Project | Data Management Plan |
---|---|
The Ecology of Prochlorococcus: Toward a Model System for Microbial Oceanography |
Principal Investigator: Sallie W. Chisholm (Massachusetts Institute of Technology)
Co-Principal Investigator: Daniele Veneziano
Nature~2005~--~Lindell, D., J.D. Jaffe, Z.I. Johnson, G.M. Church, S.W. Chisholm~~~~In revision~~Photosynthesis genes in marine viruses yield proteins during host infection.~N~~~~~~
PLoS Biology~2005~3 (5)~Sullivan, M.B., M. Coleman, P. Weigele, and S.W. Chisholm~~e144:0001~~~~Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations.~N~~~~~~
Curr Opin Biotechnol~2005~16~Paul, J.H., and M.B. Sullivan~~299~~~~Marine phage genomics: what have we learned?~N~~~~~~
BIOPHYSICAL JOURNAL~2007~~Marsh, MP; Cruciano, AC; Thompson, LR; Chisholm, SW; Chiu, W~~504A~505A~~http://wok-ws.isiknowledge.com/WoS?recid=155100976#000243972403209~Electron cryo-tomography of Prochlorococcus shows cytoplasmic and periplasmic structural features~Y~~~~~~
SCIENCE~2007~315~Follows, MJ; Dutkiewicz, S; Grant, S; Chisholm, SW~10.1126/science.113854~1843~1846~~http://wok-ws.isiknowledge.com/WoS?recid=155079623#000245280100043~Emergent biogeography of microbial communities in a model ocean~Y~~~~~~
MOLECULAR SYSTEMS BIOLOGY~2006~2~Tolonen, AC; Aach, J; Lindell, D; Johnson, ZI; Rector, T; Steen, R; Church, GM; Chisholm, SW~10.1038/msb410008~~~~http://wok-ws.isiknowledge.com/WoS?recid=154550995#000243245400050~Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability~Y~~~~~~
JOURNAL OF BACTERIOLOGY~2006~188~Steglich, C; Futschik, M; Rector, T; Steen, R; Chisholm, SW~10.1128/JB.01097-0~7796~7806~~http://wok-ws.isiknowledge.com/WoS?recid=153156540#000241938100009~Genome-wide analysis of light sensing in Prochlorococcus~Y~~~~~~
PLOS BIOLOGY~2006~4~Sullivan, MB; Lindell, D; Lee, JA; Thompson, LR; Bielawski, JP; Chisholm, SW~10.1371/journal.pbio.004023~1344~1357~~http://wok-ws.isiknowledge.com/WoS?recid=151910201#000240007400007~Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts~Y~~~~~~
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA~2006~103~Martiny, AC; Coleman, ML; Chisholm, SW~10.1073/pnas.060130110~12552~12557~~http://wok-ws.isiknowledge.com/WoS?recid=151789797#000239867500063~Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptation~Y~~~~~~
NATURE BIOTECHNOLOGY~2006~24~Zhang, K; Martiny, AC; Reppas, NB; Barry, KW; Malek, J; Chisholm, SW; Church, GM~10.1038/nbt121~680~686~~http://wok-ws.isiknowledge.com/WoS?recid=150663630#000238187300030~Sequencing genomes from single cells by polymerase cloning~Y~~~~~~
SCIENCE~2006~311~Johnson, ZI; Zinser, ER; Coe, A; McNulty, NP; Woodward, EMS; Chisholm, SW~10.1126/science.111805~1737~1740~~http://wok-ws.isiknowledge.com/WoS?recid=149466891#000236204300033~Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients~Y~~~~~~
SCIENCE~2006~311~Coleman, ML; Sullivan, MB; Martiny, AC; Steglich, C; Barry, K; DeLong, EF; Chisholm, SW~10.1126/science.112205~1768~1770~~http://wok-ws.isiknowledge.com/WoS?recid=149466912#000236204300043~Genomic islands and the ecology and evolution of Prochlorococcus~Y~~~~~~
VIE ET MILIEU-LIFE AND ENVIRONMENT~2005~55~Bertilsson, S; Berglund, O; Pullin, MJ; Chisholm, SW~~225~231~~http://wok-ws.isiknowledge.com/WoS?recid=149126537#000235757200007~Release of dissolved organic matter by Prochlorococcus~Y~~~~~~
ENVIRONMENTAL MICROBIOLOGY~2006~8~Ahlgren, NA; Rocap, G; Chisholm, SW~10.1111/j.1462-2920.2005.00910.~441~454~~http://wok-ws.isiknowledge.com/WoS?recid=148691121#000235330900008~Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies~Y~~~~~~
SCIENCE~2006~311~DeLong, EF; Preston, CM; Mincer, T; Rich, V; Hallam, SJ; Frigaard, NU; Martinez, A; Sullivan, MB; Edwards, R; Brito, BR; Chisholm, SW; Karl, DM~10.1126/science.112025~496~503~~http://wok-ws.isiknowledge.com/WoS?recid=148641161#000235071400039~Community genomics among stratified microbial assemblages in the ocean's interior~Y~~~~~~
APPLIED AND ENVIRONMENTAL MICROBIOLOGY~2006~72~Zinser, ER; Coe, A; Johnson, ZI; Martiny, AC; Fuller, NJ; Scanlan, DJ; Chisholm, SW~10.1128/AEM.72.1.723-732.200~723~732~~http://wok-ws.isiknowledge.com/WoS?recid=148327911#000234662800093~Prochlorococcus ecotype abundances in the North Atlantic Ocean as revealed by an improved quantitative PCR method~Y~~~~~~
NATURE~2005~438~Lindell, D; Jaffe, JD; Johnson, ZI; Church, GM; Chisholm, SW~10.1038/nature0411~86~89~~http://wok-ws.isiknowledge.com/WoS?recid=147000793#000232979000046~Photosynthesis genes in marine viruses yield proteins during host infection~Y~~~~~~
APPLIED AND ENVIRONMENTAL MICROBIOLOGY~2006~72~Tolonen, AC; Liszt, GB; Hess, WR~10.1128/AEM.02034-0~7607~7613~~http://wok-ws.isiknowledge.com/WoS?recid=153614454#000242681300023~Genetic manipulation of Prochlorococcus strain MIT9313: green fluorescent protein expression from an RSF1010 plasmid and Tn5 transposition~Y~~~~~~
CURRENT BIOLOGY~2008~18~Dammeyer, T; Bagby, SC; Sullivan, MB; Chisholm, SW; Frankenberg-Dinkel, N~10.1016/j.cub.2008.02.06~442~448~~http://wok-ws.isiknowledge.com/WoS?recid=161500336#000254503300029~Efficient phage-mediated pigment biosynthesis in oceanic cyanabacteria~Y~~~~~~
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA~2008~105~Frias-Lopez, J; Shi, Y; Tyson, GW; Coleman, ML; Schuster, SC; Chisholm, SW; DeLong, EF~10.1073/pnas.070889710~3805~3810~~http://wok-ws.isiknowledge.com/WoS?recid=161285169#000253930600028~Microbial community gene expression in ocean surface waters~Y~~~~~~
TRENDS IN MICROBIOLOGY~2007~15~Coleman, ML; Chisholm, SW~10.1016/j.tim.2007.07.00~398~407~~http://wok-ws.isiknowledge.com/WoS?recid=158640542#000250125100003~Code and context: Prochlorococcus as a model for cross-scale biology~Y~~~~~~
LIMNOLOGY AND OCEANOGRAPHY~2007~52~Zinser, ER; Johnson, ZI; Coe, A; Karaca, E; Veneziano, D; Chisholm, SW~~2205~2220~~http://wok-ws.isiknowledge.com/WoS?recid=157806322#000249416200040~Influence of light and temperature on Prochlorococcus ecotype distributions in the Atlantic Ocean~Y~~~~~~
NATURE~2007~449~Lindell, D; Jaffe, JD; Coleman, ML; Futschik, ME; Axmann, IM; Rector, T; Kettler, G; Sullivan, MB; Steen, R; Hess, WR; Church, GM; Chisholm, SW~10.1038/nature0613~83~86~~http://wok-ws.isiknowledge.com/WoS?recid=157247564#000249233500040~Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution~Y~~~~~~
PLOS GENETICS~2007~3~Kettler, GC; Martiny, AC; Huang, K; Zucker, J; Coleman, ML; Rodrigue, S; Chen, F; Lapidus, A; Ferriera, S; Johnson, J; Steglich, C; Church, GM; Richardson, P; Chisholm, SW~10.1371/journal.pgen.003023~2515~2528~~http://wok-ws.isiknowledge.com/WoS?recid=160619768#000253317800016~Patterns and implications of gene gain and loss in the evolution of Prochlorococcus~Y~~~~~~
LIMNOLOGY AND OCEANOGRAPHY-METHODS~2007~5~Moore, LR; Coe, A; Zinser, ER; Saito, MA; Sullivan, MB; Lindell, D; Frois-Moniz, K; Waterbury, J; Chisholm, SW~~353~362~~http://wok-ws.isiknowledge.com/WoS?recid=159588507#000251564500007~Culturing the marine cyanobacterium Prochlorococcus~Y~~~~~~
PLOS BIOLOGY~2005~3~Sullivan, MB; Coleman, ML; Weigele, P; Rohwer, F; Chisholm, SW~10.1371/journal.pbio.003014~790~806~~http://wok-ws.isiknowledge.com/WoS?recid=144416912#000229125400009~Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations~Y~~~~~~
PLoS One~2008~3~Brag, JG and SW Chisholm~~e3550~~~~Modeling the fitness consequences of a cyanophage-encoded photosynthesis gene~N~~~~~~
Genome Biology~2008~4~Steglich, C. ME Futschik, D. Lindell, B. Boss, SW Chisholm and WR Hess~~e100017~~~~The challenge of regulation in a minimal phototroph: Non-coding RNA's in Prochlorococcus~N~~~~~~
Env. Microbiology~2008~10~Sullivan, MB, ML Coleman, V Auinlivan, JE Roesnkrantz, AS DeFrancesco, G. Tan, R Fu, JA Lee, JB Waterbury, JP. Bielawski, and SW Chisholm~~2810~~~~Portal Protein Diversity and Phage Ecology~N~~~~~~
PLOS GENETICS~2008~4~Steglich, C; Futschik, ME; Lindell, D; Voss, B; Chisholm, SW; Hess, WR~10.1371/journal.pgen.100017~~~~http://wok-ws.isiknowledge.com/WoS?recid=174136800#000260410800009~The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus~Y~~~~~~
ENVIRONMENTAL MICROBIOLOGY~2008~10~Sullivan, MB; Coleman, ML; Quinlivan, V; Rosenkrantz, JE; DeFrancesco, AS; Tan, G; Fu, R; Lee, JA; Waterbury, JB; Bielawski, JP; Chisholm, SW~10.1111/j.1462-2920.2008.01702.~2810~2823~~http://wok-ws.isiknowledge.com/WoS?recid=173157560#000259147900029~Portal protein diversity and phage ecology~Y~~~~~~
ENVIRONMENTAL MICROBIOLOGY~2009~11~Frias-Lopez, J; Thompson, A; Waldbauer, J; Chisholm, SW~10.1111/j.1462-2920.2008.01793.~512~525~~http://wok-ws.isiknowledge.com/WoS?recid=176210095#000262515800020~Use of stable isotope-labelled cells to identify active grazers of picocyanobacteria in ocean surface waters~Y~~~~~~
ENVIRONMENTAL MICROBIOLOGY~2009~11~Martiny, AC; Tai, APK; Veneziano, D; Primeau, F; Chisholm, SW~10.1111/j.1462-2920.2008.01803.~823~832~~http://wok-ws.isiknowledge.com/WoS?recid=179081902#000264881300009~Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus~Y~~~~~~
PLoS ONE~2009~4~Zinser, ER, D. Lindell, Z.I. Johnson, M.E. Futschik, C. Steglich, M.L. Coleman, M.A. Wright, T. Rector, R. Steen, N. McNulty, L.R. Thompson, and S.W. Chisholm~~5135~~~~Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus~N~~~~~~
PNAS~2009~106~Martiny, A.C., S. Kathuria, and P.M. Berube~~10787~~~~Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus~N~~~~~~
J. Mol. Biol.~2009~392~Klein, M.G., P. Zward, S.C. Bagby, F. Cai, S.W. Chisholm, S. Heinhorst, G.C. Cannon, and C. A Kerfeld~~319~~~~Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport~N~~~~~~
Global Biogeochem. Cycles~2009~23~Dutkiewicz, S., M.J. Follows. and J.G. Bragg~~GB4017~~In revision~~Modeling the coupling of ocean ecology and biogeochemistry~N~~~~~~
PLoS One~2010~5 (3)~Bragg, J. G., S. Dutkiewicz, O. Jahn, M. Follows. and S.W. Chisholm~~e9569i~~~~Modeling selective pressures on phytoplankton in the global ocean~N~~~~~~
PLoS ONE~2009~4 (9)~Rodrigue S., R.R. Malmstrom, A. Berlin, B. Birren, M. Henn and S.W. Chisholm~~e6864~~~~Whole Genome Amplification and De novo Assembly of Single Bacterial Cells~N~~~~~~
Enviromental Microbiol.~2010~12~Osburne, Marcia, Holmbeck, Brianne, Frias-Lopez, Jorge, Steen, Robert, Huang, Katherine, Waraska, Kristin, Gagne, Andrew, Chisholm, Sallie~~1978~~~~UV hyper-resistance in Prochlorococcus MED4 results from a single base pair deletion just upstream of an operon encoding nudix hydrolase and photolyase~N~~~~~~
Env. Microbiol.~2009~11 (11)~Sullivan, M., B. Krastins, J. Hughes, L. Kelly, M. Chase, D. Sarracino, S.W. Chisholm~~2935~~~~The genome and structural proteome of an ocean cyanobacterial siphovirus~N~~~~~~
Nature~2009~361~Strong, A., C, Miller, S. W. Chisholm and J. Cullen,~~347~~~~Ocean Fertilization: Time to move on~N~~~~~~
Oceanography Magazine~2009~22 (3)~Strong, A. J.J. Cullen, and S. W. Chisholm~~236~~~~Ocean fertilization: Science, policy, and commerce~N~~~~~~
Nature Structure and Mol Biol~2010~17~Liu, X. Q. Zhang, K. Murata, M.L. Baker, M.B. Sullivan, C. Fu, M.F. Schmid, M. S. Osburne, S. W. Chisholm & W. Chiu~~830~~~~Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus~N~~~~~~
PLoS ONE~2010~5 (2)~M. R. Henn, M. B. Sullivan, N. Stange-Thomann, M. S. Osburne, A. M. Berlin, L. Kelly, C. Yandava, C. Kodira, Q. Zeng, M. Weiand, T. Sparrow, S. Saif, G. Giannoukos, S. K. Young, C. Nusbaum, B. W. Birren, S. W. Chisholm.~~e9083~~~~Analysis of high-throughput sequencing and annotation strategies for phage genomes.~N~~~~~~
Genome Biology~2010~11~Steglich, C. M. Futschik, D. Lindell, T. Rector, R. Steen, and S. W. Chisholm.~~R54~~~~Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus~N~~~~~~
PNAS~2010~107~Li, B. D. Sher, L. Kelly, K. Huang, I. Joewono, D. Rusch, S.W. Chisholm and W. A. van der Donk~~10430~~~~Natural combinatorial biosynthesis of secondary metabolites in planktonic marine cyanobacteria.~N~~~~~~
PLoSONE~2010~5 (7)~Rodrigue, S. A. C. Materna, S. C. Timberlake, M. C. Blacburn, R.R. Malmstrom, E. J. Alm, and S. W. Chisholm~~e11840~~~~Unlocking Short Read Sequencing for Metagenomics~N~~~~~~
PNAS~2010~107~McCarren, J., J.W. Becker, D.J. Repeta, Y. Shia, C.R. Young, R.R. Malmstrom, S.W. Chisholm, and E. F. DeLong~~16420~~~~Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea.~N~~~~~~
PNAS~2009~106 (26~Martiny AC, Kathuria S, Berube PM.~~10787~~~~Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypes~N~~~~~~