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Tanja Woyke – Single Cells

Shedding light on the tree of life. Image credit: Zosia Rostomian, LBNL

Shedding light on the tree of life. Image credit: Zosia Rostomian, LBNL

Research in the Woyke laboratory focuses on the utility of single-cell methods to access genetic material of uncultivated taxa of interest.  One such effort is targeted at environmental cells that are from candidate phyla, major branches in the phylogenetic tree without cultivated representatives. The “Great Plate-Count Anomaly” first described by Stanley and Konopa in 1985, which highlights our skewed understanding of microbial metabolism towards a minority of cultivated bacteria, still persists to date. Phylogenetic diversity estimates show that the gap between cultivated and uncultivated Bacteria and Archaea has steadily been widening since 2005. This gap is also reflected in the strongly biased representation of sequenced genomes in the public domain, the bulk of which belong to only three phyla. The Woyke group uses single-cell sequencing as a means to begin filling this gap. A primary goal is to get insights into the coding potential of candidate phyla to decipher their possible roles in the environment, establish phylogenetic relationships and to provide valuable reference genomes in under-populated areas of the tree of life, as reference genomes are critical to serve as phylogenetic anchors for metagenomes studies.

While uncovering the metabolic potential of uncultivated lineages is of high value to establish models and hypotheses, experimental data is critical to further test such hypotheses. In particular during an era of ‘homology creep’, function prediction as purely based on annotation may not be sufficient. A more recent effort in the Woyke lab is therefore focused on the application of function-driven single-cell genomics. Here, single cells are characterized and selected as based on a specific functional trait or phenotype of interest, prior to and in conjunction with whole genome sequencing.

Research Team

Tanja Woyke Esther Singer Jessica Jarrett Janey Lee
Tanja Woyke, PI Esther Singer,
Project Scientist
 Jessica Jarett,
Postdoc		 Janey Lee,
Sr. Research Associate 
twoyke@lbl.gov
(925) 296-5839/office
(925) 876-4343/cell		 esinger@lbl.gov
(925) 296-5759		 jkjarett@lbl.gov
(925) 296-5677		 jlee2@lbl.gov
(927) 296-5689
More about Tanja. Esther studies microbially-driven biogeochemical cycles in Mediterranean grassland soils using a systems approach, combining omics tools and geochemical analyses. Jess’s research focus is to discover and characterize candidate phyla of Bacteria and Archaea using single-cell sequencing, shedding light on the evolution, metabolism, and environmental roles of these microbes. Janey provides support for custom single-cell user projects and projects within the group.

 

Robert Bowers Asaf Levy Devin Doud Frederik Schulz
Robert Bowers,
Research Scientist		 Asaf Levy,
Research Scientist		 Devin Doud,
Postdoc		 Frederik Schulz,
Research Scientist
RMBowers@lbl.gov
(925) 296-5659		 alevy@lbl.gov
(925) 296-5690		 dfdoud@lbl.gov
925-296-5853		 fschulz@lbl.gov
925-296-5609
Bob uses single-cell genomics and metagenomics to explore how microbes influence people and the environment. This includes studying the diversity, physiology and community ecology of microbes sampled from the natural environment. Asaf, a computational biologist, is interested in various aspects of environmental microbial genomics. These include plant-microbe interactions, symbiotic interactions between bacteria and bacteria-phage interactions.
One of the questions Asaf is addressing is what set of bacterial genes are important in establishing plant-bacteria interactions.		 Devin is developing function-based single cell genomics methods to identify, isolate, and analyze microorganisms of interest in a
high-throughput manner.		 Frederik is a bioinformatician interested in microbial symbiosis, evolutionary microbiology and virology. He is exploring metagenomic and single-cell genomic data to find novel host-associated bacteria and viruses and applying state-of-the-art phylogenetic tools to place them in the tree of life.

Selected Publications

  1. Woyke T. & Jarett J. Function-driven single-cell genomics. Microb Biotechnol. 8:38-9(2015).
  2. Nobu M.K., Narihiro T., Rinke C., Kamagata Y., Tringe S.G., Woyke T. & Liu W.T. Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J. (2015)
  3. Field E.K., Sczyrba A., Lyman A.E., Harris C.C., Woyke T., Stepanauskas R. & Emerson D. Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. ISME J. 9:857-70 (2015).
  4. Youssef N.H., Rinke C., Stepanauskas R., Farag I., Woyke T. & Elshahed M.S. Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’. ISME J. 9:447-60 (2015).
  5. Clingenpeel S., Clum A., Schwientek P., Rinke C. & Woyke T. Reconstructing each cell’s genome within complex microbial communities-dream or reality? Front Microbiol. 5:771 (2015).
  6. Clingenpeel S., Schwientek P., Hugenholtz P. & Woyke T. Effects of sample treatments on genome recovery via single-cell genomics. ISME J. 8:2546-9 (2014).
  7. O’Connor R.M., Fung J.M., Sharp K.H., Benner J.S., McClung C., Cushing S., Lamkin E.R., Fomenkov A.I., Henrissat B., Londer Y.Y., Scholz M.B., Posfai J., Malfatti S., Tringe S.G., Woyke T., Malmstrom R.R., Coleman-Derr D., Altamia M.A., Dedrick S., Kaluziak S.T., Haygood M.G. & Distel D.L. Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proc Natl Acad Sci U S A. 111(47):E5096-104 (2014).
  8. Woyke T. & Rubin E.M. Evolution. Searching for new branches on the tree of life. Science. 346:698-9 (2014).
  9. Roux S., Hawley A.K., Torres Beltran M., Scofield M., Schwientek P., Stepanauskas R., Woyke T., Hallam S.J. & Sullivan M.B. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. Elife. 3:e03125 (2014).
  10. Hedlund B.P., Dodsworth J.A., Murugapiran S.K., Rinke C., & Woyke T. Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”. Extremophiles. 18:865-75 (2014).
  11. Mason O.U., Han J., Woyke T., & Jansson J.K. Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill. Front Microbiol. 5,332 (2014).
  12. Rinke, C., Lee, J., Nath, N., Goudeau, D., Thompson, B., Poulton, N., Dmitrieff, E., Malmstrom, R., Stepanauskas, R. & Woyke, T. Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics. Nat Protoc 9, 1038-48 (2014).
  13. Ivanova N.N., Schwientek P., Tripp H.J., Rinke C., Pati A., Huntemann M., Visel A., Woyke T., Kyrpides N.C. & Rubin E.M. Stop codon reassignments in the wild. Science 344, 909-13 (2014).
  14. Rinke C., Schwientek P., Sczyrba A., Ivanova N.N., Anderson I.J., Cheng J.F., Darling A., Malfatti S., Swan B.K., Gies E.A., Dodsworth J.A., Hedlund B.P., Tsiamis G., Sievert S.M., Liu W.T., Eisen J.A., Hallam S.J., Kyrpides N.C., Stepanauskas R., Rubin E.M., Hugenholtz P. & Woyke T. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-7 (2013).
  15. DeMaere M.Z., Williams T.J., Allen M.A., Brown M.V., Gibson J.A., Rich J., Lauro F.M., Dyall-Smith M., Davenport K.W., Woyke T., Kyrpides N.C., Tringe S.G. & Cavicchioli R. High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc Natl Acad Sci U S A 110, 16939-44 (2013).
  16. Campbell J.H., O’Donoghue P., Campbell A.G., Schwientek P., Sczyrba A., Woyke T., Soll D. & Podar M. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci U S A 110, 5540-5 (2013).
  17. Swan B.K., Martinez-Garcia M., Preston C.M., Sczyrba A., Woyke T., Lamy D., Reinthaler T., Poulton N.J., Masland E.D., Gomez M.L., Sieracki M.E., DeLong E.F., Herndl G.J. & Stepanauskas R. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333, 1296-300 (2011).
  18. Hess M., Sczyrba A., Egan R., Kim T.W., Chokhawala H., Schroth G., Luo S., Clark D.S., Chen F., Zhang T., Mackie R.I., Pennacchio L.A., Tringe S.G., Visel A., Woyke T., Wang Z. & Rubin E.M. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331, 463-7 (2011).
  19. Woyke T., Tighe D., Mavromatis K., Clum A., Copeland A., Schackwitz W., Lapidus A., Wu D., McCutcheon J.P., McDonald B.R., Moran N.A., Bristow J. & Cheng J.F. One bacterial cell, one complete genome. PLoS One 5, e10314 (2010).
  20. Woyke T., Xie G., Copeland A., Gonzalez J.M., Han C., Kiss H., Saw J.H., Senin P., Yang C., Chatterji S., Cheng J.F., Eisen J.A., Sieracki M.E. & Stepanauskas R. Assembling the marine metagenome, one cell at a time. PLoS One 4, e5299 (2009).
  21. Newton I.L., Woyke T., Auchtung T.A., Dilly G.F., Dutton R.J., Fisher M.C., Fontanez K.M., Lau E., Stewart F.J., Richardson P.M., Barry K.W., Saunders E., Detter J.C., Wu D., Eisen J.A. & Cavanaugh C.M. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315, 998-1000 (2007).
  22. Woyke T., Teeling H., Ivanova N.N., Huntemann M., Richter M., Gloeckner F.O., Boffelli D., Anderson I.J., Barry K.W., Shapiro H.J., Szeto E., Kyrpides N.C., Mussmann M., Amann R., Bergin C., Ruehland C., Rubin E.M. & Dubilier, N. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443, 950-5 (2006).