A grant has been awarded to Drs. Mary Lidstrom, Ludmila Chistoserdova and Murray Hackett at the University of Washington, to continue their Microbial Observatories project focused on an environmentally important group of bacteria that grow on simple compounds containing a single carbon: the methylotrophs. During the prior funding period, extensive knowledge was gained on the abundance and diversity of methylotrophs in Lake Washington, WA, pointing toward the existence of a multi-tiered microbial food web involved in environmental cycling of one-carbon compounds. These studies also revealed important insights into the evolution of methylotrophic pathways in different bacteria. The new data showed that many members of the methylotrophic guild remain uncharacterized in pure cultures, some belong to novel, uncharacterized phyla, and their specific roles in the cycling of environmentally important compounds remain poorly defined. The next phase of research will use a combination of cutting edge technologies such as community DNA sequencing and analysis, microarray technology for assessing gene expression, and high throughput community protein pool analysis in order to obtain systems-level knowledge of the genomic determinants, expression patterns, and protein fingerprints of methylotrophic microorganisms, ultimately linking the genomic potential of this group to its ecological function.

This work will provide further insights into the complex communities in nature that are responsible for the cycling of one-carbon compounds. Methylotrophs play an important role in keeping natural habitats healthy and thriving, and they are the main consumers of a number of compounds that contribute to global warming, such as methane, bromomethane and chloromethane. Establishing which microbial taxa are responsible for the utilization of one-carbon compounds, understanding regulation of their activities, as well as uncovering potential synergistic relationships within their communities represent important steps in developing accurate predictions regarding the relationship between the carbon cycle and global warming. The broader impact of this project will be in presenting a model for systems-level approaches to analyzing other complex microbial communities. In addition, the project will serve as a vehicle for actively involving graduate, undergraduate and high school students, including underrepresented minority groups in environmental microbial research.

Project Report

The Microbial Observatory in Lake Washington was initially funded in 2002 and subsequently renewed in 2006. The goals of the original project were to uncover the diversity of microbial populations of methylotrophs (i.e. organisms metabolizing methylated compounds with no carbon-carbon bonds, or C1 compounds such as methane, methanol etc.) in Lake Washington sediment, as a model for global estimates for C1 utilizers in the environment, and to obtain insights into the evolution of metabolic pathways enabling methylotrophy. The major goal of the second phase of the Microbial Observatory project was to apply a systems approach to obtaining knowledge about the microbial populations involved in degradation of C1 compounds in Lake Washington, as a model for understanding functional microbial communities in general. The components of this approach included functional (meta)genomics, functional (meta)transcriptomics and functional (meta)proteomics. Over the past ten years, this project has resulted in significant advances in understanding the diversity and the complexity of methylotroph populations inhabiting lake sediments, including extensive databases of genes diagnostic of methylotrophy and identification of novel genes and pathways involved in methylotrophy, characterization of novel methylotroph species, and generation of relevant (meta)genomic, (meta)transcriptomic and (meta)proteomic datasets. The results of this project were presented at over 40 international conferences and described in over 40 publications. Six post-doctoral fellows, four graduate students, 15 undergraduate students and 10 high school students (20 women, 7 minorities) have been trained as part of this project. Most of our former students have completed, are continuing, or starting their education aiming at careers in science, engineering, bio/medical informatics or medicine. The approaches and the results of this project have been incorporated into four courses at the University of Washington, used as part of the international training course ‘Geobiology 2005’ organized by the University of Southern California and Wrigley Institute for Environmental studies, and were broadly disseminated via conference participation, publications in peer-reviewed journals, invited book articles, a feature article in ASM News, press releases and feature articles by others, and via the web site devoted to the project (http://depts.washington.edu/ microobs/). Gene, transcript, protein and (meta)genomic datasets have been deposited with appropriate depositories such as GenBank, GEO or JGI IMG databases, and the novel bacterial strains isolated as part of the project have been deposited with international culture collections. As part of this project, we have actively outreached to the community, via collaborating with local schools and local colleges and via hosting undergraduate students as well as school students in our lab. We closely collaborated with minority-oriented programs via recruiting minority students through the ‘GenOM’ (‘Genomics Outreach for Minorities’) program at the University of Washington, and providing training as part of ‘The Bioscience Experience’ program that aims at recruiting underrepresented minorities to doctoral programs. We have also developed special programs for elementary school students that introduce them to both principals of microbiology and hands-on research. In addition, results from this project were used in hands-on exercises for non-experts as part of the International Women's Forum workshop on genomics held in Seattle.

National Science Foundation (NSF)
Division of Molecular and Cellular Biosciences (MCB)
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Matthew Kane
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University of Washington
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