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  • 1
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    Emended description of the genus Rhodothalassium Imhoff et al., 1998 and proposal of Rhodothalassiaceae fam. nov. and Rhodothalassiales ord. nov (2013)
    Elsevier
    In:  Systematic and Applied Microbiology, 36 (1). pp. 28-32.
    Details
    Publication Date: 2019-09-23
    Description: Five strains (JA325, JA389, JA473, JA563 and JA582) of Gram stain-negative, vibrioid to spiral shaped, phototrophic purple bacteria were isolated from solar salterns of India. All strains contained bacteriochlorophyll-a and carotenoids of the spirilloxanthin series as photosynthetic pigments. C18:1ω7c, C18:1ω7c 11-methyl and C16:0 were the major fatty acids of all strains. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), ornithine lipid (OL), an unidentified phospholipid (PL), and an unidentified aminolipid (AL) were the major polar lipids of all the strains. According to 16S rRNA gene sequences, all strains clustered phylogenetically with the only species of the genus Rhodothalassium (99.8–99.3% sequence similarity) but only strains JA325 and JA563 were distinctly related (60 + 1.5% DNA–DNA hybridization [DDH]) to the type strain Rhodothalassium salexigens DSM 2132T. However, the genotypic data of strains JA325 and JA563 was not supported because of a large number of phenotypic differences compared to the type strain, therefore, it is proposed that all five newly isolated strains were R. salexigens-like strains. In addition, phylogenetically, the Rhodothalassium clade represented a distinct lineage and formed a deep branch with less than 90% 16S rRNA gene sequence similarity to other orders of the Alphaproteobacteria, and characteristic phenotypic properties also distinguished these bacteria from other purple non-sulfur bacteria. Therefore, the novel family Rhodothalassiaceae fam. nov. and the novel order Rhodothalassiales ord. nov. are proposed for the distinct phyletic line represented by the genus Rhodothalassium.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1016/j.syapm.2012.09.003
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  • 2
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    Tabrizicola aquatica gen. nov. sp. nov., a novel alphaproteobacterium isolated from Qurugöl Lake nearby Tabriz city, Iran (2013)
    Springer
    In:  Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 104 (6). pp. 1205-1215.
    Details
    Publication Date: 2019-09-23
    Description: A novel Gram-negative, aerobic, non-motile and rod-shaped bacterium was isolated from Qurugöl Lake near Tabriz city. The bacterium grew chemoorganolheterotrophically and chemolithoautotrophically. However, photo-organoheterotrophic, photo-lithoautotrophic and fermentative growth could not be demonstrated. The presence of photosynthesis genes pufL and pufM was not shown and photosynthesis pigments were not formed. Strain RCRI19T grew without NaCl and tolerated up to 3 % NaCl. Growth occurred at pH 6–9 (optimum, pH 7) and 15–55 °C (optimum 40–45 °C). Vitamins were not required for growth. The major fatty acids are C18:1 ω7C, 11-methyl C18:1 ω7C, C18:0 3-OH. The predominant respiratory quinone is ubiquinone Q-10. The G+C content of genomic DNA is 65.9 mol%. Analysis of 16S rRNA sequences showed that strain RCRI19T has the highest similarities with uncultured environmental sequences followed by members of the genera Rhodobacter (≤95.75 %), Haematobacter (≤95.53 %), Gemmobacter (≤95.17 %) and Falsirhodobacter (94.60 %) in the family Rhodobacteraceae. DNA–DNA relatedness between strain RCRI19T and the closest phylogenetically related strain, Rhodobacter blasticus LMG 4305T, was 20 %. Based on its phenotypic and chemotaxonomic characteristics and considering that it does not form photosynthetic pigments and is unable to grow phototrophically, it is concluded that strain RCRI19T cannot be included into the genus Rhodobacter and any of the other related genera. Therefore, we propose to place the new bacterium into a new genus and species for which the name Tabrizicola aquatica gen. nov. and sp. nov. is proposed. The type strain is RCRI19T (=BCCM/LMG 25773T = JCM 17277T = KCTC 23724T).
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1007/s10482-013-0042-y
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  • 3
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    New phylogenetic lineages of the Spirochaetes phylum associated with Clathrina species (Porifera) (2010)
    Springer
    In:  Journal of Microbiology, 48 (4). pp. 411-418.
    Details
    Publication Date: 2018-01-19
    Description: Though spirochetes have been repeatedly found in marine sponges and other invertebrates, little attention has been paid to the specificity of this association. This study demonstrates that different genoand morphotypes of spirochetes can reside within the same sponge individual and develop in considerable numbers. Specimens of the calcareous sponge Clathrina clathrus collected from the Adriatic Sea off Rovinj (Croatia) were found to harbor spirochete-like bacteria, which were characterized by scanning electron microscopy (SEM), 16S rRNA gene analysis, and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Two novel spirochete sequence types related to the Brachyspiraceae could be retrieved. By use of specifically designed CARD-FISH probes, the C. clathrus-associated sequences could be assigned to a linear and a helical spirochete morphotype. Both were located within the sponge mesohyl and resembled the spirochete-like cells identified by SEM. In addition, from a Clathrina sp., most likely C. coriacea, that originated from Indonesian coastal waters, four different spirochete type sequences were recovered. Two of these also affiliated with the Brachyspiraceae, the other two were found associated with the Spirochaetaceae, one with the genera Borrelia and Cristispira.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1007/s12275-010-0017-x
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  • 4
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    Functional genes as markers for sulfur cycling and CO2 fixation in microbial communities of hydrothermal vents of the Logatchev field (2010)
    Oxford University Press
    In:  FEMS Microbiology Ecology, 73 (3). pp. 526-537.
    Details
    Publication Date: 2019-09-23
    Description: Life at deep-sea hydrothermal vents depends on chemolithoautotrophic microorganisms as primary producers mediating the transfer of energy from hydrothermal fluids to higher trophic levels. A comprehensive molecular survey was performed with microbial communities in a mussel patch at the Irina II site of the Logatchev hydrothermal field by combining the analysis of 16S rRNA gene sequences with studies of functional key genes involved in biochemical pathways of sulfur oxidation–reduction (soxB, aprA) and autotrophic carbon fixation (aclB, cbbM, cbbL). Most significantly, major groups of chemoautotrophic sulfur oxidizers in the diffuse fluids differed in their biosynthetic pathways of both carbon fixation and sulfur oxidation. One important component of the community, the Epsilonproteobacteria, has the potential to grow chemoautotrophically by means of the reductive tricarboxylic acid cycle and to gain energy through the oxidation of reduced sulfur compounds using the Sox pathway. The majority of soxB and all retrieved aclB gene sequences were assigned to this group. Another important group in this habitat, the Gammaproteobacteria, may use the adenosine 5'-phosphosulfate pathway and the Calvin–Benson–Bassham cycle, deduced from the presence of aprA and cbbM genes. Hence, two important groups of primary producers at the investigated site might use different pathways for sulfur oxidation and carbon fixation.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1111/j.1574-6941.2010.00919.x
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  • 5
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    Secondary metabolites from Calotropis procera (Aiton) (2010)
    Elsevier
    In:  Phytochemistry Letters, 3 (4). pp. 212-216.
    Details
    Publication Date: 2019-09-23
    Description: Three new metabolites, 5-hydroxy-3,7-dimethoxyflavone-4′-O-β-glucopyranoside (1), 2β,19-epoxy-3β,14β-dihydroxy-19-methoxy-5α-card-20(22)-enolide (4) and β-anhydroepidigitoxigenin-3β-O-glucopyranoside (5), along with two known compounds, uzarigenine (2) and β-anhydroepidigitoxigenin (3), were isolated from Calotropis procera (Asclepiadaceae). The structure elucidation was accomplished mainly by nuclear magnetic resonance (NMR) spectroscopic and mass spectrometric methods. To examine putative antimicrobial or cytotoxic activities, various bioassays were performed. Uzarigenine (2) demonstrated moderate cytotoxicity.
    Type: Article , PeerReviewed
    Format: text
    Format: text
    DOI: 10.1016/j.phytol.2010.07.009
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  • 6
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    Phylogenetic and functional marker gene to study ammonia-oxidizing microorganisms (AOM) in the environment (2010)
    Springer
    In:  Applied Microbiology and Biotechnology, 85 . pp. 425-440.
    Details
    Publication Date: 2019-09-23
    Description: The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1007/s00253-009-2228-9
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  • 7
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    Phylogenetic diversity and antimicrobial activities of bryozoan-associated bacteria isolated from Mediterranean and Baltic Sea habitats (2010)
    Elsevier
    In:  Systematic and Applied Microbiology, 33 . pp. 94-104.
    Details
    Publication Date: 2020-10-16
    Description: To date, only a small number of investigations covering microbe–bryozoa associations have been carried out. Most of them have focused on a few bryozoan species and none have covered the antibacterial activities of associated bacteria. In the current study, the proportion and phylogenetic classification of Bryozoan-associated bacteria with antimicrobial properties were investigated. Twenty-one specimens of 14 different bryozoan species were collected from several sites in the Baltic and the Mediterranean Sea. A total of 340 associated bacteria were isolated, and 101 displayed antibiotic activities. While antibiosis was predominantly directed against Gram-positive test strains, 16S rRNA gene sequencing revealed affiliation of the isolates to Gram-negative classes (Flavobacteria, Alpha- and Gammaproteobacteria). One isolate was related to the Gram-positive Actinobacteria. The sequences were grouped into 27 phylotypes on the basis of similarity values ≥99.5%. A host-specific affiliation was not revealed as members of the same phylotype were derived from different bryozoan species. Site-specific patterns, however, were demonstrated. Strains of the genera Sphingomonas and Alteromonas were exclusively isolated from Mediterranean sites, whereas Shewanella, Marinomonas and Vibrio-related isolates were only from Baltic sites. Although Pseudoalteromonas affiliated strains were found in both habitats, they were separated into respective phylotypes. Isolates with 16S rDNA similarity values 〈98%, which could possibly represent new species, belonged to the genera Shewanella, Pseudoalteromonas and Tenacibaculum.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1016/j.syapm.2009.12.002
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  • 8
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    The Family Chromatiaceae (2014)
    Springer
    In:  In: The Prokaryotes. Gammaproteobacteria. , ed. by Rosenberg, E., DeLong, E. F., Lory, S., Stackebrandt, S. and Thompson, F. Springer, Berlin, Germany, pp. 151-178. 4. ed. ISBN 978-3-642-38921-4
    Details
    Publication Date: 2014-12-04
    Description: The Chromatiaceae is a family of the Chromatiales within the Gammaproteobacteria and closely related to the Ectothiorhodospiraceae. Representatives of both families are referred to as phototrophic purple sulfur bacteria and typically grow under anoxic conditions in the light using sulfide as photosynthetic electron donor, which is oxidized to sulfate via intermediate accumulation of globules of elemental sulfur. In Chromatiaceae species, the sulfur globules appear inside the cells; in Ectothiorhodospiraceae, they are formed outside the cells and appear in the medium. Characteristic properties of these bacteria are the synthesis of photosynthetic pigments, bacteriochlorophyll a or b, and various types of carotenoids and the formation of a photosynthetic apparatus with reaction center and antenna complexes localized within internal membrane systems. Phototrophic growth, photosynthetic pigment synthesis, and formation of the photosynthetic apparatus and internal membranes are strictly regulated by oxygen and light and become derepressed at low oxygen tensions. Typically, Chromatiaceae are enabled to the photolithoautotrophic mode of growth. A number of species also can grow photoheterotrophically using a limited number of simple organic molecules. Some species also can grow under chemotrophic conditions in the dark, either autotrophically or heterotrophically using oxygen as terminal electron acceptor in respiratory processes
    Type: Book chapter , NonPeerReviewed
    DOI: 10.1007/978-3-642-38922-1_295
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  • 9
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    The order Kiloniellales (2014)
    Springer
    In:  In: The Prokaryotes: Alphaproteobacteria and Betaproteobacteria. , ed. by Rosenberg, E., DeLong, E. F., Lory, S., Stackebrandt, S. and Thompson, F. Springer, Berlin, Germany, pp. 301-306. 4. ed. ISBN 978-3-642-30196-4
    Details
    Publication Date: 2019-10-09
    Description: The Kiloniellaceae family is represented currently by a single genus Kiloniella with the species Kiloniella laminariae as type species. Kiloniella laminariae was isolated from the marine macroalga Saccharina latissima (former Laminaria saccharina) obtained from the Baltic Sea. The bacterium is a mesophilic, typical marine bacterium. It is a chemoheterotrophic aerobic bacterium with the potential of denitrification. Growth optima are at 25 °C, pH 5.5, and 3 % NaCl. The distinguished phylogenetic position separates Kiloniella from other alphaproteobacterial orders. The 16S rRNA gene sequence revealed a distant relationship to species of several orders of the Alphaproteobacteria with less than 91 % sequence similarity. This gives rise to the recognition of Kiloniella as a representative of a new order of the Alphaproteobacteria, the Kiloniellales. Phylogenetic analyses revealed a distinct cluster of Kiloniella with an uncharacterized bacterium (isolate KOPRI 13522) from hydrothermal plumes. This cluster forms a larger group together with the distantly related Terasakiella pusilla (88.4 % sequence similarity of the 16S rRNA gene) and the Thalassospira species (88.9–90.2 % sequence similarity). These genera are supposed to form separate families within the Kiloniellales.
    Type: Book chapter , NonPeerReviewed
    Format: text
    DOI: 10.1007/978-3-642-30197-1_301
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  • 10
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    The family Chlorobiaceae (2014)
    Springer
    In:  In: The Prokaryotes: Other major lineages of Bacteria and Archaea. , ed. by Rosenberg, E., DeLong, E. F., Lory, S., Stackebrandt, S. and Thompson, F. Springer, Berlin, Germany, pp. 501-514. 4. ed. ISBN 978-3-642-38921-4
    Details
    Publication Date: 2019-10-09
    Description: Since the discovery of the green sulfur bacteria and the first description by Larsen (1952), this group of bacteria has gained much interest because of a number of highly interesting features. These include the unique structures of the photosynthetic apparatus and the presence of small organelles, the chlorosomes, which act as light-harvesting antenna. Chlorosomes are very powerful light receptors that can capture minute amounts of light and enable the green sulfur bacteria to perform photosynthesis and to grow at very low-light intensities. This has important ecological consequences, because the efficient light harvesting determines the ecological niche of these bacteria at the lowermost part of stratified environments, where the least of light is available. Furthermore, the strict dependency on photosynthesis to provide energy for growth and the obligate phototrophy of the green sulfur bacteria together with their characteristic sulfur metabolism has provoked much interest in their physiology, ecology, and genomics. The oxidation of sulfide as the outmost important photosynthetic electron donor of the green sulfur bacteria involves the deposition of elemental sulfur globules outside the cells and separates the process of sulfide oxidation to sulfate clearly into two steps. In the phylogenetic-based taxonomy, the green sulfur bacteria are treated as family Chlorobiaceae with the genera Chlorobium, Chlorobaculum, Prosthecochloris, and Chloroherpeton.
    Type: Book chapter , NonPeerReviewed
    Format: text
    DOI: 10.1007/978-3-642-38954-2_142
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