Research

My research interests include systems biology of microbial communities and roles of nutrient trace metals in microbial interactions. My current projects involve both algal-bacterial interactions in open algal biofuel ponds and trace metal nutrition in nitrogen fixing consortia. For my post-doctoral work, I was part of a project investigating energy flow in cyanobacterial microbial mats and understanding secreted protein signatures in these complex communities. I am interested in how microbes, photoautotrophs in particular, play a role in transforming their environment and responding to change. I am also interested in integrating data using ‘omics techniques (transcriptomics, proteomics, metabolomics), classic genetic approaches, stable isotope probing and novel imaging strategies.

Poster - Characterization of Extracellular Polymeric Substances in Hypersaline Cyanobacterial Mats and Mat-forming Cyanobacterial Isolates.

JGI User meeting presentation, 2016 on Cyanobacterial recycling of organic matter

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

Kessler, N., R. Armoza-Zvuloni, S. Wang, S. Basu, P. K. Weber, R. K. Stuart, and Y. Shaked (2019). Selective collection of iron-rich dust particles by natural Trichodesmium colonies. ISME  (link).

Fisher, C. L., C. S. Ward, P. D. Lane, J. A. Kimbrel, K. L. Sale, R. K. Stuart, X. Mayali and T. W. Lane (2019). Bacterial communities protect the alga Microchloropsis salina from grazing by the rotifer Brachionus plicatilis. Algal Research 40: 101500 (link).

Bradley, J. M., D. A. Svistunenko, J. Pullin, N. Hill, R. K. Stuart, B. Palenik, M. T. Wilson, A. M. Hemmings, G. R. Moore, N. E. Le Brun, 2019. Reaction of O₂ with a diiron protein generates a mixed-valent Fe²⁺/Fe³⁺ center and peroxide. Proceedings of the National Academy of Sciences: 201809913. (link)

Hogle, S. L., C. L. Dupont, B. M. Hopkinson, A. L. King, K. N. Buck, K. L. Roe, R. K. Stuart, A. E. Allen, E. L. Mann, Z. I. Johnson and K. A. Barbeau, 2018. Pervasive iron limitation at subsurface chlorophyll maxima of the California Current. Proceedings of the National Academy of Sciences: 201813192. (link)

Stuart, R.K, X. Mayali, M. P. Thelen, J. Pett-Ridge, P. K. Weber, 2017. Measuring Cyanobacterial Metabolism in Biofilms with NanoSIMS Isotope Imaging and Scanning Electron Microscopy (SEM). Bioprotocol (link).

Stuart, R.K., R. Bundy, K. Buck, M. Ghassemain, K. Barbeau, B. Palenik, 2017. Copper toxicity response influences mesotrophic Synechococcus community structure. Environ Microbiol 19: 756-769 (link)

Stuart, R.K., X. Mayali, A. Boaro, Adam Zemla, R.C. Everroad, D. Nilson, P.K. Weber, M. Lipton, B. Bebout, J. Pett-Ridge, M.P. Thelen, 2016. Light regimes shape utilization of extracellular organic C and N in a cyanobacterial biofilm. mBio 7: e00650-00616.(link)

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, and B. Palenik. 2014.  A putative Deg-protease in marine Synechococcus is involved in stress response and outer membrane protein organization. Front. Mar. Sci., 29 June 2014 (doi: 10.3389/fmars.2014.00016) (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 Open-Ocean Strains. Applied and Environmental Microbiology 75: 5047-5057. (link)

Warshan, D., J. Espinoza, R. K. Stuart, R. Richter, S. Kim, N. Shapiro, T. Woyke, N. Kyrpides, K. Barry, V. Singan, E. Lindquist, C. Ansong, S. Purvine, H. Brewer, P. Weyman, C. Dupont, U. Rasmussen. 2017. Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant-cyanobacteria symbiosis. ISME J DOI:10.1038/ismej.2017.134. (link)

Shivlova, I.N., J.C. Robidart, H.J.Tripp, K.Turk-Kubo, B.Wawrik, A.Post, A.W.Thompson, B.Ward, J.T.Hollibaugh, A.Millard, M.Ostrowski, D.Scanlan, R.W.Paerl, R.K. Stuart, J.P.Zehr. 2014. A microarray for assessing transcription from pelagic microbial taxa. ISME J 8, 1476–1491.  (link)

Tetu, S.G, D.A. Johnson, D.R.Varkey, K.Phillippy, R.K. Stuart, C.L.Dupont, K.A.Hassan, B.P.Palenik and I.T.Paulsen. 2013. Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species. Front. Microbiol. 4. doi: 10.3389/fmicb.2013.00232 (link)

Mao, X.Z, V. Olman, R. K. Stuart, I. T. Paulsen, B. Palenik and Y. Xu. 2010. Computational prediction of the osmoregulation network in Synechococcus sp. WH8102. BMC Genomics 11: 291. (link)

Heintzman, N. D., G. C. Hon, R. D. Hawkins, P. Kheradpour, A. Stark, L. F. Harp, Z. Ye, L. Lee, R. K. Stuart, C. Ching, K. A. Ching, J. E. Antosiewicz-Bourget, H. Liu, X. M. Zhang, R. D. Green, V. V. Lobanenkov, R. Stewart, J. A. Thomson, G.E. Crawford, M. Kellis, B. Ren. 2009. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112. (link)

Heintzman, N.D., R.K. Stuart, G. Hon, Y. T. Fu, C. W. Ching, R. D. Hawkins, L. O. Barrera, S. Van Calcar, X. C. Qu, K. A. Ching, W. Wang, Z. P. Weng, R. D. Green, G. E. Crawford, B. Ren. 2007.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genetics 39: 311-318. (link)

Maynard, N. D., J. Chen, R. K. Stuart, J. B. Fan, and B. Ren. 2008. Genome-wide mapping of allele-specific protein-DNA interactions in human cells. Nature Methods 5: 307-309. (link)

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)