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  • 1
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    PANGAEA
    In:  Supplement to: Ray, Jessica L; Töpper, Birte; An, Shu; Silyakova, Anna; Spindelböck, Joachim; Thyrhaug, Runar; DuBow, Michael S; Thingstad, Tron Frede; Sandaa, Ruth-Anne (2012): Effect of increased pCO2 on bacterial assemblage shifts in response to glucose addition in Fram Strait seawater mesocosms. FEMS Microbiology Ecology, 82(3), 713-723, https://doi.org/10.1111/j.1574-6941.2012.01443.x
    Publication Date: 2024-03-15
    Description: Ocean acidification may stimulate primary production through increased availability of inorganic carbon in the photic zone, which may in turn change the biogenic flux of dissolved organic carbon (DOC) and the growth potential of heterotrophic bacteria. To investigate the effects of ocean acidification on marine bacterial assemblages, a two-by-three factorial mescosom experiment was conducted using surface sea water from the East Greenland Current in Fram Strait. Pyrosequencing of the V1-V2 region of bacterial 16S ribosomal RNA genes was used to investigate differences in the endpoint (Day 9) composition of bacterial assemblages in mineral nutrient-replete mesocosms amended with glucose (0 µm, 5.3 µm and 15.9 µm) under ambient (250 µatm) or acidified (400 µatm) partial pressures of CO2 (pCO2). All mesocosms showed low richness and diversity by Chao1 estimator and Shannon index, respectively, with general dominance by Gammaproteobacteria and Flavobacteria. Nonmetric multidimensional scaling analysis and two-way analysis of variance of the Jaccard dissimilarity matrix (97% similarity cut-off) demonstrated that the significant community shift between 0 µm and 15.9 µm glucose addition at 250 µatm pCO2 was eliminated at 400 µatm pCO2. These results suggest that the response potential of marine bacteria to DOC input may be altered under acidified conditions.
    Keywords: Algae abundance; Alkalinity, total; Aragonite saturation state; Arctic; Bacteria, abundance; Bacterial production; Bicarbonate ion; Calcite saturation state; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Class; Community composition and diversity; Entire community; EXP; Experiment; Family; Field experiment; Fram_Strait_OA; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Gene expression (incl. proteomics); Incubation duration; Mesocosm or benthocosm; OA-ICC; Ocean Acidification International Coordination Centre; Open ocean; Operational taxonomic unit; Other metabolic rates; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; Phosphate; Polar; Salinity; Sequence abundance; Sequence coverage; Silicate; Species; Temperature, water; Treatment
    Type: Dataset
    Format: text/tab-separated-values, 112442 data points
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  • 2
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 173 (1999), S. 0 
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Escherichia coli was used as model to study initial adhesion and early biofilm development to an abiotic surface. Tn10 insertion mutants with reduced attachment to a polystyrene surface were isolated. Three adhesion mutants harbored the transposon in the dsbA gene, whose product, DsbA, catalyses folding of numerous extracytoplasmic disulfide bond-containing proteins. All three mutants were weakly adherent and grew poorly. Cell surface structure analysis showed that motility, type 1 fimbriation and lipopolysaccharide structure were affected in these mutants. The pleiotropic effect of the dsbA mutations on biofilm formation is discussed.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Archives of microbiology 156 (1991), S. 444-448 
    ISSN: 1432-072X
    Keywords: Transposon5 ; Xylose operon ; Transcriptional fusions ; ColE1 replication ; luxAB genes ; Escherichia coli ; Vibrio harveyi
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A ColE1-based plasmid for transcriptional gene fusions was constructed that contains both the promoterless luxAB genes of Vibrio harveyi and a tet marker within the inverted repeats of a left end-truncated Tn5 element. Introduction of this plasmid into an Escherichia coli strain containing a plasmid (pTF421) that overproduces ColE1 RNA1 (and thus inhibits replication of the ColE1 plasmid) allowed selection for cells that had a single copy of the luxAB operon transposed into the chromosome beginning 5 days post-transformation. The long latent period necessary for Tn5 transposition is analogous to that found in other systems, where transposition frequencies and mutation rates increase in a time-dependent manner when selected for upon prolonged incubation on Petri dishes under bacteriostatic conditions.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1432-072X
    Keywords: Bacteriophage Mu ; DNA transposition ; Cis-acting sequences ; Adjacent DNA sequences
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Bacteriophage Mu DNA, like other transposable elements, requires DNA sequences at both extremities to transpose. It has been previously demonstrated that the transposition activity of various transposons can be influenced by sequences outside their ends. We have found that alterations in the neighboring plasmid sequences near the right extremity of a Mini-Mu, inserted in the plasmid pSC101, can exert an influence on the efficiency of Mini-Mu DNA transposition when an induced helper Mu prophage contains a polar insertion in its semi-essential early region (SEER). The SEER of Mu is known to contain several genes that can affect DNA transposition, and our results suggest that some function(s), located in the SEER of Mu, may be required for optimizing transposition (and thus, replication) of Mu genomes from restrictive locations during the lytic cycle.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1432-072X
    Keywords: DNA transposition ; Virus encapsidation ; Phage Mu ; Cis-acting DNA sequences ; Escherichia coli
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The 37,000 bp double-stranded DNA genome of bacteriophage Mu behaves as a plaque-forming transposable element of Escherichia coli. We have defined the cis-acting DNA sequences required in vivo for transposition and packaging of the viral genome by monitoring the transposition and maturation of Mu DNA-containing pSC101 and pBR322 plasmids with an induced helper Mu prophage to provide the trans-acting functions. We found that nucleotides 1 to 54 of the Mu left end define an essential domain for transposition, and that sequences between nucleotides 126 and 203, and between 203 and 1,699, define two auxiliary domains that stimulate transposition in vivo. At the right extremity, the essential sequences for transposition require not more than the first 62 base pairs (bp), although the presence of sequences between 63 and 117 bp from the right end increases the transposition frequency about 15-fold in our system. Finally, we have delineated the pac recognition site for DNA maturation to nucleotides 32 to 54 of the Mu left end which reside inside of the first transposase binding site (L1) located between nucleotides 1–30. Thus, the transposase binding site and packaging domains of bacteriophage Mu DNA can be separated into two well-defined regions which do not appear to overlap.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1432-072X
    Keywords: Key words Bacterial adhesion ; Biofilm formation ; Abiotic surface ; Type 1 fimbriae ; Flagella ; Lipopolysaccharide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Escherichia coli was used as a model to study initial adhesion and early biofilm development to abiotic surface. Tn10 insertion mutants of Escherichia coli K-12 W3110 were selected for altered abilities to adhere to a polystyrene surface. Seven insertion mutants that showed a decrease in adhesion harbored insertions in genes involved in lipopolysaccharide (LPS) core biosynthesis. Two insertions were located in the rfaG gene, two in the rfaP gene, and three in the galU gene. These adhesion mutants were found to exhibit a deep-rough phenotype and to be reduced, at different levels, in type 1 fimbriae production and motility. The loss of adhesion exhibited by these mutants was associated with either the affected type 1 fimbriae production and/or the dysfunctional motility. Apart from the pleiotropic effect of the mutations affecting LPS on type 1 fimbriae and flagella biosynthesis, no evidence for an involvement of the LPS itself in adhesion to polystyrene surface could be observed.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1617-4623
    Keywords: Nickel ; celF ; katE ; luxAB
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract From a library of 3000 Escherichia coli clones, each containing a single, chromosomally located luxAB transcriptional gene fusion, one clone was found in which luminescence increased in the presence of 1 to 50 ppm of NiSO4. A molecular analysis revealed that the insertion occurred within the celF gene of E. coli. This gene encodes the phospho-β-glucosidase involved in cleavage of the sugars cellobiose, salicin and arbutin. Cloning and sequencing of DNA downstream of the celF gene revealed three open reading frames (potentially encoding polypeptides of 9.9, 14.1 and 28.5 kDa) that could be coexpressed with the celF gene and that may underlie the observed induction of the celF gene by nickel. A polypeptide of 26 kDa was produced when this region was placed under the control of the P tac promoter. Moreover, this region was found to be directly adjacent to, and transcribed in the opposite orientation from, the katE gene of E. coli.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Molecular genetics and genomics 242 (1994), S. 272-279 
    ISSN: 1617-4623
    Keywords: Bacteriophage Mu ; Transposase ; Linker mutagenesis ; Site-specific mutagenesis ; Transposition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The 663 amino acid Mu transposase protein is absolutely required for Mu DNA transposition. Mutant proteins were constructed in vitro in order to locate regions of transposase that may be important for the catalysis of DNA transposition. Deletions in the A gene, which encodes the transposase, yielded two stable mutant proteins that aid in defining the end-specific DNA-binding domain. Linker insertion mutagenesis at eight sites in the Mu A gene generated two proteins, FF6 and FF14 (resulting from two and four amino acid insertions, respectively, at position 408), which were thermolabile for DNA binding in vitro at 43°C. However, transposition activity in vivo was severely reduced for all mutant proteins at 37°C, except those with insertions at positions 328 and 624. In addition, site-specific mutagenesis was performed to alter tyrosine 414, which is situated in a region that displays amino acid homology to the active sites of a number of nicking/closing enzymes. Tyrosine 414 may reside within an important, yet non-essential, site of transposase, as an aspartate-substituted protein had a drastically reduced frequency of transposition, while the remaining mutants yielded reduced, but substantial, frequencies of μMu transposition in vivo.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Molecular genetics and genomics 141 (1975), S. 113-119 
    ISSN: 1617-4623
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Host Factor (HF)1, is a 12000 molecular weight polypeptide that is found in uninfected Escherichia coli and is required as a hexamer along with Qβ replicase for in vitro replication of Qβ phage RNA. It has recently been found to be associated with ribosomes and to bind tightly to poly(A). We report here the identification and purification of HF from Pseudomonas putida. HF can be detected in crude extracts by both functional activity in the Qβ RNA replication assay and by immunodiffusion with antibody made against E. coli HF. HF from E. coli and P. putida chromatograph similarly on DEAE-cellulose and phosphocellulose. They have similar but not identical molecular weights as judged by SDS-polyacrylamide gel electrophoresis. Like E. coli HF, P. putida HF was found to be associated with ribosomes and to bind tightly to poly (A). Furthermore, the pure protein from P. putida has full functional activity in the in vitro Qβ RNA replication assay. The findings that HF has been conserved during evolution, is associated with ribosomes, and binds poly(A), suggest that HF may be an important translational element in uninfected cells and that its role involves an interaction with RNA.
    Type of Medium: Electronic Resource
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