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Rex Malmstrom

Rex Malmstrom, JGI

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.

Education

  • B.A. – Boston University, Biology, magna cum laude (1999)
  • Ph.D. – University of Delaware, Marine Biology/Biochemistry (2006)

Selected Publications

(* co-first author; member of Micro-Scale Applications group)

Complete publication list available at Google Scholar

  1. DM Needham, S Yoshizawa, T Hosaka, C Poirier, CJ Choi, … 2019. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. PNAS doi.org/10.1073/pnas.1907517116
  2. E Couradeau, J Sasse, D Goudeau, N Nath, TC Hazen, BP Bowen, Chakraborty R., Malmstrom R.R., T.R. Northen. 2019. Probing the active fraction of soil microbiomes using BONCAT-FACS. Nature Communications doi.org/10.1038/s41467-019-10542-0
  3. F Schulz, L Alteio, D Goudeau, EM Ryan, BY Feiqiao, RR Malmstrom, Blanchard J., T. Woyke. 2018. Hidden diversity of soil giant viruses. Nature Communications doi.org/10.1038/s41467-018-07335-2
  4. S Roux, LK Chan, R Egan, RR Malmstrom, KD McMahon, MB Sullivan. 2017. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nature Communications doi.org/10.1038/s41467-017-01086-2
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.