Progress 01/01/12 to 12/31/16
Outputs
Target Audience: As in previous reporting periods, the target audience included other researchers that were reached through peer-reviewed publications and seminars and posters at professional conferences but also graduate and undergraduate students that were trained in formal classroom settings and one-on-one in the PI's laboratory. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? As in previous years, graduate students and undergaduate students were trained in the lab as well as in the classroom. Undergraduate students who did research in the laboratory, either worked on experimental aspects of the project or on bioinformatics aspects. Graduate students and undergraduate students met regularly and presented progress made in their research and discussed research articles together. How have the results been disseminated to communities of interest?As in previous years, results have been disseminated through peer-reviewed publications, through invited talks at conferences, and through news articles distributed by Virginia Tech to the public. For example, the peer-reviewed journal article by Failor et al listed under products was publicized in a Virginia Tech news article that highlighted the contribution to this work by graduate student and first author Kevin Failor. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
1. To further characterize the role and importance of the chemo/photo-taxis pathways in P. syringae - plant interactions In this final year, the focus was placed on plant-associated bacteria that colonize plants from precipitation. Graduate student Kevin Failor was the first author on a publication that described hundreds of different bacteria isolated from precipitation that can possibly damage plants because of their ice nucleation activity, which can be used by these bacteria to damage plant cell walls and, thereby, facilitate invasion of plant tissue. Over 200 of these bacteria were then tested for their potential role in competing and controlling known plant pathogens. Three of these bacteria were found to produce potent antimicrobials that may interfere with the growth of plant pathogens and that can possibly be used as biocontrol agents in the future. 2. To determine the importance of chemotaxis in host range of P. syringae strains In this final year, the genomes of hundreds of P. syringae strains were compared and the overall similarity between these genomes was determined. This approach made it possible to group P. syringae strains with similar host range into groups with similar genomes. A database is currently being developed based on these results. The goal is to develop a tool that will greatly improve the way bacterial plant pathogens are currently classified, named, and identified. This will also facilitate the study of the genomic basis of chemotaxis in this important group of plant pathogens. 3. To identify plant fractions that cue P. syringae chemotaxis and test them for effectiveness in the novel "chemodistraction" disease control technique that we propose to develop. In this final year, no additional research was performed under this goal and no additional accomplishments can thus be reported.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
KC Failor, DG Schmale, BA Vinatzer, CL Monteil(2017) Ice nucleation active bacteria in precipitation are genetically diverse and nucleate ice by employing different mechanisms. The ISME Journal 11, 27402753.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
BA Vinatzer, L Tian, LS Heath (2017) A proposal for a portal to make earths microbial diversity easily accessible and searchable. Antonie van Leeuwenhoek 10, 12711279.
|
Progress 10/01/15 to 09/30/16
Outputs
Target Audience:As in previous reporting periods, the target audience included other researchers that were reached through peer-reviewed publications and seminars and posters at professional conferences but also graduate and undergraduate students that were trained in formal calssroom settings and one-on-one in the PI's laboratory. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? As in previous years, graduate students and undergaduate students were trained in the lab as well as in the classroom. In particular, this year an emphasis was placed on training graduate students in scientific writing. Undergraduate students who do research in the laboratory, either work in experimental aspects of the project or in bioinformatics aspects. Graduate students and undergraduate students meet regularly and present progress in their research and discuss research articles together. How have the results been disseminated to communities of interest?Again, this year, results obtained as part of this project have been distributed to the scientific community through peer-reviewed research articles. The PI also presented results at international meetings, such as the International Congress of Molecular Plant - Microbe Interactions in Portlan, Oregon, the National Meeting of the American Phytopathological Society in Tampa, Florida,and the meeting of the Bergey's International Society of Microbial Systematics in Pune, India. What do you plan to do during the next reporting period to accomplish the goals?During the last project year, I expect to explore new areas of research that are still connected to chemotaxis but go beyond plant - pathogen interactions. Microbiome research is a growing field. In particular, research on the composition and function of the plant-associated microbial communities has gained a lot of attention. I thus plan to expand into this field. Moreover, the lab has accumulated a collection of rain-borne bacteria that will be tested for biocontrol activities.
Impacts
What was accomplished under these goals?
Crops are continuously exposed to a myriad of threats ranging from microbes to insects. Developing environmentally safe and affordable crop protection strategies, helps make US agriculture competitive and increases farmers' income. Therefore, the goal of this project is to develop new approaches to protect plants from diseases. The rationale is to take advantage of increasing knowledge of plant - microbe interactions at the molecular level to "trick" pathogens and interfere with the infection process. The main focus of this project is to develop chemical distractants that are based on environmentally friendly products that plants produce themselves. However, other knowledge we previously generated in the field of molecular plant microbe interactions is also leveraged. While the research at this point is basic, we predict that our research will lead to commercial products and/or improved crops in the long term. 1. Further characterize the role and importance of the chemo/photo-taxis pathways in P. syringae - plant interactions 1.1 Major activities completed / experiments conducted. For objective 1, we published our main results this year (see Clarke et al, 2016, in the list of publications). We also continued our work on testing the hypothesis that rain plays a role in P. syringae - plant interactions. In particular, we collected rain and used rain as inoculum source for tomato leaves. We then compared bacterial communities immediatey after treatment and then 7 days later using culture-independent approaches, mainly sequencing of the 16S gene as marker for microbial diversity. 1.2 Data collected. We collected DNA and outsourced the molecular analysis. The data we received from the contractor consisted in sequence files of 16S rDNA gene sequences. We then compared the 16S sequence composition between plants treated with rain at different time points and plants treated with negative controls at different time points. 1.3 Summary statistics and discussion of results. The main result of this objective was that some bacterial families increased in frequency on tomato plants when plants were treated with rain but decreased in frequency when treated with negative controls. Other bacterial families increased on tomato leaves when treated with negative controls but not when treated with rain. Yet other bacterial families never increased in frequency after any of the treatments. 1.4 Key outcomes or other accomplishments realized. The key outcome of this objective was that rain contains bacteria that can efficiently colonize tomato leaves. We conclude that rain is one source of the microbial community living on tomato leaves. Additional experiments will be needed to identify the relative importance of rain as source of the leaf microbial community compared to other sources, such as soil. 2. Determine the importance of chemotaxis in host range of P. syringae strains 2.1 Major activities completed / experiments conducted. The manuscript on cloning of the flagellin receptor FLS3 in tomato was published this year in collaboration with Dr. Greg Martin at Cornell University (see Hind et al, 2016, in the list of publications). To further determine the role of allelic diversity of flagellin in host range, we expanded our research to the tomato pathogen Ralstonia solanacearum, which infects tomato by invading its roots. Published data from the lab of Dr. Caitilyn Allen at the University of Wisconsin, suggest that roots may be able to recognize the flagellin of R. solanacearum through a pathway that is different from the one in tomato leaves. We are currently following up on these data by testing the ability of the flagellin epitopes flg22 and flgII to trigger an immune response in plant roots. 2.2 Data collected. Collected data include the quantity of reactive oxygen species released by roots after treatment with flagellin epitopes. This assay was complemented with assays to measure the release of DNA from root border cells after treatment with bacterial cells, flagellin epitopes, and other known elicitors of plant immuninty. 2.3 Summary statistics and discussion of results. We determined that tomato and pea roots can produce reactive oxygen species upon treatment with flagellin epitopes. However, we have not yet been able to see any root immune response to flagellin epitopes of R. solanacearum. 2.4 Key outcomes or other accomplishments realized. The new investigation into the role of root immune responses to flagellin epitopes and their role in host range is still at the very beginning and will need to be continued during the next reporting year. 3. Identify plant fractions that cue P. syringae chemotaxis and test them for effectiveness in the novel "chemodistraction" disease control technique that we propose to develop. 3.1 Major activities completed / experiments conducted. In continuation from last year, we continued investigating genes that we found to be present in pathogen strains but not in closely related strains isolated from the environment in order to determine their role in crop disease emergence and as potential targets in disease control. We continued testing environmental strains ectopically expressing crop pathogen genes for changes in virulence on tomato. 3.2 Data collected. Population sizes of P. syringae were determined at time point zero (the day of inoculation) and time point 4 (four days after inoculation). In addition to population sizes, severity of disease symptoms were also determined. 3.3 Summary statistics and discussion of results. As expected, expression of crop pathogen genes increased bacterial growth and rendered disease symptoms more severe. 3.4 Key outcomes or other accomplishments realized. While the outcome comfirmed our hypothesis, the changes in pathogen growth and disease symptom severity were small. Therefore, these genes do not seem to play a major role in plant disease emergence and do not appear to be promising candidates for developing new disease control techniques.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Guinard J, Vinatzer BA, Poussier S, Lefeuvre P, Wicker E (2016) Draft genome sequences of nine strains of Ralstonia solanacearum differing in virulence to eggplant (Solanum melongena). 4 (1), e01415-15.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Hind SR, Strickler SR, Boyle PC, Dunham DM, Bao Z, O'Doherty IM, Baccile JA, Hoki JS, Viox EG, Clarke CR, Vinatzer BA, Schroeder FC, Martin GB (2016) Tomato receptor FLAGELLIN-SENSING 3 binds flgII-28 and activates the plant immune system. Nature Plants 2, 16128.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Moretti C, Vinatzer BA, Onofri A, Valentini F, Buonaurio R (2016) Genetic and phenotypic diversity of Mediterranean populations of the olive knot pathogen, Pseudomonas savastanoi pv. savastanoi. Plant Pathology 10.1111/ppa.12614.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Klosterman SJ, Rollins JR, Sudarshana MR, Vinatzer BA (2016) Disease Management in the Genomics Era Summaries of Focus Issue Papers. Phytopathology 106 (10), 1068-1070.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Monteil CL, Yahara K, Studholme DJ, Mageiros L, M�ric G, Swingle B, Morris CE, Vinatzer BA, Sheppard SK (2016) Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens. Microbial Genomics 2 (10).
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Vinatzer BA, Weisberg AJ, Monteil CL, Elmarakeby HA, Sheppard SK, Heath LS (2016) A Proposal for a Genome Similarity-Based Taxonomy for Plant-Pathogenic Bacteria that Is Sufficiently Precise to Reflect Phylogeny, Host Range, and Outbreak Affiliation Applied to Pseudomonas syringae sensu lato as a Proof of Concept. Phytopathology 10.1094/PHYTO-07-16-0252-R .
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Clarke CR, Hayes BW, Runde BJ, Markel E, Swingle BM, Vinatzer BA (2016) Comparative genomics of Pseudomonas syringae pathovar tomato reveals novel chemotaxis pathways associated with motility and plant pathogenicity. PeerJ 4, e2570.
|
Progress 10/01/14 to 09/30/15
Outputs
Target Audience: The target audience of this project period included mainly other researchers but also undergraduate students at Virginia Tech who were trained in formal classroom settings or received training through participation in research in the PI's laboratory. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project continued to provide a multitude of training opportunities for undergraduate students and one graduate student. Undergraduate students were trained again this year in the lab in many different aspects of plant pathology, microbiology, and bioinformatics. Results from this project were also again integrated in the undergraduate course PPWS4114 "Microbial Forensics and Biosecurity". How have the results been disseminated to communities of interest?As can be seen from the list of products, the results from this project have been widely disseminated through peer-reviewed journal articles. The PI also gave oral presentations at two international meetings: The 9th International Conference on Pseudomonas syringae pathovars and related pathogens, Malaga, Spain; 2nd International Pseudomonas syringae pv actinidiae Symposium, Bologna, Italy. What do you plan to do during the next reporting period to accomplish the goals?I will continue with the work accomplished this year and conclude the project during the last project year. Several manuscripts are close to submission and I expect to have several more publications in press by the end of this project.
Impacts
What was accomplished under these goals?
Crops are continuously exposed to a myriad of threats ranging from microbes to insects. Developing environmentally safe and affordable crop protection strategies, helps make US agriculture competitive and increases farmers' income. Therefore, the goal of this project is to develop new approaches to protect plants from diseases. The rationale is to take advantage of increasing knowledge of plant - microbe interactions at the molecular level to "trick" pathogens and interfere with the infection process. The main focus of this project is to develop chemical distractants that are based on environmentally friendly products that plants produce themselves. However, other knowledge we previously generated in the field of molecular plant microbe interactions is also leveraged. While the research at this point is basic, we predict that our research will lead to commercial products and/or improved crops in the long term. 1. Further characterize the role and importance of the chemo/photo-taxis pathways in P. syringae - plant interactions. 1.1 Major activities completed / experiments conducted. This year we expanded this objective to include the entire bacterial community that lives on plant surfaces besides the pathogen itself. Any chemotaxis pathways that are active in P. syringae may be modulated by the presence of the myriad of other bacteria that are surrounding P. syringae. Therefore, we took advantage of another ongoing project during which we collect rain for characterization of the microbial diversity present in precipitation. We then inoculated plants with P. syringae alone, P. syringae in the presence of rain, and in the presence of rain that was previously filter-sterilized. 1.2 Data collected. We determined the biodiversity in the rain sample itself and on tomato before and after treatment with rain using a culture-independent approach. We also compared P. syringae growth after 4 days in the presence and absence of rain bacteria. 1.3 Summary statistics and discussion of results. The analysis revealed that there is a higher diversity in rain than on tomatoes. Interestingly, some bacterial families present in rain increase in population size on tomato over time significantly, while others do not. Interestingly, P. syringae grew to higher levels in the presence of rain than in the presence of sterile water. 1.4 Key outcomes or other accomplishments realized. New sequencing technologies make it now possible to obtain an inclusive picture of plant - microbe interactions beyond host and pathogen. The approach we have started using this year has great potential to be applied to our core question about chemotaxis. We plan in the future to compare wild-type P. syringae and chemotaxis mutants during competition with the natural microbial communities present on leaves. We will investigate if manipulating the microbial communities on plant surfaces can interfere with pathogen infection, in particular, chemotaxis. 2. Determine the importance of chemotaxis in host range of P. syringae strains. 2.1 Major activities completed / experiments conducted. We continued our focus on the host side for this objective. A manuscript in collaboration with Greg Martin at Cornell University on the flagellin receptor FLS3 was submitted and re-submitted twice but has not been accepted yet. A new version is in the works and the plan is to submit it by the end of 2015. In parallel, we started sequencing the FLS3 allele from pepper and designing constructs to disrupt the two tomato flagellin receptors FLS2 and FLS3 in tomato. We will then complement the mutant line with different alleles of FLS2 and FLS3 to determine the effect on plant disease resistance. 2.2 Data collected. The sequence of the pepper allele of FLS3 is currently being assembled and DNA constructs to mutate FLS2 and FLS3 are being made. 2.3 Summary statistics and discussion of results. The main focus this year was to submit the manuscript on the cloning of FLS3 and on revising the manuscript for resubmission. We expect to have obtained genetically modified tomato plants by the end of next year. 2.4 Key outcomes or other accomplishments realized. Publication of the cloning of the tomato FLS3 receptor will be a significant accomplishment. Unfortunately, it was not possible to get the manuscript accepted this year. We look forward to getting the manuscript in press next year. We expect the tomato plants expressing different alleles of FLS2 and FLS3 to give important insight into the effectiveness of these kinds of immune receptors for plant disease resistance. 3. Identify plant fractions that cue P. syringae chemotaxis and test them for effectiveness in the novel "chemodistraction" disease control technique that we propose to develop. 3.1 Major activities completed / experiments conducted. We continued our efforts from last year to identify pathogen genes that would be good candidates in disease control. We have now cloned the genes that are omnipresent in P. syringae crop pathogens but not closely related environmental strains and we have started testing them for disease control in lab conditions. 3.2 Data collected. The identified genes were cloned into test strains and plant reactions were determined. The modified pathogen strains were then tested in various plant assays to either determine contribution to virulence or induction of plant defenses. 3.3 Summary statistics and discussion of results. So far, no significant effect on plant immunity was detected. We will continue these experiments on additional plants and using additional assays in the final year of the proposal. 3.4 Key outcomes or other accomplishments realized. This year the results from this objective were inconclusive. We expect the additional experiments planned for the last project year to provide more insight into the role of the identified two genes and their potential for disease control.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Pietsch RB, David RF, Marr LC, Vinatzer, BA, Schmale DG (2015) Aerosolization of two strains of Pseudomonas syringae in a Collison nebulizer at different temperatures. Aerosol Science & Technology 49(3):159-166. DOI:10.1080/02786826.2015.1010636
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Weisberg AJ, Elmarakeby HA, Lenwood SH, Vinatzer BA (2015) Similarity-based codes sequentially assigned to ebolavirus genomes are informative of species membership, associated outbreaks, and transmission chains. Open Forum Infectious Diseases. DOI: 10.1093/ofid/ofv024
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Clarke CR, Studholme DJ, Weisberg A, Hayes B, Runde B, Cai R, Wroblewski T, Daunay MC, Castillo J, Wicker E, Vinatzer BA (2015) Genome-enabled phylogeographic investigation of the quarantine pathogen Ralstonia solanacearum race 3 biovar 2 and screening for sources of resistance against its core effectors. Phytopathology. DOI: 10.1094/PHYTO-12-14-0373-R
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Sakthivel K, Kumar A, Devendrakumar C, Vibhuti M, Neelam S, Gautam RK, Kumar K, Dam Roy S, Vinatzer BA (2015) Diversity of Ralstonia solanacearum strains on the Andaman Islands in India. Plant Disease: Posted online on 10 Sep 2015, First Look.
|
Progress 10/01/13 to 09/30/14
Outputs
Target Audience: The target audience of this project period included mainly other researchers but also undergraduate students at Virginia Tech who were trained in formal classroom settings or received training through participation in research in the PI's laboratory. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? This project continued to provide a multitude of training opportunities for undergraduate students, graduate student, and postdotoral researchers. Five undergraduate students were trained this year in the lab in many different aspects of plant pathology, microbiology, and bioinformatics. Results from this project were also integrated in the undergraduate course PPWS4114 "Microbial Forensics and Biosecurity". A graduate student was trained for the whole year and a postdoctoral researcher was also trained for part of the year. How have the results been disseminated to communities of interest? As can be seen from the list of products, the results from this project have been widely disseminated through peer-reviewed journal articles. The results of one publication were also distributed to a wider audience through a Virginia Tech press release: http://www.vtnews.vt.edu/articles/2014/02/022414-cals-dnanaming.html What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Crops are continuously exposed to a myriad of threats ranging from microbes to insects. Developing environmentally safe and affordable crop protection strategies, helps make US agriculture competitive and increases farmers' income. Therefore, the goal of this project is to develop new approaches to protect plants from diseases. The rationale is to take advantage of increasing knowledge of plant - microbe interactions at the molecular level to "trick" pathogens and interfere with the infection process. The main focus of this project is to develop chemical distractants that are based on environmenatlly friendly products that plants produce themselves. However, other knowledge we previously generated in the field of molecular plant microbe interactions is also leveraged. While the research at this point is basic, we predict that our research will lead to commercial products and/or improved crops in the long term. 1. Further characterize the role and importance of the chemo/photo-taxis pathways in P. syringae - plant interactions 1.1 Major activities completed / experiments conducted This year we focused on the role of bacterial movement, in particular the bacterial flagellin, in chemotaxis. While it is well known that one region of flagellin, called flg22, is sufficient to trigger immunity in a wide range of plants, it is not well known how other regions of flagellin modulate the interaction of flg22 with the plant receptor FLS2. Moreover, while we found that a second region of flagellin, called flgII, is recognized by many Solanaceae, it is not known how recognition of flg22 and flgII affect each other. Also, it was previously shown that glycosylation of flagellin affects the strength of the immune response triggered in plants by flagellin. We have now started to develop tools to answer these open questions. In particular, we cloned different allelic regions of flagellin that contain both, flg22 and flgII. 1.2 Data collected Using the cloned flagellin regions, we found that kiwifruit plants do neither recognize the flg22 or flgII regions by themselves, but that the larger region containing both, flg22 and flgII, are recognized. We also confirmed that plant species outside of the Solanaceae family do not recognize the flgII region. 1.3 Summary statistics and discussion of results The obtained results confirm that it is essential to include the entire flagellin protein when studying the recognition of flagellin by plants during plant - microbe interactions. 1.4 Key outcomes or other accomplishments realized Kiwifruit orchards are currently under serious threat from a recently emerged pathogen, Pseudomonas syringae pathovar actinidiae. The finding that kiwifruit plants do not recognize the already known flagellin regions suggests that expression of genes of other plant species that recognize those regions in kiwifruit could increase resistance of kiwifruit to this pathogen. 2. Determine the importance of chemotaxis in host range of P. syringae strains 2.1 Major activities completed / experiments conducted For this goal we focused our attention on the role of flagellin recognition on host range of the plant pathogen P. syringae. We previously determined that pepper plants are equally efficient in recognizing different variants of the flagellin region flgII while tomato plants are not. We hypothesized that cloning the pepper gene that is responsible for the recognition of the flagellin region flgII and expressing it in tomato could increase resistance of tomato to the plant pathogen P. syringae and other bacterial pathogens. We therefore, used genetic mapping to first identify the tomato gene that is at the basis of flgII recognition and then found the corresponding gene in pepper based on similarity. 2.2 Data collected We crossed tomato plants that either recognize flgII or do not recognize flgII and we obtained a progeny that we then selfed to obtain a second generation that segregates for recognition of flgII. In a collaboration with researchers at Cornell University (Dr. Greg Martin), we then identified the gene using the latest DNA sequencing technology and computer software. 2.3 Summary statistics and discussion of results We identified the gene that recognizes flgII in tomato and we identified - based on similarity - the gene that is probably responsible for recognition of flgII in pepper. Next, we will clone the pepper gene and transform tomato with it to try to obtain tomato plants that are more resistant to P. syringae. 2.4 Key outcomes or other accomplishments realized The expected outcome from this part of the project is to obtain tomato cultivars that are more resistant to bacterial diseases and that can thus allow farmers to obtain higher yields using less pesticides. 3. Identify plant fractions that cue P. syringae chemotaxis and test them for effectiveness in the novel "chemodistraction" disease control technique that we propose to develop 3.1 Major activities completed / experiments conducted This year we decided to determine if it would be possible to determine signs of adaptation to crops in the genome sequences of strains of the plant pathogen Pseudomonas syringae. This approach was hypothesized to indirectly lead to the identification of genes involved in the recognition of specific plant products. 3.2 Data collected Almost hundred genomes of P. syringae strains were sequenced and compared with each other. Evolutionary relationships were determined and differences in gene content and gene sequences between crop pathogens and closely related environmental isolates were determined. 3.3 Summary statistics and discussion of results It was found that crop pathogens and environmental isolates of P. syringae are closely related and that crop pathogens emerged several times independently out of an environmental reservoir. Particularly interesting was the finding that two virulence genes are only present in crop pathogens but not in environmental isolates. This suggests that these two genes make an important contribution to virulence on crop plants. 3.4 Key outcomes or other accomplishments realized The obtained results provide critical information about mechanisms used by crop pathogens to cause disease. The ubiquity of two genes among an entire group of crop pathogens suggests that these two genes are essential for pathogen virulence and should be targeted when breeding/engineering crops for increeased disease resistance.
Publications
- Type:
Book Chapters
Status:
Published
Year Published:
2014
Citation:
Vinatzer B.A., Monteil C.L (2014) Pseudomonas syringae genomics: From comparative genomics of individual crop pathogen strains toward population genomics. Eds.: Gross D.C., Lichens-Park A., Publisher: Springer, New York.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Vinatzer BA, Monteil CL, Clarke CR (2014) Harnessing Population Genomics to Understand How Bacterial Pathogens Emerge, Adapt to Crop Hosts, and Disseminate. Annu Rev Phytopathol DOI: 10.1146/annurev-phyto-102313-045907
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Kumar A, Prameela TP, Suseelabhai R, Siljo A, Anandaraj M, Vinatzer BA (2014) Host specificity and genetic diversity of race 4 strains of Ralstonia solanacearum. Plant Pathology DOI: 10.1111/ppa.12189
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Marakeby H, Badr E, Torkey H, Song Y, Leman S, Monteil CL, Heath LS, Vinatzer BA (2014) A system to automatically classify and name any individual genome-sequenced organism independently of current biological classification and nomenclature. PloS ONE 9(2):e89142 doi: 10.1371/journal.pone.0089142
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Clarke CR, Hayes BW, Runde BJ, Wicker E, Vinatzer BA (2014) Eggplant and related species are promising genetic resources to dissect the plant immune response to Pseudomonas syringae and Xanthomonas euvesicatoria and to identify new resistance determinants. Molecular Plant Pathology DOI: 10.1111/mpp.12140
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Bartoli C, Lamichhane JR, Berge O, Guilbaud C, Varvaro L, Balestra GM, Vinatzer BA, Morris CE (2014) A framework to gage the epidemic potential of plant pathogens in environmental reservoirs: the example of kiwifruit canker. Molecular Plant Pathology DOI: 10.1111/mpp. 12167
|
Progress 10/01/12 to 09/30/13
Outputs
Target Audience: The target audience of this project period included mainly other researchers but also undergraduate students at Virginia Tech who were trained in formal classroom settings or received training through participation in research in the PI’s laboratory. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? This project year one postdoc and two undergraduate students were trained in the laboratory. The postdoc has completed his PhD in the laboratory previously and performs research independently. However, he was trained in manuscript writing and in teaching. He gave two guest lectures in two graduate courses and taught an entire section consisting of three lectures in an undergraduate course. The postdoc also gained experience in mentoring himself by advising the two undergradaute students in the lab. The two students have been trained by the postdoc for over two years. They have learned many molecular biology, microbial genetics, and plant pathology techniques. Both presented their research at lab meetings and local scientific meetings. Moreover, both of them contributed to writing the methods section of a manuscript that was submitted for publication and that is currently being revised. Both undergraduate students are co-authors and the postdoc is first author of this manuscript. In summary, both the postdoc and the two undergraduate students have made significant progress in their professional development by participating in this project. How have the results been disseminated to communities of interest? The research has mainly been disseminated through peer-reviewed publications this year. However, the PI also included this project when teaching 50 students in his undergraduate course "Microbial Forensics and Biosecurity", which is taken by 50 Biology majors with little background in agricultural sciences. The PI makes an effort to convey to the students the importance of plant diseases for society with the goal of enticing the students to a career in Plant Pathology. What do you plan to do during the next reporting period to accomplish the goals? Here are the plans for the coming year organized by project goals: 1. Further characterize the role and importance of the chemo/photo-taxis pathways in P. syringae - plant interactions We almost completed this goal and the main objective next year is to write and submit a manuscript describing our results. 2. To determine the importance of chemotaxis in host range of P. syringae strains We will continue the characterization of P. syringae strains isolated from crops and the environment to identify additional genes with signatures of natural selection indicative of their role in P. syringae host range and virulence. 3. To identify plant fractions that cue P. syringae chemotaxis and test them for effectiveness in the novel "chemodistraction" disease control technique that we propose to develop. We will start testing different chemicals already identified to be recognized by P. syringae to determine their potential in the novel "chemodistraction" disease control technique. We will also continue with mapping and cloning the tomato receptor of the flgII PAMP as a parallel strategy for disease control.
Impacts
What was accomplished under these goals?
1. To further characterize the role and importance of the chemo/photo-taxis pathways in P. syringae - plant interactions The research was extended this year to new mutant strains. Previously, we had disrupted P. syringae bacteria's chemotaxis pathway genes by inserting foreign DNA, which can potentially affect the regulation of other genes. The new mutants were instead obtained by replacing chemotaxis pathway genes in a way that does not affect other genes. Morevoer, we have now also included a mutant strain which is impaired in both of the chemotaxis pathways that exist in P. syringae. Using these additional mutants we were able to confirm chemotaxis mutant phenotypes observed previously and we are now ready to publish these data and expect to submit a manuscript in the first half of 2014. 2. To determine the importance of chemotaxis in host range of P. syringae strains We further characterized the role of chemotaxis in P. syringae. We also included other aspects of P. syringae biology in this characterization. Our approach consists in analyzing the natural diversity that exists amon P. syringae strains isolated from crops and from the environment. We then look for genes with signatures of natural selection indicative of adaptation to crops. Using this approach we found further evidence that bacteria adapt to specific crops by altering the sequences of pathogen-associated molecular patterns (PAMPs). Intriguingly though, we found that several wild tomato plants lost the ability to recognize the PAMP flgII, wich we had identified previously. While it is not yet clear what selective advantage loss of PAMP recognition entails, the advantage for us is that we were able to perform crosses between tomato plants that either recognize the flgII PAMP or that do not recognize the flgII PAMP. We have now started analyzing seedlings of these crosses to genetically map and then clone the tomato receptor of flgII. This will be an important advance in understanding host range mechanisms in P. syringae and other plant pathogenic bacteria. 3. To identify plant fractions that cue P. syringae chemotaxis and test them for effectiveness in the novel "chemodistraction" disease control technique that we propose to develop. We have not yet started with the identification of plant fractions that cue P. syringae chemotaxis and that could be used in plant disease control applying the control techique "chemodistraction" that we are developing. However, our progress in identifying the flgII receptor in tomato can also be expected to contribute to improved plant disease control in the field.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Clarke CR, Chinchilla D, Hind SR, Taguchi F, Miki R, Ichinose Y, Martin GB, Leman S, Felix G, Vinatzer BA (2013) Allelic variation in two distinct Pseudomonas syringae flagellin epitopes modulates the strength of plant immune responses but not bacterial motility. New Phytologist DOI: 10.1111/nph.12408
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Monteil CL, Cai R, Liu H, Mechan Llontop ME, Leman S, Studholme DJ, Morris CE, Vinatzer BA (2013) Non-agricultural reservoirs contribute to emergence and evolution of Pseudomonas syringae crop pathogens. New Phytologist 199(3):800-11
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Sarris PF, Trantas EA, Baltrus DA, Bull CT, Wechter WP, Yan S, Ververidis F, Almeida, NF, Jones CD, Dangl JL, Panopoulos NJ, Vinatzer BA, Goumas DE (2013) Comparative Genomics of Multiple Strains of Pseudomonas cannabina pv. alisalensis, a Potential Model Pathogen of Both Monocots and Dicots. PLoS ONE 8(3): e59366. doi:10.1371/journal.pone.0059366
|
Progress 10/01/11 to 09/30/12
Outputs
OUTPUTS: OUTPUTS: Bacterial plant diseases are extremely difficult to control because bacteria evolve easily to overcome genetically determined resistance in crops and easily acquire resistance to antibiotics and other pesticides. Therefore, during this project the role of chemotaxis in host range and virulence of plant pathogenic bacteria is being investigated as a target for the development of alternative plant disease control strategies. The main approach used this year consisted in the comparison of wild-type bacteria of the plant pathogen Pseudomonas syringae pv. tomato with bacteria of the same pathogen that were mutated in two chemotaxis pathways. The comparisons performed included virulence assays on the host plant tomato and on non-host plants, like the model plant species Arabidopsis thaliana. Moreover, the hypothesis was tested that spraying plants with a relative high concentration of chemicals known to act as an attractant for this plant pathogen would disorient the pathogen and interfere with plant leaf invasion. Bacteria mutated in chemotaxis pathways were hypothesized to be unaffected by the same chemicals. Moreover, the role of flagellin in triggering plant immunity and the diversity in the kiwifruit pathogen P. syringae pv. actininidiae was also investigated. MENTORING: three undergraduate students, one graduate student, and two postdoctoral researchers were advised during the project this year. DISSEMINATION: Results were disseminated at the Annual Potomac Division Meeting of the American Phytopathological Society in Winchester (VA), at the American Phytopathological Society Annual Meeting in Providence (RI), and at the International Congress on Plant - Microbe Interactions, Kyoto (Japan). PARTICIPANTS: Individuals: No change Partner Organizations: USDA ARS Salinas, California INRA, Avignon, France Sainsbury Laboratory, Norwich, UK Department of Science and Technologies for Agriculture, Forestry, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy Biosciences, University of Exeter, Exeter, Devon, United Kingdom Collaborators and contacts: Within the PI's department: Chris Clarke (post-doc) Caroline Monteil (post-doc) Anastasia Naumenko (graduate student) Haijie Liu (technician) Withing the PI's institution: Scotland Leman (Statistics Department) At other institutions: Carolee Bull (USDA ARS Salinas, California) Cindy Morris (INRA, Avignon, France) Kee Sohn (Sainsbury Laboratory, Norwich, UK) Giorgio Mazzaglia (DAFNE, University of Tuscia, Viterbo, Italy) David Studholme (Biosciences, University of Exeter, Exeter, Devon, United Kingdom) Training or professional development: The above listed graduate student was trained within the project and three undergraduates participated in the project also. TARGET AUDIENCES: The target audience of this project consists mainly in other researchers but also in undergraduate students at Virginia Tech. Undergraduate students were trained in formal classroom settings or received training by participating in the research in the PI's laboratory. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Pseudomonas syringae bacteria have two groups of genes that code for the components necessary to transduce a signal generated when an attractant is detected outside of the bacterial cell all the way to the flagellum, which is the organ that allows bacteria to swim. One gene from each of the two groups of genes was mutated to test the role of these two signal transduction pathways. As expected, the mutated bacteria were affected in their ability to infect their host plant tomato. Surprisingly though, the mutated bacteria became more virulent on the non-host plant Arabidopsis thaliana, on which they reached significantly higher population densities 4 days after inoculation. In particular, the plants reacted differently to the mutated bacteria than to non-mutated bacteria. While A. thaliana plants reacted with the expected hypersensitive defense response to wild-type P. syringae pv. tomato, they did not react with a visible defense response to the mutated bacteria. This result could be either due to a change in expression of the gene in the pathogen that triggers this response or due to a change in the ability of the mutated bacteria to closely interact with the host plant making it less detectable by the plant immune system. The two hypotheses will be tested in the next year. Treating plants with chemicals known to attract the pathogen did, as expected, reduce bacterial growth of the pathogen. The bacteria mutated in their chemotaxis signal transduction pathways were not reduced in growth when plants were pretreated with the same chemicals. This strongly suggests that pathogens can in fact be distracted by harmless chemicals reducing their success in invading crop plants and thus reducing disease incidence. In parallel, recognition of bacterial flagellum by tomato and other plants species was also investigated and it was found that different bacteria have different versions of flagellum that are detected with different efficiency by different plants. The existence of a new flagellin receptor gene was detected and we will attempt to clone this gene in the future. This gene can then be used to increase plant disease resistance. Another P. syringae pathogen that was studied is P. syringae pv. actinidiae. It was possible to identify differences in the genome of different pathogen isolates from different countries, which will facilitate disease diagnostics.
Publications
- Sohn KH, Saucet SB, Clarke CR, Vinatzer BA, O'Brien HE, Guttman DS, Jones JD (2012) HopAS1 recognition significantly contributes to Arabidopsis nonhost resistance to Pseudomonas syringae pathogens. New Phytologist doi: 10.1111/j.1469-8137.2011.03950.x.
- Vinatzer BA(2012) Listening in on How a Bacterium Takes Over the Plant Vascular System. mBio 3(5)e00269-12
- Balestra GM, Taratufolo MC, Vinatzer BA, Mazzaglia A (2012) A Multiplex PCR Assay for Detection of Pseudomonas syringae pv. actinidiae and Differentiation of Populations with Different Geographic Origin. Plant Disease, DOI:10.1094/PDIS-06-12-0590-RE
- Mazzaglia A, Studholme DJ, Taratufolo MC, Cai R, Almeida NF, Goodman, T, Guttman DS, Vinatzer BA, Balestra GM (2012) Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of kiwifruit outbreaks belong to the same genetic lineage. PLoS ONE 7(5): e36518. doi:10.1371/journal.pone.0036518
- Diallo MD, Monteil CL, Vinatzer BA, Clarke CR, Glaux C, Guilbaud C, Desbiez C, Morris CE. (2012) Pseudomonas syringae naturally lacking the canonical type III secretion system are ubiquitous in non agricultural habitats, are phylogenetically diverse and can be pathogenic. The ISME Journal doi:10.1038/ismej.2011.202
|
|