Dr. Ryan Mueller, Assistant Professor

Mueller Office 448 Nash Hall
Phone 541-737-2950
FAX 541-737-0496
Email ryan.mueller@oregonstate.edu
Education      
Ph.D., University of California, San Diego

Research Interests: Horizontal gene transfer, Nutrient cycling, Environmental succession, Niche adaptation,
Physiological adaptation to environmental change

Courses Taught:  New faculty

RESEARCH

I am interested in using inter-disciplinary approaches to study interactions of microorganisms with natural communities. By applying emerging and traditional molecular biology and optics methods (e.g., -omics, genetics, epifluorescence and confocal laser scanning microscopy), I am attempting to define the molecular mechanisms underlying evolutionary and ecological processes occurring within these communities.horizontal gene transfer mueller

I received my Ph.D. from University of California, San Diego in Professor Douglas Bartlett's lab where I studied the molecular traits of the waterborne pathogen Vibrio cholerae that enable its survival within different niches of marine reservoirs. After graduating, I completed a postdoc with Prof. Jill Banfield at the University of California, Berkeley. This research involved using high-throughput genomic, mass spectrometry (MS)-based proteomic, and metabolomic techniques to gain insight into in situ molecular adaptations of microbial communities as environmental conditions change. At the CEAB, I was involved in a project to examine how patterns of microbial community diversity (defined by 165 pyrosequencing) in alpine lakes related to a variety of factors including spatial, seasonal, climatic, physical and chemical variables.

 

REPRESENTATIVE PUBLICATIONS

Pub Med

  • Guo, X., Li, Z., Biswas, A., Yao, Q., Mueller, R.S., Eng, J.K., Tabb, D.L., Hervey IV, W.J., and Pan, C.  2017.  Ensemble learning improves database searching and filtering for complex metaproteomics.  Bioinformatics, in revision.
  • Bryson, S., Li, Z., Chavez, F., Weber, P.K., Pett-Ridge, J.P., Hettich, R.L., Pan, C., Mayali, X., and Mueller, R.S.  2017.  Phylogenetically conserved resource partitioning in the coastal microbial loop.  ISMEJ, in press.
  • Bryson, S., Li, Z., Pett-Ridge, J., Hettich, R.L., Mayali, X., Pan C., and Mueller, R.S.  2016.  Proteomic-based stable isotope probing reveals taxonomically conserved patterns in amino acid assimilation by coastal marine bacterioplankton.  mSystems 1(2).
  • Brown, N.S., Mueller, R.S., Shepardson, J.W., Landry, Z.C., Maier, C.S., Morre, J.T., Hardy, J., and Dreher, T.W.  2016.  Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102.  BMC Genomics 17(1):1-18.
  • Denef, V.J., Mueller, R.S., Chiang, E., Liebig, J.R., and Vanderploeg, H.A.  2015.  Chloroflexi CL500-11 populations that predominate deep lake hypolimnion bacterioplankton rely on nitrogen-rich DOM metabolism and C1 compound oxidation.  Appl. Environ. Microbiol. 82(5): 1423-1432.
  • Brooks, B., Mueller, R.S., Young, J.C., Morowitz, M.J., Hettich, R.L., and Banfield, J.F.  2015.  Strain-resolved microbial communit proteomics reveals simultaneous aerobic and anaerobic function during early stage gastrointestinal tract colonization.  Frontiers in Microbiol. 6; http://dx.doi.org/10.3389/fmicb.2015.00654.
  • Mueller, R.S., Bryson, S., Kieft, B., Li, Z., Pett-Ridge, J., Chavez, F., Hettich, R.L., Pan, C., and Mayali, X.  2015.  Metagenome sequencing of a coastal marine microbial community from Monterey Bay, California.  Genome Announc. 3(2):pii:e00341-15. 
  • Mueller, R.S., and Pan, C.   2013.  Sample handling and mass spectrometry for microbial metaproteomic analyses, Method. Enzymol., 531:299-303.
  • Justice, N., Pan, C., Mueller, R.S., Spaulding, S., Shah, V., Sun, C., Yelton, A., Miller, C., Thomas, B., Shah, M., VerBerkmoes, N., Hettich, R. and Banfield, J.F.   2012.  Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities. Appl. Environ. Microbiol., 78(23):8321-8330.
  • Wheeler, K.E., Erickson, B.K., Mueller, R.S., Singer, S.W., VerBerkmoes, N.C., Hwang, M.,  Thelen, M.P., and Hettich, R.L.   2011.  Metal affinity enrichment increases the range and depth of proteome identification for extracellular microbial proteins. J. Proteome Res., 11(2):861-870.
  • Mueller, R.S., Dill, B., Pan, C., Belnap, C., Thomas, B.C., VerBerkmoes, N.C., Hettich, R.L. and Banfield, J.F.   2011.  Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community. Environ. Microbiol., 13(8):2279-2292. *Featured in Faculty of 1000 – 6.0 Recommended Rating  http://f1000.com/prime/13294007
  • Wilmes, P., Bowen, B.P., Thomas, B.C., Mueller, R.S., Denef, V.J., VerBerkmoes, N.P., Hettich, R.L., Northen, T.R. and  Banfield, J.F.   2010.  Metabolome-proteome differentiation coupled to microbial divergence. mBio, 1(5):e00246-10.
  • Mueller, R.S., Denef, V.J., Kalnejais, L.H., Suttle, K.B., Thomas, B.C., Wilmes, P., Smith, R., Nordstrom, D.K., McKleskey, R.B., Shah, M., VerBerkmoes, N.C., Hettich, R.L. and Banfield, J.F.  2010a.  Ecological distribution and population physiology defined by proteomics in a natural microbial community. Molec. Systems Biol., 6(364):1-12.
  • Denef, V.J., Mueller, R.S., Jillian F. Banfield. 2010.  AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. The ISME Journal, 4(5):599-610.
  • Erickson, B.K., Mueller, R.S., VerBerkmoes, N.C., Shah, M., Singer, S., Thelen, M.P., Banfield, J.F. and Hettich R.L.  2010.   Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community.  J. Proteome Res., 9(5):2148-2159. 
  • Denef, V.J., Kalnejais, L.H., Mueller, R.S., Wilmes, P., Baker, B.J., Thomas, B.C., VerBerkmoes, N.C., Hettich, R.L. and Banfield, J.F. 2010.  Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proceed. of the Natl. Acad. of Sci. U.S.A. 107(6):2383-2390.
  • Lowery, C.A., Park, J., Gloeckner, C., Meijler, M., Mueller, R.S., Barry, C.E., Bartlett, D.H.,  Kravchenko, V., Kaufmann, G.F. and Janda, K.D. 2009.  Defining the mode of action of tetramic acid antibacterials derived from Pseudomonas aeruginosa quorum sensing signals. J. Am. Chem. Soc., 131(40):14473-14479.
  • Mueller, R.S., Beyhan, S., Yildiz, F. and Bartlett, D.H. 2009.  Indole acts as an extracellular cue regulating gene expression in Vibrio cholerae, J. Bacteriol., 191(11):3504-3516.
  • Aliaga Goltsman, D.S., Denef, V.J., Singer, S.W., VerBerkmoes, N.C., Lefsrud, M., Abraham, P., Wheeler, K., Mueller, R.S., Dick, G., Hauser, L., Land, M., Shah, M., Thelen, M.P., Hettich, R.L. and Banfield, J.F.  2008. Comparative proteogenomic analyses of biofilm communities dominated by chemoautotrophic, iron-oxidizing  Leptospirillum rubarum and Leptospirillum ferrodiazotrophum populations.  Appl. Environ. Microbiol., 75(13):4599-4615.
  • Mueller, R.S.*, Danielle Cusumano, D., Nidhi Sodhi, N., McDougald, D., Kjelleberg, S., Azam, F. and Bartlett, D.H.   2007. From the Cover: Vibrio cholerae strains possess multiple strategies for abiotic and biotic surface colonization. J. Bacteriol., 189(14):5348-5360.

*Featured in Faculty of 1000 – 9.0 Exceptional Rating;  http://www.f1000biology.com/article/id/1089003/evaluation