Dr. Ryan Mueller, Associate Professor

Mueller Office 448 Nash Hall
Phone 541-737-2950
FAX 541-737-0496
Email ryan.mueller@oregonstate.edu
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:  MB 311 Molecular Microbiology Lab, a writing intensive course; MB 312 Bacterial Physiology and Metabolism; MB 668 Microbial Bioinformatics and Genome Evolution


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.


Pub Med

David, M.M., Tataru, C., Pope, Q., Baker, L.J., English, M.K., Epstein, H.E., Kent, M., Sieler, Jr., M.J., Mueller, R.S., Sharpton, T.J., Tomas, F., Vega Thurber, R., and Fern, X.Z.,   2022.  Revealing general patterns of microbiomes that transcend systems:  Potential and challenges of deep transfer learning.  Computational Biol.  DOI:  https://doi.org/10.1128/msystems.01058-21.

Messyasz, A., Rosales, S., Mueller, R., Sawyer, T., Correa, A., Thurber, A., and Vega Thurber, R.  2020.  Coral bleaching phenotypes associated with differential abundances of nucleocytoplasmic large DNA viruses.  Front. in Mar. Sci.  7:2296-7745.

Kieft, B., Crump, B., White, A., Goni, M. and Mueller, R.  2020.  Winter river plumes shape community composition and activity of heterotrophic microorganisms on the Oregon Coast.  Aquatic Microbial Ecol. 84:15-29.

Kehlet-Delgado, H. Häse, C.C. and Mueller, R.S.  2020.  Comparative genomic analysis of Vibrios yields insights into genes associated with virulence towards C. gigas larvae. BMC Genomics.  21(1):599

Wang, L., Tomas, F., and Mueller, R.  2020.  Nutrient enrichment increases size of Zostera marina shoots and enriches for sulfur and nitrogen cycling bacteria in root-associated microbiomes.  FEMS Microbiol. Ecol. 96(8).

Wang, L., English, M., Tomas, F., and Mueller, R.  2020.  Recovery and community succession of the Zostera marina rhizobiome after transplantation.  bioRxiv. 202/04.052357.

Trang, T.H. Nguyen, Myrold, D.D. and Mueller, R.S.  2019.  Distributions of extracellular peptidases across prokaryotic genomes reflect phylogeny and habitat.  Front. Microbiol. doi.org/10.3389/fmicb.2019.00413.

Dreher, T.H., Collart, L.P., Mueller, R.S., Halsey, K.H., Bildfell, R.J. Schreder, P., Sobhakumari, A., and Ferry, R.  2018.  Anabaena/Dolichospermum as the source of lethal microcystin levels responsible for a large cattle toxicosis event.  Elsevier/Toxicon:  X; 1:100003. 

Smith, A.R., Kieft, B., Mueller, R., Fisk, M.R., Mason, O.U., Popa, R., and Colwell, F.S.  2018.  Carbon fixation and energy metabolisms of a subseafloor olivine biofilm.  The ISME J.  https://doi.org/10.1038/s41396-019-0385-0.

Guo, X., Li, Z., Yao, Q., Mueller, R.S., Eng, J.K., Tabb, D.L., Hervey, W.J.  2018.  Sipros ensemble improves database searching and filtering for complex metaproteomics.  Bioinformatics 34(5):795-802.

Crump, B.C., Wojahn, J.M., Tomas, F., and Mueller, R.S.  2018.  Metatranscriptomics and amplicon sequencing reveal mutualisms in seagrass microbiomes.  Frontiers in Microbiol. 9:388.

Kieft, B., Zhou, L., Bryson, S., Crump, B., Hettich, R., Chongle, P, Xavier, M. and Mueller, R.  2018.  Microbial community structure-function relationships in Yaquina Bay Estuary reveal spatially distinct carbon and nitrogen cycling capacities.  Front Microbiol.  9:1282.

Kehlet-Delgado, H., Richards, G.P., Häse, C. and Mueller, R.S.  2017. Three draft genome sequences of Vibrio coralliilyticus strains isolated from bivalve hatcheries.  Genome Announcements 5(41).

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.

Goltsman, D.S., Denef, V.J., Singer, S.W., VerBerkmoes, N.C., Lefsrud, M., Mueller, R.S., Dick, G.J., Sun, C.L., Wheeler, K.E., Zemla, A., Baker, B.J., Hauser, L., Land, M., Shah, M.B., Thelen, M.P., Hettich, R.L. and Banfield, J.F.  2009.  Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms.  Appl. and Environ. Microbiol. 75(13):4599-615.

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