52. Marshall, A, L Phillips, A Longmore, HL Haden, C Tang, KB Heidelberg, P Mele 2023. Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediments. Env. Microbiology Reports. 1– 16 (PDF)

51. Marshall, AJ, L Phillips, A Longmore, HL Hayden, KB Heidelberg, C Tang, and P Mele. 2023. Temporal profiling resolves the drivers of microbial nitrogen cycling variability in sediments. Sci Total. Env. 856: 159057 (PDF)


50. Marshall, A, L Phillips, A Longmore, LA Phillips, C Tang, G Croatto, H Hayden, KB Heidelberg, P Mele. 2021. Nitrogen cycling in coastal sediment microbial communities with seasonally variable benthic nutrient fluxes. Aquat. Microb. Ecol. 86:1-19. doi:10.3354/ame01954 (PDF)


49. Hu, SK, H Alexander, Z Liu, KB Heidelberg, S Dyhrman, DA Caron. (in revision) Distinct transcriptional signatures of the protistan community at the SPOT and ALOHA ocean time-series stations. 


48. Pasulka, A, S *Hu, PD Countway, KJ Coyne, SC Cary, KB Heidelberg and DA Caron. 2019. SSU-rRNA sequencing survey of benthic microbial eukaryotes from Guaymas Basin hydrothermal vent. J. Eukary. Microbiol. doi: 10.1111/jeu.12711. (PDF)


47. Ginsburg DW, KB Heidelberg. 2018. Scientific research diving: Engaging students with unique STEM training opportunities and place-based field experiences. In: Diving for Science 2018. Proceedings of the American Academy of Underwater Sciences 37th Symposium. Eds. Gochfeld DJ, TJ Herrlinger. AAUS, Tahoe City, CA. (PDF)

46. Marshall, A, L Phillips, A Longmore, C Tang, K Heidelberg, P Mele. 2018. Primer selection influences abundance estimates of ammonia oxidizing archaea in coastal marine sediments. (PDF)

45. Carpenter, KJ, M Bose, L Polerecky, AAYLie, KB Heidelberg and DA Caron. 2018. Single-cell view of carbon and nitrogen acquisition in the mixotrophic alga Prymnesium parvum (Haptophyta) inferred from stable isotope tracers and nanoSIMS Front. Mar. Sci. 5:157 doi:10.3389/fmars.2018.00157. (PDF)

44. Hu, SK, Z Liu, H Alexander, V Campbell, P Connell, ST Dyhrman, KB Heidelberg, DA Caron. 2018. Shifting metabolic priorities among key protistan taxa within and below the euphotic zone. (Preprint PDF)

43. Lie AAY, Z Liu, R Terrado, AO Tatters, KB Heidelberg, DA Caron. 2018. A tale of two mixotrophic chrysophytes: Insights into the metabolisms of two Ochromonas species (Chrysophyceae) through a comparison of gene expression. PLoS ONE 13(2): e0192439. (PDF).


42. Terrado, R, AL Pasulka, *A Lie, V Orphan, KB Heidelberg, D Caron. 2017. Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte. ISME J. doi:10.1038/ismej.2017.68 (PDF)

41. Lie, AAY, Z Liu, R Terrado, AO Tatters, KB Heidelberg, DA Caron. 2017. Effect of light and prey availability on the gene expression of the mixotrophic chrysophyte, Ochromonas sp. BMC Genomics. 18:163 (PDF)

40. Liu, Z, SK Hu, V Campbell, AO Tatters, KB Heidelberg, DA Caron. 2017. Single-cell transcriptomics of small microbial eukaryotes: insights and limitations. ISME J. doi: 10.1038/ismej.2016.190 (PDF)

39. Caron, DA, H Alexander, AE Allen, JM Archibald, EV Armbrust, C Bachy, A Bharti, CJ Bell, ST Dyhrman, S Guida, KB Heidelberg, JZ Kaye, J Metzner, SR Smith, AZ Worden. 2017. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat. Rev. Microbiol. doi:10.1038/nrmicro.2016.160  Published online 21 Nov 2016 (PDF)


38. Holm, J and KB Heidelberg. 2016. Metagenomic evaluation of the microbial holobiome of the temperate Octocorals, Muricea californica and Muricea fruticosaprovides insight into the ecological roles of bacterial communities and their hosts. Front. Microbiol. (PDF)

37. Liu, Z, V Campbell, KB Heidelberg, DA Caron. 2016. Gene expression demonstrates different nutritional strategies among three mixotrophic protists. FEMS Microbiol. Ecol. DOI: fiw106. (PDF)


36. Liu, Z, AE Koid, R Terrado, V Campbell, DA Caron, KB Heidelberg. 2015. Changes in gene expression of Prymnesium parvum induced by nitrogen and phosphorus limitation. Front Microbiol. 6:631. doi: 10.3389/fmicb.2015.00631. (PDF)

35. Andrade, K. Logemann, J., KB Heidelberg, JB Emerson, LR Comolli, LA Hug, AJ Probst, A Keillar, BC Thomas, CS Miller, EE Allen, JM Moreau, JJ Brocks, JF Banfield. 2015. Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. ISME J. 1-15 (PDF)

34. Liu, Z, AC Jones, V Campbell, KD Hambright, KB Heidelberg, DA Caron. 2015. Gene expression in the mixotrophic prymnesiophyte, Prymnesium parvum, responds to prey availability. Front. Microbiol. 6:319. doi: 10.3389/fmicb.2015.00319 (PDF)

33. Tully, B, J Emerson, K Andrade, EE Allen, J Banfield, KB Heidelberg. 2015. De Novo Sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape. Archaea, 12 pages, doi:10.1155/2015/875784. (PDF)


32. Podell, S, JB Emerson, CM Jones, JA Ugalde, S Welch, KB Heidelberg, JF Banfield, EE Allen. 2014. Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J. 8:979-90. doi: 10.1038/ismej.2013.221. (PDF)

31. Tully B, R. Sanchdevah, KB Heidelberg, and JF Heidelberg. 2014. Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using environmentally derived genomes. Microbiome. 2:34. doi:10.1186/2049-2618-2-34. (PDF)

30. Koid, AE, Z Liu, R Terrado, AC Jones, DA Caron, KB Heidelberg. 2014. Comparative Transcriptome Analysis of Four Prymnesiophyte Algae. PLoS ONE 9(6): e97801. doi:10.1371/journal.pone.0097801. (PDF)

29. Kim, D and KB Heidelberg. 2014. USC Wrigley Institute for Environmental Studies Research Experiences for Undergraduates (REU): Coastal Ocean Processes Program Handbook for Mentors and REUs (provided as a resource for other REU programs).


28. Emerson, JB, BC Thomas, K Andrade, KB Heidelberg, and JF Banfield. 2013. New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake. Appl. Environ. Microbiol. 79: 6755-6764 doi: 10.1128/AEM.01946-13. (PDF)

27. Emerson, JB, K Andrade, BC Thomas, A Norman, EE Allen, KB Heidelberg, JF Banfield. 2013. Virus-host and CRISPR dynamics in hypersaline Lake Tyrrell, Victoria, Australia. Archaea.  2013:370871. doi: 10.1155/2013/370871. (PDF)

26. Heidelberg, KB, WC Nelson, JB Holm, N Eisenkolb, K Andrade, and J Emerson. 2013. Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia. Front.   Microbio. 4:115. doi:10.3389/fmicb.2013.00115. (PDF)

25. Podell, S, JA Ugalde, P Narasingarao, JF Banfield, KB Heidelberg, EE Allen. 2013. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS ONE 8: e61692. doi:10.1371/journal.pone.0061692. (PDF)

24. López-Lozano, NE, KB Heidelberg, WC Nelson, G Bonilla-Rosso, F Garcia-Oliva, LE Eguiarte and V Souza. 2013. Microbial secondary succession in soil microcosms of a desert oasis in the Cuatro Cienegas Basin, Mexico. Peer J. doi: 10.7717/peerj.47. (PDF)


23. Emerson, JB, BC Thomas, K. Andrade, EE Allen, KB Heidelberg, JF Banfield. 2012. Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl. Env. Microbiol. 78: 6309-6320. (PDF)

22. Koid, A, WC Nelson, A Mraz, KB Heidelberg. 2012. Comparative analysis of eukaryotic marine microbial assemblages from 18S rRNA gene and gene transcript clone libraries by using different methods of extraction. Appl. Env. Microbiol. 78: 3958-3965. (PDF)

21. Narasingarao, P, S Podell, JA Ugalde, C Brochier-Armanet, JB Emerson, JJ Brocks, KB Heidelberg, JF Banfield, EE Allen. 2012. De Novo Metagenomic Assembly Reveals Abundant Novel Major Lineage of Archaea in Hypersaline Microbial Communities. ISME J. 6:81–93. (PDF)


20. Heidelberg, KB. 2011. Octocorals and Ocean Acidification Studies at Catalina. Ocean Bights: Magazine of the Catalina Mar. Soc. 2:3-5. (PDF)


19. Heidelberg, KB, JA Gilbert, I Joint. 2010. Marine Genomics: At the Interface of Marine Microbial Ecology and Biodiscovery. J. Microb. Biotech. 3: 531-543. (PDF)

18. Heidelberg, KB, O’Neil, KL, JC Bythell, KP Sebens. 2010. Vertical distribution and diel patterns of zooplankton abundance and biomass at Conch Reef, Florida Keys (USA). J. Plank. Res. 32: 75-91. (PDF)

17. Mele, P, T Sawbridge, H Hayden, B Methe, T Stockwell, C Pfannkoch, M Lewis, D Tanenbaum, D Rusch and KB Heidelberg. 2010. How does surface soil geomorphology and land-use influence the soil microbial ecosystems in southeastern Australia? Insights gained from DNA sequencing of the soil metagenome. Proc. 19th World Congress of Soil Science, Soil Solutions for a Changing World. 1-6 August 2010, Brisbane, Australia. pp. 12-15. (PDF)

16. Thomas, T, D Rusch, MZ DeMaere, PY Yung, M Lewis, A Halpern, KB Heidelberg, S Egan, PD Steinberg, and S Kjelleberg. 2010. Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis. ISME J. 4: 1557-1567. (PDF)


15. Caron DA, AZ Worden, PD Countway, E Demir, KB Heidelberg. 2009. Protists are Microbes Too: A Perspective. ISME J. 3: 4-12. (PDF)

14. Caron, DA, RJ Gast, PD Countway, KB Heidelberg. 2009. Microbial Eukaryote Diversity and Biogeography. Microbe. 4:71-77. (PDF)

13. Edgcomb, VP, J Biddle, DA Caron, KB Heidelberg, PD Countway, A Teske. 2009.  New Frontiers: The Evaluation of Eukaryotic Populations in the Deep Marine Subsurface: Scientific Goals and Approaches for Future Ocean Drilling Projects. White Paper INVEST: IODP Renewal Meeting, University of Bremen, Germany, Sept. 23-25, 2009 (PDF)


12. Williamson, SJ, DB Rusch, S Yooseph, AL Halpern, KB Heidelberg, J Glass, C Andrews- Pfannkoch, D Fadrosh, C Miller, G Sutton, M Frazier and JC Venter. 2008.  The Sorcerer II  Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples. PLoS ONE. 3(1): e1456. doi:10.1371/journal.pone.0001456. (PDF)

11. Heidelberg, KB, A Allen, R Stepanauskas, F Yildiz, A Murray, M Sullivan, M Yakimov. 2008. Marine Molecular Microbiology - The Great Questions. Report for the Joint US/CIESM Workshop on Marine Genomics: At the Interface of Marine Microbial Ecology and Biotechnological Applications, Monaco 12-14 Oct 2008. (PDF)


10. Yooseph S, G Sutton, DB Rusch, AL Halpern, S Williamson, K Remington, JA Eisen, KB Heidelberg, G Manning, W Li, L Jaroszewski, P Cieplak, CS Miller, H Li, ST Mashiyama, MP Joachimiak, C van Belle, J-M Chandonia, DA Soergel, Y Zhai, K Natarajan, S Lee, BJ Raphael, V Bafna, R Friedman, SE Brenner, A Godzik, D Eisenberg, JE Dixon, SS Taylor, RL Strausberg, M Frazier, JC Venter. 2007. The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. PLoS Biol. 5(3):432-466. (Journal Cover). (PDF)

9. Rusch, DB, AL Halpern, G Sutton, KB Heidelberg, S Williamson, S Yooseph, D Wu, JA Eisen, JM Hoffman, K Remington, K Beeson, B Tran, H Smith, H Baden-Tillson, C Stewart, J Thorpe, J Freeman, C Andrews-Pfannkoch, JE Venter, K Li, S Kravitz, JF Heidelberg, T Utterback, Y-H Rogers, LI Falcón, V Souza, G Bonilla-Rosso, LE Eguiarte, DM Karl, S Sathyendranath, T Platt, E Bermingham, V Gallardo, G Tamayo-Castillo, MR Ferrari, RL Strausberg, K Nealson, R Friedman, M Frazier, JC Venter. 2007. The Sorcerer II Global Ocean Sampling Expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5(3):398-431.  e77.doi:10.1371/journal.pbio.0050077. (Journal Cover). (PDF)


8. Remington, KA, KB Heidelberg, JC Venter. 2005. Taking metagenomic studies in context. Trends Microbiol. 13: 404. (PDF)

7. Heidelberg KB, JF Heidelberg. 2005. Environmental genomics: new secrets from a mysterious ocean. Mar. Tech. Soc J.  39:94-98. (PDF)


6. Heidelberg KB, KP Sebens, JE Purcell. 2004. Composition and sources of near reef zooplankton on a Jamaican forereef, with implications for coral feeding. Coral Reefs. 23: 263-276. doi: 10.1007/s00338-004-0375-0. (PDF)


5. Heidelberg JF, KB Heidelberg, RR Colwell. 2002. Seasonality of Chesapeake Bay bacterioplankton species. Appl. Env. Microbiol. 68:5488-5497. doi:10.1128/AEM.68.11.5488-5497.2002. (PDF)

4. Heidelberg JF, KB Heidelberg, RR Colwell. 2002. Bacteria of the gamma-subclass Proteobacteria associated with zooplankton in Chesapeake Bay. Appl. Env. Microbiol. 68:5498-5507. doi: 10.1128/AEM.68.11.5498-5507.2002. (PDF)


3. Heidelberg, KB, KP Sebens and JE Purcell. 1997. Effects of prey escape behavior and water flow on prey capture by the scleractinian coral Meandrina meandrites, p. 1081-1086. In: HA Lessios and IG Macintyre (eds.) Proc. 8th Int. Coral Reef Symp. Vol. 2. Smithsonian Tropical Research Institute, Panama. (PDF)

2. Kreps T, JE Purcell, KB Heidelberg. 1997. Escape of the Ctenophore Mnemiopsis leidyi from the Scyphomedusa Predator Chrysaora quinquecirrha. Mar. Biol. 128:441-446. (PDF)

1. Ford MD, JH Costello, KB Heidelberg, JE Purcell. 1997. Swimming and feeding by the Scyphomedusa, Chrysaora quinquecirrha. Mar. Biol. 129: 355-362. (PDF)