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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
MIAMI UNIVERSITY the Graduate School Certificate for Approving The
MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Qiuyuan Huang Candidate for the Degree: Doctor of Philosophy _______________________________________ Hailiang Dong, Director ________________________________________ Yildirim Dilek, Reader ________________________________________ Jonathan Levy, Reader ______________________________________ Chuanlun Zhang, External examiner ______________________________________ Annette Bollmann, Graduate School Representative ABSTRACT GEOMICROBIAL INVESTIGATIONS ON EXTREME ENVIRONMENTS: LINKING GEOCHEMISTRY TO MICROBIAL ECOLOGY IN TERRESTRIAL HOT SPRINGS AND SALINE LAKES by Qiuyuan Huang Terrestrial hot springs and saline lakes represent two extreme environments for microbial life and constitute an important part of global ecosystems that affect the biogeochemical cycling of life-essential elements. Despite the advances in our understanding of microbial ecology in the past decade, important questions remain regarding the link between microbial diversity and geochemical factors under these extreme conditions. This dissertation first investigates a series of hot springs with wide ranges of temperature (26-92oC) and pH (3.72-8.2) from the Tibetan Plateau in China and the Philippines. Within each region, microbial diversity and geochemical conditions were studied using an integrated approach with 16S rRNA molecular phylogeny and a suite of geochemical analyses. In Tibetan springs, the microbial community was dominated by archaeal phylum Thaumarchaeota -
Access to Electronic Thesis
Access to Electronic Thesis Author: Khalid Salim Al-Abri Thesis title: USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS Qualification: PhD This electronic thesis is protected by the Copyright, Designs and Patents Act 1988. No reproduction is permitted without consent of the author. It is also protected by the Creative Commons Licence allowing Attributions-Non-commercial-No derivatives. If this electronic thesis has been edited by the author it will be indicated as such on the title page and in the text. USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS By Khalid Salim Al-Abri Msc., University of Sultan Qaboos, Muscat, Oman Mphil, University of Sheffield, England Thesis submitted in partial fulfillment for the requirements of the Degree of Doctor of Philosophy in the Department of Molecular Biology and Biotechnology, University of Sheffield, England 2011 Introductory Pages I DEDICATION To the memory of my father, loving mother, wife “Muneera” and son “Anas”, brothers and sisters. Introductory Pages II ACKNOWLEDGEMENTS Above all, I thank Allah for helping me in completing this project. I wish to express my thanks to my supervisor Professor Milton Wainwright, for his guidance, supervision, support, understanding and help in this project. In addition, he also stood beside me in all difficulties that faced me during study. My thanks are due to Dr. D. J. Gilmour for his co-supervision, technical assistance, his time and understanding that made some of my laboratory work easier. In the Ministry of Regional Municipalities and Water Resources, I am particularly grateful to Engineer Said Al Alawi, Director General of Health Control, for allowing me to carry out my PhD study at the University of Sheffield. -
And Thermo-Adaptation in Hyperthermophilic Archaea: Identification of Compatible Solutes, Accumulation Profiles, and Biosynthetic Routes in Archaeoglobus Spp
Universidade Nova de Lisboa Osmo- andInstituto thermo de Tecnologia-adaptation Química e Biológica in hyperthermophilic Archaea: Subtitle Subtitle Luís Pedro Gafeira Gonçalves Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. OH OH OH CDP c c c - CMP O O - PPi O3P P CTP O O O OH OH OH OH OH OH O- C C C O P O O P i Dissertation presented to obtain the Ph.D degree in BiochemistryO O- Instituto de Tecnologia Química e Biológica | Universidade Nova de LisboaP OH O O OH OH OH Oeiras, Luís Pedro Gafeira Gonçalves January, 2008 2008 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. This dissertation was presented to obtain a Ph. D. degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. By Luís Pedro Gafeira Gonçalves Supervised by Prof. Dr. Helena Santos Oeiras, January, 2008 Apoio financeiro da Fundação para a Ciência e Tecnologia (POCI 2010 – Formação Avançada para a Ciência – Medida IV.3) e FSE no âmbito do Quadro Comunitário de apoio, Bolsa de Doutoramento com a referência SFRH / BD / 5076 / 2001. ii ACKNOWNLEDGMENTS The work presented in this thesis, would not have been possible without the help, in terms of time and knowledge, of many people, to whom I am extremely grateful. Firstly and mostly, I need to thank my supervisor, Prof. Helena Santos, for her way of thinking science, her knowledge, her rigorous criticism, and her commitment to science. -
Extremophiles — Link Between Earth and Astrobiology
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Directory of Open Access Journals Zbornik Matice srpske za prirodne nauke / Proc. Nat. Sci, Matica Srpska Novi Sad, ¥ 114, 5—16, 2008 UDC 133.52:57 Dejan B. Stojanoviã1 , Oliver O. Fojkar2 , Aleksandra V. Drobac-Åik1 , Kristina O. Åajko3 , Tamara I. Duliã1 ,ZoricaB.Sviråev1 1 Faculty of Sciences, Department of Biology and Ecology, Trg Dositeja Obradoviãa 2, 21000 Novi Sad, Serbia 2 Institute for nature conservation of Serbia, Radniåka 20A, 21000 Novi Sad, Serbia 3 Faculty of Sciences, Department of Physics, Trg Dositeja Obradoviãa 4, 21000 Novi Sad, Serbia EXTREMOPHILES — LINK BETWEEN EARTH AND ASTROBIOLOGY ABSTRACT: Astrobiology studies the origin, evolution, distribution and future of life in the universe. The most promising worlds in Solar system, beyond Earth, which may har- bor life are Mars and Jovian moon Europa. Extremophiles are organisms that thrive on the edge of temperature, hypersalinity, pH extremes, pressure, dryness and so on. In this paper, some extremophile cyanobacteria have been discussed as possible life forms in a scale of astrobiology. Samples were taken from solenetz and solonchak types of soil from the Voj- vodina region. The main idea in this paper lies in the fact that high percentage of salt found in solonchak and solonetz gives the possibility of comparison these types of soil with “soil" on Mars, which is also rich in salt. KEYWORDS: Astrobiology, extremophiles, cyanobacteria, halophiles 1. INTRODUCTION 1.1. About astrobiology Astrobiology studies the origin, evolution, distribution and future of life in the universe. -
Pyrolobus Fumarii Type Strain (1A)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A). Permalink https://escholarship.org/uc/item/89r1s0xt Journal Standards in genomic sciences, 4(3) ISSN 1944-3277 Authors Anderson, Iain Göker, Markus Nolan, Matt et al. Publication Date 2011-07-01 DOI 10.4056/sigs.2014648 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2011) 4:381-392 DOI:10.4056/sigs.2014648 Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1AT) Iain Anderson1, Markus Göker2, Matt Nolan1, Susan Lucas1, Nancy Hammon1, Shweta Deshpande1, Jan-Fang Cheng1, Roxanne Tapia1,3, Cliff Han1,3, Lynne Goodwin1,3, Sam Pitluck1, Marcel Huntemann1, Konstantinos Liolios1, Natalia Ivanova1, Ioanna Pagani1, Konstantinos Mavromatis1, Galina Ovchinikova1, Amrita Pati1, Amy Chen4, Krishna Pala- niappan4, Miriam Land1,5, Loren Hauser1,5, Evelyne-Marie Brambilla2, Harald Huber6, Montri Yasawong7, Manfred Rohde7, Stefan Spring2, Birte Abt2, Johannes Sikorski2, Reinhard Wirth6, John C. Detter1,3, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,8, Victor Markowitz4, Philip Hugenholtz1,9, Nikos C. Kyrpides1, Hans-Peter Klenk2, and Alla Lapidus1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, -
Life in Extreme Environments
insight review articles Life in extreme environments Lynn J. Rothschild & Rocco L. Mancinelli NASA Ames Research Center, Moffett Field, California 94035-1000, USA (e-mail: [email protected]; [email protected]) Each recent report of liquid water existing elsewhere in the Solar System has reverberated through the international press and excited the imagination of humankind. Why? Because in the past few decades we have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life. What we previously thought of as insurmountable physical and chemical barriers to life, we now see as yet another niche harbouring ‘extremophiles’. This realization, coupled with new data on the survival of microbes in the space environment and modelling of the potential for transfer of life between celestial bodies, suggests that life could be more common than previously thought. Here we examine critically what it means to be an extremophile, and the implications of this for evolution, biotechnology and especially the search for life in the Universe. ormal is passé; extreme is chic. While thriving in biological extremes (for example, nutritional Aristotle cautioned “everything in extremes, and extremes of population density, parasites, moderation”, the Romans, known for their prey, and so on). excesses, coined the word ‘extremus’, the ‘Extremophile’ conjures up images of prokaryotes, yet the superlative of exter (‘being on the outside’). taxonomic range spans all three domains. Although all NBy the fifteenth century ‘extreme’ had arrived, via Middle hyperthermophiles are members of the Archaea and French, to English. At the dawning of the twenty-first Bacteria, eukaryotes are common among the psychrophiles, century we know that the Solar System, and even Earth, acidophiles, alkaliphiles, piezophiles, xerophiles and contain environmental extremes unimaginable to the halophiles (which respectively thrive at low temperatures, low ‘ancients’ of the nineteenth century. -
Extremophiles 90C
Limits of Life on Earth Archaea and bacteria can thrive in extreme environment (heat, cold, acidity, high pressure) and can use unusual energy source Distinguish between growth and survival (e.g., seeds, spores) Analogs for extraterrestrial environments Origin of life in extreme environments? Origin of Yellowstone National Park pH scale pH 3 Temperature 60 C Rich in sulfur Nymph Creek Hydrogenobacter gets energy by reacting oxygen from the air with hydrogen gas and/or sulfide in the water. It uses the energy to make carbohydrate (sugar) from atmospheric carbon dioxide and hydrogen in the water: CO2 + 2 H2 = CH2O + H2O (where CH2O is part of a carbohydrate). Nymph Creek flowing into Nymph Lake, Yellowstone National Park; green mat of Cyanidium (pH 3, 40 to 45oC) Nymph Lake Hydrogenobacter acidocaldarius Hyperthermophile (T > 80 C), pH ≈ 3 H2 metabolism, low nutrient tolerant Hot springs in YNP, New Zealand & Australia + oil wells “Boiling Lake” Grand Prismatic 70 C Filled with thermophiles Sulphobus: optimum T~80C Orange “mats” of pigmented Minimum 60 C, maaximum extremophiles 90C. Lives by oxidizing sulfur (carotenoids) which is abundant near hot springs Adaptations of Thermophilies Similar to “ordinary” archaea and bacteria (DNA, same amino acids) Subtle differences: Cell membranes are made of lipids that are more stable to high temperature Additional enzyme (reverse DNA gyrase) causes DNA to fold up in a way that is more stable against heat The absolute maximum temperature is around 150 C--- DNA breaks up very readily above this temperature Slow growth of bacteria in thermafrost down to -20C YNP-Octopus Spring (White Creek area) Microbial mat. -
The Draft Genome of the Hyperthermophilic Archaeon Pyrodictium Delaneyi Strain Hulk, an Iron and Nitrate Reducer, Reveals the Capacity for Sulfate Reduction Lucas M
Demey et al. Standards in Genomic Sciences (2017) 12:47 DOI 10.1186/s40793-017-0260-4 EXTENDED GENOME REPORT Open Access The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction Lucas M. Demey1, Caitlin R. Miller1, Michael P Manzella1,4, Rachel R. Spurbeck2, Sukhinder K. Sandhu3, Gemma Reguera1 and Kazem Kashefi1* Abstract Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (47.9501 latitude, −129.0970 longitude, depth 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared 99.77% similarity with the complete genome of the type strain Su06T, which shares with strain Hulk the ability to reduce iron and nitrate for respiration. The annotation of the genome of strain Hulk identified genes for the reduction of several sulfur-containing electron acceptors, an unsuspected respiratory capability in this species that was experimentally confirmed for strain Hulk. This makes P. delaneyi strain Hulk the first hyperthermophilic archaeon known to gain energy for growth by reduction of iron, nitrate, and sulfur-containing electron acceptors. Here we present the most notable features of the genome of P. delaneyi strain Hulk and identify genes encoding proteins critical to its respiratory versatility at high temperatures. The description presented here corresponds to a draft genome sequence containing 2,042,801 bp in 9 contigs, 2019 protein-coding genes, 53 RNA genes, and 1365 hypothetical genes. Keywords: Pyrodictium delaneyi strain Hulk, Pyrodictiaceae, Sulfate reducer, Hyperthermophile, Juan de Fuca ridge Introduction archaeon known to respire iron, nitrate, and sulfur- The unifying metabolic feature of the first five species containing electron acceptors. -
Comparative Genomic Analysis of The
de Crécy-Lagard et al. Biology Direct 2012, 7:32 http://www.biology-direct.com/content/7/1/32 RESEARCH Open Access Comparative genomic analysis of the DUF71/ COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage Valérie de Crécy-Lagard1*, Farhad Forouhar2, Céline Brochier-Armanet3, Liang Tong2 and John F Hunt2 Abstract Background: The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distribution profiles, physical clustering, gene fusion, co-expression profiles, structural information and other genomic or post-genomic derived associations can be now used to make very strong functional hypotheses. Here, we illustrate this shift with the analysis of the DUF71/COG2102 family, a subgroup of the PP-loop ATPase family. Results: The DUF71 family contains at least two subfamilies, one of which was predicted to be the missing diphthine-ammonia ligase (EC 6.3.1.14), Dph6. This enzyme catalyzes the last ATP-dependent step in the synthesis of diphthamide, a complex modification of Elongation Factor 2 that can be ADP-ribosylated by bacterial toxins. Dph6 orthologs are found in nearly all sequenced Archaea and Eucarya, as expected from the distribution of the diphthamide modification. The DUF71 family appears to have originated in the Archaea/Eucarya ancestor and to have been subsequently horizontally transferred to Bacteria. Bacterial DUF71 members likely acquired a different function because the diphthamide modification is absent in this Domain of Life. -
Function and Adaptation of Acidophiles in Natural and Applied Communities
Stephan Christel Linnaeus University Dissertations No 328/2018 Stephan Christel and Appliedand Communities Acidophiles in Natural of Adaptation and Function Function and Adaptation of Acidophiles in Natural and Applied Communities Lnu.se ISBN: 978-91-88761-94-1 978-91-88761-95-8 (pdf ) linnaeus university press Function and Adaptation of Acidophiles in Natural and Applied Communities Linnaeus University Dissertations No 328/2018 FUNCTION AND ADAPTATION OF ACIDOPHILES IN NATURAL AND APPLIED COMMUNITIES STEPHAN CHRISTEL LINNAEUS UNIVERSITY PRESS Abstract Christel, Stephan (2018). Function and Adaptation of Acidophiles in Natural and Applied Communities, Linnaeus University Dissertations No 328/2018, ISBN: 978-91-88761-94-1 (print), 978-91-88761-95-8 (pdf). Written in English. Acidophiles are organisms that have evolved to grow optimally at high concentrations of protons. Members of this group are found in all three domains of life, although most of them belong to the Archaea and Bacteria. As their energy demand is often met chemolithotrophically by the oxidation of basic ions 2+ and molecules such as Fe , H2, and sulfur compounds, they are often found in environments marked by the natural or anthropogenic exposure of sulfide minerals. Nonetheless, organoheterotrophic growth is also common, especially at higher temperatures. Beside their remarkable resistance to proton attack, acidophiles are resistant to a multitude of other environmental factors, including toxic heavy metals, high temperatures, and oxidative stress. This allows them to thrive in environments with high metal concentrations and makes them ideal for application in so-called biomining technologies. The first study of this thesis investigated the iron-oxidizer Acidithiobacillus ferrivorans that is highly relevant for boreal biomining. -
Exploring the Taxonomical and Functional Profile of As Burgas Hot Spring Focusing on Thermostable Β-Galactosidases
www.nature.com/scientificreports OPEN Exploring the taxonomical and functional profle of As Burgas hot spring focusing on thermostable β‑galactosidases María‑Eugenia DeCastro1, Michael P. Doane2,4, Elizabeth Ann Dinsdale2,3, Esther Rodríguez‑Belmonte1 & María‑Isabel González‑Siso1* In the present study we investigate the microbial community inhabiting As Burgas geothermal spring, located in Ourense (Galicia, Spain). The approximately 23 Gbp of Illumina sequences generated for each replicate revealed a complex microbial community dominated by Bacteria in which Proteobacteria and Aquifcae were the two prevalent phyla. An association between the two most prevalent genera, Thermus and Hydrogenobacter, was suggested by the relationship of their metabolism. The high relative abundance of sequences involved in the Calvin–Benson cycle and the reductive TCA cycle unveils the dominance of an autotrophic population. Important pathways from the nitrogen and sulfur cycle are potentially taking place in As Burgas hot spring. In the assembled reads, two complete ORFs matching GH2 beta‑galactosidases were found. To assess their functional characterization, the two ORFs were cloned and overexpressed in E. coli. The pTsbg enzyme had activity towards o‑Nitrophenyl‑β‑d‑galactopyranoside (ONPG) and p‑Nitrophenyl‑ β‑d‑fucopyranoside, with high thermal stability and showing maximal activity at 85 °C and pH 6, nevertheless the enzyme failed to hydrolyze lactose. The other enzyme, Tsbg, was unable to hydrolyze even ONPG or lactose. This fnding highlights the challenge of fnding novel active enzymes based only on their sequence. Termophiles, growing optimally at temperatures over 55 °C, are found in hot environments such as fumaroles, hydrothermal vents, hot springs, or deserts1–4.