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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. -
Cryptic Inoviruses Are Pervasive in Bacteria and Archaea Across Earth's
bioRxiv preprint doi: https://doi.org/10.1101/548222; this version posted February 15, 2019. 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. Cryptic inoviruses are pervasive in bacteria and archaea across Earth’s biomes Simon Roux1*, Mart Krupovic2, Rebecca A. Daly3, Adair L. Borges4, Stephen Nayfach1, Frederik Schulz1, Jan-Fang Cheng1, Natalia N. Ivanova1, Joseph Bondy-Denomy4,5, Kelly C. Wrighton3, Tanja Woyke1, Axel Visel1, Nikos C. Kyrpides1, Emiley A. Eloe-Fadrosh1* 1 5 DOE Joint Genome Institute, Walnut Creek, CA 94598, USA 2Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Paris, 75015, France 3Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80521, USA 4Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA 5 10 Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA *Correspondence to: EAE-F [email protected], SR [email protected] Abstract 15 Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content, and infection cycle. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications such as phage display, or because of their impact on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here we show that the current 56 members of the Inoviridae family represent a minute 20 fraction of a highly diverse group of inoviruses. -
Biology, Ecology, and Biotechnological Applications of Anaerobic Bacteria Adapted to Environmental Stresses in Temperature, Ph, Salinity, Or Substrates SUSAN E
MICROBIOLOGIcAL REVIEWS, June, 1993, p. 451-509 Vol. 57, No. 2 0146-0749/93/020451-59$02.00/0 Copyright X) 1993, American Society for Microbiology Biology, Ecology, and Biotechnological Applications of Anaerobic Bacteria Adapted to Environmental Stresses in Temperature, pH, Salinity, or Substrates SUSAN E. LOWE,lt* MAHENDRA K. JAIN,2 AND J. GREGORY ZEIKUS1'2'3 Department ofBiochemistry' and Department ofMicrobiology and Public Health,3 Michigan State University, East Lansing, Michigan 48824, and Michigan Biotechnology Institute, Lansing, Michigan 489092 INTRODUCTION ........................................................................... 453 THERMOPHILES .......................................................................... 454 Ecology, Diversity, and Taxonomy........................................................................... 454 Physiology, Biochemistry, and Genetics ........................................................................... 461 Downloaded from Overview.......................................................................... 461 Catabolism and autotrophy of methanogens and acetogens.......................................................461 (i) Methanogenesis and autotrophy........................................................................... 461 (ii) Acetogenesis and autotrophy of C. thermoaceticum .........................................................462 (iii) Novel properties of sulfur/sulfate/thiosulfate reducers and other species..............................462 Ethanolic fermentation of saccharides.......................................................................... -
Characterization of Methanosarcina Mazei JL01 Isolated from Holocene
Proceedings Characterization of Methanosarcina mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta associata GLS2T † Viktoriia Oshurkova 1,*, Olga Troshina 1, Vladimir Trubitsyn 1, Yana Ryzhmanova 1, Olga Bochkareva 2 and Viktoria Shcherbakova 1 1 Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, prospect Nauki 5, Pushchino, 142290 Moscow, Russia; [email protected] (O.T.); [email protected] (V.T.); [email protected] (Y.R.); [email protected] (V.S.) 2 Institute of Science and Technology (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria; [email protected] * Correspondence: [email protected] † Presented at the 1st International Electronic Conference on Microbiology, 2–30 November 2020; Available online: https://ecm2020.sciforum.net/. Published: 18 December 2020 Abstract: A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic. After long-term extensive cultivation at 15 °C, it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains. Strain JL01 was a strict anaerobe and grew on methanol, acetate, and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stain-positive. Optimum conditions for growth were 24–28 °C, pH 6.8–7.3, and 0.075–0.1 M NaCl. Phylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly conserved protein- coding genes revealed 16S rRNA’s close relation to Methanosarcina mazei S-6T (similarity 99.5%). -
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]. -
View This Section Focuses on the Genomic and Proteomic Analyses That Were Performed on Methanolobus Vulcani B1d
MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Adam John Creighbaum Candidate for the Degree Doctor of Philosophy ______________________________________ Dr. Donald J. Ferguson Jr, Director ______________________________________ Dr. Annette Bollmann, Reader ______________________________________ Dr. Xin Wang, Reader ______________________________________ Dr. Rachael Morgan-Kiss ______________________________________ Dr. Richard Page, Graduate School Representative ABSTRACT EXAMINATION AND RECONSTITUTION OF THE GLYCINE BETAINE- DEPENDENT METHANOGENESIS PATHWAY FROM THE OBLIGATE METHYLOTROPHIC METHANOGEN METHANOLOBUS VULCANI B1D by Adam J. Creighbaum Recent studies indicate that environmentally abundant quaternary amines (QAs) are a primary source for methanogenesis, yet the catabolic enzymes are unknown. We hypothesized that the methanogenic archaeon Methanolobus vulcani B1d metabolizes glycine betaine through a corrinoid-dependent glycine betaine:coenzyme M (CoM) methyl transfer pathway. The draft genome sequence of M. vulcani B1d revealed a gene encoding a predicted non- pyrrolysine MttB homolog (MV8460) with high sequence similarity to the glycine betaine methyltransferase encoded by Desulfitobacterium hafniense Y51. MV8460 catalyzes glycine betaine-dependent methylation of free cob(I)alamin indicating it is an authentic MtgB enzyme. Proteomic analysis revealed that MV8460 and a corrinoid binding protein (MV8465) were highly abundant when M. vulcani B1d was grown -
The Genome Sequence of Methanohalophilus Mahii SLPT
Hindawi Publishing Corporation Archaea Volume 2010, Article ID 690737, 16 pages doi:10.1155/2010/690737 Research Article TheGenomeSequenceofMethanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments Stefan Spring,1 Carmen Scheuner,1 Alla Lapidus,2 Susan Lucas,2 Tijana Glavina Del Rio,2 Hope Tice,2 Alex Copeland,2 Jan-Fang Cheng,2 Feng Chen,2 Matt Nolan,2 Elizabeth Saunders,2, 3 Sam Pitluck,2 Konstantinos Liolios,2 Natalia Ivanova,2 Konstantinos Mavromatis,2 Athanasios Lykidis,2 Amrita Pati,2 Amy Chen,4 Krishna Palaniappan,4 Miriam Land,2, 5 Loren Hauser,2, 5 Yun-Juan Chang,2, 5 Cynthia D. Jeffries,2, 5 Lynne Goodwin,2, 3 John C. Detter,3 Thomas Brettin,3 Manfred Rohde,6 Markus Goker,¨ 1 Tanja Woyke, 2 Jim Bristow,2 Jonathan A. Eisen,2, 7 Victor Markowitz,4 Philip Hugenholtz,2 Nikos C. Kyrpides,2 and Hans-Peter Klenk1 1 DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 5 Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA 6 HZI—Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany 7 Davis Genome Center, University of California, Davis, CA 95817, USA Correspondence should be addressed to Stefan Spring, [email protected] and Hans-Peter Klenk, [email protected] Received 24 August 2010; Accepted 9 November 2010 Academic Editor: Valerie´ de Crecy-Lagard´ Copyright © 2010 Stefan Spring et al. -
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................................................................................................................ -
Predictedmethylators 20130327.Pdf
Predicted Methylators Experimental Locus Tag Strain Phylum Taxonomic Class Gold Card ID Verification hgcA hgcB Desulfovibrio desulfuricans ND132 (1) Proteobacteria Deltaproteobacteria Gi03061 DND132_1056 DND132_1057 Desulfovibrio aespoeensis Aspo-2 (2) Proteobacteria Deltaproteobacteria Gc01651 Daes_2662 Daes_2663 Desulfovibrio africanus str. Walvis Bay ATCC 19997 (3) Proteobacteria Deltaproteobacteria Gi03062 Desaf_0117 Desaf_0115 Desulfomicrobium baculatum X DSM 4028 Proteobacteria Deltaproteobacteria Gc01026 Dbac_0376 Dbac_0375 Desulfonatronospira thiodismutans ASO3-1 Proteobacteria Deltaproteobacteria Gi02999 Dthio_PD1043 Dthio_PD1042 Desulfonatronum lacustre Z-7951 DSM 10312 Proteobacteria Deltaproteobacteria Gi03017 DeslaDRAFT_0127 DeslaDRAFT_0126 Desulfovibrio oxyclinae DSM 11498 Proteobacteria Deltaproteobacteria Gi11435 B149DRAFT_02526 B149DRAFT_02527 Desulfobulbus propionicus 1pr3 DSM 2032 (4) Proteobacteria Deltaproteobacteria Gc01599 Despr_0439 Despr_0438 uncultured Desulfobacterium sp. Proteobacteria Deltaproteobacteria N47_A07900 N47_A07910 Geobacter sulfurreducens PCA DSM 12127 ATCC 51573 (5) Proteobacteria Deltaproteobacteria Gc00166 GSU1440 GSU1441 Geobacter sulfurreducens DL-1 / KN400 Proteobacteria Deltaproteobacteria Gc01305 KN400_1466 KN400_1468 Geobacter metallireducens GS-15 (5) Proteobacteria Deltaproteobacteria Gc00314 Gmet_1240 Gmet_1241 Geobacter metallireducens RCH3 Proteobacteria Deltaproteobacteria Gi06445 GeomeDRAFT_0749 GeomeDRAFT_0748 Geobacter sp. daltonii FRC-32 Proteobacteria Deltaproteobacteria Gc00945 -
Methylotrophic Methanogenesis Governs the Biogenic Coal Bed Methane Formation in Eastern Ordos Basin, China
Appl Microbiol Biotechnol (2012) 96:1587–1597 DOI 10.1007/s00253-012-3889-3 ENVIRONMENTAL BIOTECHNOLOGY Methylotrophic methanogenesis governs the biogenic coal bed methane formation in Eastern Ordos Basin, China Hongguang Guo & Zhisheng Yu & Ruyin Liu & Hongxun Zhang & Qiding Zhong & Zhenghe Xiong Received: 23 October 2011 /Revised: 29 December 2011 /Accepted: 2 January 2012 /Published online: 28 January 2012 # Springer-Verlag 2012 Abstract To identify the methanogenic pathways present in a biodegradation of coal by methylotrophic methanogens and deep coal bed methane (CBM) reservoir associated with East- syntrophic bacteria, as well as thermogenic CBM production, ern Ordos Basin in China, a series of geochemical and micro- contributed to the Liulin CBM reserves associated with the biological studies was performed using gas and water samples Eastern Ordos Basin. produced from the Liulin CBM reservoir. The composition and stable isotopic ratios of CBM implied a mixed biogenic Keywords Coal bed methane . Methanogenesis . Deep and thermogenic origin of the methane. Archaeal 16S rRNA subsurface environment . Ordos Basin gene analysis revealed the dominance of the methylotrophic methanogen Methanolobus in the water produced. The high potential of methane production by methylotrophic methano- Introduction gens was found in the enrichments using the water samples amended with methanol and incubated at 25 and 35 °C. Coal bed methane (CBM) is a major clean energy resource Methylotrophic methanogens were the dominant archaea in worldwide and which