Monterey Bay Aquarium Research Institute
Molecular Microbial Ecology
Publications - Worden Lab

Clayton SC, Lin Y-C, Follows MJ & AZ Worden (submitted). Western boundary current fronts: a phytoplankton melting-pot?

van Baren MJ, Bachy C, Reistetter EN, Purvine SO, Grimwood J, Sudek S, Yu H, Kuo A, Wong C-H, Smith RD, Schmutz J, Wei C-L, Callister SJ & AZ Worden (submitted). Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.

Simmons MP, Sudek S, Monier A, Limardo AJ, Jimenez V, Perle C, Elrod VA, Pennington JT & AZ Worden (submitted). Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the Eastern North Pacific Ocean.

Orsi WD, Smith JM, Liu S, Liu Z, Sakamoto CM, Wilken S, Poirier C, Richards TA, Keeling PJ, Worden AZ & AE Santoro (submitted). Highly diverse microbial communities underlie marine biogeochemical cycling of dissolved protein.

Ribalet F, Swalwell JE, Clayton S, Jimenez V, Sudek S, Lin Y, Johnson ZI, Worden AZ & EV Armbrust (2015). Light-driven synchrony of Prochlorococcus growth and mortality in the north Pacific gyre. Proceedings of the National Academy of Sciences USA. Vol. 112:8008-8012. doi: 10.1073/pnas.1424279112.

Simmons^ MP, Bachy^ C, Sudek S, Baren MJ, Sudek L, Ares M & AZ Worden* (2015). Intron invasions trace algal speciation and reveal nearly identical Arctic and Antarctic Micromonas populations. Molecular Biology and Evolution. doi: 10.1093/molbev/msv122. ^Co-first authors

Limardo AJ & AZ Worden (2015). News and Views Microbiology: Exclusive networks in the sea. Nature. Vol. 522:36–37. doi:10.1038/nature14530.

Ševčíková T, Horák A, Klimeš V, Zbránková V, Demir-Hilton E, Sudek S, Jenkins J, Schmutz J, Přibyl P, Fousek J, Vlček C, Lang BF, Oborník M, Worden AZ & M Eliáš (2015). Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte? Scientific Reports. Vol. 5. doi: 10.1038/srep10134.

Derelle E, Monier A, Cooke R, Worden AZ, Grimsely NH & H Moreau (2015). Diversity of viruses infecting the green micro-alga Ostreococcus lucimarinus. Journal of Virology. Vol. 89:5812-5821. doi: 10.1128/JVI.00246-15.

Worden AZ, Follows MJ, Giovannoni SJ, Wilken S, Zimmerman AE & PJ Keeling (2015). Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes. Science. Vol. 347. doi: 10.1126/science.1257594.

Orsi WD, Smith JM, Wilcox HM, Swalwell JE, Carini P, Worden AZ & AE Santoro (2015). Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. The ISME Journal. doi: 10.1038/ismej.2014.260.

Sudek^ S, Everroad^ RC, Gehman A, Smith JM, Poirier C, Chavez FP & AZ Worden (2015). Cyanobacterial distributions along a physico-chemical gradient in the northeastern Pacific Ocean. Environmental Microbiology. doi: 10.1111/1462-2920.12742. ^Co-first authors

Duanmu^ D, Bachy^ C, Sudek S, Wong CH, Jimenez V, Rockwell NC, Martin SS, Ngan CY, Reistetter E, van Baren MJ, Price DC, Wei CL, Reyes-Prieto A, Lagarias JC & AZ Worden (2014). Marine algae and land plants share conserved phytochrome signaling systems. Proceedings of the National Academy of Sciences USA. Vol. 111:15827-15832. doi: 10.1073/pnas.1416751111. ^Co-first authors

McRose^ D, Guo^ J, Monier^ A, SudekS, Wilken S, Yan S, Mock T, Archibald JM, Begley TP, Reyes-Prieto A & AZ Worden (2014). Alternatives to Vitamin B1 uptake revealed with discovery of riboswitches in multiple marine unicellular eukaryotes. The ISME Journal. Vol. 8:2517-2529. doi:10.1038/ismej.2014.146. ^Co-first authors.

Keeling PJ, Burki F, Wilcox HM, 75 others & AZ Worden (2014). The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLOS Biology. doi:10.1371/journal.pbio.1001889.

Bachy C & AZ Worden (2014). Microbial ecology: Finding structure in the rare biosphere. Current Biology. Vol. 24:R315–R31. doi:10.1016/j.cub.2014.03.029.

Rockwell NC, Duanmu D, Martin SS, Bachy C, Price DC, Bhattacharya D, Worden AZ & JC Lagarias (2014). Eukaryotic algal phytochromes span the visible spectrum. Proceedings of the National Academy of Sciences USA. Vol. 111:3871-3876. doi:10.1073/pnas.1401871111

Read BA*, Kegel^ J, Klute^ MJ, Kuo^ A, Lefebvre^ SC, Maumus^ F, Mayer^ C, Miller^ J, Monier^ A, Salamov^ A, Emiliania huxleyi Annotation Consortium, Dacks* JB, Delwiche* CF, Dyhrman* ST, Glockner* G, John* U, Richards* TA, Worden* AZ, Zhang* X & IV Grigoriev* (2013). Emiliania's pan genome drives the phytoplankton's global distribution. Nature. doi:10.1038/nature12221 ^Equal contributions as co-second authors; *Co-senior authors.

Santoro AE, Sakamoto CM, Smith JM, Plant JN, Gehman AL, Worden AZ, Johnson KS, Francis CA & KL Casciotti (2013). Measurements of nitrite production and nitrite-producing organisms in and around the primary nitrite maximum in the central California Current. Biogeosciences Discussions. Vol 10:5803-5840. doi:10.5194/bgd-10-5803-2013.

Monier A, Sudek S, Fast N & AZ Worden (2013). Gene invasion in distant eukaryotic lineages: discovery of mutually exclusive genetic elements reveals marine biodiversity. The ISME Journal. Vol. 7:764-774. doi:10.1038/ismej.2013.70. Topic: Inteins and intron presence absence polymorphisms

Vergin KL, Beszteri B, Monier A, Thrash JC, Treusch AH, Kilpert F, Worden AZ & SJ Giovannoni (2013). High resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site as determined by phylogenetic placement of pyrosequences. The ISME Journal. Vol. 7:1322-1332. doi: 10.1038/ismej.2013.32

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

Worden AZ, Janouskovec J, McRose D, Engman A, Welsh RM, Malfatti S, Tringe SG & PJ Keeling (2012). Global distribution of a wild alga revealed by targeted metagenomics. Current Biology. doi:10.1016/j.cub.2012.07.054. Topic: Complete Pelagomonas plastid genome sequence and ecology

See the highlight article by John Raven on our above pelagophyte research/publication here

Lin YC, Campbell T, Chung CC, Gong G, Chiang KP & AZ Worden (2012). Distribution patterns and phylogeny of novel marine stramenopiles (MAST) in the North Pacific Ocean. Applied and Environmental Microbiology. Vol. 78: 3387-3399.

Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA & AZ Worden (2012). Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environmental Microbiology. 'Omics Driven Microbial Ecology' Special Issue. doi: 10.1111/j.1462-2920.2011.02576.x. Epub Sept 2011 Topic: Bathycoccus genome (targeted metagenome sequence) and viral ecology pdf

Treusch AH, Demir-Hilton E, Vergin KL, Worden AZ, Carlson CA, Donatz MG, Burton RM & SJ Giovannoni (2012). Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids. ISME Journal. Vol. 6:481-492. doi: 10.1038/ismej.2011.117

Worden AZ, Dupont C & AE Allen (2011). Genomics of uncultured eukaryotes: sorting FACS from fiction. Genome Biology. Vol. 12:117. Invited Research Highlight

Paerl RW, Johnson KS, Welsh RM, Worden AZ, Chavez FP & JP Zehr (2011). Differential distributions of Synechococcus subgroups across the California Current System. Frontiers in Microbiology. pdf

Demir-Hilton E, Sudek S, Cuvelier ML, Gentemann C, Zehr JP & AZ Worden (2011). Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus. The ISME Journal. Vol. 5: 1095-1107. pdf

Kim^ E, Harrison^ J, Sudek^ S, Jones MDM, Wilcox HM, Richards* T, Worden* AZ & JM Archibald* (2011). Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proceedings of the National Academy of Sciences USA. Vol. 108: 1496-1500. ^These authors contributed equally as co-first authors. *co-corresponding. pdf correction, important but not published by PNAS because does not alter conclusions

Worden AZ & AE Allen (2010). The voyage of the microbial eukaryote. Current Opinion in Microbiology. Vol. 13: 652-660.

Cuvelier ML, Allen^ AE, Monier^ A, McCrow JP, Messie M, Tringe SG, Woyke T, Welsh RM, Ishoey T, Lee JH, Binder BJ, DuPont CL, Latasa M, Guigand C, Buck KR, Hilton J, Thiagarajan M, Caler E, Read B, Lasken RS, Chavez FP & AZ Worden (2010). Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences USA. ^These authors contributed equally as co-second authors. Genomes, Diversity & Production by Uncultured Pico-prymnesiophytes pdf

McDonald SM, Plant JN & AZ Worden (2010). The mixed lineage nature of nitrogen transport and assimilation in marine eukaryotic phytoplankton: a case study of Micromonas. Molecular Biology and Evolution. Vol. 27: 2268-2283. pdf

Worden AZ & D McRose (2009). The otherness of the oceans. Nature. Vol. 459:166-167. Book Review & Commentary pdf

Worden* AZ, Lee^ JH, Mock^ T, Rouze^ P, Simmons^ MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KFX, 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 EV, Bhattacharya D, Goodenough UW, Van de Peer Y & IV Grigoriev (2009). Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science. Vol. 324: 268-272; DOI: 10.1126/science.1167222 ^these authors contributed equally as second authors; *corresponding author.

See the highlight perspective in Science on our above Micromonas genome publication here

Caron DA, Worden AZ, Countway PD, Demir E & KB Heidelberg (2009). Protists are microbes too: a perspective. The ISME Journal. Vol. 3:4-12; doi:10.1038/ismej.2008.101

Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, Massana R, Scanlan DJ & AZ Worden (2008). Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environmental Microbiology. DOI: 10.1111/j.1462-2920.2008.01731.x

Worden AZ & F Not (2008). Ecology and Diversity of Picoeukaryotes. Book Chapter in: Microbial Ecology of the Ocean, 2nd Edition. Ed. D. Kirchman. Wiley.

Cuvelier ML, Ortiz A, Kim E, Moehlig H, Richardson DE, Heidelberg JF, Archibald JM, Worden AZ (2008). Widespread distribution of a unique marine protistan lineage. Environmental Microbiology. Vol. 10:1621-1634. Topic: Biliphytes - a Novel Protistan Lineage pdf

Deschamps P, Moreau H, Worden AZ, Dauvillée D & S. Ball S (2008). Early Gene Duplication within Chloroplastida and its correspondence with Relocation of Starch Metabolism to Chloroplasts. Genetics. Vol. 178:2373-2387.Topic: Evolution of Photosynthesis

Robbens S, Rouzé P, Cock JM, Spring J, Worden AZ & YJ Van de Peer (2008). The FTO gene, implicated in human obesity, is found only in vertebrates and marine algae. Journal of Molecular Evolution. Vol. 66:80-84. Topic: Obesity/Evolution

Sherr BF, Sherr EB, Caron DA, Vaulot D & AZ Worden (2007). Oceanic Protists. Oceanography. Vol 20:130-134. Topic: General Review

Not F, Gausling R, Azam F, Heidelberg JF & AZ Worden (2007). Vertical distribution of picoeukaryotic diversity in the Sargasso Sea. Environmental Microbiology. Vol 9:1233-1252. Topic: Diversity/Ecology

Derelle E*, Ferraz C*, Rombauts S*, Rouzé P*, Worden AZ, Partensky F, Degroeve S, Echeynié S, Cooke R, Robbens S, Wuyts J, Saeys Y, Jabbari K, Bowler C, Ball S, Ral JP, Bouget FY, Piganeau G, De Baets B, Picard A, Delseny M, Demaille J, Van de Peer Y & H Moreau (2006). Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils unique genome heterogeneity. Proceedings of the National Academy of Sciences USA. Vol 103:11647-11652. *Equal contribution, co-first authors. Topic: Genomics/Evolution

Worden AZ (2006). Picoeukaryote diversity in coastal waters of the Pacific Ocean. Aquatic Microbial Ecology. Vol. 43:165-175. Topic: Diversity/Ecology pdf

Worden AZ, Cuvelier ML & DH Bartlett (2006). In-depth marine microbial community genomics. Trends in Microbiology. Vol. 14:331-336. Topic: Environmental Metagenomics pdf

Worden AZ, Seidel M, Smriga S, Wick A, Malfatti F, Bartlett D & F Azam (2006). Trophic regulation of Vibrio cholerae in coastal marine waters. Environmental Microbiology. Vol. 8:21-29. Topic: Pathogen Proliferation

Six C*, Worden AZ*, Rodriguez F, Moreau H and F Partensky (2005). New insights into the nature and phylogeny of prasinophyte antennae proteins: Ostreococcus tauri, a case study. Molecular Biology and Evolution. Vol. 22:2217-2230. Topic: Light Harvesting/Photosynthesis *Equal contribution, co-first authors. pdf

Azam F and Worden AZ (2004). Microbes, molecules and marine ecosystems. Science. Vol. 303:1622-24. Topic: Integrating New Approaches to Marine Ecology pdf

Worden AZ, Nolan JK and B Palenik (2004). Assessing the dynamics and ecology of marine picophytoplankton: the importance of the eukaryotic component. Limnology and Oceanography. Vol. 49:168-179. Topic: Picoplankton Ecology/Carbon Contributions pdf

Mouriño RR, Worden AZ and F Azam (2003). Growth of Vibrio cholerae in Red Tide waters off California. Applied and Environmental Microbiology. Vol. 69:6923-6931. Topic: Pathogen Proliferation pdf

Worden AZ and BJ Binder (2003). Growth regulation of rRNA content of Prochlorococcus and Synechococcus (marine cyanobacteria) measured by whole-cell hybridization of rRNA targeted peptide nucleic acids. Journal of Phycology. Vol. 39:527-534. Topic: Physiology - rRNA Content in Marine Cyanos pdf

Worden AZ and BJ Binder (2003). Application of dilution experiments for measuring growth and mortality rates among Prochlorococcus and Synechococcus populations in oligotrophic environments. Aquatic Microbial Ecology. Vol. 30:159-174. Topic: Picoplankton Ecology pdf

Worden AZ, Chisholm SW and BJ Binder (2000). In situ hybridization of Prochlorococcus and Synechococcus (marine cyanobacteria) with rRNA-targeted Peptide Nucleic Acid Probes. Applied and Environmental Microbiology. Vol. 66:284-289. Topic: Methods - rRNA Probing in Marine Cyanos pdf

Binder BJ, Chisholm SW, Olson RJ, Frankel SL, and AZ Worden (1996). Dynamics of pico-phytoplankton, ultra-phytoplankton, and bacteria in the central equatorial Pacific. Deep-Sea Research Part II. Vol. 43:907-931. Topic: Picoplankton Ecology pdf

Last updated: Nov. 17, 2015