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Ding S, Hamm JN, Bale NJ, Sinninghe Damsté JS, Spang A. Selective lipid recruitment by an archaeal DPANN symbiont from its host. Nat Commun 2024; 15:3405. [PMID: 38649682 PMCID: PMC11035636 DOI: 10.1038/s41467-024-47750-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
The symbiont Ca. Nanohaloarchaeum antarcticus is obligately dependent on its host Halorubrum lacusprofundi for lipids and other metabolites due to its lack of certain biosynthetic genes. However, it remains unclear which specific lipids or metabolites are acquired from its host, and how the host responds to infection. Here, we explored the lipidome dynamics of the Ca. Nha. antarcticus - Hrr. lacusprofundi symbiotic relationship during co-cultivation. By using a comprehensive untargeted lipidomic methodology, our study reveals that Ca. Nha. antarcticus selectively recruits 110 lipid species from its host, i.e., nearly two-thirds of the total number of host lipids. Lipid profiles of co-cultures displayed shifts in abundances of bacterioruberins and menaquinones and changes in degree of bilayer-forming glycerolipid unsaturation. This likely results in increased membrane fluidity and improved resistance to membrane disruptions, consistent with compensation for higher metabolic load and mechanical stress on host membranes when in contact with Ca. Nha. antarcticus cells. Notably, our findings differ from previous observations of other DPANN symbiont-host systems, where no differences in lipidome composition were reported. Altogether, our work emphasizes the strength of employing untargeted lipidomics approaches to provide details into the dynamics underlying a DPANN symbiont-host system.
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Affiliation(s)
- Su Ding
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands.
| | - Joshua N Hamm
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands.
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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2
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Abuter R, Allouche F, Amorim A, Bailet C, Berdeu A, Berger JP, Berio P, Bigioli A, Boebion O, Bolzer ML, Bonnet H, Bourdarot G, Bourget P, Brandner W, Cao Y, Conzelmann R, Comin M, Clénet Y, Courtney-Barrer B, Davies R, Defrère D, Delboulbé A, Delplancke-Ströbele F, Dembet R, Dexter J, de Zeeuw PT, Drescher A, Eckart A, Édouard C, Eisenhauer F, Fabricius M, Feuchtgruber H, Finger G, Förster Schreiber NM, Garcia P, Garcia Lopez R, Gao F, Gendron E, Genzel R, Gil JP, Gillessen S, Gomes T, Gonté F, Gouvret C, Guajardo P, Guieu S, Hackenberg W, Haddad N, Hartl M, Haubois X, Haußmann F, Heißel G, Henning T, Hippler S, Hönig SF, Horrobin M, Hubin N, Jacqmart E, Jocou L, Kaufer A, Kervella P, Kolb J, Korhonen H, Lacour S, Lagarde S, Lai O, Lapeyrère V, Laugier R, Le Bouquin JB, Leftley J, Léna P, Lewis S, Liu D, Lopez B, Lutz D, Magnard Y, Mang F, Marcotto A, Maurel D, Mérand A, Millour F, More N, Netzer H, Nowacki H, Nowak M, Oberti S, Ott T, Pallanca L, Paumard T, Perraut K, Perrin G, Petrov R, Pfuhl O, Pourré N, Rabien S, Rau C, Riquelme M, Robbe-Dubois S, Rochat S, Salman M, Sanchez-Bermudez J, Santos DJD, Scheithauer S, Schöller M, Schubert J, Schuhler N, Shangguan J, Shchekaturov P, Shimizu TT, Sevin A, Soulez F, Spang A, Stadler E, Sternberg A, Straubmeier C, Sturm E, Sykes C, Tacconi LJ, Tristram KRW, Vincent F, von Fellenberg S, Uysal S, Widmann F, Wieprecht E, Wiezorrek E, Woillez J, Zins G. A dynamical measure of the black hole mass in a quasar 11 billion years ago. Nature 2024; 627:281-285. [PMID: 38286342 DOI: 10.1038/s41586-024-07053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024]
Abstract
Tight relationships exist in the local Universe between the central stellar properties of galaxies and the mass of their supermassive black hole (SMBH)1-3. These suggest that galaxies and black holes co-evolve, with the main regulation mechanism being energetic feedback from accretion onto the black hole during its quasar phase4-6. A crucial question is how the relationship between black holes and galaxies evolves with time; a key epoch to examine this relationship is at the peaks of star formation and black hole growth 8-12 billion years ago (redshifts 1-3)7. Here we report a dynamical measurement of the mass of the black hole in a luminous quasar at a redshift of 2, with a look back in time of 11 billion years, by spatially resolving the broad-line region (BLR). We detect a 40-μas (0.31-pc) spatial offset between the red and blue photocentres of the Hα line that traces the velocity gradient of a rotating BLR. The flux and differential phase spectra are well reproduced by a thick, moderately inclined disk of gas clouds within the sphere of influence of a central black hole with a mass of 3.2 × 108 solar masses. Molecular gas data reveal a dynamical mass for the host galaxy of 6 × 1011 solar masses, which indicates an undermassive black hole accreting at a super-Eddington rate. This suggests a host galaxy that grew faster than the SMBH, indicating a delay between galaxy and black hole formation for some systems.
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Affiliation(s)
- R Abuter
- European Southern Observatory, Garching, Germany
| | - F Allouche
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - A Amorim
- Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- CENTRA - Centro de Astrofísica e Gravitação, Instituto Superior Técnico (IST), Universidade de Lisboa, Lisboa, Portugal
| | - C Bailet
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - A Berdeu
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - J-P Berger
- Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - P Berio
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - A Bigioli
- Institute of Astronomy, KU Leuven, Leuven, Belgium
| | - O Boebion
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - M-L Bolzer
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
- Department of Physics, Technical University Munich, Garching, Germany
- Univ. Lyon, Univ. Lyon 1, ENS de Lyon, CNRS, Centre de Recherche Astrophysique de Lyon UMR5574, Saint-Genis-Laval, France
| | - H Bonnet
- European Southern Observatory, Garching, Germany
| | - G Bourdarot
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - P Bourget
- European Southern Observatory, Santiago, Chile
| | - W Brandner
- Max Planck Institute for Astronomy, Heidelberg, Germany
| | - Y Cao
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - R Conzelmann
- European Southern Observatory, Garching, Germany
| | - M Comin
- European Southern Observatory, Garching, Germany
| | - Y Clénet
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - B Courtney-Barrer
- European Southern Observatory, Santiago, Chile
- Research School of Astronomy and Astrophysics, College of Science, Australian National University, Canberra, Australian Capital Territory, Australia
| | - R Davies
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - D Defrère
- Institute of Astronomy, KU Leuven, Leuven, Belgium
| | - A Delboulbé
- Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | | | - R Dembet
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - J Dexter
- Department of Astrophysical & Planetary Sciences, JILA, University of Colorado Boulder, Boulder, CO, USA
| | | | - A Drescher
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - A Eckart
- Max Planck Institute for Radio Astronomy, Bonn, Germany
- 1st Institute of Physics, University of Cologne, Cologne, Germany
| | - C Édouard
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - F Eisenhauer
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - M Fabricius
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - H Feuchtgruber
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - G Finger
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | | | - P Garcia
- CENTRA - Centro de Astrofísica e Gravitação, Instituto Superior Técnico (IST), Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Engenharia, Universidade do Porto, Porto, Portugal
| | - R Garcia Lopez
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - F Gao
- Max Planck Institute for Radio Astronomy, Bonn, Germany
| | - E Gendron
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - R Genzel
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
- Departments of Physics, University of California, Berkeley, Berkeley, CA, USA
- Department of Astronomy, University of California, Berkeley, Berkeley, CA, USA
| | - J P Gil
- European Southern Observatory, Santiago, Chile
| | - S Gillessen
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - T Gomes
- CENTRA - Centro de Astrofísica e Gravitação, Instituto Superior Técnico (IST), Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Engenharia, Universidade do Porto, Porto, Portugal
| | - F Gonté
- European Southern Observatory, Garching, Germany
| | - C Gouvret
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - P Guajardo
- European Southern Observatory, Santiago, Chile
| | - S Guieu
- Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - W Hackenberg
- European Southern Observatory, Garching, Germany
| | - N Haddad
- European Southern Observatory, Santiago, Chile
| | - M Hartl
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - X Haubois
- European Southern Observatory, Santiago, Chile
| | - F Haußmann
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - G Heißel
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
- Advanced Concepts Team, European Space Agency, TEC-SF, ESTEC, Noordwijk, The Netherlands
| | - Th Henning
- Max Planck Institute for Astronomy, Heidelberg, Germany
| | - S Hippler
- Max Planck Institute for Astronomy, Heidelberg, Germany
| | - S F Hönig
- School of Physics and Astronomy, University of Southampton, Southampton, UK
| | - M Horrobin
- 1st Institute of Physics, University of Cologne, Cologne, Germany
| | - N Hubin
- European Southern Observatory, Garching, Germany
| | - E Jacqmart
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - L Jocou
- Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - A Kaufer
- European Southern Observatory, Santiago, Chile
| | - P Kervella
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - J Kolb
- European Southern Observatory, Garching, Germany
| | - H Korhonen
- European Southern Observatory, Santiago, Chile
- Max Planck Institute for Astronomy, Heidelberg, Germany
| | - S Lacour
- European Southern Observatory, Garching, Germany
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - S Lagarde
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - O Lai
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - V Lapeyrère
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - R Laugier
- Institute of Astronomy, KU Leuven, Leuven, Belgium
| | | | - J Leftley
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - P Léna
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - S Lewis
- European Southern Observatory, Garching, Germany
| | - D Liu
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - B Lopez
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - D Lutz
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - Y Magnard
- Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - F Mang
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
- Department of Physics, Technical University Munich, Garching, Germany
| | - A Marcotto
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - D Maurel
- Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - A Mérand
- European Southern Observatory, Garching, Germany
| | - F Millour
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - N More
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - H Netzer
- School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | - H Nowacki
- Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - M Nowak
- Institute of Astronomy, University of Cambridge, Cambridge, UK
| | - S Oberti
- European Southern Observatory, Garching, Germany
| | - T Ott
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - L Pallanca
- European Southern Observatory, Santiago, Chile
| | - T Paumard
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - K Perraut
- Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - G Perrin
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - R Petrov
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - O Pfuhl
- European Southern Observatory, Garching, Germany
| | - N Pourré
- Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - S Rabien
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - C Rau
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - M Riquelme
- European Southern Observatory, Garching, Germany
| | - S Robbe-Dubois
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - S Rochat
- Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - M Salman
- Institute of Astronomy, KU Leuven, Leuven, Belgium
| | - J Sanchez-Bermudez
- Max Planck Institute for Astronomy, Heidelberg, Germany
- Instituto de Astronomía, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - D J D Santos
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - S Scheithauer
- Max Planck Institute for Astronomy, Heidelberg, Germany
| | - M Schöller
- European Southern Observatory, Garching, Germany
| | - J Schubert
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - N Schuhler
- European Southern Observatory, Santiago, Chile
| | - J Shangguan
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | | | - T T Shimizu
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany.
| | - A Sevin
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | - F Soulez
- Univ. Lyon, Univ. Lyon 1, ENS de Lyon, CNRS, Centre de Recherche Astrophysique de Lyon UMR5574, Saint-Genis-Laval, France
| | - A Spang
- Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France
| | - E Stadler
- Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - A Sternberg
- School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
- Center for Computational Astrophysics, Flatiron Institute, New York, NY, USA
| | - C Straubmeier
- 1st Institute of Physics, University of Cologne, Cologne, Germany
| | - E Sturm
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - C Sykes
- School of Physics and Astronomy, University of Southampton, Southampton, UK
| | - L J Tacconi
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | | | - F Vincent
- LESIA - Observatoire de Paris, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Meudon, France
| | | | - S Uysal
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - F Widmann
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - E Wieprecht
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - E Wiezorrek
- Max Planck Institute for Extraterrestrial Physics, Garching, Germany
| | - J Woillez
- European Southern Observatory, Garching, Germany
| | - G Zins
- European Southern Observatory, Garching, Germany
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3
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Baum B, Spang A. On the origin of the nucleus: a hypothesis. Microbiol Mol Biol Rev 2023; 87:e0018621. [PMID: 38018971 PMCID: PMC10732040 DOI: 10.1128/mmbr.00186-21] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
SUMMARYIn this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions-emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.
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Affiliation(s)
- Buzz Baum
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
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4
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Mahendrarajah TA, Moody ERR, Schrempf D, Szánthó LL, Dombrowski N, Davín AA, Pisani D, Donoghue PCJ, Szöllősi GJ, Williams TA, Spang A. ATP synthase evolution on a cross-braced dated tree of life. Nat Commun 2023; 14:7456. [PMID: 37978174 PMCID: PMC10656485 DOI: 10.1038/s41467-023-42924-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.
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Affiliation(s)
- Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Dominik Schrempf
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
| | - Lénárd L Szánthó
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Karolina ut 29, H-1113, Budapest, Hungary
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Adrián A Davín
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Gergely J Szöllősi
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK.
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands.
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
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5
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Spang A. Uncovering the hidden world of nanosized archaea. Nat Rev Microbiol 2023; 21:638. [PMID: 37700049 DOI: 10.1038/s41579-023-00912-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Affiliation(s)
- Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Netherlands Institute for Sea Research, Den Burg, Netherlands.
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands.
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6
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Donoghue PCJ, Kay C, Spang A, Szöllősi G, Nenarokova A, Moody ERR, Pisani D, Williams TA. Defining eukaryotes to dissect eukaryogenesis. Curr Biol 2023; 33:R919-R929. [PMID: 37699353 DOI: 10.1016/j.cub.2023.07.048] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
The origin of eukaryotes is among the most contentious debates in evolutionary biology, attracting multiple seemingly incompatible theories seeking to explain the sequence in which eukaryotic characteristics were acquired. Much of the controversy arises from differing views on the defining characteristics of eukaryotes. We argue that eukaryotes should be defined phylogenetically, and that doing so clarifies where competing hypotheses of eukaryogenesis agree and how we may test among aspects of disagreement. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes and are distinguishable on that basis. However, other hypotheses differ only in the order of key evolutionary steps, like mitochondrial endosymbiosis and nuclear assembly, which cannot currently be distinguished phylogenetically. Stages within eukaryogenesis may be made identifiable through the absolute dating of gene duplicates that map to eukaryotic traits, such as in genes of host or mitochondrial origin that duplicated and diverged functionally prior to emergence of the last eukaryotic common ancestor. In this way, it may finally be possible to distinguish heat from light in the debate over eukaryogenesis.
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Affiliation(s)
- Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | - Chris Kay
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg 1790 AB, The Netherlands
| | - Gergely Szöllősi
- Department of Biological Physics, Eötvös Lorand University, H-1117 Budapest, Hungary; MTA-ELTE "Lendü let" Evolutionary Genomics Research Group, H-1117 Budapest, Hungary; Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Hungary
| | - Anna Nenarokova
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK; Bristol Palaeobiology Group, School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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7
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Williams TA, Davin AA, Morel B, Szánthó LL, Spang A, Stamatakis A, Hugenholtz P, Szöllősi GJ. Parameter estimation and species tree rooting using ALE and GeneRax. Genome Biol Evol 2023:evad134. [PMID: 37463417 PMCID: PMC10373948 DOI: 10.1093/gbe/evad134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 06/05/2022] [Revised: 07/05/2023] [Accepted: 07/13/2023] [Indexed: 07/20/2023] Open
Abstract
ALE and GeneRax are tools for probabilistic gene tree-species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene versus species tree discordance to infer gene duplication, transfer and loss events, map gene family origins and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root; in Bacteria - where there is less certainty about the root position - ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.
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Affiliation(s)
- Tom A Williams
- School of Biological Sciences, University of Bristol, BS81TQ, UK
| | - Adrian A Davin
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Lénárd L Szánthó
- Dept. of Biological Physics, Eötvös Loránd University, 1117 Budapest, Hungary
- MTA-ELTE "Lendület" Evolutionary Genomics Research Group, 1117 Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, 1121 Budapest, Hungary
| | - Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry; AB Den Burg, The Netherlands
| | - Alexandros Stamatakis
- Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology Hellas, 70013, Heraklion, Greece
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gergely J Szöllősi
- Dept. of Biological Physics, Eötvös Loránd University, 1117 Budapest, Hungary
- MTA-ELTE "Lendület" Evolutionary Genomics Research Group, 1117 Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, 1121 Budapest, Hungary
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8
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van der Gulik PT, Egas M, Kraaijeveld K, Dombrowski N, Groot AT, Spang A, Hoff WD, Gallie J. On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes. RNA Biol 2023; 20:48-58. [PMID: 36727270 PMCID: PMC9897764 DOI: 10.1080/15476286.2023.2172370] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Automated genome annotation is essential for extracting biological information from sequence data. The identification and annotation of tRNA genes is frequently performed by the software package tRNAscan-SE, the output of which is listed for selected genomes in the Genomic tRNA database (GtRNAdb). Here, we highlight a pervasive error in prokaryotic tRNA gene sets on GtRNAdb: the mis-categorization of partial, non-canonical tRNA genes as standard, canonical tRNA genes. Firstly, we demonstrate the issue using the tRNA gene sets of 20 organisms from the archaeal taxon Thermococcaceae. According to GtRNAdb, these organisms collectively deviate from the expected set of tRNA genes in 15 instances, including the listing of eleven putative canonical tRNA genes. However, after detailed manual annotation, only one of these eleven remains; the others are either partial, non-canonical tRNA genes resulting from the integration of genetic elements or CRISPR-Cas activity (seven instances), or attributable to ambiguities in input sequences (three instances). Secondly, we show that similar examples of the mis-categorization of predicted tRNA sequences occur throughout the prokaryotic sections of GtRNAdb. While both canonical and non-canonical prokaryotic tRNA gene sequences identified by tRNAscan-SE are biologically interesting, the challenge of reliably distinguishing between them remains. We recommend employing a combination of (i) screening input sequences for the genetic elements typically associated with non-canonical tRNA genes, and ambiguities, (ii) activating the tRNAscan-SE automated pseudogene detection function, and (iii) scrutinizing predicted tRNA genes with low isotype scores. These measures greatly reduce manual annotation efforts, and lead to improved prokaryotic tRNA gene set predictions.
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Affiliation(s)
- Peter T.S. van der Gulik
- Department of Algorithms and Complexity, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands,CONTACT Peter T.S. van der Gulik Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
| | - Martijn Egas
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Ken Kraaijeveld
- Leiden Centre for Applied Bioscience, University of Applied Sciences Leiden, Leiden, The Netherlands
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Astrid T. Groot
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Anja Spang
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands,Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA,Wouter Hoff
| | - Jenna Gallie
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany,Jenna Gallie
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9
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Abstract
The origin of complex cellular life is a key puzzle in evolutionary research, which has broad implications for various neighbouring scientific disciplines. Naturally, views on this topic vary widely depending on the world view and context from which this topic is approached. In the following, I will share my perspective about our current scientific knowledge on the origin of eukaryotic cells, that is, eukaryogenesis, from a biological point of view focusing on the question as to whether an archaeon was the ancestor of eukaryotes.
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Affiliation(s)
- Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, AB Den Burg, The Netherlands.,Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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10
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Krause S, Gfrerer S, von Kügelgen A, Reuse C, Dombrowski N, Villanueva L, Bunk B, Spröer C, Neu TR, Kuhlicke U, Schmidt-Hohagen K, Hiller K, Bharat TAM, Rachel R, Spang A, Gescher J. The importance of biofilm formation for cultivation of a Micrarchaeon and its interactions with its Thermoplasmatales host. Nat Commun 2022; 13:1735. [PMID: 35365607 PMCID: PMC8975820 DOI: 10.1038/s41467-022-29263-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 05/04/2021] [Accepted: 02/28/2022] [Indexed: 01/05/2023] Open
Abstract
Micrarchaeota is a distinctive lineage assigned to the DPANN archaea, which includes poorly characterised microorganisms with reduced genomes that likely depend on interactions with hosts for growth and survival. Here, we report the enrichment of a stable co-culture of a member of the Micrarchaeota (Ca. Micrarchaeum harzensis) together with its Thermoplasmatales host (Ca. Scheffleriplasma hospitalis), as well as the isolation of the latter. We show that symbiont-host interactions depend on biofilm formation as evidenced by growth experiments, comparative transcriptomic analyses and electron microscopy. In addition, genomic, metabolomic, extracellular polymeric substances and lipid content analyses indicate that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host. Our study of the cell biology and physiology of a Micrarchaeon and its host adds to our limited knowledge of archaeal symbioses. The Micrarchaeota lineage includes poorly characterized archaea with reduced genomes that likely depend on host interactions for survival. Here, the authors report a stable co-culture of a member of the Micrarchaeota and its host, and use multi-omic and physiological analyses to shed light on this symbiosis.
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Affiliation(s)
- Susanne Krause
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany
| | - Sabrina Gfrerer
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany.,Institute for Biological Interfaces, Karlsruhe, Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Carsten Reuse
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Boyke Bunk
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Thomas R Neu
- Helmholtz-Centre for Environmental, Research UFZ, Magdeburg, Germany
| | - Ute Kuhlicke
- Helmholtz-Centre for Environmental, Research UFZ, Magdeburg, Germany
| | - Kerstin Schmidt-Hohagen
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Karsten Hiller
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom.,Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Reinhard Rachel
- Center for Electron Microscopy, University of Regensburg, Regensburg, Germany
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johannes Gescher
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany. .,Institute for Biological Interfaces, Karlsruhe, Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany. .,Institute of Technical Microbiology, Technical University of Hamburg, Hamburg, Germany.
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11
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Spang A, Mahendrarajah TA, Offre P, Stairs CW. Evolving perspective on the origin and diversification of cellular life and the virosphere. Genome Biol Evol 2022; 14:6537539. [PMID: 35218347 PMCID: PMC9169541 DOI: 10.1093/gbe/evac034] [Citation(s) in RCA: 3] [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] [Accepted: 02/18/2022] [Indexed: 11/14/2022] Open
Abstract
The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.
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Affiliation(s)
- Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, The Netherlands and 1790 AB Den Burg.,Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden SE-75123, Uppsala
| | - Tara A Mahendrarajah
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, The Netherlands and 1790 AB Den Burg
| | - Pierre Offre
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, The Netherlands and 1790 AB Den Burg
| | - Courtney W Stairs
- Department of Biology, Lund University, Sweden Sölvegatan 35, 223 62 Lund
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12
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Moody ERR, Mahendrarajah TA, Dombrowski N, Clark JW, Petitjean C, Offre P, Szöllősi GJ, Spang A, Williams TA. An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes. eLife 2022; 11:66695. [PMID: 35190025 PMCID: PMC8890751 DOI: 10.7554/elife.66695] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [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: 01/19/2021] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
Abstract
Core gene phylogenies provide a window into early evolution, but different gene sets and analytical methods have yielded substantially different views of the tree of life. Trees inferred from a small set of universal core genes have typically supported a long branch separating the archaeal and bacterial domains. By contrast, recent analyses of a broader set of non-ribosomal genes have suggested that Archaea may be less divergent from Bacteria, and that estimates of inter-domain distance are inflated due to accelerated evolution of ribosomal proteins along the inter-domain branch. Resolving this debate is key to determining the diversity of the archaeal and bacterial domains, the shape of the tree of life, and our understanding of the early course of cellular evolution. Here, we investigate the evolutionary history of the marker genes key to the debate. We show that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set. By contrast, analysis of a broad range of manually curated marker gene datasets from an evenly sampled set of 700 Archaea and Bacteria reveals that current methods likely underestimate the AB branch length due to substitutional saturation and poor model fit; that the best-performing phylogenetic markers tend to support longer inter-domain branch lengths; and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable. Furthermore, our phylogeny inferred from the 27 highest-ranked marker genes recovers a clade of DPANN at the base of the Archaea and places the bacterial Candidate Phyla Radiation (CPR) within Bacteria as the sister group to the Chloroflexota.
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Affiliation(s)
- Edmund R R Moody
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - James W Clark
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Celine Petitjean
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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13
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Abstract
The origin of cellular complexity characterizing eukaryotic cells remains a central unresolved issue in the study of diversification of cellular life on Earth. The isolation by Imachi et al.1 of a member of the Asgard archaea2 - a contemporary relative of organisms thought to have given rise to eukaryotic cells about 2 billion years ago - now promises new insight. The complete genome sequence of the isolated Lokiarchaeum strain confirms that the eukaryotic signature proteins (ESPs) previously identified in the Lokiarchaeota3 and other Asgard archaea2 are indeed encoded by these archaeal genomes and do not represent contamination from eukaryotes. These ESPs encode homologs of eukaryotic actins, small GTPases and the ESCRT complex proteins and are required for the functioning of complex eukaryotic cells. The new, slowly growing, anaerobic laboratory strain allows a first direct look at these organisms and provides key insights into the morphology and metabolism of an Asgard archaeal organism. The work has provided valuable information for other laboratories that aim to isolate and characterize related organisms from other environments.
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Affiliation(s)
| | | | | | - Anja Spang
- Netherlands Institute of Sea Research (NIOZ)
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14
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Coleman GA, Davín AA, Mahendrarajah TA, Szánthó LL, Spang A, Hugenholtz P, Szöllősi GJ, Williams TA. A rooted phylogeny resolves early bacterial evolution. Science 2021; 372:372/6542/eabe0511. [PMID: 33958449 DOI: 10.1126/science.abe0511] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/05/2020] [Accepted: 04/01/2021] [Indexed: 12/17/2022]
Abstract
A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene families to identify the root, extent of horizontal gene transfer (HGT), and the nature of the last bacterial common ancestor (LBCA). Our analyses root the tree between the major clades Terrabacteria and Gracilicutes and suggest that LBCA was a free-living flagellated, rod-shaped double-membraned organism. Contrary to recent proposals, our analyses reject a basal placement of the Candidate Phyla Radiation, which instead branches sister to Chloroflexota within Terrabacteria. While most gene families (92%) have evidence of HGT, overall, two-thirds of gene transmissions have been vertical, suggesting that a rooted tree provides a meaningful frame of reference for interpreting bacterial evolution.
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Affiliation(s)
- Gareth A Coleman
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Adrián A Davín
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, 1790 AB Den Burg, Netherlands
| | - Lénárd L Szánthó
- Department of Biological Physics, Eötvös Loránd University, 1117 Budapest, Hungary.,MTA-ELTE "Lendület" Evolutionary Genomics Research Group, 1117 Budapest, Hungary
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, 1790 AB Den Burg, Netherlands.,Department of Cell- and Molecular Biology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, 1117 Budapest, Hungary. .,MTA-ELTE "Lendület" Evolutionary Genomics Research Group, 1117 Budapest, Hungary.,Institute of Evolution, Centre for Ecological Research, 1121 Budapest, Hungary
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK.
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15
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Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 6:136. [PMID: 33184503 PMCID: PMC7752755 DOI: 10.1038/s41564-020-00827-2] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA.
| | - John Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
| | | | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - R Thane Papke
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jean Armengaud
- CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.,Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Paul Carini
- Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Christopher A Dunlap
- National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ute Hentschel
- GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
| | | | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Elena P Ivanova
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | | | | | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Andrew D Steen
- Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anja Spang
- Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Feng-Ping Wang
- International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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16
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Martijn J, Schön ME, Lind AE, Vosseberg J, Williams TA, Spang A, Ettema TJG. Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition. Nat Commun 2020; 11:5490. [PMID: 33127909 PMCID: PMC7599335 DOI: 10.1038/s41467-020-19200-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/01/2020] [Indexed: 01/09/2023] Open
Abstract
Halobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. In contrast, the last Haloarchaea common ancestor gained a large number of genes and expanded its aerobic respiration and salt/UV resistance gene repertoire. Our results suggest that complex and gradual patterns of gain and loss shaped the methanogen-to-halophile transition.
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Affiliation(s)
- Joran Martijn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Max E Schön
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Anders E Lind
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Julian Vosseberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Anja Spang
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Thijs J G Ettema
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
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17
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Dombrowski N, Williams TA, Sun J, Woodcroft BJ, Lee JH, Minh BQ, Rinke C, Spang A. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nat Commun 2020; 11:3939. [PMID: 32770105 PMCID: PMC7414124 DOI: 10.1038/s41467-020-17408-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/25/2020] [Indexed: 01/08/2023] Open
Abstract
The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly and early emergence of the various DPANN clades and their role in life's evolution are debated. Here, we reconstructed and analysed genomes of an uncharacterized archaeal phylum (Candidatus Undinarchaeota), revealing that its members have small genomes and, while potentially being able to conserve energy through fermentation, likely depend on partner organisms for the acquisition of certain metabolites. Our phylogenomic analyses robustly place Undinarchaeota as an independent lineage between two highly supported 'DPANN' clans. Further, our analyses suggest that DPANN have exchanged core genes with their hosts, adding to the difficulty of placing DPANN in the tree of life. This pattern can be sufficiently dominant to allow identifying known symbiont-host clades based on routes of gene transfer. Together, our work provides insights into the origins and evolution of DPANN and their hosts.
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Affiliation(s)
- Nina Dombrowski
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB, Den Burg, The Netherlands
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Benjamin J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jun-Hoe Lee
- Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Bui Quang Minh
- Research School of Computer Science and Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB, Den Burg, The Netherlands.
- Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden.
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18
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Stairs CW, Dharamshi JE, Tamarit D, Eme L, Jørgensen SL, Spang A, Ettema TJG. Chlamydial contribution to anaerobic metabolism during eukaryotic evolution. Sci Adv 2020; 6:eabb7258. [PMID: 32923644 PMCID: PMC7449678 DOI: 10.1126/sciadv.abb7258] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
The origin of eukaryotes is a major open question in evolutionary biology. Multiple hypotheses posit that eukaryotes likely evolved from a syntrophic relationship between an archaeon and an alphaproteobacterium based on H2 exchange. However, there are no strong indications that modern eukaryotic H2 metabolism originated from archaea or alphaproteobacteria. Here, we present evidence for the origin of H2 metabolism genes in eukaryotes from an ancestor of the Anoxychlamydiales-a group of anaerobic chlamydiae, newly described here, from marine sediments. Among Chlamydiae, these bacteria uniquely encode genes for H2 metabolism and other anaerobiosis-associated pathways. Phylogenetic analyses of several components of H2 metabolism reveal that Anoxychlamydiales homologs are the closest relatives to eukaryotic sequences. We propose that an ancestor of the Anoxychlamydiales contributed these key genes during the evolution of eukaryotes, supporting a mosaic evolutionary origin of eukaryotic metabolism.
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Affiliation(s)
- Courtney W. Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jennah E. Dharamshi
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Daniel Tamarit
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, Netherlands
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
- Unité d’Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Orsay, France
| | - Steffen L. Jørgensen
- Department of Earth Science, Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, NL-1790 AB Den Burg, Netherlands
| | - Thijs J. G. Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, Netherlands
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19
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Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 5:987-994. [PMID: 32514073 PMCID: PMC7381421 DOI: 10.1038/s41564-020-0733-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [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: 06/14/2019] [Accepted: 05/01/2020] [Indexed: 11/09/2022]
Abstract
The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.
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Affiliation(s)
- Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA.
| | - John Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
| | | | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - R Thane Papke
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jean Armengaud
- CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.,Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Paul Carini
- Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Christopher A Dunlap
- National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ute Hentschel
- GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
| | | | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Elena P Ivanova
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | | | | | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Andrew D Steen
- Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anja Spang
- Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Feng-Ping Wang
- International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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20
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Dharamshi JE, Tamarit D, Eme L, Stairs CW, Martijn J, Homa F, Jørgensen SL, Spang A, Ettema TJG. Marine Sediments Illuminate Chlamydiae Diversity and Evolution. Curr Biol 2020; 30:1032-1048.e7. [PMID: 32142706 DOI: 10.1016/j.cub.2020.02.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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: 09/23/2019] [Revised: 12/22/2019] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
Abstract
The bacterial phylum Chlamydiae is so far composed of obligate symbionts of eukaryotic hosts. Well known for Chlamydiaceae, pathogens of humans and other animals, Chlamydiae also include so-called environmental lineages that primarily infect microbial eukaryotes. Environmental surveys indicate that Chlamydiae are found in a wider range of environments than anticipated previously. However, the vast majority of this chlamydial diversity has been underexplored, biasing our current understanding of their biology, ecological importance, and evolution. Here, we report that previously undetected and active chlamydial lineages dominate microbial communities in deep anoxic marine sediments taken from the Arctic Mid-Ocean Ridge. Reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic units, these Chlamydiae represent important community members. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, expanding by over a third the known genomic diversity in this phylum. Phylogenomic analyses revealed several novel clades across the phylum, including a previously unknown sister lineage of the Chlamydiaceae, providing new insights into the origin of pathogenicity in this family. We were unable to identify putative eukaryotic hosts for these marine sediment chlamydiae, despite identifying genomic features that may be indicative of host-association. The high abundance and genomic diversity of Chlamydiae in these anoxic marine sediments indicate that some members could play an important, and thus far overlooked, ecological role in such environments and may indicate alternate lifestyle strategies.
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Affiliation(s)
- Jennah E Dharamshi
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Daniel Tamarit
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Orsay 91400, France
| | - Courtney W Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Felix Homa
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Steffen L Jørgensen
- Department of Earth Science, Centre for Deep Sea Research, University of Bergen, Bergen 5020, Norway
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg 1790 AB, the Netherlands
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands.
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21
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Schwank K, Bornemann TLV, Dombrowski N, Spang A, Banfield JF, Probst AJ. An archaeal symbiont-host association from the deep terrestrial subsurface. ISME J 2019; 13:2135-2139. [PMID: 31048756 PMCID: PMC6776059 DOI: 10.1038/s41396-019-0421-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/26/2019] [Accepted: 03/29/2019] [Indexed: 01/27/2023]
Abstract
DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.
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Affiliation(s)
- Katrin Schwank
- Department of Chemistry, Biofilm Centre, Group for Aquatic Microbial Ecology (GAME), University of Duisburg-Essen, Duisburg, Germany
| | - Till L V Bornemann
- Department of Chemistry, Biofilm Centre, Group for Aquatic Microbial Ecology (GAME), University of Duisburg-Essen, Duisburg, Germany
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry (MMB), Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, Netherlands
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry (MMB), Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, Netherlands
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Jillian F Banfield
- Department for Earth and Planetary Sciences, University of California, Berkeley, USA
| | - Alexander J Probst
- Department of Chemistry, Biofilm Centre, Group for Aquatic Microbial Ecology (GAME), University of Duisburg-Essen, Duisburg, Germany.
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22
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Spang A, Offre P. Towards a systematic understanding of differences between archaeal and bacterial diversity. Environ Microbiol Rep 2019; 11:9-12. [PMID: 30394664 PMCID: PMC7379672 DOI: 10.1111/1758-2229.12701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 06/12/2018] [Accepted: 10/02/2018] [Indexed: 06/08/2023]
Abstract
In this crystal ball, we discuss emerging methodologies that can help reaching a synthesis on the biodiversity of Archaea and Bacteria and thereby inform a central enigma in microbiology, i.e. the fundamental split between these primary domains of life and the apparent lower diversity of the Archaea.
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Affiliation(s)
- Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistryand Utrecht UniversityNL‐1790 ABDen BurgThe Netherlands
- Department of Cell and Molecular Biology, Science for Life LaboratoryUppsala UniversitySE‐75123UppsalaSweden
| | - Pierre Offre
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistryand Utrecht UniversityNL‐1790 ABDen BurgThe Netherlands
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23
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Dombrowski N, Lee JH, Williams TA, Offre P, Spang A. Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiol Lett 2019; 366:5281434. [PMID: 30629179 PMCID: PMC6349945 DOI: 10.1093/femsle/fnz008] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [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: 09/19/2018] [Accepted: 01/07/2019] [Indexed: 12/16/2022] Open
Abstract
Archaea-a primary domain of life besides Bacteria-have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.
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Affiliation(s)
- Nina Dombrowski
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Jun-Hoe Lee
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, P.O. Box 596, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, Bristol BS8 1TQ, UK
| | - Pierre Offre
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
| | - Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, P.O. Box 596, Husargatan 3, SE-75123 Uppsala, Sweden
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Narrowe AB, Spang A, Stairs CW, Caceres EF, Baker BJ, Miller CS, Ettema TJG. Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids. Genome Biol Evol 2018; 10:2380-2393. [PMID: 30060184 PMCID: PMC6143161 DOI: 10.1093/gbe/evy154] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/22/2022] Open
Abstract
Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.
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Affiliation(s)
- Adrienne B Narrowe
- Department of Integrative Biology, University of Colorado Denver, Denver
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, AB Den Burg, The Netherlands
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Courtney W Stairs
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Eva F Caceres
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas
| | | | - Thijs J G Ettema
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
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Spang A, Eme L, Saw JH, Caceres EF, Zaremba-Niedzwiedzka K, Lombard J, Guy L, Ettema TJG. Asgard archaea are the closest prokaryotic relatives of eukaryotes. PLoS Genet 2018; 14:e1007080. [PMID: 29596421 PMCID: PMC5875740 DOI: 10.1371/journal.pgen.1007080] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/17/2017] [Indexed: 11/18/2022] Open
Affiliation(s)
- Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jimmy H Saw
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Eva F Caceres
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Jonathan Lombard
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Abstract
The concept of symbiosis – defined in 1879 by de Bary as ‘the living together of unlike organisms’ – has a rich and convoluted history in biology. In part, because it questioned the concept of the individual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, diverse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for example, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists’ workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired. Summary: At a recent Company of Biologists workshop, evolutionary biologists discussed the major outstanding questions in symbiosis research.
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Affiliation(s)
- Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - F Joseph Pollock
- Eberly College of Science, Department of Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden.,NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
| | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TH, UK
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Spang A, Caceres EF, Ettema TJG. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 2017; 357:357/6351/eaaf3883. [DOI: 10.1126/science.aaf3883] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Affiliation(s)
- Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, SE-75123, Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, SE-75123, Uppsala, Sweden
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Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley TM. Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proc Natl Acad Sci U S A 2017; 114:E4602-E4611. [PMID: 28533395 PMCID: PMC5468678 DOI: 10.1073/pnas.1618463114] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood-Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.
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Affiliation(s)
- Tom A Williams
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom;
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Gergely J Szöllősi
- MTA-ELTE Lendület Evolutionary Genomics Research Group, 1117 Budapest, Hungary
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Sarah E Heaps
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- School of Mathematics & Statistics, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Bastien Boussau
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622 Villeurbanne, France
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
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Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJG. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 2017; 541:353-358. [PMID: 28077874 DOI: 10.1038/nature21031] [Citation(s) in RCA: 597] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/02/2016] [Indexed: 01/17/2023]
Abstract
The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.
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Affiliation(s)
| | - Eva F Caceres
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Disa Bäckström
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Lina Juzokaite
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Emmelien Vancaester
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Kiley W Seitz
- Department of Marine Science, University of Texas-Austin, Marine Science Institute, Port Aransas, Texas 78373, USA
| | - Karthik Anantharaman
- Department of Earth and Planetary Sciences, and Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Piotr Starnawski
- Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark
| | - Kasper U Kjeldsen
- Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark
| | - Matthew B Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, and Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Andreas Schramm
- Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark
| | - Brett J Baker
- Department of Marine Science, University of Texas-Austin, Marine Science Institute, Port Aransas, Texas 78373, USA
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
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32
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Saw JH, Spang A, Zaremba-Niedzwiedzka K, Juzokaite L, Dodsworth JA, Murugapiran SK, Colman DR, Takacs-Vesbach C, Hedlund BP, Guy L, Ettema TJG. Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes. Philos Trans R Soc Lond B Biol Sci 2016; 370:20140328. [PMID: 26323759 PMCID: PMC4571567 DOI: 10.1098/rstb.2014.0328] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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] [Indexed: 12/26/2022] Open
Abstract
The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal ‘dark matter’, is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.
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Affiliation(s)
- Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Lina Juzokaite
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jeremy A Dodsworth
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | | | - Dan R Colman
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Abstract
In contrast to prokaryotes, eukaryotic cells are characterized by a complex set of internal membrane-bound compartments. A subset of these, and the protein machineries that move material between them, define the membrane-trafficking system (MTS), the emergence of which represents a landmark in eukaryotic evolution. Unlike mitochondria and plastids, MTS organelles have autogenous origins. Much of the MTS machinery is composed of building blocks, including small GTPase, coiled-coil, beta-propeller + alpha-solenoid, and longin domains. Despite the identification of prokaryotic proteins containing these domains, only few represent direct orthologues, leaving the origins and early evolution of the MTS poorly understood. Here, we present an in-depth analysis of MTS building block homologues in the composite genome of Lokiarchaeum, the recently discovered archaeal sister clade of eukaryotes, yielding several key insights. We identify two previously unreported Eukaryotic Signature Proteins; orthologues of the Gtr/Rag family GTPases, involved in target of rapamycin complex signaling, and of the RLC7 dynein component. We could not identify golgin or SNARE (coiled-coil) or beta-propeller + alpha-solenoid orthologues, nor typical MTS domain fusions, suggesting that these either were lost from Lokiarchaeum or emerged later in eukaryotic evolution. Furthermore, our phylogenetic analyses of lokiarchaeal GTPases support a split into Ras-like and Arf-like superfamilies, with different prokaryotic antecedents, before the advent of eukaryotes. While no GTPase activating proteins or exchange factors were identified, we show that Lokiarchaeum encodes numerous roadblock domain proteins and putative longin domain proteins, confirming the latter's origin from Archaea. Altogether, our study provides new insights into the emergence and early evolution of the eukaryotic membrane-trafficking system.
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Affiliation(s)
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJG. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 2015; 521:173-179. [PMID: 25945739 PMCID: PMC4444528 DOI: 10.1038/nature14447] [Citation(s) in RCA: 672] [Impact Index Per Article: 74.7] [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: 12/15/2014] [Accepted: 04/01/2015] [Indexed: 12/22/2022]
Abstract
The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.
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Affiliation(s)
- Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Steffen L Jørgensen
- Department of Biology, Centre for Geobiology, University of Bergen, N-5020 Bergen, Norway
| | | | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Anders E Lind
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Roel van Eijk
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Christa Schleper
- Department of Biology, Centre for Geobiology, University of Bergen, N-5020 Bergen, Norway.,Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Lionel Guy
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
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35
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Offre P, Kerou M, Spang A, Schleper C. Variability of the transporter gene complement in ammonia-oxidizing archaea. Trends Microbiol 2014; 22:665-75. [PMID: 25169021 DOI: 10.1016/j.tim.2014.07.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [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: 05/11/2014] [Revised: 07/17/2014] [Accepted: 07/30/2014] [Indexed: 12/19/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are a widespread and abundant component of microbial communities in many different ecosystems. The extent of physiological differences between individual AOA is, however, unknown. Here, we compare the transporter gene complements of six AOA, from four different environments and two major clades, to assess their potential for substrate uptake and efflux. Each of the corresponding AOA genomes encode a unique set of transporters and although the composition of AOA transporter complements follows a phylogenetic pattern, few transporter families are conserved in all investigated genomes. A comparison of ammonia transporters encoded by archaeal and bacterial ammonia oxidizers highlights the variance among AOA lineages as well as their distinction from the ammonia-oxidizing bacteria, and suggests differential ecological adaptations.
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Affiliation(s)
- Pierre Offre
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, A-1090 Wien, Austria.
| | - Melina Kerou
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, A-1090 Wien, Austria
| | - Anja Spang
- Uppsala University, Department of Cell and Molecular Biology, Science for Life Laboratory, Box 596, SE-75123, Uppsala, Sweden
| | - Christa Schleper
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, A-1090 Wien, Austria.
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36
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Goericke-Pesch S, Gentil M, Spang A, Kowalewski MP, Failing K, Hoffmann B. Status of the down-regulated canine testis using two different GNRH agonist implants in comparison with the juvenile testis. Reproduction 2013; 146:517-26. [DOI: 10.1530/rep-13-0195] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Testicular function in the dog was down-regulated using two different GNRH agonist implants, with adult and juvenile testes serving as controls. Treatment resulted in an increased percentage of the interstitial area and decreased area of Leydig cell nuclei. Expression of StAR and the steroidogenic enzymes cytochrome P450 side-chain cleavage enzyme (P450scc, CYP11A1) and cytochrome P450 17α-hydroxylase-17,20-lyase (P450c17, CYP17A1) in Leydig cells was blocked at the mRNA and protein level, showing no differences between the two agonists. Staining for androgen receptor (AR) by immunohistochemistry was positive in Sertoli, Leydig and peritubular cells and some spermatogonia, with in situ hybridization confirming expression in Sertoli cells. At the mRNA level, expression of AR was not affected; however, translation was blocked (reduced percentage of AR-positive Sertoli cells), with the number of nuclei in basal position being decreased. In the juvenile testes, mRNA expression of StAR, CYP11A1 and CYP17A1 was higher compared with the other groups but distinctly lower for the AR. At the protein level, the expression was at the limit of detection for StAR; AR-positive Sertoli cells were not detected. Our observations show that the down-regulated testis is different from the juvenile one rather resembling the testicular status in seasonal breeders out of season.
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Abstract
Archaea constitute a considerable fraction of the microbial biomass on Earth. Like Bacteria they have evolved a variety of energy metabolisms using organic and/or inorganic electron donors and acceptors, and many of them are able to fix carbon from inorganic sources. Archaea thus play crucial roles in the Earth's global geochemical cycles and influence greenhouse gas emissions. Methanogenesis and anaerobic methane oxidation are important steps in the carbon cycle; both are performed exclusively by anaerobic archaea. Oxidation of ammonia to nitrite is performed by Thaumarchaeota. They represent the only archaeal group that resides in large numbers in the global aerobic terrestrial and marine environments on Earth. Sulfur-dependent archaea are confined mostly to hot environments, but metal leaching by acidophiles and reduction of sulfate by anaerobic, nonthermophilic methane oxidizers have a potential impact on the environment. The metabolisms of a large number of archaea, in particular those dominating the subsurface, remain to be explored.
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Affiliation(s)
- Pierre Offre
- Department of Genetics in Ecology, University of Vienna, A-1090 Wien, Austria; , ,
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Poulsen M, Schwab C, Jensen BB, Engberg RM, Spang A, Canibe N, Højberg O, Milinovich G, Fragner L, Schleper C, Weckwerth W, Lund P, Schramm A, Urich T. Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun 2013; 4:1428. [PMID: 23385573 DOI: 10.1038/ncomms2432] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 01/02/2013] [Indexed: 02/07/2023] Open
Abstract
Rumen methanogens are major sources of anthropogenic methane emissions, and these archaea are targets in strategies aimed at reducing methane emissions. Here we show that the poorly characterised Thermoplasmata archaea in bovine rumen are methylotrophic methanogens and that they are reduced upon dietary supplementation with rapeseed oil in lactating cows. In a metatranscriptomic survey, Thermoplasmata 16S rRNA and methyl-coenzyme M reductase (mcr) transcripts decreased concomitantly with mRNAs of enzymes involved in methanogenesis from methylamines that were among the most abundant archaeal transcripts, indicating that these Thermoplasmata degrade methylamines. Their methylotrophic methanogenic lifestyle was corroborated by in vitro incubations, showing enhanced growth of these organisms upon methylamine supplementation paralleled by elevated methane production. The Thermoplasmata have a high potential as target in future strategies to mitigate methane emissions from ruminant livestock. Our findings and the findings of others also indicate a wider distribution of methanogens than previously anticipated.
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Affiliation(s)
- Morten Poulsen
- Department of Animal Science, Aarhus University, Blichers allé 20, 8830 Tjele, Denmark.
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Eme L, Reigstad LJ, Spang A, Lanzén A, Weinmaier T, Rattei T, Schleper C, Brochier-Armanet C. Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota. Res Microbiol 2013; 164:425-38. [DOI: 10.1016/j.resmic.2013.02.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
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Spang A, Poehlein A, Offre P, Zumbrägel S, Haider S, Rychlik N, Nowka B, Schmeisser C, Lebedeva EV, Rattei T, Böhm C, Schmid M, Galushko A, Hatzenpichler R, Weinmaier T, Daniel R, Schleper C, Spieck E, Streit W, Wagner M. The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 2012; 14:3122-45. [PMID: 23057602 DOI: 10.1111/j.1462-2920.2012.02893.x] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 09/01/2012] [Indexed: 01/21/2023]
Abstract
The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83 Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N. gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N. gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.
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Affiliation(s)
- Anja Spang
- Department of Genetics in Ecology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
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Bartossek R, Spang A, Weidler G, Lanzen A, Schleper C. Metagenomic analysis of ammonia-oxidizing archaea affiliated with the soil group. Front Microbiol 2012; 3:208. [PMID: 22723795 PMCID: PMC3379541 DOI: 10.3389/fmicb.2012.00208] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [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: 02/19/2012] [Accepted: 05/21/2012] [Indexed: 11/17/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) have recently been recognized as a significant component of many microbial communities and represent one of the most abundant prokaryotic groups in the biosphere. However, only few AOA have been successfully cultivated so far and information on the physiology and genomic content remains scarce. We have performed a metagenomic analysis to extend the knowledge of the AOA affiliated with group I.1b that is widespread in terrestrial habitats and of which no genome sequences has been described yet. A fosmid library was generated from samples of a radioactive thermal cave (46°C) in the Austrian Central Alps in which AOA had been found as a major part of the microbial community. Out of 16 fosmids that possessed either an amoA or 16S rRNA gene affiliating with AOA, 5 were fully sequenced, 4 of which grouped with the soil/I.1b (Nitrososphaera-) lineage, and 1 with marine/I.1a (Nitrosopumilus-) lineage. Phylogenetic analyses of amoBC and an associated conserved gene were congruent with earlier analyses based on amoA and 16S rRNA genes and supported the separation of the soil and marine group. Several putative genes that did not have homologs in currently available marine Thaumarchaeota genomes indicated that AOA of the soil group contain specific genes that are distinct from their marine relatives. Potential cis-regulatory elements around conserved promoter motifs found upstream of the amo genes in sequenced (meta-) genomes differed in marine and soil group AOA. On one fosmid, a group of genes including amoA and amoB were flanked by identical transposable insertion sequences, indicating that amoAB could potentially be co-mobilized in the form of a composite transposon. This might be one of the mechanisms that caused the greater variation in gene order compared to genomes in the marine counterparts. Our findings highlight the genetic diversity within the two major and widespread lineages of Thaumarchaeota.
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Affiliation(s)
- Rita Bartossek
- Centre for Geobiology, Department of Biology, University of Bergen Bergen, Norway
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Schmitz-Esser S, Penz T, Spang A, Horn M. A bacterial genome in transition--an exceptional enrichment of IS elements but lack of evidence for recent transposition in the symbiont Amoebophilus asiaticus. BMC Evol Biol 2011; 11:270. [PMID: 21943072 PMCID: PMC3196728 DOI: 10.1186/1471-2148-11-270] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [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: 05/17/2011] [Accepted: 09/26/2011] [Indexed: 11/18/2022] Open
Abstract
Background Insertion sequence (IS) elements are important mediators of genome plasticity and are widespread among bacterial and archaeal genomes. The 1.88 Mbp genome of the obligate intracellular amoeba symbiont Amoebophilus asiaticus contains an unusually large number of transposase genes (n = 354; 23% of all genes). Results The transposase genes in the A. asiaticus genome can be assigned to 16 different IS elements termed ISCaa1 to ISCaa16, which are represented by 2 to 24 full-length copies, respectively. Despite this high IS element load, the A. asiaticus genome displays a GC skew pattern typical for most bacterial genomes, indicating that no major rearrangements have occurred recently. Additionally, the high sequence divergence of some IS elements, the high number of truncated IS element copies (n = 143), as well as the absence of direct repeats in most IS elements suggest that the IS elements of A. asiaticus are transpositionally inactive. Although we could show transcription of 13 IS elements, we did not find experimental evidence for transpositional activity, corroborating our results from sequence analyses. However, we detected contiguous transcripts between IS elements and their downstream genes at nine loci in the A. asiaticus genome, indicating that some IS elements influence the transcription of downstream genes, some of which might be important for host cell interaction. Conclusions Taken together, the IS elements in the A. asiaticus genome are currently in the process of degradation and largely represent reflections of the evolutionary past of A. asiaticus in which its genome was shaped by their activity.
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Affiliation(s)
- Stephan Schmitz-Esser
- Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
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Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, Schleper C. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 2010; 18:331-40. [PMID: 20598889 DOI: 10.1016/j.tim.2010.06.003] [Citation(s) in RCA: 393] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/26/2010] [Accepted: 06/04/2010] [Indexed: 11/25/2022]
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Goericke-Pesch S, Spang A, Schulz M, Ozalp G, Bergmann M, Ludwig C, Hoffmann B. Recrudescence of spermatogenesis in the dog following downregulation using a slow release GnRH agonist implant. Reprod Domest Anim 2010; 44 Suppl 2:302-8. [PMID: 19754591 DOI: 10.1111/j.1439-0531.2009.01378.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present study examined the degree to which downregulation with a GnRH agonist impaired spermatogenesis and the time course of morphological and hormonal changes that occurred during recrudescence of spermatogenesis. Using a control group (group 1, n = 5) of dogs, the effect of a removable slow release GnRH-agonist implant was investigated in beagle dogs (group 2, n = 30). The implant was removed after 5 months (week 0) and three to four dogs were castrated at weeks 0, 3, 6, 9, 12, 15, 18, 21 and 24. The degree of downregulation and recrudescence of spermatogenesis was assessed by evaluation of 200 tubular cross-sections, resulting in an assigning of dogs of group 2 to testis developmental groups (DG) according to the most developed germ cell observed: DG A, spermatocytes; DG B, round spermatids; DG C, elongating spermatids and DG D, elongated spermatids. Downregulation led to an arrest of spermatogenesis at the level of spermatogonia/primary spermatocytes. The time course of recrudescence showed high individual variations and the number of dogs falling into DG A, B, C and D was 4, 3, 6 and 17 respectively. Spermatogenesis in group 2, DG D was not different from group 1 (control). In DG A, mean area of Leydig-cell nuclei was lower (p < 0.001) than in the other DG and group 1 and resembled that of juvenile dogs (group 3, n = 3); nuclei of Sertoli cells had changed from more flat/polygonal (group 1, group 2, DG C and D) to round/ovoid and had moved to a more luminal position. As indicated by basal testosterone (T), luteinizing hormone (LH) and follicle stimulating hormone (FSH) concentrations at implant removal, full downregulation had been obtained. Testosterone, LH and FSH concentrations [X(g) (DF), ng/ml] increased (p < 0.05) from implant removal to DG B [T: 0.1 (1.24) vs 2.12 (2.31); LH: 0.2 (2.15) vs 1.11 (1.7); FSH: 0.37 (3.50) vs 6.37 (1.68)] and were more or less constant thereafter indicating that onset of spermatogenesis was related to an increase of plasma T occurring in a very narrow time window. Following GnRH implantation, the size of the testes and the prostate decreased by approximately 55% (p < 0.001), they increased to sizes similar to pre-treatment values following implant removal.
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Affiliation(s)
- S Goericke-Pesch
- Clinic for Obstetrics, Gynecology and Andrology of Large and Small Animals, Justus-Liebig-University, Giessen, Germany.
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Abstract
Vesicular transport is the basic communication mechanism between different compartments in a cell and with the environment. In this review I discuss the principles of vesicle generation and consumption with particular emphasis on the different types of coat proteins and the timing of the shedding of the coat proteins from transport containers. In recent years it has become clear that there are more coat complexes than the classical COPI, COPII and clathrin coats. These additional coats may generate vesicles that transport cargo in a temporally and/or spatially controlled manner. Work over the last years suggests that GTP hydrolysis occurs early during vesicle biogenesis, destabilizing the coat perhaps before fission of the vesicle from the donor membrane occurs. Recent findings imply, however, that tethers at the receiving compartment specifically detect the coat on vesicle.
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Affiliation(s)
- A Spang
- Biozentrum, Growth and Development, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
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Abstract
Caenorhabditis elegans has recently been used as an attractive model system to gain insight into mechanisms of endocytosis in multicellular organisms. A combination of forward and reverse genetics has identified a number of new membrane trafficking factors. Most of them have mammalian homologues which function in the same transport events. We describe a novel C. elegans gene sand-1, whose loss of function causes profound endocytic defects in many tissues. SAND-1 belongs to a conserved family of proteins present in all eukaryotic species, whose genome is sequenced. However, SAND family has not been previously characterized in metazoa. Our comparison of C. elegans SAND-1 and its yeast homologue, Mon1p, showed a conserved role of the SAND-family proteins in late steps of endocytic transport.
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Affiliation(s)
- D Poteryaev
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tuebingen D-72076, Germany.
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Spang A, Herrmann JM, Hamamoto S, Schekman R. The ADP ribosylation factor-nucleotide exchange factors Gea1p and Gea2p have overlapping, but not redundant functions in retrograde transport from the Golgi to the endoplasmic reticulum. Mol Biol Cell 2001; 12:1035-45. [PMID: 11294905 PMCID: PMC32285 DOI: 10.1091/mbc.12.4.1035] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [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: 11/11/2022] Open
Abstract
The activation of the small ras-like GTPase Arf1p requires the action of guanine nucleotide exchange factors. Four Arf1p guanine nucleotide exchange factors have been identified in yeast: Sec7p, Syt1p, Gea1p, and its homologue Gea2p. We identified GEA2 as a multicopy suppressor of a sec21-3 temperature-sensitive mutant. SEC21 encodes the gamma-subunit of coatomer, a heptameric protein complex that together with Arf1p forms the COPI coat. GEA1 and GEA2 have at least partially overlapping functions, because deletion of either gene results in no obvious phenotype, whereas the double null mutant is inviable. Conditional mutants defective in both GEA1 and GEA2 accumulate endoplasmic reticulum and Golgi membranes under restrictive conditions. The two genes do not serve completely overlapping functions because a Deltagea1 Deltaarf1 mutant is not more sickly than a Deltaarf1 strain, whereas Deltagea2 Deltaarf1 is inviable. Biochemical experiments revealed similar distributions and activities for the two proteins. Gea1p and Gea2p exist both in membrane-bound and in soluble forms. The membrane-bound forms, at least one of which, Gea2p, can be visualized on Golgi structures, are both required for vesicle budding and protein transport from the Golgi to the endoplasmic reticulum. In contrast, Sec7p, which is required for protein transport within the Golgi, is not required for retrograde protein trafficking.
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Affiliation(s)
- A Spang
- Friedrich Miescher Laboratorium, Max Planck Gesellschaft, D-72076 Tübingen, Germany.
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Todorow Z, Spang A, Carmack E, Yates J, Schekman R. Active recycling of yeast Golgi mannosyltransferase complexes through the endoplasmic reticulum. Proc Natl Acad Sci U S A 2000; 97:13643-8. [PMID: 11095735 PMCID: PMC17629 DOI: 10.1073/pnas.250472397] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mnn9p is a component of two distinct multiprotein complexes in the Saccharomyces cerevisiae cis-Golgi that have both been shown to have alpha-1,6-mannosyltransferase activity in vitro. In one of these complexes, Mnn9p associates with four other membrane proteins, Anp1p, Mnn10p, Mnn11p, and Hoc1p, whereas the other complex consists of Mnn9p and Van1p. Members of the Mnn9p-containing complexes were incorporated into COPII vesicles made in vitro from endoplasmic reticulum (ER) membranes isolated from cycloheximide-treated cells. This behavior is consistent with an active Golgi to ER recycling process. To examine this path in vivo, we monitored retrograde transport of subunits of the complex in cells blocked in anterograde transport from the ER. In this situation, specific relocation of the proteins from the Golgi to the ER was observed in the absence of new protein synthesis. Conversely, when retrograde transport was blocked in vivo, subunits of the mannosyltransferase complex accumulated in the vacuole. Packaging of Mnn9p in COPI-coated vesicles from purified Golgi membranes was also investigated using a coatomer-dependent vesicle budding assay. Gradient fractionation experiments showed that Mnn9p and the retrograde v-SNARE, Sec22p, were incorporated into COPI-coated vesicles. These observations indicate that the Mnn9p-containing mannosyltransferase complexes cycle back and forth between the ER and Golgi.
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Affiliation(s)
- Z Todorow
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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