Progress 08/15/06 to 08/14/11
Outputs
OUTPUTS: Our work has focused on characterizing the diversity and phenotypes of rhizosphere microbial communities associated with native prairie plants. We completed multiple 454 sequencing projects of bacterial, actinobacterial, and fungal communities associated with prairie plant species. Sequencing was also completed on rhizosphere bacterial communities associated with A. gerardii and the agricultural host Secale cereale (rye) when grown in 9 different source soils in greenhouse conditions. In addition to plant-species effects on microbial communities, this work is providing insight into variation in microbial communities associated with target hosts when grown in plant communities varying in total plant diversity (1 to 32 species), and variation associated with different microbial `starting' communities. To date, we have generated more than 3,000,000 sequences for bacteria and actinobacteria in the rhizosphere, and have used this information to explore the role of plant host, soil characteristics, plant diversity, or microbial co-associates in determining microbial diversity and composition in the rhizosphere. In related work, signaling interactions among actinobacteria have been explored to determine their role in disease suppression. We recently completed a novel study to characterize the potential that antibiotics themselves act as signaling compounds by altering microbial nutrient utilization patterns when present at low, sublethal concentrations. A bacterial reporter system is being used to characterize the relative abundance of gamma-butyrolactone signaling among our actinobacterial isolates, and we are collaborating with scientists to develop two additional reporter systems to increase the diversity of signaling compounds detected rapidly in vitro. This work provides insight into the diversity and specificity of bacterial signaling interactions and, ultimately, to plant disease suppression in soil microbial communities. In related work, we have explored the potential for plant-produced compounds to act as signaling molecules. We have found multiple plant compounds that are highly active in inducing antibiotic activities in bacteria. Another major effort on this project has shown significant local adaptation of nutrient and antibiotic phenotypes among soil bacteria. In total, this work is providing broad insight into the ecology and evolutionary biology of microbes in the rhizosphere, and on the manner in which microbial interactions and plant-microbe interactions mediate disease suppressive activities in soil. Seven Ph.D. students participated in various aspects of this project over the course of the project, as well as many undergraduate research interns, two post-docs, and technical support staff. Over the life of this project, dozens of presentations based on this work were made at scientific meetings or as invited lectures at Universities in the United States and internationally (Germany, France, The Netherlands, Panama, China, Italy, India, England). Publications from this work continue to come out, with a significant collection of publications forthcoming. PARTICIPANTS: PARTICIPANTS: Linda L. Kinkel (Professor in the Department of Plant Pathology at the University of Minnesota)leads this research effort. James Bradeen is an Associate Professor in the Department of Plant Pathology and is a co-PI. Debby Samac (Professor in the Department of Plant Pathology), Christine Salomon (Assistant Professor in the University of Minnesota Center for Drug Design), Dr. Eriko Takano (Professor in the Department of Microbial Physiology at the University of Groningen The Netherlands) are collaborators on the project. Lindsey Hanson, Kun Xiao, AJ Lange, Jennifer Kang, Megan Bearman, and Jon Anderson have all been either research technicians or junior scientists on the project at varying times. Matt Bakker, Atenea Garza, Dan Schlatter, Laura Felice, Adil Essarioui, Pingping Sun, and Patricia Vaz are Ph.D. students who have contributed to the work. More than a dozen undergraduates were trained in and contributed to this project. In addition, post-doctoral scientists contributing to the project included Dr. Noah Rosenzweig and Dr. Brett Arenz. The University of Minnesota Biodale facility providing sequence data, and the UM MSI provided access to supercomputing facilities required for data analysis. TARGET AUDIENCES: Target audience: Microbial biologists, plant pathologists, plant scientists. PROJECT MODIFICATIONS: The major change in approach over the life of this project was the application of 454 sequencing approaches to the characterization of soil microbial communities. This technique was not available at the time the grant was originally funded, but has fundamentally changed our capacities to explore microbial communities in complex environmental samples. This has tremendously enhanced the scale of our sampling efforts and our capacity to develop in-depth understanding of the diversity and composition of rhizosphere microbial communities.
Impacts
Our research has documented the hierarchy of biotic interactions that mediate microbial community composition and function. Specifically, our work shows a clear role for microbial species interactions, plant-microbe interactions, and plant-plant interactions in mediating rhiosphere community diversity and composition. Simple two-way plant-microbe models are inadequate for understanding plant-microbe non-obligate symbioses. This work also highlights the significance of microbial and plant-microbe signaling interactions to community-wide disease-suppressive phenotypes and plant fitness. Based upon these results we have developed a model for managing microbial community coevolution in soil to maximize disease suppressive activities. While the capacity of plants to select for distinct microbial communities has been reasonably well-established, our model recognizes the significant manner in which plant selection is mediated through microbial species interactions in soil. This provides us with novel approaches for enhancing disease suppressive capacity of agricultural soils to contribute to more sustainable agricultural production systems. Though microbial communities in soil remain relatively poorly understood, our work contributes to the development of a broad and systematic database on microbial community composition and function across natural and agricultural landscapes; such information is crucial to enhancing our capacity to manage these communities.
Publications
- SA Schnitzer, JN Klironomos, J HilleRisLambers, LL Kinkel, PB Reich, K Xiao, M C Rillig, BA Sikes, R M Callaway, SA Mangan, EH van Nes, and M Scheffer (2011). Soil microbes drive the classic plant diversity-productivity pattern. Ecology 92(2): 296-303.
- LL Kinkel, MG Bakker, and D Schlatter (2011) A coevolutionary framework for managing disease-suppressive soils. Annu. Rev. Phytopathol. 49: 47-67.
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Progress 08/15/09 to 08/14/10
Outputs
OUTPUTS: In 2010, our work focused on characterizing the diversity and phenotypes of rhizosphere microbial communities associated with the native prairie plants Andropogon gerardii and Lespedeza capitata. Significant progress was made in pyrosequencing of bacterial and Actinobacterial communities. In addition to plant-species effects on microbial communities, variation in microbial communities associated with each of the target hosts when grown in plant communities varying in total plant diversity (1 to 32 species) was explored. This work was performed at the Cedar Creek Ecosystem Science Reserve in east-central Minnesota, and builds on the long-standing biodiversity experiment established in 1994. To date, we have generated more than 700,000 sequences for bacteria and actinobacteria in the rhizosphere, and are using this information to explore the role of plant host, soil characteristics, plant diversity, or microbial co-associates in predicting the presence or abundance of target groups in the rhizosphere. In related work, signaling interactions among actinobacteria from the rhizosphere have been explored to determine the role that local adaptation plays in mediating species interactions. This work includes a novel study to characterize the potential that antibiotics themselves act as signaling compounds by altering microbial nutrient utilization patterns when present at low, sublethal concentrations. A bacterial reporter system is being used to characterize the relative abundance of gamma-butyrolactone signaling among our actinobacterial isolates. This work provides insight into the diversity and specificity of bacterial signaling interactions and, ultimately, to plant disease suppression in soil microbial communities. In related work, we have explored the potential for root exudates to act as signaling molecules. We have found some root exudates that are highly active in inducing antibiotic activities in bacteria. Another major effort on this project has focused on systematic characterization of the antibiotic and nutrient utilization phenotypes of the bacteria associated with different plant hosts. In total, this work is providing broad insight into the ecology and evolutionary biology of microbes in the rhizosphere, and on the manner in which microbial interactions and plant-microbe interactions mediate disease suppressive activities in soil. Four Ph.D. students participated in various aspects of this project over the past year, as well as five undergraduate research interns. In 2010, we presented 7 invited presentations both in the U.S. and Europe, and participated in poster presentations at two international scientific meetings. PARTICIPANTS: Linda L. Kinkel is a Professor in the Department of Plant Pathology at the University of Minnesota and leads this research effort. James Bradeen is an Associate Professor in the Department of Plant Pathology and is a collaborator on this effort. Debby Samac is a Professor in the Department of Plant Pathology and is a collaborator on this effort. Dr. Christine Salomon is an Assistant Professor in the Center for Drug Design (University of Minnesota), Dr. Eriko Takano is an Associate Professor in the Department of Microbial Physiology at the University of Groningen (The Netherlands), and Dr. Jason Sello is an Assistant Professor in the Department of Chemistry at Brown University (Rhode Island). All three are collborators on this project. Lindsey Hanson is a Research Technician on the project who is responsible for coordinating all laboratory efforts. AJ Lange is a junior scientist who provides project support. Matt Bakker is a graduate student studying signaling interactions on the project. Atenea Garza's research contributes to the microbial phenotypic analyses. Dan Schlatter is coordinating a component of the sequencing work associated with this project. Summer interns contributing to this project included Katie Neshek, Kayla Miller, Megan Overland, Craig See, and Samantha Peterson. The University of Minnesota Biodale facility providing sequence data, and the UM MSI provided access to supercomputing facilities required for data analysis. TARGET AUDIENCES: Microbial biologists, plant pathologists, plant biologists PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Our research documents the significant roles of microbial species interactions in organizing community structure within the rhizosphere of diverse plant hosts. This work also highlights the effects of microbial species interactions and plant-microbe signaling interactions on the disease-suppressive potential of soil microbial communities, and, ultimately, on plant fitness. While the capacity of plants to select for distinct microbial communities is well-established, the manner in which plant selection is mediated through microbial species interactions in soil has not been well-described. This work provides insight into the cascade of species interactions that are critical to mediating disease suppressive activity, and offers a framework for developing novel approaches for enhancing disease suppressive activities in agricultural soils. Our work also documents the tremendous diversity of rhizosphere communities and identified some of the significant biotic and abiotic covariates of diversity and composition. Microbial communities in soil remain relatively poorly understood, and systematic data on composition and function across natural and agricultural landscapes is crucial to enhancing our capacity to manage these communities.
Publications
- Bakker, M. G., Glover, J. D., Mai, J. G., and Kinkel, L. L. 2010. Plant community effects on the diversity and pathogen suppressive activity of soil streptomycetes. Applied Soil Ecoloy 46: 35-42.
- Schlatter, D. C., Samac, D. A., Tesfaye, M., and Kinkel, L. L. 2010. Rapid and specific method for evaluating Streptomyces competitive dynamics in complex soil communities. Applied and Environmental Microbiology 76: 2009-2012.
- Morris, C. E., Bardin, M., Kinkel, L. L., Moury, B., Nicot, P. C., and Sands, D. C. 2009. Expanding the paradigms of pathogen life history and evolution of parasitic fitness beyond agricultural boundaries. PLoS Pathogens 5 (12): e1000693.
- Bakker, M. G., Tu, Z. J., Bradeen, J. M., and Kinkel, L.L. 2010. Evaluation and implications of PyroNoise, a program for error correction in 454 pyrosquence data. 13th International Symposium on Microbial Ecology Conference Book, Seattle, Washington, Aug 2010.
- Bakker, M. G., Bradeen, J. M., and Kinkel, L. L. 2010. Plant host influences on associated actinobacterial communities vary with plant diversity. 13th International Symposium on Microbial Ecology Conference Proceedings, Seattle, Washington, Aug 2010.
- Bakker, M. G., Bradeen, J. M., and Kinkel, L. L. Plant host influences on associated actinobacterial communities vary with plant diversity. 2nd Annual Argonne Soils Workshop Proceedings, Lemont, Illinois, Oct 2010.
- Neshek, K., Otto-Hanson, L., and Kinkel, L. 2010. Horton Hears a Who, Leaves Host Communities, Too!: Leaves as sources and sinks for fungi in diverse plant communities. 70th Annual Meeting of the North Central Branch of the American Society for Microbiology Proceedings, October 1 &2, 2010. Minnesota State University-Mankato, Mankato, MN.
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Progress 08/15/08 to 08/14/09
Outputs
OUTPUTS: New information on: (i) the ecology and biodiversity of microbial communities associated with the native prairie plant species Andropogon gerardii and Lespedeza capitata; (ii) the use of molecular sequencing strategies for getting broad-based (prokaryotes) and targeted (Streptomyces-only) information on microbial community and population sequenced diversity; (iii) the effects of plant community on the rhizosphere microbial communities associated with Andropogon gerardii and Lespedeza capitata; (iv) the role of microbe-microbe and plant-microbe signaling interactions in determining Streptomyces interaction phenotypes. PARTICIPANTS: Matt Bakker, Dan Schlatter, Atenea Garza, and Patricia Vaz-Jauri are graduate students whose research contributed to our understanding of microbial communities in prairie soils. Lindsey Hanson is junior scientist whose work contributed significantly to our understanding of rhizosphere microbial communities in prairie soil. AJ Lange, Maia Dedrick, and Zane Grabau are undergraduate students whose work contributed to our understanding of microbial communities in prairie soil. TARGET AUDIENCES: Plant pathologists and microbial ecologists. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Though there is substantial information suggesting that plant hosts can `create' soil microbial communities that differ in composition, there is little information on whether these compositional differences result in different microbial community functional activities. In prairie soils at Cedar Creek Ecosystem Science Reserve, microbial communities associated with the legume host Lespedeza capitata were significantly larger (cfu/g soil) than communities associated with Andropogon gerardii. However, microbial communities in the rhizosphere of Andropogon gerardii were significantly more inhibitory towards plant pathogens than were communities in the rhizosphere of Lespedeza capitata. These data contrast with agricultural system data suggesting a strong positive correlation between community density and pathogen inhibitory activity. This suggests the possibility that Andropogon gerardii plants select for pathogen inhibitory populations in the rhizosphere through a direct (non-density-dependent) mechanism. Selection for pathogen-inhibitory communities may confer a significant fitness benefit to the grass host via protection against root disease. However, for the legume host, the potential benefits of a pathogen-suppressive community may be counterbalanced by a reduction in nitrogen-fixing bacterial populations in the rhizosphere, and thus that selection for a strongly-inhibitory community may be less desirable for the legume. Extensive community analyses using 454 pyrosequencing data documented significant differences among communities associated with the two plants hosts as well as significant differences among locations for each plant host. These differences suggest key bacterial candidates for understanding the functional roles that soil bacteria play in plant development, health, and productivity. Evidence also suggests that nutrient utilization differs among Streptomyces isolates from the rhizosphere of Andropogon gerardii. In total, these data illustrate not only the compositional differences among microbial communities associated with distinct plant hosts but also shed light into the potential fitness dynamics that mediate plant-microbe interactions in soil. The plant species being studied are models for important crop plants including soybean (a legume) and corn (a grass), thus our findings have the potential to contribute significantly to the development of sustainable practices for production agriculture.
Publications
- Rosenzweig N., Tu Z. J., Bradeen J., Kinkel L. 2009. Microbial diversity associated with the long- lived perennial plant species Andropogon gerardii and Lespedeza capitata: Impacts of plant host species on rhizosphere bacterial consortium diversity and composition. ISS 6th International Symbiosis Society Congress, Ecology: Community Ecology of Symbionts Session.
- Bakker, M. G., and Kinkel, L. L. 2009. Plant signaling compounds alter secondary metabolite production among antagonistic Streptomyces. Phytopathology 99:S7-8.
- Schlatter, D., and Kinkel, L. L. 2009. Local adaptation and global biogeography of antagonistic Streptomyces. Phytopathology 99:S15.
- Schlatter, D., Fubuh, A., Xiao, K., Hernandez, D., Hobbie, S., and Kinkel, L. 2009. Resource amendments influence density and competitive phenotypes of Streptomyces in soil. Microbial Ecology 57:413-420.
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Progress 08/15/07 to 08/14/08
Outputs
OUTPUTS: 1. Characterize microbial communities associated with Andropogon gerardii and Lespedeza capitata roots in native prairie habitats. We continued to expand our collection of streptomycetes, pseudomonads, and other bacteria from two target prairie species (Lespedeza capitata and Andropogon gerardii). We continued to explore alternative culturing strategies to enhance collection of rare isolates. We are exploring bacterial diversity associated with these two plant hosts using pyrosequencing. Within the existing collection of cultured isolates, nutrient utilization phenotype analysis is underway. 2. Characterize interactions and interaction phenotypes among consortia associated with A. gerardii and L.capitata in native prairie habitats. We are also exploring the effects of plant extracts on streptomycete inhibitory activities and secondary metabolite profiles in vitro. We have been working to develop HPLC profiling as a means of characterizing the metabolomic profile for our collection of streptomycete isolates from the two different plant species. 3. Contrast the impacts of individual rhizosphere isolates on plant growth or fitness with impacts of isolate combinations/consortia. We are working on refining the plant assay to accomplish this objective. 4. Contrast the impacts of inoculated microbial consortia on the source vs. non-source plant hosts, and on agriculturally significant plant species (grasses: wheat, corn; legumes: soybean, alfalfa). Results of our work have been disseminated through published manuscripts, presentations at national meetings, and invited seminar presentations in the United States and elsewhere. PARTICIPANTS: Graduate students: Matt Bakker Dan Schlatter Atenea Garza Undergraduate students: Laura McCarrville David Manning Junior Scientist: Megan Bearman Collaborators: James Bradeen Dirk Hoffmeister Christine Salomon Helene Muller-Landau Carl Rosen Partner organization: Bioworks Training and professional development was provided to graduate and undergraduate students during the course of the project. TARGET AUDIENCES: Scientists PROJECT MODIFICATIONS: We have pursued pyrosequencing as an alternative to cloning and sequencing 16S genes from soil bacteria.
Impacts
Outcomes from the past year's work include: student training (3 graduate students, 2 undergraduate students); expanded database on the ecology of microbial communities associated with A. gerardii and L. capitata; data used to submit 6 subsequent funding proposals for submission to national, regional, and state funding agencies; and manuscripts including those published (see below) and in preparation (5 in preparation). Results of our project evaluation resulted in the development of the HPLC approach for characterizing streptomycete metabolomic profiles, and development of enhanced approaches for culturing novel streptomycetes from soil.
Publications
- Gil, I. S., Sheldon, W., Schmidt, T., Servilla, M,. Aguilar, R., Gries, C., Gray, T.,n Field, Dl., Cole, J., Pan, J. Y., Palanisamy, G., Henshaw, D., OBrien, M., Kinkel, L., McMahon, K., Kottmann, R., Amaral-Zettler, L., Hobbie, J., Goldstein, P., Guralnick, R. P., Brunt, J., and Michener, W. K. 2008. Defining linkages between the GSC and NSFs LTER program: How the Ecological Metadata language (EML) relates to GCDML and other outcomes. Omics-A Journal of Integrative Biology 12:151-156.
- Perez, C., Dill-Macky, R., and Kinkel, L. L. 2008. Management of soil microbial communities to enhance populations of Fusarium graminearum antagonists in soil. Plant and Soil 302:53-69.
- Schlatter, D., Fubuh, A., Xiao, K., Hernandez, D., Hobbie, S., and Kinkel, L. L. 2008. Resources amentdments influence density and competitive phenotypes of Streptomyces in soil. Microbial Ecology: Online First.
- Kinkel, L., and Kang, J. 2008. Variation in nutrient utilization and sensitivity to antibiotic inhibition within a global collection of Streptomyces scabies. Phytopathology 98:S82.
- Rosezweig, N., Kang, J., Kinkel, L. L., and Bradeen, J. 2008. Molecular approaches for taxa discovery in plant-associated soil microbial communities. Phytopathology 98:S136.
- Schlatter, D. C., Fubuh, A., Xiao, K., Hernandez, D., Hobbie, S., and Kinkel, L. L. 2008. Influence of carbon source amendments on population density, resource use, and antibiotic phenotypes of soilborne Streptomyces. 2008. Phytopathology 98:S140-141.
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Progress 08/15/06 to 08/14/07
Outputs
OUTPUTS: This project focuses on a comprehensive exploration of the rhizosphere microflora of two prairie plant hosts, the grass Andropogon gerardii (big bluestem), and the legume Lespedeza capitata (prairie bush clover). During the past year, we initiated characterization of the rhizosphere communities using a combination of molecular and culturing strategies, providing a collection of microbes which will be characterized phylogenetically and relative to their impacts on plant `hosts'. Personnel were hired onto the project, and field sampling methods were established.
PARTICIPANTS: Linda Kinkel: Principal investigator James Bradeen: Co-Principal investigator Debby Samac: Co-Principal investigator Noah Rosenzweig: Post-doctoral research associate Jee Kang: Technical support scientist Atenea Garza: Collaborator, graduate student Dan Schlatter: Collaborator, graduate student Training and professional development opportunities: research on this project supports the training and development of 2 graduate students and one post-doctoral scientist.
Impacts
The proposed research will advance our understanding of rhizosphere microorganisms, on the selective effects of plant hosts on soil microbes, and on the potential impacts of novel plant-associated microbes on plant fitness.
Publications
- No publications reported this period
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