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  • Articles  (168)
  • Bacteria
  • Dissolved organic carbon
  • Springer  (166)
  • American Chemical Society
  • Molecular Diversity Preservation International
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  • 1
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Walsh, A. N., Reddy, C. M., Niles, S. F., McKenna, A. M., Hansel, C. M., & Ward, C. P. Plastic formulation is an emerging control of its photochemical fate in the ocean. Environmental Science & Technology, 55(18), (2021): 12383–12392, https://doi.org/10.1021/acs.est.1c02272.
    Description: Sunlight exposure is a control of long-term plastic fate in the environment that converts plastic into oxygenated products spanning the polymer, dissolved, and gas phases. However, our understanding of how plastic formulation influences the amount and composition of these photoproducts remains incomplete. Here, we characterized the initial formulations and resulting dissolved photoproducts of four single-use consumer polyethylene (PE) bags from major retailers and one pure PE film. Consumer PE bags contained 15–36% inorganic additives, primarily calcium carbonate (13–34%) and titanium dioxide (TiO2; 1–2%). Sunlight exposure consistently increased production of dissolved organic carbon (DOC) relative to leaching in the dark (3- to 80-fold). All consumer PE bags produced more DOC during sunlight exposure than the pure PE (1.2- to 2.0-fold). The DOC leached after sunlight exposure increasingly reflected the 13C and 14C isotopic composition of the plastic. Ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry revealed that sunlight exposure substantially increased the number of DOC formulas detected (1.1- to 50-fold). TiO2-containing bags photochemically degraded into the most compositionally similar DOC, with 68–94% of photoproduced formulas in common with at least one other TiO2-containing bag. Conversely, only 28% of photoproduced formulas from the pure PE were detected in photoproduced DOC from the consumer PE. Overall, these findings suggest that plastic formulation, especially TiO2, plays a determining role in the amount and composition of DOC generated by sunlight. Consequently, studies on pure, unweathered polymers may not accurately represent the fates and impacts of the plastics entering the ocean.
    Description: Funding was provided by the Seaver Institute, the Gerstner Family Foundation, Woods Hole Oceanographic Institution, and the National Science Foundation Graduate Research Fellowship Program (A.N.W.). The Ion Cyclotron Resonance user facility at the National High Magnetic Field Laboratory is supported by the National Science Foundation Division of Chemistry and Division of Materials Research through DMR-1644779 and the State of Florida.
    Keywords: Plastic pollution ; Marine debris ; Additives ; Dissolved organic carbon ; Photochemical oxidation ; FT-ICR-MS ; Titanium dioxide
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gosselin, K. M., Nelson, R. K., Spivak, A. C., Sylva, S. P., Van Mooy, B. A. S., Aeppli, C., Sharpless, C. M., O’Neil, G. W., Arrington, E. C., Reddy, C. M., & Valentine, D. L. Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum. ACS Omega, 6(35), (2021): 22803–22810, https://doi.org/10.1021/acsomega.1c03196.
    Description: The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism.
    Description: This work was funded with grants from the National Science Foundation grants OCE-1333148, OCE-1333162, and OCE-1756254 and the Woods Hole Oceanographic Institution (IR&D). GCxGC analysis made possible by WHOI’s Investment in Science Fund.
    Keywords: Lipids ; Alkyls ; Bacteria ; Genetics ; Chromatography
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2022-05-26
    Description: © The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Functional & Integrative Genomics 10 (2010): 97-110, doi:10.1007/s10142-009-0142-y.
    Description: Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.
    Description: This research was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research under the Genomics: GTL Program via the Shewanella Federation consortium.
    Keywords: Phenotypic trait ; Bacteria ; Molecular mechanisms of cold tolerance ; Shewanella ; Protein families
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Journal of industrial microbiology and biotechnology 8 (1991), S. 201-207 
    ISSN: 1476-5535
    Keywords: Diffusion chamber ; Cadmium-sensitive ; Cadmium-resitant ; Sediment ; Bacteria ; Cadmium-sorption
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Sorption of cadmium by sediment bacteria and freshwater sediment was investigated using diffusion chambers to simulate the water-sediment interface. Diffusion chambers were constructed to provide two compartments separated by a dialysis membrane. Diffusion of cadmium across the membrane was monitored after pure cultures of sediment bacteria or lake sediments were added to the sediment side of a diffusion chamber. Cellular accumulation of cadmium by cadmium-sensitive and cadmium-resistant bacteria removed between 20% and 80% of the dissolved cadmium from the simulated water column and pore water. Cellular accumulation of cadmium was greatest for cadmium-sensitive isolates that were tested. Sediment with an intact microbial community sequestered 80% of the cadmium added to sediment, whereas autoclaved sediment retained 97% of the metal that was added. Addition of glucose to cadmium-amended sediment decreased retention of cadmium by untreated and autoclaved sediments, resulting in elevated concentrations of dissolved cadmium in the simulated water column.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of industrial microbiology and biotechnology 8 (1991), S. 223-227 
    ISSN: 1476-5535
    Keywords: Deionized water ; Ultra-pure water ; Ozone ; Ultra-violet sterilization ; Oligotroph ; Bacteria ; R2A medium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Presently, tryptic soy agar (TSA) medium is used in the semiconductor industry to determine the concentration of viable oligotrophic bacteria in ultra-pure water systems. Deionized water from an ultra-pure water pilot plant was evaluated for bacterial growth at specific locations, using a non-selective medium (R2A) designed to detect injured heterotrophic as well as oligotrophic bacteria. Results were compared to those obtained using Tryptic Soy Agar. Statistically greater numbers of bacteria were observed when R2A was used as the growth medium. Total viable bacterial numbers were compared both before and after each treatment step of the recirculating loop to determine their effectiveness in removing bacteria. The reduction in bacterial numbers for the reverse osmosis unit, the ion exchange bed, and the ultraviolet sterilizer were 97.4%, 31.3%, and 72.8%, respectively, using TSA medium, and 98.4%, 78.4%, and 35.8% using R2A medium. The number of viable bacteria increased by 60.7% based on TSA medium and 15.7% based on R2A medium after passage of the water through an in-line 0.2-μm pore size nylon filter, probably because of the growth of bacteria on the filter. Our results suggest that R2A medium may give a better representation of the microbial water quality in ultra-pure water systems and therefore a better idea of the effectiveness of the various treatment processes in the control of bacteria.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Journal of industrial microbiology and biotechnology 5 (1990), S. 79-84 
    ISSN: 1476-5535
    Keywords: Bacteria ; Soil ; Conjugation ; Gene transfer ; Plasmids ; Survival
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Experiments conducted in microcosms containing loam soil samples inoculated with eitherE. coli orPseudomonas spp. donor and recipient cells showed that bacterial cells survived and conjugated over a 24-h incubation period.E. coli transconjugants were detected 6 h after donor and recipient strains were introduced into sterile soil samples. In non-sterile soil samples, transconjugants were detected between 8 and 24 h incubation.Pseudomonas transconjugants were recovered from sterile soil samples between 6 and 12 h after their introduction and as early as 2 h in non-sterile soil. The results show that genetic interactions occur in non-sterile soil in relatively short periods of time at relatively high transfer frequencies (10−3 to 10−4). Studies on genetic interactions in soil are becoming necessary in risk assessment/environmental impact studies prior to the release of genetically engineered or modified organisms into uncontained environments.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    BioMetals 3 (1990), S. 151-154 
    ISSN: 1572-8773
    Keywords: Silver ; Nickel ; Bacteria ; Toxicity ; Metal tolerance ; Accumulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary This review examines interactions between bacteria and the biologically non-essential metal, silver. Aspects of silver toxicity, tolerance and accumulation (possible binding and uptake as opposed to energy-dependent transport) in bacteria are discussed. In addition, plasmid biology is examined briefly since little information is available on the exact mechanism(s) of plasmid-endoced silver resistance in bacteria.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1433-4909
    Keywords: Key words Extreme thermophile ; Thermosipho ; Thermotogales ; Deep-sea hydrothermal vent ; Bacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A novel barophilic, extremely thermophilic bacterium was isolated from a deep-sea hydrothermal vent chimney at the Iheya Basin, in the Okinawa area, Japan. The cells were found to be rod shaped and surrounded by a sheath-like outer structure; the organism did not possess flagella and was not motile. Growth was observed between 45° and 80°C (optimum, 72°C, 45 min doubling time), pH 5.3 and 9.3 (optimum, pH 7.2–7.6), 6.6 and 79 g/l sea salts (optimum, 40 g/l), and 0.1 and 60 MPa (optimum, 20 MPa). Strain IHB1 was found to be a strictly anaerobic chemoorganotroph capable of utilizing yeast extract and proteinaceous substrates such as peptone and tryptone. Elemental sulfur or thiosulfate acted as electron acceptors improving growth. The isolate was able to utilize casein as a sole carbon and energy source in the presence of thiosulfate. The G + C content of the genomic DNA was 31.4 mol%. Phylogenetic analysis based on 16S rDNA sequences and DNA–DNA hybridization analysis indicated that the isolate is closely related to Thermosipho africanus; however, it represents a species distinct from the previously described members of the genus Thermosipho. On the basis of the physiological and molecular properties, we propose that the new isolate represents a new species, which we name Thermosipho japonicus sp. nov. (type strain: IHB1; JCM10495).
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Aquatic sciences 57 (1995), S. 70-80 
    ISSN: 1420-9055
    Keywords: Dissolved organic carbon ; UV spectrophotometry ; A/DOC ratio ; Rhône River
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract To detect temporal changes and the origin of the refractory dissolved organic matter in the Upper Rhône River, UV light absorbance (A) at 285 nm and quantitative dissolved organic carbon (DOC) measurements were carried out. Data from 63 visits to the main channel over a period of two years and from visits to different waterbodies in the alluvial plain before and after a flood are presented. There was a good correlation between A (0.019–0.160) and the DOC content (1.40–9.81 mg/L) for the waterbodies, but not for the river axis with lower A (0.013–0.044) and DOC content (1.13–2.20 mg/L). Due to this good correlation, the DOC content could be quantified for the waterbodies by absorbance measurements only. For the river water this indirect determination of the DOC content was not possible. However, the A/DOC ratio showed changes in the composition of DOC of river water and provided indications about the origin of the dissolved organic matter in the Upper Rhône River.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1420-9055
    Keywords: Dissolved organic carbon ; bio-degradation test ; pedogenic (allochthonous) ; authochthonous ; UV-absorbance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The seasonal and spatial changes in dissolved organic carbon (DOC) in Lake Kasumigaura, a shallow, eutrophic lake, were analyzed and the lability of DOC was tested by long-term incubations. There was a nearly 1 mgCl−1 downstream increase in refractory DOC in the lake; at the center it fluctuated little seasonally. The characteristic UV-absorbance: DOC ratios were determined for samples from the influent rivers (pedogenic: used interchangeably with “allochthonous”) and outdoor experimental ponds (autochthonous) during incubations. These ratios were then used to calculate the proportion of total measured lake water DOC in each of four components: pedogenic-refractory (PR), pedogenic-labile (PL), autochthonous-refractory (AR) and autochthonous-labile (AL). PR was uniform (around 1.5 mgCl−1) or diminished very slightly over time. AR increased from nearly zero at the station closest to an influent river to 1 mgCl−1 at the lake center. PL declined downstream from 0.3 mgCl−1 to zero. AL was virtually constant at 0.8 mgCl−1 except at the station closest to the influent river. The constancy of the UV-absorbance: DOC ratio during the biodegradation process was confirmed for Lake Kasumigaura; hence a two-component model (pedogenic-autochthonous) could be applied here without consideration of DOC lability. However, this assumption is not always met for other water bodies, and therefore it should be checked before applying a two-component model elsewhere.
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