and Washington. Phytopathology. 105(5):684-694.
Impact of Pratylenchus penetrans on establishment of red raspberry - (Peer Reviewed Journal)
Zasada, I.A., Weiland, G.E., Han, Z., Walters, T.W., Moore, P.P. 2015. Impact of Pratylenchus penetrans on establishment of red raspberry. Plant Disease. 99(7):939-946.
Effect of storage environment on hatching of Globodera ellingtonae - (Peer Reviewed Journal)
Ingham, R.E., Kroese, D.R., Zasada, I.A. 2015. Effect of storage environment on hatching of Globodera ellingtonae. Journal of Nematology. 47:45-51.
The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis - (Peer Reviewed Journal)
Song, C., Van Der Voort, M., Van De Mortel, J., Hassan, K.A., Elbourne, L.D., Paulsen, I.T., Loper, J.E., Raaijmakers, J.M. 2014. The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis. Microbial Biotechnology. 8(2):296-310.
Spatial distribution of plant-parasitic nematodes in semi-arid Vitis vinifera vineyards in Washington - (Peer Reviewed Journal)
Howland, A.D., Schreiner, R.P., Zasada, I.A. 2014. Spatial distribution of plant-parasitic nematodes in semi-arid Vitis vinifera vineyards in Washington. Journal of Nematology. 46:321-330.
First report of Phytophthora cactorum and P. citrophthora causing root rot of Ribes lobbii (Gray) in Oregon - (Peer Reviewed Journal)
Weiland, G.E. 2015. First report of Phytophthora cactorum and P. citrophthora causing root rot of Ribes lobbii (Gray) in Oregon. Plant Disease. 99(1):157.
Host status of Rubus species and hybrids for the root lesion nematode, Pratylenchus penetrans - (Peer Reviewed Journal)
Zasada, I.A., Moore, P.P. 2014. Host status of Rubus species and hybrids for the root lesion nematode, Pratylenchus penetrans. HortScience. 49:1128-1131.
Analysis of genome sequences from plant pathogenic Rhodococcus reveals genetic novelties in virulence loci - (Peer Reviewed Journal)
Creason, A.L., Vandeputte, O.M., Savory, E.A., Davis, E.W., Putnam, M.L., Hu, E., Swader-Hines, D., Mol, A., Baucher, M., Prinsen, E., Zdanowska, M., Givan, S.A., El Jaziri, M., Loper, J.E., Mahmud, T., Chang, J.H. 2014. Analysis of genome sequences from plant pathogenic Rhodococcus reveals genetic novelties in virulence loci. PLoS One. 9(7):e101996.
Pathogenicity, fungicide resistance, and genetic variability of Phytophthora rubi isolates from raspberry (Rubus idaeus) in the Western United States - (Peer Reviewed Journal)
Stewart, J.E., Kroese, D.R., Tabima, J.F., Larsen, M.M., Fieland, V.J., Press, C.M., Zasada, I.A., Grunwald, N.J. 2014. Pathogenicity, fungicide resistance, and genetic variability of Phytophthora rubi isolates from raspberry (Rubus idaeus) in the Western United States. Plant Disease. 98:1702-1708.
Variation in response among Pythium species and isolates to Streptomyces lydicus - (Abstract Only)
Weiland, G.E. 2014. Variation in response among Pythium species and isolates to Streptomyces lydicus. APS Annual Meeting. August 9-13, 2014, Minneapolis, Minnesota.
Impact of Pratylenchus penetrans on established red raspberry productivity - (Peer Reviewed Journal)
Han, Z., Walters, T.W., Zasada, I.A. 2014. Impact of Pratylenchus penetrans on established red raspberry productivity. Plant Disease. 98:1514-1520.
Identifying rates of meadowfoam (Limnanthes alba) seed meal needed for suppression of Meloidogyne hapla and Pythium irregulare in soil - (Peer Reviewed Journal)
Ersahin, Y.S., Weiland, G.E., Zasada, I.A., Reed, R.L., Stevens, J.F. 2014. Identifying rates of meadowfoam (Limnanthes alba) seed meal needed for suppression of Meloidogyne hapla and Pythium irregulare in soil. Plant Disease. 98(9):1253-1260.
Pseudomonas protegens Pf-5 causes discoloration and pitting of mushroom caps due to the production of antifungal metabolites - (Peer Reviewed Journal)
Henkels, M.D., Kidarsa, T.A., Shaffer, B.T., Goebel, N.C., Burlinson, P., Mavrodi, D.V., Bentley, M.A., Rangel, L.I., Davis Ii, E.W., Thomashow, L.S., Zabriskie, T., Preston, G.M., Loper, J.E. 2014. Pseudomonas protegens Pf-5 causes discoloration and pitting of mushroom caps due to the production of antifungal metabolites. Molecular Plant-Microbe Interactions. 27(7):733-746.
Using mitogenomic and nuclear ribosomal sequence data to investigate the phylogeny of the Xiphinema americanum species complex - (Peer Reviewed Journal)
Zasada, I.A., Peetz, A.B., Howe, D.K., Wilhelm, L.J., Cheam, D., Denver, D.R., Smythe, A.B. 2014. Using mitogenomic and nuclear ribosomal sequence data to investigate the phylogeny of the Xiphinema americanum species complex. PLoS One. 9:e90035.
Sensitivity of Pythium irregulare, P. sylvaticum, and P. ultimum from forest nurseries to mefenoxam and fosetyl-al, and control of Pythium damping-off - (Peer Reviewed Journal)
Weiland, G.E., Santamaria, L., Grunwald, N.J. 2014. Sensitivity of Pythium irregulare, P. sylvaticum, and P. ultimum from forest nurseries to mefenoxam and fosetyl-al, and control of Pythium damping-off. Plant Disease. 98:937-942.
Understanding the pathology of Douglas-fir seedlings in Pacific Northwest nurseries - (Proceedings)
Weiland, G.E. 2015. Understanding the pathology of Douglas-fir seedlings in Pacific Northwest nurseries. In: Rocky Mountain Research Station Proceedings 72. Annual Meeting of Western Forest and Conservation Nursery Association, August 6-7, 2013, Olympia, Washington. p. 38-40.
Methyl bromide phase out could affect future reforestation efforts - (Trade Journal)
Weiland, G.E. 2014. Methyl bromide phase out could affect future reforestation efforts. Western Forester. 59:8-10.
Pythium species and isolate diversity influence inhibition by the biological control agent Streptomyces lydicus - (Peer Reviewed Journal)
Weiland, G.E. 2014. Pythium species and isolate diversity influence inhibition by the biological control agent Streptomyces lydicus. Plant Disease. 98(5):653-659.
Verticillium wilt in the Pacific Northwest - (Review Article)
Dung, J., Weiland, G.E., Pscheidt, J.W. 2014. Verticillium wilt in the Pacific Northwest. Pacific Northwest Plant Disease Control Handbook. p. 3-22 to 3-28.
pA506: A conjugative plasmid of the plant epiphyte Pseudomonas fluorescens A506 - (Peer Reviewed Journal)
Stockwell, V.O., Davis, E.W., Carey, A.B., Shaffer, B.T., Mavrodi, D.V., Hassan, K.A., Hockett, K.L., Thomashow, L.S., Paulsen, I.T., Loper, J.E. 2013. pA506: A conjugative plasmid of the plant epiphyte Pseudomonas fluorescens A506. Applied and Environmental Microbiology. 79:5272-5282.
The Gac Regulon of Pseudomonas fluorescens SBW25 - (Peer Reviewed Journal)
Cheng, X., De Bruijn, I., Van Der Voort, M., Loper, J.E., Raaijmakers, J.M. 2013. The Gac Regulon of Pseudomonas fluorescens SBW25. Environment Microbiology Reports. 5:608-619.
Exploring the characteristics of Pythium communities: Can knowledge about pathogen communities improve disease control? - (Abstract Only)
Weiland, G.E., Garrido, P., Grunwald, N.J., Garzon, C. 2013. Exploring the characteristics of Pythium communities: Can knowledge about pathogen communities improve disease control?. In: Phytopathology. Annual Meeting of the American Phytopathological Society, August 10-14, 2013, Austin, Texas.
Effect of tannic acid on the transcriptome of the soil bacterium Pseudomonas protegens Pf-5 - (Peer Reviewed Journal)
Lim Kent, L., Penesyan, A., Hassan, K.H., Loper, J.E., Paulsen, I. 2013. Effect of tannic acid on the transcriptome of the soil bacterium Pseudomonas protegens Pf-5. Applied and Environmental Microbiology. 79:3141-3145.
Dealing with damping-off - (Trade Journal)
Weiland, G.E., Santamaria, L. 2013. Dealing with damping-off. Digger. April 2013: 41-45.
Pathogenicity and virulence of Pythium species obtained from forest nursery soils on Douglas-fir seedlings - (Peer Reviewed Journal)
Weiland, G.E., Beck, B.R., Davis, E.A. 2013. Pathogenicity and virulence of Pythium species obtained from forest nursery soils on Douglas-fir seedlings. Plant Disease. 97: 744-748.
An aversion to Verticillium - (Trade Journal)
Weiland, G.E. 2013. An aversion to Verticillium. Digger. February 2013: 33-37.
Genes expressed by the biological control bacterium Pseudomonas protegens Pf-5 on seed surfaces under the control of the global regulators GacA and RpoS - (Peer Reviewed Journal)
Kidarsa, T.A., Shaffer, B.T., Goebel, N.C., Roberts, D.P., Buyer, J.S., Johnson, A., Kobayashi, D.Y., Paulsen, I., Loper, J.E. 2013. Genes expressed by the biological control bacterium Pseudomonas protegens Pf-5 on seed surfaces under the control of the global regulators GacA and RpoS. Environmental Microbiology. 15:716-735.
Integration of brassicaceous seed meals into red raspberry production systems - (Peer Reviewed Journal)
Gigot, J., Zasada, I.A., Walters, T.W. 2012. Integration of brassicaceous seed meals into red raspberry production systems. Applied Soil Ecology. 64:23-31.
The effect of zinc limitation on the transcriptome of Pseudomonas protegens Pf-5 - (Peer Reviewed Journal)
Lim, C., Hassan, K.A., Penesyan, A., Loper, J.E., Paulsen, I. 2013. The effect of zinc limitation on the transcriptome of Pseudomonas protegens Pf-5. Environmental Microbiology. 15:702-715.
Last Modified: 8/24/2016
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