Research

My research interests include systems biology of microbial communities and roles of nutrient exchange in microbial interactions and symbioses. I lead a DOE-OBER funded Scientific Focus Area (the µBiospheres SFA, link below) focused on understanding host-microbe interactions in bioenergy relevant systems. The project seeks to uncover context-dependent regulation of these microscale interactions and their systems-level consequences. I am interested in integrating data using stable isotope probing, high-resolution imaging mass spectrometry (nanoSIMS), and ‘omics techniques (transcriptomics, proteomics, metabolomics), and working with computational modelers to gain a predictive understanding of complex environmental communities.

LLNL Biofuels Scientific Focus Area webpage

Scripps Institution of Oceanography, University of California, San Diego, Marine Biology, Ph.D., 2012

University of California San Diego, Ecology, Behavior, Evolution, B.Sc., 2003

https://scholar.google.com/citations?user=ROWumhkAAAAJ&hl=en

Selected publications

Brisson, V., C. Swink, J. Kimbrel, X. Mayali, T. Samo, S.M. Kosina, M. Thelen, T.R. Northen, and R.K. Stuart, Dynamic Phaeodactylum tricornutum exometabolites shape surrounding bacterial communities. New Phytologist, 2023. 239(4): p. 1420-1433 DOI: https://doi.org/10.1111/nph.19051.

Stuart R. K., E. R. A Pederson., P. D. Weyman, P. K. Weber, U. Rassmussen, C. L. Dupont (2020). Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism. ISME J 14: 3068–3078.

Stuart, R.K., X. Mayali, J.Z. Lee, R.C. Everroad, B. Bebout, P.K. Weber, J. Pett-Ridge, M.P. Thelen, 2015. Cyanobacterial reuse of extracellular organic carbon in microbial mats. ISME J 10: 1240-1251.(link)

Stuart, R.K., B. Brahamsha, K. Busby and B. Palenik. 2013. Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress.  ISME J 7: 1139-1149 (link)

Stuart, R. K., C. L. Dupont, D. A. Johnson, I. T. Paulsen, and B. Palenik. 2009. Coastal Strains of Marine Synechococcus Species Exhibit Increased Tolerance to Copper Shock and a Distinctive Transcriptional Response Relative to Those of

Birney, E. …R. K. Stuart…and others. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816 (link)