Marine Ecology

Ocean EcoSystems Biology publications

Click here for publications from the Experimental Ecology - Food Webs (2004 - 2018).

 

2019

Needham DM, Poirier C, Hehenberger E, Jimenez V, Swalwell JE, Santoro AE & Worden AZ. Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes. Philosophical Transactions B. in press

Zimmermann AE, Howard-Varona C, Needham DM, John S, Worden AZ, Sullivan MB, Waldbauer JR & Coleman ML. Physiological controls and biogeochemical impacts of viral infection in aquatic systems. Nature Reviews in Microbiology. in press

Wilken S, Choi CJ &Worden AZ. Contrasting mixotrophic lifestyles reveal different ecological niches in two closely related marine protists. Journal of Phycology. in press

Wilken S, Yung C, Hamilton M, Hoadley K, Nzongo J, Eckmann C, Corrochano Luque M, Poirier C & Worden AZ. The need to account for cell biology on characterising predatory mixotrophs in aquatic environments. Philosophical transactions B. in press

Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi CJ, Hehenberger E, Irwin NTA, Wilken S, Yung C-M, Bachy C, Kurihara R, Nakajima Y, Kojima K, Kimura-Someya T, Leonard G, Malmstrom RR, Mende D, Olson DK, Sudo Y, Sudek S, Richards TA, DeLong EF, Keeling PJ, Santoro AE, Shirouzu M, Iwasaki W & Worden AZ. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proceedings of the National Academy of Sciences USA. https://doi.org/10.1073/pnas.1907517116.

Kolody BJ, McCrow J, Zeigler Allen L, Aylward FO, Fontanez KM, Moustafa A, Moniruzzaman M, Chavez FP, Scholin CA, Allen EE, Worden AZ, DeLong EF. Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. The ISME Journal. doi: 10.1038/s41396-019-0472-2.https://www.nature.com/articles/s41396-019-0472-2

Zimmerman AE, Bachy C, Ma X, Roux S, Jang HB, Sullivan MB, Waldbauer JR & Worden AZ. Closely-related viruses of the marine picoeukaryotic alga, ostreococcus lucimarinus,exhibit different ecological strategies. Environmental Microbiology. Vol 21:2148-2170.https://doi.org/10.1111/1462-2920.14608

Okamoto N, Gawryluk RMR, del Campo J, Strassert JFH, Lukeš J, Richards TA, Worden AZ, Santoro AE &PJ Keeling. A Revised Taxonomy of Diplonemids Including the Eupelagonemidae n. fam. and a Type Species, Eupelagonema oceanica n. gen. &sp. The Journal of Eukaryotic Microbiology. Vol 66:519-524. https://doi.org/10.1111/jeu.12679.

Strassert JFH, Hehenberger E, del Campo J,  Okamoto N,  Kolisko M, Richards TA,  Worden AZ,  Santoro AE & PJ Keeling. Phylogeny, evidence for a cryptic plastid, and distribution of Chytriodinium parasites (Dinophyceae) infecting copepods. Journal of Eukaryotic Microbiology. https://doi.org/10.1111/jeu.12701

 

2018

Joo S, Wang MH, Lui G, Lee J, Barnas A, Kim E, Sudek S, Worden AZ & JH Lee. Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida. BMC Biology. 16:136. doi: 10.1186/s12915-018-0605-5

Bachy C, Charlesworth CJ, Chan AM, Finke JF, Wong C-H, Wei C-L, Sudek S, Coleman ML, Suttle CA & AZ Worden. Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions. Environmental Microbiology. Vol 20:2898-2912.

Guo J, Wilken S, Jimenez V, Choi CJ, Ansong CK, Dannebaum R, Sudek L, Milner D, Bachy C, Reistetter EN, Elrod VA, Klimov D, Purvine SO, Wei C-L, Kunde-Ramamoorthy G, Richards TA, Goodenough U, Smith RD, Callister SJ & AZ Worden. Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation. Nature Microbiology. Vol 3:781–790.

Okamoto N,  Gawryluk RMR, del Campo J,  Strassert JFH, Lukeš J, Richards TA,  Worden AZ, Santoro AE & PJ Keeling. A revised taxonomy of diplonemids Including the Eupelagonemidae n. fam. and a Type Species, Eupelagonema oceanica n. gen. & sp. The Journal of Eukaryotic Microbiology. https://doi.org/10.1111/jeu.12679

Orsi WD, Wilken S, del Campo J, Heger T, James E, Richards TA, Keeling PJ, Worden AZ & AE. Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing. Environmental Microbiology. Vol 20:815-827. http://doi.org/10.1111/1462-2920.14018

Strassert JFH, Karnkowska A, Hehenberger E, del Campo J, Kolisko M, Okamoto N, Burki F, Janouškovec J, Poirier C, Leonard G, Hallam S, Richards TA, Worden AZ, Santoro A & PJ Keeling. Single cell genomics of uncultured Marine Alveolates (MALVs) shows paraphyly of basal dinoflagellates. The ISME Journal. Vol 12:304-308.

 

2017

Gutowska MA, Shome B, McRose D, Sudek S, Hamilton M, Giovannoni SJ, Begley TP & AZ Worden. Ecologically important marine haptophyte algae use exogenous pyrimidine compounds more efficiently than thiamin. mBio Vol 8: e01459-17.doi: 10.1128/mBio.01459-17

Limardo AJ, Sudek S, Choi CJ, Poirier C, Rii YM, Blum M, Roth R, Goodenough U, Church MJ & AZ Worden. Quantitative biogeography of picoprasinophytes establishes differential ecotype and significant contributions to marine phytoplankton. Environmental Microbiology 19:3219-3234. doi: 10.1111/1462-2920

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. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nature Reviews Microbiology 15:6-20. early online doi:10.1038/nrmicro.2016.160

Choi CJ, Bachy C, Jaeger GS, Poirier C, Sudek L, Sarma VVSS, Mahadevan A, Giovannoni SJ & AZ Worden. Newly discovered deep-branching marine plastid lineages are numerically rare but globally distributed. Current Biology 27:R17–R18. Co-first authors.

Cuvelier ML, Guo J, Ortiz AC, van Baren MJ, Tariq MA, Partensky F & AZ Worden. Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress. PLoS One. 27 pgs. doi: 10.1371/journal.pone.0172135

Mock T, Otillar RP, Strauss J, Allen AE, Dupont CL, Frickenhaus S, Maumus F, McMullan M, A, Sanges R, Schmutz J, Toseland A, Veluchamy A, Ward BJ, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech MG, Kroth P, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Armbrust EV, Bowler C, Green BR, Moulton V, van Oosterhout C & IV Grigoriev. Evolutionary genomics of a cold-adapted diatom, Fragilariopsis cylindrus. Nature 541:536-540. doi: 10.1038/nature20803

Clayton SC, Lin Y-C, Follows MJ & AZ Worden. Co-existence of distinct Ostreococcus ecotypes at an oceanic front. Limnology & Oceanography 62:75–88. doi: 10.1002/lno.10373

 

2016

Gawryluk R, del Campo J, Okamoto N, Strassert JFH, Lukes J, Richards TA, Worden AZ, Santoro AE & PJ Keeling. Morphological identification and single-cell genomics of marine diplonemids. Current Biology 26:3053–3059.

Gregory AC, Solonenko S, LaButti K, Copeland A, Sudek S, Maitland A, Chittick L, dos Santos F, Weitz JS, Worden AZ, Woyke T & MB Sullivan. Genomic differentiation amongst wild cyanophages despite widespread horizontal gene transfer. BMC Genomics 17:930 (13 pgs). doi: 10.1186/s12864-016-3286-x

Orsi WD, Smith JM, Liu S, Liu Z, Sakamoto CM, Wilken S, Poirier C, Richards TA, Keeling PJ, Worden AZ & AE Santoro. Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean. The ISME Journal 10:2158-2173. doi: 10.1038/ismej.2016.20

Simmons MP, Sudek S, Monier A, Limardo AJ, Jimenez V, Perle C, Elrod VA, Pennington JT & AZ Worden. Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the Eastern North Pacific Ocean. Applied & Environmental Microbiology 82:1693-1705.

van Baren MJ, Bachy C, Reistetter EN, Purvine SO, Grimwood J, Sudek S, Yu H, Poirier C, Kuo A, Grigoriev IV, Wong C-H, Smith RD, Schmutz J, Wei C-L, Callister SJ & AZ Worden. Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC Genomics 17:267 (22 pgs). doi: 10.1186/s12864-016-2585-6

Monier A, Worden AZ & TA Richards. Phylogenetic diversity and biogeography of the Mamiellophyceae lineage of eukaryotic marine phytoplankton across the oceans. Environmental Microbiology Reports 8:461-469. doi: 10.1111/1758-2229.12390

Waltman PH, Guo J, Reistetter EN, Purvine S, Ansong CK, van Baren MJ, Wong C-H, Wei C-H, Smith RD, Callister SJ, Stuart JM & AZ Worden. Identifying aspects of the post-transcriptional program governing the proteome of the green alga Micromonas pusilla. PLoS One. doi: 10.1371/journal.pone.0155839

 

2015

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

Simmons MP, Bachy C, Sudek S, Baren MJ, Sudek L, Ares M & AZ Worden. Intron invasions trace algal speciation and reveal nearly identical Arctic and Antarctic Micromonas populations. Molecular Biology and Evolution 32:2219-2235.

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

Derelle E, Monier A, Cooke R, Worden AZ, Grimsely NH & H Moreau. Diversity of viruses infecting the green micro-alga Ostreococcus lucimarinus. Journal of Virology 89:5812-21.

Orsi WD, Smith JM, Wilcox HM, Swalwell JE, Carini P, Worden AZ & AE Santoro. Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. The ISME Journal 9: 1747-1763.

Sudek S, Everroad RC, Gehman A, Smith JM, Poirier C, Chavez FP & AZ Worden. Cyanobacterial distributions along a physico-chemical gradient in the northeastern Pacific Ocean. Environmental Microbiology 17:3692-3707.

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*. Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endo-symbiosis of an ochrophyte? Scientific Reports 5: doi: 10.1038/srep10134. *co-corresponding.

 

2014

McRose D, Guo J, Monier A, Sudek S, Wilken S, Yan S, Mock T, Archibald JM, Begley TP, Reyes-A & AZ Worden. Alternatives to Vitamin B1 uptake revealed with discovery of riboswitches in multiple marine unicellular eukaryotes. The ISME Journal 17:3692-3707. 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*. Marine algae and plants share conserved phytochrome signaling systems. Proceedings of the National Academy of Sciences, USA doi: 111:15827–15832. Co-first authors, *co-corresponding.

Keeling* PJ, Burki F, Wilcox HM, Allam B, Allen EE, 75 others & AZ Worden*. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. PLoS Biology 12(6): e1001889. *co-corresponding.

Rockwell, NC, Duanmu D, Martin SS, Bachy C, Price DC, Bhattacharya D, Worden AZ & JC Lagarias. Eukaryotic algal phytochromes span the visible spectrum. Proceedings of the National Academy of Sciences, USA 11:3871-3876.

 

2013

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, Glöckner G, John U, Richards TA, Worden AZ, Zhang X and IV Grigoriev. Emiliania’s pan genome drives the global distribution. Nature 499: 209-213.Co-senior authors.

Monier A, Sudek S, Fast N & AZ Worden. Gene invasion in distant eukaryotic lineages: discovery of mutually exclusive genetic elements reveal marine biodiversity. The ISME Journal 7:1764–1774.

Santoro AE, Sakamoto CM, Smith JM, Plant JN, Gehman AL, Worden AZ, Johnson KS, Francis CA & KL Casciotti. Measurements of nitrite production and nitrite-producing organisms in and around the primary nitrite maximum in the central California Current. Biogeosci. Disc. 10:5803-5840.

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

 

2012

Worden AZ, Janouskovec J, McRose D, Engman A, Welsh RM, Malfatti S, Tringe SG & PJ Keeling. Global distribution of a wild alga revealed by targeted metagenomics. Current Biology 22:R675-R677.

Curtis BA, and 72 others (including McRose D & AZ Worden). Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492:59–65.

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

Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA & AZ. Phosphate transport in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environmental Microbiology 14:162–176.

Treusch AH, Demir-Hilton E, Vergin KL, Worden AZ, Carlson CA & SJ Giovannoni. Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids. The ISME Journal 6:481-492.

 

2011

Paerl RW, Johnson KS, Welsh RM, Worden AZ, Chavez FP & JP Zehr. Differential distributions of Synechococcus subgroups across the California Current System. Frontiers in Microbiology. doi: 10.3389/fmicb.2011.00059

Demir-Hilton E, Sudek S, Cuvelier ML, Gentemann C, Zehr JP & AZ Worden. Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus. The ISME Journal5:1095–1107.

Kim E, Harrison J, Sudek S, Jones MDM, Wilcox HM, Richards T*, Worden AZ* & JM Archibald*. Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proceedings of the National Academy of Sciences, USA 108:1496-1500. *co-corresponding.

 

2010

Cuvelier ML, Allen AE, Monier A, McCrow JP, Messié 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. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences, USA 107:14679-14684.

McDonald SM, Plant JN & AZ Worden. 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.

 

2009

Caron DA, Worden AZ, Countway PD, Demir E & KB Heidelberg. Protists are microbes too: a perspective. The ISME Journal 3:4-12.

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. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryote Micromonas. Science 324:268-272.

 

2008

Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, Massana R, Scanlan DJ & AZ Worden. Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environmental Microbiology 10:3349-3365.

Deschamps P, Moreau H, Worden AZ, Dauvillée D & SG Ball. Early gene duplication within chloroplastida and its correspondence with relocation of starch metabolism to chloroplasts. Genetics 178:2373-2387.

Cuvelier ML, Ortiz A, Kim E, Moehlig H, Richardson DE, Heidelberg JF, Archibald JM & AZ Worden.
Widespread distribution of a unique marine protistan lineage. Environmental Microbiology 10:1621–1634.

Worden AZ & F Not. Ecology and diversity of picoeukaryotes. In: Microbial Ecology of the Ocean, 2nd Edition. Ed. D. Kirchman. Wiley.

 

2007

Robbens S, Rouze P. Cock JM, Spring J, Worden* AZ & Y Van de Peer*. The FTO gene, implicated in human obesity, is found only in vertebrates and marine algae. Journal of Molecular Evolution 66:80-84. *co-corresponding.

Not F, Gausling R, Azam F, Heidelberg, JF & AZ Worden. Vertical distribution of picoeukaryotic  diversity in the Sargasso Sea. Environmental Microbiology 9:1233-1252.

Sherr BF, Sherr EB, Caron DA, Vaulot D & AZ Worden. Oceanic protists. Oceanography 20:130-134.

 

2006

Worden AZ, Cuvelier ML & DH Bartlett. In depth marine microbial community genomics. Trends in Microbiology 14:331-336.

Derelle E, Ferraz C, Rombauts S, Rouzé P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynié S, Cooke R, 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 many unique features. Proceedings of the National Academy of Sciences, USA 103:11647-11652.

Worden AZ. Picoeukaryote diversity in coastal waters of the Pacific Ocean. Aquatic Microbial Ecology 43:165-175.

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

 

2005

Six C, Worden AZ, Rodriguez F, Moreau H & F Partensky. New insights into the nature and of prasinophyte antennae proteins: Ostreococcus tauri, a case study. Molecular Biology and Evolution 22:2217-2230. Co-first authors.

 

2004

Azam F & AZ Worden. Microbes, molecules and marine ecosystems. Science 303:1622-1624.

Worden AZ, Nolan JK & B Palenik. Assessing the dynamics and ecology of marine picophyto-plankton: the importance of the eukaryotic component. Limnology & Oceanography 49:168-179.

 

2003

Mouriño RR, Worden AZ & F Azam. Growth of Vibrio cholerae in Red Tide waters off California. Applied and Environmental Microbiology 69:6923-6931.

Worden AZ & BJ Binder. 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 39:527-534.

Worden AZ & BJ Binder. Application of dilution experiments for measuring growth and mortality rates among Prochlorococcus and Synechococcus populations in oligotrophic environments. Aquatic Microbial Ecology 30:159-174.

 

2000

Worden AZ, Chisholm SW & BJ Binder. In situ hybridization of Prochlorococcus and Synechococcus (Marine Cyanobacteria) with rRNA-targeted Peptide Nucleic Acid Probes. Applied and Environmental Microbiology 66:284-289.

 

1996

Binder BJ, Chisholm SW, Olson RJ, Frankel SL & AZ Worden. Dynamics of pico-phytoplankton, ultra-phytoplankton, and bacteria in the central equatorial Pacific. Deep-Sea Research Part II 43:907-931.

Contact

Head of the Research Unit:

Prof. Dr. Alexandra Z. Worden
GEOMAR | Helmholtz Centre for Ocean Research Kiel
Düsternbrooker Weg 20 
D-24105 Kiel 
Germany
email: azworden(at)geomar.de

Assistant / Office:
Kristin Voss
Room: DW-310
Phone: 0431 600-4405
E-Mail: kvoss(at)geomar.de