Dr. Joshua Steele
Dr. Joshua Steele is a microbiologist specializing in environmental microbiology, specifically identifying and tracking pathogens and naturally-occurring microbes in wastewater, coastal ocean water, and coastal watersheds using cutting edge molecular techniques (next generation sequencing and digital PCR). His research focuses on developing methods to detect and track human-associated bacteria and viruses and identify their sources in stormwater and coastal water, developing and standardizing methods for wastewater based epidemiology of pathogens including SARS-CoV-2, applying molecular techniques to track antibiotic resistance genes in wastewater and the environment, and using bioinformatics tools to link eDNA from natural populations to ecosystem health. He serves on the Wastewater Based Epidemiology Committee of the California Water Quality Montioring Council. While at the California Institute of Technology, he focused on applying next-generation sequencing, metagenomics, metaproteomics, and biogeochemical rate measurements to study deep-sea methane seep microbial communities.
He received his Ph.D. in biological oceanography from the University of Southern California and his B.S. in molecular biology from the University of California, San Diego. He joined SCCWRP in January 2014.
Ph.D., marine environmental biology, University of Southern California, 2010
B.S., molecular biology, University of California, San Diego, 2000
Senior Scientist, Southern California Coastal Water Research Project, Costa Mesa, CA, 2021-present
Scientist, Southern California Coastal Water Research Project, Costa Mesa, CA. 2014-2021
Associate Research Scientist, Geobiology, California Institute of Technology, Pasadena, CA. 2013-2014
Postdoctoral Scholar in Geobiology, California Institute of Technology, Pasadena, CA. 2010-2013
Research Assistant, University of Southern California, Los Angeles, CA. 2001-2010
Knauss Marine Policy Fellow: Legislative Assistant for Rep. Sam Farr (CA-17), U.S. House of Representatives, Washington, DC. 2008-2009
Teaching Assistant, University of Southern California, Los Angeles, CA. 2001-2006
Doctoral Fellow, NSF Integrative Graduate Education, Research, and Training: Environmental Studies, Policy and Engineering- Sustainable Cities Program, University of Southern California, Los Angeles, CA 2003-2004
Participant USC Sustainable Cities Internship in Hong Kong SAR, China 2004
Sea Grant Trainee, Beach Water Quality Study, 2002
Laboratory Technician, CalBioMarine Technologies, Inc. Carlsbad, CA 2000-2001
Associate Editor, Aquatic Microbiology Section, Frontiers in Microbiology/Frontiers in Marine Science, 2021-present
California Water Quality Monitoring Council Wastewater Based Epidemiology Committee, 2021-present
Honors and Awards
Knauss Sea Grant Fellowship in Marine Policy 2008-2009
Rose Hills Graduate Internship 2005, 2006
National Science Foundation IGERT Doctoral Fellowship in Sustainable Cities 2003-2004
Student travel Award ASLO Ocean Sciences Conference, Honolulu, HI 2004
Traineeship, USC Sea Grant Program 2002
Professional Societies and Certifications
American Geophysical Union
American Society for Microbiology
Association for the Sciences of Limnology and Oceanography
Coastal and Estuarine Research Federation
Selected Presentations and Conference Proceedings
Steele, J.A. COVID-19 Epidemiological Monitoring in Wastewater - Methods Development and Standardization AWWA CA-NV Fall Meeting Virtual Conference October 19, 2021
Han, L., M. Atkinson, J. Chu, M. Tilahun, J. Steele, J. Griffith, A. Zimmer-Faust. Refining Sars-cov-2 RNA Wastewater Data Analysis For Improved Relationships With Covid-19 Case Counts American Society for Microbiology and Federation of European Microbiological Societies World Microbe Forum Virtual Conference June 20, 2021
Rothman, J. A. T. B. Loveless, J. Kapcia, III, E. D. Adams, J. A. Steele, A. G. Zimmer-Faust, J. F. Griffith, N. Boyajian, J. Oval, V. J. Sharavanan, K. L. Whiteson. RNA Viromics Of Southern California Wastewater And Single Nucleotide Variant Detection Of SARS-CoV-2 American Society for Microbiology and Federation of European Microbiological Societies World Microbe Forum Virtual Conference June 20, 2021
Steele, J.A. , A. G. Zimmer-Faust, J. F. Griffith, S. B. Weisberg. Sources Of Variability In Methods For Processing, Storing, And Concentrating SARS-CoV-2 In Influent From Urban Wastewater Treatment Plants American Society for Microbiology and Federation of European Microbiological Societies World Microbe Forum Virtual Conference June 20, 2021
Steele, J.A., R.E. Diner, A.G. Zimmer-Faust, M.L. Griffith, T. Harper, J. Chokry, D. Wanless, J.F. Griffith. Antimicrobial Resistance in Wastewater Effluent Streams and in Urban Coastal Waters Influenced by Effluent Discharge. Oceans and Human Health Session Co-Chair. ASLO/AGU/TOS Ocean Sciences Meeting February 16-21, 2020, San Diego CA.
Steele, J.A., D. Ebentier McCarger, A.G. Zimmer-Faust, J.F. Griffith, R.T. Noble, K.C. Schiff. Tracking human fecal sources in an urban, coastal watershed during wet weather. Coastal Estuarine Research Federation Biennial Meeting. 3–7 November, 2019 Mobile, AL, USA
Steele, J.A., A. G. Zimmer-Faust, M.L. Griffith, L.E. Darjany, P. Chen, D. Wanless, J. F. Griffith. Distinct Biofilm Communities in Separate Sewer and Storm Drain Infrastructure in Urbanized Watersheds. ASM Microbe 2019. June 20-24, 2019. San Francisco, CA, USA
Steele, J.A. Scaling the issues across culture-based methods and whole environmental matrix based bioinformatics, an overview. Impacts of Bioinformatics on Water Quality Research and Management Side Event. Co-Conveners: J.A. Steele, J.F. Griffith, R.T. Noble UNC Water Microbiology Conference 2019. May 16, 2019. Chapel Hill, NC, USA
Steele, J.A., P. Chen, M.L. Griffith, A.G. Zimmer-Faust, D. Wanless, J.F. Griffith. An Antimicrobial Resistance Survey: Primary-Tertiary Treated Wastewater, UNC Water Microbiology Conference 2019. May 14-16, 2019. Chapel Hill, NC, USA
Steele, J.A., P.A. Greenfield, L.R. Thompson, J. Martinson, D. Kacev, A. Bush, M. Hajibabaei, D. Baird, E.M. Pilgrim, E.D. Stein, A.A. Chariton. Inter-laboratory comparative study of bioinformatics pipelines: Initial Results. Second Annual Environmental DNA Technical Exchange Workshop (Virtual) January 9-10, 2018.
Marlow JJ, Steele JA, Ziebis W, Scheller S, Case D, Reynard LM, Orphan VJ. 2017. Monodeuterated Methane, an Isotopic Tool To Assess Biological Methane Metabolism Rates. mSphere 2(4): e00309–17–19 doi:10.1128/mSphereDirect.00309-17.
Pasulka, A.L; Levin, L.A; Steele, J.A; Case, D.H; Landry, M. R; Orphan, V.J. 2016 Microbial eukaryotic distributions and diversity patterns in a deep‐sea methane seep ecosystem. Environ Microbiol, 18: 3022–3043. doi:10.1111/1462-2920.13185
Cram, J. A., Chow, C.-E. T., Sachdeva, R., Needham, D. M., Parada, A. E., Steele, J. A., & Fuhrman, J. A. 2015. Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. Isme Journal 9 (3), 563-580 doi:10.1038/ismej.2014.153
Marlow JJ, Steele JA, Case DH, Connon SA, Levin LA and Orphan VJ 2014 Microbial abundance and diversity patterns associated with sediments and carbonates from the methane seep environments of Hydrate Ridge, OR. Front. Mar. Sci. 1:44. doi: 10.3389/fmars.2014.00044
Marlow, J. J., Steele, J. A., Ziebis, W., Thurber, A. R., Levin, L. A., & Orphan, V. J. 2014 Carbonate-hosted methanotrophy represents an unrecognized methane sink in the deep sea. Nature Communications, 5, 5094. doi:10.1038/ncomms6094
Glass, J.B., H. Yu, J.A. Steele, K.S. Dawson, S. Sun, K.Chourey, R.L. Hettich, V.J. Orphan. 2014 Geochemical, metagenomic and metaproteomic insights into trace metal utilization of methane-oxidizing microbial consortia in sulfidic marine sediments. Environmental Microbiology 16(6), 1592–1611. doi:10.1111/1462-2920.12314
Hatosy, S.M., J.B.H. Martiny, R. Sachdeva, J. Steele, J.A. Fuhrman, A.C. Martiny 2013 Beta-diversity of marine bacteria depends on temporal scale. Ecology 94 (9), 1898-1904
Chow, C.E.T., R. Sachdeva, J.A. Cram, J.A. Steele, D.M. Needham, A. Patel, A.E. Parada, J.A. Fuhrman. 2013. Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight ISME Journal 7, 2259–2273; doi:10.1038/ismej.2013.122
Tavormina, P.L., W. Ussler III, J.A. Steele, S.A. Connon, M.G. Klotz, V. J. Orphan. 2013. Depth distribution of Cu-MMO variants through the oxygen minimum zone along the Costa Rica convergent margin. Environmental Microbiology Reports 5 (3), 414-423
Gilbert, J.A., J.A. Steele, J.G. Caporaso, L. Steinbrück, P. Somerfield, J. Reeder, B. Temperton, S. Huse, I. Joint, A.C. McHardy, R. Knight, J.A. Fuhrman, D. Field. 2012 Defining seasonal marine microbial community dynamics. ISME Journal 6:298-308.
Steele, J.A., P.D. Countway, L. Xia, P. D. Vigil, J.M. Beman, D.Y. Kim, C. T. Chow, R. Sachdeva, A.C. Jones, M.S. Schwalbach, J. M. Rose, I. Hewson, A. Patel, F. Sun, D.A. Caron, J.A. Fuhrman. 2011 Marine bacterial, archaeal, and protistan association networks reveal ecological linkages ISME Journal 5:1414-1425.
Xia, L. C., J.A. Steele, J. Cram, Z.G. Cardon, S.L. Simmons, J.J. Vallino , J.A. Fuhrman, F. Sun 2011. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Systems Biology 5:S15.
Beman, J.M., J.A. Steele, and J.A. Fuhrman. 2011 Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California. ISME Journal 5:1077-1085.
Fuhrman J.A., J.A. Steele. 2008 Community Structure of Marine Bacterioplankton: Patterns, Networks, and Relationships to Function. Aquatic Microbial Ecology 53:69-81.
Fuhrman, J.A., J.A. Steele, I. Hewson, M. S. Schwalbach, M.V. Brown, J. Green, Brown, J.H. 2008 A Latitude Diversity Gradient in Planktonic Marine Bacteria. Proceedings of the National Academy of Sciences 105:7774-7778.
Patel, A., R. Noble, J.A. Steele, M.S. Schwalbach, I. Hewson, J.A. Fuhrman 2007 Virus and Prokaryote Enumeration from Planktonic Marine Environments by Epifluorescence Microscopy with SYBR Green I. Nature Protocols 2:269-276.
Ruan, Q., D. Dutta, M.S. Schwalbach, J.A. Steele, J.A. Fuhrman, F. Sun 2006 Local Similarity Analysis Reveals Unique Associations Among Marine Bacterioplankton Species and Environmental Factors. Bioinformatics 22: 2532-2538.
Fuhrman, J. A., Hewson, I., Schwalbach, M. S., Steele, J. A., Brown, M. V., & Naeem, S. 2006. Annually reoccurring bacterial communities are predictable from ocean conditions. Proceedings of the National Academy of Sciences, 103(35): 13104–13109.
Ruan, Q., Steele, J. A., Schwalbach, M. S., Fuhrman, J. A., & Sun, F. 2006. A dynamic programming algorithm for binning microbial community profiles. Bioinformatics, 22(12), 1508–1514.
Hewson, I., D.G. Capone, J. A. Steele, J.A. Fuhrman. 2006 Influence of Amazon and Orinoco Offshore Surface Water Plumes on Oligotrophic Bacterioplankton Diversity in the West Tropical Atlantic. Aquatic Microbial Ecology 43:11-22.
Hewson, I, J.A. Steele, D.G. Capone, J.A. Fuhrman. 2006 Remarkable Heterogeneity in Meso- and Bathypelagic Bacterioplankton Community Composition. Limnol. Oceanography 51:1274-1283.
Hewson, I, J.A. Steele, D.G. Capone, J.A. Fuhrman. 2006 Temporal and Spatial Scales of Oligotrophic Surface Water Bacterioplankton Assemblage Variation. Marine Ecology Progress Series 311:67-77.
Steele, J.A., F. Ozis, J.A. Fuhrman, J.S. Devinny. 2005. Structure of Microbial Communities in Ethanol Biofilters. Chemical Engineering Journal 113:135-143.