Dr. Joshua Steele
Dr. Joshua Steele is a microbiologist who specializes in environmental microbiology and microbial ecology, including cultivation-independent tracking of pathogens and natural microorganisms in the coastal ocean and watersheds. 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. His research involves development and application of molecular techniques to detect and track pathogenic bacteria and viruses, determine their viability and infectivity, and link them to beachgoer risk using statistical models; application of next-generation sequencing and metagenomics to connect the environmental microbiome and antibiotic resistome to water quality, ecosystem health, and health risk; and using bioinformatics tools to measure natural populations and community-wide changes in genes or gene expression in response to environmental changes.
He received his B.S. in molecular biology in 2000 from the University of California, San Diego and his Ph.D. in biological oceanography in 2010 from the University of Southern California. 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
Scientist, Southern California Coastal Water Research Project, Costa Mesa, CA. 2014-present
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
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
Association for the Sciences of Limnology and Oceanography
American Geophysical Union
American Society for Microbiology
Coastal and Estuarine Research Federation
International Society for Microbial Ecology
Society for Applied Microbiology
Selected Presentations and Conference Proceedings
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., M.R. Raith, L.E. Darjany, J.F. Griffith. Application of a cultivable halophilic archaeon as an extraction and quantification control for the measurement of bacteria using qPCR and digital PCR in wastewater and environmental waters. UNC Water Microbiology Conference 2018. May 22-24, 2018. 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.
Steele, J.A., M.R. Raith, J.F. Griffith, K.C. Schiff. Molecular Fecal Source Investigation at an Urban Marine Beach with Chronic Microbial Water Quality Problems in support of a Quantitative Microbial Risk Assessment. UNC Water Microbiology Conference 2017: May 15-17, 2017 Chapel Hill, NC
Steele, J. A., A.A. Chariton, S. M. Theroux, E.D. Stein. Inter-laboratory comparative study of bioinformatics pipelines. 2017 International Workshop on Environmental Genomics. June 8-9, 2017 St. John’s, NL, Canada.
Steele, J.A., Theroux, S.M, Kacev, D., Mazor, R. , Cao, Y., J.F. Griffith, E.D. Stein. Towards standards for sequence and bioinformatic analysis quality control when using eDNA for metabarcoding and taxonomic identification. First Annual Environmental DNA Training
& Technical Exchange Workshop, 2-3 August 2016. Denver, Colorado, USA
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.