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  • 1
    Online Resource
    Online Resource
    American Society for Microbiology ; 2019
    In:  Applied and Environmental Microbiology Vol. 85, No. 22 ( 2019-11-15)
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 85, No. 22 ( 2019-11-15)
    Abstract: In deep-sea hydrothermal vent environments, sulfur-oxidizing bacteria belonging to the clade SUP05 are crucial symbionts of invertebrate animals. Marine viruses, as the most abundant biological entities in the ocean, play essential roles in regulating the sulfur metabolism of the SUP05 bacteria. To date, vent sponge-associated SUP05 and their phages have not been well documented. The current study analyzed microbiomes of Haplosclerida sponges from hydrothermal vents in the Okinawa Trough and recovered the dominant SUP05 genome, designated VS-SUP05. Phylogenetic analysis showed that VS-SUP05 was closely related to endosymbiotic SUP05 strains from mussels living in deep-sea hydrothermal vent fields. Homology and metabolic pathway comparisons against free-living and symbiotic SUP05 strains revealed that the VS-SUP05 genome shared many features with the deep-sea mussel symbionts. Supporting a potentially symbiotic lifestyle, the VS-SUP05 genome contained genes involved in the synthesis of essential amino acids and cofactors that are desired by the host. Analysis of sponge-associated viral sequences revealed putative VS-SUP05 phages, all of which were double-stranded viruses belonging to the families Myoviridae , Siphoviridae , Podoviridae , and Microviridae . Among the phage sequences, one contig contained metabolic genes ( iscR , iscS , and iscU ) involved in iron-sulfur cluster formation. Interestingly, genome sequence comparison revealed horizontal transfer of the iscS gene among phages, VS-SUP05, and other symbiotic SUP05 strains, indicating an interaction between marine phages and SUP05 symbionts. Overall, our findings confirm the presence of SUP05 bacteria and their phages in sponges from deep-sea vents and imply a beneficial interaction that allows adaptation of the host sponge to the hydrothermal vent environment. IMPORTANCE Chemosynthetic SUP05 bacteria dominate the microbial communities of deep-sea hydrothermal vents around the world, SUP05 bacteria utilize reduced chemical compounds in vent fluids and commonly form symbioses with invertebrate organisms. This symbiotic relationship could be key to adapting to such unique and extreme environments. Viruses are the most abundant biological entities on the planet and have been identified in hydrothermal vent environments. However, their interactions with the symbiotic microbes of the SUP05 clade, along with their role in the symbiotic system, remain unclear. Here, using metagenomic sequence-based analyses, we determined that bacteriophages may support metabolism in SUP05 bacteria and play a role in the sponge-associated symbiosis system in hydrothermal vent environments.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    RVK:
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2019
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  • 2
    In: Limnology and Oceanography, Wiley, Vol. 66, No. 10 ( 2021-10), p. 3714-3727
    Abstract: Underwater soundscapes, though invisible, are crucial in shaping the biodiversity of marine ecosystems by acting as habitat‐specific settlement cues for larvae. The deep sea has received little attention in soundscape research, but it is being targeted for mineral extraction to feed the ever‐growing needs of our society. Anthropogenic impacts on soundscapes influence the resilience of key shallow‐water habitats, and the same likely applies to the deep. Japan is a forerunner in deep‐sea mining, but virtually no deep soundscape baselines exist for Japanese waters. Here, we report baseline soundscapes from four deep‐sea locations in Japan, including the Suiyo Seamount hydrothermal vent, the abyssal plain around the Minamitorishima Island home to manganese nodule fields and muds rich in rare‐earth elements, twilight depths off Sanriku, as well as a typical bathyal system in Suruga Bay. Long‐duration audio recordings were visualized and factorized by an unsupervised machine learning model, revealing differing characteristics among the habitats. Two locations near the coast are highly influenced by shipping noise. The Suiyo vent is characterized by low‐frequency sounds from venting, and the abyssal Minamitorishima is quiet with a flat spectral shape. Noise from observation platforms is likely sufficient to alter soundscape characteristics, especially in offshore locations, suggesting offshore mining‐targeted areas are susceptible to impacts from anthropogenic noise. We argue that the monitoring of soundscapes is an indispensable component for assessing potential mining impacts on deep‐sea ecosystems. Our results establish reference points for future soundscape monitoring and assessment in Japanese waters as well as similar ecosystems globally.
    Type of Medium: Online Resource
    ISSN: 0024-3590 , 1939-5590
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
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  • 3
    In: Biogeosciences, Copernicus GmbH, Vol. 18, No. 19 ( 2021-10-01), p. 5351-5362
    Abstract: Abstract. Isotope fractionation factors associated with various biogeochemical processes are important in ensuring the reliable use of isotope tracers in biogeosciences at large. Methane is a key component of the subsurface biosphere and a notable greenhouse gas, making the accurate evaluation of methane cycles, including microbial methanotrophy, imperative. Although the isotope fractionation factors associated with methanotrophy have been examined under various conditions, the dual-isotope fractionation factors of aerobic methanotrophy in oxic seawater remain unclear. Here, we investigated hydrogen and carbon isotope ratios of methane as well as the relevant biogeochemical parameters and microbial community compositions in hydrothermal plumes in the Okinawa Trough. Methanotrophs were found to be abundant in plumes above the Hatoma Knoll vent site, and we succeeded in simultaneously determining hydrogen and carbon isotope fractionation factors associated with the aerobic oxidation of methane (εH=49.4±5.0 ‰, εC=5.2±0.4 ‰) – the former being the first of its kind ever reported. This εH value is comparable with values reported from terrestrial ecosystems but clearly lower than those from aerobic and anaerobic methanotroph enrichment cultures, as well as incubations of methanotrophic isolates. The covariation factor between δ13CCH4 and δDCH4, Λ (9.4 or 8.8 determined using two different methods), was consistent with those from methanotrophic isolate incubations. These values are valuable for understanding dynamics of methane cycling in the marine realm, and future applications of the approach to other habitats with methanotrophic activity will help reveal whether the small εH value observed is a ubiquitous feature across all marine systems.
    Type of Medium: Online Resource
    ISSN: 1726-4189
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2021
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  • 4
    In: Microbes and Environments, Japanese Society of Microbial Ecology, Vol. 38, No. 2 ( 2023), p. n/a-
    Type of Medium: Online Resource
    ISSN: 1342-6311 , 1347-4405
    Language: English
    Publisher: Japanese Society of Microbial Ecology
    Publication Date: 2023
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    SSG: 12
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  • 5
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 379, No. 6634 ( 2023-02-24)
    Abstract: The Hayabusa2 spacecraft retrieved surface and subsurface samples from the carbonaceous near-Earth asteroid (162173) Ryugu, which was expected to be enriched in volatile species. The samples were collected from two locations, one undisturbed surface and the other including material excavated by an artificial impact. Unlike meteorites, these samples have experienced minimal alteration by Earth’s atmosphere. Ryugu is thought to have formed from material ejected (by an impact) from a parent body, which had experienced aqueous alteration (reactions with liquid water) ~4.56 billion years (Gyr) ago. Ryugu’s orbit later migrated from the main asteroid belt to become a near-Earth asteroid. RATIONALE Noble gases and nitrogen isotopes in Ryugu grains are inherited from Ryugu’s parent body and potentially provide information about the source of Earth’s volatile elements. Noble gas isotopes can also be used to assess the orbital evolution and recent surface activities of Ryugu. We pelletized ~0.8-mm-diameter Ryugu grains and investigated their mineralogy before carrying out isotope measurements. We measured the concentrations and isotopic compositions of noble gases and nitrogen, extracted by stepped heating, with mass spectrometers. RESULTS The mineralogy of the Ryugu grains is similar to Ivuna-type carbonaceous (CI) chondrite meteorites. Fine-grained hydrous silicates (phyllosilicates), produced through aqueous alteration of primary minerals, compose the major fraction of the samples. This is consistent with infrared spectroscopic observations of the asteroid. Iron oxide, iron sulfides, and carbonates are also found within the matrix. Noble gas isotopes are dominated by primordially trapped gases. Their abundances are mostly similar to the highest found in a CI chondrite, with some grains having several times higher concentrations than the highest CI value. Isotopic compositions and concentrations of nitrogen vary between the Ryugu grains, with divergence from the CI chondrite composition. The nitrogen concentrations in four Ryugu grains are one-half to one-third the CI values, and the 15 N/ 14 N ratio is also lower. The Ryugu grains with compositions farthest from the CI values are similar to the composition of a dehydrated CI chondrite. Only two surface samples, out of the 16 Ryugu grains measured, have clear signs of noble gases derived from solar wind (SW). Their abundances correspond to SW exposure durations of ≳3500 and ≳250 years at the current orbit, whereas most of the grains were exposed for ≳1 to ≳50 years. Cosmic ray–produced 21 Ne concentrations vary, with no systematic difference between the sample collection sites. The estimated cosmic ray exposure (CRE) ages for the surface and subsurface samples are 5.3 ± 0.9 and 5.2 ± 0.8 million years (Myr), assuming irradiations at 2 to 5 g cm −2 and 150 g cm −2 , respectively. This is consistent with the expected surface residence time under near-Earth impact rates. We infer that Ryugu’s orbit migrated from the main asteroid belt to the near-Earth region ~5 Myr ago. About 30% of cosmogenic 21 Ne, corresponding to a CRE age of ~1 Myr, was released in gas-extraction steps at 100°C, indicating that the Ryugu samples have not experienced heating above 100°C within the past 1 Myr. Previous studies have suggested that Ryugu experienced an orbital excursion much closer to the Sun. If this is the case, this excursion must have occurred ≳1 Myr ago. CONCLUSION The mineralogical and noble gas measurements show that the Ryugu samples are similar to CI chondrites. The nitrogen data indicate a heterogeneous distribution of nitrogen-carrying materials with different compositions, one of which has been lost from Ryugu grains to varying degrees. The CRE age of ~5 Myr and the implanted SW are records of the recent irradiation at the current near-Earth orbit of Ryugu. Inferred formation and history of Ryugu. Ryugu’s parent body formed in the early Solar System, incorporating primordial noble gases and nitrogen, followed by aqueous alteration ~4.56 Gyr ago. Ryugu formed from the accumulation of fragments of the parent body ejected by an impact, at an unknown date. Ryugu migrated to its current near-Earth orbit ~5 Myr ago. Ryugu might have experienced another change in orbit, bringing it closer to the Sun (“Path A”), or remained in the same near-Earth orbit (“Path B”).
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
    RVK:
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2023
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    detail.hit.zdb_id: 2066996-3
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  • 6
    Online Resource
    Online Resource
    Elsevier BV ; 2019
    In:  Trends in Ecology & Evolution Vol. 34, No. 12 ( 2019-12), p. 1066-1069
    In: Trends in Ecology & Evolution, Elsevier BV, Vol. 34, No. 12 ( 2019-12), p. 1066-1069
    Type of Medium: Online Resource
    ISSN: 0169-5347
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2019
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    SSG: 12
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  • 7
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2022
    In:  Nucleic Acids Research Vol. 50, No. 3 ( 2022-02-22), p. 1531-1550
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 50, No. 3 ( 2022-02-22), p. 1531-1550
    Abstract: DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time sequencing, we conducted culture-independent ‘metaepigenomic’ analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. A total of 233 and 163 metagenomic-assembled genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTase genes were not genetically linked with the endonuclease genes predicted to be involved in defense mechanisms against extracellular DNA. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative specificities in MTases that are highly conserved in Alphaproteobacteria, which may enhance our understanding of the co-evolutionary history of the methylation systems and the genomes. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Microbiology Society ; 2014
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 64, No. Pt_11 ( 2014-11-01), p. 3668-3675
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 64, No. Pt_11 ( 2014-11-01), p. 3668-3675
    Abstract: A novel psychrophilic, marine, bacterial strain designated BJ-1 T was isolated from the Iheya North hydrothermal field in the Okinawa Trough off Japan. Cells were Gram-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 16 °C, with the optimum between 9 and 12 °C. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the closest relatives of strain BJ-1 T were Shewanella denitrificans OS-217 T (93.5 % similarity), Shewanella profunda DSM 15900 T (92.9 %), Shewanella gaetbuli TF-27 T (92.9 %), Paraferrimonas sedimenticola Mok-106 T (92.1 %) and Ferrimonas kyonanensis Asr22-7 T (91.7 %). The major respiratory quinone was Q-8. The predominant fatty acids were C 16 : 1 ω7 c and C 16 : 0 . The G+C content of the novel strain was 40.5 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, it is proposed that strain BJ-1 T represents a novel species in a new genus, for which the name Psychrobium conchae gen. nov., sp. nov. is proposed. The type strain of Psychrobium conchae is BJ-1 T ( = JCM 30103 T  = DSM 28701 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2014
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    detail.hit.zdb_id: 2056611-6
    SSG: 12
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