The Micro-Scale Applications group explores the genetic makeup of natural microbial communities using a variety of cutting-edge approaches. For example, we operate a high throughput pipeline for sorting and amplifying the genomes of individual cells. Using this culture independent approach, we have performed whole genome amplification on 10,000’s of microbes collected from a diverse range of environments (e.g. hot springs, forest soils, subterranean aquifers, Antarctic lakes, plant roots, etc.), and recovered microbial genomes from uncultivated clades.
Our group also seeks out new approaches that utilize microfluidics/microdroplet technology in order to enhance the quality of single-cell genomes and directly link functional information with individual cells. We are particularly interested in new techniques that can assign functional activities to new groups of microbes or that can reveal links between uncultivated viruses and their microbial hosts.
Finally, we combine shotgun metagenomic sequencing with multi-year time series studies in order to follow changes in the genetic composition of natural microbial communities. In collaboration with Dr. Katherine McMahon at the University of Wisconsin, we have used this approach to assemble hundreds of population genomes, and we are now able to track the evolution of these populations over several years.
|Rex Malmstrom||Danielle Goudeau||Nandita Nath||Kanwar Singh||Andy Tomatsu|
|Read more about Rex.||Danielle operates the single-cell genomics pipeline for JGI collaborators. This work combines custom flow cytometric analysis, cell sorting, genome amplification, PCR screening, and 16S sequencing. She also develops novel flow cytometry protocols for targeted recovery of specific microbes.||Nandita is involved in developing new methods to improve genome recovery from single cells and to build sequencing libraries from minimal DNA input without amplification.||Kanwar spends part of his time assisting JGI users by processing their single cell samples using our high throughput pipeline. He also explores new methods for creating sequencing libraries and optimizing various processes.||Andy’s work focuses on the miniaturization and automation various molecular techniques using microfluidic devices. This includes DNA and RNA library creation from microbial cells captured using custom microfluidic chips, and single-cell transcriptomics of eukaryotes (e.g. Drop-seq).|
- B.A. – Boston University, Biology, magna cum laude (1999)
- Ph.D. – University of Delaware, Marine Biology/Biochemistry (2006)
As a microbial ecologist, Rex explores the composition of bacterial communities and the environmental activities these communities carry out. This represents a daunting task when you consider that <1% of bacteria will grow in the lab. Thus, he relies on a variety of culture-independent approaches including metagenomics, flow cytometry, microscopy, microfluidics, genome amplification chemistries, and the latest DNA sequencing techniques during his investigations. As part of his dissertation he made the first ever measurements of in situ growth rates and carbon consumption of SAR11 bacteria, the most abundant bacterial group in the world’s oceans. Later during his postdoctoral work at the Massachusetts Institute of Technology, he developed a high throughput approach for isolating individual bacterial cells and amplifying their genetic material, thus bypassing the need to culture these microbes in the lab. At the JGI he his currently investigating links between environmental changes and carbon cycling using long-term time-series metagenomic analyses of aquatic microbial communities, and exploring the genomes of uncultured microbes via single-cell whole genome amplification and sequencing.
(* co-first author; ¶ member of Micro-Scale Applications group)
Complete publication list available at Google Scholar
- Tsementzi, D., J. Wu, S. Deutsch, S. Nath, L.M. Rodriguez-R, A.S. Burns, P. Ranjan, N. Sarode, R.R. Malmstrom, C. Padilla, B.K. Stone, L.A. Bristow, M. Larsen, J.B. Glass, B. Thamdrup, T. Woyke, K.T. Konstatinidis, F.J. Stewart. 2016. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature doi:10.1038/nature19068.
- Hatzenpichler, R., S.A. Connon, D. Goudeau¶, R.R. Malmstrom, T. Woyke, V.J. Orphan. 2016. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia. PNAS doi: 10.1073/pnas.1603757113.
- Eloe-Fadrosh, E.A., D. Paez-Espino, J. Jarett, P.F. Dunfield, B.P. Hedlund, A.E. Dekas, S.E. Grasby, A.L. Brady, H.Dong, B.R. Briggs, W.J. Li, D. Goudeau¶, R. Malmstrom, A. Pati, J. Pett-Ridge, E.M. Rubin, T. Woyke, N.C. Kyrpides, N.N. Ivanova. 2016. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nature Communications doi:10.1038/ncomms10476.
- Bendall, M.L.¶, S. Stevens, L. Chan¶, S. Malfatti, P. Schwientek, J. Tremblay, W. Schackwitz, J. Martin, A. Pati, B. Bushnell, J. Froula, D. Kang, S.G. Tringe, S. Bertilsson, M. Moran, A. Shade, R.J. Newton, K.D. McMahon, R.R. Malmstrom. 2016. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME Journal doi:10.1038/ismej.2015.241.
- R.M. O’Connor, J.M. Fung, K.H. Sharp, J.S. Benner, C. McClung, S. Cushing, E.R. Lamkin, A.I. Fomenkov, B. Henrissat, Y.Y. Londer, M.B. Scholz, J. Posfai, S. Malfatti, S.G. Tringe, T. Woyke, R.R. Malmstrom, D. Coleman-Derr, M.A. Altamia, S. Dedrick, S.T. Kaluziak, M.G. Haygood, D.L. Distel. 2014. Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. PNAS 111 (47) E5096-E5104.
- Kashtan, N., S.E. Roggensack, S. Rodrigue, J.W. Thompson, S.J. Biller, A. Coe, H. Ding, P. Marttinen, R.R. Malmstrom, R. Stocker, M.J. Follows, R. Stepanauskas, and S.W. Chisholm. 2014. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344 (6182): 416-420.
- Rinke, C., J. Lee, N. Nath¶, D. Goudeau¶, B. Thompson, N. Poulton, E. Dmitrieff, R.R. Malmstrom, R. Stepanauskas, and T. Woyke. 2014. Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics. Nature Protocols 9 (5): 1038-1048.
- Bendall, M.L¶, K. Luong, K.M. Wetmore, M. Blow, J. Korlach, A. Deutschbauer, and R.R. Malmstrom. 2013. Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1. J. Bacteriol. 195 (2): 4966-4974.
- Malmstrom, R.R., S. Rodrigue, K.H. Huang, L. Kelly, S.E. Kern, A. Thompson, S. Roggensack, P.M. Berube, M.R. Henn, and S.W. Chisholm. 2013. Ecology of uncultured Prochlorococcus revealed through single-cell genomics and biogeographic analysis. ISME Journal 7 (1): 184-198.
- Malmstrom, R.R, A. Coe, G. Kettler, A. Martiny, J. Frias-Lopez, E. Zinser, and S.W. Chisholm. 2010. Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. ISME Journal 4 (10): 1252-1264.
- Rodrigue, S., A.C. Materna, S.C. Timberlake, M.C. Blackburn, R.R. Malmstrom, E.J. Alm, S.W. Chisholm. 2010. Unlocking short read sequencing for metagenomics. PLoS ONE 5(7) e11840.
- McCarren, J., J. Becker, D. Repeta, Y. Shi, R. Young, R.R. Malmstrom, S.W. Chisholm, and E.F. DeLong. 2010. Microbial metatranscriptomics reveals microbes and metabolic pathways associated with high molecular weight dissolved organic matter turnover in the sea. PNAS 107 (38) 1420-16427.
- Rodrigue* S., R.R. Malmstrom*, A. Berlin, B.W. Birren, M. Henn, and S.W. Chisholm. 2009. Whole genome amplification and de novo assembly of single bacterial cells. PLoS ONE 4(9): e6864.
- Malmstrom, R.R., T.R.A. Straza, M.T. Cottrell, and D.L. Kirchman. 2007. Diversity, abundance, and biomass production of bacterial groups in the western Arctic Ocean. Aquat. Microb. Ecol. 47 (1): 45-55.
- Malmstrom, R. R., R. P. Kiene, M. Vila, and D. L. Kirchman. 2005. Dimethyl-sulfoniopropionate (DMSP) assimilation by Synechococcus in the Gulf of Mexico and northwest Atlantic Ocean. Limnol. Oceanogr. 50: 1924-1931.
- Malmstrom, R.R., M.T. Cottrell, H. Elifantz, and D.L. Kirchman. 2005. Biomass production and dissolved organic matter assimilation by SAR11 bacteria in the northwest Atlantic Ocean. Appl. Environ. Microbiol. 71(6): 2979-2986.
- Malmstrom, R.R., R.P. Kiene, M.T. Cottrell, and D.L. Kirchman. 2004. Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate (DMSP) and amino acid uptake in the North Atlantic Ocean. Appl. Environ. Microbiol. 70 (7): 4129-4135.
- Malmstrom, R.R., R.P. Kiene, and D.L. Kirchman. 2004. Identification and enumeration of bacteria assimilating dimethylsulfoniopropionate (DMSP) in the North Atlantic and Gulf of Mexico. Limnol. Oceanogr. 49: 597-606.