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  • 1
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    Comparative genomics highlights symbiotic capacities and high metabolic flexibility of the marine genus Pseudovibrio (2018)
    Oxford University Press
    In:  Genome Biology and Evolution, 10 (1). pp. 125-142.
    Details
    Publication Date: 2021-02-08
    Description: Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesised that Pseudovibrio spp. form mutualistic relationships with their hosts. Here, we studied Pseudovibrio phylogeny and genetic adaptations that may play a role in host colonization by comparative genomics of 31 Pseudovibrio strains, including 25 sponge isolates. All genomes were highly similar in terms of encoded core metabolic pathways, albeit with substantial differences in overall gene content. Based on gene composition, Pseudovibrio spp. clustered by geographic region, indicating geographic speciation. Furthermore, the fact that isolates from the Mediterranean Sea clustered by sponge species suggested host-specific adaptation or colonization. Genome analyses suggest that Pseudovibrio hongkongensis UST20140214-015BT is only distantly related to other Pseudovibrio spp., thereby challenging its status as typical Pseudovibrio member. All Pseudovibrio genomes were found to encode numerous proteins with SEL1 and tetratricopeptide repeats, which have been suggested to play a role in host colonization. For evasion of the host immune system, Pseudovibrio spp. may depend on type III, IV and VI secretion systems that can inject effector molecules into eukaryotic cells. Furthermore, Pseudovibrio genomes carry on average seven secondary metabolite biosynthesis clusters, reinforcing the role of Pseudovibrio spp. as potential producers of novel bioactive compounds. Tropodithietic acid, bacteriocin and terpene biosynthesis clusters were highly conserved within the genus, suggesting an essential role in survival e.g. through growth inhibition of bacterial competitors. Taken together, these results support the hypothesis that Pseudovibrio spp. have mutualistic relations with sponges.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
    Format: archive
    DOI: 10.1093/gbe/evx271
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 2
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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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  • 3
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    Comparative in silico analysis of PCR primers suited for diagnostics and cloning of ammonia monooxygenase genes from ammonia-oxidizing bacteria (2008)
    Oxford University Press
    In:  FEMS Microbiology Ecology, 64 . pp. 141-152.
    Details
    Publication Date: 2019-09-23
    Description: Over recent years, several PCR primers have been described to amplify genes encoding the structural subunits of ammonia monooxygenase (AMO) from ammonia-oxidizing bacteria (AOB). Most of them target amoA, while amoB and amoC have been neglected so far. This study compared the nucleotide sequence of 33 primers that have been used to amplify different regions of the amoCAB operon with alignments of all available sequences in public databases. The advantages and disadvantages of these primers are discussed based on the original description and the spectrum of matching sequences obtained. Additionally, new primers to amplify the almost complete amoCAB operon of AOB belonging to Betaproteobacteria (betaproteobacterial AOB), a primer pair for DGGE analysis of amoA and specific primers for gammaproteobacterial AOB, are also described. The specificity of these new primers was also evaluated using the databases of the sequences created during this study.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1111/j.1574-6941.2007.00437.x
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  • 4
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    Communities of purple sulfur bacteria in a Baltic Sea coastal lagoon analyzed by pufLM gene libraries and the impact of temperature and NaCl concentration in experimental enrichment cultures (2011)
    Oxford University Press
    In:  FEMS Microbiology Ecology, 78 (3). pp. 428-438.
    Details
    Publication Date: 2019-09-23
    Description: Shallow coastal waters, where phototrophic purple sulfur bacteria (PSB) regularly form massive blooms, are subjected to massive diurnal and event-driven changes of physicochemical conditions including temperature and salinity. To analyze the ability of PSB to cope with these environmental factors and to compete in complex communities we have studied changes of the environmental community of PSB of a Baltic Sea lagoon under experimental enrichment conditions with controlled variation of temperature and NaCl concentration. For the first time, changes within a community of PSB were specifically analyzed using the photosynthetic reaction center genes pufL and M by RFLP and cloning experiments. The most abundant PSB phylotypes in the habitat were found along the NaCl gradient from freshwater conditions up to 7.5% NaCl. They were accompanied by smaller numbers of purple nonsulfur bacteria and aerobic anoxygenic phototrophic bacteria. Major components of the PSB community of the brackish lagoon were affiliated to PSB genera and species known as marine, halophilic or salt-tolerant, including species of Marichromatium, Halochromatium, Thiorhodococcus, Allochromatium, Thiocapsa, Thiorhodovibrio, and Thiohalocapsa. A dramatic shift occurred at elevated temperatures of 41 and 44°C when Marichromatium gracile became most prominent which was not detected at lower temperatures.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1111/j.1574-6941.2011.01175.x
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  • 5
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    Phylogenetic analysis of bacteria associated with Laminaria saccharina. (2008)
    Oxford University Press
    In:  FEMS Microbiology Ecology, 64 . pp. 65-77.
    Details
    Publication Date: 2019-09-23
    Description: Bacterial communities associated with the brown alga Laminaria saccharina from the Baltic Sea and from the North Sea were investigated using denaturing gradient gel electrophoresis and 16S rRNA gene clone libraries. The rhizoid, cauloid, meristem and phyloid revealed different 16S rRNA gene denaturing gradient gel electrophoresis banding patterns indicating a specific association of bacterial communities with different parts of the alga. Associations with cauloid and meristem were more specific, while less specific associations were obtained from the old phyloid. In addition, seasonal and geographical differences in the associated communities were observed. Results from 16S rRNA gene libraries supported these findings. Bacterial phylotypes associated with the alga were affiliated with the Alphaproteobacteria (nine phylotypes), Gammaproteobacteria (nine phylotypes) and the Bacteroidetes group (four phylotypes). A number of bacteria associated with other algae and other marine macroorganisms were among the closest relatives of phylotypes associated with L. saccharina.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1111/j.1574-6941.2008.00445.x
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  • 6
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    Unique clusters of Archaea in Salar de Huasco, an athalassohaline evaporitic basin of the Chilean Altiplano (2010)
    Oxford University Press
    In:  FEMS Microbiology Ecology, 73 (2). pp. 291-302.
    Details
    Publication Date: 2019-09-23
    Description: Analyses of clone libraries from water and sediments of different sites from Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano, revealed the presence of five unique clusters of uncultured Archaea that have not been previously reported or specifically assigned. These sequences were distantly related (83–96% sequence identity) to a limited number of other clone sequences and revealed no identity to cultured Archaea. The abundance of Archaea and Bacteria was estimated using qPCR and community composition was examined through the construction of clone libraries of archaeal 16S rRNA gene. Archaea were found to be dominant over Bacteria in sediments from two saline sites (sites H4: 6.31 × 104 and site H6: 1.37 × 104 μS cm−1) and in one of the water samples (freshwater from site H0: 607 μS cm−1). Euryarchaeotal sequences were more abundant than crenarchaeotal sequences. Many of the clone sequences (52%) were similar to uncultured archaeal groups found in marine ecosystems having identity values between 99% and 97%. A major fraction of the sequences (40%) were members of Methanobacteria, while others were included in the Marine Benthic Groups B and D, the Miscellaneous Crenarchaeotic Group, the Terrestrial Miscellaneous Euryarchaeotal Group, Marine Group I and Halobacteria. The presence of uncultured archaeal groups in Salar de Huasco extends their known distribution in inland waters, providing new clues about their possible function in the environment.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1111/j.1574-6941.2010.00891.x
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  • 7
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    Unique communities of anoxygenic phototrophic bacteria in saline lakes of Salar de Atacama (Chile): evidence for a new phylogenetic lineage of phototrophic Gammaproteobacteria from pufLM gene analyses (2010)
    Oxford University Press
    In:  FEMS Microbiology Ecology, 74 (3). pp. 510-522.
    Details
    Publication Date: 2019-09-23
    Description: Phototrophic bacteria are important primary producers of salt lakes in the Salar de Atacama and at times form visible mass developments within and on top of the lake sediments. The communities of phototrophic bacteria from two of these lakes were characterized by molecular genetic approaches using key genes for the biosynthesis of the photosynthetic apparatus in phototrophic purple bacteria (pufLM) and in green sulfur bacteria (fmoA). Terminal restriction fragment length polymorphism of the pufLM genes indicated high variability of the community composition between the two lakes and subsamples thereof. The communities were characterized by the dominance of a novel, so far undescribed lineage of pufLM containing bacteria and the presence of representatives related to known halophilic Chromatiaceae and Ectothiorhodospiraceae. In addition, the presence of BChl b-containing anoxygenic phototrophic bacteria and of aerobic anoxygenic bacteria was indicated. Green sulfur bacteria were not detected in the environmental samples, although a bacterium related to Prosthecochloris indicum was identified in an enrichment culture. This is the first comprehensive description of phototrophic bacterial communities in a salt lake of South America made possible only due to the application of the functional pufLM genes.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1111/j.1574-6941.2010.00966.x
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  • 8
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    Comparative analysis of ammonia monooxygenase (amoA) genes in the water column and sediment-water interface of two lakes and the Baltic Sea (2008)
    Oxford University Press
    In:  FEMS Microbiology Ecology, 66 . pp. 367-378.
    Details
    Publication Date: 2019-09-24
    Description: The functional gene amoA was used to compare the diversity of ammonia-oxidizing bacteria (AOB) in the water column and sediment-water interface of the two freshwater lakes Plusssee and Schöhsee and the Baltic Sea. Nested amplifications were used to increase the sensitivity of amoA detection, and to amplify a 789-bp fragment from which clone libraries were prepared. The larger part of the sequences was only distantly related to any of the cultured AOB and is considered to represent new clusters of AOB within the Nitrosomonas/Nitrosospira group. Almost all sequences from the water column of the Baltic Sea and from 1-m depth of Schöhsee were related to different Nitrosospira clusters 0 and 2, respectively. The majority of sequences from Plusssee and Schöhsee were associated with sequences from Chesapeake Bay, from a previous study of Plusssee and from rice roots in Nitrosospira-like cluster A, which lacks sequences from Baltic Sea. Two groups of sequences from Baltic Sea sediment were related to clonal sequences from other brackish/marine habitats in the purely environmental Nitrosospira-like cluster B and the Nitrosomonas-like cluster. This confirms previous results from 16S rRNA gene libraries that indicated the existence of hitherto uncultivated AOB in lake and Baltic Sea samples, and showed a differential distribution of AOB along the water column and sediment of these environments
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1111/j.1574-6941.2008.00565.x
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  • 9
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    Cyanobacterial diversity in Salar de Huasco, a high altitude saline wetland in Northern Chile, are highly similar to Antarctic cyanobacteria (2008)
    Oxford University Press
    In:  FEMS Microbiology Ecology, 64 . pp. 419-432.
    Details
    Publication Date: 2019-09-23
    Description: The diversity of Cyanobacteria in water and sediment samples from four representative sites of the Salar de Huasco was examined using denaturing gradient gel electrophoresis and analysis of clone libraries of 16S rRNA gene PCR products. Salar de Huasco is a high altitude (3800 m altitude) saline wetland located in the Chilean Altiplano. We analyzed samples from a tributary stream (H0) and three shallow lagoons (H1, H4, H6) that contrasted in their physicochemical conditions and associated biota. Seventy-eight phylotypes were identified in a total of 268 clonal sequences deriving from seven clone libraries of water and sediment samples. Oscillatoriales were frequently found in water samples from sites H0, H1 and H4 and in sediment samples from sites H1 and H4. Pleurocapsales were found only at site H0, while Chroococcales were recovered from sediment samples of sites H0 and H1, and from water samples of site H1. Nostocales were found in sediment samples from sites H1 and H4, and water samples from site H1 and were largely represented by sequences highly similar to Nodularia spumigena. We suggest that cyanobacterial communities from Salar de Huasco are unique - they include sequences related to others previously described from the Antarctic, along with others from diverse, but less extreme environments.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1111/j.1574-6941.2008.00483.x
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  • 10
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    Osmoregulation and compatible solutes in eubacteria (1986)
    Oxford University Press
    In:  Fems Microbiology Reviews, 39 . pp. 57-66.
    Details
    Publication Date: 2020-07-31
    Description: Osmotic adaption by halophilic and halotolerant bacteria is generally achieved by the accumulation or synthesis of several organic solutes. Accumulation by uptake from the medium is preferred over biosynthesis. The chemical nature of the major solute is important in determining the degree of osmotolerance of the organism. Glycine betaine accumulation confers a greater degree of osmotolerance than proline, which in turn confers more osmotolerance than glutamate accumulation. The occurrence and uptake of these solutes in a variety of eubacteria is reviewed.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1016/0378-1097(86)90061-3
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