Research Topics
| Edward F DeLongSummaryAffiliation: Massachusetts Institute of Technology Country: USA Publications
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Publications
Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine CrenarchaeotaSteven J Hallam
Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
PLoS Biol 4:e95. 2006..These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems...
Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communitiesFrank J Stewart
School of Biology, Georgia Institute of Technology, Ford ES and T Building, Rm 1242, 311 Ferst Drive, Atlanta, GA 30332, USA
Genome Biol 12:R26. 2011..The link between gene expression level and sequence conservation was examined using shotgun pyrosequencing of microbial community DNA and RNA from diverse marine environments, and from forest soil...- Archaeal mysteries of the deep revealedEdward F DeLong
Division of Biological Engineering and Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 103:6417-8. 2006 
Community genomics among stratified microbial assemblages in the ocean's interiorEdward F DeLong
Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Science 311:496-503. 2006..Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics...- Genomic perspectives in microbial oceanographyEdward F DeLong
Department of Civil and Environmental Engineering and Division of Biological Engineering, 48 427 Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nature 437:336-42. 2005..Integration of these new genome-enabled insights into the broader framework of ocean science represents one of the great contemporary challenges for microbial oceanographers... - Microbiology. Life on the thermodynamic edgeEdward F DeLong
Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Science 317:327-8. 2007 - Microbial community genomics in the oceanEdward F DeLong
Division of Biological Engineering and Department of Civil and Environmental Engineering, Room 48 427, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Nat Rev Microbiol 3:459-69. 2005..Besides providing new perspectives on oceanic microbial communities, these new studies are now poised to reveal the fundamental principles that drive microbial ecological and evolutionary processes... 
Modern microbial seascapes. ForwardEdward F DeLong
Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA E mail
Nat Rev Microbiol 5:755-7. 2007..Here, Edward DeLong discusses the selection of articles in this Focus issue, in the context of the challenges and opportunities that face microbial oceanographers today...- The microbial ocean from genomes to biomesEdward F DeLong
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nature 459:200-6. 2009.... - Microbiology. Microbial life breathes deepEdward F DeLong
Department of Civil and Environmental Engineering and Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Science 306:2198-200. 2004 - Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyreKonstantinos T Konstantinidis
Department of Civil and Environmental Engineering and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Appl Environ Microbiol 75:5345-55. 2009.... - Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analysesAsuncion Martinez
Department of Civil and Environmental Engineering, Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
Environ Microbiol 12:222-38. 2010.... - Microbial community gene expression in ocean surface watersJorge Frias-Lopez
Departments of Civil and Environmental Engineering and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 105:3805-10. 2008..Thus, microbial community transcriptomic analyses revealed not only indigenous gene- and taxon-specific expression patterns but also gene categories undetected in previous DNA-based metagenomic surveys... - Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical GyreVinh D Pham
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Environ Microbiol 10:2313-30. 2008.... - Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methodsVinh D Pham
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Environ Microbiol 11:176-87. 2009..These data suggest that acetate may be a key intermediary metabolite in this subsurface anaerobic food chain, which leads to methane production as the primary terminal electron sink... - Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and ArchaeaNiels-Ulrik Frigaard
Department of Civil and Environmental Engineering and Division of Biological Engineering, Massachusetts Institute of Technology, Building 48, 15 Vassar Street, Cambridge, Massachusetts 02139, USA
Nature 439:847-50. 2006.... - Metatranscriptomics reveals unique microbial small RNAs in the ocean's water columnYanmei Shi
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nature 459:266-9. 2009.... - Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical GyreTracy J Mincer
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, MA 02139, USA
Environ Microbiol 9:1162-75. 2007..Additionally, distributional patterns of planktonic Crenarchaea and Nitrospina species suggest potential metabolic interactions between these groups in the ocean's water column... - Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open oceanYanmei Shi
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02139, USA
ISME J 5:999-1013. 2011..In total, the data support the utility of coupled DNA and cDNA analyses for describing taxonomic and functional attributes of microbial communities in their natural habitats... - Genomic islands and the ecology and evolution of ProchlorococcusMaureen L Coleman
Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, 15 Vassar Street, Cambridge, MA 02139, USA
Science 311:1768-70. 2006..Genomic islands in this free-living photoautotroph share features with pathogenicity islands of parasitic bacteria, suggesting a general mechanism for niche differentiation in microbial species... - Design and testing of 'genome-proxy' microarrays to profile marine microbial communitiesVirginia I Rich
The MIT WHOI Joint Program in Biological Oceanography, MIT, 48 427, 15 Vassar St, Cambridge, MA 02139, USA
Environ Microbiol 10:506-21. 2008.... - Genomic patterns of recombination, clonal divergence and environment in marine microbial populationsKonstantinos T Konstantinidis
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
ISME J 2:1052-65. 2008.... - Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the seaJay McCarren
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 107:16420-7. 2010.... - Time-series analyses of Monterey Bay coastal microbial picoplankton using a 'genome proxy' microarrayVirginia I Rich
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Environ Microbiol 13:116-34. 2011..The array provided a relatively cost-effective approach (∼$15 per array) for surveying the natural history of uncultivated lineages... - Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplanktonElizabeth A Ottesen
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
ISME J 5:1881-95. 2011..These laboratory and field tests confirmed that autonomous collection and preservation is a feasible and useful approach for characterizing the expressed genes and environmental responses of marine microbial communities... - Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendmentYanmei Shi
Department of Civil and Environmental Engineering Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Environ Microbiol 14:191-206. 2012..In total, the results provide new insight into short-term responses of picoplankton to DSW mixing, which occur prior to the more well-studied, longer-term growth responses of larger phytoplankton species... - Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomicsFrank J Stewart
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Parsons Laboratory, Cambridge, MA 02139, USA
ISME J 4:896-907. 2010..These results indicate that pyrosequencing captures a small subset of total mRNA diversity and underscores the importance of reliable rRNA subtraction procedures to enhance sequencing coverage across the functional transcript pool... - Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosumSteven J Hallam
Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 103:18296-301. 2006..In total, the C. symbiosum genome was remarkably distinct from those of other known Archaea and shared many core metabolic features in common with its free-living planktonic relatives... - Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zoneJessica A Bryant
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Parsons Laboratory 48, 15 Vassar Street, Cambridge, Massachusetts 02139, USA
Ecology 93:1659-73. 2012..Finally, we discuss how our results may relate to niche theory, diversity-energy relationships and stress gradients... - Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacteriumHiroyuki Kimura
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
ISME J 5:1641-51. 2011..In total, the results suggested the importance of both the PR-enabled, light-driven proton gradient, as well as the generation of a Na(+) ion gradient, as essential components for light-enhanced growth in these flavobacteria... - Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phylaJay McCarren
Department of Civil and Environmental Engineering and Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Environ Microbiol 9:846-58. 2007..Strong selection pressure apparently acts to preserve these light-dependent photosystems in diverse marine microbial lineages... - Phosphite utilization by the marine picocyanobacterium Prochlorococcus MIT9301Asuncion Martinez
Department of Civil and Environmental Engineering Division of Biological Engineering Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
Environ Microbiol 14:1363-77. 2012..These results strongly suggest that phosphite represents a previously unrecognized component of the marine P cycle... - Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysisThomas Danhorn
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
ISME J 6:2056-66. 2012.... - Metatranscriptomic analysis of sulfur oxidation genes in the endosymbiont of solemya velumFrank J Stewart
School of Biology, Georgia Institute of Technology Atlanta, GA, USA
Front Microbiol 2:134. 2011.... - Microbial metatranscriptomics in a permanent marine oxygen minimum zoneFrank J Stewart
School of Biology, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332, USA
Environ Microbiol 14:23-40. 2012..g. sulfur oxidation), highlight gene-specific expression patterns in the context of the entire community transcriptome, as well as identify key functional groups for taxon-specific genomic profiling... - Microbial population genomics and ecology: the road aheadEdward F DeLong
Massachusetts Institute of Technology, Cambridge, MA, USA
Environ Microbiol 6:875-8. 2004 - Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provincesOded Beja
Monterey Bay Aquarium Research Institute, Moss Landing, California 95039, USA
Appl Environ Microbiol 68:335-45. 2002..Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated... - Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissolutaAndreas Schirmer
Kosan Biosciences Inc, 3832 Bay Center Place, Hayward, CA 94545, USA
Appl Environ Microbiol 71:4840-9. 2005..The filamentous bacterial community of D. dissoluta consists mainly of Entotheonella spp., an unculturable sponge-specific taxon previously implicated in the biosynthesis of bioactive peptides... - Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuous-flow bioreactorPeter R Girguis
Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California 95039, USA
Appl Environ Microbiol 71:3725-33. 2005.... - Microbiology: reconstructing the wild typesEdward F DeLong
Nature 428:25-6. 2004 - Different SAR86 subgroups harbour divergent proteorhodopsinsGazalah Sabehi
Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
Environ Microbiol 6:903-10. 2004.... - Reverse methanogenesis: testing the hypothesis with environmental genomicsSteven J Hallam
Monterey Bay Aquarium Research Institute, Moss Landing, CA 95064, USA
Science 305:1457-62. 2004..These genome-based observations support previous hypotheses and provide an informed foundation for metabolic modeling of anaerobic methane oxidation... - Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaeaAnnelie Pernthaler
Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
Appl Environ Microbiol 68:661-7. 2002..g., coastal surface waters during spring and summer... - Proteorhodopsin genes are distributed among divergent marine bacterial taxaJosé R de la Torre
Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
Proc Natl Acad Sci U S A 100:12830-5. 2003..Our analyses also demonstrate the utility of cultivation-independent comparative genomic approaches for assessing gene content and distribution in naturally occurring microbes... - Unsuspected diversity among marine aerobic anoxygenic phototrophsOded Beja
Monterey Bay Aquarium Research Institute, Moss Landing, California 95039 0628, USA
Nature 415:630-3. 2002.... - Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactorPeter R Girguis
Monterey Bay Aquarium Research Institute, Moss Landing, California 95039, USA
Appl Environ Microbiol 69:5472-82. 2003..The AMIS may also enable the enrichment, purification, and isolation of methanotrophic archaea as pure cultures or defined syntrophic consortia... - Microbial population genomics and ecologyEdward F DeLong
Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
Curr Opin Microbiol 5:520-4. 2002..Genome-enabled approaches are now significantly advancing current knowledge of genome content, diversity, population biology and evolution in natural microbial populations... - Low genomic diversity in tropical oceanic N2-fixing cyanobacteriaJonathan P Zehr
Department of Ocean Sciences, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
Proc Natl Acad Sci U S A 104:17807-12. 2007..Although genomic diversity seems to be the rule in many, if not most, marine microbial lineages, different forces may control the evolution and diversification in low abundance microorganisms, such as the nitrogen-fixing cyanobacteria... - Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaeaSteven J Hallam
Monterey Bay Aquarium Research Institute, Moss Landing, California 95039-9644, USA
Appl Environ Microbiol 69:5483-91. 2003..These results provide a basis for identifying methanotrophic archaea with mcrA sequences and define a functional genomic link between methanogenic and methanotrophic archaea... - Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomesDagmar Woebken
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
ISME J 1:419-35. 2007..stuttgartiensis plus the surprising lack of almost any planctomycete-specific gene within this organism reveals an unexpected distinctiveness of anammox bacteria from all other Planctomycetes... - Power from the deepEdward F DeLong
Nat Biotechnol 20:788-9. 2002 - The microbial engines that drive Earth's biogeochemical cyclesPaul G Falkowski
Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
Science 320:1034-9. 2008..A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales... - Comparative genomics of DNA fragments from six Antarctic marine planktonic bacteriaJoseph J Grzymski
Desert Research Institute, 2215 Raggio Parkway, Reno, NV 89512, USA
Appl Environ Microbiol 72:1532-41. 2006..These characteristics were not specific to any one phylum, COG role category, or G+C content and imply that underlying genotypic and biochemical adaptations to the cold are inherent to life in the permanently subzero Antarctic waters... - Multiple archaeal groups mediate methane oxidation in anoxic cold seep sedimentsVictoria J Orphan
Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
Proc Natl Acad Sci U S A 99:7663-8. 2002..Other microbial groups, including ANME-1 archaea, are capable of anaerobic methane consumption either as single cells, in monospecific aggregates, or in multispecies consortia... - Molecular diversity among marine picophytoplankton as revealed by psbA analysesGil Zeidner
Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
Environ Microbiol 5:212-6. 2003..Furthermore, using environmental bacterial artificial chromosome (BAC) libraries, we were able to correlate psbA genes with small subunit rRNAs and, therefore, to confirm their phylogenetic affiliation... - Histones in crenarchaeaKathleen Sandman
Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
J Bacteriol 187:5482-5. 2005..The discovery of histones in Crenarchaea supports the argument that histones evolved before the divergence of Archaea and Eukarya... - Novel Proteorhodopsin variants from the Mediterranean and Red SeasGazalah Sabehi
Department of Biology, Technion- Israel Institute of Technology, Haifa 32000, Israel
Environ Microbiol 5:842-9. 2003..These variants could represent functionally divergent paralogous genes, derived from the same or similar species, or orthologous proteorhodopsins that are distributed amongst divergent planktonic microbial taxa... - Microbiology: all in the packagingEdward F DeLong
Nature 419:676-7. 2002 - Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonucleaseShigeo Yoshinari
Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
Biochem Biophys Res Commun 346:1024-32. 2006..tokodaii. These observations are consistent with previous reports indicating that subunit composition of the splicing endonuclease contributes to substrate specificity...