Camille Daniels

Research and Interests

I currently use metranscriptomics to describe function in reef-building corals and their associates through the lens of pathogenic infection. We have established a holobiont centric RNASeq workflow to determine global gene expression patterns across the coral metaorganism (i.e. coral, symbiotic algae, and bacteria compartments), and compare healthy specimens and those with phenotypic presentation of a previously described 'bacterial' infection, White Plague Disease. This approach allows us to link specific gene functions associated with this disease to specific taxa and resolve any interplay occurring between holobiont members.

A second project explores coral larval settlement and the functional role of gene transfer agents (GTAs). GTAs are non-lytic, phage-like particles that package host material, and are produced by marine Alphaprotebacteria. These particles promote enhanced settlement of coral larvae onto biofilms. RNASeq data is also employed to identify differentially expressed genes between control and GTA treatments from settlement assays to determine the mechanism(s) involved in larval settlement, and if cross-kingdom signalling plays a role.

My interests are in working with non-model organisms and microbial communities to address functional questions in the marine environment. 

Work History

Work History
Feb 2012 - Mar 2015

Post Doctoral Fellow

King Abdullah University of Science and Technology (KAUST)

Red Sea Research Center

Coral Reef Genomics Lab

PI: Dr. Christian Voolstra


Aug 2006 - Dec 2011


University of South Florida

Dissertation: Microbial Landscapes of Cnidarians and Ctenophores

Major Professor: Dr. Mya Breitbart

Aug 2003 - Aug 2005


University of South Florida

Thesis: Reef Assessment: An Index for Utilizing Reef Sediments

Major Professor: Dr. Pamela Hallock-Muller

Aug 1997 - May 2002


Louisiana State University


McKnight Doctoral Fellow, Florida Education Fund, (2006-2011)

Bridge to the Doctorate Endowed Fellow, USF College of Marine Science, (2006-2008)

Gulf Oceanic Trust Fellow, USF College of Marine Science, (2006-2007)

FS-LAMP Bridge to the Doctorate Project NSF Fellow, USF College of Marine Science (2004-2006)


McDaniel, L., Daniels, C., Baumgarten, S., Henderson, T., Ritchie, K.B., Paul, J., and C.R. Voolstra. (submitted). Gene transfer agents from a marine alphaproteobacteria selectively package mobile genetic elements and transporters. PNAS.

Daniels, C., Bayer, T., Roder, C., Arif, C., Baumgarten, S., Aranda, M.C., Michell, C., Weil, E., and C.R. Voolstra. 2015. Metatranscriptome analysis of the reef-building coral, Orbicella faveolata, indicates holobiont response to coral disease. Frontiers In Marine Science.

Antunes, A., Alam, I., Simes, M.F., Daniels, C., Ferreira, A.J.S., El-Dorry, H., Siam, R., and V.B. Bajic. 2015. First insights on the viral communities of the deep-sea anoxic brines of the Red Sea. Genomics, Proteomics & Bioinformatics. doi:10.1016/j.gpb.2015.06.004

Arif, C., Daniels, C., Bayer, T., Banguera-Hinestroza, E., Howe, C., LaJeunesse, T., and C.R. Voolstra. 2014. Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region. Molecular Ecology 23(17): 4418-33. doi: 10.1111/mec.12869

Burghart, S., Van Woudenberg L., Daniels, C., Meyers, S.D., Peebles, E.B., and M. Breitbart. 2014. Disparity between planktonic fish egg and larval communities as indicated by DNA barcoding. Marine Ecology Progress Series 503:195-204. doi: 10.3354/meps10752

Roder, C., Arif, C., Daniels, C., Weil E., and C.R. Voolstra. 2014. Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome. Molecular Ecology 23(4): 965-74. doi: 10.1111/mec.12638

Roder, C., Arif, C., Bayer, T., Aranda, M, Daniels, C., Shibl, A., Chavanich, S. and C.R. Voolstra. 2013. Bacterial profiling of White Plague Disease (WPD) in a comparative framework. ISME Journal 8: 31-39. doi: 10.1038/ismej.2013.127

Daniels, C. and M. Breitbart. 2012. Microbial communities associated with the ctenophore, Mnemiopsis leidyi. FEMS Microbiology Ecology 82(1): 90-101. doi:10.1111/j.1574-6941.2012.01409

Nitti, A., Daniels, C., Siefert, J., Souza, V., Hollander, D., and M. Breitbart. 2012. Spatially-resolved genomic, molecular organic, and stable isotopic analyses of an actively accreting freshwater microbialite from Cuatro Ciénegas, Mexico. Astrobiology 12(7): 685-698. doi:10.1089/ast.2011.0812

Daniels, C., Zeifman, A., Heym, K., Ritchie, K.B., Watson, C.A., Berzins, I., and M. Breitbart. 2011. Spatial heterogeneity in bacterial communities associated with Montastraea annularis. Marine Ecology Progress Series 426: 29-40. doi:10.3354/meps09024

Selected Presentations

Oral Presentation

November 2013- Transcriptomic landscape of the coral holobiont in White Plague Disease

KAUST Bioscience Seminar Series, Thuwal, Saudi Arabia

February 2013- Novel Effects of Gene Transfer Agents in the Reef Environment

(Paul, JH; Young, EC; McDaniel, LD; Daniels, CA; Voolstra, CR; Ritchie, KB)

American Society of Limnology and Oceanography (ASLO) meeting, New Orleans, LA

July/August 2012- Transcriptomic landscape of the coral holobiont in White Plague Disease

International Coral Reef Conference (ICRS), Carins, Australia

Argonne National Laboratory, Chicago, Illinois

Oct 2010- Bacterial Communities Associated With Mnemiopsis leidyi*

*Outstanding Student Presentation (1st place)

Florida Branch of the American Society for Microbiology Meeting, Islamorada, FL     

July 2008/Jan 2009- Bacterial Community Profiling for Coral Restoration

International Coral reef Symposium (ICRS), Fort Lauderdale, FL   

American Society for Limnology and Oceanography (ASLO) Aquatic Sciences Meeting, Nice, France                                                                                                               

Feb 2006- Bridge to the Doctorate: A Student Perspective

National Science Foundation Joint Annual Meeting, Washington, DC (panelist)   


August 2012- Transcriptomic landscape of the coral holobiont in White Plague Disease

International Society for Microbial Ecology (ISME), Copenhagen, Denmark

Aug 2010- Bacterial Communities Associated With Mnemiopsis leidyi

International Society for Microbial Ecology (ISME-13) Meeting, Seattle, WA

Apr 2007- From Culture to Transplantation: Microbial Profiling for Coral Restoration

Small Matters: Microbes and Their Role In Conservation Sympoisum, American Musuem

of Natural History Center for Biodiversity, New York, NY

Teaching/Mentoring Experience

2012-2014: Supervising KAUST PhD student (Chatchanit Arif) on Red Sea coral symbiont diversity project. Molecular Ecology article published and student completed PhD in Dec 2014.

2008-12: Training undergraduates in molecular techniques. One student is a co-author on the Marine Ecology Progress Series manuscript mentioned above, and graduated in 2011. A second student assisted on a biogeographic study of bacterial communities and associated with Pocillopora damicornis, and is now pursuing an M.S.

Research Cruises

Sept 2009- R/V HSBC Atlantic Explorer : Large scale seawater collections and tangential flow filtration to obtain viral concentrates from Bermuda Atlantic Time Series sites for a viral diversity project

May 2008- R/V Bellows : Coral mucus collection at reef sites in Dry Tortugas National Park, Florida

Laboratory Techniques


Nucleic Acid Extraction/PCR/Cloning

Community Profiling

 - Automated Ribosomal Intergenic Spacer Analysis (ARISA)

 - Terminal Restriction Fragment Length Polymorphism (T-RFLP)

 - 454 pyrosequencing (bacterial 16S and algal ITS2 genes)

Bacterial Culturing

Tangential Flow Filtration

Epifluorescence Microscopy

Selected Software

Bowtie2, eXpress, DeSeq/edgeR (RNASeq analysis)

Mothur  (community analysis for pyrosequencing data sets)

CLC Genomics Workbench, Codon Code Aligner (genomics/sequence) 

PeakScanner(Size calling software for community profiling data)

PRIMER (Ecological Statistics package)

EndNote, Corel DRAW



UNIX, Perl (novice in both)


Christian Voolstra, PhD

(Faculty supervisor)

KAUST Red Sea Research Center

Building 2, 2226

Thuwal, Saudi Arabia


office: +966 02 808 2377

Mya Breitbart, PhD

(PhD major professor)

University of South Florida

College of Marine Science

140 7th Avenue SouthSt. Petersburg, Florida 33701

office: +1 (727) 553-3520

Pam Hallock-Muller, PhD

(PhD committee member)

University of South Florida

College of Marine Science

140 7th Avenue South

St. Petersburg, Florida 33701

office: +1 (727) 553-1567

Kim Ritchie, PhD

(PhD committee member)

Mote Marine Laboratory

1600 Ken Thompson Parkway

Sarasota, Florida 34236

office: +1 (941) 388-4441