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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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2
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Vaksmaa A, Polerecky L, Dombrowski N, Kienhuis MVM, Posthuma I, Gerritse J, Boekhout T, Niemann H. Polyethylene degradation and assimilation by the marine yeast Rhodotorula mucilaginosa. ISME Commun 2023; 3:68. [PMID: 37423910 PMCID: PMC10330194 DOI: 10.1038/s43705-023-00267-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/16/2023] [Accepted: 05/26/2023] [Indexed: 07/11/2023]
Abstract
Ocean plastic pollution is a severe environmental problem but most of the plastic that has been released to the ocean since the 1950s is unaccounted for. Although fungal degradation of marine plastics has been suggested as a potential sink mechanism, unambiguous proof of plastic degradation by marine fungi, or other microbes, is scarce. Here we applied stable isotope tracing assays with 13C-labeled polyethylene to measure biodegradation rates and to trace the incorporation of plastic-derived carbon into individual cells of the yeast Rhodotorula mucilaginosa, which we isolated from the marine environment. 13C accumulation in the CO2 pool during 5-day incubation experiments with R. mucilaginosa and UV-irradiated 13C-labeled polyethylene as a sole energy and carbon source translated to degradation rates of 3.8% yr-1 of the initially added substrate. Furthermore, nanoSIMS measurements revealed substantial incorporation of polyethylene-derived carbon into fungal biomass. Our results demonstrate the potential of R. mucilaginosa to mineralize and assimilate carbon from plastics and suggest that fungal plastic degradation may be an important sink for polyethylene litter in the marine environment.
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Affiliation(s)
- Annika Vaksmaa
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands.
| | - Lubos Polerecky
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Michiel V M Kienhuis
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Ilsa Posthuma
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Jan Gerritse
- Deltares, Unit Subsurface and Groundwater Systems, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
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3
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Eme L, Tamarit D, Caceres EF, Stairs CW, De Anda V, Schön ME, Seitz KW, Dombrowski N, Lewis WH, Homa F, Saw JH, Lombard J, Nunoura T, Li WJ, Hua ZS, Chen LX, Banfield JF, John ES, Reysenbach AL, Stott MB, Schramm A, Kjeldsen KU, Teske AP, Baker BJ, Ettema TJG. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature 2023; 618:992-999. [PMID: 37316666 PMCID: PMC10307638 DOI: 10.1038/s41586-023-06186-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [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: 04/23/2021] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.
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Affiliation(s)
- Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratoire Écologie, Systématique, Évolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Daniel Tamarit
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Eva F Caceres
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Courtney W Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biology, Lund University, Lund, Sweden
| | - Valerie De Anda
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Max E Schön
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kiley W Seitz
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nina Dombrowski
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - William H Lewis
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Felix Homa
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Jonathan Lombard
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Emily St John
- Department of Biology, Portland State University, Portland, OR, USA
| | | | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas P Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
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4
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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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5
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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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6
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Langwig MV, De Anda V, Dombrowski N, Seitz KW, Rambo IM, Greening C, Teske AP, Baker BJ. Correction to: Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups. ISME J 2022; 16:899. [PMID: 34811518 PMCID: PMC8857281 DOI: 10.1038/s41396-021-01091-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Marguerite V Langwig
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA.
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, AB Den Burg, The Netherlands
| | - Kiley W Seitz
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- EMBL Heidelberg, Meyerhofstraße 1, Heidelberg, Germany
| | - Ian M Rambo
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Andreas P Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA.
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7
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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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8
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Suominen S, Dombrowski N, Sinninghe Damsté JS, Villanueva L. A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone. Environ Microbiol 2021; 23:2709-2728. [PMID: 31858660 PMCID: PMC8359207 DOI: 10.1111/1462-2920.14902] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 11/27/2022]
Abstract
Organic matter degradation in marine environments is essential for the recycling of nutrients, especially under conditions of anoxia where organic matter tends to accumulate. However, little is known about the diversity of the microbial communities responsible for the mineralization of organic matter in the absence of oxygen, as well as the factors controlling their activities. Here, we determined the active heterotrophic prokaryotic community in the sulphidic water column of the Black Sea, an ideal model system, where a tight coupling between carbon, nitrogen and sulphur cycles is expected. Active microorganisms degrading both dissolved organic matter (DOM) and protein extracts were determined using quantitative DNA stable isotope probing incubation experiments. These results were compared with the metabolic potential of metagenome-assembled genomes obtained from the water column. Organic matter incubations showed that groups like Cloacimonetes and Marinimicrobia are generalists degrading DOM. Based on metagenomic profiles the degradation proceeds in a potential interaction with members of the Deltaproteobacteria and Chloroflexi Dehalococcoidia. On the other hand, microbes with small genomes like the bacterial phyla Parcubacteria, Omnitrophica and of the archaeal phylum Woesearchaeota, were the most active, especially in protein-amended incubations, revealing the potential advantage of streamlined microorganisms in highly reduced conditions.
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Affiliation(s)
- Saara Suominen
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
| | - Nina Dombrowski
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
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9
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Mayer T, Mari A, Almario J, Murillo-Roos M, Syed M Abdullah H, Dombrowski N, Hacquard S, Kemen EM, Agler MT. Obtaining deeper insights into microbiome diversity using a simple method to block host and nontargets in amplicon sequencing. Mol Ecol Resour 2021; 21:1952-1965. [PMID: 33905604 DOI: 10.1111/1755-0998.13408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/28/2021] [Accepted: 04/13/2021] [Indexed: 11/29/2022]
Abstract
Profiling diverse microbiomes is revolutionizing our understanding of biological mechanisms and ecologically relevant problems, including metaorganism (host + microbiome) assembly, functions and adaptation. Amplicon sequencing of multiple conserved, phylogenetically informative loci has therefore become an instrumental tool for many researchers. Investigations in many systems are hindered, however, since essential sequencing depth can be lost by amplification of nontarget DNA from hosts or overabundant microorganisms. Here, we introduce "blocking oligos", a low-cost and flexible method using standard oligonucleotides to block amplification of diverse nontargets and software to aid their design. We apply them primarily in leaves, where exceptional challenges with host amplification prevail. A. thaliana-specific blocking oligos applied in eight different target loci reduce undesirable host amplification by up to 90%. To expand applicability, we designed universal 16S and 18S rRNA gene plant blocking oligos for targets that are conserved in diverse plant species and demonstrate that they efficiently block five plant species from five orders spanning monocots and dicots (Bromus erectus, Plantago lanceolata, Lotus corniculatus, Amaranth sp., Arabidopsis thaliana). These can increase alpha diversity discovery without biasing beta diversity patterns and do not compromise microbial load information inherent to plant-derived 16S rRNA gene amplicon sequencing data. Finally, we designed and tested blocking oligos to avoid amplification of 18S rRNA genes of a sporulating oomycete pathogen, demonstrating their effectiveness in applications well beyond plants. Using these tools, we generated a survey of the A. thaliana leaf microbiome based on eight loci targeting bacterial, fungal, oomycete and other eukaryotic microorganisms and discuss complementarity of commonly used amplicon sequencing regions for describing leaf microbiota. This approach has potential to make questions in a variety of study systems more tractable by making amplicon sequencing more targeted, leading to deeper, systems-based insights into microbial discovery. For fast and easy design for blocking oligos for any nontarget DNA in other study systems, we developed a publicly available R package.
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Affiliation(s)
- Teresa Mayer
- Plant Microbiosis Laboratory, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Alfredo Mari
- Plant Microbiosis Laboratory, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Department of Microbial Interactions, IMIT/ZMBP, Eberhardt Karl University of Tübingen, Tübingen, Germany
| | - Juliana Almario
- Department of Microbial Interactions, IMIT/ZMBP, Eberhardt Karl University of Tübingen, Tübingen, Germany
| | - Mariana Murillo-Roos
- Plant Microbiosis Laboratory, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hafiz Syed M Abdullah
- Plant Microbiosis Laboratory, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Nina Dombrowski
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Stephane Hacquard
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Eric M Kemen
- Department of Microbial Interactions, IMIT/ZMBP, Eberhardt Karl University of Tübingen, Tübingen, Germany
| | - Matthew T Agler
- Plant Microbiosis Laboratory, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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10
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De Anda V, Chen LX, Dombrowski N, Hua ZS, Jiang HC, Banfield JF, Li WJ, Baker BJ. Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways. Nat Commun 2021; 12:2404. [PMID: 33893309 PMCID: PMC8065059 DOI: 10.1038/s41467-021-22736-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 07/02/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.
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Affiliation(s)
- Valerie De Anda
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
| | - Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Den Burg, Netherlands
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People's Republic of China.
| | - Brett J Baker
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA.
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11
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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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12
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Rambo IM, Dombrowski N, Constant L, Erdner D, Baker BJ. Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus. Environ Microbiol 2019; 22:1764-1783. [PMID: 31775181 DOI: 10.1111/1462-2920.14878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 11/13/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Abstract
Microbial communities inhabit algae cell surfaces and produce a variety of compounds that can impact the fitness of the host. These interactions have been studied via culturing, single-gene diversity and metagenomic read survey methods that are limited by culturing biases and fragmented genetic characterizations. Higher-resolution frameworks are needed to resolve the physiological interactions within these algal-bacterial communities. Here, we infer the encoded metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assembly and binning) associated with the marine dinoflagellates Gambierdiscus carolinianus and G. caribaeus. Phylogenetic analyses revealed that two of the genomes belong to the commonly algae-associated families Rhodobacteraceae and Flavobacteriaceae. The other two genomes belong to the Phycisphaeraceae and include the first algae-associated representative within the uncultured SM1A02 group. Analyses of all four genomes suggest these bacteria are facultative aerobes, with some capable of metabolizing phytoplanktonic organosulfur compounds including dimethylsulfoniopropionate and sulfated polysaccharides. These communities may biosynthesize compounds beneficial to both the algal host and other bacteria, including iron chelators, B vitamins, methionine, lycopene, squalene and polyketides. These findings have implications for marine carbon and nutrient cycling and provide a greater depth of understanding regarding the genetic potential for complex physiological interactions between microalgae and their associated bacteria.
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Affiliation(s)
- Ian M Rambo
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA.,NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Lauren Constant
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Deana Erdner
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
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13
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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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14
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Garrido-Oter R, Nakano RT, Dombrowski N, Ma KW, McHardy AC, Schulze-Lefert P. Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia. Cell Host Microbe 2019; 24:155-167.e5. [PMID: 30001518 PMCID: PMC6053594 DOI: 10.1016/j.chom.2018.06.006] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/16/2018] [Accepted: 06/15/2018] [Indexed: 11/19/2022]
Abstract
Rhizobia are a paraphyletic group of soil-borne bacteria that induce nodule organogenesis in legume roots and fix atmospheric nitrogen for plant growth. In non-leguminous plants, species from the Rhizobiales order define a core lineage of the plant microbiota, suggesting additional functional interactions with plant hosts. In this work, genome analyses of 1,314 Rhizobiales isolates along with amplicon studies of the root microbiota reveal the evolutionary history of nitrogen-fixing symbiosis in this bacterial order. Key symbiosis genes were acquired multiple times, and the most recent common ancestor could colonize roots of a broad host range. In addition, root growth promotion is a characteristic trait of Rhizobiales in Arabidopsis thaliana, whereas interference with plant immunity constitutes a separate, strain-specific phenotype of root commensal Alphaproteobacteria. Additional studies with a tripartite gnotobiotic plant system reveal that these traits operate in a modular fashion and thus might be relevant to microbial homeostasis in healthy roots.
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Affiliation(s)
- Ruben Garrido-Oter
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany; Cluster of Excellence on Plant Sciences, Dusseldorf 40225, Germany
| | - Ryohei Thomas Nakano
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany; Cluster of Excellence on Plant Sciences, Dusseldorf 40225, Germany
| | - Nina Dombrowski
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany; University of Texas Austin, Marine Science Institute, Port Aransas, TX 78373, USA
| | - Ka-Wai Ma
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Alice C McHardy
- Department of Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig 38124, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany; Cluster of Excellence on Plant Sciences, Dusseldorf 40225, Germany.
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15
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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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16
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Chen LX, Méndez-García C, Dombrowski N, Servín-Garcidueñas LE, Eloe-Fadrosh EA, Fang BZ, Luo ZH, Tan S, Zhi XY, Hua ZS, Martinez-Romero E, Woyke T, Huang LN, Sánchez J, Peláez AI, Ferrer M, Baker BJ, Shu WS. Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. ISME J 2018; 12:756-775. [PMID: 29222443 PMCID: PMC5864196 DOI: 10.1038/s41396-017-0002-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 08/26/2017] [Accepted: 10/09/2017] [Indexed: 11/17/2022]
Abstract
Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64-1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.
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Affiliation(s)
- Lin-Xing Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Celia Méndez-García
- Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas Austin, Marine Science Institute, Port Aransas, TX, 78373, USA
| | - Luis E Servín-Garcidueñas
- Laboratory of Microbiomics, National School of Higher Studies Morelia, National University of Mexico, Morelia, Michoacan, 58190, Mexico
| | | | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Esperanza Martinez-Romero
- Department of Ecological Genomics, Center for Genomic Sciences, National University of Mexico, Cuernavaca, Morelos, 62210, Mexico
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jesús Sánchez
- Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain
| | - Ana Isabel Peláez
- Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Brett J Baker
- Department of Marine Science, University of Texas Austin, Marine Science Institute, Port Aransas, TX, 78373, USA.
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China.
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17
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Affiliation(s)
- Marcel G A van der Heijden
- Plant-Soil Interactions, Division of Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
- Plant-Microbe Interactions, Institute of Environmental Biology, Faculty of Science, Utrecht University, 3508 TB Utrecht, The Netherlands
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
| | - Nina Dombrowski
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX 78373
| | - Klaus Schlaeppi
- Plant-Soil Interactions, Division of Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland;
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18
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Dombrowski N, Seitz KW, Teske AP, Baker BJ. Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments. Microbiome 2017; 5:106. [PMID: 28835260 PMCID: PMC5569505 DOI: 10.1186/s40168-017-0322-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [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: 03/02/2017] [Accepted: 08/01/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis and circulation produce fluids rich in hydrocarbons and reduced compounds that stimulate microbial activity in surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf of California) sediment-inhabiting microorganisms; however, many of the identified taxa lack cultures or genomic representations. Here, we resolved the metabolic potential and community-level interactions of these diverse communities by reconstructing and analyzing microbial genomes from metagenomic sequencing data. RESULTS We reconstructed 115 microbial metagenome-assembled genomes comprising 27 distinct archaeal and bacterial phyla. The archaea included members of the DPANN and TACK superphyla, Bathyarchaeota, novel Methanosarcinales (GoM-Arc1), and anaerobic methane-oxidizing lineages (ANME-1). Among the bacterial phyla, members of the Bacteroidetes, Chloroflexi, and Deltaproteobacteria were metabolically versatile and harbored potential pathways for hydrocarbon and lipid degradation and a variety of respiratory processes. Genes encoding enzymes that activate anaerobic hydrocarbons for degradation were detected in Bacteroidetes, Chloroflexi, Latescibacteria, and KSB1 phyla, while the reconstructed genomes for most candidate bacteria phyla (Aminicenantes, Atribacteria, Omnitrophica, and Stahlbacteria) indicated a fermentative metabolism. Newly obtained GoM-Arc1 archaeal genomes encoded novel pathways for short-chain hydrocarbon oxidation by alkyl-coenzyme M formation. We propose metabolic linkages among different functional groups, such as fermentative community members sharing substrate-level interdependencies with sulfur- and nitrogen-cycling microbes. CONCLUSIONS Overall, inferring the physiologies of archaea and bacteria from metagenome-assembled genomes in hydrothermal deep-sea sediments has revealed potential mechanisms of carbon cycling in deep-sea sediments. Our results further suggest a network of biogeochemical interdependencies in organic matter utilization, hydrocarbon degradation, and respiratory sulfur cycling among deep-sea-inhabiting microbial communities.
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Affiliation(s)
- Nina Dombrowski
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX USA
| | - Kiley W. Seitz
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX USA
| | - Andreas P. Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Brett J. Baker
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX USA
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Dombrowski N, Donaho JA, Gutierrez T, Seitz KW, Teske AP, Baker BJ. Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill. Nat Microbiol 2016; 1:16057. [DOI: 10.1038/nmicrobiol.2016.57] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/29/2016] [Indexed: 01/25/2023]
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Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, Dombrowski N, Münch PC, Spaepen S, Remus-Emsermann M, Hüttel B, McHardy AC, Vorholt JA, Schulze-Lefert P. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 2015; 528:364-9. [DOI: 10.1038/nature16192] [Citation(s) in RCA: 700] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/09/2015] [Indexed: 01/07/2023]
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Zamioudis C, Korteland J, Van Pelt JA, van Hamersveld M, Dombrowski N, Bai Y, Hanson J, Van Verk MC, Ling HQ, Schulze-Lefert P, Pieterse CMJ. Rhizobacterial volatiles and photosynthesis-related signals coordinate MYB72 expression in Arabidopsis roots during onset of induced systemic resistance and iron-deficiency responses. Plant J 2015; 84:309-22. [PMID: 26307542 PMCID: PMC5019235 DOI: 10.1111/tpj.12995] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [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: 12/02/2014] [Revised: 07/07/2015] [Accepted: 08/14/2015] [Indexed: 05/19/2023]
Abstract
In Arabidopsis roots, the transcription factor MYB72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (ISR) and plant survival under conditions of limited iron availability. Previously, it was shown that MYB72 coordinates the expression of a gene module that promotes synthesis and excretion of iron-mobilizing phenolic compounds in the rhizosphere, a process that is involved in both iron acquisition and ISR signaling. Here, we show that volatile organic compounds (VOCs) from ISR-inducing Pseudomonas bacteria are important elicitors of MYB72. In response to VOC treatment, MYB72 is co-expressed with the iron uptake-related genes FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER 1 (IRT1) in a manner that is dependent on FER-LIKE IRON DEFICIENCY TRANSCRIPTION FACTOR (FIT), indicating that MYB72 is an intrinsic part of the plant's iron-acquisition response that is typically activated upon iron starvation. However, VOC-induced MYB72 expression is activated independently of iron availability in the root vicinity. Moreover, rhizobacterial VOC-mediated induction of MYB72 requires photosynthesis-related signals, while iron deficiency in the rhizosphere activates MYB72 in the absence of shoot-derived signals. Together, these results show that the ISR- and iron acquisition-related transcription factor MYB72 in Arabidopsis roots is activated by rhizobacterial volatiles and photosynthesis-related signals, and enhances the iron-acquisition capacity of roots independently of the iron availability in the rhizosphere. This work highlights the role of MYB72 in plant processes by which root microbiota simultaneously stimulate systemic immunity and activate the iron-uptake machinery in their host plants.
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Affiliation(s)
- Christos Zamioudis
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Jolanda Korteland
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Johan A Van Pelt
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Muriël van Hamersveld
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Nina Dombrowski
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Yang Bai
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Johannes Hanson
- Molecular Plant Physiology, Department of Biology, Faculty of Science, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden
| | - Marcel C Van Verk
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
- Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Hong-Qing Ling
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
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Dombrowski N, Foumeny EA, Ookawara S, Riza A. The influence of reynolds number on the entry length and pressure drop for laminar pipe flow. CAN J CHEM ENG 1993. [DOI: 10.1002/cjce.5450710320] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Andrew S, Damani M, Dombrowski N. The flow characteristics of thin sheets of water containing sodium lauryl sulfate. J Colloid Interface Sci 1979. [DOI: 10.1016/0021-9797(79)90342-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Fraser R, Dombrowski N, Routley J. The production of uniform liquid sheets from spinning cups. Chem Eng Sci 1963. [DOI: 10.1016/0009-2509(63)85053-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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