Extreme Halophilic Archaea Derive from Two Distinct Methanogen Class
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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). -
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. -
Functionalized Membrane Domains: an Ancestral Feature of Archaea? Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger
Functionalized Membrane Domains: An Ancestral Feature of Archaea? Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger To cite this version: Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger. Functionalized Membrane Domains: An Ancestral Feature of Archaea?. Frontiers in Microbiology, Frontiers Media, 2020, 11, pp.526. 10.3389/fmicb.2020.00526. hal-02553764 HAL Id: hal-02553764 https://hal.archives-ouvertes.fr/hal-02553764 Submitted on 20 May 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. fmicb-11-00526 March 30, 2020 Time: 21:44 # 1 ORIGINAL RESEARCH published: 31 March 2020 doi: 10.3389/fmicb.2020.00526 Functionalized Membrane Domains: An Ancestral Feature of Archaea? Maxime Tourte1†, Philippe Schaeffer2†, Vincent Grossi3† and Phil M. Oger1*† 1 Université de Lyon, INSA Lyon, CNRS, MAP UMR 5240, Villeurbanne, France, 2 Université de Strasbourg-CNRS, UMR 7177, Laboratoire de Biogéochimie Moléculaire, Strasbourg, France, 3 Université de Lyon, ENS Lyon, CNRS, Laboratoire de Géologie de Lyon, UMR 5276, Villeurbanne, France Bacteria and Eukarya organize their plasma membrane spatially into domains of distinct functions. Due to the uniqueness of their lipids, membrane functionalization in Archaea remains a debated area. -
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. -
Archaea and the Origin of Eukaryotes
REVIEWS Archaea and the origin of eukaryotes Laura Eme, Anja Spang, Jonathan Lombard, Courtney W. Stairs and Thijs J. G. Ettema Abstract | Woese and Fox’s 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor. Sister groups Two descendants that split The pioneering work by Carl Woese and colleagues In this Review, we discuss how culture- independent from the same node; the revealed that all cellular life could be divided into three genomics has transformed our understanding of descendants are each other’s major evolutionary lines (also called domains): the archaeal diversity and how this has influenced our closest relative. -
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]. -
Downloaded 522 from the NCBI Genome Database in September 2018
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.16.207365; this version posted July 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 Early acquisition of conserved, lineage-specific proteins currently lacking functional 3 predictions were central to the rise and diversification of archaea 4 5 Raphaël Méheust+1,4, Cindy J. Castelle1,2, Alexander L. Jaffe5 and Jillian F. Banfield+,1,2,3,4,5 6 7 +Corresponding authors: [email protected], raphael.meheust@berkeley,edu 8 9 1Department of Earth and Planetary Science, University of California, Berkeley, CA 10 2Chan Zuckerberg Biohub, San Francisco, CA 11 3Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 12 4Innovative Genomics Institute, University of California, Berkeley, CA 13 5Department of Plant and Microbial Biology, University of California, Berkeley, CA 14 15 16 Abstract 17 Recent genomic analyses of Archaea have profoundly reshaped our understanding of their 18 distribution, functionalities and roles in eukaryotic evolution. Within the domain, major 19 supergroups are Euryarchaeota, which includes many methanogens, the TACK, which includes 20 Thaumarchaeaota that impact ammonia oxidation in soils and the ocean, the Asgard, which 21 includes lineages inferred to be ancestral to eukaryotes, and the DPANN, a group of mostly 22 symbiotic small-celled archaea. Here, we investigated the extent to which clustering based on 23 protein family content recapitulates archaeal phylogeny and identified the proteins that distinguish 24 the major subdivisions. We also defined 10,866 archaeal protein families that will serve as a 25 community resource. -
How Many Kingdoms of Life? Eukaryotic Phylogeny and Philosophy of Systematics
How many kingdoms of life? Eukaryotic phylogeny and philosophy of systematics Łukasz Lamża Copernicus Center for Interdisciplinary Studies, Jagiellonian University Abstract According to contemporary understanding of the universal tree of life, the traditionally recognized kingdoms of eukaryotic organisms— Protista, Fungi, Animalia and Plantae—are irregularly interspersed in a vast phylogenetic tree. There are numerous groups that in any Linnaean classification advised by phylogenetic relationships (i.e. a Hennigian system) would form sister groups to those kingdoms, therefore requiring us to admit them the same rank. In practice, this would lead to the creation of ca. 25-30 new kingdoms that would now be listed among animals and plants as “major types of life”. This poses problems of an aesthetic and educational nature. There are, broadly speaking, two ways to deal with that issue: a) ignore the aesthetic and educational arguments and propose classification sys- tems that are fully consistent with the Hennigian principles of phylo- genetic classification, i.e. are only composed of monophyletic taxa; CC-BY-NC-ND 4.0 b) ignore Hennigian principles and bunch small, relatively uncharac- • teristic groups into paraphyletic taxa, creating systems that are more 227 – convenient. In the paper, I present the debate and analyze the pros 203 and cons of both options, briefly commenting on the deeper, third resolution, which would be to abandon classification systems entirely. Philosophical Problems in Science (Zagadnienia FilozoficzneNo w Nauce) 66 (2019), pp. 204 Łukasz Lamża Recent advances in eukaryotic classification and phylogeny are com- mented in the light of the philosophical question of the purpose and design principles of biological classification systems. -
Biosynthetic Capacity, Metabolic Variety and Unusual Biology in the CPR and DPANN Radiations Cindy J
Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations Cindy J. Castelle 1,2, Christopher T. Brown 1, Karthik Anantharaman 1,5, Alexander J. Probst 1,6, Raven H. Huang3 and Jillian F. Banfield 1,2,4* 1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. 2Chan Zuckerberg Biohub, San Francisco, CA, USA. 3Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA. 4Department of Environmental Science, Policy, and Management, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. 5Department of Bacteriology, University of WisconsinMadison, Madison, WI, USA. 6Department of Chemistry, Biofilm Center, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany. *e-mail: [email protected] Abstract Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth’s environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. -
Genome-Resolved Metagenomics Analysis Provides Insights Into the Ecological Role of Thaumarchaeota in the Amazon River and Its Plume Otávio H
Pinto et al. BMC Microbiology (2020) 20:13 https://doi.org/10.1186/s12866-020-1698-x RESEARCH ARTICLE Open Access Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume Otávio H. B. Pinto1, Thais F. Silva1, Carla S. Vizzotto1,2, Renata H. Santana3, Fabyano A. C. Lopes4, Bruno S. Silva5, Fabiano L. Thompson5 and Ricardo H. Kruger1* Abstract Background: Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume. Results: The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. -
With Inferred Horizontal Gene Transfers and Co-Occurrence Networks
RESEARCH ARTICLE Deciphering Symbiotic Interactions of “Candidatus Aenigmarchaeota” with Inferred Horizontal Gene Transfers and Co-occurrence Networks Yu-Xian Li,a Yang-Zhi Rao,a Yan-Ling Qi,a Yan-Ni Qu,a Ya-Ting Chen,a Jian-Yu Jiao,a Wen-Sheng Shu,b Hongchen Jiang,c Brian P. Hedlund,d,e Zheng-Shuang Hua,f Wen-Jun Lia,g aState 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 bSchool of Life Sciences, South China Normal University, Guangzhou, People’s Republic of China cState Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People’s Republic of China dSchool of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA eNevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA fDepartment of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People’s Republic of China gState Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People’s Republic of China Yu-Xian Li and Yang-Zhi Rao contributed equally to this work. Author order was determined based on alphabetical order of authors’ last names. ABSTRACT “Candidatus Aenigmarchaeota” (“Ca. Aenigmarchaeota”) represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interac- tions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth com- parative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases.