Project | Data Management Plan |
---|---|
MO: Assembly of Marine Microbial Communities |
Principal Investigator: David A. Caron (University of Southern California)
Co-Principal Investigator: Jed A Fuhrman
Environmental Microbiology~2007~9~Hewson, I., Myrna E. Jacobson/Meyers and J. A. Fuhrman~~923~~~~Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands~N~~~~~~
Oceanography~2007~20~Sherr, B., E. Sherr, D. Caron, D. Vaulot and A. Worden~~102~~~~A sea of microbes: oceanic protists~N~~~~~~
Nature Reviews Microbiology~2008~6~Fuhrman, J.A., M.S. Schwalbach, U. Stingl~~488~~~~Proteorhodopsins: an array of physiological roles?~N~~~~~~
Proc. Nat. Acad. Sci. USA~2008~105~Fuhrman, J.A., J. A. Steele, I. Hewson, M. S. Schwalbach, M.V. Brown, J. L. Green, J. H. Brown~~7774~~~~Latitudinal richness gradient in planktonic marine bacteria~N~~~~~~
Proc. Nat. Acad. Sci. USA~2008~105~Fuhrman, J.A., J. A. Steele, I. Hewson, M. S. Schwalbach, M.V. Brown, J. L. Green, J. H. Brown~~7774~~~~A latitudinal diversity gradient in planktonic marine bacteria~N~~~~~~
Aquatic Microbial Ecology~2008~53~Fuhrman, J.A. and J.A. Steele~~69~~~~Community structure of marine bacterioplankton: patterns, networks, and relationships to function~N~~~~~~
Journal of Eukaryotic Microbiology~2009~56~Caron, D.A.~~105~~~~Protistan biogeography: why all the fuss?~N~~~~~~
The ISME Journal~2009~3~Caron, D.A., A.Z. Worden, P.D. Countway, E. Demir and K.B. Heidelberg~~4~~~~Protists are microbes too: a commentary~N~~~~~~
Accessing uncultivated microorganisms: From the environment to organisms and genomes and back~2008~~Caron, D. A.;Gast, R. J.;~~67-93~~~~The diversity of free-living protists: seen and unseen, cultured and uncultured~U~~~~~~
Limnology and Oceanography~2008~53~Caron, D.A.;Rose, J.M.;~~2048-2049~~~~The metabolic theory of ecology and algal bloom formation (Reply to comment by López-Urrutia)~U~~~~~~
Applied and Environmental Microbiology~2009~In pres~Caron, D.A.;Countway, P.D.;Savai, P.;Gast, R.J.;Schnetzer, A.;Moorthi, S.D.;Dennett, M.R.;Jones, A.C.;~~~~~~Defining molecular taxonomic units for microbial eukaryote ecology~U~~~~~~
Microbe~2009~4~Caron, D.A.;Gast, R.J.;Countway, P.D.;Heidelberg, K.B.;~~71-77~~~~Microbial eukaryote ecology: questions of diversity and biogeography~U~~~~~~
BioScience~2009~59~Caron, D.A.;~~287-299~~~~New accomplishments and approaches for assessing protistan diversity and ecology in natural ecosystems~U~~~~~~
Aquatic Microbial Ecology~2009~~Caron,D.A.;Countway, P. D.;~~~~~~The protistan Rare Biosphere in aquatic microbial ecology: hypotheses on the role of diversity in a changing world~U~~~~~~
Nature Reviews Microbiology~2008~6~Fuhrman, J. A.;Schwalbach, M. S.;Stingl, U.;~~488-494~~~~Proteorhodopsins: an array of physiological roles?~U~~~~~~
Aquatic Microbial Ecology~2008~53~Fuhrman, J. A.;Steel, J.;~~69-81~~~~Community structure of marine bacterioplankton: patterns, networks, and relationships to function~U~~~~~~
Nature~2009~459~Fuhrman, J. A.;~~193-199~~~~Deriving functional insights from microbial community structure~U~~~~~~
The ISME Journal~2009~~Brown, M.V.;Philip, G.K.;Bunge, J.A.;Smith, M.C.;Bissett, A.;Lauro, F.M.;Fuhrman, J. A.;Donachie, S.P.;~~~~~~Microbial community structure in the North Pacific Ocean~U~~~~~~
The ISME Journal~2009~3~Böer, S.;Hedtkamp, S.;van Beusekom, J.;Fuhrman, J. A.;Boetius, A.;Ramette, A.;~~780-791~~~~Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sandy sediments~U~~~~~~
Applied and Environmental Microbiology~2009~75~Caron, D.A.;Countway, P.D.;Savai, P.;Gast, R.J.;Schnetzer, A.;Moorthi, S.D.;Dennett, M.R.;Jones, A.C.;~~5797~~~~Defining molecular taxonomic units for microbial eukaryote ecology~N~~~~~~
Aquatic Microbial Ecology~2009~57~Caron,D.A.;Countway, P. D.;~~227~~~~Hypotheses on the role of the protistan Rare Biosphere in a changing world~N~~~~~~
The ISME Journal~2009~~Brown, M.V.;Philip, G.K.;Bunge, J.A.;Smith, M.C.;Bissett, A.;Lauro, F.M.;Fuhrman, J. A.;Donachie, S.P.;~~~~~~Microbial community structure in the North Pacific Ocean~N~~~~~~
The ISME Journal~2009~3~Boer, S.;Hedtkamp, S.;van Beusekom, J.;Fuhrman, J.A.;Boetius, A.;Ramette, A.;~~780-791~~~~Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sandy sediments~N~~~~~~
Trends in Microbiology~2009~17~Gast, R.J.; Sanders, R.W.; Caron, D.A.~~563~~~~Ecological strategies of protists and their symbiotic relationships with prokaryotic microbes~N~~~~~~
Protist~2010~161~Gilg, I.C.; Amaral-Zettler, L.A.; Countway, P.D.; Moorthi, S.; Schnetzer, A.; Caron, D.A.~~197~~~~Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the Southern California coast~N~~~~~~
Environmental Microbiology~2010~12~Beman, J.M.; Sachdeva R.; Fuhrman, J.A.~~1282~~~~Population ecology of nitrifying Archaea and Bacteria in the Southern California Bight~N~~~~~~
Limnology and Oceanography~2010~55~Countway, P.D.; Vigil, P.; Schnetzer, A.; Moorthi, S.; Caron, D.A.~~2~~~~Seasonal analysis of protistan community structure and diversity at the USC Microbial Observatory (San Pedro Channel, Pacific Ocean)~N~~~~~~
Deep-Sea Research~2010~58~Schnetzer, A.; Moorthi, S.; Countway, P.D.; Gast, R.J.; Gilg, I.C.; Caron, D.A.~~16~~~~Depth matters: microbial eukaryote diversity and community structure in the eastern North Pacific revealed through environmental gene libraries~N~~~~~~
Proceedings of the National Academy of Sciences~2010~108~Beman, J.M.; Chow, C.E.; Popp, B.N.; Fuhrman, J.A.; Andersson, A.; Feng, Y.; King, A.L.; Hutchins, D.A.~~208~~~~Global declines in ammonia oxidation as a consequence of ocean acidification~N~~~~~~
The ISME Journal~2010~~Steele, J.A.; Countway, P.D.; Xia, L.; Vigil, P.D.; Beman, J.M.; Kim, D.Y.; Chow, C-E.T.; Sachdeva, R.; Jonesm, A.C.; Schwalbach, M.S.; Rose, J.M.; Hewson, I.; Patel, A.; Sun, F.; Caron, D.A.; Fuhrman, J.A.~doi:10.1038/ismej.2011.24~~~~~Three-domain marine microbial association networks reveal ecological linkages.~N~~~~~~
The ISME Journal~2011~~Beman, J. Michael;Steele, J.;Fuhrman, J. A.;~10.1038/ismej.2010.204~~~~~Co-occurrence patterns for abundant marine archaeal and bacterial lingeages in the deep chlorophyll maximum of coastal California~N~~~~~~
The ISME Journal~2011~5~Steele, J.A.; Countway, P.D.; Xia, L.; Vigil, P.D.; Beman, J.M.; Kim, D.Y.; Chow, C-E.T.; Sachdeva, R.; Jonesm, A.C.; Schwalbach, M.S.; Rose, J.M.; Hewson, I.; Patel, A.; Sun, F.; Caron, D.A.; Fuhrman, J.A.~~~~~~Three-domain marine microbial association networks reveal ecological linkages.~N~~~~~~
PLoS One~2011~6~Xia, L.C, J. Cram, T. Chen, J. Fuhrman and F. Sun~ 10.1371/journal.pone.0027992~~~~~Accurate genome relative abundance estimation based on shotgun metagenomic reads~N~~~~~~
Microbial Ecology~2011~62~Kim, D.Y., P.D. Countway, R.J. Gast and D.A. Caron~~383~~~~Rapid shifts in protistan community structure and composition during bottle incubations~N~~~~~~
Annual Review of Marine Science~2012~4~Caron, D.A., P.D. Countway, A.C. Jones, D.Y. Kim and A. Schnetzer~~467~~~~Marine protistan diversity~N~~~~~~
Enivronmental Microbiology~2012~~Chow, C-E.T., and J.A. Fuhrman~~~~~~Seasonality and monthly dynamics of marine myovirus communities~N~~~~~~
Nature Reviews Microbiology~2012~~Hanson, C., C. Horner-Devine, J.A. Fuhrman, J.B.H. Martiny~doi:10.1038/nrmicro2795~~~~~Beyond biogeographic patterns: evolutionary and ecological processes that shape the microbial landscape~N~~~~~~
F1000 Biology Reports~2012~4~Fuhrman, J.A.~~15~~~~Metagenomics and its connection to microbial community organization~N~~~~~~
BMC Systems Biology~2011~5(Suppl~Xia, L.C., J.A. Steele, Jacob A. Cram, Z.G. Cardon , S.L. Simmons , J.J. Vallino, J.A. Fuhrman , F. Sun~10.1186/1752-0509-5-S2-S15~~~~~Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates~N~~~~~~
Applied and Environmental Microbiology~2011~77~Garneau, M.-Ã?Â?., A. Schnetzer, P.D. Countway, A.C. Jones, E.L. Seubert, D.A. Caron~~7669~~~~Seasonal dynamics of the toxic dinoflagellate Alexandrium catenella at Redondo Beach, California, examined by quantitative PCR~N~~~~~~
Journal of Phycology~2012~48~Howard, M.D.A., A.C. Jones, A. Schnetzer, P.D. Countway, C.R. Tomas, R.M. Kudela, K. Hayashi, P. Chia, D.A. Caron~~384~~~~Quantitative real-time PCR for Cochlodinium fulvescens (Dinophyceae), a potentially harmful dinoflagellate from California coastal waters~N~~~~~~
Microbe~2011~6~Fuhrman, J.A.~~531~~~~Crenarchaeota: a personal history describing this paradigm shift~N~~~~~~
The ISME Journal~2012~6~Gilbert, J.A., J. Steele, J.G. Caporaso, L. Steinbr�¼ck, J. Reeder, B. Temperton, S. Huse, I. Joint, A.C. McHardy, R. Knight, P. Somerfield, J.A. Fuhrman, D. Field~~298~~~~Defining seasonal marine microbial community dynamics~N~~~~~~
Journal of Biogeogeography~2013~40~Amend, A.S., T.A. Oliver, L.A. Amaral-Zettler, A. Boetius, J.A. Fuhrman, M.C. Horner-Devine, S.M. Huse, D.B. M. Welch, A.C. Martiny, A. Ramette, L. Zinger, M.L. Sogin, and J.H. Martiny~~800~~~~Macroecological patterns of marine Bacteria on a global scale~~~~~~~
Annual Review of Marine Science~2012~4~Caron, D.A. P.D. Countway, A.C. Jones, D.Y. Kim, A. Schnetzer~~467~~~~Marine protistan diversity~~~~~~~
Journal of Plankton Research~2013~35~Caron, D.A. and D.A. Hutchins~~235~~~~The effects of changing climate on microzooplankton grazing and community structure: drivers, predictions and knowledge gaps~~~~~~~
Journal of Eukaryotic Microbiology~2013~60~Caron, D.A.~~407~~~~Towards a molecular taxonomy for protists: benefits, risks and applications in plankton ecology~~~~~~~
Frontiers in Bioscience~2012~S4~Chang, Q., Y. Luan, T. Chen, J.A. Fuhrman, F. Sun~~1333~~~~Computational methods for the analysis of tag sequences in metagenomics studies~~~~~~~
Environmental Microbiology~2012~14~Chow, C-E.T., and J.A. Fuhrman~~2171~~~~Seasonality and monthly dynamics of marine myovirus communities~~~~~~~
The ISME Journal~2012~6~Freitas, S., S. Hatosy, J.A. Fuhrman, S.M. Huse, D.B. M. Welch, M.L. Sogin, and A.C. Martin~~1499~~~~Global distribution and diversity of marine Verrucomicrobia~~~~~~~
F1000 Biology Reports~2012~4~Fuhrman, J.A.~~15~~~~Metagenomics and its connection to microbial community organization~~~~~~~
Applied and Environmental Microbiology~2011~77~Garneau, M.-È., A. Schnetzer, P.D. Countway, A.C. Jones, E.L. Seubert and D.A. Caron~~7669~~~~Seasonal dynamics of the toxic dinoflagellate Alexandrium catenella at Redondo Beach, California, examined by quantitative PCR~~~~~~~
Nature Reviews Microbiology~2012~10~Hanson, C., C. Horner-Devine, J.A. Fuhrman, J.B.H. Martiny~~497~~~~Beyond biogeographic patterns: evolutionary and ecological processes that shape the microbial landscape~~~~~~~
Journal of Phycology~2012~48~Howard, M.D.A., A.C. Jones, A. Schnetzer, P.D. Countway, C.R. Tomas, R.M. Kudela, K. Hayashi, P. Chia and D.A. Caron~~384~~~~Quantitative real-time PCR for Cochlodinium fulvescens (Dinophyceae), a potentially harmful dinoflagellate from California coastal waters~~~~~~~
Microbial Ecology~2011~62~Kim, D.Y., P.D. Countway, R.J. Gast and D.A. Caron~~383~~~~Rapid shifts in protistan community structure and composition during bottle incubations~~~~~~~
Journal of Microbiological Methods~2012~91~Kim, D.Y., P.D. Countway, W. Yamashita and D.A. Caron~~527~~~~A combined sequence-based and fragment-based characterization of microbial eukaryote assemblages provides taxonomic context for the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method~~~~~~~
Aquatic Microbial Ecology~2013~70~Lie, A.A.Y., D.Y. Kim, A. Schnetzer and D.A. Caron~~93~~~~Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-series station off the coast of southern California~~~~~~~
Deep-Sea Research I~2011~58~Schnetzer, A., S.D. Moorthi, P.D. Countway R.J. Gast, I.C. Gilg and D.A. Caron~~16~~~~Depth matters: microbial eukaryote diversity and community structure in the eastern North Pacific revealed through environmental gene libraries~~~~~~~
The ISME Journal~2011~5~Steele, J.A., P.D. Countway, L. Xia, P.D.Vigil, J.M. Beman, D.Y. Kim, C.-E. T. Chow, R. Sachdeva, A.C. Jones, M.S. Schwalbach, J.M. Rose, I. Hewson, A. Patel, F. Sun, D.A. Caron, J.A. Fuhrman~~1414~~~~Marine bacterial, archaeal, and protistan assocation networks reveal ecological linkages~~~~~~~
Bioinformatics~2013~29~Xia, L., A. Dongmei, J. Cram, J. Fuhrman and F. Sun~~230~~~~Efficient statistical significance approximation for local association analysis of high-throughput time series data~~~~~~~