Publications (129)

Title Author Journal Date PubMed Project
Functional metagenomic profiling of nine biomes Elizabeth A. Dinsdale Nature 2008 Apr 3 18337718 Viral and Microbial Metagenomes from Salterns of Differing Salinities
Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges A Monier Environmental microbiology 2012 Jan 21914098  
Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria K Anantharaman Proceedings of the National Academy of Sciences of the United States of America 2013 Jan 2 23263870  
Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume Brett J. Baker The ISME journal 2012 Dec 22695863  
The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs R A Lesniewski The ISME journal 2012 Dec 22695860  
Diel gene expression profiles of a phosphorus limited mountain lake using metatranscriptomics M Villa-Costa Environmental microbiology 2013 Apr 23176588 Diel gene expression profiles of a phosphorus limited mountain lake using metatranscriptomics
Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill Adam R Rivers The ISME journal 2013 Dec 23902988 Transcriptional Response of Bathypelagic Marine Bacteria to the Deepwater Horizon Oil Spill
Pattern and synchrony of gene expression among sympatric marine microbial populations EA Ottesen Proceedings of the National Academy of Sciences of the United States of America 2013 Feb 5 23345438  
Sequencing platform and library preparation choices impact viral metagenomes Sergei A Solonenko BMC genomics 2013 May 10 23663384  
A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes Linda A. Amaral-Zettler PloS one 2009 Jul 27 19633714 Eukaryal V9 Tag Sequencing Methodology
Virus population dynamics and acquired virus resistance in natural microbial communities Anders F. Andersson Science (New York, N.Y.) 2008 May 23 18497291  
The marine viromes of four oceanic regions Florent E. Angly PLoS biology 2006 Nov 17090214 Ocean Viruses
Lineages of acidophilic archaea revealed by community genomic analysis Brett J. Baker Science (New York, N.Y.) 2006 Dec 22 17185602  
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria Ian Lo Nature 2007 Mar 29 17344860  
Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes Natalya Yutin Environmental microbiology 2007 Jun 17504484 Global Ocean Sampling Expedition (GOS)
Viral photosynthetic reaction center genes and transcripts in the marine environment Oded Beja The ISME journal 2007 Oct 18043651  
Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses Devaki Bhaya The ISME journal 2007 Dec 18059494  
Biogeography of photosynthetic light-harvesting genes in marine phytoplankton Thomas S. Bibby PloS one 2009 19240807  
Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment Jennifer F. Biddle Proceedings of the National Academy of Sciences of the United States of America 2008 Jul 29 18650394 Metagenomic signatures of the Peru Margin
Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm William J. Brazelton The ISME journal 2009 Dec 19571895 Hydrothermal Vent Metagenome
Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico Mya Breitbart Environmental microbiology 2009 Jan 18764874 Microbial metagenome from Rios Mesquites microbiolite
Community genomics among stratified microbial assemblages in the ocean's interior Edward F. DeLong Science (New York, N.Y.) 2006 Jan 27 16439655 Microbial Community Genomics at the HOT/ALOHA
Biodiversity and biogeography of phages in modern stromatolites and thrombolites Christelle Desnues Nature 2008 Mar 20 18311127 Viral Stromatolite Metagenome
Microbial ecology of four coral atolls in the Northern Line Islands Elizabeth A. Dinsdale PloS one 2008 Feb 27 18301735 Marine Metagenome from Line Islands
Microbial community gene expression in ocean surface waters Jorge Frias-Lopez Proceedings of the National Academy of Sciences of the United States of America 2008 Mar 11 18316740  
Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities Jack A. Gilbert PloS one 2008 Aug 22 18725995 Marine Metagenome from Coastal Waters project at Plymouth Marine Laboratory
Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters Jack A. Gilbert Environmental microbiology 2009 Jan 18783384  
The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation Jack A. Gilbert PloS one 2010 Nov 29 21124740 Western Channel Observatory Microbial Metagenomic Study
Metagenomic analysis of the human distal gut microbiome Steven R. Gill Science (New York, N.Y.) 2006 Jun 2 16741115 Human Distal Gut Biome project
Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility Joseph J. Grzymski Proceedings of the National Academy of Sciences of the United States of America 2008 Nov 11 18987310 Epibiont Metagenome
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities Philip Hugenholtz Nature biotechnology 2006 Oct 16998472 Phosphorus Removing (EBPR) Sludge Community
Surface Distribution and Population-Genetic Structure of Marine Microbes in the Indian Ocean Gyre (unpublished) J. Craig Venter Institute Unknown NA    
High-resolution metagenomics targets specific functional types in complex microbial communities Marina G Kalyuzhnaya Nature biotechnology 2008 Sep 18711340 Washington Lake Metagenomes
Chronic cigarette smoke causes oxidative damage and apoptosis to retinal pigmented epithelial cells in mice Natarajan Kannan PloS one 2008 Sep 1 18769672  
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans Nicole King Nature 2008 Feb 14 18273011 Alternative splicing in the choanoflagellate M. bre
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat Victor Kunin Molecular systems biology 2008 18523433 Metagenome isolated from Guerrero Negro hypersaline microbial mat in Mexico
Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species Boris A Legault BMC genomics 2006 Jul 4 16820057 Metagenome of Marine NaCl-Saturated Brine
Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering Shibu Yooseph BMC bioinformatics 2008 Apr 10 18402669  
Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses Asuncion Martinez Environmental microbiology 2010 Jan 19788654  
It's all relative: ranking the diversity of aquatic bacterial communities AK Shaw Environmental microbiology 2008 Sep 18637951  
Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression Lauren D. McDaniel PloS one 2008 Sep 23 18810270 Tampa Bay Induced Viral Metagenome
Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent S. L. McLellan Environmental microbiology 2010 Feb 19840106 Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent
Environmental drivers of a genomic transition zone in the ocean’s interior Mende D.R., Bryant J.A., Aylward F.O., Eppley J.M., Nielsen T.N., Karl D.M., DeLong E.F. Nature Microbiology 2017-08-14   Station ALOHA Gene Catalogue v1
Metagenomic diagnosis of bacterial infections Shota Nakamura Emerging infectious diseases 2008 Nov 18976571  
Patterns of damage in genomic DNA sequences from a Neandertal Joseph J. Grzymski Proceedings of the National Academy of Sciences of the United States of America 2007 Sep 11 17715061  
Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity Brian Palenik Environmental microbiology 2009 Feb 19196269 Marine Synechococcus metagenome experiment
Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics Annelie Pernthaler Proceedings of the National Academy of Sciences of the United States of America 2008 May 13 18467493 Diverse syntrophic partnerships by direct cell capture and metagenomics
Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome Ani Qu PloS one 2008 Aug 13 18698407 Chicken Cecum Microbiome
Community proteomics of a natural microbial biofilm Rachna J. Ram Science (New York, N.Y.) 2005 Jun 24 15879173  
Comparative metagenomics of microbial communities Susannah G. Tringe Science (New York, N.Y.) 2005 Apr 22 15845853  
Symbiosis insights through metagenomic analysis of a microbial consortium Tanja Woyke Nature 2006 Oct 26 16980956 Mediterranean Gutless Worm Metagenome
Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing Nina Sanapareddy Applied and environmental microbiology 2009 Mar 19114525 Wastewater Metagenome Mallard Creek
Matriptase-deficient mice exhibit ichthyotic skin with a selective shift in skin microbiota Tiffany C. Scharschmidt The Journal of investigative dermatology 2009 Oct 19387477  
Photosystem I gene cassettes are present in marine virus genomes Itai Sharon Nature 2009 Sep 10 19710652  
Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome Carola Simon Applied and environmental microbiology 2009 Dec 19801459 Ice Metagenome of the Northern Schneeferner
The airborne metagenome in an indoor urban environment Susannah G. Tringe PloS one 2008 Apr 2 18382653 Singapore Air Metagenome
An obesity-associated gut microbiome with increased capacity for energy harvest Peter J. Turnbaugh Nature 2006 Dec 21 17183312 Mouse Gut Community
A core gut microbiome in obese and lean twins Peter J. Turnbaugh Nature 2009 Jan 22 19043404 A core gut microbiome in obese and lean twins
Community structure and metabolism through reconstruction of microbial genomes from the environment Gene W. Tyson Nature 2004 Mar 4 14961025  
Genomic plasticity in prokaryotes: the case of the square haloarchaeon Francisco Rodriguez-Valera The ISME journal 2007 Jul 18043634  
Metagenomics of the deep Mediterranean, a warm bathypelagic habitat Ana-Belen Martin-Cuadrado PloS one 2007 Sep 19 17878949 Mediterranean Bathypelagic Habitat Metagenome
Environmental genome shotgun sequencing of the Sargasso Sea J. Craig Venter Science (New York, N.Y.) 2004 Apr 2 15001713  
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite Falk Warnecke Nature 2007 Nov 22 18033299 Termite Gut Metagenome
The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples Shannon J. Williamson PloS one 2008 Jan 23 18213365  
Metagenomic Characterization of Chesapeake Bay Virioplankton Shellie R. Bench Unknown NA 17921274 Chesapeake Bay Virioplankton Metagenome
Metagenomics: Read Length Matters K. Eric Wommack Unknown NA 18192407  
In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii Ian Hewson The ISME journal 2009 May 19225552  
RNA viral community in human feces: prevalence of plant pathogenic viruses Tao Zhang PLoS biology 2006 Jan 16336043 Uncultured Human Fecal Virus Metagenome
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes Ken Kurokawa DNA research : an international journal for rapid publication of reports on genes and genomes 2007 Aug 31 17916580 13 Healthy Human Gut Metagenomes
Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre Rachel S. Poretsky Environmental microbiology 2009 Jun 19207571 Comparative day/night metatranscriptomic analysis of microbial communities
Metabolically active eukaryotic communities in extremely acidic mine drainage. Baker BJ, Lutz MA, Dawson SC, Bond PL, Banfield JF Applied and environmental microbiology 2004 Oct 15466574 Acid Mine Drainage Metagenome
An integrative study of a meromictic lake ecosystem in Antarctica. Lauro FM, DeMaere MZ, Yau S, Brown MV, Ng C, Wilkins D, Raftery MJ, Gibson JA, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Thomas T, Cavicchioli R The ISME journal 2011 May 21124488 Antarctica Aquatic Microbial Metagenome
Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griffithsii. Lucero ME, Unc A, Cooke P, Dowd S, Sun S PloS one 2011 Mar 17 21437280 Host-microbe interactions in an Atriplex microbiome
Seasonality in ocean microbial communities. Giovannoni SJ, Vergin KL Science (New York, N.Y.) 2012 Feb 10 22323811 Metagenomic Analysis of the North Atlantic Spring Bloom
Microbial oceanography in a sea of opportunity. Bowler C, Karl DM, Colwell RR Nature 2009 May 14 19444203 Marine Bacterioplankton Metagenomes
The genomic basis of trophic strategy in marine bacteria. Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S, DeMaere MZ, Ting L, Ertan H, Johnson J, Ferriera S, Lapidus A, Anderson I, Kyrpides N, Munk AC, Detter C, Han CS, Brown MV, Robb FT, Kjelleberg S, Cavicchioli R Proceedings of the National Academy of Sciences of the United States of America 2009 Sep 15 19805210 Botany Bay Metagenomes
Metagenomic analysis of stressed coral holobionts. Vega Thurber R, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, Angly F, Dinsdale E, Kelly L, Rohwer F Environmental microbiology 2009 Aug 19397678 Metagenomic analysis of stressed coral holobionts
Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Poinar HN, Schwarz C, Qi J, Shapiro B, Macphee RD, Buigues B, Tikhonov A, Huson DH, Tomsho LP, Auch A, Rampp M, Miller W, Schuster SC Science (New York, N.Y.) 2006 Jan 20 16368896 Fossil Metagenome
The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Science (New York, N.Y.) 2004 Oct 1 15459382 Intra-Species Genetic Diversity of the Centric Diatom Thalassiosira Pseudonana: Genome-Wide Comparisons via Massively Parallel Short-Read DNA Sequencing
High diversity of the viral community from an Antarctic lake. López-Bueno A, Tamames J, Velázquez D, Moya A, Quesada A, Alcamí A Science (New York, N.Y.) 2009 Nov 6 19892985 Viral Metagenome from the Freshwater Lake Limnopolar
Ferritin is used for iron storage in bloom-forming marine pennate diatoms. Marchetti A, Parker MS, Moccia LP, Lin EO, Arrieta AL, Ribalet F, Murphy ME, Maldonado MT, Armbrust EV Nature 2009 Jan 22 19037243 The use and regulation of ferritin for iron sequestration in marine pennate diatoms
Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Mincer TJ, Church MJ, Taylor LT, Preston C, Karl DM, DeLong EF Environmental microbiology 2007 May 17472632 Monterey Bay Microbial Study
The skin microbiome. Grice EA, Segre JA Nature reviews. Microbiology 2011 Apr 21407241 Mouse Skin Metagenome
Metagenomic analysis of viruses in reclaimed water. Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M Environmental microbiology 2009 Nov 19555373 Metagenomic analysis of viruses in reclaimed water
One carbon metabolism in SAR11 pelagic marine bacteria. Sun J, Steindler L, Thrash JC, Halsey KH, Smith DP, Carter AE, Landry ZC, Giovannoni SJ PloS one 2011 21886845 AAP gene operon study of SAR11 clades
Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. Gifford SM, Sharma S, Rinta-Kanto JM, Moran MA The ISME journal 2011 Mar 20844569 Sapelo Island Microbial Observatory (SIMO) metatranscriptomes pt I
Bacterial taxa that limit sulfur flux from the ocean. Howard EC, Henriksen JR, Buchan A, Reisch CR, Bürgmann H, Welsh R, Ye W, González JM, Mace K, Joye SB, Kiene RP, Whitman WB, Moran MA Science (New York, N.Y.) 2006 Oct 27 17068264 Sapelo Island Bacterioplankton Metagenome
Environmental, biochemical and genetic drivers of DMSP degradation and DMS production in the Sargasso Sea. Levine NM, Varaljay VA, Toole DA, Dacey JW, Doney SC, Moran MA Environmental microbiology 2012 May 22324779 Microbial controls on DMSP degradation and DMS formation in the Sargasso Sea
Rapid diversification of coevolving marine Synechococcus and a virus. Marston MF, Pierciey FJ Jr, Shepard A, Gearin G, Qi J, Yandava C, Schuster SC, Henn MR, Martiny JB Proceedings of the National Academy of Sciences of the United States of America 2012 Mar 20 22388749 Synechococcus Study
Assembly of viral metagenomes from yellowstone hot springs. Schoenfeld T, Patterson M, Richardson PM, Wommack KE, Young M, Mead D Applied and environmental microbiology 2008 Jul 18441115 Viral Metagenomes from Terrestrial Hot Springs
Metagenomics: DNA sequencing of environmental samples. Tringe SG, Rubin EM Nature reviews. Genetics 2005 Nov 16304596 Whale Fall Metagenome
In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats. Steunou AS, Bhaya D, Bateson MM, Melendrez MC, Ward DM, Brecht E, Peters JW, Kühl M, Grossman AR Proceedings of the National Academy of Sciences of the United States of America 2006 Feb 14 16467157 Yellowstone National Park Octopus/Mushroom Hot Springs Metagenome
The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. Hurwitz BL, Sullivan MB PloS one 2013 23468974 Pacific Ocean Virus (POV) Protein Clusters
Community and proteomic analysis of methanogenic consortia degrading terephthalate. Wu JH, Wu FY, Chuang HP, Chen WY, Huang HJ, Chen SH, Liu WT Applied and environmental microbiology 2013 Jan 23064332 Metagenomic sequencing of terephthalate-degrading consortia from mother reactor (TA_mother_DNA)
Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, Nelson KE, Torralba M, Henrissat B, Coutinho PM, Cann IK, White BA, Fahey GC Jr The ISME journal 2011 Apr 20962874 Canine fecal metagenome
Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume. Dick GJ, Tebo BM Environmental microbiology 2010 May 20192971 Guaymas Basin deep-sea Metagenome
Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: Devil's Hole, Bermuda. Parsons RJ, Nelson CE, Carlson CA, Denman CC, Andersson AJ, Kledzik AL, Vergin KL, McNally SP, Treusch AH, Giovannoni SJ Environmental microbiology 2014 Mar 3 24589037 Bermuda Oceanic Microbial Observatory Course
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR, Chisholm SW, DeLong EF Proceedings of the National Academy of Sciences of the United States of America 2010 Sep 21 20807744 Bloomer DOM addition experiment
Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus. Demir-Hilton E, Sudek S, Cuvelier ML, Gentemann CL, Zehr JP, Worden AZ The ISME journal 2011 Jul 21289652 Monterey Bay transect CN207 sampling sites
Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment. Shi Y, McCarren J, DeLong EF Environmental microbiology 2012 Jan 21981709 Bloomer DSW addition experiment
Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning. Steward GF, Preston CM Virology journal 2011 Jun 9 21651822 Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning
Metatranscriptomic analysis of sulfur oxidation genes in the endosymbiont of solemya velum. Stewart FJ, Dmytrenko O, Delong EF, Cavanaugh CM Frontiers in microbiology 2011 21738524 Solemya velum symbiont gill transcriptome
Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis. Danhorn T, Young CR, DeLong EF The ISME journal 2012 Nov 22534608 Two HOT Fosmid end depth profiles (HOT179 and HOT186)
Antibiotics in feed induce prophages in swine fecal microbiomes. Allen HK, Looft T, Bayles DO, Humphrey S, Levine UY, Alt D, Stanton TB mBio 2011 22128350 Swine fecal viromes with and without in-feed antibiotics
Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil. de Menezes A, Clipson N, Doyle E Environmental microbiology 2012 Sep 22625871 Metatranscriptomics of contaminated soil
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Duhaime MB, Deng L, Poulos BT, Sullivan MB Environmental microbiology 2012 Sep 22713159 Linker amplification for quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples
Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Hurwitz BL, Deng L, Poulos BT, Sullivan MB Environmental microbiology 2013 May 22845467 Comparative evaluation of methods to concentrate and purify wild ocean virus communities through replicated metagenomics
Stimulated bacterioplankton growth and selection for certain bacterial taxa in the vicinity of the ctenophore Mnemiopsis leidyi. Dinasquet J, Granhag L, Riemann L Frontiers in microbiology 2012 22912629 Mleidyi_bacteria
Global patterns of diversity and community structure in marine bacterioplankton. Pommier T, Canbäck B, Riemann L, Boström KH, Simu K, Lundberg P, Tunlid A, Hagström A Molecular ecology 2007 Feb 17284217 Community succession in DOC utilization experiment reflects functional adaptation in marine bacterioplankton
Soil microbial diversity in the vicinity of desert shrubs. Saul-Tcherkas V, Unc A, Steinberger Y Microbial ecology 2013 Apr 23192699 Bacterial Diversity in Soils under Artemisia sieberi and Noaea mucronata plants in the Negev Desert
Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes. Hewson I, Barbosa JG, Brown JM, Donelan RP, Eaglesham JB, Eggleston EM, LaBarre BA Applied and environmental microbiology 2012 Sep 22773646 Trichodesmium Viral Community Metagenome
Nitrogen biogeochemistry in the Caribbean sponge, Xestospongia muta: a source or sink of dissolved inorganic nitrogen? Fiore CL, Baker DM, Lesser MP PloS one 2013 23991166 Symbiotic prokaryotic communities in sponges
Fluorescent epibiotic microbial community on the carapace of a Bahamian ostracod. Jarett J, Fiore C, Mazel C, Lesser M Archives of microbiology 2013 Sep 23861150 Fluorescent epibiotic biofilm on Bahamaian ostracods
Near real-time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California, using rRNA-targeted DNA probes. Preston CM, Marin R 3rd, Jensen SD, Feldman J, Birch JM, Massion EI, Delong EF, Suzuki M, Wheeler K, Scholin CA Environmental microbiology 2009 May 19210704 Lagrangian sampling of Monterey Bay Surface waters
Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging. Deng L, Gregory A, Yilmaz S, Poulos BT, Hugenholtz P, Sullivan MB mBio 2012 Oct 30 23111870 Population structure of wild ocean cyanobacterial viruses revealed by viral-tagged metagenomics
Alternatives to vitamin B1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages. McRose D, Guo J, Monier A, Sudek S, Wilken S, Yan S, Mock T, Archibald JM, Begley TP, Reyes-Prieto A, Worden AZ The ISME journal 2014 Dec 25171333 Micromonas sp. CCMP2099, Pyramomonas parkeae CCMP725 and Prasinoderma coloniale CCMP1413 transcriptomes
Metagenomics of the water column in the pristine upper course of the Amazon river. Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D, Rinke R, Cristina Souza de Oliveira T, Wagner Garcia J, Pellon de Miranda F, Henrique-Silva F PloS one 2011 21915244 RIVER AMAZON METAGENOME
Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. Ghai R, Martin-Cuadrado AB, Molto AG, Heredia IG, Cabrera R, Martin J, Verdú M, Deschamps P, Moreira D, López-García P, Mira A, Rodriguez-Valera F The ISME journal 2010 Sep 20393571 Deep Chlorophyll Maximum Metagenome
The Santa Pola saltern as a model for studying the microbiota of hypersaline environments. Ventosa A, Fernández AB, León MJ, Sánchez-Porro C, Rodriguez-Valera F Extremophiles : life under extreme conditions 2014 Sep 25129545 Santa Pola Saltern 37 percent
Metagenomes of Mediterranean coastal lagoons. Ghai R, Hernandez CM, Picazo A, Mizuno CM, Ininbergs K, Díez B, Valas R, DuPont CL, McMahon KD, Camacho A, Rodriguez-Valera F Scientific reports 2012 22778901 Hypersaline_Lagoon_MarMenor
The transcriptional response of prokaryotes to phytoplankton-derived dissolved organic matter in seawater. Beier S, Rivers AR, Moran MA, Obernosterer I Environmental microbiology 2014 Feb 25 24612402 A biomolecular approach to the cycling of carbon and iron in the ocean
Culture-dependent and culture-independent analyses reveal no prokaryotic community shifts or recovery of Serratia marcescens in Acropora palmata with white pox disease. Lesser MP, Jarett JK FEMS microbiology ecology 2014 Jun 24597458 White pox in Acropora palmata
Microbial diversity under extreme euxinia: Mahoney Lake, Canada. Klepac-Ceraj V, Hayes CA, Gilhooly WP, Lyons TW, Kolter R, Pearson A Geobiology 2012 May 22329601 Mahoney Lake Metagenome
Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. Hurwitz BL, Westveld AH, Brum JR, Sullivan MB Proceedings of the National Academy of Sciences of the United States of America 2014 Jul 22 25002514 Southern Ocean Viromes (SOV)
Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the Eastern North Pacific Ocean Melinda P. Simmons, Sebastian Sudek, Adam Monier, Alexander J. Limardo, Valeria Jimenez, Christopher R. Perle, Virginia A. Elrod, J. Timothy Pennington, and Alexandra Z. Worden Unpublished NA   North Pacific metatranscriptomes from Monterey Bay to Open Ocean (CalCOFI Line 67) October 2009
Ocean plankton. Patterns and ecological drivers of ocean viral communities. Acinas SG, Alberti A, Bork P, Bowler C, Brum JR, Chaffron S, Cruaud C, Dimier C, Doulcier G, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Ignacio-Espinoza JC, Iudicone D, Kandels-Lewis S, Karsenti E, Not F, Ogata H, Pesant S, Picheral M, Poulos BT, Roux S, Schwenck SM, Searson S, Speich S, Sullivan MB, Sunagawa S, Wincker P, de Vargas C Science 2015 May 22 25999515 Tara Ocean Viromes (TOV)
The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. Bushman FD, Grice EA, Hannigan GD, Hodkinson BP, Meisel JS, Minot S, SanMiguel AJ, Tyldsley AS, Zheng Q MBio 2015 Oct 20 26489866 The Human Skin Double-Stranded DNA Virome
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. Allen AE, Bai J, Barbeau KA, Dupont CL, Goodenough U, Hogle SL, Johnson ZI, Mann E, McCrow JP, Moustafa A, Palenik B, Roth R, Valas R, Venter JC, Walworth N ISME J 2015 May 25333462 Southern California Bight microbial metagenomics
Community genomics among stratified microbial assemblages in the ocean’s interior DeLong, E. F., Preston, C. M.., Martinez, A., Mincer, T., Frigaard, N.U., Rich, V., Hallam, S. J., Sullivan, M., Edwards, R., Beltran, R.B., Chisholm, S. W., and D. M. Karl Science NA 16439655 Station ALOHA Gene Catalogue v1