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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
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    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
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    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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Home › Our Science › Science Programs & Platforms Leads › Single Cells Group

Single Cells Group

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, PI Robert Bowers,
Research Scientist
Maria Dzunkova,
Postdoc
Janey Lee,
Sr. Research Associate 
twoyke@lbl.gov
rmbowers@lbl.gov mdzunkova@lbl.gov jlee2@lbl.gov
More about Tanja. 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. Maria identifies links between phages and their bacterial hosts by the “single-cell viral tagging” method Janey provides support for custom single-cell user projects and projects within the group.
Frederik Schulz
Frederik Schulz,
Research Scientist
Esther Singer,
Research Scientist
Tomas Tyml,
Postdoc
Jean-Marie Volland Visiting Scientist
fschulz@lbl.gov esinger@lbl.gov ttyml@lbl.gov jvolland@lbl.gov
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. Esther studies plant microbiome interactions in field and lab combining omics tools, plant genetics and phenotyping, as well as soil geochemistry analyses. Tomas uses traditional cultivation methods along with microscopy and genomics for studying endosymbiotic associations within microbial eukaryotes. With his research, he hopes to broaden our understanding of the roles that these associations have played in the evolutionary history of life. Jean-Marie uses classic and cutting-edge imaging approaches in conjunction with sequencing technologies to investigate unusual life strategies and symbiotic interactions in uncultivated bacteria and small eukaryotes

Former Lab Members

  • Scott Clingenpeel: Industrial Hygienist, Washington River Protection Solutions
  • Devin Doud:  Principal Scientist, Kintai Therapeutics, Cambridge, MA
  • Jessica Jarett: Computational Biologist, AnimalBiome
  • Asaf Levy: Assistant Professor,  Hebrew University of Jerusalem, Israel
  • Chris Rinke: Research Officer,  Australian Centre for Ecogenomics
  • Patrick Schwientek: Cofounder & CTO, Oralta

Selected Publications

  1. Schulz F., Roux S., Paez-Espino D., Jungbluth S., Walsh D. A., Denef V. J., McMahon K. D., Konstantinidis K. T., Eloe-Fadrosh E. A., Kyrpides N. C., Woyke T. Giant virus diversity and host interactions through global metagenomics.” Nature 578(7795): 432-436 (2020).
  2. Seshadri R., Leahy S. C., Attwood G. T., Teh K. H., Lambie S. C., Cookson A. L., Eloe-Fadrosh E. A., Pavlopoulos G. A., Hadjithomas M., Varghese N. J., Paez-Espino D., Hungate project, collaborators Perry R., Henderson G., Creevey C. J., Terrapon N., Lapebie P., Drula E., Lombard V., Rubin E., Kyrpides N. C., Henrissat B., Woyke T., Ivanova N. N., Kelly W. J. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.” Nat Biotechnol 36(4): 359-367 (2018).
  3. Woyke T., Doud D. F. R., Schulz F. The trajectory of microbial single-cell sequencing. Nat Methods 14(11): 1045-1054 (2017).
  4. Schulz F., Yutin N., Ivanova N. N., Ortega D. R., Lee T. K., Vierheilig J., Daims H., Horn M., Wagner M., Jensen G. J., Kyrpides N. C., Koonin E. V., Woyke T. Giant viruses with an expanded complement of translation system components.” Science 356(6333): 82-85 (2017).
  5. Mukherjee S., Seshadri R., Varghese N. J., Eloe-Fadrosh E. A., Meier-Kolthoff J. P., Goker M., Coates R. C., Hadjithomas M., Pavlopoulos G. A., Paez-Espino D., Yoshikuni Y., Visel A., Whitman W. B., Garrity G. M., Eisen J. A., Hugenholtz P., Pati A., Ivanova N. N., Woyke T., Klenk H. P., Kyrpides N. C. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.” Nat Biotechnol 35(7): 676-683 (2017).
  6. Bowers R. M., Kyrpides N. C., Stepanauskas R., … Banfield J. F., Hugenholtz P., Woyke T. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 35(8): 725-731 (2017).
  7. Woyke T. & Rubin E.M. Evolution. Searching for new branches on the tree of life. Science. 346:698-9 (2014).
  8. 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).
  9. 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).
  10. 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).
  11. 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).
  12. 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).
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