Supplemental Information Assembly and Binning an Iterative Assembly
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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). -
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. -
Xenorhodopsins, an Enigmatic New Class of Microbial Rhodopsins Horizontally Transferred Between Archaea and Bacteria
UC San Diego UC San Diego Previously Published Works Title Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between Archaea and Bacteria Permalink https://escholarship.org/uc/item/8rg5f54b Journal Biology Direct, 6(1) ISSN 1745-6150 Authors Ugalde, Juan A Podell, Sheila Narasingarao, Priya et al. Publication Date 2011-10-10 DOI http://dx.doi.org/10.1186/1745-6150-6-52 Supplemental Material https://escholarship.org/uc/item/8rg5f54b#supplemental Peer reviewed eScholarship.org Powered by the California Digital Library University of California Ugalde et al. Biology Direct 2011, 6:52 http://www.biology-direct.com/content/6/1/52 DISCOVERYNOTES Open Access Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria Juan A Ugalde1, Sheila Podell1, Priya Narasingarao1 and Eric E Allen1,2* Abstract Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena sensory rhodopsin (ASR) protein, including multiple homologs not previously recognized. We propose the name xenorhodopsin for this class, reflecting a taxonomically diverse membership spanning five different Bacterial phyla as well as the Euryarchaeotal class Nanohaloarchaea. The patchy phylogenetic distribution of xenorhodopsin homologs is consistent with historical dissemination through horizontal gene transfer. Shared characteristics of xenorhodopsin-containing microbes include the absence of flagellar motility and isolation from high light habitats. Reviewers: This article was reviewed by Dr. Michael Galperin and Dr. Rob Knight. Findings disseminated photoreceptor and photosensory activities Microbial rhodopsins are a widespread family of photo- across large evolutionary distances [1]. -
The Distribution and Evolution of Small Non-Coding Rnas in Archaea in Light of New Archaeal Phyla
THE DISTRIBUTION AND EVOLUTION OF SMALL NON-CODING RNAS IN ARCHAEA IN LIGHT OF NEW ARCHAEAL PHYLA A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Science in Biological Sciences at the University of Canterbury by Laura A.A. Grundy University of Canterbury 2016 Table of Contents Table of Contents...................................................................................................... 2 Acknowledgements ................................................................................................... 4 Abstract..................................................................................................................... 5 Chapter One - Introduction ..................................................................................... 6 Overview ............................................................................................................... 6 The Archaeal Domain of Life ................................................................................. 6 Metagenomics and the Availability of Genomic Data ......................................... 6 The History of Archaeal Taxa ............................................................................ 7 Archaeal Similarities to the Bacteria and Eukaryotes......................................... 9 Small Non-Coding RNA....................................................................................... 10 RNA................................................................................................................ -
Global Phylogenomic Analysis Disentangles the Complex Evolutionary History of DNA Replication in Archaea
Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea. Kasie Raymann, Patrick Forterre, Céline Brochier-Armanet, Simonetta Gribaldo To cite this version: Kasie Raymann, Patrick Forterre, Céline Brochier-Armanet, Simonetta Gribaldo. Global phy- logenomic analysis disentangles the complex evolutionary history of DNA replication in archaea.. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2014, 6 (1), pp.192-212. 10.1093/gbe/evu004. hal-00957432 HAL Id: hal-00957432 https://hal.archives-ouvertes.fr/hal-00957432 Submitted on 11 Mar 2014 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. Distributed under a Creative Commons Attribution - NonCommercial| 4.0 International License GBE Global Phylogenomic Analysis Disentangles the Complex Evolutionary History of DNA Replication in Archaea Kasie Raymann1,2, Patrick Forterre1,Ce´line Brochier-Armanet3, and Simonetta Gribaldo1,* 1De´partement de Microbiologie, Institut Pasteur, Unite´ Biologie Mole´culaire du Gene chez les Extreˆmophiles, Paris, France 2Universite´ Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France 3Universite´ de Lyon, Universite´ Lyon 1, CNRS, UMR5558, Laboratoire de Biome´trie et Biologie Evolutive, Villeurbanne, France *Corresponding author: E-mail: [email protected]. Downloaded from Accepted: December 29, 2013 Abstract The archaeal machinery responsible for DNA replication is largely homologous to that of eukaryotes and is clearly distinct from its http://gbe.oxfordjournals.org/ bacterial counterpart. -
Close Encounters of the Third Domain: the Emerging Genomic View of Archaeal Diversity and Evolution
Hindawi Publishing Corporation Archaea Volume 2013, Article ID 202358, 12 pages http://dx.doi.org/10.1155/2013/202358 Review Article Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution Anja Spang, Joran Martijn, Jimmy H. Saw, Anders E. Lind, Lionel Guy, and Thijs J. G. Ettema Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, P.O. Box 596, 75123 Uppsala, Sweden Correspondence should be addressed to Thijs J. G. Ettema; [email protected] Received 24 July 2013; Accepted 21 September 2013 Academic Editor: Gustavo Caetano-Anolles´ Copyright © 2013 Anja Spang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life. 1. Introduction information-processing machineries [7–14]. These findings were later supported by genome sequences and compara- The description of the three (cellular) domains of life— tive analyses of genes coding for replication, transcription, Eukarya, Bacteria, and Archaea—by Carl Woese and George and translation machineries as well as by protein crystal Fox [1] represents a milestone in the modern era of micro- structures [15–21]. -
Lokiarchaea Are Close Relatives of Euryarchaeota, Not
Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes Violette da Cunha, Morgan Gaia, Danièle Gadelle, Arshan Nasir, Patrick Forterre To cite this version: Violette da Cunha, Morgan Gaia, Danièle Gadelle, Arshan Nasir, Patrick Forterre. Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. PLoS Ge- netics, Public Library of Science, 2017, 13 (6), pp.e1006810. 10.1371/journal.pgen.1006810. pasteur- 01570207 HAL Id: pasteur-01570207 https://hal-pasteur.archives-ouvertes.fr/pasteur-01570207 Submitted on 28 Jul 2017 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. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes Violette Da Cunha1,2³, Morgan Gaia1³, Daniele Gadelle2, Arshan Nasir3, Patrick Forterre1,2* 1 Institut Pasteur, Unite de Biologie MoleÂculaire du Gène chez les Extrêmophiles (BMGE), DeÂpartement de Microbiologie Paris, France, 2 Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris- Sud, Universite Paris-Saclay, Gif-sur-Yvette cedex, France, 3 Department of Biosciences, COMSATS a1111111111 Institute of Information Technology, Islamabad, Pakistan a1111111111 ³ These authors share first authorship on this work. -
Resolving Widespread Incomplete and Uneven Archaeal Classifications
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.01.972265; this version posted February 17, 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-NC-ND 4.0 International license. 1 2 Resolving widespread incomplete and uneven archaeal 3 classifications based on a rank-normalized genome-based 4 taxonomy 5 Christian Rinke1, Maria Chuvochina1, Aaron J. Mussig1, Pierre-Alain Chaumeil1, Adrian A. Davin1, David W. 6 Waite2, William B Whitman3, Donovan H. Parks1, Philip Hugenholtz1 7 8 1 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia 9 2 School of Biological Sciences, The University of Auckland, New Zealand 10 3 Department of Microbiology, University of Georgia Athens, GA, USA 11 12 Abstract 13 An increasing wealth of genomic data from cultured and uncultured microorganisms provides the opportunity 14 to develop a systematic taxonomy based on evolutionary relationships. Here we propose a standardized 15 archaeal taxonomy, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated 16 protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary 17 divergence (RED). The resulting archaeal taxonomy is stable under a range of phylogenetic variables, 18 including marker genes, inference methods, corrections for rate heterogeneity and compositional bias, tree 19 rooting scenarios, and expansion of the genome database. Rank normalization was shown to robustly correct 20 for substitution rates varying up to 30-fold using simulated datasets. -
Hydrogenotrophic Methanogenesis in Archaeal Phylum Verstraetearchaeota Reveals the Shared Ancestry of All Methanogens
Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens Bojk A. Berghuisa, Feiqiao Brian Yua,b, Frederik Schulzc, Paul C. Blaineyd,e, Tanja Woykec, and Stephen R. Quakea,b,f,1 aDepartment of Bioengineering, Stanford University, Stanford, CA 94305; bChan Zuckerberg Biohub, San Francisco, CA 94158; cDepartment of Energy Joint Genome Institute, Walnut Creek, CA 94598; dDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; eBroad Institute of Harvard and MIT, Cambridge, MA 02142; and fDepartment of Applied Physics, Stanford University, Stanford, CA 94305 Contributed by Stephen R. Quake, December 29, 2018 (sent for review September 27, 2018; reviewed by Jared R. Leadbetter and Marc Strous) Methanogenic archaea are major contributors to the global carbon electron donor (1, 11). To conserve energy, hydrogenotrophs couple cycle and were long thought to belong exclusively to the euryarchaeal the WLP to methanogenesis. This coupling is established by N5- phylum. Discovery of the methanogenesis gene cluster methyl- methyl-tetrahydromethanopterin:coenzyme M methyltransferase coenzyme M reductase (Mcr) in the Bathyarchaeota, and thereafter (Mtr; also known as tetrahydromethanopterin S-methyltransferase), the Verstraetearchaeota, led to a paradigm shift, pushing back the which transfers the methyl group from the WLP to coenzyme M. Mtr + evolutionary origin of methanogenesis to predate that of the uses the free energy of methyl transfer to establish a Na -motive Euryarchaeota. The methylotrophic methanogenesis found in force across the membrane (14). Methyl coenzyme M reductase then the non-Euryarchaota distinguished itself from the predomi- reduces methyl-coenzyme M to methane, using coenzyme B as an nantly hydrogenotrophic methanogens found in euryarchaeal orders as the former do not couple methanogenesis to carbon fixation through electron donor. -
Pubication Board.Qxp
This article may be downloaded for personal use only. Any other use requires prior permission of the author or publisher. The following article appeared in International Microbiology 15(1): 33-41 (2012); and may be found at https://doi.org/10.2436/20.1501.01.155 RESEARCH ARTICLE INTERNATIONAL MICROBIOLOGY (2012) 15:33-41 DOI: 10.2436/20.1501.01.155 ISSN: 1139-6709 www.im.microbios.org Phylogenetic diversity of methyl-coenzyme M reductase (mcrA) gene and methanogenesis from trimethylamine in hypersaline environments José Q. García-Maldonado,1 Brad M. Bebout,2 Lourdes B. Celis,3 Alejandro López-Cortés1* 1Laboratory of Molecular Microbial Ecology, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico. 2Exobiology Branch, Ames Research Center, National Aeronautics and Space Administration, Moffett Field, CA, USA. 3Applied Geosciences Division, Scientific and Technological Research Institute of San Luis Potosi (IPICYT), San Luis Potosi, Mexico Received 13 January 2012 · Accepted 28 February 2012 Summary. Methanogens have been reported in complex microbial communities from hypersaline environments, but little is known about their phylogenetic diversity. In this work, methane concentrations in environmental gas samples were deter- mined while methane production rates were measured in microcosm experiments with competitive and non-competitive sub- strates. In addition, the phylogenetic diversity of methanogens in microbial mats from two geographical locations was ana- lyzed: the well studied Guerrero Negro hypersaline ecosystem, and a site not previously investigated, namely Laguna San Ignacio, Baja California Sur, Mexico. Methanogenesis in these microbial mats was suspected based on the detection of methane (in the range of 0.00086 to 3.204 %) in environmental gas samples. -
Metabolic Versatility of Small Archaea Micrarchaeota and Parvarchaeota
Lawrence Berkeley National Laboratory Recent Work Title Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. Permalink https://escholarship.org/uc/item/1vc6t690 Journal The ISME journal, 12(3) ISSN 1751-7362 Authors Chen, Lin-Xing Méndez-García, Celia Dombrowski, Nina et al. Publication Date 2018-03-01 DOI 10.1038/s41396-017-0002-z Peer reviewed eScholarship.org Powered by the California Digital Library University of California The ISME Journal (2018) 12:756–775 https://doi.org/10.1038/s41396-017-0002-z ARTICLE Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota 1 2,3 4 5 Lin-Xing Chen ● Celia Méndez-García ● Nina Dombrowski ● Luis E. Servín-Garcidueñas ● 6 1 1 1 7 1 Emiley A. Eloe-Fadrosh ● Bao-Zhu Fang ● Zhen-Hao Luo ● Sha Tan ● Xiao-Yang Zhi ● Zheng-Shuang Hua ● 8 6 1 2 2 Esperanza Martinez-Romero ● Tanja Woyke ● Li-Nan Huang ● Jesús Sánchez ● Ana Isabel Peláez ● 9 4 10 Manuel Ferrer ● Brett J. Baker ● Wen-Sheng Shu Received: 5 April 2017 / Revised: 26 August 2017 / Accepted: 9 October 2017 / Published online: 8 December 2017 © The Author(s) 2018. This article is published with open access 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 1234567890 world. 16S rRNA gene based analyses revealed that Electronic supplementary material The online version of this article Parvarchaeota were only detected in AMD and hot spring (https://doi.org/10.1038/s41396-017-0002-z) contains supplementary habitats, while Micrarchaeota were also detected in others material, which is available to authorized users. -
Assessment of 16S Rrna Gene-Based Phylogenetic Diversity
biology Article Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia Afef Najjari 1,*, Panagiota Stathopoulou 2 , Khaled Elmnasri 3, Faten Hasnaoui 1, Ines Zidi 1, Haitham Sghaier 3,4, Hadda Imene Ouzari 1, Ameur Cherif 3 and George Tsiamis 2 1 Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; [email protected] (F.H.); [email protected] (I.Z.); [email protected] (H.I.O.) 2 Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece; [email protected] (P.S.); [email protected] (G.T.) 3 Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia; [email protected] (K.E.); [email protected] (H.S.); [email protected] (A.C.) 4 Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), 2020 Sidi Thabet, Tunisia * Correspondence: [email protected] Citation: Najjari, A.; Stathopoulou, Simple Summary: In the current investigation, we determine the archaeal diversity from halite- P.; Elmnasri, K.; Hasnaoui, F.; Zidi, I.; crystal salts sampled from Chott Djerid and Chott Douz, two saline Chotts in the Tunisian Sahara, Sghaier, H.; Ouzari, H.I.; Cherif, A.; using both culture-dependent and independent approaches citing DGGE (V3 regions), 16S rRNA- Tsiamis, G. Assessment of 16S rRNA gene (full length gene ~ 1500 bp) based clone libraries and high-throughput sequencing technology of Gene-Based Phylogenetic Diversity of Illumina MiSeq platform (V3–V4 regions).