Research

warning: Creating default object from empty value in /mount/ebs/www/html/modules/taxonomy/taxonomy.pages.inc on line 33.
All about our research

Publications

 

Sohm, J. A., Ahlgren, N. A., Thomson, Z., Williams, C., Moffett, J.W., Saito, M.A., Webb, E.A., and G. Rocap. Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients, and iron. ISME Journal in press doi: 10.1038/ismej.2015.115

Saunders, J. K. and G. Rocap. Arsenic detoxification strategies vary with environmental phosphate concentrations in global Prochlorococcus populations. ISME Journal in press doi:10.1038/ismej.2015.85

Guannel, M. L., Haring, D, Twiner, M.J., Wang, Z., Noble, A., Lee, P., Saito, M.A., and G. Rocap. 2015. Toxigenicity and biogeography of the diatom Pseudo-nitzschia across distinct environmental regimes in the South Atlantic Ocean. Marine Ecology Progress Series 526:67-87 doi:10.3354/meps11027

Gruber, A., G. Rocap, P. G. Kroth, E. V. Armbrust and T. Mock.  2015. Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage. The Plant Journal 81: 519-528 DOI: 10.1111/tpj.12734

Ahlgren, N. A., Noble A., Patton, A.P., Roache-Johnson, K., Jackson, L., Robinson, D., McKay, C., Moore, L.R., Saito, M.A. and G. Rocap. 2014. The unique trace metal and mixed layer conditions of the Costa Rica upwelling dome support a distinct and dense community of Synechococcus. Limnology and Oceanography 59(6), 2014, 2166-2184 | DOI: 10.4319/lo.2014.59.6.2166

Biller, S.J., Berube, P. M., Berta-Thompson, J. W., Kelly, L., Roggensack, S.E., Awad, L., Roache-Johnson, K. H., Ding, H., Giovannoni, S. J., Rocap, G., Moore, L.R. and S. W. Chisholm. 2014. Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus Scientific Data 1, Article number: 140034 ​doi:10.1038/sdata.2014.34

Starkenburg, S.R., Kwon, K.J., Jha, R.A., McKay, C., Jacobs, M. Chertkov, O., Twary, S., Rocap, G. and Cattolico, R.A. 2014. A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes. BMC Genomics, 15:212  (2014) doi:10.1186/1471-2164-15-212

Nahas Reistetter, E., Krumhardt, K., Callnan, K., Roache-Johnson, K., Saunders, J. Moore, L. R. and G. Rocap. 2013. Effects of phosphorus starvation versus limitation on the marine cyanobacterium Prochlorococcus MED4 II: gene expression. Environmental Microbiology doi:10.1111/1462-2920.12129 (pdf)

Krumhardt, K., Callnan, K., Roache-Johnson, K., Swett, T., Robinson, D., Nahas Reistetter, E., Saunders, J. Rocap, G. and L. R. Moore. 2013. Effects of phosphorus starvation versus limitation on the marine cyanobacterium Prochlorococcus MED4 I: Uptake Physiology. Environmental Microbiology doi:10.1111/1462-2920.12079 (pdf)

Rodríguez-Martínez, R., G. Rocap, G. Salazar and R. Massana. 2013. Biogeography of the uncultured marine picoeukaryote MAST-4: temperature-driven distribution patterns. ISME Journal doi:10.1038/ismej.2013.53 (pdf)

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

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 (pdf)

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 (pdf)

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)

Diversity

Growing Cultures

The unicellular marine Cyanobacteria Prochlorococcus and Synechococcus are closely related genera that are extremely abundant in open ocean waters and account for a significant portion of global primary production.  Both groups consist of multiple physiological and genetic types.   We are using parts of the ribosomal RNA operon as a neutral marker to investigate the phylogenetic relationships of strains within each genus, and attempt to correlate the genetic diversity with observed physiological diversity.  We have developed real-time quantitative PCR assays to specifically enumerate ecotypes of both Prochlorococcus and Synechococcus in natural samples.  By examining the distributions of the different ecotypes over a variety of seasonal and spatial scales we hope to understand the environmental factors that have driven the genetic differentiation we observe. 

 
Specific Projects:

Identification, enumeration and biogeography of ecotypes of Prochlorococcus and Synechococcus (led by Nathan Ahlgren, in collaboration with Jill Sohm and Eric Webb)

Diversity of bacterial communities in a seasonally hypoxic fjord, Hood Canal Washington, using 454 tag sequencing (part of International Census Of Marine Microbes, in collaboration with Claire Horner-Devine)

Biogeography of the uncultured marine heterotrophic protist group MAST-4 (led by Raquel Rodriquez-Martinez, in collaboration with Ramon Massana)

Function

 

 

Pn_australis

 


Specific Projects:

  • Phosphorus uptake, physiology and gene expression in Prochlorococcus (in collaboration with Lisa Moore)
  • Arsenic detoxification strategies in marine cyanobacteria  (led by Jaci Saunders)
  • Shotgun proteomics to assess community function in the field and response to stress in cultured experiments (in collaboration with Bob Morris)

Evolution

 

 


Specific Projects

Genome evolution of the marine cyanobacteria (Nathan Ahlgren)

Comparative genomics of archaea and bacteria to gain insight into the role of lateral transfer in environmental adaptations (led by Clara Fuchsman)

Resolving the relationships of the many classes of of the heterokont algae, using organelle genome sequences (part of an Assembling the Tree of Life project, in collaboration with Rose Ann Cattolico)

Evolutionary relationships of Pseudo-nitzschia species  (Michele Guannel)

 

Distribution of Ecotypes

 

QPCR 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

 

We study 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).  A major focus of the lab are the unicellular marine Cyanobacteria Prochlorococcus and Synechococcus, closely related genera that are extremely abundant in open ocean waters and account for a significant portion of global primary production. We also study the toxic diatom Pseudo-nitzschia, and are developing a virus-host system to understand the role viral lysis may play in the outbreak or supression of toxic blooms.

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.

Syndicate content