Dr. Susanna Theroux

Dr. Susanna Theroux is an ecologist specializing in microbiology and bioassessment, specifically the interactions between microbial communities and nutrient stressors. She specializes in the use of high-throughput DNA sequencing to untangle microbial interactions, from nutrient food webs and carbon cycling to novel species characterization. Her research focuses on the development of molecular methods (next-generation DNA and RNA sequencing) for bioassessment, with a special focus on microbial community response to anthropogenic disturbance and the use of algal assemblages as indicators of environmental degradation. She has worked in a range of aquatic systems with a special focus on photosynthetic microalgae as sentinels of anthropogenic disturbance and climate change

She received her B.A. in biology and geology from Williams College in 2005, and M.S. and Ph.D. in geological sciences from Brown University in 2009 and 2012, respectively. She joined SCCWRP in 2016.


Ph.D., geological sciences, Brown University, 2012

M.S., geological sciences, Brown University, 2009

B.A., biology and geology, Williams College, 2005

Professional Experience

Principal Scientist, Southern California Coastal Water Research Project Authority. Costa Mesa, CA. 2022-present.

Senior Scientist, Southern California Coastal Water Research Project Authority. Costa Mesa, CA. 2020-2022.

Scientist, Southern California Coastal Water Research Project Authority. Costa Mesa, CA. 2016-2019.

Computational biology postdoctoral fellow, DOE Joint Genome Institute. Walnut Creek, CA. 2012-2015.

Graduate research assistant, Brown University Department of Geological Sciences. Providence, RI. 2007-2012.

Research technician, Woods Hole Marine Biological Laboratory. Woods Hole, MA. 2005-2007.

Honors and Awards

DOE Joint Genome Institute Director’s Discretion Proposal, 2014.
American Association of University Women (AAUW) Dissertation Fellowship, 2011.
Geological Society of America (GSA) Student Research Grant, 2010.
Brown-MBL Graduate Fellowship, Brown University, 2007-2009.
Professor Jack L. Strominger Graduate Fellowship, Brown University, 2008.

Professional Societies and Certifications

American Association of University Women (AAUW).
Earth Science Women’s Network (ESWN).
Sigma XI Scientific Research Society.
International Society for Microbial Ecology (ISME).
Phycological Society of America (PSA).

Selected Presentations and Conference Proceedings

Theroux, S. molecular methods standardization for biomonitoring and bioassessment. California Environmental Laboratory Accreditation Program (ELAP) Conference. June 2, 2021. Via webinar.

Theroux, S. California Dreaming of Molecular Methods for Bioassessment. National Water Monitoring Conference. April 20, 2021. Via webinar.

Theroux, S. Advancing eDNA Tools for Bioassessment Applications. California Aquatic Bioassessment Workgroup (CABW). October 13-14, 2020. Davis, CA. 

Theroux, S. Mind the gap: bridging the distance between eDNA research and regulatory integration. International Workshop on Environmental Genomics. June 24-25, 2020. St John’s, Newfoundland, Canada. 

Theroux, S. Mazor, R., Stein, E. 2019. Incorporating molecular ecology tools into coastal and estuarine monitoring programs. Paper presented at the Coastal & Estuarine Research Federation annual meeting. Mobile, AL.

Theroux, S. 2019. Efforts to standardize molecular approaches to bioassessment in California and beyond. Paper presented at the COST Action CA15219 ('DNAqua-Net') Meeting, Limassol, Cyprus.

Theroux, S., Vasselon, V., Bouchez, A., Stein, E. 2019. Effect of bioinformatic pipeline on bioassessment index performance. International Barcode of Life (iBoL) conference. Trondheim, Norway.

Theroux, S., Steele, J., Griffith, J., Stein, E. 2019. A tale of two taxonomies: comparing morpho- and molecular taxonomy for stream algal bioassessment. Paper presented at the Society for Freshwater Science (SFS) Annual Conference. Salt Lake City, UT.

Theroux, S., Mazor, R., Stein, E., Sutula, M. 2017. A DNA-based approach for stream algal bioassessment: a case study in Southern California. Paper presented at the Phycological Society of America Annual Meeting. Monterey Bay, CA.

Theroux, S. 2017. A High-Throughput DNA Sequencing Approach to Algae Monitoring Allows for Enhanced Bioassessment. Paper presented at the Southern California SETAC Annual Conference. Dana Point, CA.

Theroux, S. Hartman, W., Tringe, S. 2015. Marsh madness: Microbial Communities Driving Greenhouse Gas Cycling in Coastal Wetlands. Paper presented at the Genomics of Energy & Environment. Walnut Creek, CA.

Theroux, S. Hartman, W., He, S., Windham-Myers, L., Tringe, S. 2014. Microbial diversity and carbon cycling in San Francisco Bay wetlands. Paper presented at the Joint Aquatic Sciences Meeting. Portland, OR.


Journal Articles

Kelly, R.P., D.M. Lodge, K.N. Lee, S. Theroux, A.J. Sepulveda, C.A. Scholin, J.M. Craine, E.A. Allan, K.M. Nichols, K.M. Parsons, K.D. Goodwin, Z. Gold, F.P. Chavez, R.T. Noble, C.L. Abbott, M.R. Baerwald, A.M. Naaum, P.M. Thielen, A.L. Simons, C.L. Jerde, J.J. Duda, M.E. Hunter, J.A. Hagan, R.S. Meyer, J.A. Steele, M.Y. Stoeckle, H.M. Bik, C.P. Meyer, E.D. Stein, K.E. James, A.C. Thomas, E. Demir-Hilton, M.A. Timmers, J.F. Griffith, M.J. Weise, S.B. Weisberg. 2024. Toward a national eDNA strategy for the United States. Environmental DNA DOI:10.1002/edn3.432.

Simons, A.L., S. Theroux, M. Osborne, S. Nuzhdin, R.D. Mazor, J.A. Steele. 2023. Zeta diversity patterns in metabarcoded lotic algal assemblages as a tool for bioassessment. Ecological Applications DOI:10.1002/eap.2812.

Stepien, C.A., S. Theroux, S.B. Weisberg. 2022. The Second National Workshop on Marine eDNA: A workshop to accelerate the incorporation of eDNA science into environmental management application. Environmental DNA DOI:10.1002/edn3.379.

Mazor, R.D., M. Sutula, S. Theroux, M. Beck, P.R. Ode. 2022. Eutrophication thresholds associated with protection of biological integrity in California wadeable streams. Ecological Indicators 142:109180.

Howard, M.D.A., J. Smith, D.A. Caron, R.M. Kudela, K. Loftin, K. Hayashi, R. Fadness, S. Fricke, J. Kann, M. Roethler, A. Tatters, S. Theroux. 2022. Integrative monitoring strategy for marine and freshwater harmful algal blooms and toxins across the freshwater‐to‐marine continuum. Integrated Environmental Assessment and Management DOI:10.1002/ieam.4651.

Irving, K., K.T. Taniguchi-Quan, A. Aprahamian, C. Rivers, G. Sharp, R.D. Mazor, S. Theroux, A. Holt, R. Peek, E.D. Stein. 2022. Application of Flow-Ecology Analysis to Inform Prioritization for Stream Restoration and Management Actions. Frontiers in Environmental Science 9:787462.

Bueno de Mesquita, C.P., J. Zhou, S. Theroux, S.G. Tringe. 2021. Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern. Genes 12:1609.

Zhou, J., S. Theroux, C.P. Bueno de Mesquita, W.H. Hartman, Y. Tian, S.G. Tringe. 2021. Microbial drivers of methane emissions from unrestored industrial salt ponds. The ISME Journal DOI:10.1038/s41396-021-01067-w.

Charles, D.F., M.G. Kelly, R.J. Stevenson, S. Poikane, S. Theroux, A. Zgrundo, M. Cantonati. 2021. Benthic algae assessments in the EU and the US: Striving for consistency in the face of great ecological diversity . Ecological Indicators DOI:10.1016/j.ecolind.2020.107082.

Howard, M.D.A., R.M. Kudela, K. Hayashi, A.O. Tatters, D.A. Caron, S. Theroux, S. Oehrle, M. Roethler, A. Donovan, K. Loftin, Z. Laughrey. 2021. Multiple co-occurring and persistently detected cyanotoxins and associated cyanobacteria in adjacent California lakes. Toxicon 192:1-14.

Theroux, S., R.D. Mazor, M.W. Beck, P.R. Ode, E.D. Stein, M. Sutula. 2020. Predictive biological indices for algae populations in diverse stream environments. Ecological Indicators DOI:10.1016/j.ecolind.2020.106421.

Paul, M.J., B. Jessup, L.R. Brown, J.L. Carter, M. Cantonati, D.F. Charles, J. Gerritsen, D.B. Herbst, R. Stancheva, J. Howard, B. Isham, R. Lowe, R.D. Mazor, P.K. Mendex, P.R. Ode, A. O'Dowd, J. Olson, Y. Pan, A.C. Rehn, S. Spaulding, M. Sutula, S. Theroux. 2020. Characterizing benthic macroinvertebrate and algal biological condition gradient models for California wadeable Streams, USA. Ecological Indicators DOI:10.1016/j.ecolind.2020.106618.

Aylagas, E., A. Borja, X. Pochon, A. Zaiko, N. Keeley, K. Bruce, P. Hong, G.M. Ruiz, E.D. Stein, S. Theroux, N. Geraldi, A. Ortega, L. Gajdzik, D.J. Coker, Y. Katan, T. Hikmawan, A. Saleem, S. Alamer, B.H. Jones, C.M. Duarte, J. Pearman, S. Carvalho. 2020. Translational Molecular Ecology in practice: Linking DNA-based methods to actionable marine environmental management. Science of the Total Environment DOI:10.1016/j.scitotenv.2020.140780.

Beck, M.W., C. O'Hara, J.S. Stewart-Lowndes, R.D. Mazor, S. Theroux, D.J. Gillett, B. Lane, G. Gearheart. 2020. The importance of open science for biological assessment of aquatic environments. PeerJ DOI:10.7717/peerj.9539.

Simons, A.L., R.D. Mazor, S. Theroux. 2019. Using Co‐occurrence Network Topology in Assessing Ecological Stress in Benthic Macroinvertebrate Communities. Ecology and Evolution DOI:10.1002/ece3.5751.

Beck, M., R.D. Mazor, S. Theroux, K.C. Schiff. 2019. The Stream Quality Index: A multi-indicator tool for enhancing environmental management. Environmental and Sustainability Indicators DOI:10.1016/j.indic.2019.100004.

Longo, W., Theroux, S., Giblin, A.E., Zheng, Y., Dillon, J.T., Huang, Y. 2016. Temperature calibration and phylogenetically distinct distributions for freshwater alkenones: Evidence from northern Alaskan lakes. Geochimica et Cosmochimica Acta 180: 177-196.

D’Andrea, W., Theroux, S., Bradley, R., Huang, X. 2016. Does phylogeny control Uk37-temperature sensitivity? Implications for lacustrine alkenone paleothermometry. Geochimica et Cosmochimica Acta 175:168-180.

Theroux, S., Toney, J.L., Amaral-Zettler, L., Huang, Y. 2013. Production and temperature sensitivity of long chain alkenones cultured haptophyte Pseudoisochrysis paradoxa. Organic Geochemistry. http://dx.doi.org/10.1016/j.orggeochem.2013.07.006.

Theroux, S. 2012. Diversity and ecology of lacustrine haptophyte algae: implications for paleothermometry. Ph.D. dissertations, Brown University. Providence, RI.

Theroux, S., Huang, Y., Amaral-Zettler. 2012. Comparative molecular microbial ecology of spring haptophyte blooms in an arctic oligosaline lake in Greenland. Frontiers in Microbiology. doi: 10.3389/fmicb.2012.00415.

Toney, J., Theroux, S., Andersen, R., Coleman, A., Amaral-Zettler, L., Huang, Y. 2012. Culturing of the first 37:4 predominant lacustrine haptophyte: Geochemical, biochemical, and genetic implications. Geochimica et Cosmochimica Acta 78:51-64.

Technical Reports

Smith, J., D. Shultz, A. Lie, S. Theroux. 2023. Diversity and Prevalence of Cyanobacteria and Cyanotoxins in Los Angeles Region Recreational Lakes and Reservoirs. Technical Report 1309. Southern California Coastal Water Research Project. Costa Mesa, CA.

Beck, M., R.D. Mazor, S. Theroux, K.C. Schiff. 2019. The Stream Quality Index: A Multi-Indicator Tool for Enhancing Environmental Management Communication. Technical Report 1080. Southern California Coastal Water Research Project. Costa Mesa, CA.