Microorganisms from Deep-Sea Hydrothermal Vents
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Bioenergetics of Mixotrophic Metabolisms: a Theoretical Analysis
Bioenergetics of mixotrophic metabolisms: A theoretical analysis by Stephanie Slowinski A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Master of Science in Earth Sciences (Water) Waterloo, Ontario, Canada, 2019 © Stephanie Slowinski 2019 Author’s Declaration This thesis consists of material all of which I authored or co-authored: see Statement of Contributions included in the thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Statement of Contributions This thesis consists of two co-authored chapters. I contributed to the study design and execution in chapters 2 and 3. Christina M. Smeaton (CMS) and Philippe Van Cappellen (PVC) provided guidance during the study design and analysis. I co-authored both of these chapters with CMS and PVC. iii Abstract Many biogeochemical reactions controlling surface water and groundwater quality, as well as greenhouse gas emissions and carbon turnover rates, are catalyzed by microorganisms. Representing the thermodynamic (or bioenergetic) constraints on the reduction-oxidation reactions carried out by microorganisms in the subsurface is essential to understand and predict how microbial activity affects the environmental fate and transport of chemicals. While organic compounds are often considered to be the primary electron donors (EDs) in the subsurface, many microorganisms use inorganic EDs and are capable of autotrophic carbon fixation. Furthermore, many microorganisms and communities are likely capable of mixotrophy, switching between heterotrophic and autotrophic metabolisms according to the environmental conditions and energetic substrates available to them. -
Geomicrobiological Processes in Extreme Environments: a Review
202 Articles by Hailiang Dong1, 2 and Bingsong Yu1,3 Geomicrobiological processes in extreme environments: A review 1 Geomicrobiology Laboratory, China University of Geosciences, Beijing, 100083, China. 2 Department of Geology, Miami University, Oxford, OH, 45056, USA. Email: [email protected] 3 School of Earth Sciences, China University of Geosciences, Beijing, 100083, China. The last decade has seen an extraordinary growth of and Mancinelli, 2001). These unique conditions have selected Geomicrobiology. Microorganisms have been studied in unique microorganisms and novel metabolic functions. Readers are directed to recent review papers (Kieft and Phelps, 1997; Pedersen, numerous extreme environments on Earth, ranging from 1997; Krumholz, 2000; Pedersen, 2000; Rothschild and crystalline rocks from the deep subsurface, ancient Mancinelli, 2001; Amend and Teske, 2005; Fredrickson and Balk- sedimentary rocks and hypersaline lakes, to dry deserts will, 2006). A recent study suggests the importance of pressure in the origination of life and biomolecules (Sharma et al., 2002). In and deep-ocean hydrothermal vent systems. In light of this short review and in light of some most recent developments, this recent progress, we review several currently active we focus on two specific aspects: novel metabolic functions and research frontiers: deep continental subsurface micro- energy sources. biology, microbial ecology in saline lakes, microbial Some metabolic functions of continental subsurface formation of dolomite, geomicrobiology in dry deserts, microorganisms fossil DNA and its use in recovery of paleoenviron- Because of the unique geochemical, hydrological, and geological mental conditions, and geomicrobiology of oceans. conditions of the deep subsurface, microorganisms from these envi- Throughout this article we emphasize geomicrobiological ronments are different from surface organisms in their metabolic processes in these extreme environments. -
Intra-Field Variation of Prokaryotic Communities on and Below the Seafloor 24 in the Back-Arc Hydrothermal System of the Southern Mariana Trough
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Springer - Publisher Connector Intra-Field Variation of Prokaryotic Communities On and Below the Seafloor 24 in the Back-Arc Hydrothermal System of the Southern Mariana Trough Shingo Kato, Moriya Ohkuma, and Akihiko Yamagishi Abstract Deep-sea hydrothermal vents harbor diverse prokaryotes. There are a variety of habitat types in a deep-sea hydrothermal field, e.g., active and inactive chimneys, iron-rich mats, venting fluid and hydrothermal plume. Numerous studies have shown the diversity and composition of prokaryotic communities in individual habitats. However, it is still unclear whether and how the characteristics of prokaryotic communities in their respective habitats are different. Previously, we reported 16S rRNA genes in a variety of habitats, i.e., hydrothermally active and inactive chimneys, iron-rich mats, a vent fluid, crustal fluids from boreholes, as well as ambient seawater in a back-arc basin hydrothermal field of the Southern Mariana Trough. Here we summarize the prokaryotic communities in the col- lected samples at higher taxonomic resolution (up to family level) using the detected 16S rRNA gene sequences and compare them using recently developed bioinformatics tools. The comparative analysis clearly highlights differences in prokaryotic communities among the habitat types on and below the seafloor in the Southern Mariana Trough. Furthermore, descriptions of cultured species and environmental clones close to the detected sequences provide valuable information for understanding of their distribution and potential of ecological roles in deep-sea hydrothermal fields. Keywords 16S rRNA gene Archaea Back-arc basin Bacteria Chemosynthetic ecosystem Deep- sea hydrothermal vents Prokaryotic community 24.1 Introduction The online version of this chapter (doi:10.1007/978-4-431-54865-2_24) Deep-sea hydrothermal vents are oases for organisms on the contains supplementary material, which is available to authorized users. -
Archaeoglobus Profundus Type Strain (AV18T)
Standards in Genomic Sciences (2010) 2:327-346 DOI:10.4056/sigs.942153 Complete genome sequence of Archaeoglobus profundus type strain (AV18T) Mathias von Jan1, Alla Lapidus2, Tijana Glavina Del Rio2, Alex Copeland2, Hope Tice2, Jan-Fang Cheng2, Susan Lucas2, Feng Chen2, Matt Nolan2, Lynne Goodwin2,3, Cliff Han2,3, Sam Pitluck2, Konstantinos Liolios2, Natalia Ivanova2, Konstantinos Mavromatis2, Galina Ovchinnikova2, Olga Chertkov2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Elizabeth Saunders2, Thomas Brettin2,3, John C. Detter2,3, Patrick Chain2,4, Konrad Eichinger6, Harald Huber6, Ste- fan Spring1, Manfred Rohde7, Markus Göker1, Reinhard Wirth6, Tanja Woyke2, Jim Bristow2, Jonathan A. Eisen2,8, Victor Markowitz4, Philip Hugenholtz2, Nikos C Kyrpides2, and Hans-Peter Klenk1* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 University of Regensburg, Microbiology – Archaeenzentrum, Regensburg, Germany 7 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 8 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: hyperthermophilic, marine, strictly anaerobic, sulfate respiration, hydrogen utili- zation, hydrothermal systems, Archaeoglobaceae, GEBA Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the eu- ryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeog- lobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no va- lidly published name. -
Specific Enrichment of Hyperthermophilic Electroactive Archaea From
bioRxiv preprint doi: https://doi.org/10.1101/272039; this version posted February 27, 2018. 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 Specific enrichment of hyperthermophilic electroactive Archaea from 2 deep-sea hydrothermal vent on electrically conductive support. 3 4 Guillaume Pillot1, Eléonore Frouin1, Emilie Pasero1, Anne Godfroy2, Yannick Combet-Blanc1, 5 Sylvain Davidson1 & Pierre-Pol Liebgott1* 6 1 Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, Marseille, France. 7 2 Laboratoire de Microbiologie des Environnements Extrêmes - UMR6197 IFREMER, CNRS, 8 UBO Centre de Brest–CS10070/IUEM, Plouzané, France. 9 *Corresponding author: [email protected]; Mediterranean Institute of 10 Oceanography, Campus de Luminy, Bâtiment OCEANOMED, 13288 Marseille Cedex 09. 11 Abstract 12 While more and more investigations are done to isolate hyperthermophilic exoelectrogenic 13 communities from environments, none have been performed yet on deep-sea hydrothermal vent. 14 Samples of black smoker chimney from Rainbow site on the Atlantic mid-oceanic ridge have 15 been harvested for enriching exoelectrogens in microbial electrolysis cells under hyperthermophilic 16 (80°C) condition. Two enrichments have been performed: one from direct inoculation of crushed 17 chimney and the other one from inoculation of a pre-cultivation on iron (III) oxide. In both 18 experiments, a current production was observed from 2.4 A/m² to 5.8 A/m² with a set anode 19 potential of +0.05 vs SHE. Taxonomic affiliation of the exoelectrogen communities obtained 20 exhibited a specific enrichment of Archaea from Thermococcales and Archeoglobales orders on the 21 electrode, even when both inocula were dominated by Bacteria. -
Marine Extremophiles: a Source of Hydrolases for Biotechnological Applications
Mar. Drugs 2015, 13, 1925-1965; doi:10.3390/md13041925 OPEN ACCESS marine drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Marine Extremophiles: A Source of Hydrolases for Biotechnological Applications Gabriel Zamith Leal Dalmaso 1,2, Davis Ferreira 3 and Alane Beatriz Vermelho 1,* 1 BIOINOVAR—Biotechnology laboratories: Biocatalysis, Bioproducts and Bioenergy, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil; E-Mail: [email protected] 2 Graduate Program in Plant Biotechnology, Health and Science Centre, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil 3 BIOINOVAR—Biotechnology Laboratories: Virus-Cell Interaction, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +55-(21)-3936-6743; Fax: +55-(21)-2560-8344. Academic Editor: Kirk Gustafson Received: 1 December 2014 / Accepted: 25 March 2015 / Published: 3 April 2015 Abstract: The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons. -
Lectures 2020
Dr. Warshi Dandeniya Environmental microbiology SS 5113 Dr. Warshi Dandeniya Bioenergetics of microorganisms 2 h WS Evolution of metabolic pathways 2 h Reading assignment Techniques in environmental 3 h microbiology Presentation Microbial communities 3 h Biogeocycling of nutrients 4 h Enzymes in the soil env. 4 h Midterm paper All assessments 60% Microorganisms as sinks and 7 h WB sources of pollutants Presentation (15%) Principles of biological treatments 3 h End term examination 2h 25% Dr. Warshi Dandeniya Environmental microbiology The study of microorganisms that inhabit the Earth and their roles in carrying out processes in both natural and human made systems Ecology Physiology Environmental Microbial Sciences Ecology Thermodynamics Habitat diversity Evolution Dr. Warshi Dandeniya Traits of Microorganisms • Small size • Wide distribution throughout Earth’s habitat • High specific surface area • High rate of metabolic activity • Physiological responsiveness • Genetic malleability • Potential rapid growth rate • Incomparable nutritional diversity • Unbeatable enzymatic diversity What are the ecological consequences of traits? Can you name major taxonomic groups? Dr. Warshi Dandeniya Ubiquitous in the environment Dr. Warshi Dandeniya So much to explore • Estimated global diversity of microorganisms ~5 million species • So far cultured and characterized ~6,500 species • Documented based on biomarkers ~100,000 species Dr. Warshi Dandeniya An example from polar environment A metagenomic study with sea water revealed: • Very high microbial diversity in polar ocean • OTUs – 16S RNA gene markers with 97% similarity Cao et al., 2020 https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00826-9 Dr. Warshi Dandeniya Sri Lankan experience: Diversity of fungi in dry mixed evergreen forests (Dandeniya and Attanayake 2017) Maximum of 10 different CFU/plate 177 species Undisturbed forest Regenerating forest Chena 8 Culture based approach Metagenomic approach 8 Dr. -
Dominio Archaea
FILOGENIA DE LOS SERES VIVOS: DOMINIO ARCHAEA Nuria Garzón Pinto Facultad de Farmacia Universidad de Sevilla Septiembre de 2017 FILOGENIA DE LOS SERES VIVOS: DOMINIO ARCHAEA TRABAJO FIN DE GRADO Nuria Garzón Pinto Tutores: Antonio Ventosa Ucero y Cristina Sánchez-Porro Álvarez Tipología del trabajo: Revisión bibliográfica Grado en Farmacia. Facultad de Farmacia Departamento de Microbiología y Parasitología (Área de Microbiología) Universidad de Sevilla Sevilla, septiembre de 2017 RESUMEN A lo largo de la historia, la clasificación de los seres vivos ha ido variando en función de las diversas aportaciones científicas que se iban proponiendo, y la historia evolutiva de los organismos ha sido durante mucho tiempo algo que no se lograba conocer con claridad. Actualmente, gracias sobre todo a las ideas aportadas por Carl Woese y colaboradores, se sabe que los seres vivos se clasifican en 3 dominios (Bacteria, Eukarya y Archaea) y se conocen las herramientas que nos permiten realizar estudios filogenéticos, es decir, estudiar el origen de las especies. La herramienta principal, y en base a la cual se ha realizado la clasificación actual es el ARNr 16S. Sin embargo, hoy día sedispone de otros métodos que ayudan o complementan los análisis de la evolución de los seres vivos. En este trabajo se analiza cómo surgió el dominio Archaea, se describen las características y aspectos más importantes de las especies este grupo y se compara con el resto de dominios (Bacteria y Eukarya). Las arqueas han despertado un gran interés científico y han sido investigadas sobre todo por su capacidad para adaptarse y desarrollarse en ambientes extremos. -
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. -
Laboratory of Marine Environmental Microbiology
Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University 12/09/2017 Laboratory of Marine Environmental Microbiology Professor:Shigeki SAWAYAMA, Associate professor:Satoshi NAKAGAWA This laboratory is doing researches on microalgal productions of ω-3 fatty acids, carotenoids and third-generation biofuels by genetic engineering. ω-3 Fatty acids and carotenoids have physiological functions and are used for dietary supplements. We are also searching novel and useful fungi from marine environments. In addition, we have studied ecophysiology and evolution of ‘earth-eating’ microorganisms inhabiting various extreme marine environments such as deep-sea hydrothermal fields. ω-3 Fatty acids, carotenoids and biofuel production using microalgae Chlorella spp. produce ω-3 fatty acids and Dunaliella spp. produce β-carotene known as a vitamin A pre-cursor. We are doing researches on molecular biology of these microalgae to produce useful compounds. Dunaliella salina Marine fungi and methanogens Fungi producing large amount of enzymes are widely used for fermentation industries. We are conducting research on screening of novel marine fungi. We are also studying ecological roles of methanogens in aquatic environments. Marine fungus with melon flavor Microbial ecophysiology and evolution in extreme marine environments. Rich microbial ecosystems exist in deep-sea and oceanic sediments, and even in rock deep inside Earth’s crust, where not long ago it was thought that life could not exist. We have studied ecophysiology and evolution of microorganisms inhabiting extreme marine environments. ©JAMSTEC DSV Shinkai6500 Key words Microalgae, ω-3 Fatty acid, Carotenoid, Biofuel, Fungi, Yeast, Methanogen, Deep-sea vents, Symbiosis, Extremophiles Research Achievements 2017 Overexpression of DnaJ-like chaperone enhances carotenoid synthesis in Chlamydomonas reinhardtii. -
Aciduliprofundum Boonei’’, a Cultivated Obligate Thermoacidophilic Euryarchaeote from Deep-Sea Hydrothermal Vents
Extremophiles (2008) 12:119–124 DOI 10.1007/s00792-007-0111-0 ORIGINAL PAPER Tetraether membrane lipids of Candidatus ‘‘Aciduliprofundum boonei’’, a cultivated obligate thermoacidophilic euryarchaeote from deep-sea hydrothermal vents Stefan Schouten Æ Marianne Baas Æ Ellen C. Hopmans Æ Anna-Louise Reysenbach Æ Jaap S. Sinninghe Damste´ Received: 11 June 2007 / Accepted: 28 August 2007 / Published online: 28 September 2007 Ó Springer 2007 Abstract The lipid composition of Candidatus ‘‘Acidu- vents contain ecosystems, which are predominantly fueled liprofundum boonei’’, the only cultivated representative of by geochemical energy and are host to many newly archaea falling in the DHVE2 phylogenetic cluster, a group described free-living microbes, which are often associated of microorganisms ubiquitously occurring at hydrothermal with actively venting porous deep-sea vent deposits or vents, was studied. The predominant core membrane lipids ‘‘chimneys’’. The steep chemical and thermal gradients in this thermophilic euryarchaeote were found to be com- within the walls of these deposits provide a wide range of posed of glycerol dibiphytanyl glycerol tetraethers microhabitats for microorganisms with suitable conditions (GDGTs) containing 0–4 cyclopentyl moieties. In addition, for aerobic and anaerobic thermophiles and mesophiles GDGTs with an additional covalent bond between the (e.g. McCollom and Schock 1997). Indeed, both culture- isoprenoid hydrocarbon chains, so-called H-shaped dependent and -independent approaches have exposed a GDGTs, were present. The latter core lipids have been vast diversity of Bacteria and Archaea associated with rarely reported previously. Intact polar lipid analysis deep-sea vent deposits (e.g. Reysenbach and Shock 2002; revealed that they predominantly consist of GDGTs with a Schrenk et al. -
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a 50 40 DSB 30 DSS HSB OTUs 20 10 HSS 0 REB 0 20406080RES Number of clones 20 DSB b 15 DSS 10 HSB OTUs 5 HSS 0 REB 0 204060 RES Number of clones Fig. S1. Rarefaction curves for bacterial (a) and archaeal (b) clone libraries. 1 Fig. S2. Communities clustered using normalized weighted-UniFrac PCA for bacterial communities (a). Each point represents an individual sample. 2 a b Jaccard Chao cd Jaccard Chao Fig. S3. Communities clustered using multidimensional scaling method for bacterial (a and b, Jaccard- and Chao-indices, respectively) and archaeal communities (c and d, Jaccard- and Chao-indices, respectively). Each point represents an individual sample. 3 Table S1. Summary of archaeal 16S rRNA gene clone sequences identified from the Yamagawa coastal hydrothermal field. Number of clones Pylogenetic group Representative clone Closest match (NCBI BLAST) Source Accession no. Similarity (%) HSS HSB DSS DSB RES REB Crenarchaeota Desulfurococcacae DSB_A38 1 Aeropyrum camini strain SY1 deep-sea hydrothermal vent chimney NR_040973 95 HSB_A50 1 Aeropyrum camini strain SY1 deep-sea hydrothermal vent chimney NR_040973 95 HSB_A77 6 Aeropyrum camini strain SY1 deep-sea hydrothermal vent chimney NR_040973 96 HSS_A02 1 10 Aeropyrum camini strain SY1 deep-sea hydrothermal vent chimney NR_040973 97 HSB_A38 2 clone HTM1036Pn-A124 microbial mats on polychaete nests at the Hatoma Knoll AB611454 99 HSB_A68 1 clone HTM1036Pn-A124 microbial mats on polychaete nests at the Hatoma Knoll AB611454 93 Pyrodictiaceae HSB_A20 2 Geogemma indica strain 296 deep-sea hydrothermal vent sulfide chimney DQ492260 98 HSB_A46 1 clone TOTO-A1-15 Pacific Ocean, Mariana Volcanic Arc AB167480 95 HSB_A23 1 clone F99a113 nascent hydrothermal chimney DQ228527 99 Thermoproteaceae HSB_A18 3 Pyrobaculum aerophilum str.