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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. -
Originally Published As
Originally published as: Westphal, A., Lerm, S., Miethling-Graff, R., Seibt, A., Wolfgramm, M., Würdemann, H. (2016): Effects of plant downtime on the microbial community composition in the highly saline brine of a geothermal plant in the North German Basin. - Applied Microbiology and Biotechnology, 100, 7, pp. 3277—3290. DOI: http://doi.org/10.1007/s00253-015-7181-1 1 Effects of plant downtime on the microbial community composition in the highly saline brine 2 of a geothermal plant in the North German Basin 3 4 Anke Westphala, Stephanie Lerma, Rona Miethling-Graffa, Andrea Seibtb, Markus 5 Wolfgrammc, Hilke Würdemannad# 6 7 a GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, 14473 Pots- 8 dam, Germany 9 b BWG Geochemische Beratung GmbH, 17041 Neubrandenburg, Germany 10 c Geothermie Neubrandenburg (GTN), 17041 Neubrandenburg, Germany 11 d Environmental Technology, Water- and Recycling Technology, Department of Engineering 12 and Natural Sciences, University of Applied Sciences Merseburg, 06217 Merseburg, Germa- 13 ny 14 15 16 17 18 19 20 21 22 23 24 # Address correspondence to Hilke Würdemann 25 [email protected] 26 Phone: +49 331 288 1516 27 Fax: ++49 331 2300662 1 28 Abstract 29 The microbial biocenosis in highly saline fluids produced from the cold well of a deep geo- 30 thermal heat store located in the North German Basin was characterized during regular plant 31 operation and immediately after plant downtime phases. Genetic fingerprinting revealed the 32 dominance of sulfate-reducing bacteria (SRB) and fermentative Halanaerobiaceae during 33 regular plant operation, whereas after shut-down phases, sequences of sulfur-oxidizing bacte- 34 ria (SOB) were also detected. -
Isolation and Characterization of a Thermophilic Sulfate-Reducing Bacterium, Desuvotomaculum Themosapovorans Sp
- INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1995, p. 218-221 Vol. 45, No. 2 0020-7713/95/$04.00+0 Copyright O 1995, International Union of Microbiological Societies Isolation and Characterization of a Thermophilic Sulfate-Reducing Bacterium, Desuvotomaculum themosapovorans sp. nov. MARIE-LAURE FARDEAU,1,''' BERNARD OLLIVIER: BHARAT K. C. PATEL?3 PREM DWIVEDI? MICHEL RAGOT? AND JEAN-LOUIS GARCIA' Laboratoire de Chimie Bactérienne, Centre National de la Recherche ScieiitiJque, 13277 Marseille cedex 9, and Laboratoire de Microbiologie ORSTOM, Université de Provence, 13331 Marseille cedex 3, France, and Faculty of Science and Technology, Crifith University, Biisbane, Queensland 4111, Australia3 Strain MLFT (T = type strain), a new thermophilic, spore-forming sulfate-reducing bacterium, was char- acterized and was found to be phenotypically, genotypically, and phylogenetically related to the genus Desul- fotornaculurn. This organism was isolated from a butyrate enrichment culture that had been inoculated with a mixed compost containing rice hulls and peanut shells. The optimum temperature for growth was 50°C. The G+C content of the DNA was 51.2 mol%. Strain MLFT incompletely oxidized pyruvate, butyrate, and butanol to acetate and presumably CO,. It used long-chain fatty acids and propanediols. We observed phenotypic and phylogenetic differences between strain MLFT and other thermophilic Desulfotornaculum species that also oxidize long-chain fatty acids. On the basis of our results, we propose that strain MLFT is a member of a new species, Desulfotornaculum tliermosapovorarzs. In environments where conditions for the survival of the The organisms wcre cultivated under strictly anoxic conditions at 55°C. The basal strictly anaerobic sulfate-reducing bacteria are not provided medium contained (per liter of distilled water) 1.0 g of NH,Cl, 0.15 g of continuously, the sporulating species of the genus Desulfo- CaCI,. -
Desulfotomaculum Arcticum Sp. Nov., a Novel Spore-Forming, Moderately
International Journal of Systematic and Evolutionary Microbiology (2006), 56, 687–690 DOI 10.1099/ijs.0.64058-0 Desulfotomaculum arcticum sp. nov., a novel spore-forming, moderately thermophilic, sulfate- reducing bacterium isolated from a permanently cold fjord sediment of Svalbard Verona Vandieken,1 Christian Knoblauch2 and Bo Barker Jørgensen1 Correspondence 1Max-Planck-Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany Verona Vandieken 2University of Hamburg, Institute of Soil Science, Allende-Platz 2, 20146 Hamburg, Germany [email protected] Strain 15T is a novel spore-forming, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard. Sulfate could be replaced by sulfite or thiosulfate. Hydrogen, formate, lactate, propionate, butyrate, hexanoate, methanol, ethanol, propanol, butanol, pyruvate, malate, succinate, fumarate, proline, alanine and glycine were used as electron donors in the presence of sulfate. Growth occurred with pyruvate as sole substrate. Optimal growth was observed at T pH 7?1–7?5 and concentrations of 1–1?5 % NaCl and 0?4 % MgCl2. Strain 15 grew between 26 and 46?5 6C and optimal growth occurred at 44 6C. Therefore, strain 15T apparently cannot grow at in situ temperatures of Arctic sediments from where it was isolated, and it was proposed that it was present in the sediment in the form of spores. The DNA G+C content was 48?9 mol%. Strain 15T was most closely related to Desulfotomaculum thermosapovorans MLFT (93?5% 16S rRNA gene sequence similarity). Strain 15T represents a novel species, for which the name Desulfotomaculum arcticum sp. nov. is proposed. The type strain is strain 15T (=DSM 17038T=JCM 12923T). -
Desulfohalobium Retbaense Gen. Nov. Sp. Nov. a Halophilic Sulfate-Reducing Bacterium from Sediments of a Hypersaline Lake in Senegal
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1991, p. 74-81 Vol. 41, No. 1 0020-7713/91/010074-08$02.OO/O Copyright 0 1991, International Union of Microbiological Societies Desulfohalobium retbaense gen. nov. sp. nov. a Halophilic Sulfate-Reducing Bacterium from Sediments of a Hypersaline Lake in Senegal B. OLLIVIER,, C. E. HATCHIKIAN,, G. PRENSIER,3 J. GUEZENNEC,, AND J.-L. GARCIA1* Laboratoire de Microbiologie ORSTOM, Universite' de Provence, 13331 Marseille Ce'dex 3, Laboratoire de Chimie Bacte'rienne, Centre National de la Recherche Scientifique, 13277 Marseille Ce'dex 9,, Laboratoire de Microbiologie, Universite' Blaise Pascal, 63177 A~biPre,~and Departement DEROIEP IFREMER, 29280 Plou~ane,~France Sulfate-reducingbacterial strain HR,, was isolated from sediments of Retba Lake, a pink hypersaline lake in Senegal. The cells were motile, nonsporulating, and rod shaped with polar flagella and incompletely oxidized a limited range of substrates to acetate and CO,. Acetate and vitamins were required for growth and could be replaced by Biotrypcase or yeast extract. Sulfate, sulfite, thiosulfate, and elemental sulfur were used as electron acceptors and were reduced to H,S. Growth occurred at pH values ranging from 5.5 to 8.0. The optimum temperature for growth was 37 to 4OOC. NaCl and MgCI, were required for growth; the optimum NaCl concentration was near 10%.The guanine-plus-cytosinecontent of the DNA was 57.1 f 0.2 mol%. On the basis of the morphological and physiological properties of this strain, we propose that it should be classified in a new genus, Desulfohalobium, which includes a single species, Desulfohalobium retbaense. The type strain is strain DSM 5692. -
Desulfotomaculum Alkaliphilum Sp. Nov., a New Alkaliphilic, Moderately Thermophilic, Sulfate-Reducing Bacterium
International Journal of Systematic and Evolutionary Microbiology (2000), 50, 25–33 Printed in Great Britain Desulfotomaculum alkaliphilum sp. nov., a new alkaliphilic, moderately thermophilic, sulfate-reducing bacterium E. Pikuta,1 A. Lysenko,1 N. Suzina,2 G. Osipov,4 B. Kuznetsov,3 T. Tourova,1 V. Akimenko2 and K. Laurinavichius2 Author for correspondence: E. Pikuta. Tel: 7 95 135 0421. Fax: 7 095 135 65 30. e-mail: pikuta!inmi.host.ru 1 Institute of Microbiology, A new moderately thermophilic, alkaliphilic, sulfate-reducing, Russian Academy of chemolithoheterotrophic bacterium, strain S1T, was isolated from a mixed Sciences, prospekt 60-let Octiabria, 7/2, Moscow, cow/pig manure with neutral pH. The bacterium is an obligately anaerobic, 117811, Russia non-motile, Gram-positive, spore-forming curved rod growing within a pH 2 Institute of Biochemistry range of 8<0–9<15 (optimal growth at pH 8<6–8<7) and temperature range of and Physiology of 30–58 SC (optimal growth at 50–55 SC). The optimum NaCl concentration for Microorganisms, growth is 0<1%. Strain S1T is an obligately carbonate-dependent alkaliphile. Russian Academy of Sciences, Pushchino, Russia The GMC content of the DNA is 40<9 mol%. A limited number of compounds are utilized as electron donors, including H Macetate, formate, ethanol, lactate and 3 Centre ‘Bioengineering’, 2 Russian Academy of pyruvate. Sulfate, sulfite and thiosulfate, but not sulfur or nitrate, can be used Sciences, Moscow, Russia as electron acceptors. Strain S1T is able to utilize acetate or yeast extract as T 4 Academician Yu. Isakov sources of carbon. Analysis of the 16S rDNA sequence allowed strain S1 Scientific Group, Russian (¯ DSM 12257T) to be classified as a representative of a new species of the Academy of Medical genus Desulfotomaculum, Desulfotomaculum alkaliphilum sp. -
1 Characterization of Sulfur Metabolizing Microbes in a Cold Saline Microbial Mat of the Canadian High Arctic Raven Comery Mast
Characterization of sulfur metabolizing microbes in a cold saline microbial mat of the Canadian High Arctic Raven Comery Master of Science Department of Natural Resource Sciences Unit: Microbiology McGill University, Montreal July 2015 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master in Science © Raven Comery 2015 1 Abstract/Résumé The Gypsum Hill (GH) spring system is located on Axel Heiberg Island of the High Arctic, perennially discharging cold hypersaline water rich in sulfur compounds. Microbial mats are found adjacent to channels of the GH springs. This thesis is the first detailed analysis of the Gypsum Hill spring microbial mats and their microbial diversity. Physicochemical analyses of the water saturating the GH spring microbial mat show that in summer it is cold (9°C), hypersaline (5.6%), and contains sulfide (0-10 ppm) and thiosulfate (>50 ppm). Pyrosequencing analyses were carried out on both 16S rRNA transcripts (i.e. cDNA) and genes (i.e. DNA) to investigate the mat’s community composition, diversity, and putatively active members. In order to investigate the sulfate reducing community in detail, the sulfite reductase gene and its transcript were also sequenced. Finally, enrichment cultures for sulfate/sulfur reducing bacteria were set up and monitored for sulfide production at cold temperatures. Overall, sulfur metabolism was found to be an important component of the GH microbial mat system, particularly the active fraction, as 49% of DNA and 77% of cDNA from bacterial 16S rRNA gene libraries were classified as taxa capable of the reduction or oxidation of sulfur compounds. -
Dispersal of Thermophilic Desulfotomaculum Endospores Into Baltic Sea Sediments Over Thousands of Years
The ISME Journal (2012), 1–13 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years Ju´ lia Rosa de Rezende1, Kasper Urup Kjeldsen1, Casey RJ Hubert2, Kai Finster3, Alexander Loy4 and Bo Barker Jørgensen1 1Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark; 2School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, UK; 3Microbiology Section, Department of Bioscience, Aarhus University, Aarhus, Denmark and 4Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria Patterns of microbial biogeography result from a combination of dispersal, speciation and extinction, yet individual contributions exerted by each of these mechanisms are difficult to isolate and distinguish. The influx of endospores of thermophilic microorganisms to cold marine sediments offers a natural model for investigating passive dispersal in the ocean. We investigated the activity, diversity and abundance of thermophilic endospore-forming sulfate-reducing bacteria (SRB) in Aarhus Bay by incubating pasteurized sediment between 28 and 85 1C, and by subsequent molecular diversity analyses of 16S rRNA and of the dissimilatory (bi)sulfite reductase (dsrAB) genes within the endospore-forming SRB genus Desulfotomaculum. The thermophilic Desulfotomaculum community in Aarhus Bay sediments consisted of at least 23 species-level 16S rRNA sequence phylotypes. In two cases, pairs of identical 16S rRNA and dsrAB sequences in Arctic surface sediment 3000 km away showed that the same phylotypes are present in both locations. Radiotracer- enhanced most probable number analysis revealed that the abundance of endospores of thermophilic SRB in Aarhus Bay sediment was ca. -
Desulfotomaculum Halophilum Sp. Now, a Halophi I Ic Sulfate-Reducing
International Journal of Systematic Bacteriology (1 998), 48, 333-338 Printed in Great Britain Desulfotomaculum halophilum sp. now, a halophiI ic sulfate-reducing bacterium isolated from oil production facilities C. Tardy-Jacquenod,' M. Magot,' B. K. C. Patel,3 R. Matheron4 and P. Caumette' Author for correspondence: P. Caumette. Tel: + 33 5 56 22 39 01. Fax: + 33 5 56 83 51 04. 1 La boratoire A halophilic endospore-forming,sulfate-reducing bacterium was isolated from d'OcCa nograp h ie an oilfield brine in France. The strain, designated SEBR 3139, was composed of Biologique, UniversitC Bordeaux 1, 2 rue du long, straight to curved rods. It grew in 1-14% NaCl with an optimum at 6%. Professeur Jolyet, F-33120 On the basis of morphological, physiologicaland phylogenetical Arcachon, France characteristics, strain SEBR 3139 should be classified in the genus 2 Sanofi Recherche, Centre Desulfotomaculum. However, it is sufficiently different from the hitherto de Lab&ge, F-31676 described Desulfotomaculum species to be considered as a new species. Strain Labege, France SEBR 3139' (= DSM 115593 represents the first moderate halophilic species of 3 Faculty of Science and the genus Desulfofomaculum. The name Desulfotomaculum halophilum Technology, Griff ith University, Nathan, sp. nov. is proposed. Brisbane, Australia 41 11 4 Laboratoire de Microbiologie, UniversitC Keywords: Desulfotomaculum halophilum, halophile, sulfate-reducing bacterium, oil des Sciences et Techniques production de Saint-JCrdme, F-13397 Marseille cedex 20, France INTRODUCTION NaCl. Strain SEBR 3 139 represents the first halophilic spore-forming, sulfate-reducing bacterium described Sulfate-reducing bacteria that form heat-resistant so far. Based on 16s rDNA sequence comparisons, endospores are classified in the genus Desulfoto- strain SEBR 3139 was found to be phylogenetically rnaculum (3). -
MICRO-ORGANISMS and RUMINANT DIGESTION: STATE of KNOWLEDGE, TRENDS and FUTURE PROSPECTS Chris Mcsweeney1 and Rod Mackie2
BACKGROUND STUDY PAPER NO. 61 September 2012 E Organización Food and Organisation des Продовольственная и cельскохозяйственная de las Agriculture Nations Unies Naciones Unidas Organization pour организация para la of the l'alimentation Объединенных Alimentación y la United Nations et l'agriculture Наций Agricultura COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE MICRO-ORGANISMS AND RUMINANT DIGESTION: STATE OF KNOWLEDGE, TRENDS AND FUTURE PROSPECTS Chris McSweeney1 and Rod Mackie2 The content of this document is entirely the responsibility of the authors, and does not necessarily represent the views of the FAO or its Members. 1 Commonwealth Scientific and Industrial Research Organisation, Livestock Industries, 306 Carmody Road, St Lucia Qld 4067, Australia. 2 University of Illinois, Urbana, Illinois, United States of America. This document is printed in limited numbers to minimize the environmental impact of FAO's processes and contribute to climate neutrality. Delegates and observers are kindly requested to bring their copies to meetings and to avoid asking for additional copies. Most FAO meeting documents are available on the Internet at www.fao.org ME992 BACKGROUND STUDY PAPER NO.61 2 Table of Contents Pages I EXECUTIVE SUMMARY .............................................................................................. 5 II INTRODUCTION ............................................................................................................ 7 Scope of the Study ........................................................................................................... -
Desulfotomaculum Acetoxidans Type Strain (5575)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575). Permalink https://escholarship.org/uc/item/53z4r149 Journal Standards in genomic sciences, 1(3) ISSN 1944-3277 Authors Spring, Stefan Lapidus, Alla Schröder, Maren et al. Publication Date 2009-11-22 DOI 10.4056/sigs.39508 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2009) 1: 242-253 DOI:10.4056/sigs.39508 Complete genome sequence of Desulfotomaculum acetox- idans type strain (5575T) Stefan Spring1, Alla Lapidus2, Maren Schröder1, Dorothea Gleim1, David Sims3, Linda Meincke3, Tijana Glavina Del Rio2, Hope Tice2, Alex Copeland2, Jan-Fang Cheng2, Susan Lucas2, Feng Chen2, Matt Nolan2, David Bruce2,3, Lynne Goodwin2,3, Sam Pitluck2, Natalia Ivanova2, Konstantinos Mavromatis2, Natalia Mikhailova2, Amrita Pati2, Amy Chen4, Krish- na Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Patrick Chain2,6, Elizabeth Saunders2,3, Thomas Brettin2,3, John C. Detter2,3, Markus Göker1, Jim Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2, Nikos C Kyr- pides2, Hans-Peter Klenk1*, and Cliff Han2,3 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 Labora- tory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 Lawrence Livermore National Laboratory, Livermore, California, USA 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: sulfate-reducer, hydrogen sulfide, piggery waste, mesophile, motile, sporulating, obligate anaerobic, Peptococcaceae, Clostridiales, Firmicutes. -
Desulfonatronovibrio Halophilus Sp. Nov., a Novel Moderately Halophilic Sulfate-Reducing Bacterium from Hypersaline Chloride–Sulfate Lakes in Central Asia
Extremophiles (2012) 16:411–417 DOI 10.1007/s00792-012-0440-5 ORIGINAL PAPER Desulfonatronovibrio halophilus sp. nov., a novel moderately halophilic sulfate-reducing bacterium from hypersaline chloride–sulfate lakes in Central Asia D. Y. Sorokin • T. P. Tourova • B. Abbas • M. V. Suhacheva • G. Muyzer Received: 10 February 2012 / Accepted: 22 March 2012 / Published online: 10 April 2012 Ó The Author(s) 2012. This article is published with open access at Springerlink.com Abstract Four strains of lithotrophic sulfate-reducing soda lakes. The isolates utilized formate, H2 and pyruvate as bacteria (SRB) have been enriched and isolated from electron donors and sulfate, sulfite and thiosulfate as electron anoxic sediments of hypersaline chloride–sulfate lakes in acceptors. In contrast to the described species of the genus the Kulunda Steppe (Altai, Russia) at 2 M NaCl and pH Desulfonatronovibrio, the salt lake isolates could only tolerate 7.5. According to the 16S rRNA gene sequence analysis, high pH (up to pH 9.4), while they grow optimally at a neutral the isolates were closely related to each other and belonged pH. They belonged to the moderate halophiles growing to the genus Desulfonatronovibrio, which, so far, included between 0.2 and 2 M NaCl with an optimum at 0.5 M. On the only obligately alkaliphilic members found exclusively in basis of their distinct phenotype and phylogeny, the described halophilic SRB are proposed to form a novel species within the genus Desulfonatronovibrio, D. halophilus (type strain T T T Communicated by A. Oren. HTR1 = DSM24312 = UNIQEM U802 ). The GenBank/EMBL accession numbers of the 16S rRNA gene Keywords Sulfate-reducing bacteria (SRB) Á sequences of the HTR strains are GQ922847, HQ157562, HQ157563 and JN408678; the dsrAB gene sequences of (halo)alkaliphilic SRB Desulfonatronovibrio Á Hypersaline lakes Á Halophilic obtained in this study are JQ519392-JQ519396.