Microbial Systems

Group within the Metagenomics Program.

Research in the Tringe group focuses on sequence-based approaches to studying microbial community assembly, function and dynamics.  Members of the group aid in communicating and interpreting sequencing results to collaborators in addition to performing collaborative and independent research in microbial community genomics.  Major foci of these research efforts are the roles of microbial communities in wetland carbon cycling and the interactions of plants with their associated microbiomes.

Wetland greenhouse gas cycling

Wetlands occupy less than 10% of the Earth’s land surface but harbor up to a third of soil organic carbon.  Wetland preservation and restoration has the potential to sequester significant amounts of terrestrial carbon, but they can also produce the potent greenhouse gas methane, meaning different types of wetlands may serve as either greenhouse gas sources or sinks.  This uncertainty leads to considerable variability in predictions from climate models, both in the overall carbon budget and in how wetlands are expected to respond to climate change.

More accurate prediction of wetland carbon dynamics requires better understanding of the belowground microbial communities that are key to recycling or storing biomass carbon and producing greenhouse gases.  To gain insight into these systems we are applying microbial community genomics to wetland microbial communities in coastal wetlands across the San Francisco Bay / Delta region, including in-depth metagenome and metatranscriptome sequencing of natural and restored wetlands. (Watch the video here.) These studies are revealing organisms and genes involved in promoting or repressing greenhouse gas emissions, enabling a mechanistic understanding of belowground carbon cycling. Ultimately these findings are expected to aid in planning wetland restoration projects to maximize carbon storage. Download a copy of the JGI wetlands handout.

Plant-microbe interactions

The interactions of plants with microbial communities found in the endosphere and rhizosphere (within plant tissues and adjacent to the roots) have been shown to be critical to plant growth, health and disease resistance and manipulation of these organisms could potentially improve yields of both bioenergy and food crops.  Yet how these communities form and to what extent plants exert active control over the organisms involved is largely unknown, and genomic investigation of endophytic and rhizosphere microbes has been largely confined to culture-based methods due to both the challenges associated with soil metagenomics described above, and the close association with plant cells which harbor large and complex genomes.  In close collaboration with Jeff Dangl at the University of North Carolina, we are addressing these obstacles with high-throughput 16S profiling of rhizosphere and endophyte communities combined with single cell genomics, metagenomics and metatranscriptomics to characterize key plant-associated microbes, using Arabidopsis thaliana as a plant model system.  These investigations have revealed reproducible rhizosphere and endophyte community assemblage and plant genotype-specific associations with rhizosphere organisms. Ultimately, this work will allow us to identify genes, proteins and molecules involved in plant-microbe and microbe-microbe interactions in the plant root environment.

Group Members

Susannah Green Tringe, PI	Dawn Chiniquy, Postdoctoral Fellow	Wyatt Hartman, Postdoctoral Fellow	Edward Kirton, Systems Analyst	Qingpeng Zhang, Postdoctoral Fellow
More about Susannah.

Group Alumni

• Filipa Godoy-Vitorino is currently Assistant Professor at the Inter American University of Puerto Rico (filipagodoyvitorino@gmail.com)
• Julien Tremblay is Bioinformatician at National Research Council Canada (jtremblay514@gmail.com)
• Devin Coleman-Derr is Principal Investigator at the Plant Gene Expression Center (devin.coleman-derr@ars.usda.gov)

Publications

1. O’Connor, R.M., Fung, J.M., Sharp, K.H., Benner, J., McClung, C., Cushing, S., Lamkin, E., Fomenkov, A., Henrissat, B., Londer, 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.  Proceedings of the National Academy of Sciences 111(47):E5096-104, 2014.
2. Coleman-Derr, D., Tringe, S.G. Building the crops of tomorrow: advantage of symbiont-based approaches to improving abiotic stress tolerance. Frontiers in Microbiology 5: 283, 2014.
3. Wagner, M.R., Lundberg, D.S., Coleman-Derr, D., Tringe, S.G., Dangl, J.L., Mitchell-Olds, T. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecology Letters 17:717-726, 2014.
4. Howe, A.C., Jansson, J.K., Malfatti, S.A., Tringe, S.G., Tiedje, J.M., Brown, C.T. Tackling soil diversity with the assembly of large, complex metagenomes. Proceedings of the National Academy of Sciences 111: 4904-4909, 2014.
5. Castelle, C.J., Hug, L.A., Wrighton, K.C., Thomas, B.C., Williams, K.H., Wu, D., Tringe, S.G., Singer, S., Eisen, J., Banfield, J.F. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications  4:2120, 2013.
6. Rivers, A.R., Sharma, S., Tringe, S.G., Martin, J., Joye, S., Moran, M.A. Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon Oil Spill.  ISME Journal 7: 2315-2329, 2013.
7. Flowers, J.J., He, S., Malfatti, S., Glavina del Rio, T., Tringe, S.G., Hugenholtz, P., McMahon, K.D. Comparative genomics of two “Candidatus Accumulibacter” clades performing biological phosphorus removal. ISME Journal 7: 2301-2314, 2013.
8. Inskeep, W.P., Jay, Z.J., Tringe, S.G., Herrgard, M., Rusch, D.B., YNP Metagenome Project Steering Committee and Working Group Members. The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem. Frontiers in Microbiology 4: 67, 2013.
9. He, S., Ivanova, N., Kirton, E., Allgaier, M., Bergin, C., Scheffrahn, R.H., Kyrpides, N.C., Warnecke, F.,  Tringe, S.G., Hugenholtz, P.  Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood-feeding and dung-residing higher termite species (Nasutitermes corniger and Amitermes wheeleri).  PLOS One 8: e61126, 2013.
10. Peiffer, J.A., Spor, A., Koren, O., Jin, Z., Tringe, S.G., Dangl, J.L., Buckler, E.S., Ley, R.E. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences 110: 6548-6553, 2013.
11. Lundberg, D.S., Lebeis, S.L., Herrera Paredes, S., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Glavina del Rio, T., Eickhorst, T., Ley, R.E., Hugenholtz, P., Tringe, S.G., Dangl, J.L. Defining the core Arabidopsis thaliana root microbiome.  Nature 488: 86-90, 2012.
12. Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C., Bork, P., Hugenholtz, P., and Rubin, E.M.  Comparative Metagenomics of Microbial Communities.  Science 308: 554-557, 2005.