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  • 1
    Online Resource
    Online Resource
    Funktionelle Genomanalyse umweltrelevanter mariner und terrestrischer Bakterien, Vorhaben: Bioinformatische und funktionelle Genomanalyse : Schlussbericht ; Laufzeit des Vorhabens/Berichtszeitraum: 01.04.2000 - 31.03.2002 (2003)
    Bremen : Max-Planck-Inst. für Marine Mikrobiologie
    Details Availability
    Keywords: Forschungsbericht ; Genanalyse ; Pirellula
    Type of Medium: Online Resource
    Pages: Online-Ressource (12 S., 278 KB) , graph. Darst
    URL: https://edocs.tib.eu/files/e01fb05/48486713X.pdf
    URL: https://doi.org/10.2314/GBV:48486713X
    URL: https://edocs.tib.eu/files/e01fb05/48486713Xl.pdf
    DOI: 10.2314/GBV:48486713X
    Language: German
    Note: Förderkennzeichen BMBF 03 F0 279 A. - Verbund-Nr. 01017534 , Unterschiede zwischen dem gedruckten Dokument und der elektronischen Ressource können nicht ausgeschlossen werden , Auch als gedr. Ausg. vorh , Systemvoraussetzungen: Acrobat reader.
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  • 2
    Electronic Resource
    Electronic Resource
    The transcriptional regulator pool of the marine bacterium Rhodopirellula baltica SH 1T as revealed by whole genome comparisons (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 242 (2005), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Rhodopirellula baltica (strain SH 1T) is a free-living marine representative of the phylogenetically independent and environmentally relevant phylum Planctomycetes. Little is known about the regulatory strategies of free-living bacteria with large (7.15 Mb) genomes. Therefore, a consistent, quantitative and qualitative description was produced by comparing R. baltica's transcriptional regulator pool with that of 123 publicly available bacterial genomes. The overall results are congruous with earlier observations that in Bacteria, the proportion of genes encoding transcriptional regulators generally increases with genome size. However, R. baltica distinctly stands out from this trend with only 2.4% (174) of all genes predicted to encode transcriptional regulators. The qualitative investigation of R. baltica's transcriptional regulators revealed a clear shift towards high numbers of two-component systems (66) as well as high numbers of sigma factors (49), with more than 76% (37) belonging to the extra-cytoplasmic function subfamily of sigma-70. Only one predicted sigma factor showed a relatively close phylogenetic relationship to that of another bacterium, the sigma factor SigZ of Bacillus subtilis. In summary, analysis of the R. baltica genome revealed disparate regulatory mechanisms and a clear bias towards direct environmental sensing. This strategy might provide a selective advantage for organisms living in habitats with frequently changing environmental conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsle.2004.10.049
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    Paper (German National Licenses)
    Fulltext
  • 3
    Electronic Resource
    Electronic Resource
    Modern methods in subsurface microbiology: in situ identification of microorganisms with nucleic acid probes (1997)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology reviews 20 (1997), S. 0 
    Details
    ISSN: 1574-6976
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Like many other parts of microbial ecology, subsurface microbiology has entered the molecular age. As one example of various powerful molecular techniques, fluorescently labeled rRNA-targeted nucleic acid probes today allow an in situ identification of individual microbial cells in their natural habitats. The technique relies on the specific hybridization of the nucleic acid probes to the naturally amplified intracellular rRNA. Fluorescently labeled, rRNA-targeted oligonucleotide probes are perfect tools for many areas of microbial ecology since they can monitor specific populations in environmental samples based on constant genotypic features and not on variable phenotypic features like morphology. In case of immobilized communities like biofilms, exact spatial distributions of microorganisms can be analyzed on a micrometer scale. Recent technical improvements have increased the number of potential applications considerably. Today, better fluorescent dyes enable identification of routinely more than 50% of the cells even in oligotrophic aquatic samples in which the visualization of small cells with low numbers of ribosomes had been problematic. This compares favorably with the usually less than 1% of microorganisms which can be characterized based on cultivation-dependent methods.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6976.1997.tb00308.x
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    Paper (German National Licenses)
    Fulltext
  • 4
    Electronic Resource
    Electronic Resource
    Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization (2000)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 34 (2000), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: We report here on novel groups of Archaea in the bacterioplankton of a small boreal forest lake studied by the culture-independent analysis of the 16S rRNA genes amplified directly from lake water in combination with fluorescent in situ hybridization (FISH). Polymerase chain reaction products were cloned and 28 of the 160 Archaea clones with around 900-bp-long 16S rRNA gene inserts, were sequenced. Phylogenetic analysis, including 642 Archaea sequences, confirmed that none of the freshwater clones were closely affiliated with known cultured Archaea. Twelve Archaea sequences from lake Valkea Kotinen (VAL) belonged to Group I of uncultivated Crenarchaeota and affiliated with environmental sequences from freshwater sediments, rice roots and soil as well as with sequences from an anaerobic digestor. Eight of the Crenarchaeota VAL clones formed a tight cluster. Sixteen sequences belonged to Euryarchaeota. Four of these formed a cluster together with environmental sequences from freshwater sediments and peat bogs within the order Methanomicrobiales. Five were affiliated with sequences from marine sediments situated close to marine Group II and three formed a novel cluster VAL III distantly related to the order Thermoplasmales. The remaining four clones formed a distinct clade within a phylogenetic radiation characterized by members of the orders Methanosarcinales and Methanomicrobiales on the same branch as rice cluster I, detected recently on rice roots and in anoxic bulk soil of flooded rice microcosms. FISH with specifically designed rRNA-targeted oligonucleotide probes revealed the presence of Methanomicrobiales in the studied lake. These observations indicate a new ecological niche for many novel ‘non-extreme’ environmental Archaea in the pelagic water of a boreal forest lake.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2000.tb00753.x
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    Paper (German National Licenses)
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  • 5
    Electronic Resource
    Electronic Resource
    A conspicuous nickel protein in microbial mats that oxidize methane anaerobically (2003)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 426 (2003), S. 878-881 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Anaerobic oxidation of methane (AOM) in marine sediments is an important microbial process in the global carbon cycle and in control of greenhouse gas emission. The responsible organisms supposedly reverse the reactions of methanogenesis, but cultures providing biochemical proof of this have ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature02207
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    Paper (German National Licenses)
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  • 6
    Electronic Resource
    Electronic Resource
    Symbiosis insights through metagenomic analysis of a microbial consortium (2006)
    [s.l.] : Nature Publishing Group
    Nature 443 (2006), S. 950-955 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature05192
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    Paper (German National Licenses)
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  • 7
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    The ocean sampling day consortium (2015)
    Oxford Univ. Press
    In:  GigaScience, 4 (1). Art.Nr. 27.
    Details
    Publication Date: 2019-09-23
    Description: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
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    DOI: 10.1186/s13742-015-0066-5
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 8
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    Microbial Diversity of the Freshwater Sponge Spongilla lacustris (2005)
    Springer
    In:  Microbial Ecology, 50 (2). pp. 206-212.
    Details
    Publication Date: 2015-08-25
    Description: To provide insight into the phylogenetic bacterial diversity of the freshwater sponge Spongilla lacustris, a 16S rRNA gene libraries were constructed from sponge tissues and from lake water. Restriction fragment length polymorphism (RFLP) analysis of 〉190 freshwater sponge-derived clones resulted in six major restriction patterns, from which 45 clones were chosen for sequencing. The resulting sequences were affiliated with the Alphaproteobacteria (n = 19), the Actinobacteria (n = 15), the Betaproteobacteria (n = 2), and the Chloroflexi (n = 2) lineages. About half of the sequences belonged to previously described actinobacterial (hgc-I) and betaproteobacterial (beta-II) sequence clusters of freshwater bacteria that were also present in the lake water 16S rRNA gene library. At least two novel, deeply rooting alphaproteobacterial lineages were recovered from S. lacustris that showed 〈89% sequence similarity to known phylogenetic groups. Electron microscopical observations revealed that digested bacterial remnants were contained within food vacuoles of sponge archaeocytes, whereas the extracellular matrix was virtually free of bacteria. This study is the first molecular diversity study of a freshwater sponge and adds to a growing database on the diversity and community composition of sponge-associated microbial consortia.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1007/s00248-004-0172-x
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 9
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    Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data (2015)
    Public Library of Science
    In:  PLoS ONE, 10 (7). e0134377.
    Details
    Publication Date: 2020-10-26
    Description: Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This dataset has been created with the intention to serve as a valuable reference dataset for aquatic fungi including a phylogenetic reference tree. The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.
    Type: Article , PeerReviewed
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    DOI: 10.1371/journal.pone.0134377
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 10
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    Environmental conditions and habitats of GOS sites and bottle data of HOT-ALOHA station
    PANGAEA
    In:  Supplement to: Yilmaz, Pelin; Iversen, Morten Hvitfeldt; Hankeln, Wolfgang; Kottmann, Renzo; Quast, Christian; Glöckner, Frank Oliver (2012): Ecological structuring of bacterial and archaeal taxa in surface ocean waters. FEMS Microbiology Ecology, 81(2), 373-385, https://doi.org/10.1111/j.1574-6941.2012.01357.x
    Details
    Publication Date: 2023-06-07
    Description: The Global Ocean Sampling (GOS) expedition is currently the largest and geographically most comprehensive metagenomic dataset, including samples from the Atlantic, Pacific, and Indian Oceans. This study makes use of the wide range of environmental conditions and habitats encompassed within the GOS sites in order to investigate the ecological structuring of bacterial and archaeal taxon ranks. Community structures based on taxonomically classified 16S ribosomal RNA (rRNA) gene fragments at phylum, class, order, family, and genus rank levels were examined using multivariate statistical analysis, and the results were inspected in the context of oceanographic environmental variables and structured habitat classifications. At all taxon rank levels, community structures of neritic, oceanic, estuarine biomes, as well as other exotic biomes (salt marsh, lake, mangrove), were readily distinguishable from each other. A strong structuring of the communities with chlorophyll a concentration and a weaker yet significant structuring with temperature and salinity were observed. Furthermore, there were significant correlations between community structures and habitat classification. These results were used for further investigation of one-to-one relationships between taxa and environment and provided indications for ecological preferences shaped by primary production for both cultured and uncultured bacterial and archaeal clades.
    Keywords: Center for Marine Environmental Sciences; MARUM
    Type: Dataset
    Format: application/zip, 9 datasets
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