Isolation, Characterization, and Ecology
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Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms. -
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. -
Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma Divulgatum
microorganisms Article Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum Rafael Bargiela 1 , Karin Lanthaler 1,2, Colin M. Potter 1,2 , Manuel Ferrer 3 , Alexander F. Yakunin 1,2, Bela Paizs 1,2, Peter N. Golyshin 1,2 and Olga V. Golyshina 1,2,* 1 School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; [email protected] (R.B.); [email protected] (K.L.); [email protected] (C.M.P.); [email protected] (A.F.Y.); [email protected] (B.P.); [email protected] (P.N.G.) 2 Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK 3 Systems Biotechnology Group, Department of Applied Biocatalysis, CSIC—Institute of Catalysis, Marie Curie 2, 28049 Madrid, Spain; [email protected] * Correspondence: [email protected]; Tel.: +44-1248-388607; Fax: +44-1248-382569 Received: 27 April 2020; Accepted: 15 May 2020; Published: 19 May 2020 Abstract: The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation. -
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 -
Differences in Lateral Gene Transfer in Hypersaline Versus Thermal Environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1
Rhodes et al. BMC Evolutionary Biology 2011, 11:199 http://www.biomedcentral.com/1471-2148/11/199 RESEARCH ARTICLE Open Access Differences in lateral gene transfer in hypersaline versus thermal environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1 Abstract Background: The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these “long distance” LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles. Results: We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles. Conclusions: Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA. -
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. -
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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. -
Metagenomic Sequence Assembly Via Iterative Reclassification
MetaPar: Metagenomic Sequence Assembly via Iterative Reclassification Minji Kim∗, Jonathan G. Ligo∗, Amin Emad, Farzad Farnoud (Hassanzadeh) Olgica Milenkovic and Venugopal V. Veeravalli ∗The first two authors contributed equally to this paper. Department of Electrical and Computer Engineering, University of Illinois, Urbana-Champaign Email: fmkim158,ligo2,emad2,hassanz1,milenkov,vvvg [at] illinois.edu Abstract—We introduce a parallel algorithmic architecture for step, some reads may remain unaligned, and require alternative means metagenomic sequence assembly, termed MetaPar, which allows of processing. for significant reductions in assembly time and consequently Two options may be pursued in the second round of classification, enables the processing of large genomic datasets on computers depending on the number of unaligned reads. If the number of reads with low memory usage. The gist of the approach is to iteratively is prohibitively large so as not to allow one-pass assembly with a perform read (re)classification based on phylogenetic marker standard metagenomic assembler, the reads are randomly partitioned genes and assembler outputs generated from random subsets into subgroups small enough to be assembled. All assemblies are per- of metagenomic reads. Once a sufficiently accurate classification formed in parallel. Unaligned reads are iteratively reassigned between within genera is performed, de novo metagenomic assemblers assemblers until no changes in the assembled contigs are reported or (such as Velvet or IDBA-UD) or reference based assemblers may until a maximum number of iterations is reached. On the other hand, be used for contig construction. We analyze the performance if the number of reads is small enough to allow for one pass assembly, of MetaPar on synthetic data consisting of 15 randomly chosen the same procedure as outlined for the initial step is performed. -
4 Metabolic and Taxonomic Diversification in Continental Magmatic Hydrothermal Systems
Maximiliano J. Amenabar, Matthew R. Urschel, and Eric S. Boyd 4 Metabolic and taxonomic diversification in continental magmatic hydrothermal systems 4.1 Introduction Hydrothermal systems integrate geological processes from the deep crust to the Earth’s surface yielding an extensive array of spring types with an extraordinary diversity of geochemical compositions. Such geochemical diversity selects for unique metabolic properties expressed through novel enzymes and functional characteristics that are tailored to the specific conditions of their local environment. This dynamic interaction between geochemical variation and biology has played out over evolu- tionary time to engender tightly coupled and efficient biogeochemical cycles. The timescales by which these evolutionary events took place, however, are typically in- accessible for direct observation. This inaccessibility impedes experimentation aimed at understanding the causative principles of linked biological and geological change unless alternative approaches are used. A successful approach that is commonly used in geological studies involves comparative analysis of spatial variations to test ideas about temporal changes that occur over inaccessible (i.e. geological) timescales. The same approach can be used to examine the links between biology and environment with the aim of reconstructing the sequence of evolutionary events that resulted in the diversity of organisms that inhabit modern day hydrothermal environments and the mechanisms by which this sequence of events occurred. By combining molecu- lar biological and geochemical analyses with robust phylogenetic frameworks using approaches commonly referred to as phylogenetic ecology [1, 2], it is now possible to take advantage of variation within the present – the distribution of biodiversity and metabolic strategies across geochemical gradients – to recognize the extent of diversity and the reasons that it exists. -
Microbiology and Geochemistry of Smith Creek and Grass Valley Hot
Journal of Earth Science, Vol. 21, Special Issue, p. 315–318, June 2010 ISSN 1674-487X Printed in China Microbiology and Geochemistry of Smith Creek and Grass Valley Hot Springs: Emerging Evidence for Wide Distribution of Novel Thermophilic Lineages in the US Great Basin Jeremy A Dodsworth, Brian P Hedlund* School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA INTRODUCTION the Southern Smith Creek Valley springs region and The endorheic Great Basin (GB) region in the GVS1 is just southeast of Hot Spring Point, as desig- western US is host to a variety of non-acidic geother- nated by the Nevada Bureau of Mines and Geology mal spring systems. Heating of the majority of these website (http://www.nbmg.unr.edu/geothermal/ systems is due to their association with range-front gthome. tm). Sample collection, DNA extraction, field faults, in contrast to caldera-associated hot springs in measurements and water chemistry analysis were per- systems such as Yellowstone National Park and formed with source pool samples essentially as de- Kamchatka (Faulds et al., 2006). Previous characteri- scribed (Vick et al., 2010). 16S rRNA gene libraries zation of two geothermal systems in the GB, Great were constructed using PCR forward primers 9bF Boiling/Mud Hot springs (Costa et al., 2009) and Lit- (specific for Bacteria; L2) or 8aF (specific for Ar- tle Hot Creek (Vick et al., 2010), indicated that they chaea; L4) in conjunction with reverse primer 1406uR host several novel deep lineages of potentially abun- as described in Costa et al. (2009). 48 clones from dant Bacteria and Archaea. -
Characterizing and Classifying Prokaryotes
PowerPoint® Lecture Presentations prepared by Mindy Miller-Kittrell, North Carolina State University C H A P T E R 11 Characterizing and Classifying Prokaryotes © 2014 Pearson Education, Inc. Bacteria as Plastic Recyclers http://www.cnn.com/2016/03/11/world/b acteria-discovery-plastic/index.html http://www.the- scientist.com/?articles.view/articleNo/4 5556/title/Microbial-Recycler-Found/ © 2014 Pearson Education, Inc. General Characteristics of Prokaryotic Organisms • Reproduction of Prokaryotic Cells • All reproduce asexually • Three main methods • Binary fission (most common) • Snapping division • Budding © 2014 Pearson Education, Inc. Figure 11.3 Binary fission. 1 Cell replicates its DNA. Cell wall Cytoplasmic Nucleoid membrane Replicated DNA 2 The cytoplasmic membrane elongates, separating DNA molecules. 3 Cross wall forms; membrane invaginates. 4 Cross wall forms completely. 5 Daughter cells may separate. © 2014 Pearson Education, Inc. Figure 11.4 Snapping division, a variation of binary fission. Older, outer portion of cell wall Newer, inner portion of cell wall Rupture of older, outer wall Hinge © 2014 Pearson Education, Inc. Figure 11.6 Budding Parent cell retains its identity © 2014 Pearson Education, Inc. General Characteristics of Prokaryotic Organisms • Arrangements of Prokaryotic Cells • Result from two aspects of division during binary fission • Planes in which cells divide • Separation of daughter cells © 2014 Pearson Education, Inc. Figure 11.7 Arrangements of cocci. Plane of division Diplococci Streptococci Tetrads Sarcinae Staphylococci © 2014 Pearson Education, Inc. Figure 11.8 Arrangements of bacilli. Single bacillus Diplobacilli Streptobacilli Palisade V-shape © 2014 Pearson Education, Inc. Modern Prokaryotic Classification • Currently based on genetic relatedness of rRNA sequences • Three domains • Archaea • Bacteria • Eukarya © 2014 Pearson Education, Inc. -
Downloaded from Appl
University of Massachusetts Amherst From the SelectedWorks of Derek Lovley November 2, 2007 Growth of Thermophilic and Hyperthermophilic Fe(III)-Reducing Microorganisms on a Ferruginous Smectite as the Sole Electron Acceptor Derek Lovley, University of Massachusetts - Amherst Kazem Kashefi Evgenya S Shelobolina W. Crawford Elliott Available at: https://works.bepress.com/derek_lovley/100/ Growth of Thermophilic and Hyperthermophilic Fe(III)-Reducing Microorganisms on a Ferruginous Smectite as the Sole Electron Acceptor Kazem Kashefi, Evgenya S. Shelobolina, W. Crawford Elliott and Derek R. Lovley Downloaded from Appl. Environ. Microbiol. 2008, 74(1):251. DOI: 10.1128/AEM.01580-07. Published Ahead of Print 2 November 2007. Updated information and services can be found at: http://aem.asm.org/ http://aem.asm.org/content/74/1/251 These include: REFERENCES This article cites 53 articles, 28 of which can be accessed free at: http://aem.asm.org/content/74/1/251#ref-list-1 on March 14, 2013 by Univ of Massachusetts Amherst CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» Information about commercial reprint orders: http://journals.asm.org/site/misc/reprints.xhtml To subscribe to to another ASM Journal go to: http://journals.asm.org/site/subscriptions/ APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Jan. 2008, p. 251–258 Vol. 74, No. 1 0099-2240/08/$08.00ϩ0 doi:10.1128/AEM.01580-07 Copyright © 2008, American Society for Microbiology. All Rights Reserved. Growth of Thermophilic and Hyperthermophilic Fe(III)-Reducing Microorganisms on a Ferruginous Smectite as the Sole Electron Acceptorᰔ Kazem Kashefi,1* Evgenya S.