Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

Dupont, Chris L.; McCrow, John P.; Valas, Ruben; Moustafa, Ahmed; Walworth, Nathan; Goodenough, Ursula; Roth, Robyn; Hogle, Shane L.; Bai, Jing; Johnson, Zackary I.; Mann, Elizabeth; Palenik, Brian; Barbeau, Katherine A.; Venter, J. Craig; Allen, Andrew E.

doi:10.1038/ismej.2014.198

Title: Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

Journal Article · Tue Oct 21 04:00:00 UTC 2014 · The ISME Journal

DOI: https://doi.org/10.1038/ismej.2014.198 · OSTI ID:1346924

Dupont, Chris L. ^[1]; McCrow, John P. ^[2]; Valas, Ruben ^[2]; Moustafa, Ahmed ^[3]; Walworth, Nathan ^[4]; Goodenough, Ursula ^[5]; Roth, Robyn ^[5]; Hogle, Shane L. ^[6]; Bai, Jing ^[2]; Johnson, Zackary I. ^[7]; Mann, Elizabeth ^[8]; Palenik, Brian ^[6]; Barbeau, Katherine A. ^[6]; Venter, J. Craig ^[2]; Allen, Andrew E. ^[9]

J. Craig Venter Inst., La Jolla, CA (United States); Office of Scientific and Technical Information (OSTI)
J. Craig Venter Inst., La Jolla, CA (United States)
American Univ. in Cairo, New Cairo (Egypt)
J. Craig Venter Inst., La Jolla, CA (United States); Univ. of Southern California, Los Angeles, CA (United States)
Washington Univ., St. Louis, MO (United States)
Univ. of California, San Diego, La Jolla, CA (United States)
Nicholas School of the Environment, Beaufort, NC (United States); Duke Univ., Durham, NC (United States)
Skidaway Institute of Oceanography, Savannah, GA (United States)
J. Craig Venter Inst., La Jolla, CA (United States); Univ. of California, San Diego, La Jolla, CA (United States)

Here, transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO₂ uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteria enriched in the>3.0-μm size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM.

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Research Organization:: J. Craig Venter Inst., La Jolla, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: FC02-02ER63453

OSTI ID:: 1346924

Journal Information:: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 5 Vol. 9; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (107)

Correlation of oxygen consumption, cytochrome c oxidase, and cytochrome c oxidase subunit I gene expression in the termination of larval diapause in the bamboo borer, Omphisa fuscidentalis Singtripop, Tippawan; Saeangsakda, Manasawan; Tatun, Nujira Journal of Insect Physiology, Vol. 53, Issue 9 https://doi.org/10.1016/j.jinsphys.2007.03.005	journal	September 2007
Phytoplankton carbon fixation gene (RuBisCO) transcripts and air-sea CO2 flux in the Mississippi River plume John, David E.; Wang, Zhaohui A.; Liu, Xuewu The ISME Journal, Vol. 1, Issue 6 https://doi.org/10.1038/ismej.2007.70	journal	August 2007
Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics Stewart, Frank J.; Ottesen, Elizabeth A.; DeLong, Edward F. The ISME Journal, Vol. 4, Issue 7 https://doi.org/10.1038/ismej.2010.18	journal	March 2010
Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean Shi, Yanmei; Tyson, Gene W.; Eppley, John M. The ISME Journal, Vol. 5, Issue 6 https://doi.org/10.1038/ismej.2010.189	journal	December 2010
Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic Allen, Lisa Zeigler; Allen, Eric E.; Badger, Jonathan H. The ISME Journal, Vol. 6, Issue 7 https://doi.org/10.1038/ismej.2011.201	journal	January 2012
The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs Lesniewski, Ryan A.; Jain, Sunit; Anantharaman, Karthik The ISME Journal, Vol. 6, Issue 12 https://doi.org/10.1038/ismej.2012.63	journal	June 2012
Mixotrophic haptophytes are key bacterial grazers in oligotrophic coastal waters Unrein, Fernando; Gasol, Josep M.; Not, Fabrice The ISME Journal, Vol. 8, Issue 1 https://doi.org/10.1038/ismej.2013.132	journal	August 2013
Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone Ganesh, Sangita; Parris, Darren J.; DeLong, Edward F. The ISME Journal, Vol. 8, Issue 1 https://doi.org/10.1038/ismej.2013.144	journal	September 2013
High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences Vergin, Kevin L.; Beszteri, Bánk; Monier, Adam The ISME Journal, Vol. 7, Issue 7 https://doi.org/10.1038/ismej.2013.32	journal	March 2013
The significance of nitrification for oceanic new production Yool, Andrew; Martin, Adrian P.; Fernández, Camila Nature, Vol. 447, Issue 7147 https://doi.org/10.1038/nature05885	journal	June 2007
Characterization of Prochlorococcus clades from iron-depleted oceanic regions Rusch, D. B.; Martiny, A. C.; Dupont, C. L. Proceedings of the National Academy of Sciences, Vol. 107, Issue 37 https://doi.org/10.1073/pnas.1009513107	journal	August 2010
Pattern and synchrony of gene expression among sympatric marine microbial populations Ottesen, E. A.; Young, C. R.; Eppley, J. M. Proceedings of the National Academy of Sciences, Vol. 110, Issue 6 https://doi.org/10.1073/pnas.1222099110	journal	January 2013
Microspatial gene expression patterns in the Amazon River Plume Satinsky, B. M.; Crump, B. C.; Smith, C. B. Proceedings of the National Academy of Sciences, Vol. 111, Issue 30 https://doi.org/10.1073/pnas.1402782111	journal	July 2014
Microbial diversity and the lability of dissolved organic carbon Nelson, C. E.; Wear, E. K. Proceedings of the National Academy of Sciences, Vol. 111, Issue 20 https://doi.org/10.1073/pnas.1405751111	journal	May 2014
A Rapid Bootstrap Algorithm for the RAxML Web Servers Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques Systematic Biology, Vol. 57, Issue 5 https://doi.org/10.1080/10635150802429642	journal	October 2008
Phenotypic Correlates of Genomic DNA Content in Unicellular Eukaryotes and Other Cells Shuter, B. J.; Thomas, J. E.; Taylor, W. D. The American Naturalist, Vol. 122, Issue 1 https://doi.org/10.1086/284116	journal	July 1983
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Katoh, K.; Standley, D. M. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mst010	journal	January 2013
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Pruitt, K. D. Nucleic Acids Research, Vol. 33, Issue Database issue https://doi.org/10.1093/nar/gki025	journal	December 2004
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Pruesse, E.; Quast, C.; Knittel, K. Nucleic Acids Research, Vol. 35, Issue 21 https://doi.org/10.1093/nar/gkm864	journal	November 2007
The integrated microbial genomes system: an expanding comparative analysis resource Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp887	journal	October 2009
Ensembl 2011 Flicek, P.; Amode, M. R.; Barrell, D. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1064	journal	November 2010
FragGeneScan: predicting genes in short and error-prone reads Rho, Mina; Tang, Haixu; Ye, Yuzhen Nucleic Acids Research, Vol. 38, Issue 20 https://doi.org/10.1093/nar/gkq747	journal	August 2010
The Pfam protein families database Punta, M.; Coggill, P. C.; Eberhardt, R. Y. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1065	journal	November 2011
GenBank Benson, D. A.; Karsch-Mizrachi, I.; Clark, K. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1202	journal	December 2011
The Genome Portal of the Department of Energy Joint Genome Institute Grigoriev, I. V.; Nordberg, H.; Shabalov, I. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr947	journal	November 2011
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach Whelan, Simon; Goldman, Nick Molecular Biology and Evolution, Vol. 18, Issue 5 https://doi.org/10.1093/oxfordjournals.molbev.a003851	journal	May 2001
Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes Zwirglmaier, Katrin; Jardillier, Ludwig; Ostrowski, Martin Environmental Microbiology, Vol. 0, Issue 0 https://doi.org/10.1111/j.1462-2920.2007.01440.x	journal	September 2007
Niche Partitioning Among Prochlorococcus Ecotypes Along Ocean-Scale Environmental Gradients Johnson, Z. I. Science, Vol. 311, Issue 5768 https://doi.org/10.1126/science.1118052	journal	March 2006
Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior DeLong, E. F. Science, Vol. 311, Issue 5760 https://doi.org/10.1126/science.1120250	journal	January 2006
Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones Walsh, D. A.; Zaikova, E.; Howes, C. G. Science, Vol. 326, Issue 5952 https://doi.org/10.1126/science.1175309	journal	October 2009
Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria Hazen, Terry C.; Dubinsky, Eric A.; DeSantis, Todd Z. Science, Vol. 330, Issue 6001 https://doi.org/10.1126/science.1195979	journal	August 2010
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota Iverson, V.; Morris, R. M.; Frazar, C. D. Science, Vol. 335, Issue 6068 https://doi.org/10.1126/science.1212665	journal	February 2012
Relationship between Abundance and Specific Activity of Bacterioplankton in Open Ocean Surface Waters Hunt, Dana E.; Lin, Yajuan; Church, Matthew J. Applied and Environmental Microbiology, Vol. 79, Issue 1 https://doi.org/10.1128/aem.02155-12	journal	October 2012
Geochemical Rate-RNA Integration Study: Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Gene Transcription and Photosynthetic Capacity of Planktonic Photoautotrophs Corredor, J. E.; Wawrik, B.; Paul, J. H. Applied and Environmental Microbiology, Vol. 70, Issue 9 https://doi.org/10.1128/aem.70.9.5459-5468.2004	journal	September 2004
Polyadenylation and Degradation of Human Mitochondrial RNA: the Prokaryotic Past Leaves Its Mark Slomovic, S.; Laufer, D.; Geiger, D. Molecular and Cellular Biology, Vol. 25, Issue 15 https://doi.org/10.1128/mcb.25.15.6427-6435.2005	journal	July 2005
Artificial and natural duplicates in pyrosequencing reads of metagenomic data Niu, Beifang; Fu, Limin; Sun, Shulei BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-187	journal	January 2010
A simple, fast, and accurate method of phylogenomic inference Wu, Martin; Eisen, Jonathan A. Genome Biology, Vol. 9, Issue 10 https://doi.org/10.1186/gb-2008-9-10-r151	journal	January 2008
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing Keeling, Patrick J.; Burki, Fabien; Wilcox, Heather M. PLoS Biology, Vol. 12, Issue 6 https://doi.org/10.1371/journal.pbio.1001889	journal	June 2014
Accelerated Profile HMM Searches Eddy, Sean R. PLoS Computational Biology, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pcbi.1002195	journal	October 2011
Metagenomic Sequencing of an In Vitro-Simulated Microbial Community Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A. PLoS ONE, Vol. 5, Issue 4 https://doi.org/10.1371/journal.pone.0010209	journal	April 2010
Energy Starved Candidatus Pelagibacter Ubique Substitutes Light-Mediated ATP Production for Endogenous Carbon Respiration Steindler, Laura; Schwalbach, Michael S.; Smith, Daniel P. PLoS ONE, Vol. 6, Issue 5 https://doi.org/10.1371/journal.pone.0019725	journal	May 2011
The Phylogenetic Diversity of Metagenomes Kembel, Steven W.; Eisen, Jonathan A.; Pollard, Katherine S. PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0023214	journal	August 2011
Cytochrome c Oxidase as a Cause of Variation in Oxygen Uptake Rates Among Vegetables Makino, Yoshio; Ichimura, Masayuki; Kawagoe, Yoshinori Journal of the American Society for Horticultural Science, Vol. 132, Issue 2 https://doi.org/10.21273/jashs.132.2.239	journal	March 2007
A Synechococcus serotype is found preferentially in surface marine waters Toledo, Gerardo; Palenik, Brian Limnology and Oceanography, Vol. 48, Issue 5 https://doi.org/10.4319/lo.2003.48.5.1744	journal	September 2003
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree Matsen, Frederick A.; Kodner, Robin B.; Armbrust, E. Virginia arXiv https://doi.org/10.48550/arxiv.1003.5943	preprint	January 2010
Prediction of effective genome size in metagenomic samples Raes, J.; Korbel, J. O.; Lercher, M. J. BioMed Central https://doi.org/10.5167/uzh-1017	text	January 2007
Phycoerythrin-containing picoplankton in the Southern California Bight Collier, Jackie L.; Palenik, Brian Deep Sea Research Part II: Topical Studies in Oceanography, Vol. 50, Issue 14-16 https://doi.org/10.1016/S0967-0645(03)00127-9	journal	August 2003
Global distribution of a wild alga revealed by targeted metagenomics Worden, Alexandra Z.; Janouskovec, Jan; McRose, Darcy Current Biology, Vol. 22, Issue 17 https://doi.org/10.1016/j.cub.2012.07.054	journal	September 2012
Correlation of oxygen consumption, cytochrome c oxidase, and cytochrome c oxidase subunit I gene expression in the termination of larval diapause in the bamboo borer, Omphisa fuscidentalis Singtripop, Tippawan; Saeangsakda, Manasawan; Tatun, Nujira Journal of Insect Physiology, Vol. 53, Issue 9 https://doi.org/10.1016/j.jinsphys.2007.03.005	journal	September 2007
Particulate organic matter flux and planktonic new production in the deep ocean Eppley, Richard W.; Peterson, Bruce J. Nature, Vol. 282, Issue 5740 https://doi.org/10.1038/282677a0	journal	December 1979
Phytoplankton carbon fixation gene (RuBisCO) transcripts and air-sea CO2 flux in the Mississippi River plume John, David E.; Wang, Zhaohui A.; Liu, Xuewu The ISME Journal, Vol. 1, Issue 6 https://doi.org/10.1038/ismej.2007.70	journal	August 2007
Quantitative analysis of a deeply sequenced marine microbial metatranscriptome Gifford, Scott M.; Sharma, Shalabh; Rinta-Kanto, Johanna M. The ISME Journal, Vol. 5, Issue 3 https://doi.org/10.1038/ismej.2010.141	journal	September 2010
Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics Stewart, Frank J.; Ottesen, Elizabeth A.; DeLong, Edward F. The ISME Journal, Vol. 4, Issue 7 https://doi.org/10.1038/ismej.2010.18	journal	March 2010
Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean Shi, Yanmei; Tyson, Gene W.; Eppley, John M. The ISME Journal, Vol. 5, Issue 6 https://doi.org/10.1038/ismej.2010.189	journal	December 2010
Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing Ghai, Rohit; Martin-Cuadrado, Ana-Belén; Molto, Aitor Gonzaga The ISME Journal, Vol. 4, Issue 9 https://doi.org/10.1038/ismej.2010.44	journal	April 2010
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage Dupont, Chris L.; Rusch, Douglas B.; Yooseph, Shibu The ISME Journal, Vol. 6, Issue 6 https://doi.org/10.1038/ismej.2011.189	journal	December 2011
Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic Allen, Lisa Zeigler; Allen, Eric E.; Badger, Jonathan H. The ISME Journal, Vol. 6, Issue 7 https://doi.org/10.1038/ismej.2011.201	journal	January 2012
The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs Lesniewski, Ryan A.; Jain, Sunit; Anantharaman, Karthik The ISME Journal, Vol. 6, Issue 12 https://doi.org/10.1038/ismej.2012.63	journal	June 2012
Expression patterns reveal niche diversification in a marine microbial assemblage Gifford, Scott M.; Sharma, Shalabh; Booth, Melissa The ISME Journal, Vol. 7, Issue 2 https://doi.org/10.1038/ismej.2012.96	journal	August 2012
Mixotrophic haptophytes are key bacterial grazers in oligotrophic coastal waters Unrein, Fernando; Gasol, Josep M.; Not, Fabrice The ISME Journal, Vol. 8, Issue 1 https://doi.org/10.1038/ismej.2013.132	journal	August 2013
Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone Ganesh, Sangita; Parris, Darren J.; DeLong, Edward F. The ISME Journal, Vol. 8, Issue 1 https://doi.org/10.1038/ismej.2013.144	journal	September 2013
High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences Vergin, Kevin L.; Beszteri, Bánk; Monier, Adam The ISME Journal, Vol. 7, Issue 7 https://doi.org/10.1038/ismej.2013.32	journal	March 2013
The significance of nitrification for oceanic new production Yool, Andrew; Martin, Adrian P.; Fernández, Camila Nature, Vol. 447, Issue 7147 https://doi.org/10.1038/nature05885	journal	June 2007
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets Chitsaz, Hamidreza; Yee-Greenbaum, Joyclyn L.; Tesler, Glenn Nature Biotechnology, Vol. 29, Issue 10 https://doi.org/10.1038/nbt.1966	journal	September 2011
Assimilation of upwelled nitrate by small eukaryotes in the Sargasso Sea Fawcett, Sarah E.; Lomas, Michael W.; Casey, John R. Nature Geoscience, Vol. 4, Issue 10 https://doi.org/10.1038/ngeo1265	journal	September 2011
Characterization of Prochlorococcus clades from iron-depleted oceanic regions Rusch, D. B.; Martiny, A. C.; Dupont, C. L. Proceedings of the National Academy of Sciences, Vol. 107, Issue 37 https://doi.org/10.1073/pnas.1009513107	journal	August 2010
Pattern and synchrony of gene expression among sympatric marine microbial populations Ottesen, E. A.; Young, C. R.; Eppley, J. M. Proceedings of the National Academy of Sciences, Vol. 110, Issue 6 https://doi.org/10.1073/pnas.1222099110	journal	January 2013
Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean Pedler, B. E.; Aluwihare, L. I.; Azam, F. Proceedings of the National Academy of Sciences, Vol. 111, Issue 20 https://doi.org/10.1073/pnas.1401887111	journal	April 2014
Microspatial gene expression patterns in the Amazon River Plume Satinsky, B. M.; Crump, B. C.; Smith, C. B. Proceedings of the National Academy of Sciences, Vol. 111, Issue 30 https://doi.org/10.1073/pnas.1402782111	journal	July 2014
A Rapid Bootstrap Algorithm for the RAxML Web Servers Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques Systematic Biology, Vol. 57, Issue 5 https://doi.org/10.1080/10635150802429642	journal	October 2008
Phenotypic Correlates of Genomic DNA Content in Unicellular Eukaryotes and Other Cells Shuter, B. J.; Thomas, J. E.; Taylor, W. D. The American Naturalist, Vol. 122, Issue 1 https://doi.org/10.1086/284116	journal	July 1983
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Katoh, K.; Standley, D. M. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mst010	journal	January 2013
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Pruitt, K. D.; Tatusova, T.; Maglott, D. R. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl842	journal	January 2007
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Pruesse, E.; Quast, C.; Knittel, K. Nucleic Acids Research, Vol. 35, Issue 21 https://doi.org/10.1093/nar/gkm864	journal	November 2007
The integrated microbial genomes system: an expanding comparative analysis resource Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp887	journal	October 2009
Ensembl 2011 Flicek, P.; Amode, M. R.; Barrell, D. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1064	journal	November 2010
FragGeneScan: predicting genes in short and error-prone reads Rho, Mina; Tang, Haixu; Ye, Yuzhen Nucleic Acids Research, Vol. 38, Issue 20 https://doi.org/10.1093/nar/gkq747	journal	August 2010
The Pfam protein families database Punta, M.; Coggill, P. C.; Eberhardt, R. Y. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1065	journal	November 2011
GenBank Benson, D. A.; Karsch-Mizrachi, I.; Clark, K. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1202	journal	December 2011
The Genome Portal of the Department of Energy Joint Genome Institute Grigoriev, I. V.; Nordberg, H.; Shabalov, I. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr947	journal	November 2011
KEGG for integration and interpretation of large-scale molecular data sets Kanehisa, M.; Goto, S.; Sato, Y. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr988	journal	November 2011
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach Whelan, Simon; Goldman, Nick Molecular Biology and Evolution, Vol. 18, Issue 5 https://doi.org/10.1093/oxfordjournals.molbev.a003851	journal	May 2001
Polyadenylation and Degradation of mRNA in the Chloroplast Schuster, Gadi; Lisitsky, Irena; Klaff, Petra Plant Physiology, Vol. 120, Issue 4 https://doi.org/10.1104/pp.120.4.937	journal	August 1999
ULTRASTRUCTURE AND 18S _R RNA GENE SEQUENCE FOR PELAGOMONAS CALCEOLATA GEN. ET SP. NOV. AND THE DESCRIPTION OF A NEW ALGAL CLASS, THE PELAGOPHYCEAE CLASSIS NOV. ¹ Andersen, Robert A.; Saunders, Gary W.; Paskind, Michael P. Journal of Phycology, Vol. 29, Issue 5 https://doi.org/10.1111/j.0022-3646.1993.00701.x	journal	October 1993
Microbial metatranscriptomics in a permanent marine oxygen minimum zone: OMZ community gene expression Stewart, Frank J.; Ulloa, Osvaldo; DeLong, Edward F. Environmental Microbiology, Vol. 14, Issue 1 https://doi.org/10.1111/j.1462-2920.2010.02400.x	journal	January 2011
Basin-scale patterns in the abundance of SAR11 subclades, marine Actinobacteria (OM1), members of the Roseobacter clade and OCS116 in the South Atlantic: Bacterioplankton communities in the South Atlantic Morris, Robert M.; Frazar, Christian D.; Carlson, Craig A. Environmental Microbiology, Vol. 14, Issue 5 https://doi.org/10.1111/j.1462-2920.2011.02694.x	journal	January 2012
Niche Partitioning Among Prochlorococcus Ecotypes Along Ocean-Scale Environmental Gradients Johnson, Z. I. Science, Vol. 311, Issue 5768 https://doi.org/10.1126/science.1118052	journal	March 2006
Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior DeLong, E. F. Science, Vol. 311, Issue 5760 https://doi.org/10.1126/science.1120250	journal	January 2006
Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones Walsh, D. A.; Zaikova, E.; Howes, C. G. Science, Vol. 326, Issue 5952 https://doi.org/10.1126/science.1175309	journal	October 2009
Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria Hazen, Terry C.; Dubinsky, Eric A.; DeSantis, Todd Z. Science, Vol. 330, Issue 6001 https://doi.org/10.1126/science.1195979	journal	August 2010
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota Iverson, V.; Morris, R. M.; Frazar, C. D. Science, Vol. 335, Issue 6068 https://doi.org/10.1126/science.1212665	journal	February 2012
Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom Teeling, H.; Fuchs, B. M.; Becher, D. Science, Vol. 336, Issue 6081 https://doi.org/10.1126/science.1218344	journal	May 2012
Relationship between Abundance and Specific Activity of Bacterioplankton in Open Ocean Surface Waters Hunt, Dana E.; Lin, Yajuan; Church, Matthew J. Applied and Environmental Microbiology, Vol. 79, Issue 1 https://doi.org/10.1128/AEM.02155-12	journal	October 2012
Geochemical Rate-RNA Integration Study: Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Gene Transcription and Photosynthetic Capacity of Planktonic Photoautotrophs Corredor, J. E.; Wawrik, B.; Paul, J. H. Applied and Environmental Microbiology, Vol. 70, Issue 9 https://doi.org/10.1128/AEM.70.9.5459-5468.2004	journal	September 2004
Polyadenylation and Degradation of Human Mitochondrial RNA: the Prokaryotic Past Leaves Its Mark Slomovic, S.; Laufer, D.; Geiger, D. Molecular and Cellular Biology, Vol. 25, Issue 15 https://doi.org/10.1128/MCB.25.15.6427-6435.2005	journal	July 2005
Artificial and natural duplicates in pyrosequencing reads of metagenomic data Niu, Beifang; Fu, Limin; Sun, Shulei BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-187	journal	January 2010
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree Matsen, Frederick A.; Kodner, Robin B.; Armbrust, E. Virginia BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-538	journal	October 2010
A simple, fast, and accurate method of phylogenomic inference Wu, Martin; Eisen, Jonathan A. Genome Biology, Vol. 9, Issue 10 https://doi.org/10.1186/gb-2008-9-10-r151	journal	January 2008
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