Project | Data Management Plan |
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Ocean's dark energy: Global inventory of chemoautotrophs in the aphotic realm |
Principal Investigator: Ramunas Stepanauskas (Bigelow Laboratory for Ocean Sciences)
PNAS~2013~TBD~Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson BP, Poulton NJ, Schwientek P, Acinas SG, Giovannoni SJ, Moran MA, Hallam SJ, Cavicchioli R, Woyke T, Stepanauskas, R~10.1073/pnas.1304246110~TBD~~~~Prevalent genome streamlining and latitudinal divergence of marine planktonic bacteria in the surface ocean~~~~~~~
Nature~2013~499~Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam S, Kyrpides N, Stepanauskas R, Rubin E, Hugenholtz P, Woyke T~10.1038/nature12352~431~~~~Insights into the phylogeny and coding potential of microbial dark matter.~~~~~~~
PLoS ONE~2014~9~Swan, BK, M Chaffin, M Martinez-Garcia, HG Morrison, E Field, NJ Poulton, EDP Masland, CC Harris, A Sczyrba, PSG Chain, S Koren, T Woyke and R Stepanauskas~10.1371/journal.pone.0095380~e95380~~~~Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres~~~~~~~
Proceedings of the National Academy of Sciences~2013~~Swan, Brandon K. and Tupper, Ben and Sczyrba, Alexander and Lauro, Federico M. and Martinez-Garcia, Manuel and González, José M. and Luo, Haiwei and Wright, Jody J. and Landry, Zachary C. and Hanson, Niels W. and Thompson, Brian P. and Poulton, Nicole J.~10.1073/pnas.1304246110~~~~~Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean~~~~~~~
{ISME} J~2014~~Cameron Thrash, J and Temperton, Ben and Swan, Brandon K and Landry, Zachary C and Woyke, Tanja and DeLong, Edward F and Stepanauskas, Ramunas and Giovannoni, Stephan J~1751-7370~~~~~Single-cell enabled comparative genomics of a deep ocean {SAR11} bathytype~~~~~~~
{ISME} J~2014~8~Luo, Haiwei and Tolar, Bradley B and Swan, Brandon K and Zhang, Chuanlun L and Stepanauskas, Ramunas and Ann Moran, Mary and Hollibaugh, James T~1751-7362~732--736~~~~Single-cell genomics shedding light on marine Thaumarchaeota diversification~~~~~~~
Environmental Microbiology~2014~16~Eiler A, Zaremba-Niedzwiedzka K, Martinez-Garcia M, McMahon KD, Stepanauskas R, Andersson SGE, Bertilsson S.~~2682~~~~Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics.~~~~~~~
The ISME Journal~2014~8~Ghylin TW, Garcia SL, Moya F, Oyserman BO, Schwientek P, Forest KT, Mutschler J, Dwulit-Smith J, Chan LK, Martinez-Garcia M, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F, Malmstrom R, Bertilsson S, McMahon KD.~~2503~~~~Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage.~~~~~~~
Science~2014~344~Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom R, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW~~416~~~~Single cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus~~~~~~~
Life Sciences in Space Research~2014~2~Kminek G, Conley C, Allen CC, Bartlett DH, Beaty DW, Benning LG, Bhartia R, Boston PJ, Duchaine C, Farmer JD, Flynn GJ, Glavin DP, Gorby Y, Hallsworth JE, Mogul R, Moser D, Buford Price P, Pukall R, Fernandez-Remolar D, Smith CL, Stedman K, Steele A, Step~~1~~~~Report of the workshop for life detection in samples from Mars~~~~~~~
Frontiers in Microbiology~2015~6~Labonte JM, Field EK, Lau M, Chivian D, van Heerden E, Wommack KE, Kieft TL, Onstott TC, Stepanauskas R.~~649~~~~Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population~~~~~~~
The ISME Journal~2015~~Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, Sullivan MB, Woyke T, Wommack KE, Stepanauskas R.~~~~~~Single cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton.~~~~~~~
Environmental Microbiology Reports~2014~6~Luo H, Swan BK, Stepanauskas R, Hughes AL, Moran MA~~167~~~~Comparing Effective Population Sizes of Dominant Marine Alphaproteobacteria Lineages.~~~~~~~
The ISME Journal~2014~8~Luo H, Swan BK, Stepanauskas R, Hughes AL, Moran MA~~1428~~~~Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters~~~~~~~
The ISME Journal~2015~~Martijn J, Schullz F, Zaremba-Niedzwiedzka K, Viklund J, Stepanauskas R, Andersson SGE, Horn M, Guy L, Ettema TJG.~~~~~~Single cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution.~~~~~~~
Nature Protocols~2014~9~Rinke C, Lee J, Nath N, Goudeau D, Thompson B, Poulton N, Ferguson E, Malmstrom R, Stepanauskas R, Woyke T.~~1038~~~~Obtaining genomes from uncultivated environmental microorganisms.~~~~~~~
eLife~2014~3~Roux S, Hawley AK, Beltran MT, Scofield M, Schwientek P, Stepanauskas R, Woyke T, Hallam SJ, Sullivan MB.~~03125~~~~Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics.~~~~~~~
Frontiers in Microbiology~2015~6~Stepanauskas R~~258~~~~Wiretapping into microbial interactions by single cell genomics~~~~~~~
Environmental Microbiology Reports~2015~7~Stepanauskas R.~~36~~~~Crystal Ball: Re-defining microbial diversity from its single-celled building blocks.~~~~~~~
The ISME Journal~2014~8~Wasmund K, Schreiber L, Lloyd KG, Petersen DG, Schramm A, Stepanauskas R, Jørgensen BB, Adrian L.~~383~~~~Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi.~~~~~~~
The ISME journal~2016~~Dyksma, Stefan and Bischof, Kerstin and Fuchs, Bernhard M and Hoffmann, Katy and Meier, Dimitri and Meyerdierks, Anke and Pjevac, Petra and Probandt, David and Richter, Michael and Stepanauskas, Ramunas and Mu{\ss}mann, Marc~10.1038/ISMEJ.2015.257~1--15~~~~{Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments}~~~~~~2016-12-02 17:26:51.913~
Environmental Microbiology~2014~16~Eiler, Alexander and Zaremba-Niedzwiedzka, Katarzyna and Martinez-Garcia, Manuel and Mcmahon, Katherine D. and Stepanauskas, Ramunas and Andersson, Siv G E and Bertilsson, Stefan~10.1111/1462-2920.12301~2682--269~~~~{Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics}~~~~~~2016-12-02 17:26:51.990~
Isme j~2014~8~Ghylin, T W and Garcia, S L and Moya, F and Oyserman, B O and Schwientek, P and Forest, K T and Mutschler, J and Dwulit-Smith, J and Chan, L K and Martinez-Garcia, M and Sczyrba, A and Stepanauskas, R and Grossart, H P and Woyke, T and Warnecke, F and Mal~10.1038/ismej.2014.135~2503--251~~~~{Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage}~~~~~~2016-12-02 17:26:51.996~
Science (New York, N.Y.)~2014~344~Kashtan, Nadav and Roggensack, Sara E and Rodrigue, S{\'{e}}bastien and Thompson, Jessie W and Biller, Steven J and Coe, Allison and Ding, Huiming and Marttinen, Pekka and Malmstrom, Rex R and Stocker, Roman and Follows, Michael J and Stepanauskas, Ramuna~10.1126/science.1248575~416--20~~~~{Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus.}~~~~~~2016-12-02 17:26:52.3~
Life Sciences in Space Research~2014~2~Kminek, Gerhard and Conley, Catherine and Allen, Carlton C. and Bartlett, Douglas H. and Beaty, David W. and Benning, Liane G. and Bhartia, Rohit and Boston, Penelope J. and Duchaine, Caroline and Farmer, Jack D. and Flynn, George J. and Glavin, Daniel P.~10.1016/j.lssr.2014.05.001~1--5~~~~{Report of the workshop for life detection in samples from Mars}~~~~~~2016-12-02 17:26:52.10~
The ISME Journal~2015~9~Labont{\'{e}}, Jessica M and Swan, Brandon K and Poulos, Bonnie and Luo, Haiwei and Koren, Sergey and Hallam, Steven J and Sullivan, Matthew B and Woyke, Tanja and {Eric Wommack}, K and Stepanauskas, Ramunas~10.1038/ismej.2015.48~2386--239~~~~{Single-cell genomics-based analysis of virus?host interactions in marine surface bacterioplankton}~~~~~~2016-12-02 17:26:52.16~
Frontiers in Microbiology~2015~6~Labont{\'{e}}, Jessica M. and Field, Erin K. and Lau, Maggie and Chivian, Dylan and {Van Heerden}, Esta and Wommack, K. Eric and Kieft, Thomas L. and Onstott, Tullis C. and Stepanauskas, Ramunas~10.3389/fmicb.2015.00349~~~~~{Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population}~~~~~~2016-12-02 17:26:52.50~
Nature~2013~496~Lloyd, Karen G and Schreiber, Lars and Petersen, Dorthe G and Kjeldsen, Kasper U and Lever, Mark A and Steen, Andrew D and Stepanauskas, Ramunas and Richter, Michael and Kleindienst, Sara and Lenk, Sabine and Schramm, Andreas and J{\o}rgensen, Bo Barker~10.1038/nature12033~215--218~~~~{Predominant archaea in marine sediments degrade detrital proteins}~~~~~~2016-12-02 17:26:52.53~
The ISME journal~2014~8~Luo, Haiwei and Swan, Brandon K and Stepanauskas, Ramunas and Hughes, Austin L and Moran, Mary Ann~10.1038/ismej.2013.248~1428--39~~~~{Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters.}~~~~~~2016-12-02 17:26:52.56~
Environmental Microbiology Reports~2014~6~Luo, Haiwei and Swan, Brandon K. and Stepanauskas, Ramunas and Hughes, Austin L. and Moran, Mary Ann~10.1111/1758-2229.12129~167--172~~~~{Comparing effective population sizes of dominant marine alphaproteobacteria lineages}~~~~~~2016-12-02 17:26:52.63~
The ISME journal~2014~8~Luo, Haiwei and Tolar, Bradley B and Swan, Brandon K and Zhang, Chuanlun L and Stepanauskas, Ramunas and {Ann Moran}, Mary and Hollibaugh, James T~10.1038/ismej.2013.202~732--6~~~~{Single-cell genomics shedding light on marine Thaumarchaeota diversification.}~~~~~~2016-12-02 17:26:52.66~
The ISME journal~2015~9~Martijn, Joran and Schulz, Frederik and Zaremba-Niedzwiedzka, Katarzyna and Viklund, Johan and Stepanauskas, Ramunas and Andersson, Siv G E and Horn, Matthias and Guy, Lionel and Ettema, Thijs J G~10.1038/ismej.2015.46~2373--85~~~~{Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution.}~~~~~~2016-12-02 17:26:52.73~
The ISME Journal~2015~~Ngugi, D.K. and Blom, J. and Stepanauskas, R. and Stingl, U.~10.1038/ismej.2015.214~1--17~~~~{Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines}~~~~~~2016-12-02 17:26:52.76~
Nat. Protocols~2014~9~Rinke, Christian and Lee, Janey and Nath, Nandita and Goudeau, Danielle and Thompson, Brian and Poulton, Nicole and Dmitrieff, Elizabeth and Malmstrom, Rex and Stepanauskas, Ramunas and Woyke, Tanja~1754-2189~1038--104~~~~{Obtaining genomes from uncultivated environmental microorganisms using FACS?based single-cell genomics}~~~~~~2016-12-02 17:26:52.80~
Nature~2013~499~Rinke, Christian and Schwientek, Patrick and Sczyrba, Alexander and Ivanova, Natalia N and Anderson, Iain J and Cheng, Jan-Fang and Darling, Aaron E and Malfatti, Stephanie and Swan, Brandon K and Gies, Esther a and Dodsworth, Jeremy a and Hedlund, Brian~10.1038/nature12352~431--437~~~~{Insights into the phylogeny and coding potential of microbial dark matter.}~~~~~~2016-12-02 17:26:52.83~
eLife~2014~2014~Roux, Simon and Hawley, Alyse K. and Beltran, Monica Torres and Scofeld, Melanie and Schwientek, Patrick and Stepanauskas, Ramunas and Woyke, Tanja and Hallam, Steven J. and Sullivan, Matthew B.~10.7554/eLife.03125.001~~~~~{Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics}~~~~~~2016-12-02 17:26:52.86~
Environmental Microbiology Reports~2015~7~Stepanauskas, Ramunas~10.1111/1758-2229.12226~36--37~~~~Re-defining microbial diversity from its single-celled building blocks~~~~~~2016-12-02 17:26:52.90~
Proceedings of the National Academy of Sciences of the United States of America~2013~110~Swan, Brandon K and Tupper, Ben and Sczyrba, Alexander and Lauro, Federico M and Martinez-Garcia, Manuel and Gonzalez, Jose M and Luo, Haiwei and Wright, Jody J and Landry, Zachary C and Hanson, Niels W and Thompson, Brian P and Poulton, Nicole J and Schw~10.1073/pnas.1304246110~11463--8~~~~{Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean.}~~~~~~2016-12-02 17:26:52.93~
PLoS ONE~2014~9~Swan, Brandon K. and Chaffin, Mark D. and Martinez-Garcia, Manuel and Morrison, Hilary G. and Field, Erin K. and Poulton, Nicole J. and Masland, E. Dashiell P and Harris, Christopher C. and Sczyrba, Alexander and Chain, Patrick S G and Koren, Sergey and W~10.1371/journal.pone.0095380~~~~~{Genomic and metabolic diversity of marine group i thaumarchaeota in the mesopelagic of two subtropical gyres}~~~~~~2016-12-02 17:26:52.96~
The ISME journal~2014~8~Thrash, J Cameron and Temperton, Ben and Swan, Brandon K and Landry, Zachary C and Woyke, Tanja and DeLong, Edward F and Stepanauskas, Ramunas and Giovannoni, Stephan J~10.1038/ismej.2013.243~1440--51~~~~{Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype.}~~~~~~2016-12-02 17:26:52.103~
mBio~2016~7~Wasmund, Kenneth and Cooper, Myriel and Schreiber, Lars and Lloyd, Karen G. and Baker, Brett J. and Petersen, Dorthe G. and Joergensen, Bo Barker and Stepanauskas, Ramunas and Reinhardt, Richard and Schramm, Andreas and Loy, Alexander and Adrian, Lorenz~10.1128/mBio.00266-16~~~~~{Single-cell genome and group-specific dsrAB sequencing implicate marine members of the class Dehalococcoidia (phylum Chloroflexi) in sulfur cycling}~~~~~~2016-12-02 17:26:52.103~
The ISME journal~2014~8~Wasmund, Kenneth and Schreiber, Lars and Lloyd, Karen G and Petersen, Dorthe G and Schramm, Andreas and Stepanauskas, Ramunas and Joergensen, Bo Barker and Adrian, Lorenz~10.1038/ismej.2013.143~383--97~~~~{Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi.}~~~~~~2016-12-02 17:26:52.106~
Applied and Environmental Microbiology~2016~82~Zhang, Yao and Sun, Ying and Jiao, Nianzhi and Stepanauskas, Ramunas and Luo, Haiwei~10.1128/AEM.03678-15~2100--211~~~~Ecological genomics of the uncultivated marine Roseobacter lineage CHAB-I-5~~~~~~2016-12-02 17:26:52.110~
Frontiers in Microbiology~2015~6~Stepanauskas Ramunas~10.3389/fmicb.2015.00258~~~~~Wiretapping into microbial interactions by single cell genomics~~~~~~2016-12-02 17:26:52.113~