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  • 1
    Electronic Resource
    Electronic Resource
    Distribution of the pressure-regulated operons in deep-sea bacteria (1998)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 159 (1998), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: DNA regions corresponding to portions of two different pressure-regulated operons previously identified in two deep-sea barophilic bacteria were separately PCR amplified from a variety of deep-sea microorganisms and sequenced. With the two sets of primers employed, amplification was particularly successful from the more barophilic bacteria examined. 16S rRNA sequence analysis revealed that these bacteria are all phylogenetically related and belong in a sub-branch of the genus Shewanella containing only the deep-sea Shewanella barophilic bacteria. We define this sub-branch as the ‘Shewanella barophile branch’ containing at least two different species. Our results suggest that the DNA sequences of the pressure-regulated operons can be regarded as marker sequences to identify the Shewanella barophilic strains.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1998.tb12855.x
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  • 2
    Electronic Resource
    Electronic Resource
    Identification and analysis of the amylase-binding protein B (AbpB) and gene (abpB) from Streptococcus gordonii (2002)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 212 (2002), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The binding of salivary amylase to Streptococcus gordonii has previously been shown to involve a 20-kDa amylase-binding protein (AbpA). S. gordonii also releases an 82-kDa protein into the supernatant that binds amylase. To study this 82-kDa component, proteins were precipitated from bacterial culture supernatants by the addition of acetone or purified amylase. Precipitated proteins were separated by SDS–PAGE and transferred to a sequencing membrane. The P2 kDa band was then sequenced, yielding a 25 N-terminal amino acid sequence, CGFIFGRQLTADGSTMFGPTEDYP. Primers derived from this sequence were used in an inverse PCR strategy to clone the full-length gene from S. gordonii chromosomal DNA. An open reading frame of 1959 bp was noted that encoded a 652 amino acid protein having a predicted molecular mass of 80 kDa. The first 24 amino acid residues were consistent with a hydrophobic signal peptide, followed by a 25 amino acid N-terminal sequence that shared identity (24 of 25 residues) with the amino acid sequence of purified AbpB. The abpB gene from strains of S. gordonii was interrupted by allelic exchange with a 420-bp fragment of the abpB gene linked to an erythromycin cassette. The 82-kDa protein was not detected in supernatants from these mutants. These abpB mutants retained the ability to bind soluble amylase. Thus, AbpA, but not AbpB, appears sufficient to be the major receptor for amylase binding to the streptococcal surface. The role of AbpB in bacterial colonization remains to be elucidated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.2002.tb11259.x
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  • 3
    Electronic Resource
    Electronic Resource
    Changes in the microbial community in Japan Trench sediment from a depth of 6292 m during cultivation without decompression (1999)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 170 (1999), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: A sample of deep-sea sediment was obtained from the Japan Trench at a depth of 6292 m using a pressure-retaining sediment sampler. Microorganisms in the sediment sample were cultivated in marine broth 2216 at ambient pressure (65 MPa) without decompression, and at atmospheric pressure (0.1 MPa) as a control experiment. 16S ribosomal RNA genes (rDNA) were amplified by PCR from DNA extracted from the original sediment sample and the mixed cultures, and the nucleotide sequences were determined. The results of phylogenetic analysis based on 16S rDNA sequences indicated that microbial diversity in the original sediment samples showed a wide distribution of types in the domain Bacteria. Furthermore, in the mixed cultures incubated at 65 MPa without decompression, bacterial strains belonging to the Shewanella barophiles branch and the genus Moritella existed together at the beginning of cultivation, and Moritella strains became dominant towards the end of the cultivation period. Finally, in the mixed cultures incubated at atmospheric pressure, strains belonging to the genus Pseudomonas were dominant at all times. Analysis of fatty acids extracted from the cultures supported the phylogenetic results.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1999.tb13384.x
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  • 4
    Electronic Resource
    Electronic Resource
    In vivo analysis of the roles of conserved aspartate and histidine residues within a complex response regulator (2005)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 55 (2005), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: RcaC is the founding member of a group of large response regulators with complex domain combinations containing at least two receiver domains, an OmpR-class winged helix-turn-helix DNA binding domain, and a histidine phosphotransfer (HPt) domain. Within its two receiver and HPt domains, RcaC contains consensus phosphorylation sites at aspartates 51, 576 and histidine 316. RcaC operates in the pathway regulating transcription of genes encoding components of photosynthetic light harvesting antenna to changes in light colour. We show that phycocyanin gene expression requires RcaC. RcaC contributes to light regulation of phycoerythrin genes, but is not part of the second light regulation pathway controlling these genes. Substitutions at aspartate 51 or histidine 316 severely impaired light responsiveness while substitutions at aspartate 576 had little effect. Complete loss of light regulation, measured by phycocyanin gene expression, only occurred in the triple mutant. We conclude that aspartate 51 primarily controls light colour responsiveness and is regulated by histidine 316, and that these residues are likely phosphorylated in red light and dephosphorylated in green light. The carboxy-terminal receiver domain has a minor role in controlling this response. RcaC abundance is also light regulated and depends on aspartate 51 and histidine 316, but not aspartate 576.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2958.2005.04491.x
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  • 5
    Electronic Resource
    Electronic Resource
    Microbial Diversity in Sediments Collected from the Deepest Cold-Seep Area, the Japan Trench (1999)
    Springer
    Marine biotechnology 1 (1999), S. 391-400 
    Details
    ISSN: 1436-2236
    Keywords: Key words: Cold-seep environment, microbial diversity, Calyptogena, Japan Trench, sulfur-reducing bacteria, sediment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract: The Japan Trench land slope at a depth of 6,400 m is the deepest cold-seep environment with Calyptogena communities. Sediment samples from inside and beside the Calyptogena communities were collected, and the microbial diversity in the sediment samples was studied by molecular phylogenetic techniques. From DNA extracted directly from the sediment samples, 16S rDNAs were amplified by the polymerase chain reaction method. The sequences of the amplified 16S rDNAs selected by restriction fragment length polymorphism analysis were determined and compared with sequences in DNA databases. The results showed that 33 different bacterial 16S rDNA sequences from the two samples analyzed fell into similar phylogenetic categories, the α-, γ-, δ-, and ɛ-subdivisions of Proteobacteria, Cytophaga, and gram-positive bacteria; some of the 16S rDNA sequences were common to both samples. δ- and ɛ-Proteobacteria-related sequences were abundant in both sediments. These sequences are mostly related to sulfate-reducing or sulfur-reducing bacteria and epibionts, respectively. Eight different archaeal 16S rDNA sequences were cloned from the sediments. The majority of the archaeal 16S rDNA sequences clustered in Crenarchaeota and showed high similarities to marine group I archaeal rDNA. A Methanococcoides burtonii–related sequence obtained from the sediment clustered in the Euryarchaeota indicating that M. burtonii–related strains in the area of Calyptogena communities may contribute to production of methane in this environment. From these results, we propose a possible model of sulfur circulation within the microbial community and that of Calyptogena clams in the cold-seep environment.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00011793
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  • 6
    Electronic Resource
    Electronic Resource
    Microbial Diversity in Nankai Trough Sediments at a Depth of 3,843 m (1999)
    Springer
    Journal of oceanography 55 (1999), S. 635-642 
    Details
    ISSN: 1573-868X
    Keywords: Deep-sea ; microbial diversity ; cold seep ; Nankai Trough ; Calyptogena ; 16S ribosomal RNA gene ; PLFA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract Dense populations of bivalves, primarily Calyptogena sp., were observed at cold seeps of the Nankai Trough. Bacterial input to the sediment was estimated through determination of phospholipid ester-linked fatty acid (PLFA) and DNA profiles. Results indicated a bacterial biomass of 109 cells (g dry wt)-1 while individual fatty acid profiles revealed a predominance of monounsaturated fatty acids, mainly 18:1 isomers. The presence of these fatty acids can be interpreted to reflect a response to low temperature and a predominance of psychrophilic bacteria. DNA fragments encoding bacterial ribosomal RNA small-subunit sequences (16S rDNA) were amplified by the polymerase chain reaction method using DNA extracted directly from the sediment samples. From the sequencing results, at least 19 kinds of bacterial 16S rDNAs related to mostly the Proteobacteria and a few gram-positive bacteria were identified. These results suggest that the bacterial community in the Nankai Trough sediments consists of mainly bacteria belonging to the Proteobacteria γ, ε, and δ subdivisions. Bacteria belonging to the ε and δ subdivisions, which are known to include epibiont and sulfate reducing bacteria, respectively, were mostly detected in the sediment obtained from inside the area of the Calyptogena community, and the δ-Proteobacteria may function to supply reduced sulfur to bacterial endosymbionts of Calyptogena.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1007897020042
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  • 7
    Electronic Resource
    Electronic Resource
    Novel archaeal phylotypes from an East African alkaline saltern (1999)
    Springer
    Extremophiles 3 (1999), S. 139-145 
    Details
    ISSN: 1433-4909
    Keywords: Key words Halophile ; Haloalkaliphile ; Phylogeny ; Phylotype ; 16S rDNA ; Alkaline saltern ; Archaea
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract DNA has been extracted on site from the brines of the final crystallizing pond of an alkaline saltern at Lake Magadi, Kenya. Amplification of 16S rRNA genes followed by cloning, sequencing, and phylogenetic analysis has revealed the presence of two distinct new archaeal lineages. The majority of cloned sequences showed greater than 95% identity to each other, but only 88%–90% similarity to any cultivated haloalkaliphilic Archaea, and form a distinct cluster within the known Haloarchaea. Two cloned genes showed close similarity to each other but only 76% similarity to any known archaeal sequence, and therefore represent a distinct phylotype only distantly related to the euryarchaeotal branch of the Archaea.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007920050109
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  • 8
    Electronic Resource
    Electronic Resource
    Taxonomy and biotransformation activities of some deep-sea actinomycetes (1998)
    Springer
    Extremophiles 2 (1998), S. 269-277 
    Details
    ISSN: 1433-4909
    Keywords: Key words Deep sea ; Actinomycetes ; Selective isolation ; Pyrolysis mass spectrometry ; Nitrile transformations ; High pressure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Deep-sea soft sediments from trench systems and depths in the northwestern Pacific Ocean ranging from less than 300 to 10 897 m in depth have been analyzed for three target genera of actinomycetes: Micromonospora, Rhodococcus, and Streptomyces. Only culturable strains, recovered at atmospheric pressure on selective isolation media, have been examined to date. Maximum recoveries of culturable bacteria were greater that 107/ml wet g sediment, but actinomycetes comprised a small proportion of this population (usually less than 1%). The target actinomycetes were isolated at all depths except from the Mariana Trench sediments. Actinomycete colonies were defined initially on the basis of colony morphologies, and preliminary identification then was made by chemotaxonomic tests. Pyrolysis mass spectrometry (PyMS) of deep-sea mycolic acid-containing actinomycetes gave excellent correspondence with numerical (phenetic) taxonomic analyses and subsequently was adopted as a rapid procedure for assessing taxonomic diversity. PyMS analysis enabled several clusters of deep-sea rhodococci to be distinguished that are quite distinct from all type strains. 16S rRNA gene sequence analysis has revealed that several of these marine rhodococci have sequences that are very similar to certain terrestrial species of Rhodococcus and to Dietzia. There is evidence for the intrusion of terrestrial runoff into these deep trench systems, and the inconsistency of the phenotypic and molecular taxonomies may reflect recent speciation events in actinomycetes under the high-pressure conditions of the deep sea. The results of DNA-DNA pairing experiments point to the novelty of Rhodococcus strains recovered from hadal depths in the Izu Bonin Trench. Biotransformation studies of deep-sea bacteria have focused on nitrile compounds. Nitrile-metabolizing bacteria, closely related to rhodococci, have been isolated that grow well at low temperature, high salt concentrations, and high pressures, suggesting that they are of marine origin or have adapted to the deep-sea environment.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007920050069
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  • 9
    Electronic Resource
    Electronic Resource
    A denitrifying bacterium from the deep sea at 11 000-m depth (1997)
    Springer
    Extremophiles 1 (1997), S. 207-211 
    Details
    ISSN: 1433-4909
    Keywords: Key words Deep-sea ; Mariana Trench ; Denitrification Extreme environment ; Pseudomonas
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The denitrifying bacterium strain MT-1 was isolated from the mud of the Mariana Trench. The optimal temperature and pressure for growth of this bacterium were found to be 30°C and 0.1 MPa, respectively. However, it showed greater tolerance to low temperature (4°C) and high hydrostatic pressure (50 MPa) as compared with denitrifiers obtained from land. From the results, it can be said that this organism is adapted to the environment of the deep sea. Strain MT-1 was shown to belong to the genus Pseudomonas by analysis of its 16S rDNA. The cytochrome contents of the bacterium were similar to those of Ps. stutzeri in spectrophotometric studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007920050035
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  • 10
    Electronic Resource
    Electronic Resource
    Molecular analyses of the sediment of the 11000-m deep Mariana Trench (1997)
    Springer
    Extremophiles 1 (1997), S. 117-123 
    Details
    ISSN: 1433-4909
    Keywords: Key words Mariana Trench ; Challenger point ; Deep-sea ; Barophilic bacteria ; Pseudomonas ; Planktonic marine archaea ; Pressure-regulated operon
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have obtained sediment samples from the world's deepest sea-bottom, the Mariana Trench challenger point at a depth of 10 898 m, using the new unmanned submersible Kaiko. DNA was extracted from the sediment, and DNA fragments encoding several prokaryotic ribosomal RNA small-subunit sequences and pressure-regulated gene clusters, typically identifed in deep-sea adapted bacteria, were amplifed by the polymerase chain reaction. From the sequencing results, at least two kinds of bacterial 16S rRNAs closely related to those of the genus Pseudomonas and deep-sea adapted marine bacteria, and archaeal 16S rRNAs related to that of a planktonic marine archaeon were identifed. The sequences of the amplifed pressure-regulated clusters were more similar to those of deep-sea barophilic bacteria than those of barotolerant bacteria. These results suggest that deep-sea adapted barophilic bacteria, planktonic marine archaea, and some of the world's most widespread bacteria (the genus Pseudomonas) coexist on the world's deepest sea-bottom.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007920050024
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