Progress 12/01/15 to 11/30/22
Outputs
Target Audience:The target audience was comprised of researchers, graduate students, and undergraduate student trainees. The research focused on scientific methods that were novel with results that could translate into industrial innovations. We primarily shared the research findings with other researchers to advance progress in microbiome research that improves plant production systems. Another important audience was the team of undergraduate and graduate students that received training in novel and cutting edge methods for microbiomes, stable isotope ecology,and plant transcriptome research. The students have now advanced in their careers into prestigious postdoctoral fellowships, graduate research fellowships, and selective doctoral programs. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project provided training and professional development to the graduate students, undergraduate students, and technicians that served on the grant. The team received lab methods training on: 1) microbiome DNA extraction, PCR, and bar-coded tagging methods for sequence preparation, 2) soil extracellular enzyme analysis for assessing nitrogen and phosphorus cycling in rhizosphere soils, and 3) plant transcriptome approaches to plant tissue RNA extraction and preparation. The team received training on microbiome sequence and plant transcriptome sequence bioinformatics and statistical analysis. How have the results been disseminated to communities of interest?We shared the results at academic conferences and universities as invited and contributed presentations. The conferences included the following: The Soil Ecology Society American Association for the Advancement of Science (AAAS) Meeting Ecological Society of America Tri-Societies Conference:The American Society of Agronomy, the Crop Science Society of America, and the Soil Science Society of America Phytobiomes Meeting The Ohio State University Virginia Tech Connecticut College Cornell University Boyce Thompson Research Institute Rutgers University University of Maryland-College Park Washington State University UC-Davis What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Goal 1:Characterize the assemblages of microbial communities over generations of selection for enhanced nitrogen use efficiency of plants. Goal 2: Experimentally test the ability of the selected microbiomes to increase nitrogen use efficiency across different types of plants and soils. Goal 3: Examine how microbiomes alter plant functioning and the potential mechanisms of how microbiomes influence plant nitrogen use efficiency. We addressed all three goals specified in the original proposal by developinga novel approach to characterize microbiome composition, diversity, and interaction profiles during the selection process for increased nitrogen use efficiency and seed yield.Microbial experimental systems provided a platform to observe how networks of groups emerged to impact plant development. We applied selective pressure on soil bacterial communities for changes in the biomass phenotype of its plant host across iterative cycles for enhanced yield. Analysis of plant phenotypes after 9 generations of selection revealed that Brassica rapa plants had altered seed yield and nitrogen use efficiency. Soil bacterial diversity declined in response to selection for high B. rapa biomass production while distinct sub-groups of interactions emerged among bacterial phyla such as Proteobacteria and Bacteroidetes. Extended Local Similarity Analysis (eLSA) and quantification of bacterial community rewiring and change showed greater connectivity of the bacterial community, with more edges, shorter path lengths, and altered modularity through the course of selection for enhanced plant biomass. In contrast, bacterial communities under random selection and no selection (control) showed less complex interaction profiles of bacterial taxa. These results suggest that group-level bacterial interactions can be modified to collectively shift microbiome functions impacting the development of plant phenotypes.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
King, W.L., L.M. Kaminsky, M.Gannett, G.L. Thompson, J. Kao-Kniffin, and T.H. Bell. 2021. Soil salinization accelerates microbiome stabilization in iterative selections for plant performance. New Phytologist. https://doi.org/10.1111/nph.17774
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Garcia, J., and J. Kao-Kniffin*. 2018. Microbial group dynamics in plant rhizospheres and their implications on nutrient cycling. Frontiers in Microbiology. 9: 1516. DOI:10.3389/fmicb.2018.01516
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Garcia J, Gannett M, Wei L, Cheng L, Hu S, Sparks J, Giovannoni J, Kao-Kniffin J. Selection pressure on the rhizosphere microbiome can alter nitrogen use efficiency and seed yield in Brassica rapa. Commun Biol. 2022 Sep 14;5(1):959. doi: 10.1038/s42003-022-03860-5. PMID: 36104398; PMCID: PMC9474469.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Garcia, J. and J. Kao-Kniffin*. 2020. Can dynamic network modelling be used to identify adaptive microbiomes? Functional Ecology. 34: 2065 2074. https://doi.org/10.1111/1365-2435.13491
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Progress 12/01/20 to 11/30/21
Outputs
Target Audience:The target audience for this project includes growers, industry stakeholders, and researchers. The ability to modify crop traits by altering the crop's microbiome is beneficial to agriculture and the various stakeholders involved in research, development, and production. The results of the study will be shared with the scientific community via peer-reviewed publications and scientific conferences, and through public engagement using extension articles and media. We provided laboratory instruction to two undergraduate students and one graduate student this past year. The graduate student is now in his final year at Cornell University and has received advanced training on microbiome analysis since joining the project. He received a three-year NSF graduate research fellowship and a diversity fellowship. The undergraduate students include two returning students that are continuing their research experience on the project. We shared research updates with a diverse audience at scientific conferences, university seminars, and with industry stakeholders. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project has provided the opportunity to train one underrepresented minority graduate student, two undergraduate researchers (one focused on large animal veterinary science as a career goal) and one woman scientist in pre-medicine The graduate student received a three year NSF GRFP and a McNair diversity fellowship. The techniques gained in plant and microbial genomics will allow the students to advance in their careers, while also providing new tools and expertise for the agricultural sciences. How have the results been disseminated to communities of interest?The results have been shared with the scientific community at academic conferences and within the university. Bearky all meetings in the past reporting period were virtual due to the pandemic travel and meeting restrictions. Assembly of highly connected microbiomes that modify plant host traits. Special Session: Coupled Experimental and Quantitative Mathematical Multiscale Modeling of the Environmental Microbiome, American Association for the Advancement of Science (AAAS) Annual Meeting, February 9th, 2021. Don't be afraid of the -omics: Easy, affordable methods to study the rhizosphere microbiome. Cornell University Biogeochemistry speaker series, February 28th, 2021. Transcriptome of tomato (Solanum lycopersicum) reveals impacts of microbiomes on host interactions. Cornell University Graduate Field Review for Horticultural Biology. August 24 th, 2021. Developing crop microbiomes for enhnaced plant productivity. American Tri-Societies Annual Meeting of Soil Science, Crop Science, and Agronomy. Nov 8th, 2021 What do you plan to do during the next reporting period to accomplish the goals?We plan to complete the final objective within the next year by submitting manuscripts for peer-review publication and uploading both microbiome and plant sequencing data to public repository sites.
Impacts
What was accomplished under these goals?
Research objective 1 (addresses goal 1): Assembling microbiomes that enhance crop yield. 100% completion The objective for the first experiment focuses on crop yield as traits that can be modulated by a plant's microbiome. We used the rapidly cycling genotype of Brassica rapa to assemble microbiomes that are associated with greater aboveground biomass. We found that the microbiomes derived from organic farms were able to assemble into communities that may have modified seed yield by the end of the experiment. We used 16S rRNA gene sequencing to track shifts in the bacterial composition of rhizospheres across the high biomass selection, random selection, and non-selection (non-adaptive microbiome) treatments. We used standard microbial ordination techniques to show that the microbiomes selected under high biomass versus random selection became distinctly different communities in the successive generations (6-8). Dynamic network modeling using LSA indicated that the interactions across the most abundant bacterial taxa show stronger associations in the high biomass selection rhizospheres in comparison to the random and non-selection treatments. The overall microbiome dataset reveals that our experimental design using directed evolution to assemble microbiomes associated with higher biomass resulted in greater seed yield under the high biomass selection lines versus the non-selection controls, while grown under constant nitrogen-limiting conditions. New data for this year indicates that the stable isotope data for soil, plant tissue, and fertilizer show greater nitrogen use efficiency for plants grown with the plant growth-promoting microbiomes compared to the controls. The manuscript is currently in review with moderate revisions requested. Research objective 2 (addresses goals 2 and 3): Microbiome transfer to field and greenhouse production settings. 80% completion, estimated full completion in final year The second objective entails transferring microbiome function to field or greenhouse settings. Specifically, we tested the robustness of one specific microbiome that showed plant growth promoting abilities. We focused on Solanum lycopersicum (tomato) as the crop for examining detailed impacts of the microbiome on plant physiology. The plants were grown in a greenhouse setting to assess the ability of the microbiomes to enhance fruit yield, NUE, and N capture across host plants. Within the past year, the following analyses were analyzed: RNA Seq analysis, ethylene measurements, fruit carotenoid measurements, extracellular enzyme activities, soil bacterial and fungal 16S rRNA and ITS sequencing, and plant transcriptional data. This final year, we are preparing a manuscript that features the results of the project--that genes associated with nitrogen utilization in tomato were upregulated in the presence of the plant-growth promoting microbiomes and that differences in plant biomass and growth responses are more evident in the earlier stages of plant development. The graduate student has presented the results at several conferences and has nearly completed a final draft of the manuscript.
Publications
|
Progress 12/01/19 to 11/30/20
Outputs
Target Audience:The target audience for this project includes growers, industry stakeholders, and researchers. The ability to modify crop traits by altering the crop's microbiome is beneficial to agriculture and the various stakeholders involved in research, development, and production. The results of the study will be shared with the scientific community via peer-reviewed publications and scientific conferences, and through public engagement using extension articles and media. We provided laboratory instruction to two undergraduate students, one graduate student, and one postdoctoral fellow. The graduate student is now in his third year at Cornell University and has received advanced training on microbiome analysis since joining the project. He received a three-year NSF graduate research fellowship and a two-year diversity fellowship. The undergraduate students include two returning students that are continuing their research experience on the project. The postdoc completed the year with advanced training in microbiome analysis. She is now a research scientist with the Environmental Protection Agency. We shared research updates with a diverse audience at virtual scientific conferences, university seminars, and with industry stakeholders. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project has provided the opportunity to train one underrepresented minority graduate student, two undergraduate researchers (one focused on large animal veterinary science as a career goal) and one woman postdoctoral fellow in new techniques in plant biology, soil science, and microbiology. The graduate student received a three year NSF GRFP and a two year McNair diversity fellowship. The techniques gained in plant and microbial genomics will allow the students to advance in their careers, while also providing new tools and expertise for the agricultural sciences. The postdoc has now successfully obtained a research scientist position with the Environmental Protection Agency on biopesticide research. How have the results been disseminated to communities of interest?The research results were presented at multiple virtual scientific conferences and university symposia. What do you plan to do during the next reporting period to accomplish the goals?We plan to complete both objectives within the next year, submit manuscripts for peer-review publication, and upload both microbiome and plant sequencing data to public repository sites.
Impacts
What was accomplished under these goals?
Research objective 1 (addresses goal 1): Assembling microbiomes that enhance crop yield. Year 1: 98% completion The objective for the first experiment focuses on crop yield as traits that can be modulated by a plant's microbiome. We used the rapidly cycling genotype of Brassica rapa to assemble microbiomes that are associated with greater aboveground biomass. We found that the microbiomes derived from organic farms were able to assemble into communities that may have modified seed yield by the end of the experiment. We used 16S rRNA gene sequencing to track shifts in the bacterial composition of rhizospheres across the high biomass selection, random selection, and non-selection (non-adaptive microbiome) treatments. We used standard microbial ordination techniques to show that the microbiomes selected under high biomass versus random selection became distinctly different communities in the successive generations (6-8). Dynamic network modeling using LSA indicated that the interactions across the most abundant bacterial taxa show stronger associations in the high biomass selection rhizospheres in comparison to the random and non-selection treatments. The overall microbiome dataset reveals that our experimental design using directed evolution to assemble microbiomes associated with higher biomass resulted in greater seed yield under the high biomass selection lines versus the non-selection controls, while grown under constant nitrogen-limiting conditions. New data for this year indicates that the stable isotope data for soil, plant tissue, and fertilizer show greater nitrogen use efficiency for plants grown with the plant growth-promoting microbiomes compared to the controls. The manuscript will be submitted in January 2021. Research objective 2 (addresses goals 2 and 3): Microbiome transfer to field and greenhouse production settings. Years 2-4: 90% completion, estimated full completion in final year The second objective entails transferring microbiome function to field or greenhouse settings. Specifically, we tested the robustness of one specific microbiome that showed plant growth promoting abilities. We focused on Solanum lycopersicum (tomato) as the crop for examining detailed impacts of the microbiome on plant physiology. The plants were grown in a greenhouse setting to assess the ability of the microbiomes to enhance fruit yield, NUE, and N capture across host plants. Within the past year, the following analyses were analyzed: RNA Seq analysis, ethylene measurements, fruit carotenoid measurements, extracellular enzyme activities, soil bacterial and fungal 16S rRNA and ITS sequencing, and plant transcriptional data. This final year, we are preparing a manuscript that features the results of the project--that genes associated with nitrogen utilization in tomato were upregulated in the presence of the plant-growth promoting microbiomes and that differences in plant biomass and growth responses are more evident in the earlier stages of plant development.
Publications
|
Progress 12/01/18 to 11/30/19
Outputs
Target Audience:The target audience for this project includes growers, industry stakeholders, and researchers. The ability to modify crop traits by altering the crop's microbiome is beneficial to agriculture and the various stakeholders involved in research, development, and production. The results of the study will be shared with the scientific community via peer-reviewed publications and scientific conferences, and through public engagement using extension articles and media. We provided laboratory instruction to a group of two undergraduate students and one graduate student. The graduate student is now in his third year at Cornell University and has received advanced training on microbiome analysis since joining the project. He received a three-year NSF graduate research fellowship and a two-year diversity fellowship. The undergraduate students include two returning students that are continuing their research experience on the project. We shared research updates with a diverse audience at scientific conferences, university seminars, and with industry stakeholders. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project has provided the opportunity to train one minority graduate student and two women scientists in new techniques in plant biology, soil science, and microbiology. The graduate student received a three year NSF GRFP and a two year McNair diversity fellowship. The women scientists are undergraduates that are pursuing careers in medical research and practice, with an interest in microbiomes in health. The techniques gained in plant and microbial genomics will allow the students to advance in their careers, while also providing new tools and expertise for the agricultural sciences. How have the results been disseminated to communities of interest?We have presented the preliminary findings and shared the experimental design and goals with scientific audiences at several seminar events: Graduate student presentation, (2019). Using group selection in the rhizosphere microbiome to enhance plant productivity. Soil Ecology Society Annual Meeting. Toledo, OH. May 29th. Invited Speaker, (2019). Applying concepts in group-level evolutionary processes to assemble plant beneficial microbiomes. International Symposium. MICROPE: Microbe-Assisted Crop Production Opportunities, Challenges, and Needs, Vienna, Austria, December 3rd. Invited Speaker, (2019). Ecological assembly of rhizosphere microbiomes to modify plant reproductive traits. International Workshop. The Fruit Microbiome: A New Frontier, Leesburg, VA, September 10th. What do you plan to do during the next reporting period to accomplish the goals?We will complete the data analysis and submit the remaining manuscripts for peer-review publications. We have an additional project to complete with the aid of the award supplement that would allow us to examine the networks of microbial taxa most associated with changes in plant biomass and seed yield of Brassica rapa.
Impacts
What was accomplished under these goals?
Research objective 1 (addresses goal 1): Assembling microbiomes that enhance crop yield. Year 1: 95% completion, estimated full completion in final year The objective for the first experiment focuses on crop yield as traits that can be modulated by a plant's microbiome. We used the rapidly cycling genotype of Brassica rapa to assemble microbiomes that are associated with greater aboveground biomass. We found that the microbiomes derived from organic farms were able to assemble into communities that may have modified seed yield by the end of the experiment. We used 16S rRNA gene sequencing to track shifts in the bacterial composition of rhizospheres across the high biomass selection, random selection, and non-selection (non-adaptive microbiome) treatments. We used standard microbial ordination techniques to show that the microbiomes selected under high biomass versus random selection became distinctly different communities in the successive generations (6-8). Dynamic network modeling using LSA indicated that the interactions across the most abundant bacterial taxa show stronger associations in the high biomass selection rhizospheres in comparison to the random and non-selection treatments. The overall microbiome dataset reveals that our experimental design using directed evolution to assemble microbiomes associated with higher biomass resulted in greater seed yield under the high biomass selection lines versus the non-selection controls, while grown under constant nitrogen-limiting conditions. We are now preparing the manuscript for peer review with a target of March 2020. Research objective 2 (addresses goals 2 and 3): Microbiome transfer to field and greenhouse production settings. Years 2-4: 90% completion, estimated full completion in final year The second objective entails transferring microbiome function to field or greenhouse settings. Specifically, we tested the robustness of one specific microbiome that showed plant growth promoting abilities. We focused on Solanum lycopersicum (tomato) as the crop for examining detailed impacts of the microbiome on plant physiology. The plants were grown in a greenhouse setting to assess the ability of the microbiomes to enhance fruit yield, NUE, and N capture across host plants. Within the past year, the following analyses were conducted: RNA Seq analysis, ethylene measurements, fruit carotenoid measurements, extracellular enzyme activities, soil bacterial and fungal 16S rRNA and ITS sequencing, and plant transcriptional data. This final year, we are linking microbiome and fruit physiological data together to better understand how soil microbiomes impact plant growth and physiology.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Garcia, J. and J. Kao?Kniffin. Can dynamic network modeling be used to identify adaptive microbiomes? Functional Ecology 2019; 00: 1 10. https://doi.org/10.1111/1365-2435.13491
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Progress 12/01/17 to 11/30/18
Outputs
Target Audience:The target audience for this project includes growers, industry stakeholders, and researchers. The ability to modify crop traits by altering the crop's microbiome is beneficial to agriculture and the various stakeholders involved in research, development, and production. The results of the study will be shared with the scientific community via peer-reviewed publications and scientific conferences, and through public engagement using extension articles and media. We provided laboratory instruction to a group of three undergraduate students and one graduate student. The graduate student is now in his second year at Cornell University and has received advanced training on microbiome analysis since joining the project. He received a three-year NSF graduate research fellowship and a two-year diversity fellowship. The undergraduate students include two returning students that are continuing their research experience on the project, as well as a new sophomore student that plans to pursue Honor's Thesis level research. We shared research updates with a diverse audience at scientific conferences, University seminars, and with industry stakeholders. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project has provided the opportunity to train one minority graduate student and two women scientists in new techniques in plant biology, soil science, and microbiology. The graduate student received a three year NSF GRFP and a two year McNair diversity fellowship. The women scientists are undergraduates that are pursuing careers in medical research and practice, with an interest in microbiomes in health. The techniques gained in plant and microbial genomics will allow the students to advance in their careers, while also providing new tools and expertise for the agricultural sciences. How have the results been disseminated to communities of interest?We have presented the preliminary findings and shared the experimental design and goals with scientific audiences at several seminar events: Graduate student presentation, (2018). Developing crop microbiomes for enhanced plant productivity. Ecological Society of America Annual Meeting. New Orleans, LA. August 7th. PI presentation, (2018). Microbiome effects on plant phenotypes. NSF Workshop: International Agricultural Microbiome Research Coordination Network. Boston, MA. July 28th. PI presentation, (2018). Extending microbiome science to agricultural systems. Boyce Thompson Institute Computational Biology Center Symposium. Ithaca, NY. May 8th. PI presentation, (2018, multiple dates). Shared research results with a multitude of industry leaders in agriculture. What do you plan to do during the next reporting period to accomplish the goals?We plan to complete both objectives within the next year, submit manuscripts for peer-review publication, and upload both microbiome and plant sequencing data to public repository sites.
Impacts
What was accomplished under these goals?
Research objective 1 (addresses goal 1): Assembling microbiomes that enhance crop yield. Year 1: 90% completion, estimated full completion in final year The objective for the first experiment focuses on crop yield as traits that can be modulated by a plant's microbiome. As a consequence, we proposed to examine changes in the plant transcriptome when inoculated with microbiomes assembled under selection for increased seed yield with higher nitrogen use efficiency. We instead found weak effects of the selected microbiomes on plant biomass and seed yield. Specifically, one of the five microbiomes examined as separate selection lines showed higher seed yield compared to the random selection and non-adaptive controls. We repeated generation eight of this selection line to examine if the higher seed yield response can be revived with cryo-preserved soil microbiome inoculants. The preliminary data show a repeat of the higher seed yield phenotype with this particular microbiome treatment, which should allow us to move forward with RNA-seq analysis. The analysis will be completed by winter 2019, upon which we will evaluate the plant transcriptome in relation to plant yield and tissue N. Research objective 2 (addresses goals 2 and 3): Microbiome transfer to field and greenhouse production settings. Years 2-4: 75% completion, estimated full completion in final year The second objective entails transferring microbiome function to field or greenhouse settings. Specifically, we tested the robustness of one specific microbiome that showed plant growth promoting abilities. We focused on Solanum lycopersicum (tomato) as the crop for examining detailed impacts of the microbiome on plant physiology. The plants were grown in a greenhouse setting to assess the ability of the microbiomes to enhance fruit yield, NUE, and N capture across host plants. Within the past year, the following analyses were conducted: RNA Seq analysis, ethylene measurements, fruit carotenoid measurements, extracellular enzyme activities, and soil bacterial and fungal 16S rRNA and ITS sequencing. In the following year, plant transcriptional data will be linked with microbiome and fruit physiological data to better understand how soil microbiomes impact plant growth and physiology.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Garcia, J., and J. Kao-Kniffin. 2018. Microbial group dynamics in plant rhizospheres and their implications on nutrient cycling. Frontiers in Microbiology. 9: 1516. DOI: https://doi.org/10.3389/fmicb.2018.01516
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Progress 12/01/16 to 11/30/17
Outputs
Target Audience:The target audience for this project includes growers, industry stakeholders, and researchers. The ability to modify crop traits by altering the crop's microbiome is beneficial to agriculture and the various stakeholders involved in research, development, and production. The results of the study will be shared with the scientific community via peer-reviewed publications and scientific conferences, and through public engagement using extension articles and media. We provided laboratory instruction to a group of four undergraduate students and one graduate student. The student is a recent graduate of UC-Davis and has received advanced training on microbiome analysis since joining the project. He received a three-year NSF graduate research fellowship and a two-year diversity fellowship. The undergraduate students include three returning students that are continuing their research experience on the project, as well as a Freshman student that specifically joined the lab to receive training in microbiome research. We shared research updates with a diverse audience at scientific conferences, university seminars, and grower/manager extension events. Changes/Problems:We do not have major problems or changes in year 2. We replaced the previous graduate student with a new student that is a better fit with the project. Progress is occurring, with one publication in 2017, and an additional two papers for 2018. What opportunities for training and professional development has the project provided?The project has provided the opportunity to train one minority graduate student and four women scientists in new techniques in plant biology, soil science, and microbiology. The graduate student received a three year NSF GRFP and a two year McNair diversity fellowship. Two of the women scientists are undergraduates that are pursuing a career in research, another is a technician that is entering the doctoral program in the agricultural sciences next year, and the fourth is continuing a career in plant and microbiome science research in an industry or academic setting. The techniques gained in plant and microbial genomics will allow the students and technicians to advance in their careers, while also providing new tools and expertise for the agricultural sciences. How have the results been disseminated to communities of interest?We have presented the preliminary findings and shared the experimental design and goals with scientific audiences at several invited seminar events: 2017. University of Nebraska-Lincoln, Department of Agronomy and Horticulture Seminar Series. Lincoln, NE. November 3rd. 2017. Tri-Societies Meeting, American Society of Agronomy. Invited Symposium. Tampa, FL. October 23rd. 2017. Washington State University, Department of Crop and Soil Science Seminar Series, Pullman, WA. June 19th. 2017. University of Maryland, Department of Plant Science and Landscape Architecture Seminar Series, College Park, MD. April 13th. 2017. Phytobiomes Meeting, National Arboretum, Washington DC. March 31st. What do you plan to do during the next reporting period to accomplish the goals?We plan to complete the microbiome and plant transcriptome datasets for objective 1 early in year 3. Manuscripts will be in review in year 3. The transfer to greenhouse and field settings will occur in year 3, as planned.
Impacts
What was accomplished under these goals?
Objective 1: Assembling microbiomes that enhance crop yield. Year 1: 80% completion, estim. completion in Year 3 The objective for the first experiment focuses on crop yield as traits that can be modulated by a plant's microbiome. As a consequence, we propose to examine changes in the plant transcriptome when inoculated with microbiomes assembled under selection for increased seed yield with higher nitrogen use efficiency. We are using a multi-generation experimental design using B. rapa to create different levels of effect of a microbiome on plant biomass. Transcriptional changes in B. rapa, upon inoculation with the selected microbiomes, will facilitate molecular understanding of the role of microbiomes in crop trait manifestations and point toward strategies enabling practical applications. In this second year of the project, we completed the plant biomass studies involving different microbiome inoculations. We are in the process of analyzing the microbial dataset and have published a paper detailing the inoculation methods we used for soil microbiome transfer. The final component of objective 1 is the plant transcriptome analysis that is currently under way. Objective 2: Microbiome transfer to field and greenhouse production settings. Year 2 and 3: 25% completion, estim. completion year 3 The second objective entails transferring microbiome function to field and greenhouse crops. Specifically, we will test the robustness of the assembled microbiomes to reproduce higher crop yield. The plants will be grown for one growing season to assess the ability of the microbiomes to enhance seed yield, NUE, and N capture across host plants. Based on preliminary data, we expect that the microbiomes will be able to induce mechanisms associated with the selected traits across the Brassica hosts. However, we will be testing the robustness of the assembled microbiomes to exert the trait effect under field conditions. In the second year of the project, we are establishing a microbiome on tomatoes and Brassica rapa plants in growth chamber settings using a steam-treatment for soils to minimize the survival of relic microbial members. The resulting colonization of the growth-promoting microbiome will then be transferred into greenhouse and field settings in the third year.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Howard, M., T. Bell, and J. Kao-Kniffin*. 2017. Soil microbiome transfer method affects microbiome composition, including dominant microorganisms, in a novel environment. FEMS Microbiology Letters. Jun 15:364(11). DOI: 10.1093/femsle/fnx092
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Progress 12/01/15 to 11/30/16
Outputs
Target Audience:During the initial year of the project, we have been setting up the plant systems for selecting microbial communities that enhance plant yield. We have been training five different undergraduate students on scientific research with a plant, soil, and microbiology focus. All five students are women and one is from an underrepresented group in the sciences. The students are gaining experience in conducting cutting edge research focusing on agricultural genomics, while learning the fundamental techniques in plant production that will aid in addressing food security in the coming decades. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project has provided the opportunity to train eight women scientists in new techniques in plant biology, soil science, and microbiology. Five of the students are undergraduates that did not have prior research experience in these scientific fields. Two of the technicians working on the project hope to enter graduate school to pursue PhDs in the agricultural sciences. The techniques gained in plant and microbial genomics will allow the students and technicians to advance in their careers, while also providing new tools and expertise for the agricultural sciences. How have the results been disseminated to communities of interest?We have presented the preliminary findings and shared the experimental design and goals with scientific audiences at several invited seminar events: Invited Speaker, (2016), Plant microbiomes: Rethinking symbiosis at the community level. Department of Biological Sciences Seminar Series, Binghamton University, Binghamton, NY. October 7th. Invited Speaker, (2016) Modifying plant-biotic interactions in rhizospheres for novel weed management approaches. Section of Horticulture, Cornell University, Ithaca, NY. August 29th. Invited Speaker, (2016) Using directed selection of plant microbiomes to enhance crop traits. Plant Breeding and Genetics Section, Cornell University, Ithaca, NY. April 19th. Invited Speaker, (2016) Managing weeds in turf and landscapes. Rutgers University Department of Plant Biology and Pathology Seminar Series, New Brunswick, NJ. January 29th. What do you plan to do during the next reporting period to accomplish the goals?We plan to complete the first goal by generating the microbiomes associated with enhanced nitrogen use efficiency. We will then analyze the plant transcriptional data of hosts exposed to the selected microbiomes and paired controls. The physiological measurements involving stable isotopes will aid in teasing apart the mechanisms for enhanced nitrogen uptake or use efficiency.
Impacts
What was accomplished under these goals?
Objective 1: Assembling microbiomes that enhance crop yield. Year 1: 30% completion, estim. completion in Year 2 The objective for the first experiment focuses on crop yield as traits that can be modulated by a plant's microbiome. As a consequence, we propose to examine changes in the plant transcriptome when inoculated with microbiomes assembled under selection for increased seed yield with higher nitrogen use efficiency. We are using a multi-generation experimental design using B. rapa to create different levels of effect of a microbiome on plant biomass. Transcriptional changes in B. rapa, upon inoculation with the selected microbiomes, will facilitate molecular understanding of the role of microbiomes in crop trait manifestations and point toward strategies enabling practical applications. What was accomplished in the initial year for objective 1: We are at the initial year of the project. Preliminary findings with a related plant species (Arabidopsis thaliana) show a strong ability of soil microbiomes to modify plant traits, such as flowering time and biomass. We have set up a new system featuring an agronomic crop (Brassica rapa), with a genotype (Wisconsin Fast Plant) that cycles rapidly to provide rapid observations of plant-microbial interactions associated with changes in plant traits. We found that the new system provides a reliable turnover time of 26 days for each generation cycle. We optimized the soil, fertility, and environmental conditions to maintain a consistent selection cycle for observing microbial modification of plant growth. We conducted a preliminary study of the rapidly cycling Brassica, paired with different types of microbial communities. After four generations of selecting for microbiomes in soils from high biomass yielding plants, the resulting microbiomes began to differentiate in their levels of effect on plant biomass. We observed that the timing of this microbiome modification of plant biomass occurred when there was a precipitous decline in microbial diversity (at generation five). We are in the process of analyzing the data set to determine if there is a clear association of microbiome composition with plant biomass. At present, we are starting a larger experimental design that examines the importance of the starting (initial) microbial community in influencing plant biomass levels over the course of selection for high yields. We are testing the effects of five different starting inoculants, paired with controls for community drift and random effects. This larger experiment will be completed in year 2. As for plant transcripts, we started the analysis of transcriptomic data on Brassica rapa to confirm the efficacy of the library preparation and bioinformatic analysis on the specific genotype used in this study. The data show that the techniques developed by Dr. Giovannoni are appropriate for B. rapa analysis. We used the results to confirm the number of biological replicates needed for the plant transcriptome analysis and the number of libraries to combine on each sequencing lane. Objective 2: Microbiome transfer to field and greenhouse production settings. Year 2 and 3: 0 % completion, estim. completion year 3 The second objective entails transferring microbiome function to field and greenhouse crops. Specifically, we will test the robustness of the assembled microbiomes to reproduce higher crop yield. The plants will be grown for one growing season to assess the ability of the microbiomes to enhance seed yield, NUE, and N capture across host plants. Based on preliminary data, we expect that the microbiomes will be able to induce mechanisms associated with the selected traits across the Brassica hosts. However, we will be testing the robustness of the assembled microbiomes to exert the trait effect under field conditions. As stated in the original proposal, we will begin addressing the second objective in year 2. The expected completion of the field and greenhouse experiment will occur in the third year.
Publications
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