5. Ecology of Hypersaline Microorganisms
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Complete Genome Sequence of the Antarctic Halorubrum Lacusprofundi Type Strain ACAM 34 Iain J
Anderson et al. Standards in Genomic Sciences (2016) 11:70 DOI 10.1186/s40793-016-0194-2 SHORT GENOME REPORT Open Access Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34 Iain J. Anderson1, Priya DasSarma2*, Susan Lucas1, Alex Copeland1, Alla Lapidus1, Tijana Glavina Del Rio1, Hope Tice1, Eileen Dalin1, David C. Bruce3, Lynne Goodwin3, Sam Pitluck1, David Sims3, Thomas S. Brettin3, John C. Detter3, Cliff S. Han3, Frank Larimer1,4, Loren Hauser1,4, Miriam Land1,4, Natalia Ivanova1, Paul Richardson1, Ricardo Cavicchioli5, Shiladitya DasSarma2, Carl R. Woese6 and Nikos C. Kyrpides1 Abstract Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. WereportherethecompletegenomesequenceofH. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea. Keywords: Archaea, Halophile, Halorubrum, Extremophile, Cold adaptation, Tree of life Abbreviations: TE, Tris-EDTA buffer; CRITICA, Coding region identification tool invoking comparative analysis; PRIAM, PRofils pour l’Identification Automatique du Métabolisme; KEGG, Kyoto Encyclopedia of Genes and Genomes; COG, Clusters of Orthologous Groups; TMHMM, Transmembrane hidden Markov model; CRISPR, Clustered regularly interspaced short palindromic repeats Introduction 2006 Joint Genome Institute Community Sequencing Halorubrum lacusprofundi is an extremely halophilic Program project because of its ability to grow at low archaeon belonging to the class Halobacteria within the temperature and its phylogenetic distance from other phylum Euryarchaeota. -
Multiple Lateral Transfers of Dissimilatory Sulfite Reductase
JOURNAL OF BACTERIOLOGY, Oct. 2001, p. 6028–6035 Vol. 183, No. 20 0021-9193/01/$04.00ϩ0 DOI: 10.1128/JB.183.20.6028–6035.2001 Copyright © 2001, American Society for Microbiology. All Rights Reserved. Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes MICHAEL KLEIN,1 MICHAEL FRIEDRICH,2 ANDREW J. ROGER,3 PHILIP HUGENHOLTZ,4 SUSAN FISHBAIN,5 1 4 6 1 HEIKE ABICHT, LINDA L. BLACKALL, DAVID A. STAHL, AND MICHAEL WAGNER * 1 Lehrstuhl fu¨r Mikrobiologie, Technische Universita¨t Mu¨nchen, D-85350 Freising, and Department of Biogeochemistry, Max Planck Downloaded from Institute for Terrestrial Microbiology, D-35043-Marburg,2 Germany; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada3; Advanced Wastewater Management Centre, Department of Microbiology and Parasitology, The University of Queensland, Brisbane 4072, Queensland, Australia4; Department of Civil Engineering, Northwestern University, Evanston, Illinois 60208-31095; and Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195-27006 Received 26 February 2001/Accepted 3 July 2001 http://jb.asm.org/ A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. In addition, the sequence of the dsrAB gene homologs of the sulfite reducer Desulfitobacterium dehalogenans was determined. In contrast to previous reports, comparative analysis of all available DsrAB sequences produced a tree topology partially inconsistent with the corresponding 16S rRNA phylogeny. For example, the DsrAB sequences of -several Desulfotomaculum species (low G؉C gram-positive division) and two members of the genus Thermode sulfobacterium (a separate bacterial division) were monophyletic with ␦-proteobacterial DsrAB sequences. -
Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide
antioxidants Review Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide Ivan Kushkevych 1,* , Veronika Bosáková 1,2 , Monika Vítˇezová 1 and Simon K.-M. R. Rittmann 3,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] (V.B.); [email protected] (M.V.) 2 Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic 3 Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Vienna, Austria * Correspondence: [email protected] (I.K.); [email protected] (S.K.-M.R.R.); Tel.: +420-549-495-315 (I.K.); +431-427-776-513 (S.K.-M.R.R.) Abstract: Hydrogen sulfide is a toxic compound that can affect various groups of water microorgan- isms. Photolithotrophic sulfur bacteria including Chromatiaceae and Chlorobiaceae are able to convert inorganic substrate (hydrogen sulfide and carbon dioxide) into organic matter deriving energy from photosynthesis. This process takes place in the absence of molecular oxygen and is referred to as anoxygenic photosynthesis, in which exogenous electron donors are needed. These donors may be reduced sulfur compounds such as hydrogen sulfide. This paper deals with the description of this metabolic process, representatives of the above-mentioned families, and discusses the possibility using anoxygenic phototrophic microorganisms for the detoxification of toxic hydrogen sulfide. Moreover, their general characteristics, morphology, metabolism, and taxonomy are described as Citation: Kushkevych, I.; Bosáková, well as the conditions for isolation and cultivation of these microorganisms will be presented. V.; Vítˇezová,M.; Rittmann, S.K.-M.R. -
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. -
Archaeology of Eukaryotic DNA Replication
Downloaded from http://cshperspectives.cshlp.org/ on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Archaeology of Eukaryotic DNA Replication Kira S. Makarova and Eugene V. Koonin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 Correspondence: [email protected] Recent advances in the characterization of the archaeal DNA replication system together with comparative genomic analysis have led to the identification of several previously un- characterized archaeal proteins involved in replication and currently reveal a nearly com- plete correspondence between the components of the archaeal and eukaryotic replication machineries. It can be inferred that the archaeal ancestor of eukaryotes and even the last common ancestor of all extant archaea possessed replication machineries that were compa- rable in complexity to the eukaryotic replication system. The eukaryotic replication system encompasses multiple paralogs of ancestral components such that heteromeric complexes in eukaryotes replace archaeal homomeric complexes, apparently along with subfunctionali- zation of the eukaryotic complex subunits. In the archaea, parallel, lineage-specific dupli- cations of many genes encoding replication machinery components are detectable as well; most of these archaeal paralogs remain to be functionally characterized. The archaeal rep- lication system shows remarkable plasticity whereby even some essential components such as DNA polymerase and single-stranded DNA-binding protein are displaced by unrelated proteins with analogous activities in some lineages. ouble-stranded DNA is the molecule that Okazaki fragments (Kornberg and Baker 2005; Dcarries genetic information in all cellular Barry and Bell 2006; Hamdan and Richardson life-forms; thus, replication of this genetic ma- 2009; Hamdan and van Oijen 2010). -
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. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
Int J Syst Evol Microbiol 67 1
Author version : International Journal of Systematic and Evolutionary Microbiology, vol.67(6); 2017; 1949-1956 Imhoffiella gen. nov.. a marine phototrophic member of family Chromatiaceae including the description of Imhoffiella purpurea sp. nov. and the reclassification of Thiorhodococcus bheemlicus Anil Kumar et al. 2007 as Imhoffiella bheemlica comb. nov. Nupur1, Mohit Kumar Saini1, Pradeep Kumar Singh1, Suresh Korpole1, Naga Radha Srinivas Tanuku2, Shinichi Takaichi3 and Anil Kumar Pinnaka1* 1Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh – 160 036, INDIA 2CSIR-National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam-530017, INDIA 3Nippon Medical School, Department of Biology, Kyonan-cho, Musashino 180-0023, Japan Address for correspondence* Dr. P. Anil Kumar Microbial Type Culture Collection and Gene Bank, Institute of Microbial Technology (CSIR), Sector 39A, Chandigarh – 160 036, INDIA Email: [email protected] Telephone: 00-91-172-6665170 Running title Imhoffiella purpurea sp. nov. Subject category New taxa (Gammaproteobacteria) The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain AK35T is HF562219. A coccoid-shaped phototrophic purple sulfur bacterium was isolated from a coastal surface water sample collected from Visakhapatnam, India. Strain AK35T was Gram-negative, motile, purple colored, containing bacteriochlorophyll a and the carotenoid rhodopinal as major photosynthetic pigments. Strain AK35T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically. Strain AK35T was able to utilize sulfide and thiosulfate as electron donors. The main fatty acids present were identified as C16:0, C18:1 T 7c and C16:1 7c and/or iso-C15:0 2OH (Summed feature 3) were identified. -
A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis
Microorganisms 2015, 3, 500-517; doi:10.3390/microorganisms3030500 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Article A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis Violetta La Cono 1, Erika Arcadi 1, Gina La Spada 1, Davide Barreca 2, Giuseppina Laganà 2, Ersilia Bellocco 2, Maurizio Catalfamo 1, Francesco Smedile 1, Enzo Messina 1, Laura Giuliano 1,3 and Michail M. Yakimov 1,* 1 Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina 98122, Italy; E-Mails: [email protected] (V.L.C.); [email protected] (E.A.); [email protected] (G.L.S.); [email protected] (M.C.); [email protected] (F.S.); [email protected] (E.M.); [email protected] (L.G.) 2 Department of Organic and Biological Chemistry, University of Messina, Salita Sperone 31, Villaggio S. Agata, Messina 98166, Italy; E-Mails: [email protected] (D.B.); [email protected] (G.L.); [email protected] (E.B.) 3 Mediterranean Science Commission (CIESM), 16 bd de Suisse, MC 98000, Monaco * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +39-090-6015-437. Academic Editors: Ricardo Amils and Elena González Toril Received: 1 July 2015 / Accepted: 1 September 2015 / Published: 9 September 2015 Abstract: Microbial communities inhabiting the deep-sea salt-saturated anoxic lakes of the Eastern Mediterranean operate under harsh physical-chemical conditions that are incompatible with the lifestyle of common marine microorganisms. -
The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. -
Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules
Brigham Young University BYU ScholarsArchive Theses and Dissertations 2014-07-01 Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biochemistry Commons, and the Chemistry Commons BYU ScholarsArchive Citation Taylor, Ryan M., "Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules" (2014). Theses and Dissertations. 5585. https://scholarsarchive.byu.edu/etd/5585 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor A dissertation submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Doctor of Philosophy John T. Prince, Chair Mark Clement Steven W. Graves Barry M. Willardson Dixon J. Woodbury Department of Chemistry and Biochemistry Brigham Young University July 2014 Copyright © 2014 Ryan M. Taylor All Rights Reserved ABSTRACT Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor Department of Chemistry and Biochemistry, BYU Doctor of Philosophy Biological research has benefitted greatly from the advent of omic methods. For many biomolecules, mass spectrometry (MS) methods are most widely employed due to the sensitivity which allows low quantities of sample and the speed which allows analysis of complex samples. Improvements in instrument and sample preparation techniques create opportunities for large scale experimentation. -
Genome Size Evolution in the Archaea
Kellner, S., Spang, A., Offre, P., Szollosi, G. J., Petitjean, C., & Williams, T. (2018). Genome size evolution in the Archaea. Emerging Topics in Life Sciences. https://doi.org/10.1042/ETLS20180021 Publisher's PDF, also known as Version of record License (if available): CC BY Link to published version (if available): 10.1042/ETLS20180021 Link to publication record in Explore Bristol Research PDF-document This is the final published version of the article (version of record). It first appeared online via Portland Press at http://www.emergtoplifesci.org/content/early/2018/11/13/ETLS20180021 . Please refer to any applicable terms of use of the publisher. University of Bristol - Explore Bristol Research General rights This document is made available in accordance with publisher policies. Please cite only the published version using the reference above. Full terms of use are available: http://www.bristol.ac.uk/red/research-policy/pure/user-guides/ebr-terms/ Emerging Topics in Life Sciences (2018) https://doi.org/10.1042/ETLS20180021 Review Article Genome size evolution in the Archaea Siri Kellner1, Anja Spang2,3, Pierre Offre2, Gergely J. Szöllo˝si4,5, Celine Petitjean6 and Tom A. Williams6 1School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, U.K.; 2NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands; 3Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden; 4MTA-ELTE Lendület Evolutionary Genomics Research Group, 1117 Budapest, Hungary; 5Department of Biological Physics, Eötvös Loránd University, 1117 Budapest, Hungary; 6School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, U.K.