Progress 09/01/14 to 08/31/19
Outputs Target Audience:Same as in previous reports. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Students and postdocs were trained in an interdisciplinary research program. How have the results been disseminated to communities of interest?As described in a previous section, a variety of presentations to diverse audiences were delivered. These included extension pathologists, research scientsts (graduate students/postdocs/academic researchers), congressional staffers. Presentations were at departmental, national and international conferences. Publications included peer-reviewed primary research articles, review articles, and articles in stakeholder-relevant journals. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts What was accomplished under these goals?
We completed the proposed online course. This course will create awareness about plant diseases by teaching concepts and relating them to daily work activities in nursery or greenhouse settings. Completion of this course will hopefully lead nursery workers to begin to develop strategic practices to prevent pests and diseases in their own system of production. At the end of the course, the students will receive a certification they can use to demonstrate their knowledge. The course prototype will be fully executed by August 31, 2019, with the full English language course available to the general public on or before October 9, 2019. The Spanish language course will be available to learners in early 2020.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Thapa et al., (2019) The Evolution, Ecology, and Mechanisms of Infection by Gram-Positive, Plant-Associated Bacteria. Annu. Rev. Phytopathol. Epub ahead of print.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Wu, C-F., Santos, M. N. M., Cho, S-T., Chang, H-H., Tsai, Y-M., Smith, D. A., Kuo, C-H., Chang, J. H., and Lai, E-M. (2019) Plant pathogenic Agrobacterium tumefaciens strains have diverse type VI effector-immunity pairs and vary in in planta competitiveness. MPMI. 32(8):961-971.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Putnam (2019). The Lowdown on Leafy Gall. GrowerTalks. 83:70-74
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Progress 09/01/17 to 08/31/18
Outputs Target Audience:Same as in previous reports. Changes/Problems:The major problem we encountered was that nurseries tend not to record input and output at a scale sufficient for our needs, as proposed in the economic outreach aim. As a consequence, we have engaged in conversations with nurseries to provide opportunities for us to track time and cost associated on plant unit basis. What opportunities for training and professional development has the project provided?Postdocs and students were trained in an interdisciplinary program that spanned basic to applied research. Nursery workers continue to be taught in bilingual programs. How have the results been disseminated to communities of interest?https://www.the-scientist.com/notebook/scientists-cant-agree-on-whats-making-pistachio-trees-sick-64526 http://www.nurserymag.com/article/bacterium-breakthrough/ https://content.govdelivery.com/accounts/USDANIFA/bulletins/1d37681 https://blog.plantwise.org/2017/12/15/rhodococcus-jekyll-and-hyde-bacteria-discovered-in-plant-nurseries/ http://extension.oregonstate.edu/news/release/2017/12/osu-plant-pathologists-discover-unusual-evolutionary-transition-common-bacteria https://www.asm.org/index.php/podcasts/bacteriofiles/item/7305-plasmid-promotes-plant-pathogenesis-bacteriofiles-340 http://www.nurserymag.com/article/osu-discover-rhodococcus-bacteria-evolves/ https://www.sciencedaily.com/releases/2017/12/171212125356.htm http://www.capitalpress.com/Nursery/20171219/researchers-developing-tools-to-track-harmful-bacteria https://phys.org/news/2017-12-pathologists-unusual-evolutionary-transition-common.html https://plantae.org/evolutionary-transitions-between-beneficial-and-phytopathogenic-rhodococcus/ http://www.westernfarmerstockman.com/technology/researchers-uncover-bacteria-change-tactic What do you plan to do during the next reporting period to accomplish the goals?We have applied for a no-cost extenstion to complete the proposed aims. Consistent with the proposed timeline, we are in the late stages of experimentation and most of our efforts will be directed at finalizing our work and preparing data for release and publication.
Impacts What was accomplished under these goals?
We have completed testing the tool-mediated transmission of Rhodococcus and Agrobacterium and are currently writing up the work for publication. We have completed our evaluation of commercially-available products for controlling Rhodococcus and Agrobacterium and are currently writing up the work for publication. We have identified natural products from two species of plants and one species of bacteria. We have determined the structure for one product. We have also demonstrated that the natural product from bacteria controls Agrobacterium in planta. We will be writing up the work for publiction over the next year. We have completed the genomic epidemiological survey of nursery plants for Agrobacteria. We will be writing up the work for publication over the next year. We are currently writing up the work on the evolution of agrobacteria and its oncogenic plasmids. Specific aims 3 and 4 were previously completed. We continue to offer courses on plant health and preventive methods. We learned that for AgBiz Logic to work, that we need to collect more data (see changes/problems).
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2017
Citation:
Savory, EA., Fuller, S.L., Weisberg, A.J., Thomas, W.J., Gordon, M.I., Stevens, D.M., Creason, A.L., Belcher, M.S., Serdani, M., Wiseman, M.S., Grunwald, N.J., Putnam, M.L., and Chang, J.H. 2017. Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management. Elife 6:e30925.
- Type:
Other
Status:
Accepted
Year Published:
2018
Citation:
Chang, J. H., Putnam, M. L., Grunwald, N. J., Savory, E. A., Fuller, S. L., and Weisberg, A. J. (2018) Response to comments on Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management eLife 7:e35852.
- Type:
Book Chapters
Status:
Accepted
Year Published:
2018
Citation:
Wu, C-F., Smith, D. A., Lai, E-M., and Chang, J. H. (2018) The Agrobacterium type VI secretion system: a contractile nanomachine for interbacterial competition in Current Topics in Microbiology and Immunology S. Gelvin Editor, Springer Nature: Heidelberg, Germany.
- Type:
Book Chapters
Status:
Awaiting Publication
Year Published:
2018
Citation:
Savory, E. A., Chang, J. H.6, and Putnam, M. L. Rhodococcus fascians in The Laboratory Guide for Identification of Plant Pathogenic Bacteria, 4th Ed. APS press: St. Paul, MN.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2018
Citation:
Putnam, M.L. 2018. Rhodococcus revisited: Does it have any role in PBTS? Pacific Nut Producer 24:40-42.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2018
Citation:
Putnam, M.L. Treating and Tracking the Intractable Rhodococcus. Digger (submitted, June 2018) [to be published in September]
- Type:
Book Chapters
Status:
Published
Year Published:
2017
Citation:
Putnam, M.L. 2017. Detection of Rhodococcus fascians in ornamental plants. Chapter 46 In: Detection of Plant-Pathogenic Bacteria in Seed and Other Planting Material, 2nd ed., M. Fatmi, R.R. Walcott, and N.W. Schaad (Eds.). St. Paul: American Phytopathological Society, St. Paul, MN.
- Type:
Book Chapters
Status:
Published
Year Published:
2017
Citation:
Putnam, M.L. 2017. Detection of Agrobacterium tumefaciens in ornamental plants. Chapter 47 In: Detection of Plant-Pathogenic Bacteria in Seed and Other Planting Material, 2nd ed., M. Fatmi, R.R. Walcott, and N.W. Schaad (Eds.). St. Paul: American Phytopathological Society, St. Paul, MN.
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Progress 09/01/16 to 08/31/17
Outputs Target Audience:Same as in previous reports Changes/Problems:We repeatedly and consistently detected pathogenic Rhodococcus on plants donated to us for use in in planta assays. This was a systemic problem and we had to resort to propagating our own plants to produce uninfected material for our work. This did not result in a major change in approach but it significantly delayed our efforts to address aspects of Specific Objective 1a and b. Results from the nursery industry workshop revealed the challenges for individual nursery owners to collect field data for labor, inputs, etc. to develop accurate enterprise budgets, which is the foundation of AgBiz Logic. Consensus was reached that "getting close enough" with data collection and allocation to enterprise budgets was the best nursery operations could do at this time (which means allocating most costs equally across the number of plants sold and adjusting the costs of selected inputs). One larger nursery representative wrote in an email after the session "There isno waythat tracking each individual cultivar is worth the time and effort. In my opinion there is also little benefit in tracking each labor activity or each material expense per cultivar. We attempted that at the nursery years ago and came away with numbers that were more biased and further away from reality." We will assist nursery owners in identifying the most important input variables to "best guess" in allocating costs to generate enterprise budgets for analysis. The challenge in data collection for nursery owners will also impact the economic assessment of this project. An industry meeting towards the end of this project should be held to ask industry owners, from their viewpoint, how the results of this research impacts their business' bottom line. What opportunities for training and professional development has the project provided?The training of postdocs, graduate students, undergraduate students, and high school students is framed in a cross-disciplinary, translational research program. Five workshops (in Spanish) were delivered to 70 nursery workers and helped in their professional development. Ten nursery operations will be using this AgBiz LogicTM to gather and collect cost of production data for their own operations and using these budgets in decision making strategies. How have the results been disseminated to communities of interest?Researchers refine diagnostic tool to quickly identify plant pathogen http://www.capitalpress.com/Nursery/20170711/researchers-refine-diagnostic-tool-to-quickly-identify-plant-pathogen NIFA fresh from the field: Success Stories of the week https://content.govdelivery.com/accounts/USDANIFA/bulletins/1a9cb3f OSU College of Agriculture: The Source http://agsci.oregonstate.edu/source/summer-2017 Oregon State University Extension Service http://extension.oregonstate.edu/news/release/2017/07/osu-research-leads-detection-method-crown-gall-disease Washington Ag Network http://washingtonagnetwork.com/2017/07/20/work-oregon-state-speed-crown-gall-diagnosis/ Good Fruit Grower http://www.goodfruit.com/osu-researchers-develop-field-test-for-crown-gall/ Western Farmer-Stockman http://www.westernfarmerstockman.com/crop-disease/oregon-research-finds-crown-gall-detection-method AgInfo.net http://www.aginfo.net/index.cfm/event/report/id/Fruit-Grower-Report-37591 Four separate presentations at the 37th Annual Crown Gall conference. Presentations were on: 1) genetic similarity between agrobacteria and rhizobia, 2) evolution of Ti plasmids, 3) new diagnostic tools for pathogenic agrobacteria, and 4) ecological role of type VI secretion systems of agrobacteria. Agricultural and Horticulture Development Board/British Protected Ornamentals Association Study Tour: a group of 22 growers visited and attended an update on our SCRI research. Interest was high, given the international nature of both Rhodococcus and Agrobacterium problems in the commercial ornamental plant trade. AgBiz LogicTM: An Economic and Financial Tool for the Nursery Industry. Nursery industry meeting, North Willamette Research and Extension Center, Aurora, Oregon AgBiz LogicTM: An Economic, Financial and Environmental Decision Tool for Farmers, Ranchers and Land Managers. Southern Region Extension. San Antonio, Texas. Wasco County Orchard Manager's Breakfast Meeting. The Dalles, Oregon. AgBizClimateTM: Its Use in Cereal Grain Production. REACCH Fall Focus Group meeting, Coeur d'alene, Idaho. AgBiz LogicTM: An Economic, Financial and Environmental Decision Tool for Fruit Producers. Washington State Horticultural Society Annual Meeting, Wenatchee, Washington. What does Climate Change Mean for Specialty Fruit Crops of the Pacific Northwest?: Adaptation Strategies for a Changing Climate. Houston, L. S. Capalbo, C. Seavert, M. Dalton, D. Bryla, and R. Sagili. Poster available at:Link Here. Poster presented at the 7thannual Pacific Northwest Climate Science Conference, Stevenson, WA. What do you plan to do during the next reporting period to accomplish the goals?Several specific objectives have been completed. In the next funding period, we will complete the study on tool-mediated transmission and the efficacy of commercial products on pathogenic bacteria; one more replicate is necessary to complete an in vitro assay. We will complete one more genomic epidemiological study on transmission of Agrobacterium. We will continue to work towards identifying compounds that control against the broad host range, gall-causing phytopathogenic bacteria. Easy to follow protocols will be optimized. For outreach, we will implement the online certification course and complete the development of the economic, financial and environmental decision tools.
Impacts What was accomplished under these goals?
Specific objective 1 (Aim 1a): The assay to determine tool-mediated transmission of Rhodococcus and Agrobacterium is currently in progress (please see "Changes Problems"). Specific objective 1 (Aim 1b): We have evaluated 16 commercially-available products (three concentrations and in three separate assays) for efficacy in control against pathogenic Agrobacterium and Rhodococcus. Several products showed control in in vitro assays. However, none were effective in in planta assays. It is possible for the high inoculum levels of bacteria to overcome control, but lower inoculum levels could make infection more variable and results more difficult to interpret. Specific objective 1 (Aim 1c): We have identified the structure of an active compound from Withania somnifera. This coumpound exhibits anti-bacterial activity against pathogenic Rhodococcus. We have also fractionated an active compound from Celtis boninensis that exhibits anti-bacterial activity against pathogenic Rhodococcus. Lastly, we discovered isolates of Bacillus that exhibit in vitro and in planta biocontrol activity against both pathogenic Agrobacterium and pathogenic Rhodococcus. These isolates produce two separate classes of compounds, that control against one or the other pathogen tested. We have identified the classes of compounds Specific objective 2 (Aim 2a/b): We completed a genomic epidemiological study of approximatelhy 80 Rhodococcus cultured from diseased plants grown in managed, nursery settings. A significant finding was that analyses of chromosomal sequences is insufficient. Understanding plasmid transmission patterns is equally important. We suggest that plant production practices are promoting the generation of new lineages. We have also completed the analyses of approximately 130 isolates of Agrobacterium, mostly from culture collections. The data were used to model the evolution of Agrobacterial species and their Ti plasmids. Specific objective 3 (Aim 3a): This aim was completed. Molecular diagnostic markers were developed to detect pathogenic Agrobacterium (Fuller et al., 2017) and pathogenic Rhodococcus (Savory et al., in review). Briefly, oligonucleotides and probes were developed to detect conserved sequences of virulence genes. When used in the commercial Twist kits and lateral flow cells, detection was demonstrated to be extremely sensitive, robust, and rapid. A patent (Agrobacterium; 6297004-17-0008) has been filed and an invention disclosure (Rhodococcus) has been submitted to the Office of Commercialization and Corporate Development at OSU. Specific Objective 4 (Aim 3b): Completed during last funding period. Specific Objective 5 (Outreach 1): Learning outcomes and structure for certification course have been developed. Met with focus group to help develop the course. Specific Objective 5 (Outreach 2): Nursery/Greenhouse enterprise has been incorporated into software and AgBizClimate has been released. Beta version of AgBizProfit is targeted for release on October, 2017.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Fuller SL, Savory EA, Weisberg AJ, Buser JZ, Gordon MI, Putnam ML, Chang JH. 2017. Isothermal Amplification and Lateral-Flow Assay for Detecting Crown-Gall-Causing Agrobacterium spp. Phytopathology 107:10621068.
- Type:
Book Chapters
Status:
Awaiting Publication
Year Published:
2017
Citation:
Susan M. Capalbo, Clark Seavert, John M. Antle, Jenna Way and Laurie L. Houston. 2017. Understanding Tradeoffs in the Context of Farm-Scale and Regional Impacts: An Application of Decision-Support Tools for assessing Climate Smart Agriculture. In D. Zilberman, L. Lipper, N. McCarthy, S. Asfaw, G. Branca, editors. Climate Smart Agriculture - Building Resilience to Climate Change. Elsevier.
- Type:
Other
Status:
Published
Year Published:
2017
Citation:
Georgine Yorgey, Chad Kruger, Brooke Saari, Sonia A. Hall, Elizabeth Whitefield, Nichole Embertson, Vincent P. Jones, Kirti Rajagopalan, Elizabeth Allen, Gabrielle Roesch-McNally, Beatrice Van Horne, John Abatzoglou, Hal Collins, Laurie Houston, Clark Seavert, Timothy Ewing. (February 2017).�Agriculture in a Changing Climate: Research and Extension Priorities in the Northwest. Washington State University Extension.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2017
Citation:
Savory EA, Fuller SL, Weisberg AJ, Thomas, WJ, Gordon MI, Stevens, DM, Creason, AL, Belcher, MS, Serdani, M, Wiseman, MS, Putnam ML, Grunwald, NJ, Chang JH. 2017.Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management. Elife. Under review
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Houston, Laurie, Susan Capalbo, Clark Seavert, Meghan Dalton, David R. Bryla and Ramesh Sagili. 2017. Specialty Fruit Products of the Pacific Northwest:� Adaptation Strategies for a Changing Climate.� Climatic Change. 1-13. First Online:�03 April 2017.��DOI��10.1007/s10584-017-1951-y
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Susan M. Capalbo, John M. Antle, and Clark Seavert. 2017. Next generation data systems and knowledge products to support agricultural producers and science-based policy decision making. Agricultural Systems, Volume 155:191-199
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Progress 09/01/15 to 08/31/16
Outputs Target Audience:The target audience is diverse and the same as that reported in the previous report. Changes/Problems:We had major problems testing transmission of Rhodococcus. The plants that we received, to be used for testing, came infected with Rhodococcus. This showed to us that many nurseries are unaware of Rhodococcus and its ubiquity. Additionally, we discovered that Rhodococcus is easily disseminated and can be recovered from watering devices and benches. We are attempting to repeat these studies and have worked with the greenhouse crew to be more careful in working with our plants. What opportunities for training and professional development has the project provided?In addition to training professionals in inter-disciplinary research skills and collaborating between research and extension, this project has provided opportunities for professionals (UG and Grad students/postdocs): to visit production sites, interact directly with stakeholders, to participate in formal teaching to high school students, and to mentor. How have the results been disseminated to communities of interest?Publications Trade journals Workshops Face-to-face interactions Conferences; basic and applied research-centric (MPMI and Crown Gall, APS, NPDN meeting) What do you plan to do during the next reporting period to accomplish the goals?1. Test extracts for in planta control against Rhodococcus. 2. Continue screening extracts for additional control compounds. 3. Continue sampling diseased tissues and sequence genomes from isolates. 4. Develop on site instruments to facilitate use of diagnostic dipsticks. 5. Introduce online modules for certification program. 6. Continue developing AgBiz and working with nurseries to test its efficacy.
Impacts What was accomplished under these goals?
Our accomplishments were recently described during a site visit so I will be brief and bullet accomplishments. 1) We have demonstrated that few commercially available control compounds have in vitro anti-bacterial activity against Agrobacterium and Rhodococcus but no in planta activity. 2) We have identified three extracts that have anti-bacterial activity. These were extracted from medicinal plants. We have determined the structure for one of the active compounds. All three show activity against Rhodococcus, but not Agrobacterium. 3) We have developed a dipstick method to rapidly detect pathogenic Agrobacterium. We have developed markers that detect all known genetic variants of plant pathogenic Rhodococcus. 4) We have successfully classified Ti plasmids into "genetic units" and identified correlations between Ti plasmid type, bacterial type, and host plant species. We have also identified novel combinations as well as derivatives of the Ti plasmid. 5) We have piloted a hybrid course, which involves face-to-face and online learning. We had a focus group to identify specific needs of the nursery industry; discussions were centered around training needs of front-line workers. 6) We continue to advance AgBiz specifically for the nursery industry. Key additions are chunking of budgets into smaller units to address the varied products in the industry and the inclusions of biotic and abiotic stresses as variables.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Davis EW II, Weisberg AJ, Tabima JF, Gr�nwald NJ, Chang JH. 2016. Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria. PeerJ 4:e2222.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Tabima JF, Everhart SE, Larsen MM, Weisberg AJ, Kamvar ZN, Tancos MA, Smart CD, Chang JH, Gr�nwald NJ. 2016. Microbe-ID: an open source toolbox for microbial genotyping and species identification. PeerJ, 3rd ed. 4:e2279.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2016
Citation:
Almabruk KH, Chang, JH, Mahmud, T. 2016. Total Synthesis of (+/-)-Isoperbergins and Correction of the Chemical Structure of Perbergin
- Type:
Other
Status:
Published
Year Published:
2016
Citation:
Putnam, ML, Santamaria, L. (2016) Disinfectants: In search of a silver bullet. Digger. May; 41-45
- Type:
Book Chapters
Status:
Submitted
Year Published:
2016
Citation:
Savory, E. A.**, Chang, J. H.6, and Putnam, M. L. Rhodococcus fascians in The Laboratory Guide for Identification of Plant Pathogenic Bacteria, 4th Ed. APS press: St. Paul, MN.
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Progress 09/01/14 to 08/31/15
Outputs Target Audience:The target audience includes a diversity of groups of individuals: 1) frontline nursery workers, foremen, supervisors, managers, and sales managers of growers, producers, retailers and landscapers; 2) agricultural industry scientists, consultants, extension specialists/agents, diagnosticians and regulatory personnel, and government policy makers; and 3) plant pathologists, students, and educators. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has provided scientists opportunities to develop skills in computational biology, generate and analyze big datasets, curate databases, develop web-based tools, learn to work and communicate effectively across disciplines, and mentor graduate, undergraduate, and high school students. How have the results been disseminated to communities of interest?Information is disseminated via standard mechanisms in peer-reviewed journals (Microbe-ID and Gall-ID in preparation in open-access journals) and at conferences (posters and oral presentation). We also disseminate information in trade journals (see products) and via electronic means (Microbe-ID is available for download from Github and Gall-ID and AgBiz Logic are usable via the internet). We will also work directly with 10 nursery operations to use the AgBiz Logic decision tool to gather and collect cost of production data for their own operations and use these budgets in decision making strategies. What do you plan to do during the next reporting period to accomplish the goals?For the next reporting period, we will: 1. Complete testing transmission of bacteria from plant to plant and via cutting tools, as well as efficacy of commercially available control compounds. For the extracts from plant sources, we will test their efficacy as preventative compounds on plant hosts and develop simple methods that allow growers to make the extracts. 2. Begin sampling diseased tissues from nurseries across the US. The causative bacterium will be isolated and their genomes will be sequenced and analyzed to determine population structure and migration patterns. We will also leverage the whole genome sequences to develop target sequences as molecular diagnostic markers, which will be further advanced for on-site diagnostic kits. 3. Implement modules online as the next step towards developing a certificate program. 4. Begin integrating effects of disease and training/prevention in Agbizlogic and working with nurseries to test the software.
Impacts What was accomplished under these goals?
Aim I) We determined whether Rhodococcus fascians or Agrobacterium tumefaciens are carried on cutting tools, as has been assumed in the industry and by educators. Hosts tested were Veronica and Oenothera speciosa for R. fascians and Rosa sp. and Leucanthemum for Agrobacterium. Preliminary results suggest that R. fascians has the potential to be transmitted between herbaceous tissues via cutting tools whereas A. tumefaciens is not easily transmitted between woody tissues via cutting tools. We also tested whether bacteria can be recovered directly from cutting tools after cutting through infected plant material. One trial using rose and Agrobacterium has been completed. We were able to recover bacteria from the clippers used. We have completed assays to test the efficacy of six registered products in controlling against in vitro growth of bacteria. The products were tested at three concentrations with both bacteria at five different concentrations. An additional six products have been tested at three concentrations and two bacterial suspensions of R. fascians only. The products were applied to sterile paper discs which were then placed on lawns of bacteria, and any zones of inhibition were measured. Initial results show that three commercial products have at least some activity against R. fascians and one product has some activity against A. tumefaciens. We used three different methods to extract potentially active substances from macerated tissues from six plant sources. The extracts were tested in an assay similar to the one previously described, except that only one concentration of the extracts was tested against one concentration of R. fascians. Based on preliminary results, extracts from two plant sources showed strong inhibition of bacterial growth. Three plant sources showed weak to medium activity. One plant source showed none to weak activity. Aim II) In preparation for assaying environments for reservoirs of phytopathogenic Rhodococcus at major production facilities, we first determined whether R. fascians can be recovered from soil. Soil is hypothesized to be the environment where the pathogen persists over seasons. We examined natural, unpasteurized field soil and an artificial peat-based potting mix. Both media were inoculated separately with three concentrations of bacteria. After three days, the soils were assayed for R. fascians, using PCR and oligonucleotides specific to R. fascians as well as a culture-dependent method to detect live cells. Additionally, the spiked soil was allowed to air dry, after which recovery was attempted using PCR and culturing. We found that the populations of bacteria declined during the course of the six day experiment, but were recoverable under some conditions. We have determined the genome sequences for nearly 50 isolates of Agrobacterium that were obtained from a variety of culture collections (primarily the "Larry Moore" collection), and selected to maximize diversity based on host isolated from, geographic location of isolation, and date of isolation. The purpose of this was to develop a framework for accomplishing the goal of determining the population structure, migration patterns, and evolution of A. tumefaciens. Aim III) We have also developed Microbe-ID, which was used as a platform for Gall-ID. The latter website provides tools for using molecular markers as well as whole genome sequencing reads to group isolates into taxonomic units in order to infer their identity. The website also provides tools to align short reads to identify potential homologs of known virulence genes. The website also provides downloadable tools that automate the use of whole genome sequences to determine genetic relatedness. These tools are derived from the pipeline we developed to accomplish the goals of Aim II. Two manuscripts are in preparation. For educational outreach, we have worked with OSU PACE to advance current workshops into an online certificate program. We have identified the following topics for the certificate program: 1) Pesticide application, 2) Proper use of disinfectants, 3) Distinguishing between biotic and abiotic symptoms, 4) Basic biology of plant pathogens, and 5) Sanitation and management methods. The first topic will first be offered as a hybrid course in fall of 2015 and then repurposed for an online module. All courses will be offered in English and Spanish. We are working with the OSU survey group to develop assessment tools to understand usefulness of training workshops, for the certification program, and to help advertise the online courses. For economic outreach, we have advanced our AgBiz Logic tools and website and met with local nurseries to establish cost categories and sub-categories for nursery owners to easily construct nursery crop specific enterprise budgets. We met with the external advisory board on August 26th, 2015 and received feedback on our progress and future directions.
Publications
- Type:
Other
Status:
Accepted
Year Published:
2015
Citation:
Putnam, M.L. 2015. Crown gall still confounding scientists and growers alike. (Accepted) Grower Talks.�
- Type:
Other
Status:
Published
Year Published:
2015
Citation:
Putnam, M.L. 2015. How to prevent leafy gall before you lose plants. GreenhouseGrower 33:57-60.
- Type:
Websites
Status:
Other
Year Published:
2015
Citation:
Gall-ID.cgrb.oregonstate.edu
- Type:
Websites
Status:
Published
Year Published:
2015
Citation:
http://www.agbizlogic.com/
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