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  • 1
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    Bacterial carbon processing by generalist species in the coastal ocean (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-01-29
    Description: The assimilation and mineralization of dissolved organic carbon (DOC) by marine bacterioplankton is a major process in the ocean carbon cycle. However, little information exists on the specific metabolic functions of participating bacteria and on whether individual taxa specialize on particular components of the marine DOC pool. Here we use experimental metagenomics to show that coastal communities are populated by taxa capable of metabolizing a wide variety of organic carbon compounds. Genomic DNA captured from bacterial community subsets metabolizing a single model component of the DOC pool (either dimethylsulphoniopropionate or vanillate) showed substantial overlap in gene composition as well as a diversity of carbon-processing capabilities beyond the selected phenotypes. Our direct measure of niche breadth for bacterial functional assemblages indicates that, in accordance with ecological theory, heterogeneity in the composition and supply of organic carbon to coastal oceans may favour generalist bacteria. In the important interplay between microbial community structure and biogeochemical cycling, coastal heterotrophic communities may be controlled less by transient changes in the carbon reservoir that they process and more by factors such as trophic interactions and physical conditions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mou, Xiaozhen -- Sun, Shulei -- Edwards, Robert A -- Hodson, Robert E -- Moran, Mary Ann -- England -- Nature. 2008 Feb 7;451(7179):708-11. doi: 10.1038/nature06513. Epub 2008 Jan 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18223640" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/classification/genetics/*metabolism ; Carbon/*metabolism ; Gene Dosage ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Marine Biology ; Molecular Sequence Data ; Oceans and Seas ; Plankton/classification/genetics/metabolism ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sulfonium Compounds/metabolism ; Vanillic Acid/metabolism
    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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  • 2
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    Functional metagenomic profiling of nine biomes (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-03-14
    Description: Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dinsdale, Elizabeth A -- Edwards, Robert A -- Hall, Dana -- Angly, Florent -- Breitbart, Mya -- Brulc, Jennifer M -- Furlan, Mike -- Desnues, Christelle -- Haynes, Matthew -- Li, Linlin -- McDaniel, Lauren -- Moran, Mary Ann -- Nelson, Karen E -- Nilsson, Christina -- Olson, Robert -- Paul, John -- Brito, Beltran Rodriguez -- Ruan, Yijun -- Swan, Brandon K -- Stevens, Rick -- Valentine, David L -- Thurber, Rebecca Vega -- Wegley, Linda -- White, Bryan A -- Rohwer, Forest -- England -- Nature. 2008 Apr 3;452(7187):629-32. doi: 10.1038/nature06810. Epub 2008 Mar 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, San Diego State University, San Diego, California 92182, USA. elizabeth_dinsdale@hotmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337718" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthozoa/physiology ; Archaea/genetics/isolation & purification/metabolism ; Bacteria/*genetics/isolation & purification/*metabolism ; Chemotaxis/genetics ; Computational Biology ; Culicidae/physiology ; *Ecosystem ; Fishes/physiology ; Fresh Water ; *Gene Expression Profiling ; Genome, Archaeal ; Genome, Bacterial ; Genome, Viral ; *Genomics ; Microbiology ; Seawater ; Viruses/*genetics/isolation & purification/*metabolism
    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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  • 3
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    Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-05-13
    Description: Dimethylsulphoniopropionate (DMSP) accounts for up to 10% of carbon fixed by marine phytoplankton in ocean surface waters, producing an estimated 11.7-103 Tmol S per year, most of which is processed by marine bacteria through the demethylation/demethiolation pathway. This pathway releases methanethiol (MeSH) instead of the climatically active gas dimethylsulphide (DMS) and enables marine microorganisms to assimilate the reduced sulphur. Despite recognition of this critical microbial transformation for over two decades, the biochemical pathway and enzymes responsible have remained unidentified. Here we show that three new enzymes related to fatty acid beta-oxidation constitute the pathway that assimilates methylmercaptopropionate (MMPA), the first product of DMSP demethylation/demethiolation, and that two previously unknown coenzyme A (CoA) derivatives, 3-methylmercaptopropionyl-CoA (MMPA-CoA) and methylthioacryloyl-CoA (MTA-CoA), are formed as novel intermediates. A member of the marine roseobacters, Ruegeria pomeroyi DSS-3, requires the MMPA-CoA pathway for MMPA assimilation and MeSH production. This pathway and the ability to produce MeSH from MMPA are present in diverse bacteria, and the ubiquitous SAR11 clade bacterium Pelagibacter ubique possesses enzymes for at least the first two steps. Analysis of marine metagenomic data indicates that the pathway is widespread among bacterioplankton in the ocean surface waters, making it one of the most important known routes for acquisition of reduced carbon and sulphur by surface ocean heterotrophs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reisch, Chris R -- Stoudemayer, Melissa J -- Varaljay, Vanessa A -- Amster, I Jonathan -- Moran, Mary Ann -- Whitman, William B -- England -- Nature. 2011 May 12;473(7346):208-11. doi: 10.1038/nature10078.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21562561" target="_blank"〉PubMed〈/a〉
    Keywords: Aquatic Organisms/classification/enzymology/*genetics/*metabolism ; Bacteria/classification/enzymology/*genetics/*metabolism ; Bacterial Proteins/genetics/isolation & purification/metabolism ; Coenzyme A/metabolism ; Metagenomics ; Phylogeny ; Roseobacter/genetics/metabolism ; Sulfhydryl Compounds/metabolism ; Sulfonium Compounds/*metabolism
    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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  • 4
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    Bacterial taxa that limit sulfur flux from the ocean (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-10-28
    Description: Flux of dimethylsulfide (DMS) from ocean surface waters is the predominant natural source of sulfur to the atmosphere and influences climate by aerosol formation. Marine bacterioplankton regulate sulfur flux by converting the precursor dimethylsulfoniopropionate (DMSP) either to DMS or to sulfur compounds that are not climatically active. Through the discovery of a glycine cleavage T-family protein with DMSP methyltransferase activity, marine bacterioplankton in the Roseobacter and SAR11 taxa were identified as primary mediators of DMSP demethylation to methylmercaptopropionate. One-third of surface ocean bacteria harbor a DMSP demethylase homolog and thereby route a substantial fraction of global marine primary production away from DMS formation and into the marine microbial food web.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Howard, Erinn C -- Henriksen, James R -- Buchan, Alison -- Reisch, Chris R -- Burgmann, Helmut -- Welsh, Rory -- Ye, Wenying -- Gonzalez, Jose M -- Mace, Kimberly -- Joye, Samantha B -- Kiene, Ronald P -- Whitman, William B -- Moran, Mary Ann -- New York, N.Y. -- Science. 2006 Oct 27;314(5799):649-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, University of Georgia, Athens, GA 30602, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17068264" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/classification/enzymology/*genetics/*metabolism ; Food Chain ; Genes, Bacterial ; Genome, Bacterial ; Molecular Sequence Data ; Oceans and Seas ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Phytoplankton/metabolism ; Plankton/classification/enzymology/genetics/metabolism ; Propionates/metabolism ; Rhodobacteraceae/classification/enzymology/*genetics/*metabolism ; *Seawater/microbiology ; Sulfhydryl Compounds/metabolism ; Sulfides/metabolism ; Sulfonium Compounds/*metabolism ; Sulfur Compounds/*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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  • 5
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    The global ocean microbiome (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-12-15
    Description: The microbiome of the largest environment on Earth has been gradually revealing its secrets over four decades of study. Despite the dispersed nature of substrates and the transience of surfaces, marine microbes drive essential transformations in all global elemental cycles. Much has been learned about the microbes that carry out key biogeochemical processes, but there are still plenty of ambiguities about the factors important in regulating activity, including the role of microbial interactions. Identifying the molecular "currencies" exchanged within the microbial community will provide key information on microbiome function and its vulnerability to environmental change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moran, Mary Ann -- New York, N.Y. -- Science. 2015 Dec 11;350(6266):aac8455. doi: 10.1126/science.aac8455.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Marine Sciences, University of Georgia, Athens, GA 30602-3636, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26659059" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Cycle ; Earth (Planet) ; Energy Metabolism ; Microbiota/genetics/*physiology ; Oceans and Seas ; 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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  • 6
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    Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-05-29
    Description: Interactions between primary producers and bacteria impact the physiology of both partners, alter the chemistry of their environment, and shape ecosystem diversity. In marine ecosystems, these interactions are difficult to study partly because the major photosynthetic organisms are microscopic, unicellular phytoplankton. Coastal phytoplankton communities are dominated by diatoms, which generate approximately 40% of marine primary production and form the base of many marine food webs. Diatoms co-occur with specific bacterial taxa, but the mechanisms of potential interactions are mostly unknown. Here we tease apart a bacterial consortium associated with a globally distributed diatom and find that a Sulfitobacter species promotes diatom cell division via secretion of the hormone indole-3-acetic acid, synthesized by the bacterium using both diatom-secreted and endogenous tryptophan. Indole-3-acetic acid and tryptophan serve as signalling molecules that are part of a complex exchange of nutrients, including diatom-excreted organosulfur molecules and bacterial-excreted ammonia. The potential prevalence of this mode of signalling in the oceans is corroborated by metabolite and metatranscriptome analyses that show widespread indole-3-acetic acid production by Sulfitobacter-related bacteria, particularly in coastal environments. Our study expands on the emerging recognition that marine microbial communities are part of tightly connected networks by providing evidence that these interactions are mediated through production and exchange of infochemicals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amin, S A -- Hmelo, L R -- van Tol, H M -- Durham, B P -- Carlson, L T -- Heal, K R -- Morales, R L -- Berthiaume, C T -- Parker, M S -- Djunaedi, B -- Ingalls, A E -- Parsek, M R -- Moran, M A -- Armbrust, E V -- England -- Nature. 2015 Jun 4;522(7554):98-101. doi: 10.1038/nature14488. Epub 2015 May 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] School of Oceanography, University of Washington, Seattle, Washington 98195, USA [2] Chemistry Faculty, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates. ; Department of Microbiology, University of Washington, Seattle, Washington 98195, USA. ; School of Oceanography, University of Washington, Seattle, Washington 98195, USA. ; Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA. ; Department of Marine Science, University of Georgia, Athens, Georgia 30602, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26017307" target="_blank"〉PubMed〈/a〉
    Keywords: Diatoms/cytology/genetics/*metabolism/*microbiology ; *Ecosystem ; Indoleacetic Acids/*metabolism ; Metabolomics ; Molecular Sequence Data ; Oceans and Seas ; Photosynthesis ; Phytoplankton/cytology/genetics/*metabolism/*microbiology ; Rhodobacteraceae/genetics/*metabolism ; Seawater/chemistry ; Transcriptome ; Tryptophan/metabolism
    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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  • 7
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    Biomass energy from crop and forest residues (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-06-05
    Description: Residues remaining after the harvest of crop and forestry products are being proposed as a substantial energy source for the nation. An estimated 22 percent of the residues might be utilized, providing a renewable source of high-grade energy with the potential of supplying 1 percent of the current U.S. gasoline consumption as ethanol or 4 percent of the total electrical energy used. These net energy benefits are limited by high energy costs to collect, transport, and process the residues. Environmental threats include soil erosion, water runoff, and nutrient loss.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pimentel, D -- Moran, M A -- Fast, S -- Weber, G -- Bukantis, R -- Balliett, L -- Boveng, P -- Cleveland, C -- Hindman, S -- Young, M -- New York, N.Y. -- Science. 1981 Jun 5;212(4499):1110-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17815203" target="_blank"〉PubMed〈/a〉
    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
    Electronic Resource
    Electronic Resource
    Productivities of microbial decomposers during early stages of decomposition of leaves of a freshwater sedge (1995)
    Oxford, UK : Blackwell Publishing Ltd
    Freshwater biology 34 (1995), S. 0 
    Details
    ISSN: 1365-2427
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: 1. We examined standing-senescing, standing-dead and recently fallen leaf blades of Carex walteriana in fens of the Okefenokee Swamp to determine the nature of the microbial decomposers in the early stages of decomposition, measuring both standing crops and productivities ([3H]leucineprotein method for bacteria, [14C]acetateergosterol for fungi).2. Fungal standing crops (ergosterol) became detectable at the mid-senescence stage (leaves about half yellow-brown) and rose to 14–31 mg living-fungal C g−1 organic mass of the decaying system; bacterial standing crops (direct microscopy) were ± 0.2 mgC g−1 until the fallen-leaf stage, when they rose to as high as 0.9 mgC g−1.3. Potential microbial specific growth rates were similar between fungi and bacteria, at about 0.03–0.06 day−1, but potential production of fungal mass was 115–512 μgC g−1 organic mass day−1, compared with 0–22 μgC g−1 day−1 for bacteria. Rates of fungal production were about 6-fold lower on average than previously found for a saltmarsh grass, perhaps because much lower phosphorus concentratiofis in the freshwater fen limit fungal activity.4. There was little change in lignocellulose (LC) percentage of decaying leaves, although net loss of organic mass at the fallen, broken stage was estimated to be 59%, suggesting that LC was lost at rates proportional to those for total organics during decay. Monomers of fungal-wall polymers (glucosamine and mannose) accumulated 2- to 4-fold during leaf decay. This may indicate that an increase found for proximate (acid-detergent) lignin could be at least partially due to accumulation of refractory fungal-wall material, including melanin.5. A common sequence in decaying aquatic grasses is suggested: principally fungal alteration of LC during standing decay, followed by a trend toward bacterial decomposition of the LC after leaves fall and break into particles.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2427.1995.tb00430.x
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  • 9
    Electronic Resource
    Electronic Resource
    Seed dispersal and seedling emergence in an old field community in central New York (USA) (1986)
    Springer
    Oecologia 70 (1986), S. 92-99 
    Details
    ISSN: 1432-1939
    Keywords: Seed dispersal ; Emergence ; Old field communities ; Solidago spp. ; Asteraceae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Seed dispersal and seedling emergence of common taxa growing in a Solidago-dominated old field in central New York (USA) were monitored from May 1982 to June 1984. Over 3.5x104 seeds per m2 were captured on seed traps in each of the two years, with peaks occuring in July (due to Hieracium) and in November (due to Solidago). About 4.0x103 seedling/m2 emerged beneath the intact community in each of the two years. Although seedlings emerged predominantly in the early spring, a secondary peak occurred in September and October when many seedlings of introduced grasses appeared. Two additional aspects of the reproductive biology of the major taxa were related to the seasonal timing of seed dispersal: As the date of peak seed dispersal (among taxa) became progressively later in the season, (1) the duration of dispersal increased from about one week to about one-half year, and (2) the delay between the peak of seed dispersal and the peak of seedling emergence increased from a few days to about one-half year.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00377115
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  • 10
    Electronic Resource
    Electronic Resource
    Bacterial populations in replicate marine enrichment cultures: assessing variability in abundance using 16S rRNA-based probes (1999)
    Springer
    Hydrobiologia 401 (1999), S. 69-75 
    Details
    ISSN: 1573-5117
    Keywords: microcosms ; bacterial populations ; 16S rRNA oligonucleotide probes ; lignin ; coastal seawater
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Most studies of marine bacterial communities focus on functional attributes of the community, rather than on population or community structure, at least in part, because of the difficulty in enumerating individual species within complex communities. Here, we describe a study in which populations of three bacterial species were followed over time in replicate marine enrichment cultures using 16S rRNA-based oligonucleotide probes. Three identical enrichment microcosms were established with lignin-rich pulp mill waste as a sole carbon source, inoculated with coastal seawater, and transferred at two-week intervals. Population levels were assessed throughout a six-week period using species-specific 16S rRNA-based oligonucleotide probes directed toward three bacterial species that were numerically important (and culturable) members of the enrichments. Substantial differences in the population levels of each bacterial species were found among the triplicate incubations, despite the fact that the enrichments were inoculated and treated identically. Stochastic differences in the composition of the inoculum and/or ecological interactions within the enrichment replicates may have been important in determining final population levels. Functional ability, assessed as rates of degradation of a synthetic lignin preparation, were fairly similar among the three replicate enrichments (within 70%), despite the substantial differences in population levels of the representative lignin-degrading species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003771318693
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