Progress 10/01/19 to 09/30/20
Outputs
Target Audience:Target audiences for this project during the period under review included various stakeholders, including scientists, students, and industry. Events where such target audiences were reached are shown below. December 5, 2019: 'Towards microbiota-informed predictive monitoring and preventive managament of soilborne diseases in processing tomato fields', presentation at the 2019-2020 Annual Research Meeting of the California Tomato Research Institute (CTRI), UC Davis campus. December 6, 2019: 'Microbial associations with plants: bio-based services for sustainable protection of California crops', meeting of Multistate Research Project W4147: Managing Plant Microbe Interactions in Soil to Promote Sustainable Agriculture, Puyallup WA. December 17, 2019: 'Deconstructing the complexity of the plant microbial biome', John Lawrence Seminar at the Berkeley Lab, Aquatic Park, Berkeley CA. February 5, 2020: 'Scales, types, and outcomes of microbial interactions in the phytobiome', flash talk at the Tri-Institutional Partnership in Microbiome Research networking event, Lawrence Berkeley National Laboratory, Berkeley, CA. Several engagements allowing interaction with additional target audiences were cancelled due to COVID-19. These include the participation of Dr. Leveau as instructor in the four-week CALIFORNIA STATE SUMMER SCHOOL FOR MATHEMATICS AND SCIENCE (COSMOS) 2020 at UC Davis (cancelled), in a graduate student workshop on functional genomics at Ohio State University (postponed), and in the Microbiome For Agriculture Congress (postponed). Changes/Problems:COVID-19 has halted or slowed down many of our research projects. What opportunities for training and professional development has the project provided?During the period of review, Dr. Leveau had the opportunity to mentor Dr. Akum and Dr. Mosquera and help them get their research published. Both have secured employment, one in industry, the other in academia. How have the results been disseminated to communities of interest?Results and accomplishments from the project have been disseminated though research articles, presentations, lectures, and lab courses, as described in the various sections of this report. What do you plan to do during the next reporting period to accomplish the goals?The plan for the next reporting period is to catch up on lost time due to COVID-19, with a focus on research related to Objectives 3 and 4, and to continue seeking interest of industry in the promise of Collimonas-Bacillus-based biocontrol of plant diseases.
Impacts
What was accomplished under these goals?
This project's main focus remains on bacteria from the genus Collimonas as potential biocontrol agents, by themselves or mixed with other bacteria, for the management of soilborne fungal diseases with economic relevance to the state of California. This focus is based on research that was performed in Lab Leveau and was published recently (Doan et al., 2020; see `Products'), showing that Collimonas arenae (C. arenae) Cal35 in combination with Bacillus bacteria is able to protect tomato plants from a fungal root pathogen (Fusarium oxysporum f.sp. lycopersici, or Fol) in greenhouse and field trials. We consider this Collimonas-Bacillus synergism an example of `biocombicontrol'. The objectives of this project are as follows: 1. Generate a transposon mutant library of Collimonas arenae Cal35 and screen it for mutants with diminished ability to suppress fungal growth; test these mutants for biocombicontrol activity; identify genes that contribute to the antifungal and biocombicontrol activity of Cal35. 2. Sample soils in California and isolate bacteria belonging to the species Collimonas arenae; compare the antifungal and biocombicontrol activity of these isolates to that of Cal35. 3. Establish an experimental setup to elucidate the mode of action that underlies Collimonas-based biocombicontrol. 4. Discover new genes and gene products coding for plant-beneficial activities in bacteria from the genus Collimonas. Objective 1 has been completed and the results of this research have been published during this review period (Akum et al., 2020; see `Products'). In short, we identified two mutants of Cal35 that were impaired completely or partially in their ability to halt the growth of a wide range of fungal species. In mutant 46A06, the transposon insertion was located in a biosynthetic gene cluster that was predicted to code for a hybrid polyketide synthase -non?ribosomal peptide synthetase, while mutant 60C09 was impacted in a gene cluster for the synthesis and secretion of sugar repeat units. Our data were consistent with a model in which both gene clusters are necessary for the production of an antifungal compound we refer to as carenaemins. We also showed that the ability to produce carenaemin contributed significantly to the observed synergy between Cal35 and Bacillus velezensis FZB42 in protecting tomato plants from Fol. Our research highlights the potential for supplementing Bacillus?based biocontrol products with Collimonas bacteria to boost efficacy of such products. For Objective 2, we secured permits to sample soils in a number of forest sites maintained by the College of Natural Resources, Center for Forestry at the University of California, Berkeley. Unfortunately, funding for the sampling expedition (French-Berkeley Fund proposal `MINING GENOMES AND MODES OF ACTION OF BACTERIA WITH PLANT?BENEFICIAL PROPERTIES", with collaborator Stephane Uroz, INRAE, France) did not come through. We continue to explore alternative sources of funding in support of this objective. For Objective 3, Dr Leveau spent his Fall 2019/Winter 2020 sabbatical at Lawrence Berkeley National Laboratory to gain practical experience in the use of EcoFABs, which are standardized, reproducible root chambers that allow the study of rhizosphere colonization during controlled experimentation. These EcoFABs are ideal for testing hypotheses related to the observed Collimonas-Bacillus biocombicontrol. One specific hypothesis is that the inhibition of fungal spore germination by Collimonas bacteria (as documented by Mosquera et al., 2020; see `Products') contributes to the suppression of Fol on tomato roots. Unfortunately, preliminary experiments were halted due to COVID-19-related closure of Lab Leveau in March 2020. The hope is that once the lab reopens such experiments can resume. Entitled `Collimonas-derived enhancement of plant-protective performance by Bacillus-based biofungicides', a proposal related to the use of EcoFABs for understanding Collimonas-Bacillus synergism was submitted to the UC Davis STAIR grant competition but it was not awarded. We continue to explore alternative sources of funding in support of this objective. For Objective 4, we are actively collaborating with Dr. Stephane Uroz at INRAE, France to apply a comparative genomics approach to the Collimonas isolates in our strain collection, with the aim link the variation in antifungal activity among these same isolates to link genes to functions and to accelerate the discovery of new types of genes and gene products involved in the production of secondary metabolites with antifungal properties. Progress on this objective has been slow due to COVID-19 in both France and the US.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Akum, F.N., R. Kumar, G. Lai, C.H. Williams, H.K. Doan, and J.H.J. Leveau (2020) Identification of Collimonas gene loci involved in the biosynthesis of a diffusible secondary metabolite with broad?spectrum antifungal activity and plant?protective properties. Microbial Biotechnology https://doi.org/10.1111/1751-7915.13716
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Doan, H.K., N.N. Maharaj, K.N. Kelly, E.M. Miyao, R.M. Davis, and J.H.J. Leveau (2020) Antimycotal activity of Collimonas isolates and synergy-based biocontrol of Fusarium wilt of tomato. Phytobiomes Journal 4:64-74 https://doi.org/10.1094/PBIOMES-05-19-0027-R
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Mosquera, S., I. Stergiopoulos, and J.H.J. Leveau (2020) Interruption of Aspergillus niger spore germination by the bacterially produced secondary metabolite collimomycin. Environmental Microbiology Reports 12:306-313. https://doi.org/10.1111/1758-2229.12833
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience:Target audiences for this project during the period under review included various stakeholders, including scientists, students, and industry. Events where such target audiences were reached are shown below. October 17, 2018: 'Form and function of plant microbiota', presented by J.H.J. Leveau, MARS-organized workshop, UC Davis campus. November 6, 2018: 'Characterization and manipulation of crop microbiota', presented by J.H.J. Leveau, Society of Environmental Toxicology and Chemistry (SETAC) North America 39th Annual Meeting, Sacramento, CA, 4-8 November 2018. November 16, 2018: 'Understanding the mechanism of Collimonas dependent biocombicontrol', presented by F.N. Akum at the Plant Microbe Interaction Forum (PMIF) at UC Berkeley. December 12, 2018: 'Structure, function and scale of plant microbiota', presented by J.H.J. Leveau, Microbiome Special Research Program, Mini-Symposium with BASF, UC Davis campus. January 21, 2019: 'Application of Collimonas bacteria in biocontrol formulations for the protection of crops against soilborne fungal pathogens', presented by J.H.J. Leveau, Molecular Biology and Microbiology group of DuPont Industrial Biosciences in Palo Alto, CA. April 27, 2019: 'Identification of an additional antifungal compound produced by Collimonas arenae Cal35', presented by C.H. Williams, Undergraduate Research Conference, UC Davis campus. July 7 - August 3, 2019: students participating in the COSMOS Summer School, Cluster 7: Introduction to Plant Microbiology were introduced to the antifungal properties and biocontrol potential of Collimonas bacteria, performed hands-on experiments that demonstrated these properties, and played the Mycomuncher DNA Puzzle which is based on Collimonas research in Lab Leveau. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Dr. Leveau, together with his student Hung Doan, trained 22 high-school students on the topic of Plant Microbiology during the 2019 COSMOS Summer School. Students were introduced to the microbes that live on and in plants and learned to appreciate that all plants carry such microbes, that these microbes represent a rich and diverse assemblage of microscopic shapes and species, and that there are many ways by which these microbes might impact, for better or worse, the health of their host plant. Students were also introduced to basic concepts and laboratory techniques related to microbiology, plant disease, food security and food safety. Dr. Leveau and his postdoc Fidele Akum both were involved in the training of undergraduate student Catherine Williams as she gained professional skills related to research on bacterial-fungal interactions and comparative genomics of Collimonas strains. Ms Williams graduated with a BSc degree in Global Disease Biology from UC Davis in Summer 2019. Dr. Akum, who has been working on the Cal35 project under the supervision of Dr. Leveau since 2016, accepted a position in an ag-bio company in December 2018, continuing to work on improving plant health through plant microbiomes. How have the results been disseminated to communities of interest?Results and accomplishments from the project have been disseminated though research articles, presentations, lectures, lab courses, and the internet, as described in the various sections of this report. What do you plan to do during the next reporting period to accomplish the goals?We formulated two additional objectives for this project: 4) to establish an experimental setup to eludicate the mode of action that underlies Collimonas-based biocombicontrol, and 5) to discover new genes and gene products coding for plant-beneficial activities in bacteria from the genus Collimonas. Objective 4 refers to the observation that C. arenae Cal35 in combination with Bacillus bacteria protect tomato plants from fungal root pathogens in greenhouse and field trials (Doan et al, 2019). The mode of action underlying this synergism is unknown still. During his Fall 2019/Winter 2020 sabbatical, Dr Leveau, as an affiliate researcher at Lawrence Berkeley National Laboratory, has been gaining practical experience in the use of EcoFABs, which are standardized, reproducible root chambers that allow the study of rhizosphere colonization during controlled experimentation. These EcoFABs are ideal for testing hypotheses related to the observed Collimonas-Bacillus biocombicontrol. Objective 5 builds on the work of Catherine Williams who used comparative genomics to document the variation in gene content among Collimonas isolates collected from soils in California and other parts of the world. For this objective, we will compare this variation to the variation in antifungal activity among these same isolates, with the intent to link genes to functions and to accelerate the discovery of new types of genes and gene products involved in the production of secondary metabolites with antifungal properties.
Impacts
What was accomplished under these goals?
This project's main focus is on bacteria from the genus Collimonas as potential biocontrol agents, by themselves or mixed with other bacteria, for the management of soilborne fungal diseases with economic relevance to the state of California. The original objectives of the project were formulated as follows: 1. Generate a transposon mutant library of Collimonas arenae Cal35 and screen it for mutants with diminished ability to suppress fungal growth; test these mutants for biocombicontrol activity; identify genes that contribute to the antifungal and biocombicontrol activity of Cal35. 2. Sample soils in California and isolate bacteria belonging to the species Collimonas arenae; compare the antifungal and biocombicontrol activity of these isolates to that of Cal35. 3. Establish a strawberry-Fusarium pathosystem in the Leveau lab, and test Collimonas-Bacillus biocombicontrol for ability to reduce disease symptoms. Objective 1 has been completed: we identified 2 mutants of C. arenae Cal35 which were impaired in their ability to halt the growth of several fungi, including Fusarium oxysporum f.sp lycopersici (FOL) which causes Fusarium wilt of tomato. These mutants were disrupted in genes that code for the production of a novel secondary metabolite. Unlike wildtype Cal35, the mutants were unable to protect, in combination with biocontrol strains belonging to the genus Bacillus, tomato plants from challenge with FOL under greenhouse conditions. We are finalizing a manuscript that details our findings and expect to be able to submit it for peer review by Spring 2020. For Objective 2, we had already secured permits to sample soils in a number of forest sites maintained by the College of Natural Resources, Center for Forestry at the University of California, Berkeley. The decision to sample and mine such soils for additional Collimonas strains was made because the original permit we used to sample soils from the Jug Handle State National Reserve (which is run by California State Parks, or CSP) and from which Cal35 was isolated, stated that any collected materials `shall not be used for commercial purposes'. Seeing that the AES mission is `to conduct research that encompasses the continuum of fundamental and applied research for the purpose of developing new knowledge and technologies that address specific problems of importance to the people of California', and considering that Cal35 represented an opportunity to convert a California-based discovery into something useful for California, I worked intensively with UC Davis InnovationAccess and CSP to change California legislation to allow the CSP director, under a benefits-sharing agreement, to issue commercialization permits to qualified universities and institutions. Signing into law of Senate Bill 442 occurred on October 2, 2019 and received some press: 1) `Legislature Passes Sen. Dodd's Parks Research Partnership Bill, September 13, 2019, https://sd03.senate.ca.gov/news/20190913-legislature-passes-sen-dodd's-parks-research-partnership-bill, The "UC Davis plant professor" is Dr. Johan Leveau, the "discovered bacteria" belong to the strain Collimonas arenae Cal35, the "park" is Jug Handle State Natural Reserve, the "tomato-killing disease" is Fusarium wilt, caused by Fusarium oxysporum f.sp. lycopersici. 2) New Law Sponsored by UC Will Allow Commercialization of Discoveries in State Parks, https://www.ucdavis.edu/news/new-law-sponsored-uc-will-allow-commercialization-discoveries-state-parks/, 10/2/2019. Objective 3 has been discontinued following negative first results from greenhouse trials and with the retirement and career advancement, respectively, of two expert collaborators on this part of the project: Dr. Tom Gordon, Professor Emeritus and Dr. Peter Henry, now Research Plant Pathologist at USDA-ARS in Salinas, CA. Given the completion of Objective 1, the obsolescence of Objective 2, and the discontinuation of Objective 3, two new objectives have been formulated (Objectives 4 and 5). These will be presented and explained in more detail in the section `What do you plan to do during the next reporting period?'. Both objectives continue to build on current research in Lab Leveau on the topic of Collimonas bacteria, their antifungal properties, and their potential for use as crop protectants in California agriculture.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Bell, T., K.L. Hockett, R.I. Alcal�-Brise�o, M. Barbercheck, G.A. Beattie, M.A. Bruns, J.E. Carlson, T. Chung, A. Collins, B. Emmett, P. Esker, K.A. Garrett, L. Glenna, B.K. Gugino, M. del Mar Jim�nez-Gasco, L. Kinkel, J. Kovac, K.P. Kowalski, G. Kuldau, J.H.J. Leveau, M.J. Michalska-Smith, J. Myrick, K. Peter, M.F. Vivanco Salazar, A. Shade, N. Stopnisek, X. Tan, A.T. Welty, K. Wickings, E. Yergeau (2019) Manipulating wild and tamed phytobiomes: challenges and opportunities. Phytobiomes Journal 3:3-21.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Doan, H.K., N.N. Maharaj, K.N. Kelly, E.M. Miyao, R.M. Davis, and J.H.J. Leveau (2019) Antimycotal activity of Collimonas isolates and synergy-based biocontrol of Fusarium wilt of tomato. Phytobiomes https://doi.org/10.1094/PBIOMES-05-19-0027-R.
- Type:
Theses/Dissertations
Status:
Accepted
Year Published:
2018
Citation:
Mosquera, S. (2018) Mechanistic Characterization and Evolutionary Outcomes of the Collimonas fungivorans Ter331-Aspergillus niger N402 Antagonistic Interaction, PhD Dissertation, Plant Pathology, UC Davis
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience:Target audiences for this project during the period under review included various stakeholders, i.e. scientists, students, and commodity groups. Some events where such target audiences were reached are shown below. 1) 17 November 2017, 'Evaluating field performance of a bacterial mixture that protects processing tomato plants from Fusarium wilt', Annual Research Meeting of the California Tomato Research Institute, UC Davis campus. 2) 3 May 2018, student-invited evening presentation during Faculty Event at Tercero Hall, UC Davis campus. 3) June 21, 2018, 'Wild, tamed, then back to where the wild things are: isolation, characterization, and biocontrol application of Collimonas bacteria', 21st Penn State Plant Biology Symposium on Wild and Tamed Phytobiomes, Penn State University, University Park, PA, June 19-22, 2018. 4) June 27, 2018, 'Soil and root microbiota of field-grown processing tomatoes at various spatial scales', at the 2018 APS Pacific Division Joint Meeting with the Conference on Soilborne Plant Pathogens, Portland, OR, June 25-27, 2018. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Postdoc Fidele Akum generated the Cal35 library screening for this project and served as the day-to-day supervisor and trainer of an undergraduate student in Global Disease Biology, Catherine Williams, who contributed to the Cal35 mutant library screening. Both Dr Akum and Ms Williams took advantage of various opportunities to present their research findings to a broader audience. For example, Dr. Akum was a presenter at the UC Davis Plant Pathology retreat (19 September, 2018) and agreed to share his research findings at the Plant-Microbe Interaction meeting at UC Berkeley (16 November 2018) hwich is a venue that brings together many scientists and other parties interested in plant microbiology from around the Bay Area. How have the results been disseminated to communities of interest?Our project results are relatively new and have not achieved broad or full dissemination yet. Our expectation for the next period is to be able to write up our findings pertaining to Objective 1 as a manuscript for submission, peer-review, and publication in a scientific journal, for wide dissemination into the scientific community. Dr. Leveau also anticipates to be included as co-author on a white paper that came out of the 21st Penn State Plant Biology Symposium on Wild and Tamed Phytobiomes held in June 2018, and for which he wrote a section specifically dedicated to the discovery and utility of biocontrol agents in plant disease management. What do you plan to do during the next reporting period to accomplish the goals?Objective 1: We anticipate to reveal what mechanisms underlie the anti-FOL activity of Cal35 and whether these mechanisms contribute to the biocombicontrol phenomenon oberved with mixtures of Collimonas and Bacillus bacteria. Also, we will test the Cal35 transposon library against other plant pathogenic fungi, including Magnaporthe grisea, causative agent of rice blast. Objective 2: We are scheduled to sample the forest sites in Spring of 2019, after snow melt. As part of the research collaboration with the Center for Forestry, we are committed to present our research-in-progress annually or semi-annually at the Blodgett Forest Research Workshop, which broadens our target audience to include forest scientists and other stakeholders. Objective 3: We anticipate to repeat the greenhouse trial, but with a reduced FOF load.
Impacts
What was accomplished under these goals?
This project focuses on bacteria from the genus Collimonas as potential biocontrol agents, by themselves or mixed with other bacteria, for the management of soilborne fungal diseases with economic relevance to the state of California. This project has the following objectives: 1. Generate a transposon mutant library of Collimonas arenae Cal35 and screen it for mutants with diminished ability to suppress fungal growth; test these mutants for biocombicontrol activity; identify genes that contribute to the antifungal and biocombicontrol activity of Cal35. 2. Sample soils in California and isolate bacteria belonging to the species Collimonas arenae; compare the antifungal and biocombicontrol activity of these isolates to that of Cal35. 3. Establish a strawberry-Fusarium pathosystem in the Leveau lab, and test Collimonas-Bacillus biocombicontrol for ability to reduce disease symptoms. Accomplishments in the period 10/1/2017 - 9/30/2018: Objective 1: We created a Tn5 transposon mutant library of C. arenae Cal35 and screened this library against Fusarium oxysporum f. sp. lycopersicum (FOL) for mutants that were less able than wildtype Cal35 to inhibit the growth of FOL in co-culture. Among the approximately 6,000 mutants that were screened, two were completely ineffective in their ability to impact FOL. We identified the transposon insertion sites in both mutants, so we know what gene(s) might underlie the antagonistic activity of Cal35 toward FOL. We have started to analyze these genes and their gene products in more detail. We have also started to test the Cal35 mutants in combination with Bacillus for their ability to suppress symptoms of Fusarium wilt on tomato plants in the greenhouse, using Cal35 as a positive control. Objective 2: We reached out to Berkeley Forests (https://forests.berkeley.edu/forests) with a research proposal entitled 'Project Collifornia, continued: surveying California forest soils for novel strains of Collimonas bacteria with plant-beneficial properties'. We successfully secured permits to sample soils in a number of forest sites maintained by the College of Natural Resources, Center for Forestry at the University of California, Berkeley. These sites include Blodgett Forest, Grouse Ridge, and Whitaker's Forest. Objective 3: We tested a mixture of C. arenae Cal35 and the Bacillus-based plant-protection product Serenade (Collinade) for its ability to reduce the impact of the soilborne fungus Fusarium oxysporum f. sp. fragariae (FOF) on strawberry plants. This trial was performed in the greenhouse. We observed symptoms of Fusarium wilt of strawberry following challenge with FOF, in the absence but also presence of Collinade, suggesting that this mixture did not protect the plants from FOF.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Courty, P. E., M. Buée, J.J.T. Tech, D. Brulé, Y. Colin, J.H.J. Leveau, and S. Uroz. (2018) Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino. Mycorrhiza, 28(4): 343-356.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2019
Citation:
Maharaj, N.N., E.M. Miyao, R.M. Davis, S. Uroz, and J.H.J. Leveau. (2018) Impact of soil chemistry, nutrient supplements, and fungicides on the health and yield of field-grown processing tomatoes. European Journal of Plant Pathology, 152(4): 855-868.
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