Progress 03/15/11 to 03/14/15
Outputs Target Audience: Target audiences reached by our efforts include the scientific community, through publications, presentations at national and international meetings, invited seminars, and visits to other universities. Students were another important target audience, and were reached through research presentations as part of courses, and outreach presentations as part of summer undergraduate intern workshops, and through the provision of research experiences to undergraduate students throughout the grant. Grower groups, including potato and soybean growers, were a final target audience. Results of this research were shared during meetings with grower groups. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? This project has provided training for 2 graduate students, 2 research fellows, 3 post-doctoral scientists, and at least 6 undergraduate student researchers. These training activities focus predominantly on research skill development. In addition, both graduate students, bost research fellows, all post-doctoral scientists, and three undergraduate students participated in conferences based upon their work on this project. How have the results been disseminated to communities of interest? The results of this work have been disseminated to communities of interest via publciations, seminar presentations, poster presentations, informal discussions at grower field days, and through presentations as part of undergraduate research opportunity events. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts What was accomplished under these goals?
Soil microbial communities have significant impacts on plant productivity, but the factors that structure the phylogenetic and especially the phenotypic or functional characteristics of soil communities remain poorly understood. Our project provides novel information on the effects of plant diversity and plant host on functional and phylogenetic diversity and composition of microbial communities in soil. While crop rotation is commonly practiced to reduce the buildup of plant pathogens in soil, our work shows that extended monoculture cropping can also have positive impacts on soil communities, specifically in enriching the antagonistic capacities of soilborne Streptomyces bacteria against plant pathogens. Bacterial communities in monoculture or low-diversity plant communities had greater phylogenetic diversity and greater pathogen-inhibitory capacity than bacterial communities in high-diversity plant communities. In contrast, Fusarium communities were more inhibitory in polyculture than in monoculture plant communities. This information suggests that bacteria and fungi respond differently to cropping patterns, and specifically plant diversity. Moreover, our work shows that bacterial and fungal interactions in localized soil communities have significant impacts on antagonistic phenotypes, offering the potential for managing these interactions to enhance disease-suppressive capacities of agricultural soils. Understanding the ways in which soil microbial communities respond to variation in cropping systems, especially plant diversity, is critical to optimizing agricultural management systems for sustainable crop production. 1. We completed characterization of the fungal, bacterial, Fusarium, and Streptomyces phylogenetic composition and diversity in the rhizosphere of plants growing in 1, 4, 16, and 32-species plant communities as part of a long-term (21-year) experiment. In addition, we evaluated communities in soil on which prairie plants were non-treated or treated every-other-week with foliar fungicides over the past 8 years. These studies have generated multiple substantial metagenomic datasets, and that have contributed to over a dozen publications with at least 8 more publications in progress. 2. We determined the inhibitory capacities of Fusarium and Streptomyces populations against one another in cases where the populations were sympatric (from the same soil sample) or allopatric (from different soil samples). In addition, we evaluated the nutrient use profiles, niche width, and growth efficiency of Fusarium and Streptomyces populations growing in the same plants hosts across the plant diversity gradient. Phenotypic analyses were also completed this past year on Streptomyces populations from non-treated and foliar fungicide-treated plants across the plant diversity gradient. These studies have resulted in a substantial phenotypic database that is linked to the metagenomic data and to environmental metadata, thus providing significant insights into the correlates of soil microbial community functional characteristics. These data have contributed to over a dozen publications, with at least 8 more in progress. 3. We developed genome sequence data for diverse Fusarium isolates from native prairie plant hosts to provide insight into the genomic and phenotypic characteristics of indigenous soil populations of this important genus. Genomic data has been incorporated into 3 publications, with at least 2 more in progress.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Schlatter, D. C., Bakker, M. G., Bradeen, J. M., and Kinkel, L. L. 2015. Plant community richness and microbial interactions structure bacterial communities in soil. Ecology. DOI http://dx.doi.org/10.1890/13-1648.1
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Schlatter, D. C. and Kinkel, L. L. 2014. Conflict and communication in microbial communities: a coevolutionary perspective on antibiotics as weapons and signals. Microbe 9: 282-288.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Felice LJ, Huerd SC, Dill-Macky R, Sheaffer CC, Jordan NR, Aldrich-Wolfe L, Kinkel LL. 2015. Soil Streptomyces communities in a prairie establishment study are correlated with soil edaphic characteristics but not plant host. Plant and Soil 386: 89-98. (online 2014, hard copy January 2015)
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Becklund, K.K., L. Kinkel, and J. Powers. 2014. Landscape-scale variation in pathogen-suppressive bacteria in tropical dry forest soils of Costa Rica. Biotropica 46: 657-666. Editors Choice.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Vaz-Jauri, P., and Kinkel, L. L. 2014. Nutrient overlap, genetic relatedness and spatial origin influence interaction-mediated shifts in inhibitory phenotypes among Streptomyces spp. FEMS Microbiology Ecology 90: 264-275. DOI: 10/1111/1574-6941.12389.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
LeBlanc, N., Kinkel, L. L., and Kistler, H. C. 2014. Soil fungal communities respond to grassland plant community richness and soil edaphics. Microbial Ecology DOI 10.1007/s00248-014-0531-1.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Arenz, B. E., Bradeen, J. M., Otto-Hanson, L. K., and Kinkel, L. L. 2014. Two grass species fail to display differing species-specific effects on soil bacterial community structures after one season of greenhouse growth. Plant and Soil 385: 241-254.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Schlatter, D. S., and Kinkel, L. L. 2014. Global biogeography of Streptomyces antibiotic inhibition, resistance, and resource use. FEMS Microbiology Ecology 88: 386-397.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Bakker, M. G., Schlatter, D. S., Otto-Hanson, L., and Kinkel, L. L. 2014. Diffuse symbioses: Roles of plant-plant, plant-microbe, and microbe-microbe interactions in structuring the soil microbiome. Molecular Ecology 23: 1571-1583. DOI: 10.1111/mec.12571.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Kinkel, L. L., Schlatter, D. S., Xiao, K., and Baines, A. D. 2014. Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes. ISME 8: 249-256. doi:10.1038/ismej.2013.175
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Lofgren, L.A., Lasin, P., Roelfs, A., and Kistler, H.C. 2014. Fusarium Inhabitants of Asymptomatic Wild Grasses. Inoculum 65(3): 37. Abstract for Mycological Society of America Meeting, East Lansing, Michigan June 8-11, 2014. (Given as an oral presentation by Lotus)
- Type:
Journal Articles
Status:
Submitted
Year Published:
2015
Citation:
Jelinski, N.A., Broz, K., Jonkers, W., Ma, L.-J., and Kistler, H.C. 2015. Soil populations of Fusarium oxysporum in tomato fields undergoing a tomato wilt epidemic. Environmental Microbiology (manuscript submitted).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
N. LEBLANC, A. Essarioui, L. L. Kinkel, and H. C. Kistler, 2014. Fusarium community structure and carbon metabolism phenotypes respond to grassland plant community richness and plant host. American Phytopathological Society Annual Meeting, Minneapolis, MN.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Felice L, Dill-Macky R, Kinkel L. Effect of carbon amendments on density and pathogen-inhibition in indigenous soil Streptomycetes. American Phytopathological Society Annual Meeting, Minneapolis, MN.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
A. ESSARIOUI, N. LEBLANC, H. C. Kistler, L. Kinkel. 2014. Plant host and community diversity impact the dynamics of resource use by soil Streptomyces. American Phytopathological Society Annual Meeting, Minneapolis, MN.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Anderson, JA., Schlatter, DC., Otto-Hanson, LK., Berglund, M., Kinkel, L. 2014. Variation in Streptomyces densities and inhibitory capacities from diverse natural habitats in New Zealand. American Phytopathological Society Annual Meeting, Minneapolis, MN.
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Progress 03/15/13 to 03/14/14
Outputs Target Audience: Our project efforts targeted scientists through publication of manuscripts and presentation of posters and talks at national and local meetings. In addition, our efforts targeted students through presentations in the classroom and at local scientific field days. Changes/Problems: No major changes or problems. What opportunities for training and professional development has the project provided? Beyond training of two Ph.D. students, one undergraduate, and one research fellow, this project has provided multiple opportunities for training and professional development beyond the degree program. Students working on the project have presented results of their work at multiple conferences in the past year. In addition, graduate students have engaged actively in a `rhizosphere biology' discussion group as part of their activities on this research grant. Graduate students have mentored undergraduate research students in the laboratory, and the results of the mentorship have contributed significantly to the results of the project. How have the results been disseminated to communities of interest? Beyond the scientific publications and presentations at national meetings, results of this project have been included in a recently-developed Freshman Seminar course on the ecology, biochemistry, uses, and challenges of antibiotics in nature and in medicine. This course reached 25 brand-new Freshman students this past year, and resulted in multiple students changing (or choosing!) majors in the sciences! What do you plan to do during the next reporting period to accomplish the goals? We will complete phenotypic analyses of the isolate collection to test the final hypotheses of the proposal, and continue molecular analyses of the soil microbial communities associated with different plant hosts across the plant richness gradient. These research efforts will result in the completion of Ph.D. degrees for two students in the coming year.
Impacts What was accomplished under these goals?
Microbial communities in soil have tremendous potential to enhance plant productivity through diverse mechanisms, including their capacities to directly increase plant growth via production of plant growth-promoting hormones, and indirectly through suppression of plant pathogens. However, we understand little of the factors that influence populations of indigenous soil microbes that can support plant production. Research on this project focuses on characterizing the effects of individual plant hosts and plant community diversity on the capacities of Streptomyces bacteria and Fusarium fungi to suppress plant pathogens and enhance plant growth. This work provides a foundation for understanding how plant hosts influence selection for specific soil microbial population phenotypes, and for altering crop management practices to reduce reliance on pesticides by increasing the capacities of indigenous soil microbes to reduce crop diseases. Objective 1: Use metagenomics to characterize rhizosphere fungal, bacterial, Fusarium, and Streptomyces community composition and diversity among plant hosts grown in experimental plant communities containing 1, 4, 16, or 32 native plant species. Sequencing analyses were completed for two plants hosts growing in plots varying in plant diversity. Bacterial and Streptomyces community composition varied significantly in the rhizosphere of the same plant host when hosts were grown in plots varying in plant diversity, but not among plant hosts. In contrast, both fungal and Fusarium populations varied significantly in the rhizosphere of two plant hosts when grown in monoculture, but varied less among plots varying in plant diversity. This suggests that fungal populations, including Fusarium, respond significantly to individual plant hosts, while bacterial communities, including Streptomyces, respond to larger-scale, plant community factors more than individual plant hosts. This may reflect tighter plant-microbe linkages for fungal populations, while bacterial populations may respond more broadly to total soil nutrient characteristics (which are strongly associated with plant community diversity). KEY ACCOMPLISHMENT: These results change our knowledge and understanding of the factors that structure microbial community structure and composition in the rhizosphere. Objective 2: Determine the relative abundance of competitive phenotypes (nutrient utilization and inhibitory ability) and impacts on plant productivity of Fusarium and Streptomyces populations from the rhizosphere of plants varying in plant community diversity. Streptomyces and Fusarium populations were randomly collected from the rhizosphere of plants growing in prairie plots varying in plant community diversity. Individual isolates were characterized for phylogeny as well as nutrient use profiles and inhibitory phenotypes against populations from the same and from different rhizospheres. Streptomyces populations from the rhizosphere of plants growing in monoculture were significantly more inhibitory than populations isolated from the rhizosphere of plants growing in polyculture. In contrast, Fusarium populations were significantly more inhibitory when isolated from plants growing in polyculture than in monoculture. For both Streptomyces and Fusarium, there are apparent tradeoffs in inhibitory and nutrient use phenotypes: populations that are highly inhibitory exhibit less efficient growth on a broad cross-section of nutrients than isolates that are poor inhibitors. Both Streptomyces and Fusarium isolates show significant local adaptation. That is, these populations are both significantly better at inhibiting members of the other genus from the SAME than from different rhizospheres. This indicates significant local adaptation, reflecting the importance of interactions between these two genera to their fitness. These results provide a significant enhancement (change) in our knowledge of the role of Fusarium-Streptomyces interactions in structuring the composition and phenotype/function of these populations in the rhizosphere. Objective 3: Sequence the genome of one or more nonpathogenic Fusarium oxysporum isolates most abundant in the prairie plant communities. We have collected a large number of Fusarium oxysporum isolates from the prairie plant communities, and are in the process of characterizing these isolates genetically and phenotypically. We anticipate that these results will result in a change in knowledge.
Publications
- Type:
Journal Articles
Status:
Submitted
Year Published:
2014
Citation:
LeBlanc, N., L. L. Kinkel, and H.C. Kistler. 201x. Soil fungal communities respond to grassland plant community richness and soil edaphics. submitted Microbial Ecology.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Kinkel, L. L., Schlatter, D. S., Xiao, K., and Baines, A. D. 2014. Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes. ISME 8: 249-256. doi:10.1038/ismej.2013.175
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Bakker, M. G., Schlatter, D. S., Otto-Hanson, L., and Kinkel, L. L. 2013. Diffuse symbioses: Roles of plant-plant, plant-microbe, and microbe-microbe interactions in structuring the soil microbiome. Molecular Ecology 23:1571-1583. DOI: 10.1111/mec.12571.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Vaz-Jauri, P., Bakker, M. G., Salomon, C. E., and Kinkel, L. L. 2013. Subinhibitory antibiotic concentrations mediate nutrient use and competition among soil Streptomyces. PLoS One 8:12 e81064.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Schlatter, D. S., DavelosBaines, A.D., Xiao, K., and Kinkel, L. L. 2013. Resource use of soil Streptomycetes varies with location, phylogeny, and nitrogen amendment. Microbial Ecology 66: 961-971.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Rosenzweig, N., Bradeen, J. M., Tu, Z. J., McKay, S. J., and Kinkel, L. L. 2013. Rhizosphere bacterial communities associated with long-lived perennial prairie plants vary in diversity, composition, and structure. Canadian Journal of Microbiology 59:494-502.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Bakker, M. G., Bradeen, J. M., and Kinkel, L. l. 2013. Effects of plant host species and plant community richness on streptomycete community structure. FEMS Microbiology Ecology 83:596-506.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Bakker, M. G., Otto-Hanson, L., Lange, A. J., Bradeen, J. M., and Kinkel, L. L. 2013. Plant monocultures produce more antagonistic soil Streptomyces communities than high-diversity plant communities. Soil Biology and Biochemistry 65:304-312.
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Progress 03/15/12 to 03/14/13
Outputs Target Audience: Scientists, farmers Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Two Ph.D. student projects are focused on this project, and a third Ph.D. student has received training on this project. In addition, the project supports further training of a M.S.-level research fellow. How have the results been disseminated to communities of interest? Results have been disseminated to the scientific community through presentations at multiple scientific meetings. In addition, we have published four scientific manuscripts summarizing various aspects of the work. Finally, an overview of the research was presented as part of a discussion with Minnesota potato growers at a grower field day (Summer, 2012). What do you plan to do during the next reporting period to accomplish the goals? We will complete isolation and characterization of Streptomyces and Fusarium isolates to test key hypotheses of the proposal. In addition, we will complete further molecular analyses of the soil microbial communities associated with different plant hosts across the plant richness gradient. Finally, we will initiate sequencing of a Fusarium oxysporum genome in the coming year.
Impacts What was accomplished under these goals?
Soil samples were collected from plant hosts growing in plots varying in plant species richness (n = 1-32 plant species). Microbial densities (bacterial and fungal) as well as Streptomyces and Fusarium densities were determined for rhizosphere soil across the diveristy gradient. In addition, pathogen-inhibitory activities of Streptomyces communities associated with hosts across the diversity gradient were quantified against multiple pathogen targets. DNA was extracted from soils and processed using 454 pyrosequencing. Analyses of the sequence databases provided data for poster presentations at national meetings. Isolation of a broad collection of individual Streptomyces and Fusarium isolates for phenotypic characterization is currently underway.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
Kinkel, L. L., Schlatter, D. S., Bakker, M. B., and Arenz, B. 2012. Streptomyces competition and coevolution in relation to disease suppression. Research in Microbiology: dx.doi.org/10.1016/j.resmic.2012.07.005
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
Bakker, M. B., Tu, Z. J., Bradeen, J. M., and Kinkel, L. L. 2012. Implications of Pyrosequencing Error Correction for Biological Data Interpretation. Public Library of Science (PLoS ONE) 7(8): e44357. doi:10.1371/journal.pone.0044357.
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
Bakker, M. B., Bradeen, J. M., and Kinkel, L. L. 2012. Effects of plant host species and plant community richness on streptomycete community structure. FEMS Microbiology Ecology: DOI: 10.1111/1574-6941.12017
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Otto-Hanson, L. , Rosen, C., Salomon, C., and Kinkel, L. L. 2013. Pathogen variation and urea influence selection and success of Streptomyces mixtures in biocontrol. Phytopathology 103: 34-42.
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Progress 03/15/11 to 03/14/12
Outputs OUTPUTS: Field experiments were established at the Cedar Creek Ecosystem Science Reserve. Wheat plants were introduced into prairie plots varying in plant species richness (n = 1 - 32 plant species). Soil samples collected from the rhizosphere of prairie plants within species richness plots were processed and DNA extracted from the soils was processed using 454 pyrosequencing. DNA was also extracted from leaf and root tissues of prairie species across the plant species richness gradient, and processed using 454 pyrosequencing. Analyses of the resulting sequence databases are underway. Poster presentations based on some of the data generated in the biodiversity plots were made at international meetings. PARTICIPANTS: Nick LeBlanc, Ph.D. student in Plant Pathology Adil Essarioui, Ph.D. student in Plant Pathology Lindsey Hanson, Research Fellow in Plant Pathology Jon Anderson, junior scientist TARGET AUDIENCES: Scientists, farmers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts Sequence data resulting from this project are providing new insights into the effects of plant hosts and plant community richness on rhizosphere microbial community diversity, richness, and composition. In addition, these data are providing significant knowledge for use in developing enhanced models for managing soil microbial communities to enhance plant disease suppression.
Publications
- No publications reported this period
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