Skip to main content
Ryan Mueller in front of shrubbery

Ryan S. Mueller

Associate Professor
Department of Microbiology

Ryan S. Mueller

Associate Professor
Department of Microbiology


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.

Research Interests

  • Horizontal Gene Transfer
  • Nutrient Cycling
  • Environmental Succession
  • Niche Adaptation
  • Physiological Adaptation to Environmental Change


Ph.D., University of California, San Diego

College strategic research areas

Biomedical Science Marine Science


  • Yang, B., Hawthorne, T. L., Aoki, L., Beatty, D. S., Copeland, T., Domke, L. K., Eckert, G. L., Gomes, C. P., Graham, O. J., Harvell, C. D., Hovel, K. A., Hessing-Lewis, M., Harper, L., Mueller, R. S., Rappazzo, B., Reshitnyk, L., Stachowicz, J. J., Tomas, F., & Duffy, J. E. (2023). Low-Altitude UAV Imaging Accurately Quantifies Eelgrass Wasting Disease From Alaska to California. Geophysical Research Letters, 50(4), e2022GL101985.
  • English, M. K., Langdon, C. J., Schubiger, C. B., & Mueller, R. S. (2023). Dominant Bacterial Taxa Drive Microbiome Differences of Juvenile Pacific Oysters of the Same Age and Variable Sizes. Frontiers in Microbiomes, 2.
  • Dreher, T. W., Matthews, R., Davis, E. W., & Mueller, R. S. (2023). Woronichinia naegeliana: A Common Nontoxigenic Component of Temperate Freshwater Cyanobacterial Blooms with 30% of its Genome in Transposons. Harmful Algae, 125, 102433.
  • 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.
  • 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.
  • 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. Bioinformatis 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).