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Award Abstract #0447586
CAREER: Targeted Environmental Genomics: Stable Isotope Probing of Non-cultivated Diazotrophs in Soil
| NSF Org: |
MCB
Division of Molecular and Cellular Biosciences
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| Initial Amendment Date: |
September 7, 2005 |
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| Latest Amendment Date: |
July 27, 2009 |
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| Award Number: |
0447586 |
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| Award Instrument: |
Continuing grant |
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| Program Manager: |
Matthew Kane
MCB Division of Molecular and Cellular Biosciences
BIO Directorate for Biological Sciences
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| Start Date: |
October 1, 2005 |
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| Expires: |
September 30, 2012 (Estimated) |
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| Awarded Amount to Date: |
$686488 |
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| Investigator(s): |
Daniel Buckley dhb28@cornell.edu (Principal Investigator)
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| Sponsor: |
Cornell University - State
373 Pine Tree Road
Ithica, NY 14850 607/255-5014
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| NSF Program(s): |
BE: NON-ANNOUNCEMENT RESEARCH,
MICRO OBS & MICRO INTER & PRO
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| Field Application(s): |
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| Program Reference Code(s): |
BIOT, 9109, 7187, 1629, 1187, 1045
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| Program Element Code(s): |
1629, 1089
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ABSTRACT
Nitrogen (N) fixation is an ancient microbial process which evolved early in the history of our planet and is of central importance to the biosphere. All living things require fixed N for biosynthesis and N-fixing microbes in soils provide the dominant natural source of N in many terrestrial ecosystems. Despite their ancient and enduring ecological importance remarkably littleis known about the ecology and evolution of these microorganisms and of soil microbes in general. This research effort will implement a novel approach that combines stable isotope probing in concert with environmental genomics to target the genomes of non-cultivated diazotrophs. This approach will allow access to genomic DNA from these non-cultivated microbes, providing a remarkable opportunity to advance our understanding of the environmental and genomic mechanisms that regulate the diversity and activity of a microbial process of central importance to the global N-cycle. The genome sequences obtained will help shed light on the evolution of N-fixation and on genome evolution in general by revealing the complex structure of nitrogenase supraoperons in previously uncharacterized microorganisms. In addition, by using this microbial community as a model, this research will reveal basic principles pertaining to the functional significance of microbial diversity and the mechanisms that regulate microbial process in soils. Thus, this project will have both specific and far reaching effects that will improve understanding of microbial processes in the soil, and the ability to effectively manage terrestrial ecosystems.
As part of this project an educational program will be developed that is composed of three components designed to increase science literacy, to improve awareness of microbiology, and to train the next generation of environmental genomics researchers. The first component is a summer workshop "The Microbial Earth" that will provide high school science teachers with modules allowing them to implement open ended laboratory exercises in their curricula and will provide equipment and assistance to help them achieve their teaching goals. The second component is a web module called "Bioprospecting on the Frontiers of Microbiology" for the Cornell CyberTower site. This multimedia module will highlight the role of environmental genomics in discovering novel modes of life and valuable new enzymes. The last component is an advanced undergraduate course in environmental genomics to test the idea of using undergraduates in genomics cooperatives to achieve the dual goals of providing students with primary research experience while contributing to the analysis and annotation of raw genome data.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
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Buckley, D. H., V. Huangyutitham, S-F. Hsu and T. A. Nelson. "15N-Stable isotope probing of DNA as a tool for characterizing the functional significance of free-living diazotrophs in soil," Soil Biology and Biochemistry, v.40, 2008, p. 1272.
Buckley, D. H., S. Hsu, V. Haungyutitham and T. Nelson. "Discovery of nitrogen fixation within novel microbial groups achieved by 15N2 stable isotope probing of soil," Abstracts of the 2006 Annual Meeting of the Soil Science Society of America, 2006.
Buckley, D. H., S. Hsu, V. Haungyutitham and T. Nelson. "Stable isotope probing with 15N2 as a tool to uncover the functional significance of non-cultivated diazotrophs in soil," the Abstracts of the 18th World Congress of Soil Science, 2006.
Buckley, D. H., S. Hsu, V. Haungyutitham and T. Nelson. "Analysis of 16S rRNA and nifH genes through 15N2 stable isotope probing reveal that novel Actinobacteria mediate nitrogen fixation in soil," Abstracts of the 107th General Meeting of the American Society of Microbiology, 2007.
Buckley, D. H., V. Huangyutitham, S-F. Hsu and T. A. Nelson. "Stable isotope probing with 15N achieved by disentangling the effects of genome G + C content and isotope enrichment on DNA density," Applied and Environmental Microbiology, v.73, 2007, p. 3189.
Buckley, D. H., V. Huangyutitham, S-F. Hsu and T. A. Nelson. "Stable isotope probing with 15N2 reveals novel non-cultivated diazotrophs in soil," Applied and Environmental Microbiology, v.73, 2007, p. 3196.
Doroghazi, J. R., D. H. Buckley. "Evidence that bacterial communities in soil follow a lognormal distribution," Proceedings of the 108th General Meeting of the American Society of Microbiology, 2008.
Gaby, J. C., D. H. Buckley. "The Nitrogenase nifH Gene: Current Status of the Census," Proceedings of the 108th General Meeting of the American Society of Microbiology, 2008.
Hsu, S., T. A. Nelson, D. H. Buckley. "Temporal variation in the composition and activity of the diazotrophic community in soils associated with long term biomass energy production," Proceedings of the 108th General Meeting of the American Society of Microbiology, 2008.
J. R. Doroghazi and D. H. Buckley. "Evidence from GC-TRFLP that bacterial communities in soil are lognormally distributed," PLoS One, v.3, 2008, p. e2910.
Jude Maul, Shi-Fang Hsu, Peter Bergholtz and Daniel H. Buckley. "A targeted metagenomic approach to characterization of free-living soil diazotrophs using 15N2 stable isotope probing," Proceedings of the Soil Science Society of America Annual Meeting, 2008.
Noar, J. and D. H. Buckley. "Ideonella azotifigens sp. nov., an aerobic diazotroph of the Betaproteobacteria isolated from grass rhizosphere soil, and emended description of the genus Ideonella," International Journal of Systematic and Evolutionary Microbiology, 2009.
Noar, J., D. H. Buckley. "Ideonella azotifigens sp. nov., an aerobic nitrogen-fixing bacterium which was isolated from soil and is a member of the Burkholderiales," Proceedings of the 108th General Meeting of the American Society of Microbiology, 2008.
S. Hsu and D. H. Buckley. "Correspondence between diazotroph diversity and rates of nitrogen fixation in soil.," International Society for Microbial Ecology Journal, v.3, 2009, p. 124.
S. Hsu, T. A. Nelson and D. H. Buckley. "Linking the diversity and activity of diazotrophs across a gradient of agricultural disturbance," Abstracts of the 107th General Meeting of the American Society of Microbiology, 2007.
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