Worden lab publications

Submitted publications

Cuvelier ML, Ortiz AC, van Baren MJ, Guo J, Tariq MA, Partensky F & AZ Worden (submitted). Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress.

2016

Clayton SC, Lin Y-C, Follows MJ & AZ Worden (2016). Co-existence of distinct Ostreococcus ecotypes at an oceanic front. Limnology & Oceanographydoi:10.1002/lno.10373
Caron DA, Alexander H, Allen AE, Archibald JM, Armbrust EV, Bachy C, Bharti A, Dyhrman ST, Guida S, Heidelberg KB, Kaye JZ, Metzner J, Smith SR, & AZ Worden (in press). Insights into the evolution, ecology and physiology of marine protists from transcriptomic analyses. Nature Reviews Microbiology.
Gawryluk R, del Campo J, Okamoto N, Strassert JFH, Lukes J, Richards TA, Worden AZ, Santoro AE & PJ Keeling (in press). Morphological identification and single-cell genomics of marine diplonemids. Current Biology.
van Baren, Marijke J., Charles Bachy, Emily Nahas Reistetter, Samuel O. Purvine, Jane Grimwood, Sebastian Sudek, Hang Yu, Camille Poirier, Thomas J. Deerinck, Alan Kuo, Igor V. Grigoriev, Chee-Hong Wong, Richard D. Smith, Stephen J. Callister, Chia-Lin Wei, Jeremy Schmutz and Alexandra Z. Worden. “Evidence-Based Green Algal Genomics Reveals Marine Diversity and Ancestral Characteristics of Land Plants.” BMC Genomics 17 (2016): 1–22. doi:10.1186/s12864-016-2585-6.
Simmons, MP., Sebastian Sudek, Adam Monier, Alexander J. Limardo, Valeria Jimenez, Christopher R. Perle, Virginia A. Elrod, J. Timothy Pennington, and Alexandra Z. Worden (2016). Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the Eastern North Pacific Ocean. Applied and Environmental Microbiology. doi:10.1128/AEM.02730-15.
Monier A, Worden AZ & TA Richards (2016). Phylogenetic diversity and biogeography of the Mamiellophyceae lineage of eukaryotic marine phytoplankton across the oceans. Environmental Microbiology Reportsdoi:10.1111/1758-2229.12390.
Orsi WD, Smith JM, Liu S, Liu Z, Sakamoto CM, Wilken S, Poirier C, Richards TA, Keeling PJ, Worden AZ & AE Santoro (2016). Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean. The ISME Journal. doi:10.1038/ismej.2016.20.
Waltman PH, Guo J, Reistetter EN, Purvine S, van Baren MJ, Ansong CK, Wong CH, Wei C-L, Smith RD, Callister SJ, Stuart JM & AZ Worden (2016). Identifying aspects of the post-transcriptional program governing the proteome of the green alga Micromonas. PLoS One. doi:10.1371/journal.pone.0155839.

2015

Derelle, E., Monier, A., Cooke, R., Worden, A. Z., Grimsley, N. H., & Moreau, H. (2015). Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus. Journal of Virology, 89(11), 5812–5821. http://doi.org/10.1128/JVI.00246-15
Limardo, A. J., & Worden, A. Z. (2015). Microbiology: Exclusive networks in the sea. Nature, 522(7554), 36–37.
Orsi, W. D., Smith, J. M., Wilcox, H. M., Swalwell, J. E., Carini, P., Worden, A. Z., & Santoro, A. E. (2015). Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. ISME J, 9(8), 1747–1763.
Ribalet, F., Swalwell, J., Clayton, S., Jiménez, V., Sudek, S., Lin, Y., Johnson, Z. I., Worden, A. Z., & Armbrust, E. V. (2015). Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre. Proceedings of the National Academy of Sciences, 112(26), 8008–8012. http://doi.org/10.1073/pnas.1424279112
Ševčíková, T., Horák, A., Klimeš, V., Zbránková, V., Demir-Hilton, E., Sudek, S., Jenkins, J., Schmutz, J., Přibyl, P., Fousek, J., Vlček, Č., Lang, B. F., Oborník, M., Worden, A. Z., & Eliáš, M. (2015). Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte? Scientific Reports, 5, 10134.
Simmons, M. P., Bachy, C., Sudek, S., van Baren, M. J., Sudek, L., Ares Jr., M., & Worden, A. Z. (2015). Intron invasions trace algal speciation and reveal nearly identical Arctic and Antarctic Micromonas Populations. Molecular Biology and Evolution, 32(9), 2219–2235. http://doi.org/10.1093/molbev/msv122
Sudek, S., Everroad, R. C., Gehman, A. M., Smith, J. M., Poirier, C. L., Chavez, F. P., & Worden, A. Z. (2015). Cyanobacterial distributions along a physico-chemical gradient in the Northeastern Pacific Ocean. Environmental Microbiology. http://doi.org/10.1111/1462-2920.12742
Worden, A. Z., Follows, M. J., Giovannoni, S. J., Wilken, S., Zimmerman, A. E., & Keeling, P. J. (2015). Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes. Science, 347(6223). http://doi.org/10.1126/science.1257594

2014

Bachy, C., & Worden, A. Z. (2014). Microbial ecology: Finding structure in the rare biosphere. Current Biology, 24, R315–R317. http://doi.org/10.1016/j.cub.2014.03.029
Duanmu, D., Bachy, C., Sudek, S., Wong, C.-H., Jiménez, V., Rockwell, N. C., Martin, S. S., Ngan, C. Y., Reistetter, E. M., van Baren, M. J., Price, D. C., Wei, C.-L., Reyes-Prieto, A., Lagarias, J. C., & Worden, A. Z. (2014). Marine algae and land plants share conserved phytochrome signaling systems. Proceedings of the National Academy of Sciences, 111, 15827–15832. http://doi.org/10.1073/pnas.1416751111
Keeling, P. J., Burki, F., Wilcox, H. M., Allam, B., Allen, E. E., Amaral-Zettler, L. A., Armbrust, E. V., Archibald, J. M., Bharti, A. K., Bell, C. J., Beszteri, B., Bidle, K. D., Cameron, C. T., & Worden, A. Z. (2014). The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biology. http://doi.org/10.1371/journal.pbio.1001889
McRose, D., Guo, J., Monier, A., Sudek, S., Wilken, S., Yan, S., Mock, T., Archibald, J. M., Begley, T. P., Reyes-Prieto, A., & Worden, A. Z. (2014). Alternatives to vitamin B1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages. The ISME Journal, 8, 2517–2529. http://doi.org/10.1038/ismej.2014.146
Rockwell, N. C., Duanmu, D., Martin, S. S., Bachy, C., Price, D. C., Bhattacharya, D., Worden, A. Z., & Lagarias, J. C. (2014). Eukaryotic algal phytochromes span the visible spectrum. Proceedings of the National Academy of Sciences, 111, 3871–3876. http://doi.org/10.1073/pnas.1401871111

2013

Monier, A., Sudek, S., Fast, N. M., & Worden, A. Z. (2013). Gene invasion in distant eukaryotic lineages: discovery of mutually exclusive genetic elements reveals marine biodiversity. ISME Journal, 7, 1764–1774. http://doi.org/10.1038/ismej.2013.70
Read, B. A., Kegel, J., Klute, M. J., Kuo, A., lefebvre, S. C., Maumus, F., Mayer, C., Miller, J., Monier, A., Salamov, A., Young, J., Aguilar, M., Claverie, J. M., Frickenhaus, S., Gonzalez, K., Herman, E. K., lin, Y. C., Napier, J., Ogata, H., Sarno, A. F., Shmutz, J., Schroeder, D., de Vargas, C., Verret, F., von Dassow, P., Valentin, K., Van de Peer, Y., Wheeler, G., Emiliania huxleyi Annotation Consortium, dacks, J. B., Delwiche, C. F., dyhrman, S. T., Glockner, G., John, U., Richards, T., Worden, A. Z., Zhang, X., & Grigoriev, I. V. (2013). Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature, 499, 209–213. http://doi.org/10.1038/nature12221
Santoro, A. E., Sakamoto, C. M., Smith, J. M., Plant, J. N., Gehman, A. L., Worden, A. Z., Johnson, K. S., Francis, C. A., & Casciotti, K. L. (2013). Measurements of nitrite production and nitrite-producing organisms in and around the primary nitrite maximum in the central California Current. Biogeosciences Discussions, 10, 5803–5840. http://doi.org/10.5194/bgd-10-5803-2013
Vergin, K. L., Beszteri, B., Monier, A., Thrash, J. C., Temperton, B., Treusch, A. H., Kilpert, F., Worden, A. Z., & Giovannoni, S. J. (2013). High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-Series Study site by phylogenetic placement of pyrosequences. ISME Journal, 7, 1322–32. http://doi.org/10.1038/ismej.2013.32

2012

Curtis, B. A., Tanifuji, G., Burki, F., Gruber, A., Irimia, M., Maruyama, S., Arias, M. C., Ball, S. G., Gile, G. H., Hirakawa, Y., Hopkins, J. F., Kuo, A., Rensing, S. A., Schmutz, J., Symeonidi, A., Elias, M., Eveleigh, J. M., Herman, E. K., Klute, M. J., Nakayama, T., Obornik, M., Reyes-Prieto, A., Armbrust, E. V., Aves, S. J., Beiko, R. G., Coutinho, P., Dacks, J. B., Durnford, D. G., Fast, N. M., Green, B. R., Grisdale, C. J., Hempel, F., Henrissat, B., Höppner, M. P., Ishida, K.-I., Kim, E., Kořený, L., Kroth, P. G., Liu, Y., Malik, S.-B., Maier, U. G., McRose, D., Mock, T., Neilson, J. A. D., Onodera, N. T., Poole, A. M., Pritham, E. J., Richards, T. A., Rocap, G., Roy, S. W., Sarai, C., Schaack, S., Shirato, S., Slamovits, C. H., Spencer, D. F., Suzuki, S., Worden, A. Z., Zauner, S., Barry, K., Bell, C., Bharti, A. K., Crow, J. A., Grimwood, J., Kramer, R., Lindquist, E., Lucas, S., Salamov, A., McFadden, G. I., Lane, C. E., Keeling, P. J., Gray, M. W., Grigoriev, I. V., & Archibald, J. M. (2012). Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature, 492, 59–65. http://doi.org/10.1038/nature11681
Lin, Y. C., Campbell, T., Chung, C. C., Gong, G. C., Chiang, K. P., & Worden, A. Z. (2012). Distribution patterns and phylogeny of marine stramenopiles in the North Pacific Ocean. Applied and Environmental Microbiology, 78, 3387–3399.
Monier, A., Welsh, R. M., Gentemann, C., Weinstock, G., Sodergren, E., Armbrust, E. V., Eisen, J. A., & Worden, A. Z. (2012). Phosphate transporters in marine phytoplankton and their viruses: Cross-domain commonalities in viral-host gene exchanges. Environmental Microbiology, 14, 162–176. http://doi.org/10.1111/j.1462-2920.2011.02576.x
Worden, A. Z., Janouskovek, J., McRose, D., Engman, A., Welsh, R. M., Malfatti, S., Tringe, S. G., & Keeling, P. J. (2012). Global distribution of a wild alga revealed by targeted metagenomics. Current Biology, 22, R675–R677. http://doi.org/10.1016/j.cub.2012.07.054

2011

Demir-Hilton, E., Sudek, S., Cuvelier*, M. L., Gentemann, C. L., Zehr, J. P., & Worden, A. Z. (2011). Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus. The ISME Journal, 5, 1095–1107. http://doi.org/10.1038/ismej.2010.209
Kim, E.*, Harrison, J. W.*, Sudek, S.*, Jones, M. D. M., Wilcox, H. M., Richards, T. A.**, Worden, A. Z.**, & Archibald, J. M.** (2011). Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proceedings of the National Academy of Sciences, 109, 1469–1500. http://doi.org/10.1073/pnas.1013337108 *co-first authors **corresponding authors
Paerl, R. W., Johnson, K. S., Welsh, R. M., Worden, A. Z., Chavez, F. P., & Zehr, J. P. (2011). Differential distributions of Synechococcus subgroups across the California current system. Frontiers in Aquatic Microbiology, 2, http://doi.org/10.3389/fmicb.2011.00059
Treusch, A. H., Demir-Hilton, E., Vergin, K. L., Worden, A. Z., Carlson, C. A., Donatz, M. G., Burton, R. M., & Giovannoni, S. J. (2011). Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids. ISME Journal. http://doi.org/10.1038/ismej.2011.117

2010

Cuvelier, M. L., Allen, A. E., Monier, A., McCrow, J. P., Messié, M., Tringe, S. G., Woyke, T., Welsh, R. M., Ishoey, T., Lee, J. H., Binder, B. J., DuPont, C. L., Latasa, M., Guigand, C., Buck, K. R., Hilton, J., Thiagarajan, M., Caler, E., Read, B., Lasken, R. S., Chavez, F. P., & Worden, A. Z. (2010). Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences, 107, 14679–14684.
McDonald, S. M., Plant, J. N., & Worden, A. Z. (2010). The mixed lineage nature of nitrogen transport and assimilation in marine eukaryotic phytoplankton: A case study of Micromonas. Molecular Biology and Evolution, 27, 2268–2283. http://doi.org/10.1093/molbev/msq113
Worden, A. Z., & Allen, A. E. (2010). The voyage of the microbial eukaryote. Current Opinion in Microbiology, 13, 652–660. http://doi.org/10.1016/j.mib.2010.08.001

2009

Caron, D. A., Worden, A. Z., Countway, P. D., Demir, E., & Heidelberg, K. B. (2009). Protists are microbes too: A perspective. The ISME Journal, 3, 4–12.
Worden, A. Z., Lee, J. H., Mock, T., Rouze, P., Simmons, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Von Dassow, P., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, U., Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, S., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van de Peer, Y. J., & Grigoriev, I. V. (2009). Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science, 324, 268–272.
Worden, A. Z., & McRose, D. (2009). The otherness of the oceans. Nature, 459, 166–167.

2008

Caron, D. A., Worden, A. Z., Countway, P. D., Demir, E., & Heidelberg, K. B. (2008). Protists are microbes too: A perspective. The ISME Journal, 3, http://doi.org/10.1038/ismej.2008.101
Cuvelier, M. L., Ortiz, A., Kim, E., Moehlig, H., Richardson, D. E., Heidelberg, J. F., Archibald, J. M., & Worden, A. Z. (2008). Widespread distribution of a unique marine protistan lineage. Environmental Microbiology, 10, 1621–1634.
Deschamps, P., Moreau, H., Worden, A. Z., Dauvillée, D., & Ball, S. G. (2008). Early gene duplication within chloroplastida and its correspondence with relocation of starch metabolism to chloroplasts. Genetics, 178, 2373–2387.
Guillou, L., Viprey, M., Chambouvet, A., Welsh, R. M., Kirkham, A. R., Massanna, R., Scanlan, D. J., & Worden, A. Z. (2008). Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environmental Microbiology, 10, 3349–3365.
Robbens, S., Rouzé, P., Cock, J. M., Spring, J., Worden, A. Z., & Van de Peer, Y. J. (2008). The FTO gene, implicated in human obesity, is found only in vertebrates and marine algae. Molecular Evolution, 66, 80–84.
Worden, A. Z., & Not, F. (2008). Ecology and diversity of picoeukaryotes. In D. Kirchman (Ed.), Microbial Ecology of the Oceans, Second Edition. (pp. 159–206). Wiley Publishing.

2007

Not, F., Gausling, R., Azam, F., Heidelberg, J. F., & Worden, A. Z. (2007). Vertical distribution of picoeukaryotic diversity in the Sargasso Sea. Environmental Microbiology, 9, 1233–1252.
Sherr, B. F., Sherr, E. B., Caron, D. A., Vaulot, D., & Worden, A. Z. (2007). Oceanic protists. Oceanography, 20, 130–134.

Earlier publications

Azam, F., & Worden, A. Z. (2004). Microbes, molecules, and marine ecosystems. Science(Washington), 303(5664), 1622–1624.
Binder, B. J., Chisholm, S. W., Olson, R. J., Frankel, S. L., & Worden, A. Z. (1996). Dynamics of picophytoplankton, ultraphytoplankton and bacteria in the central equatorial Pacific. Deep Sea Research Part II: Topical Studies in Oceanography, 43(4), 907–931.
Derelle, E., Ferraz, C., Rombauts, S., Rouzé, P., Worden, A. Z., Robbens, S., Partensky, F., Degroeve, S., Echeynié, S., Cooke, R., Saeys, Y., Wuyts, J., Jabbari, K., Bowler, C., Panaud, O., Piégu, B., Ball, S. G., Ral, J.-P., Bouget, F.-Y., Piganeau, G., De Baets, B., Picard, A., Delseny, M., Demaille, J., Van de Peer, Y., & Moreau, H. (2006). Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proceedings of the National Academy of Sciences, 103(31), 11647–11652. http://doi.org/10.1073/pnas.0604795103
Mourino-Pérez, R. R., Worden, A. Z., & Azam, F. (2003). Growth of Vibrio cholerae O1 in red tide waters off California. Applied and Environmental Microbiology, 69(11), 6923–6931.
Six, C., Worden, A. Z., Rodríguez, F., Moreau, H., & Partensky, F. (2005). New Insights into the Nature and Phylogeny of Prasinophyte Antenna Proteins: Ostreococcus tauri, a Case Study. Molecular Biology and Evolution, 22(11), 2217–2230. http://doi.org/10.1093/molbev/msi220
Worden, A. Z. (2006). Picoeukaryote diversity in coastal waters of the Pacific Ocean. Aquatic Microbial Ecology, 43(2), 165–175.
Worden, A. Z., & Binder, B. J. (2003a). Application of dilution experiments for measuring growth and mortality rates among Prochlorococcus and Synechococcus populations in oligotrophic environments. Aquatic Microbial Ecology, 30(2), 159–174.
Worden, A. Z., & Binder, B. J. (2003b). Growth regulation of rRNA content in Prochlorococcus and Synechococcus (marine cyanobacteria) measured by whole-cell hybridization of rRNA‐targeted peptide nucleic acids. Journal of Phycology, 39(3), 527–534.
Worden, A. Z., Chisholm, S. W., & Binder, B. J. (2000). In Situ Hybridization of Prochlorococcusand Synechococcus (Marine Cyanobacteria) spp. with rRNA-Targeted Peptide Nucleic Acid Probes. Applied and Environmental Microbiology, 66(1), 284–289.
Worden, A. Z., Cuvelier, M. L., & Bartlett, D. H. (2006). In-depth analyses of marine microbial community genomics. Trends in Microbiology, 14(8), 331–336. http://doi.org/10.1016/j.tim.2006.06.008
Worden, A. Z., Nolan, J. K., & Palenik, B. (2004). Assessing the dynamics and ecology of marine picophytoplankton: the importance of the eukaryotic component. Limnology and Oceanography, 49(1), 168–179.
Worden, A. Z., Seidel, M., Smriga, S., Wick, A., Malfatti, F., Bartlett, D., & Azam, F. (2006). Trophic regulation of Vibrio cholerae in coastal marine waters. Environmental Microbiology, 8(1), 21–29. http://doi.org/10.1111/j.1462-2920.2005.00863.x

Science

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