MEB Faculty

Karla Heidelberg

Associate Professor (Teaching) of Biological Sciences and Environmental Studies
Director of USC Environmental Studies Program

Contact Information
Phone: (213) 740-0951
Office: AHF 107

Faculty Profile on Departmental Website
Wrigley Institute of Environmental Studies
Personal Lab Web page


  • B.A. (Honors) Individualized Major, Maryville College, TN, 1988
  • Ph.D. Marine-Estuarine Environmental Science (Conc: Biological Oceanography), University of Maryland, College Park, 1999

  • Postdoctoral Training

    • Department of Biology Post-Doctoral Fellow, University of Maryland, College Park, 06/1999-08/2001  

    Academic Appointment, Affiliation, and Employment History

    Tenure Track Appointments
    • Assistant Professor, Department of Biological Sciences, University of Southern California, 2006-  
    Visiting and Temporary Appointments
    • Adjunct Research Scientist, J. Craig Venter Institute, 2006-2010  
    • Adjunct Research Faculty, Department of Biology, University of Maryland, College Park, 2001-2004  
    • Adjunct Teaching Faculty, Department of Biology, Hood College, Frederick, MD, 2002-2003   
    Other Employment
    • Resident Faculty, USC Wrigley Marine Science Center, 2006-  
    • Scientists and Coodinator of Global Program, Rockville, MD, J. Craig Venter Institute, 2003-2006  
    • International Marine Science Policy Advisor (AAAS Science and Diplomacy Fellow), U.S. Department of State, Office of Oceans Affairs, 2001-2003  

    Description of Research

    Summary Statement of Research Interests
    I research the genetic, biochemical, and metabolic properties of naturally occurring prokaryotic and eukaryotic microbial assemblages by pairing contemporary genomic technologies with more traditional lab and field approaches. The knowledge gained through genomic approaches provides the basis to evaluate microbial diversity and the fundamental physiological and ecological principles governing the activities and interactions of microbial taxa in studied habitats. Understanding these interactions and their resultant biogeochemical activities is an exciting avenue of research given that much of the energy flow and elemental cycling is not only conducted by microorganisms, but dictated by their trophic interactions. Current research programs focus on microbial consortia from hypersaline environments and functional properties of microbial mixotrophs.
    Research Keywords
    Marine and environmental microbiology and ecology; Microbial diversity, including microbial eukaryotes; Environmental genomics; Effects of environmental change on microbial assemblages.

    Affiliations with Research Centers, Labs, and Other Institutions

    • Wrigley Institute of Marine Studies, Resident Faculty,


    Journal Article
    • Koid, A. E., Terrado, R., Liu, Z., Caron, D. A., Heidelberg, K. B. (2015). Changes in gene expression of Prymnesium parvum due to nitrogen and phosphorus limitation. Front. Aquat. Micro. Ecol..
    • Andrade, K., Logemann, J., Heidelberg, K. B., Emerson, J. B., Comolii, L. R., Huq, L. A., Keillar, A., Thomas, B. C., Miller, C. S., Allen, E. E., Moreau, J., Brocks, J., Banfield, J. F. (2015). Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. ISME J. pp. 1-15. PubMed Web Address Article
    • Liu, Z., Jones, A. C., Campbell, V., Hambright, K. D., Heidelberg, K. B., Caron, D. A. (2015). Gene expression in the mixotrophic haptophyte, Prymnesium parvum, responds to prey availability. Front. Microb.. (6), pp. 319. Article
    • Holm, J., Heidelberg, K. B. (2014). Metagenomic evaluation of the microbial holobiome of the temperate Octocorals, Muricea californica and Muricea fruticosa provides insight into the ecological roles of bacterial communities and their hosts (submitted Dec 2014, NPJ Biofilms and Microbiomes). NPJ Biofilms and Microbiomes.
    • Tully, B. J., Andrade, K., Brocks, J., Emerson, J., Allen, E. E., Banfield, J. F., Heidelberg, K. B. (2014). Genome wide variation in Haloquadratum ecotypes across spatial and temporal gradients. Archaea. (Article ID 875784) Article
    • Tully, B. J., Sachdeva, R., Heidelberg, K. B., Heidelberg, J. F. (2014). Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data. Microbiome. Vol. 2, pp. 34. Article
    • Koid, A. E., Liu, Z., Terrado, R., Jones, A. C., Caron, D., Heidelberg, K. B. (2014). Comparative transcriptome analysis of four prymnesiophyte algae. PLoS ONE. Vol. 9, pp. e97801. publication
    • Podell, S., Emerson, J. B., Jones, C. M., Ugalde, J. A., Welch, S., Heidelberg, K. B., Banfield, J. F. (2013). Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J. article
    • Emerson, J., Andrade, K., Thomas, B. C., Norman, A., Allen, E., Heidelberg, K. B., Banfield, J. F. (2013). Virus-host and CRISPR dynamics in hypersaline Lake Tyrrell, Victoria, Australia (Accepted). Archaea.
    • Emerson, J. B., Thomas, B. C., Andrade, K., Heidelberg, K. B., Banfield, J. F. (2013). Characterizing the diversity and dynamics of natural viral assemblages, as demonstrated in a hypersaline lake system. J. Virology..
    • Heidelberg, K. B., Nelson, W. C., Holm, J. B., Eisenkolb, N., Andrade, K., Emerson, J. (2013). Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia. Front. Microbiol. Vol. 4, pp. 1-14. doi: 10.3389/fmicb.2013.00115
    • Lopez-Lozano, N. E., Heidelberg, K. B., Nelson, W. C., Garcia-Oliva, F., Eguiarte, L. E., Souza, V. (2013). Microbial secondary sucession in soil microcosms of a desert oasis in the Cuatro Cienegas Basin, Mexico. Peer J. Vol. 1, pp. e47. 10.7717/peerj.47
    • Podell, S., Ugalde, J. A., Narasingarao, P., Banfield, J. F., Heidelberg, K. B., Allen, E. E. (2013). Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS ONE. Vol. 8 (4), pp. e61692. PLoS ONE
    • Emerson, J. B., Thomas, B. C., Andrade, K., Heidelberg, K. B., Banfield, J. F. (2013). New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake. Appl. Environ. Microbiol.. Vol. 79, pp. 6755-6764. PubMed Web Address
    • Koid, A. E., Nelson, W. C., Mraz, A., Heidelberg, K. B. (2012). Comparative analysis of eukaryotic marine microbial assemblages from 18S rRNA gene or gene transcript clone libraries using different methods of extraction. Appl. Env. Microbiol.. Vol. 78, pp. 3958-3965. PubMed Web Address
    • Narasingarao, P., Podell, S., Ugalde, J. A., Brochier-Armanet, C., Emmerson, J. B., Brocks, J. J., Heidelberg, K. B., Banfield, J. F., Allen, E. E. (2012). De Novo Metagenomic Assembly Reveals Abundant Novel Archaea in Hypersaline Microbial Communities. ISME J.. pp. 1-13. PubMed Web Address
    • Emerson, J. B., Thomas, B. C., Andrade, K., Allen, E. E., Heidelberg, K. B., Banfield, J. F. (2012). Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl. Environ. Microbiol.. Vol. 78, pp. 6309-6320. PubMed Web Address
    • Heidelberg, K. B. (2011). Octocorals and ocean acidification studies at Catalina. Ocean Bights: The Magazine of the Catalina Marine Society. Vol. 2, pp. 3-5.
    • Heidelberg, K. B., Gilbert, J. A., Joint, I. (2010). Marine genomics: at the interface of marine microbial ecology and biodiscovery. Microbial Biotechnology. doi:10.1111/j.1751-7915.2010.00193.x
    • Thomas, T., Rusch, D., Damaere, M. Z., Young, P. Y., Lewis, M., Halpern, A., Heidelberg, K. B., Egan, S., Steinberg, P. D., Kjelleberg, S. (2010). Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis. ISME J. (Epub) PubMed Web Address
    • Heidelberg, K. B., Bythell, J., Oneill, K. L., Sebens, K. P. (2009). Vertical Distribution and Diel Patterns of Zooplankton over a Florida Coral Reef. J. Plank. Res. Journal
    • Caron, D. A., Gast, R. J., Countway, P. D., Heidelberg, K. B. (2009). Microbial Eukaryote Ecology: Questions of Diversity and Biogeography. Microbe. Vol. 4 (2), pp. 71-77.
    • Caron, D. A., Worden, A. Z., Countway, P. D., Demir, E., Heidelberg, K. B. (2009). Protists are Microbes Too: A Perspective. Int. Soc. Microbial Ecol.. Vol. 3, pp. 4-12. PubMed Web Address
    • Williamson, S., Rusch, D., Yooseph, S., Halpern, A., Heidelberg, K., Glass, J., Andrews-Pfannkoch, C., Fadrosh, D., Miller, C., Sutton, G., Frazier, M., Venter, J. C. (2008). The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples. PLoS ONE. Vol. 3 (1), pp. e1456. PubMed Web Address
    • Yooseph, S., Sutton, G., Rusch, D. B., Halpern, A. L., Williamson, S. J., Remington, K., Eisen, J. A., Heidelberg, K. B., Manning, G., Li, W., Jaroszewski, L., Cieplak, P., Miller, C. S., Li, H., Mashiyama, S. T., Joachimiak, M. P., van Belle, C., Chandonia, J., Soergel, D. A., Zhai, Y., Natarajan, K., Lee, S., Raphael, B. J., Bafna, V., Friedman, R., Brenner, S. E., Godzik, A., Eisenberg, D., Dixon, J. E., Taylor, S. S., Strausberg, R. L., Frazier, M., Venter, J. C. (2007). The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (Cover). PLoS Biology. Vol. 5, pp. e16. PubMed Web Address
    • Rusch, D. B., Halpern, A. L., Sutton, G., Heidelberg, K. B., Williamson, S., Yooseph, S., Wu, D., Eisen, J. A., Hoffman, J. M., Remington, K., Beeson, K., Tran, B., Smith, H., Baden-Tillson, H., Stewart, C., Thorpe, J., Freeman, J., Andrews-Pfannkoch, C., Venter, J. E., Li, K., Kravitz, S., Heidelberg, J. F., Utterback, T., Rogers, Y., Falcon, L. I., Souza, V., Bonilla-Rosso, G., Eguiarte, L. E., Karl, D. M., Sathyendranath, S., Platt, T., Bermingham, E., Gallardo, V., Tamayo-Castillo, G., Ferrari, M. R., Strausberg, R. L., Nealson, K., Friedman, R., Frazier, M., Venter, J. C. (2007). The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific (Cover). PLoS Biology. Vol. 5, pp. e77. PubMed Web Address
    • Remington, K. A., Heidelberg, K. B., Venter, J. C. (2005). Taking Metagenomic Studies in Context. Trends Microbiol. Vol. 13, pp. 404. PubMed Web Address
    • Heidelberg, K. B., Heidelberg, J. F. (2005). Marine Environmental Genomics: New Secretes from a Mysterious Ocean. Marine Technology Society Journal. Vol. 39 (3), pp. 94-98.
    • Heidelberg, K. B., Sebens, K. P., Purcell, J. E. (2004). Composition and Sources of Near Reef Zooplankton on a Jamaican Forereef, with Implications for Coral Feeding. Coral Reefs. Vol. 23, pp. 263-276.
    • Heidelberg, J. F., Heidelberg, K. B., Colwell, R. R. (2002). Bacteria of the gamma-Subclass Proteobacteria Associated with Zooplankton in Chesapeake Bay. Appl. Env. Microbiol.. Vol. 68, pp. 5498-5507. PubMed Web Address
    • Heidelberg, J. F., Heidelberg, K. B., Colwell, R. R. (2002). Seasonality of Chesapeake Bay Bacterioplankton Species. Appl. Environ. Microbiol.. Vol. 68 (11), pp. 5488-5497. PubMed Web Address
    • Kreps, T., Purcell, J. E., Heidelberg, K. B. (1997). Escape of the Ctenophore Mnemiopsis leidyi from the Scyphomedusa Predator Chrysaora quinquecirrha. Mar. Biol.. Vol. 128, pp. 441-446.
    • Heidelberg, K. B., Sebens, K. P., Purcell, J. E. (1997). Effects of Prey Escape Behavior and Water Flow on Prey Capture by the Scleractinian Coral, Meandrina meandrites. Proc. 8th Int Coral Reef Symp.. Vol. 2, pp. 1081-1086.
    • Ford, M. D., Costello, J. H., Heidelberg, K. B., Purcell, J. E. (1997). Swimming and Feeding by the Scyphomedusa, Chrysaora quinquecirrha. Mar. Biol.. Vol. 129, pp. 355-362.

    • Heidelberg, K. B. (2008). NSF Sponsored Interactive Outreach for a Deep Sea Hydrothermal vent cruise using DSV Alvin (participation by 23 elem. schools). Website
    • Heidelberg, K. B. (2008). Antarctica Research Expedition (Jan/Feb 2008) Interactive Educational Outreach (14 elementary. website
    • Heidelberg, K. B. (1999). Effects of water flow and zooplankton prey behavior on scleractinian coral heterotrophy. University of Maryland.

    • Mele, P., Sawbridge, T., Hayden, H., Methe, B., Stockwell, T., Pfannkoch, C., Lewis, M., Tanenbaum, D., Rusch, D., Heidelberg, K. (2010). How does surface soil geomorphology and land-use influence the soil microbial ecosystems in south eastern Australia? Insights gained from DNA sequencing of the soil metagenome. pp. 12-15. Brisbane. 2010 19th World Congress of Soil Sci., Soil Solutions for a Changing World.. PDF

    Technical Report

    Working Paper
    • Edgcomb, V. P., Biddle, J., Caron, D. A., Heidelberg, K. B., Countway, P. D., Teske, A. (2009). New Frontiers: The Evaluation of Eukaryotic Populations in the Deep Marine Subsurface: Scientific Goals and Approaches for Future Ocean Drilling Projects. INVEST. INVEST IODP Renewal Meeting, University of Bremen

    Multimedia Scholarship and Creative Works

    • Radio Interview, Seti Institute Science Friday Radio Program. DNA: The Nucleotide is Turning, 2006-2007   
    • Discovery Channel Documentary, Science Advisor "Cracking the Ocean Code", 2004-2005   
    • Article, Research featured in National Geographic Adventure Magazine, 2002-2003   
    • Article, Research featured on, Nature Section, 1999-2000   
    • Documentary, Research featured in Jason VII: Adapting to a Changing Sea, 1995-1996   
    • Interactive Outreach Website, NOAA Sponsored Outreach for Aquarius Underwater Habitat Saturation Research Mission:, 2000-2001   
    • Article and Training/Outreach Video, The Machine that Goes Ping: Article and web-based video, 2008-2009   
    • Magazine, Research featured in USC Trojan Family Magazine Article, "Blurring the Lines Between Earth and Life", 2008-2009   
    • Newspaper/web article, Ventura County Star highlighted a satellite Q&A with high school students from aboard the submersible Alvin. Education outreach part of 2008 hydrothermal vent cruise. Story included a photo of Heidelberg and colleagues on Alvin. , 2008-2009   

    Honors and Awards

    • USC or School/Dept Award for Teaching, Steven B. Sample Teaching and Mentoring Award, 2012-2013   
    • USC or School/Dept Award for Teaching, (Nomination) USC Steven B. Sample Teaching and Mentoring Award, 2010-2011   
    • Superior Honor Award, US Department of State, 2004  
    • Meritorious Honor Award, US Department of State, 2003  
    • Maryville College Kin Takahashi Award for Young Alumni, 2001  

    Service to the Profession

    Editorships and Editorial Boards
    • Editorial Board, Microbiome, 01/2012-  
    • Associate Editor, Frontiers in Aquatic Microbiology, 06/2010-  

  • Department of Biological Sciences
  • University of Southern California
  • Allan Hancock Foundation Building
  • Los Angeles, CA 90089-0371