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  • 1
    Online Resource
    Online Resource
    Insights into the genomes of archaea mediating the anaerobic oxidation of methane
    Wiley ; 2005
    In:  Environmental Microbiology Vol. 7, No. 12 ( 2005-12), p. 1937-1951
    Details
    In: Environmental Microbiology, Wiley, Vol. 7, No. 12 ( 2005-12), p. 1937-1951
    Abstract: The anaerobic oxidation of methane is a globally significant process which is mediated by consortia of yet uncultivated methanotrophic archaea (ANME) and sulfate‐reducing bacteria. In order to gain deeper insights into genome characteristics of the different ANME groups, large‐insert genomic libraries were constructed using DNA extracted from a methanotrophic microbial mat growing in the anoxic part of the Black Sea, and from sediments above gas hydrates at the Hydrate Ridge off the coast of Oregon. Analysis of these fosmid libraries with respect to archaeal 16S rRNA gene diversity revealed a single ANME‐1b ribotype for the Black Sea libraries, whereas the sequences derived from the Hydrate Ridge library phylogenetically affiliated with the ANME‐2a, ANME‐2c and ANME‐3 group. Genome walking for ANME‐1b resulted in a contiguous 155 kb composite genome fragment. The comparison of a set of four genomic fragments belonging to the different ANME groups revealed differences in the rRNA operon structure and the average G+C content, with the ANME‐2c contig showing the highest divergence within the set. A detailed analysis of the ANME contigs with respect to genes putatively involved in the anaerobic oxidation of methane led to the identification of: (i) a putative N 5 ,N 10 ‐methenyltetrahydromethanopterin cyclohydrolase gene, (ii) a gene cluster supposedly encoding a novel type of heterodisulfide reductase/dehydrogenase complex and (iii) a gene cluster putatively encoding a new type of CO dehydrogenase/acetyl‐CoA synthase enzyme complex.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2005.7.issue-12
    DOI: 10.1111/j.1462-2920.2005.00844.x
    Language: English
    Publisher: Wiley
    Publication Date: 2005
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Identification of the dominant sulfate‐reducing bacterial partner of anaerobic methanotrophs of the ANME‐2 clade
    Wiley ; 2010
    In:  Environmental Microbiology Vol. 12, No. 8 ( 2010-08), p. 2327-2340
    Details
    In: Environmental Microbiology, Wiley, Vol. 12, No. 8 ( 2010-08), p. 2327-2340
    Abstract: The anaerobic oxidation of methane (AOM) with sulfate as terminal electron acceptor is mediated by consortia of methanotrophic archaea (ANME) and sulfate‐reducing bacteria (SRB). Whereas three clades of ANME have been repeatedly studied with respect to phylogeny, key genes and genomic capabilities, little is known about their sulfate‐reducing partner. In order to identify the partner of anaerobic methanotrophs of the ANME‐2 clade, bacterial 16S rRNA gene libraries were constructed from cultures highly enriched for ANME‐2a and ANME‐2c in consortia with Deltaproteobacteria of the Desulfosarcina/Desulfococcus group (DSS). Phylogenetic analysis of those and publicly available sequences from AOM sites supported the hypothesis by Knittel and colleagues that the DSS partner belongs to the diverse SEEP‐SRB1 cluster. Six subclusters of SEEP‐SRB1, SEEP‐SRB1a to SEEP‐SRB1f, were proposed and specific oligonucleotide probes were designed. Using fluorescence in situ hybridization on samples from six different AOM sites, SEEP‐SRB1a was identified as sulfate‐reducing partner in up to 95% of total ANME‐2 consortia. SEEP‐SRB1a cells exhibited a rod‐shaped, vibrioid, or coccoid morphology and were found to be associated with subgroups ANME‐2a and ANME‐2c. Moreover, SEEP‐SRB1a was also detected in 8% to 23% of ANME‐3 consortia in Haakon Mosby Mud Volcano sediments, previously described to be predominantly associated with SRB of the Desulfobulbus group. SEEP‐SRB1a contributed to only 0.3% to 0.7% of all single cells in almost all samples indicating that these bacteria are highly adapted to a symbiotic relationship with ANME‐2.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2010.12.issue-8
    DOI: 10.1111/j.1462-2920.2010.02275.x
    Language: English
    Publisher: Wiley
    Publication Date: 2010
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 3
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    Online Resource
    Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov., psychrophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacteria isolated from marine Arctic sediments
    Microbiology Society ; 2005
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 55, No. 2 ( 2005-03-01), p. 781-786
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 55, No. 2 ( 2005-03-01), p. 781-786
    Abstract: Two psychrophilic, chemolithoautotrophic, sulfur-oxidizing bacteria were isolated from marine Arctic sediments sampled off the coast of Svalbard with thiosulfate as the electron donor and CO 2 as carbon source. Comparative analysis of 16S rRNA gene sequences suggested that the novel strains, designated SVAL-D T and SVAL-E T , represent members of the genus Thiomicrospira . Further genotypic (DNA–DNA relatedness, DNA G+C content) and phenotypic characterization revealed that the strains represent members of two novel species. Both organisms are obligately autotrophic and strictly aerobic. Nitrate was not used as an electron acceptor. Chemolithoautotrophic growth was observed with thiosulfate, tetrathionate and sulfur. The temperature limits for growth of both strains were between −2 °C and 20·8 °C, with optima of 11·5–13·2 °C (SVAL-E T ) and 14·6–15·4 °C (SVAL-D T ), which is about 13–15 °C lower than the optima of all other recognized Thiomicrospira species. The maximum growth rate on thiosulfate at 14 °C was 0·14 h −1 for strain SVAL-E T and 0·2 h −1 for strain SVAL-D T . Major fatty acids of SVAL-D T are C 16 : 1 , C 18 : 0 and C 16 : 0 , and those of SVAL-E T are C 16 : 1 , C 18 : 1 , C 16 : 0 and C 14 : 1 . Cells of SVAL-D T and SVAL-E T are rods, like those of their closest relatives. To our knowledge the novel strains are the first psychrophilic, chemolithoautotrophic, sulfur-oxidizing bacteria so far described. The names Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov. are proposed for SVAL-E T (=ATCC 700955 T =DSM 13458 T ) and SVAL-D T (=ATCC 700954 T =DSM 13453 T ), respectively.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijs.0.63362-0
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2005
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
    SSG: 12
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  • 4
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    Online Resource
    Bacterial communities in temperate and polar coastal sands are seasonally stable
    Springer Science and Business Media LLC ; 2021
    In:  ISME Communications Vol. 1, No. 1 ( 2021-06-28)
    Details
    In: ISME Communications, Springer Science and Business Media LLC, Vol. 1, No. 1 ( 2021-06-28)
    Abstract: Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine and terrestrial origin, thus, acting as centers of organic matter transformation. At high temporal resolution, we accessed the variability of benthic bacterial communities over two annual cycles at Helgoland (North Sea), and compared it with seasonality of communities in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter. Benthic community structure remained stable in both, temperate and polar sediments on the level of cell counts and 16S rRNA-based taxonomy. Actinobacteriota of uncultured Actinomarinales and Microtrichales were a major group, with 8 ± 1% of total reads (Helgoland) and 31 ± 6% (Svalbard). Their high activity (frequency of dividing cells 28%) and in situ cell numbers of 〉 10% of total microbes in Svalbard sediments, suggest Actinomarinales and Microtrichales as key heterotrophs for carbon mineralization. Even though Helgoland and Svalbard sampling sites showed no phytodetritus-driven changes of the benthic bacterial community structure, they harbored significantly different communities ( p   〈  0.0001, r  = 0.963). The temporal stability of benthic bacterial communities is in stark contrast to the dynamic succession typical of coastal waters, suggesting that pelagic and benthic bacterial communities respond to phytoplankton productivity very differently.
    Type of Medium: Online Resource
    ISSN: 2730-6151
    URL: Article
    DOI: 10.1038/s43705-021-00028-w
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 3041786-7
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