Rocap Lab Website

Curtis, B. et al. 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492:59-65 doi:10.1038/nature11681

Ahlgren, N.A. and G. Rocap. 2012 Diversity and distribution of marine Synechococcus: multiple gene phylogenies for consensus classification and development of qPCR assays for sensitive measurement of clades in the ocean Frontiers in Aquatic Microbiology doi: 10.3389/fmicb.2012.00213

Rodríguez-Martínez, R., G. Rocap, R. Logares, S. Romac and R. Massana. 2012 Low Evolutionary Diversification in a Widespread and Abundant Uncultured Protist (MAST-4). Molecular Biology and Evolution 29 (5): 1393-1406. doi: 10.1093/molbev/msr303

Guannel, M. L., M. C. Horner-Devine and G. Rocap.  2011. Bacterial community composition differs with species and toxigenicity of the diatom Pseudo-nitzschia Aquatic Microbial Ecology, 64: 117-133. doi:10.3354/ame01513

Morris, R. M., B. Nunn, C. Frazar, D. Goodlett, Y.S. Ting and G. Rocap. 2010. Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction ISME Journal 4:673-685 (pdf)

Ong, H. C., S. W. Wilhelm, C. J. Gobler, G. Bullerjahn, M. A. Jacobs, J. McKay, E. H. Sims, W. G. Gillett, Y. Zhou, E. Haugen, G. Rocap, R. A. Cattolico. 2010 Analyses of the complete chloroplast genome sequences of two members of the Pelagophyceae:  Aureococcus anophagefferens CCMP1984 and Aureoumbra lagunensis CCMP1507 Journal of Phycology 46:602-615  (pdf)

Collins, R. E., G. Rocap, J. Deming. 2010. Persistence of bacterial and archaeal communities in sea ice through an Arctic winter. Environmental Microbiology 12:1828-1841 (pdf)

Adams, N. G., V. L. Trainer, G. Rocap, R.P. Herwig. L. Hauser. 2009. Genetic population structure of Pseudo-nitzschia (Bacillariophyceae) from the Pacific Northwest and the North Sea.  Journal of Phycology 45:1037-1045. (pdf)

Cattolico, R.A. M. A. Jacobs, Y. Zhou, J. Chang, M. Duplessis, T. Lybrand, J. McKay, H.C. Ong, E. Sims, and G. Rocap. 2008.  Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES 293 (West Pacific) strains BMC Genomics 9:211 doi:10.1186/1471-2164-9-211  (pdf)

Hubbard, K. A. G. Rocap and E. V. Armbrust. 2008  Inter- and intra-specific community structure within the diatom genus Pseudo-nitzschia (Bacillariophyceae).  Journal of Phycology 44: 637-649 (pdf)

Collins, R.E. and G. Rocap. 2007 REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis.  Nucleic Acids Research 35 (Web server issue): W58-W62; (pdf)

Ahlgren, N. A. and G. Rocap. 2006. Culture isolation and culture-independent clone libraries reveal new marine Synechococcus ecotypes with distinctive light and N physiologies. Applied and Environmental Microbiology 72: 7193-7204. PDF file (752 kb)

Fuchsman, C. A. and G. Rocap. 2006. Whole genome reciprocal BLAST analysis reveals Planctomycetes do not share an unusually high number of genes with Eukarya and Archaea. Applied and Environmental Microbiology 72:6841-6844 PDF file (214 kb)

Van Mooy, B.A.S., G. Rocap, H. F. Fredricks, C. T. Evans and A. H. Devol. 2006. Sulfolipids dramatically decrease phosphorus demand by picocyanobacteria in oligotrophic marine environments. PNAS. 103:8607-8612. PDF file (856 kb)

Ahlgren, N. A., G. Rocap, and S. W. Chisholm. 2005. Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies Environmental Microbiology 8: 441-454 PDF file (257 kb)

Saito, M. A., G. Rocap, and J. W. Moffett. 2005. Production of Cobalt Binding Ligands in a Synechococcus Feature at the Costa Rica Upwelling Dome. Limnology and Oceanography 50: 279-290. PDF file (380 kb)

Rocap, G., F. W. Larimer, J. Lamerdin, S. Malfatti, P. Chain, N. A. Ahlgren, A. Arellano, M. Coleman, L. Hauser, W. R. Hess, Z. I. Johnson, M. Land, D. Lindell, A. F. Post, W. Regala, M. Shah, S. L. Shaw, C. Steglich, M. B. Sullivan, C. S. Ting, A. Tolonen, E. A. Webb, E. R. Zinser and S. W. Chisholm. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047. PDF file (430 kb)
Supplementary Information (418 kb)

Rocap, G., D. L. Distel, J. B.Waterbury and S. W. Chisholm. 2002. Resolution of Prochlorococcus and Synechococcus ecotypes using 16S-23S rRNA internal transcribed spacer (ITS) region sequences. Applied and Environmental Microbiology, 68: 1180-1191. PDF file (362 kb)

Ting, C. S., G. Rocap, J. King and S. W. Chisholm. 2002. Cyanobacterial Photosynthesis in the Oceans: Origins and Significance of Divergent Light Harvesting Strategies. Trends in Microbiology. 10:134-142. PDF file (136 kb)

Moore, L. R., A. F. Post, G. Rocap and S. W. Chisholm. 2002. Differential nitrogen utilization of the marine cyanobacteria Prochlorococcus and Synechococcus. Limnology and Oceanography 47: 989-996. PDF file (178 kb).

Hess, W. R., G. Rocap, C. S. Ting, F. W. Larimer, S. Stilwagon, J. Lamerdin and S. W. Chisholm. 2001. The photosynthetic apparatus of Prochlorococcus - a genomic perspective. Photosynthesis Research, 70:53-71. PDF file (717 kb)

Ting, C., G. Rocap, J. King and S. W. Chisholm. 2001. Phycobiliprotein genes of the marine prokaryote Prochlorococcus: Evidence for rapid evolution of genetic heterogeneity. Microbiology 147: 3171-3182. PDF file (1.6 Mb)

Rocap, G., L. R. Moore and S. W. Chisholm. 1999. Molecular Phylogeny of Prochlorococcus ecotypes. in Marine Cyanobacteria, L. Charpy and A. W. D. Larkum ed. Bulletin de líInstitute Océanographique, Monaco, special issue No. 19. pp. 107-116. PDF file (548 kb)

Moore, L. R., G. Rocap and S. W. Chisholm. 1998. Physiology and Molecular Phylogeny of Coexisting Prochlorococcus ecotypes. Nature 393: 464-467. PDF file (345 kb)

 
Relevant Publications

Ahlgren, N. A. and G. Rocap. 2006. Culture isolation and culture-independent clone libraries reveal new marine Synechococcus ecotypes with distinctive light and N physiologies. Applied and Environmental Microbiology 72: 7193-7204. PDF file (752 kb)

Ahlgren, N. A., G. Rocap, and S. W. Chisholm. 2005. Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies Environmental Microbiology   doi: 10.1111/j.1462-2920.2005.00910.x PDF file (257 kb)

As part of the Pacific Northwest Center for Human Health and Ocean Sciences we are studying the distributions of the pennate diatom Pseudo-nitzschia in Puget Sound and coastal Washington waters. Some species of Pseudo-nitzschia produce domoic acid, a toxin that can result in amnesiac shellfish poisoning. The goal of our research is to use molecular markers to distinguish different species and understand the environmental factors that trigger production of domoic acid. Michele Wrabel's research seeks to understand the interaction between microbial community composition and domoic acid production in Pseudo-nitzschia. Gwendolyn Hannam assisted with this project. Diana Haring received an Oceans and Human Health REU fellowship in 2008 to study Pseudo-nitzschia in the Benguela Upwelling.  Ben Johnson's REU fellowship involved the hunt for Pseudo-nitzschia viruses, and Michael Carlson is continuing this work.

Funded by the National Institute of Environmental Health Sciences (NIEHS) and the National Science Foundation (NSF)

Collaborators: Dr. Ginger Armbrust, Dr Monica Orellana, Dr. Micaela Parker and Kate Hubbard.

More info on the Center:

• Center website

• Other Centers for Oceans and Human Health

• Human Health and Ocean Studies seminar schedule (pdf)

Relevant Links:

• Latest levels of domoic acid in razor clams from the Washington Department of Fish and Wildlife

• Check beach closures due to biotoxins at the Washington Department of Health
  

Relevant Publications:

Chloroplasts, organelles derived from once free-living cyanobacteria, are the power behind all photosynthetic eukaryotes, from diatoms to oak trees. We are sequencing the chloroplast genomes from 30 algal species to better understand the evolution of the non-chlorophyll b-containing photosynthetic lineage. Cedar McKay provides the bioinformatics for this project.

This project is a collaboration with Dr. Rose Ann Cattolico, UW Biology and Dr. Mike Jacobs at the UW Genome Center. Funding from NSF microbial genome program and Assembling the Tree of Life program.

The Stramenopile Chloroplast Genome Project

Relevant Publications 

Cattolico, R.A. M. A. Jacobs, Y. Zhou, J. Chang, M. Duplessisi, T. Lybrand, J. McKay, H.C. Ong, E. Sims, and G. Rocap. 2008.  Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES 293 (West Pacific) strains BMC Genomics doi:10.1186/1471-2164-9-211  (pdf)

Relevant Links:

• The Provasoli-Guillard National Center for Culture of Marine Phytoplankton
• Chloroplast Genome DB
• Organellar genomics at JGI
• GOBASE Organelle Genome Database

The Department of Energy supported the complete genome sequencing of two strains of Prochlorococcus under the auspices of the Microbial Genome Program. The two strains, MED4 and MIT9313 were chosen because they represent the two ends of the spectrum of physiologically and genetically distinct strains available in culture.

Published Marine cyanobacterial genome pages:

Prochlorococcus MED4
Prochlorococcus MIT 9313
Prochlorococcus SS120
Synechococcus WH8102

Useful Microbial Genomics Links:

Comprehensive Microbial Resource
Integrated Microbial Genomes
CyanoBase

Relevant Publications:

Isolated strains of the genus Prochlorococcus can be divided into two main groups based on their pigment content and light dependent physiology. These two groups correspond to phylogenetic groupings as defined by the16S rRNA, and can be further subdivided genetically into two high light adaptedecotypes and four low light adapted ecotypes.   We are using real-timequantitative PCR to determine the abundances of all 6 ecotypes of Prochlorococcus in natural samples.  By examining the distributions of the differentecotypes over a variety of seasonal and spatial scales we hope to understandthe environmental factors that have driven the genetic differentiation withinthis genus.  Both Nathan Ahlgren and Cedar McKay are involved in this project.

 

Research in the lab focuses on the evolution and ecology of marine bacteria and phytoplankton. We use a variety of approaches in the lab; physiological (growth experiments and pigment analyses), molecular (quantitative PCR, sequencing and expression assays) and computational (phylogenetic analyses, comparative genomics). The multiple projects in the lab all address common questions: How does genetic diversity arise in marine microbial populations, how is it maintained, and how does it influence ecological success. See the links at the right for more details about individual projects.