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  • 1
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    Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection (2019)
    Springer Nature
    Details
    Publication Date: 2019
    Print ISSN: 1751-7362
    Electronic ISSN: 1751-7370
    Topics: Biology
    Published by Springer Nature on behalf of The International Society for Microbial Ecology (ISME).
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  • 2
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    Bacterial rhodopsin: evidence for a new type of phototrophy in the sea (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-09-16
    Description: Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential in response to light have been demonstrated only in halophilic archaea. We describe here a type of rhodopsin derived from bacteria that was discovered through genomic analyses of naturally occuring marine bacterioplankton. The bacterial rhodopsin was encoded in the genome of an uncultivated gamma-proteobacterium and shared highest amino acid sequence similarity with archaeal rhodopsins. The protein was functionally expressed in Escherichia coli and bound retinal to form an active, light-driven proton pump. The new rhodopsin exhibited a photochemical reaction cycle with intermediates and kinetics characteristic of archaeal proton-pumping rhodopsins. Our results demonstrate that archaeal-like rhodopsins are broadly distributed among different taxa, including members of the domain Bacteria. Our data also indicate that a previously unsuspected mode of bacterially mediated light-driven energy generation may commonly occur in oceanic surface waters worldwide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beja, O -- Aravind, L -- Koonin, E V -- Suzuki, M T -- Hadd, A -- Nguyen, L P -- Jovanovich, S B -- Gates, C M -- Feldman, R A -- Spudich, J L -- Spudich, E N -- DeLong, E F -- HG01775-02S1/HG/NHGRI NIH HHS/ -- R01GM27750/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 15;289(5486):1902-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039-0628, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10988064" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Amino Acid Sequence ; Archaea/classification/physiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Cloning, Molecular ; Escherichia coli ; Gammaproteobacteria/classification/genetics/*physiology ; Molecular Sequence Data ; Oceans and Seas ; Photochemistry ; Photosynthesis ; Phylogeny ; Phytoplankton/genetics/physiology ; Protein Binding ; Proton Pumps/physiology ; Retinaldehyde/metabolism ; Rhodopsin/*physiology ; Rhodopsins, Microbial ; *Water Microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-21
    Description: Microorganisms living in anoxic marine sediments consume more than 80% of the methane produced in the world's oceans. In addition to single-species aggregates, consortia of metabolically interdependent bacteria and archaea are found in methane-rich sediments. A combination of fluorescence in situ hybridization and secondary ion mass spectrometry shows that cells belonging to one specific archaeal group associated with the Methanosarcinales were all highly depleted in 13C (to values of -96 per thousand). This depletion indicates assimilation of isotopically light methane into specific archaeal cells. Additional microbial species apparently use other carbon sources, as indicated by significantly higher 13C/12C ratios in their cell carbon. Our results demonstrate the feasibility of simultaneous determination of the identity and the metabolic activity of naturally occurring microorganisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Orphan, V J -- House, C H -- Hinrichs, K U -- McKeegan, K D -- DeLong, E F -- New York, N.Y. -- Science. 2001 Jul 20;293(5529):484-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11463914" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Carbon Isotopes/analysis ; Deltaproteobacteria/chemistry/classification/*metabolism ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence ; Lipids/analysis ; Methane/*metabolism ; Methanosarcinales/chemistry/classification/*metabolism ; Oceans and Seas ; Oligonucleotide Probes ; Oxidation-Reduction ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; Spectrometry, Mass, Secondary Ion ; Sulfates/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    The microbial ocean from genomes to biomes (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-05-16
    Description: Numerically, microbial species dominate the oceans, yet their population dynamics, metabolic complexity and synergistic interactions remain largely uncharted. A full understanding of life in the ocean requires more than knowledge of marine microbial taxa and their genome sequences. The latest experimental techniques and analytical approaches can provide a fresh perspective on the biological interactions within marine ecosystems, aiding in the construction of predictive models that can interrelate microbial dynamics with the biogeochemical matter and energy fluxes that make up the ocean ecosystem.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeLong, Edward F -- England -- Nature. 2009 May 14;459(7244):200-6. doi: 10.1038/nature08059.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. delong@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444206" target="_blank"〉PubMed〈/a〉
    Keywords: *Ecosystem ; Gene Expression Profiling ; *Genomics ; *Marine Biology ; Oceans and Seas ; Phylogeny ; *Water Microbiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-05-16
    Description: Microbial gene expression in the environment has recently been assessed via pyrosequencing of total RNA extracted directly from natural microbial assemblages. Several such 'metatranscriptomic' studies have reported that many complementary DNA sequences shared no significant homology with known peptide sequences, and so might represent transcripts from uncharacterized proteins. Here we report that a large fraction of cDNA sequences detected in microbial metatranscriptomic data sets are comprised of well-known small RNAs (sRNAs), as well as new groups of previously unrecognized putative sRNAs (psRNAs). These psRNAs mapped specifically to intergenic regions of microbial genomes recovered from similar habitats, displayed characteristic conserved secondary structures and were frequently flanked by genes that indicated potential regulatory functions. Depth-dependent variation of psRNAs generally reflected known depth distributions of broad taxonomic groups, but fine-scale differences in the psRNAs within closely related populations indicated potential roles in niche adaptation. Genome-specific mapping of a subset of psRNAs derived from predominant planktonic species such as Pelagibacter revealed recently discovered as well as potentially new regulatory elements. Our analyses show that metatranscriptomic data sets can reveal new information about the diversity, taxonomic distribution and abundance of sRNAs in naturally occurring microbial communities, and indicate their involvement in environmentally relevant processes including carbon metabolism and nutrient acquisition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shi, Yanmei -- Tyson, Gene W -- DeLong, Edward F -- England -- Nature. 2009 May 14;459(7244):266-9. doi: 10.1038/nature08055.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444216" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; DNA, Complementary/genetics ; Ecosystem ; *Gene Expression Profiling ; Gene Expression Regulation, Bacterial/*genetics ; Oceans and Seas ; Plankton/genetics/isolation & purification/metabolism ; RNA, Bacterial/*analysis/*genetics/isolation & purification ; Seawater/*microbiology ; Sequence Analysis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-13
    Description: Nitrogen cycling is normally thought to dominate the biogeochemistry and microbial ecology of oxygen-minimum zones in marine environments. Through a combination of molecular techniques and process rate measurements, we showed that both sulfate reduction and sulfide oxidation contribute to energy flux and elemental cycling in oxygen-free waters off the coast of northern Chile. These processes may have been overlooked because in nature, the sulfide produced by sulfate reduction immediately oxidizes back to sulfate. This cryptic sulfur cycle is linked to anammox and other nitrogen cycling processes, suggesting that it may influence biogeochemical cycling in the global ocean.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Canfield, Don E -- Stewart, Frank J -- Thamdrup, Bo -- De Brabandere, Loreto -- Dalsgaard, Tage -- Delong, Edward F -- Revsbech, Niels Peter -- Ulloa, Osvaldo -- New York, N.Y. -- Science. 2010 Dec 3;330(6009):1375-8. doi: 10.1126/science.1196889. Epub 2010 Nov 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark. dec@biology.sdu.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21071631" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Bacteria/classification/genetics/*metabolism ; Chile ; Deltaproteobacteria/classification/genetics/metabolism ; Denitrification ; *Ecosystem ; Gammaproteobacteria/classification/genetics/metabolism ; Genes, Bacterial ; Metagenome ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Oxygen/*analysis ; Pacific Ocean ; Quaternary Ammonium Compounds/metabolism ; Seawater/chemistry/*microbiology ; Sequence Analysis, DNA ; Sulfates/metabolism ; Sulfides/metabolism ; Sulfur/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Evolution. Microbial evolution in the wild (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-04-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeLong, Edward F -- New York, N.Y. -- Science. 2012 Apr 27;336(6080):422-4. doi: 10.1126/science.1221822.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02138, USA. delong@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22539708" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*genetics ; *Biofilms ; *Biological Evolution ; *Ecosystem ; *Mining ; *Recombination, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Microbiology. Microbial life breathes deep (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeLong, Edward F -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2198-200.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil and Environmental Engineering and Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. delong@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15622564" target="_blank"〉PubMed〈/a〉
    Keywords: Archaea/growth & development/isolation & purification/metabolism ; Bacteria/growth & development/isolation & purification/*metabolism ; Biomass ; Carbon/metabolism ; Colony Count, Microbial ; *Ecosystem ; Electron Transport ; Geologic Sediments/*microbiology ; Iron/metabolism ; Manganese/metabolism ; Methane/metabolism ; Oxidants/metabolism ; Oxidation-Reduction ; Pacific Ocean ; Peru ; Seawater/chemistry ; Sulfates/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Reverse methanogenesis: testing the hypothesis with environmental genomics (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-09
    Description: Microbial methane consumption in anoxic sediments significantly impacts the global environment by reducing the flux of greenhouse gases from ocean to atmosphere. Despite its significance, the biological mechanisms controlling anaerobic methane oxidation are not well characterized. One current model suggests that relatives of methane-producing Archaea developed the capacity to reverse methanogenesis and thereby to consume methane to produce cellular carbon and energy. We report here a test of the "reverse-methanogenesis" hypothesis by genomic analyses of methane-oxidizing Archaea from deep-sea sediments. Our results show that nearly all genes typically associated with methane production are present in one specific group of archaeal methanotrophs. These genome-based observations support previous hypotheses and provide an informed foundation for metabolic modeling of anaerobic methane oxidation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hallam, Steven J -- Putnam, Nik -- Preston, Christina M -- Detter, John C -- Rokhsar, Daniel -- Richardson, Paul M -- DeLong, Edward F -- New York, N.Y. -- Science. 2004 Sep 3;305(5689):1457-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Monterey Bay Aquarium Research Institute, Moss Landing, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15353801" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Carbon Dioxide/metabolism ; Cloning, Molecular ; Gene Library ; Genes, Archaeal ; Genes, rRNA ; *Genome, Archaeal ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Pterins/metabolism ; RNA, Archaeal/genetics ; RNA, Ribosomal/genetics ; Seawater/microbiology ; Sulfates/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Genomic islands and the ecology and evolution of Prochlorococcus (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-25
    Description: Prochlorococcus ecotypes are a useful system for exploring the origin and function of diversity among closely related microbes. The genetic variability between phenotypically distinct strains that differ by less that 1% in 16S ribosomal RNA sequences occurs mostly in genomic islands. Island genes appear to have been acquired in part by phage-mediated lateral gene transfer, and some are differentially expressed under light and nutrient stress. Furthermore, genome fragments directly recovered from ocean ecosystems indicate that these islands are variable among cooccurring Prochlorococcus cells. 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coleman, Maureen L -- Sullivan, Matthew B -- Martiny, Adam C -- Steglich, Claudia -- Barry, Kerrie -- Delong, Edward F -- Chisholm, Sallie W -- New York, N.Y. -- Science. 2006 Mar 24;311(5768):1768-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, 15 Vassar Street, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16556843" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Atlantic Ocean ; Bacteriophages/*genetics/physiology ; *Biological Evolution ; *Ecosystem ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; *Genomic Islands ; Light ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Prochlorococcus/classification/*genetics/isolation & purification/*physiology ; Seawater/*microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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