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      Conspicuous Smooth and White Egg-Shaped Sulfur Structures on a Deep-Sea Hydrothermal Vent Formed by Sulfide-Oxidizing Bacteria

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      a , , b , c , a , a
      Microbiology Spectrum
      American Society for Microbiology
      sulfide oxidation, Arcobacter, sulfur filaments, hydrothermal vent

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          ABSTRACT

          Conspicuous egg-shaped, white, and smooth structures were observed at a hydrothermal vent site in the Guaymas Basin, Gulf of California. The gelatinous structures decomposed within hours after sampling. Scanning electron microscopy (SEM) and light microscopy showed that the structure consisted of filaments of less than 0.1 μm thickness, similar to those observed for “ Candidatus Arcobacter sulfidicus.” SEM-energy-dispersive X-ray spectroscopy (EDS) showed that the filaments were sulfur rich. According to 16S rRNA gene amplicon and fluorescence in situ hybridization (FISH) analyses, Arcobacter, a sulfide oxidizer that is known to produce filamentous elemental sulfur, was among the dominant species in the structure and was likely responsible for its formation. Arcobacter normally produces woolly snowflake like structures in opposed gradients of sulfide and oxygen. In the laboratory, we observed sulfide consumption in the anoxic zone of the structure, suggesting an anaerobic conversion. The sulfide oxidation and decomposition of the structure in the laboratory may be explained by dissolution of the sulfur filaments by reaction with sulfide under formation of polysulfides.

          IMPORTANCE At the deep-sea Guaymas Basin hydrothermal vent system, sulfide-rich hydrothermal fluids mix with oxygenated seawater, thereby providing a habitat for microbial sulfur oxidation. Microbial sulfur oxidation in the deep sea involves a variety of organisms and processes and can result in the excretion of elemental sulfur. Here, we report on conspicuous white and smooth gelatinous structures found on hot vents. These strange egg-shaped structures were often observed on previous occasions in the Guaymas Basin, but their composition and formation process were unknown. Our data suggest that the notable and highly ephemeral structure was likely formed by the well-known sulfide-oxidizing Arcobacter. While normally Arcobacter produces loose flocs or woolly layers, here smooth gel-like structures were found.

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          Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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            Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples.

            Microbial community analysis via high-throughput sequencing of amplified 16S rRNA genes is an essential microbiology tool. We found the popular primer pair 515F (515F-C) and 806R greatly underestimated (e.g. SAR11) or overestimated (e.g. Gammaproteobacteria) common marine taxa. We evaluated marine samples and mock communities (containing 11 or 27 marine 16S clones), showing alternative primers 515F-Y (5'-GTGYCAGCMGCCGCGGTAA) and 926R (5'-CCGYCAATTYMTTTRAGTTT) yield more accurate estimates of mock community abundances, produce longer amplicons that can differentiate taxa unresolvable with 515F-C/806R, and amplify eukaryotic 18S rRNA. Mock communities amplified with 515F-Y/926R yielded closer observed community composition versus expected (r(2)  = 0.95) compared with 515F-Y/806R (r(2)  ∼ 0.5). Unexpectedly, biases with 515F-Y/806R against SAR11 in field samples (∼4-10-fold) were stronger than in mock communities (∼2-fold). Correcting a mismatch to Thaumarchaea in the 515F-C increased their apparent abundance in field samples, but not as much as using 926R rather than 806R. With plankton samples rich in eukaryotic DNA (> 1 μm size fraction), 18S sequences averaged ∼17% of all sequences. A single mismatch can strongly bias amplification, but even perfectly matched primers can exhibit preferential amplification. We show that beyond in silico predictions, testing with mock communities and field samples is important in primer selection.
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              A communal catalogue reveals Earth’s multiscale microbial diversity

              Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity. Supplementary information The online version of this article (doi:10.1038/nature24621) contains supplementary material, which is available to authorized users.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                Microbiol Spectr
                Microbiol Spectr
                spectrum
                Microbiology Spectrum
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2165-0497
                1 September 2021
                Sep-Oct 2021
                1 September 2021
                : 9
                : 2
                : e00955-21
                Affiliations
                [a ] Max Planck Institute for Marine Microbiologygrid.419529.2, , Bremen, Germany
                [b ] Montana State University, Bozeman, Montana, USA
                [c ] Aarhus University, Aarhus, Denmark
                University of Minnesota
                Author notes

                Citation van erk MR, Krukenberg V, Bomholt Jensen P, Littmann S, de Beer D. 2021. Conspicuous smooth and white egg-shaped sulfur structures on a deep-sea hydrothermal vent formed by sulfide-oxidizing bacteria. Microbiol Spectr 9:e00955-21. https://doi.org/10.1128/Spectrum.00955-21.

                Author information
                https://orcid.org/0000-0002-7074-3729
                Article
                00955-21
                10.1128/Spectrum.00955-21
                8557937
                34468192
                b70ec9dd-5102-4ba0-b123-8dd7b7bb76b7
                Copyright © 2021 van Erk et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 23 July 2021
                : 26 July 2021
                Page count
                supplementary-material: 1, Figures: 6, Tables: 0, Equations: 0, References: 48, Pages: 10, Words: 6240
                Funding
                Funded by: Max-Planck-Gesellschaft (Max Planck Society), FundRef https://doi.org/10.13039/501100004189;
                Award Recipient : Award Recipient : Award Recipient :
                Funded by: U.S. National Science Foundation;
                Award ID: MCB-1817428 award to Roland Hatzenpichler
                Award Recipient :
                Categories
                Research Article
                environmental-microbiology, Environmental Microbiology
                Custom metadata
                September/October 2021

                sulfide oxidation,arcobacter,sulfur filaments,hydrothermal vent

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