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Rex Malmstrom

Rex Malmstrom, JGI

Dr. Malmstrom is a Staff Scientist and leader of the Microscale Applications group.  Prior to joining the JGI in 2010, he made the first ever measurements of in situ growth rates and carbon consumption of SAR11 bacteria, the most abundant bacterial group in the ocean. 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. After joining the JGI, he formed the Microscale Applications group to operate a similar single-cell genomics pipeline that provides JGI users access to the genomes of uncultured microbes.  His group also handles the Stable Isotope Probing (SIP) Metagenomics pipeline  that reveals in situ functional activities of specific microbial groups within complex communities.  The microscalle Applications group also carries out custom preparative work for difficult user projects, including those that require fluorescence activated cell sorting and non-standard molecular protocols.  Finally, Rex’s team utilizes new technologies, e.g. acoustic liquid transfer and microfluidics, to minimize molecular biology reactions, increase throughput, and enable processing of samples that would not be possible with traditional approaches.

Education

  • Ph.D. in Marine Biology/Biochemistry, University of Delaware
  • BA in Biology, Boston University (magna cum laude)

Awards and Service

  • University of Delaware’s Theodore Wolf Prize for outstanding dissertation in life sciences 2006

Selected Publications

  1. Berg, M.  et al. 2021.  Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions.  ISME Journal  doi.org/10.1038/s41396-020-00870-1
  2. Grieb, A. et al. 2020. A pipeline for targeted metagenomics of environmental bacteria. Microbiome 8(1) 1-17
  3. Needham, D.M. et al. 2019. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators.  PNAS 116 (41), 20574-20583
  4. Couradeau, J.S. et al. 2019. Probing the active fraction of soil microbiomes using BONCAT-FACS.  Nature Comm 10(1) 1-10
  5. Schulz, F. et al. 2018. Hidden diversity of soil giant viruses. Nature Comm. 9 (1), 4881
  6. Roux, S. et al. 2017. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics.  Nature Comm. 8 (1), 858
  7. Tsementzi, D. et al. 2016. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature 536 (7615), 179
  8. Hatzenpichler, R. et al. 2016. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal− bacterial consortia. PNAS 113 (28), E4069-E4078
  9. Bendall, M.L. et al. 2016. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME Journal 10 (7), 1589
  10. Kashtan, N et al. 2014. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus.  Science 344 (6182), 416-420
  11. Malmstrom, R.R. et al. 2012. Ecology of uncultured Prochlorococcus revealed through single-cell genomics and biogeographic analysis. ISME Journal 7(1), 184-198

Complete publication list available at Google Scholar