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Hribovšek P, Olesin Denny E, Dahle H, Mall A, Øfstegaard Viflot T, Boonnawa C, Reeves EP, Steen IH, Stokke R. Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field. mSystems 2023; 8:e0054323. [PMID: 37921472 PMCID: PMC10734525 DOI: 10.1128/msystems.00543-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.
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Affiliation(s)
- Petra Hribovšek
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Emily Olesin Denny
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Berge, Bergen, Norway
| | - Håkon Dahle
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Berge, Bergen, Norway
| | - Achim Mall
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Thomas Øfstegaard Viflot
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Chanakan Boonnawa
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Eoghan P. Reeves
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ida Helene Steen
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Runar Stokke
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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2
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Spilker JS, Phadke KA, Aravena M, Archipley M, Bayliss MB, Birkin JE, Béthermin M, Burgoyne J, Cathey J, Chapman SC, Dahle H, Gonzalez AH, Gururajan G, Hayward CC, Hezaveh YD, Hill R, Hutchison TA, Kim KJ, Kim S, Law D, Legin R, Malkan MA, Marrone DP, Murphy EJ, Narayanan D, Navarre A, Olivier GM, Rich JA, Rigby JR, Reuter C, Rhoads JE, Sharon K, Smith JDT, Solimano M, Sulzenauer N, Vieira JD, Vizgan D, Weiß A, Whitaker KE. Spatial variations in aromatic hydrocarbon emission in a dust-rich galaxy. Nature 2023:10.1038/s41586-023-05998-6. [PMID: 37277615 DOI: 10.1038/s41586-023-05998-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/21/2023] [Indexed: 06/07/2023]
Abstract
Dust grains absorb half of the radiation emitted by stars throughout the history of the universe, re-emitting this energy at infrared wavelengths1-3. Polycyclic aromatic hydrocarbons (PAHs) are large organic molecules that trace millimetre-size dust grains and regulate the cooling of interstellar gas within galaxies4,5. Observations of PAH features in very distant galaxies have been difficult owing to the limited sensitivity and wavelength coverage of previous infrared telescopes6,7. Here we present James Webb Space Telescope observations that detect the 3.3 μm PAH feature in a galaxy observed less than 1.5 billion years after the Big Bang. The high equivalent width of the PAH feature indicates that star formation, rather than black hole accretion, dominates infrared emission throughout the galaxy. The light from PAH molecules, hot dust and large dust grains and stars are spatially distinct from one another, leading to order-of-magnitude variations in PAH equivalent width and ratio of PAH to total infrared luminosity across the galaxy. The spatial variations we observe suggest either a physical offset between PAHs and large dust grains or wide variations in the local ultraviolet radiation field. Our observations demonstrate that differences in emission from PAH molecules and large dust grains are a complex result of localized processes within early galaxies.
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Affiliation(s)
- Justin S Spilker
- Department of Physics and Astronomy and George P. and Cynthia Woods Mitchell Institute for Fundamental Physics and Astronomy, Texas A&M University, College Station, TX, USA.
| | - Kedar A Phadke
- Department of Astronomy, University of Illinois, Urbana, IL, USA
- Center for AstroPhysical Surveys, National Center for Supercomputing Applications, Urbana, IL, USA
| | - Manuel Aravena
- Núcleo de Astronomía de la Facultad de Ingeniería y Ciencias, Universidad Diego Portales, Santiago, Chile
| | - Melanie Archipley
- Department of Astronomy, University of Illinois, Urbana, IL, USA
- Center for AstroPhysical Surveys, National Center for Supercomputing Applications, Urbana, IL, USA
| | - Matthew B Bayliss
- Department of Physics, University of Cincinnati, Cincinnati, OH, USA
| | - Jack E Birkin
- Department of Physics and Astronomy and George P. and Cynthia Woods Mitchell Institute for Fundamental Physics and Astronomy, Texas A&M University, College Station, TX, USA
| | | | - James Burgoyne
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jared Cathey
- Department of Astronomy, University of Florida, Gainesville, FL, USA
| | - Scott C Chapman
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
- National Research Council, Herzberg Astronomy and Astrophysics, Victoria, British Columbia, Canada
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Håkon Dahle
- Institute of Theoretical Astrophysics, University of Oslo, Oslo, Norway
| | | | - Gayathri Gururajan
- Aix Marseille Univ., CNRS, CNES, LAM, Marseille, France
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, Bologna, Italy
- INAF - Osservatorio di Astrofisica e Scienza dello Spazio, Bologna, Italy
| | | | - Yashar D Hezaveh
- Center for Computational Astrophysics, Flatiron Institute, New York, NY, USA
- Département de Physique, Université de Montréal, Montreal, Quebec, Canada
- Ciela - Montreal Institute for Astrophysical Data Analysis and Machine Learning, Montreal, Quebec, Canada
- Mila - Québec Artificial Intelligence Institute, Montreal, Quebec, Canada
| | - Ryley Hill
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Taylor A Hutchison
- Observational Cosmology Lab, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - Keunho J Kim
- Department of Physics, University of Cincinnati, Cincinnati, OH, USA
| | - Seonwoo Kim
- Department of Astronomy, University of Illinois, Urbana, IL, USA
| | - David Law
- Space Telescope Science Institute, Baltimore, MD, USA
| | - Ronan Legin
- Center for Computational Astrophysics, Flatiron Institute, New York, NY, USA
- Département de Physique, Université de Montréal, Montreal, Quebec, Canada
- Ciela - Montreal Institute for Astrophysical Data Analysis and Machine Learning, Montreal, Quebec, Canada
- Mila - Québec Artificial Intelligence Institute, Montreal, Quebec, Canada
| | - Matthew A Malkan
- Department of Physics and Astronomy, University of California, Los Angeles, CA, USA
| | | | - Eric J Murphy
- National Radio Astronomy Observatory, Charlottesville, VA, USA
| | - Desika Narayanan
- Department of Astronomy, University of Florida, Gainesville, FL, USA
- University of Florida Informatics Institute, Gainesville, FL, USA
- Cosmic Dawn Center, DTU Space, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alex Navarre
- Department of Physics, University of Cincinnati, Cincinnati, OH, USA
| | - Grace M Olivier
- Department of Physics and Astronomy and George P. and Cynthia Woods Mitchell Institute for Fundamental Physics and Astronomy, Texas A&M University, College Station, TX, USA
| | - Jeffrey A Rich
- The Observatories of the Carnegie Institution for Science, Pasadena, CA, USA
| | - Jane R Rigby
- Observational Cosmology Lab, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - Cassie Reuter
- Department of Astronomy, University of Illinois, Urbana, IL, USA
- Center for AstroPhysical Surveys, National Center for Supercomputing Applications, Urbana, IL, USA
| | - James E Rhoads
- Observational Cosmology Lab, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - Keren Sharon
- Department of Astronomy, University of Michigan, Ann Arbor, MI, USA
| | - J D T Smith
- Ritter Astrophysical Research Center, Department of Physics and Astronomy, University of Toledo, Toledo, OH, USA
| | - Manuel Solimano
- Núcleo de Astronomía de la Facultad de Ingeniería y Ciencias, Universidad Diego Portales, Santiago, Chile
| | | | - Joaquin D Vieira
- Department of Astronomy, University of Illinois, Urbana, IL, USA
- Center for AstroPhysical Surveys, National Center for Supercomputing Applications, Urbana, IL, USA
- Department of Physics, University of Illinois, Urbana, IL, USA
| | - David Vizgan
- Department of Astronomy, University of Illinois, Urbana, IL, USA
| | - Axel Weiß
- Max-Planck-Institut für Radioastronomie, Bonn, Germany
| | - Katherine E Whitaker
- Cosmic Dawn Center, DTU Space, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Astronomy, University of Massachusetts, Amherst, MA, USA
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3
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Drønen K, Roalkvam I, Tungland K, Dahle H, Nilsen H, Olsen A, Wergeland H. How to define fish pathogen relatives from a 16S rRNA sequence library and Pearson correlation analysis between defined OTUs from the library: Supplementary data to the research article "Presence and habitats of bacterial fish pathogen relatives in a marine salmon post-smolt RAS". Data Brief 2022; 46:108846. [PMID: 36687152 PMCID: PMC9849859 DOI: 10.1016/j.dib.2022.108846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 01/01/2023] Open
Abstract
This paper provides supplementary data to the research paper ''Presence and habitats of bacterial fish pathogen relatives in a marine salmon post-smolt RAS" [1]. Here, environmental samples from a marine recirculating aquaculture system (RAS) were subjected to microbiome studies. This data article adds value to the research article by providing open access to data files that increased information retrieval from the 16S rRNA sequence library. A fasta file of full-length 16S rRNA sequences from fish pathogenic microbes was deposited in the Mendeley data repository, a collection named "Fish Pathogen Database". Alignment of this database against the short sequences in the 16S rRNA library revealed the fish pathogen-relatives. Furthermore, a link to a CSV file containing Pearson correlation data was provided, an analysis based on the relative abundance information of all operational taxonomic units defined in the microbiome dataset. Included also, the methodological description of the Pearson correlation analysis, as well as a table where correlation data for the defined fish pathogen-relatives was retrieved from the large data file (Table 1).
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Affiliation(s)
- K. Drønen
- Department of Biological Science, University of Bergen, Thormøhlensgt. 55, N-5020, Norway,Corresponding author. @KarineNen
| | - I. Roalkvam
- Department of Biological Science, University of Bergen, Thormøhlensgt. 55, N-5020, Norway
| | - K. Tungland
- Independent Data Science Consultant, Equinor, PB 8500, N-4035, Norway
| | - H. Dahle
- Department of Biological Science, University of Bergen, Thormøhlensgt. 55, N-5020, Norway
| | - H. Nilsen
- Norwegian Veterinary Institute, Thormøhlensgt. 43C, N-5006, Norway
| | - A.B. Olsen
- Norwegian Veterinary Institute, Thormøhlensgt. 43C, N-5006, Norway
| | - H. Wergeland
- Department of Biological Science, University of Bergen, Thormøhlensgt. 55, N-5020, Norway
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Vulcano F, Hahn CJ, Roerdink D, Dahle H, Reeves EP, Wegener G, Steen IH, Stokke R. Phylogenetic and functional diverse ANME-1 thrive in Arctic hydrothermal vents. FEMS Microbiol Ecol 2022; 98:6747120. [PMID: 36190327 PMCID: PMC9576274 DOI: 10.1093/femsec/fiac117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/15/2022] [Accepted: 09/29/2022] [Indexed: 01/21/2023] Open
Abstract
The methane-rich areas, the Loki's Castle vent field and the Jan Mayen vent field at the Arctic Mid Ocean Ridge (AMOR), host abundant niches for anaerobic methane-oxidizers, which are predominantly filled by members of the ANME-1. In this study, we used a metagenomic-based approach that revealed the presence of phylogenetic and functional different ANME-1 subgroups at AMOR, with heterogeneous distribution. Based on a common analysis of ANME-1 genomes from AMOR and other geographic locations, we observed that AMOR subgroups clustered with a vent-specific ANME-1 group that occurs solely at vents, and with a generalist ANME-1 group, with a mixed environmental origin. Generalist ANME-1 are enriched in genes coding for stress response and defense strategies, suggesting functional diversity among AMOR subgroups. ANME-1 encode a conserved energy metabolism, indicating strong adaptation to sulfate-methane-rich sediments in marine systems, which does not however prevent global dispersion. A deep branching family named Ca. Veteromethanophagaceae was identified. The basal position of vent-related ANME-1 in phylogenomic trees suggests that ANME-1 originated at hydrothermal vents. The heterogeneous and variable physicochemical conditions present in diffuse venting areas of hydrothermal fields could have favored the diversification of ANME-1 into lineages that can tolerate geochemical and environmental variations.
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Affiliation(s)
- F Vulcano
- Corresponding author: Thormølens gate 53 A 5006 Bergen Postboks 7803 5020 Bergen. E-mail:
| | - C J Hahn
- Max-Plank Institute for Marine Microbiology, HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Bremen, 28359, Germany
| | - D Roerdink
- Department of Earth Science, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - H Dahle
- Computational Biological Unit, Department of Informatics, Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - E P Reeves
- Department of Earth Science, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - G Wegener
- Max-Plank Institute for Marine Microbiology, HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Bremen, 28359, Germany,MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, 28359, Germany,Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - I H Steen
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - R Stokke
- Corresponding author: Thormølens gate 53 A 5006 Bergen Postboks 7803 5020 Bergen. E-mail:
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5
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Sandaa RA, Saltvedt MR, Dahle H, Wang H, Våge S, Blanc-Mathieu R, Steen IH, Grimsley N, Edvardsen B, Ogata H, Lawrence J. Adaptive evolution of viruses infecting marine microalgae (haptophytes), from acute infections to stable coexistence. Biol Rev Camb Philos Soc 2021; 97:179-194. [PMID: 34514703 DOI: 10.1111/brv.12795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022]
Abstract
Collectively known as phytoplankton, photosynthetic microbes form the base of the marine food web, and account for up to half of the primary production on Earth. Haptophytes are key components of this phytoplankton community, playing important roles both as primary producers and as mixotrophs that graze on bacteria and protists. Viruses influence the ecology and diversity of phytoplankton in the ocean, with the majority of microalgae-virus interactions described as 'boom and bust' dynamics, which are characteristic of acute virus-host systems. Most haptophytes are, however, part of highly diverse communities and occur at low densities, decreasing their chance of being infected by viruses with high host specificity. Viruses infecting these microalgae have been isolated in the laboratory, and there are several characteristics that distinguish them from acute viruses infecting bloom-forming haptophytes. Herein we synthesise what is known of viruses infecting haptophyte hosts in the ocean, discuss the adaptive evolution of haptophyte-infecting viruses -from those that cause acute infections to those that stably coexist with their host - and identify traits of importance for successful survival in the ocean.
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Affiliation(s)
- Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Marius R Saltvedt
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Haina Wang
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Selina Våge
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Romain Blanc-Mathieu
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Université Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Nigel Grimsley
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Bente Edvardsen
- Department of Biosciences, University of Oslo, Postbox 1066, N-0316, Oslo, Norway
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Janice Lawrence
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, NB, E3B 5A3, Canada
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6
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Arsın H, Jasilionis A, Dahle H, Sandaa RA, Stokke R, Nordberg Karlsson E, Steen IH. Exploring Codon Adjustment Strategies towards Escherichia coli-Based Production of Viral Proteins Encoded by HTH1, a Novel Prophage of the Marine Bacterium Hypnocyclicus thermotrophus. Viruses 2021; 13:v13071215. [PMID: 34201869 PMCID: PMC8310279 DOI: 10.3390/v13071215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 01/15/2023] Open
Abstract
Marine viral sequence space is immense and presents a promising resource for the discovery of new enzymes interesting for research and biotechnology. However, bottlenecks in the functional annotation of viral genes and soluble heterologous production of proteins hinder access to downstream characterization, subsequently impeding the discovery process. While commonly utilized for the heterologous expression of prokaryotic genes, codon adjustment approaches have not been fully explored for viral genes. Herein, the sequence-based identification of a putative prophage is reported from within the genome of Hypnocyclicus thermotrophus, a Gram-negative, moderately thermophilic bacterium isolated from the Seven Sisters hydrothermal vent field. A prophage-associated gene cluster, consisting of 46 protein coding genes, was identified and given the proposed name Hypnocyclicus thermotrophus phage H1 (HTH1). HTH1 was taxonomically assigned to the viral family Siphoviridae, by lowest common ancestor analysis of its genome and phylogeny analyses based on proteins predicted as holin and DNA polymerase. The gene neighbourhood around the HTH1 lytic cassette was found most similar to viruses infecting Gram-positive bacteria. In the HTH1 lytic cassette, an N-acetylmuramoyl-L-alanine amidase (Amidase_2) with a peptidoglycan binding motif (LysM) was identified. A total of nine genes coding for enzymes putatively related to lysis, nucleic acid modification and of unknown function were subjected to heterologous expression in Escherichia coli. Codon optimization and codon harmonization approaches were applied in parallel to compare their effects on produced proteins. Comparison of protein yields and thermostability demonstrated that codon optimization yielded higher levels of soluble protein, but codon harmonization led to proteins with higher thermostability, implying a higher folding quality. Altogether, our study suggests that both codon optimization and codon harmonization are valuable approaches for successful heterologous expression of viral genes in E. coli, but codon harmonization may be preferable in obtaining recombinant viral proteins of higher folding quality.
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Affiliation(s)
- Hasan Arsın
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
- Correspondence: (H.A.); (I.H.S.); Tel.: +47-555-88-375 (I.H.S.)
| | - Andrius Jasilionis
- Division of Biotechnology, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (A.J.); (E.N.K.)
| | - Håkon Dahle
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
- Computational Biology Unit, University of Bergen, N-5020 Bergen, Norway
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
| | - Runar Stokke
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
| | - Eva Nordberg Karlsson
- Division of Biotechnology, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (A.J.); (E.N.K.)
| | - Ida Helene Steen
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
- Correspondence: (H.A.); (I.H.S.); Tel.: +47-555-88-375 (I.H.S.)
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7
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Aevarsson A, Kaczorowska AK, Adalsteinsson BT, Ahlqvist J, Al-Karadaghi S, Altenbuchner J, Arsin H, Átlasson ÚÁ, Brandt D, Cichowicz-Cieślak M, Cornish KAS, Courtin J, Dabrowski S, Dahle H, Djeffane S, Dorawa S, Dusaucy J, Enault F, Fedøy AE, Freitag-Pohl S, Fridjonsson OH, Galiez C, Glomsaker E, Guérin M, Gundesø SE, Gudmundsdóttir EE, Gudmundsson H, Håkansson M, Henke C, Helleux A, Henriksen JR, Hjörleifdóttir S, Hreggvidsson GO, Jasilionis A, Jochheim A, Jónsdóttir I, Jónsdóttir LB, Jurczak-Kurek A, Kaczorowski T, Kalinowski J, Kozlowski LP, Krupovic M, Kwiatkowska-Semrau K, Lanes O, Lange J, Lebrat J, Linares-Pastén J, Liu Y, Lorentsen SA, Lutterman T, Mas T, Merré W, Mirdita M, Morzywołek A, Ndela EO, Karlsson EN, Olgudóttir E, Pedersen C, Perler F, Pétursdóttir SK, Plotka M, Pohl E, Prangishvili D, Ray JL, Reynisson B, Róbertsdóttir T, Sandaa RA, Sczyrba A, Skírnisdóttir S, Söding J, Solstad T, Steen IH, Stefánsson SK, Steinegger M, Overå KS, Striberny B, Svensson A, Szadkowska M, Tarrant EJ, Terzian P, Tourigny M, Bergh TVD, Vanhalst J, Vincent J, Vroling B, Walse B, Wang L, Watzlawick H, Welin M, Werbowy O, Wons E, Zhang R. Going to extremes - a metagenomic journey into the dark matter of life. FEMS Microbiol Lett 2021; 368:6296640. [PMID: 34114607 DOI: 10.1093/femsle/fnab067] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.
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Affiliation(s)
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Josefin Ahlqvist
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Joseph Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hasan Arsin
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - David Brandt
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Magdalena Cichowicz-Cieślak
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Katy A S Cornish
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | | | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,Department of Informatics, University of Bergen, PO Box 7803, Thormøhlens gate 53 A/B, N-5020 Bergen, Norway
| | | | - Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Francois Enault
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Anita-Elin Fedøy
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Stefanie Freitag-Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | - Clovis Galiez
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eirin Glomsaker
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | - Sigurd E Gundesø
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | | | - Maria Håkansson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Christian Henke
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | | | | | - Gudmundur O Hreggvidsson
- Matis ohf, Vinlandsleid 12, Reykjavik 113, Iceland.,Faculty of Life and Environmental Sciences, University of Iceland, Askja-Sturlugata 7, Reykjavik, Iceland
| | - Andrius Jasilionis
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Annika Jochheim
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | - Agata Jurczak-Kurek
- Department of Molecular Evolution, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Lukasz P Kozlowski
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | - Mart Krupovic
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Karolina Kwiatkowska-Semrau
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Olav Lanes
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Joanna Lange
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | | | - Javier Linares-Pastén
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Ying Liu
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | | | - Tobias Lutterman
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Thibaud Mas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | - Milot Mirdita
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Agnieszka Morzywołek
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Eric Olo Ndela
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Eva Nordberg Karlsson
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Cathrine Pedersen
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Francine Perler
- Perls of Wisdom Biotech Consulting, 74 Fuller Street, Brookline, MA 02446, USA
| | | | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ehmke Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom.,Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - David Prangishvili
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jessica L Ray
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,NORCE Environment, NORCE Norwegian Research Centre AS, Nygårdsgaten 112, 5008 Bergen, Norway
| | | | | | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | - Johannes Söding
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Terese Solstad
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - Martin Steinegger
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | - Bernd Striberny
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Anders Svensson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Emma J Tarrant
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Paul Terzian
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | | | | | - Jonathan Vincent
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Bas Vroling
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | - Björn Walse
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Lei Wang
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hildegard Watzlawick
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Martin Welin
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Olesia Werbowy
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ruoshi Zhang
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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8
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Diego D, Hannisdal B, Dahle H. On how the power supply shapes microbial survival. Math Biosci 2021; 338:108615. [PMID: 33857526 DOI: 10.1016/j.mbs.2021.108615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/29/2021] [Accepted: 04/04/2021] [Indexed: 10/21/2022]
Abstract
Understanding how environmental factors affect microbial survival is an important open problem in microbial ecology. Patterns of microbial community structure have been characterized across a wide range of different environmental settings, but the mechanisms generating these patterns remain poorly understood. Here, we use mathematical modelling to investigate fundamental connections between chemical power supply to a system and patterns of microbial survival. We reveal a complex set of interdependences between power supply and distributions of survival probability across microbial habitats, in a case without interspecific resource competition. We also find that different properties determining power supply, such as substrate fluxes and Gibbs energies of reactions, affect microbial survival in fundamentally different ways. Moreover, we show how simple connections between power supply and growth can give rise to complex patterns of microbial survival across physicochemical gradients, such as pH gradients. Our findings show the importance of taking energy fluxes into account in order to reveal fundamental connections between microbial survival and environmental conditions, and to obtain a better understanding of microbial population dynamics in natural environments.
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Affiliation(s)
- David Diego
- Department of Earth Science, University of Bergen, Allégaten, NO-5007 Bergen, Norway; K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway.
| | - Bjarte Hannisdal
- Department of Earth Science, University of Bergen, Allégaten, NO-5007 Bergen, Norway; K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway
| | - Håkon Dahle
- K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway; Department of Biological Sciences, University of Bergen, Thormøhlens gate 53A, NO-5006 Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway
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9
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Stokke R, Reeves EP, Dahle H, Fedøy AE, Viflot T, Lie Onstad S, Vulcano F, Pedersen RB, Eijsink VGH, Steen IH. Tailoring Hydrothermal Vent Biodiversity Toward Improved Biodiscovery Using a Novel in situ Enrichment Strategy. Front Microbiol 2020; 11:249. [PMID: 32153535 PMCID: PMC7046548 DOI: 10.3389/fmicb.2020.00249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/03/2020] [Indexed: 11/13/2022] Open
Abstract
Deep-sea hydrothermal vents are amongst the most extreme environments on Earth and represent interesting targets for marine bioprospecting and biodiscovery. The microbial communities in hydrothermal vents are often dominated by chemolithoautotrophs utilizing simple chemical compounds, though the full extent of their heterotrophic abilities is still being explored. In the bioprocessing industry, where degradation of complex organic materials often is a major challenge, new microbial solutions are heavily needed. To meet these needs, we have developed novel in situ incubators and tested if deployment of recalcitrant materials from fish farming and wood-pulping industries introduced changes in the microbial community structure in hot marine hydrothermal sediments. The incubation chambers were deployed in sediments at the Bruse vent site located within the Jan Mayen vent field for 1 year, after which the microbial populations in the chambers were profiled by 16S rRNA Ion Torrent amplicon sequencing. A total of 921 operational taxonomic units (OTUs) were assigned into 74 different phyla where differences in community structure were observed depending on the incubated material, chamber depth below the sea floor and/or temperature. A high fraction of putative heterotrophic microbial lineages related to cultivated members within the Thermotogales were observed. However, considerable fractions of previously uncultivated and novel Thermotogales and Bacteroidetes were also identified. Moreover, several novel lineages (e.g., members within the DPANN superphylum, unidentified archaeal lineages, unclassified Thermoplasmatales and Candidatus division BRC-1 bacterium) of as-yet uncultivated thermophilic archaea and bacteria were identified. Overall, our data illustrate that amendment of hydrothermal vent communities by in situ incubation of biomass induces shifts in community structure toward increased fractions of heterotrophic microorganisms. The technologies utilized here could aid in subsequent metagenomics-based enzyme discovery for diverse industries.
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Affiliation(s)
- Runar Stokke
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Eoghan P Reeves
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Department of Earth Science, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Anita-Elin Fedøy
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Thomas Viflot
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Department of Earth Science, University of Bergen, Bergen, Norway
| | - Solveig Lie Onstad
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Department of Earth Science, University of Bergen, Bergen, Norway
| | - Francesca Vulcano
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Rolf B Pedersen
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Department of Earth Science, University of Bergen, Bergen, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
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10
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Rivera-Thorsen TE, Dahle H, Chisholm J, Florian MK, Gronke M, Rigby JR, Gladders MD, Mahler G, Sharon K, Bayliss M. Gravitational lensing reveals ionizing ultraviolet photons escaping from a distant galaxy. Science 2019; 366:738-741. [PMID: 31699936 DOI: 10.1126/science.aaw0978] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 10/17/2019] [Indexed: 11/02/2022]
Abstract
During the epoch of reionization, neutral gas in the early Universe was ionized by hard ultraviolet radiation emitted by young stars in the first galaxies. To do so, ionizing ultraviolet photons must escape from the host galaxy. We present Hubble Space Telescope observations of the gravitationally lensed post-reionization galaxy PSZ1-ARC G311.6602-18.4624 (nicknamed the "Sunburst Arc"), revealing bright, multiply imaged ionizing photon escape from a compact star-forming region through a narrow channel in an optically thick gas. The gravitational lensing magnification shows how ionizing photons escape this galaxy, contributing to the reionization of the Universe. The multiple sight lines to the source probe absorption by intergalactic neutral hydrogen on a scale of less than a few hundred parsecs.
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Affiliation(s)
| | - Håkon Dahle
- Institute of Theoretical Astrophysics, University of Oslo, 0315 Oslo, Norway
| | - John Chisholm
- Observatoire de Genève, Université de Genève, 1290 Versoix, Switzerland.,Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064, USA
| | - Michael K Florian
- Observational Cosmology Lab, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - Max Gronke
- Department of Physics, University of California, Santa Barbara, CA 93106, USA
| | - Jane R Rigby
- Observational Cosmology Lab, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - Michael D Gladders
- Department of Astronomy and Astrophysics, University of Chicago, Chicago, IL 60637, USA.,Kavli Institute for Cosmological Physics, University of Chicago, Chicago, IL 60637, USA
| | - Guillaume Mahler
- Department of Astronomy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Keren Sharon
- Department of Astronomy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew Bayliss
- Massachusetts Institute of Technology-Kavli Center for Astrophysics and Space Research, Cambridge, MA 02139, USA.,Department of Physics, University of Cincinnati, Cincinnati, OH 45221, USA
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11
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Roalkvam I, Drønen K, Dahle H, Wergeland HI. Microbial Communities in a Flow-Through Fish Farm for Lumpfish ( Cyclopterus lumpus L.) During Healthy Rearing Conditions. Front Microbiol 2019; 10:1594. [PMID: 31354681 PMCID: PMC6640156 DOI: 10.3389/fmicb.2019.01594] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 06/26/2019] [Indexed: 11/29/2022] Open
Abstract
Lumpfish can efficiently remove sea lice from Atlantic salmon in net-pens, and production of lumpfish in closed fish farms is a new, fast developing industry in Norway. However, periodic outbreaks of bacterial diseases in the fish farms represent a large problem, both economically and ethically. Therefore it is important to obtain a better understanding of how microbial communities develop in these production facilities. Knowledge on the characteristics of microbial communities associated with healthy fish could also enable detection of changes associated with disease outbreaks at an early stage. In this study we have monitored microbial communities in a fish farm for lumpfish during normal operational conditions with no disease outbreak by using 16S rRNA gene amplicon sequencing. The study involved weekly samplings of water and biofilms from fish tanks, and fish. The results revealed that the microbial communities in fish tank water were different from the intake water. The water and biofilm in fish tanks were highly similar in regards to microbial community members, but with large differences in relative abundances for some taxa. The sampled fish were associated with mostly the same taxa as in tank water and biofilm, but more variation in relative abundances of different taxonomic groups occurred. The microbial communities in the fish farm seemed stable over time, and were dominated by marine bacteria and archaea within Alphaproteobacteria, Epsilonproteobacteria, Flavobacteria, Gammaproteobacteria, Thaumarchaeota, Planctomycetes, Sphingobacteriia, and Verrucomicrobiae (>10% relative abundance). Bacterial genera known to include fish-pathogenic strains were detected in all types of sample materials, but with low relative abundances (<5%). Exceptions were some samples of fish, biofilm and water with high relative abundance of Tenacibaculum (<85.8%) and Moritella (<82%). In addition, some of the eggs had a high relative abundance of Tenacibaculum (<89.5%). Overall, this study shows that a stable microbial community dominated by various genera of non-pathogenic bacteria is associated with a healthy environment for rearing lumpfish. Taxa with pathogenic members were also part of the microbial communities during healthy conditions, but the stable non-pathogenic bacteria may limit their growth and thereby prevent disease outbreaks.
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Affiliation(s)
- Irene Roalkvam
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Karine Drønen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
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12
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Le Moine Bauer S, Sjøberg AG, L'Haridon S, Stokke R, Roalkvam I, Steen IH, Dahle H. Profundibacter amoris gen. nov., sp. nov., a new member of the Roseobacter clade isolated from Loki’s Castle Vent Field on the Arctic Mid-Ocean Ridge. Int J Syst Evol Microbiol 2019; 69:975-981. [DOI: 10.1099/ijsem.0.003234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated BAR1T, was isolated from a microbial mat growing on the surface of a barite chimney at the Loki’s Castle Vent Field, at a depth of 2216 m. Cells of strain BAR1T were rod-shaped, Gram-reaction-negative and grew on marine broth 2216 at 10–37 °C (optimum 27–35 °C), pH 5.5–8.0 (optimum pH 6.5–7.5) and 0.5–5.0 % NaCl (optimum 2 %). The DNA G+C content was 57.38 mol%. The membrane-associated major ubiquinone was Q-10, the fatty acid profile was dominated by C18 : 1ω7c (91 %), and the polar lipids detected were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid, one unidentified lipid and one unidentified phospholipid. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BAR1T clustered together with Rhodobacterales bacterium PRT1, as well as the genera
Halocynthiibacter
and Pseudohalocynthiibacter in a polyphyletic clade within the
Roseobacter
clade. Several characteristics differentiate strain BAR1T from the aforementioned genera, including its motility, its piezophilic behaviour and its ability to grow at 35 °C and under anaerobic conditions. Accordingly, strain BAR1T is considered to represent a novel genus and species within the Roseobacter clade, for which the name Profundibacter amoris gen. nov., sp. nov. is proposed. The type strain is Profundibacter amoris BAR1T (=JCM 31874T=DSM 104147T).
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Affiliation(s)
- Sven Le Moine Bauer
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
| | - Andreas Gilje Sjøberg
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
| | - Stéphane L'Haridon
- Université de Brest (UBO), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
- CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
- Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Runar Stokke
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
| | - Irene Roalkvam
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway
| | - Ida Helene Steen
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
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13
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Vander Roost J, Daae FL, Steen IH, Thorseth IH, Dahle H. Distribution Patterns of Iron-Oxidizing Zeta- and Beta-Proteobacteria From Different Environmental Settings at the Jan Mayen Vent Fields. Front Microbiol 2018; 9:3008. [PMID: 30574135 PMCID: PMC6292416 DOI: 10.3389/fmicb.2018.03008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/20/2018] [Indexed: 12/26/2022] Open
Abstract
Iron oxidizers are widespread in marine environments and play an important role in marine iron cycling. However, little is known about the overall distribution of iron oxidizers within hydrothermal systems, including settings with little hydrothermal activity. Moreover, the extent to which different phylogenetic groups of iron oxidizers exhibit niche specialization toward different environmental settings, remains largely unknown. Obtaining such knowledge is critical to unraveling the impact of the activity of iron oxidizers and how they are adapted. Here, we used 16S rRNA sequencing to characterize the distribution of iron oxidizers in different environmental settings within the Jan Mayen hydrothermal vent fields (JMVFs). Putative iron oxidizers affiliated to Zetaproteobacteria and Betaproteobacteria were detected within iron mounds, bottom seawater, basalt surfaces, and surface layers of sediments. The detected iron oxidizers were compared to sequence types previously observed in patchily distributed iron mats associated with diffuse venting at the JMVFs. Most OTUs of iron oxidizers reoccurred under different environmental settings, suggesting a limited degree of niche specialization. Consequently, most of the detected iron oxidizers seem to be generalists with a large habitat range. Our study highlights the importance of gathering information about the overall distribution of iron oxidizers in hydrothermal systems to fully understand the role of this metabolic group regarding cycling of iron. Furthermore, our results provide further evidence of the presence of iron-oxidizing members of Betaproteobacteria in marine environments.
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Affiliation(s)
- Jan Vander Roost
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Frida Lise Daae
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Ida Helene Steen
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Ingunn Hindeness Thorseth
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Earth Science, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
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14
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Dahle H, Le Moine Bauer S, Baumberger T, Stokke R, Pedersen RB, Thorseth IH, Steen IH. Energy Landscapes in Hydrothermal Chimneys Shape Distributions of Primary Producers. Front Microbiol 2018; 9:1570. [PMID: 30061874 PMCID: PMC6055050 DOI: 10.3389/fmicb.2018.01570] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 06/25/2018] [Indexed: 11/25/2022] Open
Abstract
Hydrothermal systems are excellent natural laboratories for the study of how chemical energy landscapes shape microbial communities. Yet, only a few attempts have been made to quantify relationships between energy availability and microbial community structure in these systems. Here, we have investigated how microbial communities and chemical energy availabilities vary along cross-sections of two hydrothermal chimneys from the Soria Moria Vent Field and the Bruse Vent Field. Both vent fields are located on the Arctic Mid-Ocean Ridge, north of the Jan Mayen Island and the investigated chimneys were venting fluids with markedly different H2S:CH4 ratios. Energy landscapes were inferred from a stepwise in silico mixing of hydrothermal fluids (HFs) with seawater, where Gibbs energies of relevant redox-reactions were calculated at each step. These calculations formed the basis for simulations of relative abundances of primary producers in microbial communities. The simulations were compared with an analysis of 24 samples from chimney wall transects by sequencing of 16S rRNA gene amplicons using 454 sequencing. Patterns in relative abundances of sulfide oxidizing Epsilonproteobacteria and methane oxidizing Methylococcales and ANME-1, were consistent with simulations. However, even though H2 was present in HFs from both chimneys, the observed abundances of putative hydrogen oxidizing anaerobic sulfate reducers (Archaeoglobales) and methanogens (Methanococcales) in the inner parts of the Soria Moria Chimney were considerably higher than predicted by simulations. This indicates biogenic production of H2 in the chimney wall by fermentation, and suggests that biological activity inside the chimneys may modulate energy landscapes significantly. Our results are consistent with the notion that energy landscapes largely shape the distribution of primary producers in hydrothermal systems. Our study demonstrates how a combination of modeling and field observations can be useful in deciphering connections between chemical energy landscapes and metabolic networks within microbial communities.
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Affiliation(s)
- Håkon Dahle
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Sven Le Moine Bauer
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Tamara Baumberger
- Pacific Marine Environmental Laboratory (NOAA), Newport, OR, United States
| | - Runar Stokke
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Rolf B. Pedersen
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ingunn H. Thorseth
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ida H. Steen
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
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15
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Le Moine Bauer S, Stensland A, Daae FL, Sandaa RA, Thorseth IH, Steen IH, Dahle H. Water Masses and Depth Structure Prokaryotic and T4-Like Viral Communities Around Hydrothermal Systems of the Nordic Seas. Front Microbiol 2018; 9:1002. [PMID: 29904373 PMCID: PMC5990851 DOI: 10.3389/fmicb.2018.01002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/30/2018] [Indexed: 12/04/2022] Open
Abstract
The oceanographic features of the Nordic Seas, situated between Iceland and Svalbard, have been extensively studied over the last decades. As well, the Nordic Seas hydrothermal systems situated on the Arctic Mid-Ocean Ridge System have received an increasing interest. However, there is very little knowledge on the microbial communities inhabiting the water column of the Nordic Seas, and nothing is known about the influence of the different water masses and hydrothermal plumes on the microbial community structures. In this study, we aimed at characterizing the impact of hydrothermal plumes on prokaryotic and T4-like viral communities around the island of Jan Mayen. To this end, we used 16S rRNA-gene and g23-gene profiling as well as flow cytometry counts to examine prokaryotic and viral communities in 27 samples obtained from different water masses in this area. While Thaumarchaeota and Marine group II Archaea dominated the waters deeper than 500 m, members of Flavobacteria generally dominated the shallower waters. Furthermore, extensive chemical and physical characteristics of all samples were obtained, including temperature measurements and concentrations of major ions and gases. The effect of these physiochemical variables on the communities was measured by using constrained and unconstrained multivariate analyzes, Mantel tests, network analyzes, phylogenetic analyzes, taxonomic analyzes and temperature-salinity (Θ-S) plots. Our results suggest that hydrothermal activity has little effect on pelagic microbial communities in hydrothermal plumes of the Nordic Seas. However, we provide evidences that observed differences in prokaryotic community structure can largely be attributed to which water mass each sample was taken from. In contrast, depth was the major factor structuring the T4-like viral communities. Our results also show that it is crucial to include water masses when studying the influence of hydrothermal plumes on microbial communities, as it could prevent to falsely associate a change in community structure with the presence of a plume.
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Affiliation(s)
- Sven Le Moine Bauer
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Anne Stensland
- Department of Earth Science and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Frida L Daae
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ingunn H Thorseth
- Department of Earth Science and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Ida H Steen
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
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Vander Roost J, Thorseth IH, Dahle H. Microbial analysis of Zetaproteobacteria and co-colonizers of iron mats in the Troll Wall Vent Field, Arctic Mid-Ocean Ridge. PLoS One 2017; 12:e0185008. [PMID: 28931087 PMCID: PMC5607188 DOI: 10.1371/journal.pone.0185008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 09/05/2017] [Indexed: 11/30/2022] Open
Abstract
Over the last decade it has become increasingly clear that Zetaproteobacteria are widespread in hydrothermal systems and that they contribute to the biogeochemical cycling of iron in these environments. However, how chemical factors control the distribution of Zetaproteobacteria and their co-occurring taxa remains elusive. Here we analysed iron mats from the Troll Wall Vent Field (TWVF) located at the Arctic Mid-Ocean Ridge (AMOR) in the Norwegian-Greenland Sea. The samples were taken at increasing distances from high-temperature venting chimneys towards areas with ultraslow low-temperature venting, encompassing a large variety in geochemical settings. Electron microscopy revealed the presence of biogenic iron stalks in all samples. Using 16S rRNA gene sequence profiling we found that relative abundances of Zetaproteobacteria in the iron mats varied from 0.2 to 37.9%. Biogeographic analyses of Zetaproteobacteria, using the ZetaHunter software, revealed the presence of ZetaOtus 1, 2 and 9, supporting the view that they are cosmopolitan. Relative abundances of co-occurring taxa, including Thaumarchaeota, Euryarchaeota and Proteobacteria, also varied substantially. From our results, combined with results from previous microbiological and geochemical analyses of the TWVF, we infer that the distribution of Zetaproteobacteria is connected to fluid-flow patterns and, ultimately, variations in chemical energy landscapes. Moreover, we provide evidence for iron-oxidizing members of Gallionellaceae being widespread in TWVF iron mats, albeit at low relative abundances.
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Affiliation(s)
- Jan Vander Roost
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Ingunn Hindenes Thorseth
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
- * E-mail:
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Hestetun JT, Dahle H, Jørgensen SL, Olsen BR, Rapp HT. The Microbiome and Occurrence of Methanotrophy in Carnivorous Sponges. Front Microbiol 2016; 7:1781. [PMID: 27881974 PMCID: PMC5101230 DOI: 10.3389/fmicb.2016.01781] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/24/2016] [Indexed: 12/03/2022] Open
Abstract
As shown by recent studies, filter-feeding sponges are known to host a wide variety of microorganisms. However, the microbial community of the non-filtering carnivorous sponges (Porifera, Cladorhizidae) has been the subject of less scrutiny. Here, we present the results from a comparative study of the methanotrophic carnivorous sponge Cladorhiza methanophila from a mud volcano-rich area at the Barbados Accretionary Prism, and five carnivorous species from the Jan Mayen Vent Field (JMVF) at the Arctic Mid-Ocean Ridge. Results from 16S rRNA microbiome data indicate the presence of a diverse assemblage of associated microorganisms in carnivorous sponges mainly from the Gamma- and Alphaproteobacteria, Flavobacteriaceae, and Thaumarchaeota. While the abundance of particular groups varied throughout the dataset, we found interesting similarities to previous microbiome results from non-carnivorous deep sea sponges, suggesting that the carnivorous sponges share characteristics of a previously hypothesized putative deep-sea sponge microbial community. Chemolithoautotrophic symbiosis was confirmed for C. methanophila through a microbial community with a high abundance of Methylococcales and very light isotopic δ13C and δ15N ratios (-60 to -66‰/3.5 to 5.2‰) compared to the other cladorhizid species (-22 to -24‰/8.5 to 10.5‰). We provide evidence for the presence of putative sulfur-oxidizing Gammaproteobacteria in the arctic cladorhizids; however, δ13C and δ15N signatures did not provide evidence for significant chemoautotrophic symbiosis in this case, and the slightly higher abundance of cladorhizids at the JMVF site compared to the nearby deep sea likely stem from an increased abundance of prey rather than a more direct vent association. The phylogenetic position of C. methanophila in relation to other carnivorous sponges was established using a three-gene phylogenetic analysis, and it was found to be closely related to other non-methanotrophic Cladorhiza species with a similar morphology included in the dataset, suggesting a recent origin for methanotrophy in this species. C. methanophila remains the only known carnivorous sponge with a strong, chemolithoautotrophic symbiont association, and methanotrophic symbiosis does not seem to be a widespread property within the Cladorhizidae.
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Affiliation(s)
- Jon T. Hestetun
- Marine Biodiversity Group, Department of Biology, University of BergenBergen, Norway
- Centre for Geobiology, University of BergenBergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of BergenBergen, Norway
| | | | - Bernt R. Olsen
- Marine Biodiversity Group, Department of Biology, University of BergenBergen, Norway
- Centre for Geobiology, University of BergenBergen, Norway
| | - Hans T. Rapp
- Marine Biodiversity Group, Department of Biology, University of BergenBergen, Norway
- Centre for Geobiology, University of BergenBergen, Norway
- Uni Research Environment, Uni Research ASBergen, Norway
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Le Moine Bauer S, Roalkvam I, Steen IH, Dahle H. Lutibacter profundi sp. nov., isolated from a deep-sea hydrothermal system on the Arctic Mid-Ocean Ridge and emended description of the genus Lutibacter. Int J Syst Evol Microbiol 2016; 66:2671-2677. [PMID: 27118569 DOI: 10.1099/ijsem.0.001105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated LP1T was isolated from a microbial mat growing on the surface of a black smoker chimney at the Loki's Castle hydrothermal system, which is located on the Arctic Mid-Ocean Ridge. Phylogenetic analyses based on 16S rRNA gene sequences positioned strain LP1T within the family Flavobacteriaceae with Lutibacterholmesii as the closest relative (97.5 % 16S rRNA gene sequence similarity). Strain LP1T was rod-shaped, Gram-reaction-negative and non-motile. It grew in a modified artificial seawater medium supplemented with tryptone and vitamins at pH 5.5-7.5 (optimum pH 6.0-6.5), within a temperature range of 13-34 °C (optimum 23 °C), and under microaerobic conditions. The most abundant fatty acids (>10 %) were iso-C15 : 0 (25.2 %) and iso-C15 : 0 3-OH (14.5 %). The genome of strain LP1T has a DNA G+C content of 29.8 mol%. Based on the results of the polyphasic characterization presented here, strain LP1T is considered to represent a novel species of the genus Lutibacter, for which the name Lutibacter profundi sp. nov. is proposed. The type strain is LP1T (=DSM 100437T =JCM 30585T). An emended description of the genus Lutibacter is also provided to fit the description of strain LP1T.
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Affiliation(s)
- Sven Le Moine Bauer
- Department of Biology, Center for Geobiology, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway
| | - Irene Roalkvam
- Department of Biology, Center for Geobiology, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway
| | - Ida Helene Steen
- Department of Biology, Center for Geobiology, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway
| | - Håkon Dahle
- Department of Biology, Center for Geobiology, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway
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Lin TJ, Ver Eecke HC, Breves EA, Dyar MD, Jamieson JW, Hannington MD, Dahle H, Bishop JL, Lane MD, Butterfield DA, Kelley DS, Lilley MD, Baross JA, Holden JF. Linkages between mineralogy, fluid chemistry, and microbial communities within hydrothermal chimneys from the Endeavour Segment, Juan de Fuca Ridge. Geochem Geophys Geosyst 2016; 17:300-323. [PMID: 30123099 PMCID: PMC6094386 DOI: 10.1002/2015gc006091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Rock and fluid samples were collected from three hydrothermal chimneys at the Endeavour Segment, Juan de Fuca Ridge to evaluate linkages among mineralogy, fluid chemistry, and microbial community composition within the chimneys. Mössbauer, midinfrared thermal emission, and visible-near infrared spectroscopies were utilized for the first time to characterize vent mineralogy, in addition to thin-section petrography, X-ray diffraction, and elemental analyses. A 282°C venting chimney from the Bastille edifice was composed primarily of sulfide minerals such as chalcopyrite, marcasite, and sphalerite. In contrast, samples from a 300°C venting chimney from the Dante edifice and a 321°C venting chimney from the Hot Harold edifice contained a high abundance of the sulfate mineral anhydrite. Geochemical modeling of mixed vent fluids suggested the oxic-anoxic transition zone was above 100°C at all three vents, and that the thermodynamic energy available for autotrophic microbial redox reactions favored aerobic sulfide and methane oxidation. As predicted, microbes within the Dante and Hot Harold chimneys were most closely related to mesophilic and thermophilic aerobes of the Betaproteobacteria and Gammaproteobacteria and sulfide-oxidizing autotrophic Epsilonproteobacteria. However, most of the microbes within the Bastille chimney were most closely related to mesophilic and thermophilic anaerobes of the Deltaproteobacteria, especially sulfate reducers, and anaerobic hyperthermophilic archaea. The predominance of anaerobes in the Bastille chimney indicated that other environmental factors promote anoxic conditions. Possibilities include the maturity or fluid flow characteristics of the chimney, abiotic Fe2+ and S2- oxidation in the vent fluids, or O2 depletion by aerobic respiration on the chimney outer wall.
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Affiliation(s)
- T. J. Lin
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - H. C. Ver Eecke
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - E. A. Breves
- Department of Astronomy, Mount Holyoke College, South Hadley, Massachusetts, USA
| | - M. D. Dyar
- Department of Astronomy, Mount Holyoke College, South Hadley, Massachusetts, USA
| | - J. W. Jamieson
- Department of Earth Sciences, University of Ottawa, Ottawa, Ontario, Canada
- GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany
| | - M. D. Hannington
- Department of Earth Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - H. Dahle
- Department of Biology, Centre for Geobiology, University of Bergen, Bergen, Norway
| | - J. L. Bishop
- SETI Institute/NASA Ames Research Center, Moffett Field, California, USA
| | - M. D. Lane
- Planetary Science Institute, Tucson, Arizona, USA
| | - D. A. Butterfield
- Joint Institute for the Study of the Atmosphere and Ocean, University of Washington and NOAA-PMEL, Seattle, Washington, USA
| | - D. S. Kelley
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - M. D. Lilley
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - J. A. Baross
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - J. F. Holden
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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20
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Steen IH, Dahle H, Stokke R, Roalkvam I, Daae FL, Rapp HT, Pedersen RB, Thorseth IH. Novel Barite Chimneys at the Loki's Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems. Front Microbiol 2016; 6:1510. [PMID: 26779165 PMCID: PMC4703759 DOI: 10.3389/fmicb.2015.01510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/14/2015] [Indexed: 01/23/2023] Open
Abstract
In order to fully understand the cycling of elements in hydrothermal systems it is critical to understand intra-field variations in geochemical and microbiological processes in both focused, high-temperature and diffuse, low-temperature areas. To reveal important causes and effects of this variation, we performed an extensive chemical and microbiological characterization of a low-temperature venting area in the Loki's Castle Vent Field (LCVF). This area, located at the flank of the large sulfide mound, is characterized by numerous chimney-like barite (BaSO4) structures (≤ 1 m high) covered with white cotton-like microbial mats. Results from geochemical analyses, microscopy (FISH, SEM), 16S rRNA gene amplicon-sequencing and metatranscriptomics were compared to results from previous analyses of biofilms growing on black smoker chimneys at LCVF. Based on our results, we constructed a conceptual model involving the geochemistry and microbiology in the LCVF. The model suggests that CH4 and H2S are important electron donors for microorganisms in both high-temperature and low-temperature areas, whereas the utilization of H2 seems restricted to high-temperature areas. This further implies that sub-seafloor processes can affect energy-landscapes, elemental cycling, and the metabolic activity of primary producers on the seafloor. In the cotton-like microbial mats on top of the active barite chimneys, a unique network of single cells of Epsilonproteobacteria interconnected by threads of extracellular polymeric substances (EPS) was seen, differing significantly from the long filamentous Sulfurovum filaments observed in biofilms on the black smokers. This network also induced nucleation of barite crystals and is suggested to play an essential role in the formation of the microbial mats and the chimneys. Furthermore, it illustrates variations in how different genera of Epsilonproteobacteria colonize and position cells in different vent fluid mixing zones within a vent field. This may be related to niche-specific physical characteristics. Altogether, the model provides a reference for future studies and illustrates the importance of systematic comparative studies of spatially closely connected niches in order to fully understand the geomicrobiology of hydrothermal systems.
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Affiliation(s)
- Ida H Steen
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Runar Stokke
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Irene Roalkvam
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Frida-Lise Daae
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Hans Tore Rapp
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Rolf B Pedersen
- Centre for Geobiology, University of BergenBergen, Norway; Department of Earth Science, University of BergenBergen, Norway
| | - Ingunn H Thorseth
- Centre for Geobiology, University of BergenBergen, Norway; Department of Earth Science, University of BergenBergen, Norway
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Roalkvam I, Drønen K, Stokke R, Daae FL, Dahle H, Steen IH. Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria. Front Microbiol 2015; 6:987. [PMID: 26441916 PMCID: PMC4584990 DOI: 10.3389/fmicb.2015.00987] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/04/2015] [Indexed: 01/18/2023] Open
Abstract
In this study we characterized and sequenced the genome of Arcobacter anaerophilus strain IR-1 isolated from enrichment cultures used in nitrate-amended corrosion experiments. A. anaerophilus IR-1 could grow lithoautotrophically on hydrogen and hydrogen sulfide and lithoheterothrophically on thiosulfate and elemental sulfur. In addition, the strain grew organoheterotrophically on yeast extract, peptone, and various organic acids. We show for the first time that Arcobacter could grow on the complex organic substrate tryptone and oxidize acetate with elemental sulfur as electron acceptor. Electron acceptors utilized by most Epsilonproteobacteria, such as oxygen, nitrate, and sulfur, were also used by A. anaerophilus IR-1. Strain IR-1 was also uniquely able to use iron citrate as electron acceptor. Comparative genomics of the Arcobacter strains A. butzleri RM4018, A. nitrofigilis CI and A. anaerophilus IR-1 revealed that the free-living strains had a wider metabolic range and more genes in common compared to the pathogen strain. The presence of genes for NAD(+)-reducing hydrogenase (hox) and dissimilatory iron reduction (fre) were unique for A. anaerophilus IR-1 among Epsilonproteobacteria. Finally, the new strain had an incomplete denitrification pathway where the end product was nitrite, which is different from other Arcobacter strains where the end product is ammonia. Altogether, our study shows that traditional characterization in combination with a modern genomics approach can expand our knowledge on free-living Arcobacter, and that this complementary approach could also provide invaluable knowledge about the physiology and metabolic pathways in other Epsilonproteobacteria from various environments.
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Affiliation(s)
- Irene Roalkvam
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Karine Drønen
- UniResearch, Centre for Integrated Petroleum Research Bergen, Norway
| | - Runar Stokke
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Frida L Daae
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Ida H Steen
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
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22
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Stokke R, Dahle H, Roalkvam I, Wissuwa J, Daae FL, Tooming-Klunderud A, Thorseth IH, Pedersen RB, Steen IH. Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm. Environ Microbiol 2015; 17:4063-77. [PMID: 26147346 DOI: 10.1111/1462-2920.12970] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/25/2015] [Accepted: 06/25/2015] [Indexed: 11/30/2022]
Abstract
Little is known about how lithoautotrophic primary production is connected to microbial organotrophic consumption in hydrothermal systems. Using a multifaceted approach, we analysed the structure and metabolic capabilities within a biofilm growing on the surface of a black smoker chimney in the Loki's Castle vent field. Imaging revealed the presence of rod-shaped Bacteroidetes growing as ectobionts on long, sheathed microbial filaments (> 100 μm) affiliated with the Sulfurovum genus within Epsilonproteobacteria. The filaments were composed of a thick (> 200 nm) stable polysaccharide, representing a substantial fraction of organic carbon produced by primary production. An integrated -omics approach enabled us to assess the metabolic potential and in situ metabolism of individual taxonomic and morphological groups identified by imaging. Specifically, we provide evidence that organotrophic Bacteroidetes attach to and glide along the surface of Sulfurovum filaments utilizing organic polymers produced by the lithoautotrophic Sulfurovum. Furthermore, in situ expression of acetyl-CoA synthetase by Sulfurovum suggested the ability to assimilate acetate, indicating recycling of organic matter in the biofilm. This study expands our understanding of the lifestyles of Epsilonproteobacteria in hydrothermal vents, their metabolic properties and co-operative interactions in deep-sea hydrothermal vent food webs.
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Affiliation(s)
- Runar Stokke
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Irene Roalkvam
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Juliane Wissuwa
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Frida Lise Daae
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Ave Tooming-Klunderud
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Ingunn H Thorseth
- Centre for Geobiology.,Department of Earth Science, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Rolf B Pedersen
- Centre for Geobiology.,Department of Earth Science, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Ida Helene Steen
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
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Dahle H, Økland I, Thorseth IH, Pederesen RB, Steen IH. Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge. ISME J 2015; 9:1593-606. [PMID: 25575309 PMCID: PMC4478700 DOI: 10.1038/ismej.2014.247] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 11/17/2022]
Abstract
Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent field (SMVF) and the Loki's Castle Vent Field (LCVF). Chemical energy landscapes were evaluated through modelling of the Gibbs energy from selected redox reactions under different mixing ratios between seawater and hydrothermal fluids. Our models indicate that the sediment-influenced LCVF has a much higher potential for both anaerobic and aerobic methane oxidation, as well as aerobic ammonium and hydrogen oxidation, than the SMVF. The modelled energy landscapes were used to develop microbial community composition models, which were compared with community compositions in environmental samples inside or on the exterior of hydrothermal chimneys, as assessed by pyrosequencing of partial 16S rRNA genes. We show that modelled microbial communities based solely on thermodynamic considerations can have a high predictive power and provide a framework for analyses of the link between energy availability and microbial community composition.
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Affiliation(s)
- Håkon Dahle
- 1] Centre for Geobiology, University of Bergen, Bergen, Norway [2] Department of Biology, University of Bergen, Bergen, Norway
| | - Ingeborg Økland
- 1] Centre for Geobiology, University of Bergen, Bergen, Norway [2] Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ingunn H Thorseth
- 1] Centre for Geobiology, University of Bergen, Bergen, Norway [2] Department of Earth Science, University of Bergen, Bergen, Norway
| | - Rolf B Pederesen
- 1] Centre for Geobiology, University of Bergen, Bergen, Norway [2] Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ida H Steen
- 1] Centre for Geobiology, University of Bergen, Bergen, Norway [2] Department of Biology, University of Bergen, Bergen, Norway
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Nesbø CL, S Swithers K, Dahle H, Haverkamp THA, Birkeland NK, Sokolova T, Kublanov I, Zhaxybayeva O. Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments. ISME J 2014; 9:1532-42. [PMID: 25500512 DOI: 10.1038/ismej.2014.238] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/03/2014] [Accepted: 11/10/2014] [Indexed: 11/09/2022]
Abstract
Oil reservoirs represent a nutrient-rich ecological niche of the deep biosphere. Although most oil reservoirs are occupied by microbial populations, when and how the microbes colonized these environments remains unanswered. To address this question, we compared 11 genomes of Thermotoga maritima-like hyperthermophilic bacteria from two environment types: subsurface oil reservoirs in the North Sea and Japan, and marine sites located in the Kuril Islands, Italy and the Azores. We complemented our genomes with Thermotoga DNA from publicly available subsurface metagenomes from North America and Australia. Our analysis revealed complex non-bifurcating evolutionary history of the isolates' genomes, suggesting high amounts of gene flow across all sampled locations, a conjecture supported by numerous recombination events. Genomes from the same type of environment tend to be more similar, and have exchanged more genes with each other than with geographically close isolates from different types of environments. Hence, Thermotoga populations of oil reservoirs do not appear isolated, a requirement of the 'burial and isolation' hypothesis, under which reservoir bacteria are descendants of the isolated communities buried with sediments that over time became oil reservoirs. Instead, our analysis supports a more complex view, where bacteria from subsurface and marine populations have been continuously migrating into the oil reservoirs and influencing their genetic composition. The Thermotoga spp. in the oil reservoirs in the North Sea and Japan probably entered the reservoirs shortly after they were formed. An Australian oil reservoir, on the other hand, was likely colonized very recently, perhaps during human reservoir development.
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Affiliation(s)
- Camilla L Nesbø
- 1] Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Blindern, Oslo, Norway [2] Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Kristen S Swithers
- 1] Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, USA [2] Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Håkon Dahle
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Blindern, Oslo, Norway
| | - Nils-Kåre Birkeland
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Tatiana Sokolova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Zhaxybayeva
- 1] Department of Biological Sciences, Dartmouth College, Hanover, NH, USA [2] Department of Computer Science, Dartmouth College, Hanover, NH, USA
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Daae FL, Økland I, Dahle H, Jørgensen SL, Thorseth IH, Pedersen RB. Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex. Geobiology 2013; 11:318-339. [PMID: 23551703 DOI: 10.1111/gbi.12035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/15/2013] [Indexed: 06/02/2023]
Abstract
Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions.
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Affiliation(s)
- F L Daae
- Department of Biology, Centre for Geobiology, Bergen, Norway.
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Dahle H, Roalkvam I, Thorseth IH, Pedersen RB, Steen IH. The versatile in situ gene expression of an Epsilonproteobacteria-dominated biofilm from a hydrothermal chimney. Environ Microbiol Rep 2013; 5:282-290. [PMID: 23584970 DOI: 10.1111/1758-2229.12016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 10/03/2012] [Accepted: 11/05/2012] [Indexed: 06/02/2023]
Abstract
The Epsilonproteobacteria, including members of the genus Sulfurovum, are regarded as important primary producers in hydrothermal systems. However, their in situ gene expression in this habitat has so far not been investigated. We report a metatranscriptomic analysis of a Sulfurovum-dominated biofilm from one of the chimneys at the Loki's Castle hydrothermal system, located at the Arctic Mid Ocean Ridge. Transcripts involved in hydrogen oxidation, oxidation of sulfur species, aerobic respiration and denitrification were abundant and mostly assigned to Sulfurovum, indicating that members of this genus utilize multiple chemical energy sources simultaneously for primary production. Sulfurovum also seemed to have a diverse expression of transposases, potentially involved in horizontal gene transfer. Other transcripts were involved in CO₂ fixation by the reverse TCA cycle, the CRISPR-Cas system, heavy metal resistance, and sensing and responding to changing environmental conditions. Through pyrosequencing of PCR amplified 16S rRNA genes, the Sulfurovum-dominated biofilm was compared with another biofilm from the same chimney, revealing a large shift in the community structure of Epsilonproteobacteria-dominated biofilms over a few metres.
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Affiliation(s)
- Håkon Dahle
- Department of Biology, Centre for Geobiology, University of Bergen, Norway.
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Roalkvam I, Dahle H, Chen Y, Jørgensen SL, Haflidason H, Steen IH. Fine-Scale Community Structure Analysis of ANME in Nyegga Sediments with High and Low Methane Flux. Front Microbiol 2012; 3:216. [PMID: 22715336 PMCID: PMC3375579 DOI: 10.3389/fmicb.2012.00216] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 05/28/2012] [Indexed: 11/13/2022] Open
Abstract
To obtain knowledge on how regional variations in methane seepage rates influence the stratification, abundance, and diversity of anaerobic methanotrophs (ANME), we analyzed the vertical microbial stratification in a gravity core from a methane micro-seeping area at Nyegga by using 454-pyrosequencing of 16S rRNA gene tagged amplicons and quantitative PCR. These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux. A down core stratification and high relative abundance of ANME were observed in both cores, with transition from an ANME-2a/b dominated community in low-sulfide and low methane horizons to ANME-1 dominance in horizons near the sulfate-methane transition zone. The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark. A fine-scale view into the ANME communities at each location was achieved through operational taxonomical units (OTU) clustering of ANME-affiliated sequences. The majority of ANME-1 sequences from both sampling sites clustered within one OTU, while ANME-2a/b sequences were represented in unique OTUs. We suggest that free-living ANME-1 is the most abundant taxon in Nyegga cold seeps, and also the main consumer of methane. The observation of specific ANME-2a/b OTUs at each location could reflect that organisms within this clade are adapted to different geochemical settings, perhaps due to differences in methane affinity. Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments.
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Affiliation(s)
- Irene Roalkvam
- Center for Geobiology, Department of Biology, University of Bergen Bergen, Norway
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Roalkvam I, Jørgensen SL, Chen Y, Stokke R, Dahle H, Hocking WP, Lanzén A, Haflidason H, Steen IH. New insight into stratification of anaerobic methanotrophs in cold seep sediments. FEMS Microbiol Ecol 2011; 78:233-43. [PMID: 21676010 DOI: 10.1111/j.1574-6941.2011.01153.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Methane seepages typically harbor communities of anaerobic methane oxidizers (ANME); however, knowledge about fine-scale vertical variation of ANME in response to geochemical gradients is limited. We investigated microbial communities in sediments below a white microbial mat in the G11 pockmark at Nyegga by 16S rRNA gene tag pyrosequencing and real-time quantitative PCR. A vertical stratification of dominating ANME communities was observed at 4 cmbsf (cm below seafloor) and below in the following order: ANME-2a/b, ANME-1 and ANME-2c. The ANME-1 community was most numerous and comprised single or chains of cells with typical rectangular morphology, accounting up to 89.2% of the retrieved 16S rRNA gene sequences. Detection rates for sulfate-reducing Deltaproteobacteria possibly involved in anaerobic oxidation of methane were low throughout the core. However, a correlation in the abundance of Candidate division JS-1 with ANME-2 was observed, indicating involvement in metabolisms occurring in ANME-2-dominated horizons. The white microbial mat and shallow sediments were dominated by organisms affiliated with Sulfurovum (Epsilonproteobacteria) and Methylococcales (Gammaproteobacteria), suggesting that aerobic oxidation of sulfur and methane is taking place. In intermediate horizons, typical microbial groups associated with methane seeps were recovered. The data are discussed with respect to co-occurring microbial assemblages and interspecies interactions.
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Affiliation(s)
- Irene Roalkvam
- Department of Biology, Centre for Geobiology, University of Bergen, Norway
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Dahle H, Hannisdal B, Steinsbu BO, Ommedal H, Einen J, Jensen S, Larsen O, Ovreås L, Norland S. Evolution of temperature optimum in Thermotogaceae and the prediction of trait values of uncultured organisms. Extremophiles 2011; 15:509-16. [PMID: 21638056 PMCID: PMC3119804 DOI: 10.1007/s00792-011-0381-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 05/20/2011] [Indexed: 11/28/2022]
Abstract
Quantitative characterization of the mode and rate of phenotypic evolution is rarely applied to prokaryotes. Here, we present an analysis of temperature optimum (Topt) evolution in the thermophilic family Thermotogaceae, which has a large number of cultured representatives. We use log-rate-interval analysis to show that Topt evolution in Thermotogaceae is consistent with a Brownian motion (BM) evolutionary model. The properties of the BM model are used to a establish confidence intervals on the unknown phenotypic trait value of an uncultured organism, given its distance to a close relative with known trait value. Cross-validation by bootstrapping indicates that the predictions are robust.
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Affiliation(s)
- Håkon Dahle
- Centre for Geobiology, University of Bergen, Allegaten, Norway.
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Dipippo JL, Nesbø CL, Dahle H, Doolittle WF, Birkland NK, Noll KM. Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid. Int J Syst Evol Microbiol 2009; 59:2991-3000. [PMID: 19643902 DOI: 10.1099/ijs.0.008045-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic, heterotrophic bacterium, strain TBF 19.5.1(T), was isolated from oil production fluid at the Troll B oil platform in the North Sea. Cells of strain TBF 19.5.1(T) were non-motile rods with a sheath-like structure, or toga. The strain was Gram-negative and grew at 20-80 degrees C (optimum 65 degrees C), pH 5.5-8.0 (optimum pH 6.8) and NaCl concentrations of 10-60 g l(-1) (optimum 25-30 g l(-1)). For a member of the order Thermotogales, the novel isolate is capable of unprecedented growth at low temperatures, with an optimal doubling time of 175 min (specific growth rate 0.24 h(-1)) and a final optical density of >1.4 when grown on pyruvate at 37 degrees C. Various carbohydrates, proteinaceous compounds and pyruvate served as growth substrates. Thiosulfate, but not elemental sulfur, enhanced growth of the isolate. Sulfate also enhanced growth, but sulfide was not produced. The strain grew in the presence of up to approximately 15 % oxygen, but only if cysteine was included in the medium. Growth of the isolate was inhibited by acetate, lactate and propionate, while butanol and malate prevented growth. The major fermentation products formed on maltose were hydrogen, carbon dioxide and acetic acid, with traces of ethanol and propionic acid. The G+C content of the genomic DNA was 42.5 mol%. Phylogenetic analyses of the 16S and 23S rRNA gene sequences as well as 29 protein-coding ORFs placed the strain within the bacterial order Thermotogales. Based on the phylogenetic analyses and the possession of a variety of physiological characteristics not previously found in any species of this order, it is proposed that the strain represents a novel species of a new genus within the family Thermotogaceae, order Thermotogales. The name Kosmotoga olearia gen. nov., sp. nov. is proposed. The type strain of Kosmotoga olearia is TBF 19.5.1(T) (=DSM 21960(T) =ATCC BAA-1733(T)).
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Affiliation(s)
- Jonathan L Dipippo
- Department of Molecular and Cell Biology, University of Connecticut, Unit 3125, 91 N. Eagleville Road, Storrs, CT 06269-3125, USA
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Riemer-Sørensen S, Zioutas K, Hansen SH, Pedersen K, Dahle H, Liolios A. Searching for decaying axionlike dark matter from clusters of galaxies. Phys Rev Lett 2007; 99:131301. [PMID: 17930573 DOI: 10.1103/physrevlett.99.131301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 08/10/2007] [Indexed: 05/25/2023]
Abstract
We constrain the lifetime of radiatively decaying dark matter in clusters of galaxies inspired by generic Kaluza-Klein axions, which have been invoked as a possible explanation for the solar coronal x-ray emission. These particles can be produced inside stars and remain confined by the gravitational potential of clusters. By analyzing x-ray observations of merging clusters, where gravitational lensing observations have identified massive, baryon poor structures, we derive the first cosmological lifetime constraint on this kind of particles of tau > or = 10(23) sec.
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Affiliation(s)
- Signe Riemer-Sørensen
- Dark Cosmology Centre, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, DK-2100 Copenhagen, Denmark.
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Dahle H, Garshol F, Madsen M, Birkeland NK. Microbial community structure analysis of produced water from a high-temperature North Sea oil-field. Antonie van Leeuwenhoek 2007; 93:37-49. [PMID: 17588160 DOI: 10.1007/s10482-007-9177-z] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Accepted: 05/21/2007] [Indexed: 11/30/2022]
Abstract
Molecular and culture-based methods were used to investigate the microbial diversity in produced water obtained from the high-temperature Troll oil formation in the North Sea. 16S rRNA gene libraries were generated from total community DNA, using universal archaeal or bacterial oligonucleotide primer sets. Sequence analysis of 88 clones in the bacterial library indicated that they originated from members of Firmicutes (48 sequences), Bacteroidetes (17 sequences), delta-Proteobacteria (15 sequences), Spirochaetes (5 sequences), Thermotogales (2 sequences) and gamma-Proteobacteria (1 sequence). Twenty-two sequences in the archaeal library were close relatives to members of the genera Methanococcus (18 sequences), Methanolobus (3 sequences) and Thermococcus (1 sequence). Most of the bacterial sequences shared less than 95% identity with their closest match in GenBank, indicating that the produced water harbours a unique community of novel bacterial species or genera. Members of the thermophilic genera Thermosipho, Thermotoga, Anaerophaga and Thermovirga were isolated. The Troll formations are not injected with sea water. Thus, dramatic changes of the in situ conditions have been avoided, and a common source of continuous contamination from injection water can be excluded. However, the majority of the organisms detected in the gene libraries were most closely related to cultivated organisms with optimum temperatures for growth well below the in situ reservoir temperature (70 degrees C), indicating that produced water from the Troll platform harbours a substantial amount of non-indigenous organisms. This was confirmed by the isolation of a number of mesophilic and moderately thermophilic organisms that were unable to grow at reservoir temperature.
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Affiliation(s)
- Håkon Dahle
- Department of Biology and Centre for Geobiology, University of Bergen, P.O. Box 7800, Bergen, 5020, Norway
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Dahle H, Birkeland NK. Thermovirga lienii gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, amino-acid-degrading bacterium isolated from a North Sea oil well. Int J Syst Evol Microbiol 2006; 56:1539-1545. [PMID: 16825627 DOI: 10.1099/ijs.0.63894-0] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, moderately thermophilic bacterium, strain Cas60314T, was isolated from hot oil-well production water obtained from an oil reservoir in the North Sea. The cells were Gram-negative, motile, straight rods. The salinity and pH growth optima were 2.0–3.0 % NaCl and 6.5–7.0, respectively. The optimum temperature was 58 °C. Strain Cas60314T had a fermentative type of metabolism and utilized proteinous substrates, some single amino acids and a limited number of organic acids, but not sugars, fatty acids or alcohols. Cystine and elemental sulfur were reduced to sulfide. The G+C content of the DNA was 46.6 mol%. On the basis of phenotypic and phylogenetic features, it is proposed that this isolate represents a novel genus and species with the name Thermovirga lienii gen. nov., sp. nov. within the family Syntrophomonadaceae. The proposed type strain is strain Cas60314T (=DSM 17291T=ATTC BAA-1197T).
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Affiliation(s)
- Håkon Dahle
- Department of Biology, University of Bergen, PO Box 7800, N-5020 Bergen, Norway
| | - Nils-Kåre Birkeland
- Department of Biology, University of Bergen, PO Box 7800, N-5020 Bergen, Norway
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Kvam G, Dahle H, Nordrehaug JE, Randa TI, Tillung T. The shortening fraction of myocardial fibers and its layered distribution, as derived from cine-MR imaged left ventriculograms. An approach for evaluating globar left ventricular function. Acta Radiol 1997; 38:391-9. [PMID: 9191429 DOI: 10.1080/02841859709172089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
PURPOSE To evaluate the mean shortening fraction and its SD through the wall calculated from multiple cine-MR views, as an estimate of left ventricular globar function. MATERIAL AND METHODS The average myocardial fiber shortening fraction was calculated by means of a simple truncated ellipsoid nested shell model. Left ventricular parameters, acquired by cine-MR imaging, from 20 healthy volunteers served as input. Fiber angles, ventricular torsion and a gradient increase in wall thickening from epicard to endocard were part of the model. RESULTS The average fiber shortening fraction was 0.203 (0.158-0.246) +/- 0.021 diastolic lengths. It varied only moderately with variations in fiber angle values and not at all when the torsion angles were varied within physiological limits. The average shortening fraction correlates well with the systolic increase in chamber oblonguity (k = 0.837), with the ejection fraction (k = 0.877), and even better with the calculated wall thickening (k = 0.973). The average epicardial shortening fraction 0.169 (0.142-0.202) +/- 0.016 increased gradually through the wall to the endocardial value 0.250 (0.212-0.290) +/- 0.024. The increase in chamber length-width ratio from diastole to systole reduced the SD of the shortening fraction through the wall layers to a minimum. CONCLUSION The fiber shortening fraction expresses the layered contraction of the myocardial wall, the wall thickening, and also the endocardial wall motion. The ejection fraction expresses only the latter. The shortening fraction and its SD through the wall may prove a valuable additional tool for estimating ventricular globar function.
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Affiliation(s)
- G Kvam
- Department of Radiology, Haukeland University Hospital, Bergen, Norway
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Kvam G, Dahle H, Nordrehaug JE, Randa TI, Tillung T. The shortening fraction of myocardial fibers and its layered distribution, as derived from cine-mr imaged left ventriculograms. Acta Radiol 1997. [DOI: 10.3109/02841859709172089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Berge OG, Hole K, Dahle H. Nociception is enhanced after low doses and reduced after high doses of the serotonin receptor agonist 5-methoxy-N,N-dimethyltryptamine. Neurosci Lett 1980; 19:219-23. [PMID: 6302598 DOI: 10.1016/0304-3940(80)90198-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The effects on pain sensitivity of intracerebroventricular injections of 5-methoxy-N,N-dimethyltryptamine were tested by the tail-flick method. Following administration of 1.6, 3.1, 6.3, 12.5 and 25 micrograms (n = 8 for each dose), tail-flick latencies were reduced by 13-24%. Fifty and 100 micrograms caused a biphasic response (hyperalgesia followed by analgesia), whereas 400 micrograms increased mean latencies by 28-39%. The hyperalgesia observed after low doses was most likely due to reduced activity in descending serotonergic neurons following presynaptic stimulation. Higher doses caused analgesia, probably by stimulating spinal postsynaptic serotonergic receptors as well.
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Hole K, Dahle H, Kløve H. Lead intoxication as an etiologic factor in hyperkinetic behavior in children: a negative report. Acta Paediatr Scand 1979; 68:759-60. [PMID: 525344 DOI: 10.1111/j.1651-2227.1979.tb18452.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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