The genomes of modern microbes represent natural repositories of the evolutionary history of life on Earth. My research focuses on significantly expanding our knowledge of this molecular record by accessing whole genomes of major new microbial groups that are often known by only a single gene sequence. Since these organisms inhabit primitive Earth-like environments, genomic and emergent physiological data represent key pieces in the puzzle of understanding the first stages of life on Earth and may provide important insights into the early evolution of key metabolic processes. In addition, my projects provide a framework for understanding microorganisms with potentially fundamentally different metabolisms, which is part and parcel for evaluating the question: Does life exist elsewhere in the universe?
One of the central challenges in understanding how biodiversity is shaped by the environment is the sheer complexity of microbial ecosystems. Progress in understanding biodiversity has been driven by studying carefully chosen cross-sections of complex ecosystems or focusing on a few culturable keystone organisms within the larger community. Microbes play a pivotal role in shaping ecosystems: from driving planetary-scale biogeochemical cycles to provoking the origin and evolution of functional diversity in higher organisms. My work seeks to clarify the reciprocal interactions between the microbial majority and their environment.
My research focuses on three approaches to tackle the central challenges in analyzing complex environmental communities to:
- Develop novel computational techniques to inform a new generation of genomic and community genomic data.
- Model the co-evolution of organisms and the environment
- Illuminate the evolutionary origin and history of phenotypes and environmental adaptation.
Becraft, E.D., Dodsworth, J.A., Murugapiran, S.K., Ohlsson, J.I., Briggs, B.R., Kanbar, J., De Vlaminck, I., Quake, S.R., Dong, H., Hedlund, B.P., and Swingley, W.D. (2016) Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes. Appl Environ Microbiol. 82, 992-1003.
Amrine, K.C.H., Swingley, W.D., and Ardell, D.H. (2014) tRNA signatures reveal a polyphyletic origin of SAR11 strains among Alphaproteobacteria. PLOS Comput Biol. 10, e1003454.Dodsworth, J.A., Blainey, P.C., Murugapiran, S.K., Swingley, W.D., Ross, C.A., Tringe, S.G., Chain, P.S.G., Scholz, M.B., Lo, C.-C., Raymond, J., Quake, S.R., and Hedlund, B.P. (2013) Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun. 4, 1854.
Sattley, W.M. and Swingley, W.D. (2013) “Properties and Evolutionary Implications of the Heliobacterial Genome,” In Genome Evolution of Photosynthetic Bacteria. ed Beatty, J.T. Elsevier, Amsterdam, The Netherlands. pp 67-98.
Swingley. W.D., Meyer-Dombard, D.R., Alsop, E.B., Falenski, H.D., Shock, E.L., and Raymond, J. (2011) Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem. PLoS ONE. (In Press).
Meyer-Dombard, D.R., Swingley, W., Raymond, J., Havig, J., Shock, E.L., and Summons, R.E. (2011) Hydrothermal ecotones and streamer biofilm communities in the Lower Geyser Basin, Yellowstone National Park. Environ Microbiol. 13, 2216-31.
Swingley, W.D., Iwai, M., Takizawa, K., and Minagawa, J. (2010) Characterization of photosystem I antenna proteins in the prasinophyte Ostreococcus tauri. Biochim Biophys Acta. 1797, 1458-64.
Lu Y.K., Marden J., Han M., Swingley W.D., Mastrian S.D., Chowdhury S.R., Hao J., Helmy T., Kim S., Kurdoglu A.A., Matthies H.J., Rollo D., Stothard P., Blankenship R.E., Bauer C.E., Touchman J.W. (2010) Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum. BMC Genomics. 11, 325.
Swingley, W.D., Blankenship, R.E., and Raymond, J. (2008) “Evolutionary Relationships Among Purple Photosynthetic Bacteria and the Origin of Proteobacterial Photosynthetic Systems,” In The Purple Phototrophic Bacteria. eds. Hunter, C.N., Daldal, F., Thurnauer, M.C., and Beatty, J.T. Springer, Dordrecht, The Netherlands. pp 17-29.
Raymond, J. and Swingley, W.D. (2008) Phototroph genomics ten years on. Photosynth Res. 97, 5-19.
Sattley, W.M., Madigan, M.T., Swingley, W.D., Cheung, P.C., Clocksin, K. M., Conrad, A.L., Dejesa, L.C., Honchak, B.M., Jung, D.O., Karbach, L.E., Kurdoglu, A., Lahiri, S., Mastrian, S.D., Page, L.E., Taylor, H.L., Wang, Z.T., Raymond, J., Chen, M., Blankenship, R.E., and Touchman, J.W. (2008) The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus. J Bacteriol. 190, 4687-96.
Swingley, W.D., Blankenship, R.E., Raymond, J. (2008) Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families. Mol Biol Evol. 25, 643-54.
Swingley, W.D., Chen, M., Cheung, P.C., Conrad, A.L., Dejesa, L.C., Hao, J., Honchak, B.M., Karbach, L.E., Kurdoglu, A., Lahiri, S., Mastrian, S.D., Miyashita, H., Page, L., Satoh, S., Sattley, W.M., Shimada, Y., Taylor, H.L., Tomo, T., Tsuchiya, T., Wang, Z.T., Raymond, J., Mimuro, M., Blankenship, R.E., and Touchman, J.W. (2008) Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina. Proc. Natl. Acad. Sci. USA. 105, 2005-10.
Swingley, W.D., Blankenship, R.E., and Raymond, J. (2008) “Insight into cyanobacterial evolution from comparative genomics,” In The Cyanobacteria: Molecular Biology,Genomics and Evolution. eds. Herrero, A. and Flores, E. Caister Academic Press, Norfolk, UK, pp 21-44.
Soule, T., Stout, V., Swingley, W.D., Meeks, J.C., Garcia-Pichel, F. (2007) Molecular genetics and genomic analysis of scytonemin biosynthesis in Nostoc punctiforme ATCC 29133, J. Bacteriol. 189, 4465-72.
Swingley, W.D., Gholba, S., Mastrian, S.D., Matthies, H.J., Hao, J., Ramos, H., Acharya, C.R., Conrad, A.L., Taylor, H.L., Dejesa, L.C., Shah, M.K., O’Huallachain, M.E., Lince, M.T., Beatty, J.T., Blankenship, R.E. and Touchman, J.W. (2007) The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism, J. Bacteriol. 189, 683-90.
Swingley, W.D., Hohmann-Marriott, M.F., Le Olson, T., and Blankenship, R.E. (2005) Effect of iron on growth and ultrastructure of Acaryochloris marina, Appl Environ Microbiol. 71, 8606-10.
MO 333 (office)
MO 312 (lab)
- Postdoc, University of California – Merced (2009-2012)
- Postdoc, Hokkaido University (2006-2009)
- Ph.D., Arizona State University (2006)
- B.S., Case Western Reserve University (2001)