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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. -
Supplemental Information Assembly and Binning an Iterative Assembly
Supplemental Information Assembly and binning An iterative assembly and binning process was used to reduce complexity and enrich for Haloquadratum sequences in the combined dataset. The initial round of assembly generated 5,403 contigs greater than 5,000 bp in length, for which 856 bins were generated using hierarchical clustering of tetranucleotide frequencies. Of these 856 bins, 424 were determined to be of putative Haloquadratum origin, containing 2,096 contigs. A database of reference genomes containing representatives of Class Halobacteriaceae and Class Nanohaloarchaea (Phylum Nanohaloarchaeota; [1]) was generated from the IMG genome database [2]. Haloquadratum is a distinct phylogenetic group within the Halobacteria [3, 4] and this genomic signature resulted in a sharp distinction between bins above 60% assignable Haloquadratum-like putative CDSs versus those well below 50% (data not shown). The proportion of contigs determined to be Haloquadratum-like represented a nearly identical proportion of the total number of contigs as found in a previous metagenomic study of microbial populations in Lake Tyrrell in 2007 (38.8%) [5]. This result indicates that the first round of assembly and binning captured a portion of the total metagenomic dataset that is similar to the previous relative abundance of Haloquadratum. These contigs provided an ideal situation for generating more refined genomic constructs. Sequence reads were recruited to the contigs putatively related to Haloquadratum. This reduced the number of sequence reads undergoing the second round of assembly by between 62 and 93% (Mean = 79%). Samples with multiple filter fractions had both filter fractions assembled together in an effort to include sequences that may bridge gaps in the previous assembly. -
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]. -
Genomes of “Spiribacter”, a Streamlined, Successful Halophilic
López-Pérez et al. BMC Genomics 2013, 14:787 http://www.biomedcentral.com/1471-2164/14/787 RESEARCH ARTICLE Open Access Genomes of “Spiribacter”, a streamlined, successful halophilic bacterium Mario López-Pérez1, Rohit Ghai1, Maria Jose Leon2, Ángel Rodríguez-Olmos3, José Luis Copa-Patiño3, Juan Soliveri3, Cristina Sanchez-Porro2, Antonio Ventosa2 and Francisco Rodriguez-Valera1* Abstract Background: Thalassosaline waters produced by the concentration of seawater are widespread and common extreme aquatic habitats. Their salinity varies from that of sea water (ca. 3.5%) to saturation for NaCl (ca. 37%). Obviously the microbiota varies dramatically throughout this range. Recent metagenomic analysis of intermediate salinity waters (19%) indicated the presence of an abundant and yet undescribed gamma-proteobacterium. Two strains belonging to this group have been isolated from saltern ponds of intermediate salinity in two Spanish salterns and were named “Spiribacter”. Results: The genomes of two isolates of “Spiribacter” have been fully sequenced and assembled. The analysis of metagenomic datasets indicates that microbes of this genus are widespread worldwide in medium salinity habitats representing the first ecologically defined moderate halophile. The genomes indicate that the two isolates belong to different species within the same genus. Both genomes are streamlined with high coding densities, have few regulatory mechanisms and no motility or chemotactic behavior. Metabolically they are heterotrophs with a subgroup II xanthorhodopsin as an additional energy source when light is available. Conclusions: This is the first bacterium that has been proven by culture independent approaches to be prevalent in hypersaline habitats of intermediate salinity (half a way between the sea and NaCl saturation). -
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]. -
Seasonal Dynamics of Extremely Halophilic Microbial Communities in Three Argentinian Downloaded From
FEMS Microbiology Ecology Advance Access published September 7, 2016 A manuscript submitted to FEMS Microbiology Ecology Seasonal dynamics of extremely halophilic microbial communities in three Argentinian Downloaded from salterns http://femsec.oxfordjournals.org/ Leonardo Di Meglioa, Fernando Santosb, María Gomarizb, Cristina Almansac, Cristina Lópezb, Josefa Antónb and Débora Nercessiana*. a. Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, UNMDP – CONICET, Funes 3250 4º nivel, 7600 Mar del Plata, Argentina. by guest on September 11, 2016 b. Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, 03690 San Vicente del Raspeig, España. c. Servicios Técnicos de Investigación (SSTTI), Unidad de Microscopía, Universidad de Alicante, Alicante, 03690 San Vicente del Raspeig, España *Correspondence to: Débora Nercessian E-mail: [email protected] Phone: (54) 223-4753030 Fax: (54) 223-4724143 Keywords: Halophilic microorganisms; haloviruses; microbial dynamics; prokaryotic diversity; hypersaline environments; environmental parameters. Downloaded from Running title: Microbial dynamics in three Argentinian salterns http://femsec.oxfordjournals.org/ Abstract A seasonal sampling was carried out in three Argentinian salterns: Salitral Negro (SN), Colorada Grande (CG) and Guatraché (G), aimed to analyze abiotic parameters and microbial diversity and dynamics. Microbial assemblages were correlated to environmental factors by statistical analyses. Principal- Component-Analysis -
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. -
DMSP) Demethylation Enzyme Dmda in Marine Bacteria
Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria Laura Hernández1, Alberto Vicens2, Luis E. Eguiarte3, Valeria Souza3, Valerie De Anda4 and José M. González1 1 Departamento de Microbiología, Universidad de La Laguna, La Laguna, Spain 2 Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain 3 Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Mexico 4 Department of Marine Sciences, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA ABSTRACT Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP- producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and Submitted 6 April 2020 functional divergence driven by positive selection before a coevolution between Accepted 12 August 2020 Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA Published 10 September 2020 by horizontal gene transfer prior to an environment with higher DMSP. -
Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia
Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia Dahe Zhao Institute of Microbiology Chinese Academy of Sciences Shengjie Zhang Institute of Microbiology Chinese Academy of Sciences Qiong Xue Institute of Microbiology Chinese Academy of Sciences Junyu Chen Institute of Microbiology Chinese Academy of Sciences Jian Zhou Institute of Microbiology Chinese Academy of Sciences Feiyue Cheng Institute of Microbiology Chinese Academy of Sciences Ming Li Institute of Microbiology Chinese Academy of Sciences Yaxin Zhu Institute of Microbiology Chinese Academy of Sciences Haiying Yu Beijing Institute of Genomics Chinese Academy of Sciences Songnian Hu Institute of Microbiology Chinese Academy of Sciences Yanning Zheng Institute of Microbiology Chinese Academy of Sciences Shuangjiang Liu Institute of Microbiology Chinese Academy of Sciences Hua Xiang ( [email protected] ) Institute of Microbiology Chinese Academy of Sciences https://orcid.org/0000-0003-0369-1225 Research Keywords: Soda-Saline lakes, Deep metagenomic sequencing, Microbiome, Abundant taxa, Sulfur cycling, Glucan metabolism Posted Date: December 18th, 2019 Page 1/30 DOI: https://doi.org/10.21203/rs.2.19124/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 2/30 Abstract Background: The chloride-carbonate-sulfate lakes (also called Soda-Saline lakes) are double-extreme ecological environments with high pH and high salinity values but can also exhibit high biodiversity and high productivity. The diversity of metabolic process that functioned well in such environments remains to be systematically investigated. Deep sequencing and species-level characterization of the microbiome in elemental cycling of carbon and sulfur will provide novel insights into the microbial adaptation in such saline-alkaline lakes.