Lokiarchaea Are Close Relatives of Euryarchaeota, Not
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The Syntrophy Hypothesis for the Origin of Eukaryotes Revisited Purificación López-García, David Moreira
The Syntrophy hypothesis for the origin of eukaryotes revisited Purificación López-García, David Moreira To cite this version: Purificación López-García, David Moreira. The Syntrophy hypothesis for the origin of eukaryotes revisited. Nature Microbiology, Nature Publishing Group, 2020, 5 (5), pp.655-667. 10.1038/s41564- 020-0710-4. hal-02988531 HAL Id: hal-02988531 https://hal.archives-ouvertes.fr/hal-02988531 Submitted on 3 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 1 2 Perspectives 3 4 5 6 The Syntrophy hypothesis for the origin of eukaryotes revisited 7 8 Purificación López-García1 and David Moreira1 9 10 1 Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France 11 12 13 14 *Correspondence to: [email protected] 15 16 17 18 19 1 20 The discovery of Asgard archaea, phylogenetically closer to eukaryotes than other archaea, together with 21 improved knowledge of microbial ecology impose new constraints on emerging models for the origin of the 22 eukaryotic cell (eukaryogenesis). Long-held views are metamorphosing in favor of symbiogenetic models 23 based on metabolic interactions between archaea and bacteria. These include the classical Searcy’s and 24 hydrogen hypothesis, and the more recent Reverse Flow and Entangle-Engulf-Enslave (E3) models. -
Marsarchaeota Are an Aerobic Archaeal Lineage Abundant in Geothermal Iron Oxide Microbial Mats
Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Authors: Zackary J. Jay, Jacob P. Beam, Mansur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep This is a postprint of an article that originally appeared in Nature Microbiology on May 14, 2018. The final version can be found at https://dx.doi.org/10.1038/s41564-018-0163-1. Jay, Zackary J. , Jacob P. Beam, Mensur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep. "Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats." Nature Microbiology 3, no. 6 (May 2018): 732-740. DOI: 10.1038/ s41564-018-0163-1. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Zackary J. Jay1,4,7, Jacob P. Beam1,5,7, Mensur Dlakić2, Douglas B. Rusch3, Mark A. Kozubal1,6 and William P. Inskeep 1* The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and character- ization of a phylum-level archaeal lineage proposed and herein referred to as the ‘Marsarchaeota’, after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50–80 °C. Metagenomics, single-cell sequencing, enrichment culturing and in situ transcrip- tional analyses reveal their biogeochemical role as facultative aerobic chemoorganotrophs that may also mediate the reduction of Fe(III). -
Phylogenomics Provides Robust Support for a Two-Domains Tree of Life
ARTICLES https://doi.org/10.1038/s41559-019-1040-x Phylogenomics provides robust support for a two-domains tree of life Tom A. Williams! !1*, Cymon J. Cox! !2, Peter G. Foster3, Gergely J. Szöllősi4,5,6 and T. Martin Embley7* Hypotheses about the origin of eukaryotic cells are classically framed within the context of a universal ‘tree of life’ based on conserved core genes. Vigorous ongoing debate about eukaryote origins is based on assertions that the topology of the tree of life depends on the taxa included and the choice and quality of genomic data analysed. Here we have reanalysed the evidence underpinning those claims and apply more data to the question by using supertree and coalescent methods to interrogate >3,000 gene families in archaea and eukaryotes. We find that eukaryotes consistently originate from within the archaea in a two-domains tree when due consideration is given to the fit between model and data. Our analyses support a close relation- ship between eukaryotes and Asgard archaea and identify the Heimdallarchaeota as the current best candidate for the closest archaeal relatives of the eukaryotic nuclear lineage. urrent hypotheses about eukaryotic origins generally pro- Indeed, it has previously been suggested that it is the 3D tree, rather pose at least two partners in that process: a bacterial endo- than the 2D tree, that is an artefact of long-branch attraction5,9–11, symbiont that became the mitochondrion and a host cell for both because analyses under better-fitting models have recovered C 1–4 that endosymbiosis . The identity of the host has been informed a 2D tree but also because the 3D topology is one in which the two by analyses of conserved genes for the transcription and transla- longest branches in the tree of life—the stems leading to bacteria and tion machinery that are considered essential for cellular life5. -
ARCHAEAL EVOLUTION Evolutionary Insights from the Vikings
RESEARCH HIGHLIGHTS Nature Reviews Microbiology | Published online 16 Jan 2017; doi:10.1038/nrmicro.2016.198 ARCHAEAL EVOLUTION Evolutionary insights from the Vikings The emergence of the eukaryotic cell ASGARD — after the invisible the closest known homologue of during evolution gave rise to all com- ‘Gods of Asgard’ in Norse mythology. eukaryotic epsilon DNA polymerases primordial plex life forms on Earth, including The superphylum consists of the identified thus far. eukaryotic multicellular organisms such as ani- previously identified Lokiarchaeota Members of the ASGARD super- mals, plants and fungi. However, the and Thorarchaeota phyla, and the phylum were particularly enriched vesicular and origin of eukaryotes and their char- newly identified Odinarchaeota and for eukaryotic signature proteins trafficking acteristic structural complexity has Heimdallarchaeota phyla. Using that are involved in intracellular components remained a mystery. The most recent phylogenomics, they discovered trafficking and secretion. Several are derived insights into eukaryogenesis support a strong phylogenetic association proteins contained domain signatures the endosymbiotic theory, which between ASGARD lineages and of eukaryotic transport protein from our proposes that the first eukaryotic eukaryotes that placed the eukaryote particle (TRAPP) complexes, which archaeal cell arose from archaea through the lineage in close proximity to the are involved in transport from the ancestor acquisition of an alphaproteobacterial ASGARD superphylum. endoplasmic -
Two Domains of Life, Not Three?
Asgard Archaea Two domains of life, not three? A picture of visual interpretation of the Wagner’s opera Das Rheingold, a part of Richard Wagner’s Der Ring des Nibelungen Loki's Castle is a field of five active hydrothermal vents in the mid-Atlantic Ocean, located at 73 degrees north on the Mid-Atlantic Ridge between Greenland and Norway at a depth of 2,352 metres The vents were discovered in 2008 by a multinational scientific expedition of the university of Bergen, and are the most northerly black smokers to date. The five active chimneys of Loki's Castle are venting water as hot as 300 °C and sit on a vast mound of sulfide minerals. The vent field was given the name Loki's Castle as its shape reminded its discoverers of a fantasy castle. The reference is to the ancient Norse god of trickery, Loki. The top three feet (1 m) of a vent chimney almost 40 feet (12 m) tall at Loki's Castle in mid-July 2008. Visible at left is the arm of a remotely operated vehicle, reaching in to take fluid samples. Loki’s Castle Wents Loki's Castle - a field of five active hydrothermal vents in the mid-Atlantic Ocean - at 73 degrees north on the Mid-Atlantic Ridge - at a depth of 2,352 meters In Norse mythology, Loki is a cunning trickster who has the ability to change his shape and sex. Loki is represented as the companion of the great gods Odin and Thor. Preliminary observations have shown the warm area around the Loki's Castle vents to be alive with diverse and apparently unique microorganisms, unlike vent communities observed elsewhere. -
Metagenomic Insights Into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines
Lawrence Berkeley National Laboratory Recent Work Title Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. Permalink https://escholarship.org/uc/item/9xc5s0v5 Journal Frontiers in microbiology, 7(FEB) ISSN 1664-302X Authors Vavourakis, Charlotte D Ghai, Rohit Rodriguez-Valera, Francisco et al. Publication Date 2016 DOI 10.3389/fmicb.2016.00211 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH published: 25 February 2016 doi: 10.3389/fmicb.2016.00211 Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines Charlotte D. Vavourakis 1, Rohit Ghai 2, 3, Francisco Rodriguez-Valera 2, Dimitry Y. Sorokin 4, 5, Susannah G. Tringe 6, Philip Hugenholtz 7 and Gerard Muyzer 1* 1 Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands, 2 Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain, 3 Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Ceskéˇ Budejovice,ˇ Czech Republic, 4 Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia, 5 Department of Biotechnology, Delft University of Technology, Delft, Netherlands, 6 The Department of Energy Joint Genome Institute, Walnut Creek, CA, USA, 7 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration Edited by: of sodium carbonates in the absence of major divalent cations. -
S41564-017-0083-5.Pdf
CORRECTION https://doi.org/10.1038/s41564-017-0083-5 Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Donovan H. Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J. Woodcroft, Paul N. Evans, Philip Hugenholtz* and Gene W. Tyson* Correction to: Nature Microbiology https://doi.org/10.1038/s41564-017-0012-7 (2017); published online 11 September 2017. In the original version of this Article, the authors stated that the archaeal phylum Parvarchaeota was previously represented by only two single-cell genomes (ARMAN-4_'5-way FS' and ARMAN-5_'5-way FS'). However, these are in fact unpublished, low-quality metage- nome-assembled genomes (MAGs) obtained from Richmond Mine, California. In addition, the authors overlooked two higher-quality published Parvarchaeota MAGs from the same habitat, ARMAN-4 (ADCE00000000) and ARMAN-5 (ADHF00000000) (B. J. Baker et al., Proc. Natl Acad. Sci. USA 107, 8806–8811; 2010). The ARMAN-4 and ARMAN-5 MAGs are estimated to be 68.0% and 76.7% complete with 3.3% and 5.6% contamination, respectively, based on the archaeal-specific marker sets of CheckM. The 11 Parvarchaeota genomes identified in our study were obtained from different Richmond Mine metagenomes, but are highly similar to the ARMAN-4 (ANI of ~99.7%) and ARMAN-5 (ANI of ~99.6%) MAGs. The highest-quality uncultivated bacteria and archaea (UBA) MAGs with similarity to ARMAN-4 and ARMAN-5 are 82.5% and 83.3% complete with 0.9% and 1.9% contamination, respectively. The Parvarchaeota rep- resents only 0.23% of the archaeal genome tree and addition of the ARMAN-4 and ARMAN-5 MAGs do not change the conclusions of this Article, but do impact the phylogenetic gain for this phylum. -
Lokiarchaeota: Biologists Discover 'Missing Link' Microorganism
Home About Us News Archive Copyright Privacy Policy Contact Us Newsletter RSS HOME ASTRONOMY SPACE EXPLORATION ARCHAEOLOGY PALEONTOLOGY BIOLOGY PHYSICS Lokiarchaeota: Biologists Discover ‘Missing Link’ Microorganism May 7, 2015 by Sci-News.com « PREVIOUS Published in A team of biologists, co-led by Dr Lionel Guy and Dr Thijs J. G. Ettema from Biology Uppsala University in Sweden, has discovered a new group of Tagged as microorganisms that represents an intermediate form in-between the Archaea simple cells of bacteria and the complex cell types of eukaryotes. Bacteria Eukaryote Lokiarchaeota Follow Like 16k Share Tweet 12 Like 58 41 You Might Like Bottlenose Dolphins Form Highly Complex Networks of Friends Rorqual Whales This false-color image shows a cell of thermophilic methanogenic archaea. Image credit: University of Have Unique California Museum of Paleontology. Stretchy Nerves In 1977, biochemist Dr Carl Woese and his colleagues at the University of Illinois described an entirely new group of organisms, the Archaea (originally found in extreme environments, such as hydrothermal vents and terrestrial hot springs). The scientists were studying relationships among the prokaryotes using DNA Extinction of sequences, and found that Archaea have distinct molecular characteristics World’s Largest separating them from bacteria as well as from eukaryotes. They proposed that Herbivores May Lead to Empty life can be divided into three domains: Eukaryota, Eubacteria, and Landscapes, Say Archaebacteria. Researchers Despite that archaeal cells were simple and small like bacteria, scientists found that Archaea were more closely related to organisms with complex cell types, a group collectively known as ‘eukaryotes.’ This observation has puzzled Sichuan Bush biologists for years. -
Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria)
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 2 Genomic analysis of family UBA6911 (Group 18 3 Acidobacteria) expands the metabolic capacities of the 4 phylum and highlights adaptations to terrestrial habitats. 5 6 Archana Yadav1, Jenna C. Borrelli1, Mostafa S. Elshahed1, and Noha H. Youssef1* 7 8 1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, 9 OK 10 *Correspondence: Noha H. Youssef: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 11 Abstract 12 Approaches for recovering and analyzing genomes belonging to novel, hitherto unexplored 13 bacterial lineages have provided invaluable insights into the metabolic capabilities and 14 ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent 15 and ecologically successful lineages on earth yet, currently, multiple lineages within this phylum 16 remain unexplored. Here, we utilize genomes recovered from Zodletone spring, an anaerobic 17 sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil 18 and non-soil habitats, to examine the metabolic capabilities and ecological role of members of 19 the family UBA6911 (group18) Acidobacteria. -
Coupled Reductive and Oxidative Sulfur Cycling in the Phototrophic Plate of a Meromictic Lake T
Geobiology (2014), 12, 451–468 DOI: 10.1111/gbi.12092 Coupled reductive and oxidative sulfur cycling in the phototrophic plate of a meromictic lake T. L. HAMILTON,1 R. J. BOVEE,2 V. THIEL,3 S. R. SATTIN,2 W. MOHR,2 I. SCHAPERDOTH,1 K. VOGL,3 W. P. GILHOOLY III,4 T. W. LYONS,5 L. P. TOMSHO,3 S. C. SCHUSTER,3,6 J. OVERMANN,7 D. A. BRYANT,3,6,8 A. PEARSON2 AND J. L. MACALADY1 1Department of Geosciences, Penn State Astrobiology Research Center (PSARC), The Pennsylvania State University, University Park, PA, USA 2Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA 3Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA 4Department of Earth Sciences, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA 5Department of Earth Sciences, University of California, Riverside, CA, USA 6Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Nanyang, Singapore 7Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany 8Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA ABSTRACT Mahoney Lake represents an extreme meromictic model system and is a valuable site for examining the organisms and processes that sustain photic zone euxinia (PZE). A single population of purple sulfur bacte- ria (PSB) living in a dense phototrophic plate in the chemocline is responsible for most of the primary pro- duction in Mahoney Lake. Here, we present metagenomic data from this phototrophic plate – including the genome of the major PSB, as obtained from both a highly enriched culture and from the metagenomic data – as well as evidence for multiple other taxa that contribute to the oxidative sulfur cycle and to sulfate reduction. -
Yu-Chen Ling and John W. Moreau
Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig. -
Differential Depth Distribution of Microbial Function and Putative Symbionts Through Sediment-Hosted Aquifers in the Deep Terrestrial Subsurface
ARTICLES https://doi.org/10.1038/s41564-017-0098-y Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface Alexander J. Probst1,5,7, Bethany Ladd2,7, Jessica K. Jarett3, David E. Geller-McGrath1, Christian M. K. Sieber1,3, Joanne B. Emerson1,6, Karthik Anantharaman1, Brian C. Thomas1, Rex R. Malmstrom3, Michaela Stieglmeier4, Andreas Klingl4, Tanja Woyke 3, M. Cathryn Ryan 2* and Jillian F. Banfield 1* An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome- resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep- branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.