DOCSLIB.ORG

Complete Nitrification by Nitrospira Bacteria Holger Daims1, Elena V

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Complete Nitrification by Nitrospira Bacteria Holger Daims1, Elena V ARTICLE doi:10.1038/nature16461 Complete nitrification by Nitrospira bacteria Holger Daims1, Elena V. Lebedeva2, Petra Pjevac1, Ping Han1, Craig Herbold1, Mads Albertsen3, Nico Jehmlich4, Marton Palatinszky1, Julia Vierheilig1, Alexandr Bulaev2, Rasmus H. Kirkegaard3, Martin von Bergen4,5, Thomas Rattei6, Bernd Bendinger7, Per H. Nielsen3 & Michael Wagner1 Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly expressed during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira- contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities. Nitrification is catalysed by ammonia-oxidizing bacteria (AOB)1 The globally distributed genus Nitrospira represents the most or archaea (AOA)2 and nitrite-oxidizing bacteria (NOB)1. Since diverse known group of NOB. Nitrospira members have been found the pioneering studies by Winogradsky more than a century ago3, in terrestrial8 and limnic habitats9,10, marine waters11, deep sea nitrifying microorganisms are generally perceived as specialized sediments, sponge tissue12, geothermal springs13, drinking water chemolithoautotrophs that obtain energy for growth by oxidizing distribution systems14, corroded iron pipes15, and wastewater treat- either ammonia or nitrite. The known ammonia-oxidizing microbes ment plants (WWTPs)10,16. At least six phylogenetic sublineages of (AOM) and NOB are phylogenetically not closely related, and none Nitrospira exist, of which lineage II seems to be most widely distrib- of these organisms can oxidize both substrates. This separation of the uted in both natural and engineered ecosystems10. The ecological suc- two nitrification steps in different organisms leads to a tight cross- cess of Nitrospira has been linked to an economical pathway for nitrite feeding interaction and the frequently observed co-aggregation of oxidation17 and a substantial metabolic versatility, which includes AOM with NOB in nitrifying consortia4. However, the functional the utilization of various organic compounds in addition to nitrite 10,11,17–19 separation is a puzzling phenomenon since complete nitrification and CO2 , cyanate or urea degradation and nitrification by −1 19,20 would yield more energy (∆G°′ = −349 kJ mol NH3) than either reciprocal feeding with AOM , and chemolithoautotrophic aerobic −1 21 single step (∆G°′ = −275 kJ mol NH3 for ammonia oxidation hydrogen oxidation . −1 − to nitrite and ∆G°′ = −74 kJ mol NO2 for nitrite oxidation to nitrate). Thus, an organism catalysing complete nitrification should Enrichment of conspicuous Nitrospira have growth advantages over the ‘incomplete’ AOM and NOB. Based A microbial biofilm developing on the walls of a pipe under the flow on kinetic theory of optimal pathway length5,6, Costa et al.7 argued of hot water (56 °C, pH 7.5) raised from a 1,200 m deep oil exploration that a hypothetical complete nitrifier would likely be outcompeted well (Aushiger, North Caucasus, Russia) was sampled and incubated by incomplete, cross-feeding AOM and NOB in many environments. at 46 °C in ammonium-containing mineral medium to enrich mod- However, the same authors7 also pointed out that a complete nitrifier erately thermophilic AOM. After a series of subcultivation steps, we might be competitive under conditions that favour the maximiza- obtained enrichment culture ‘ENR4’ that oxidized ammonia to nitrate tion of growth yield rather than growth rate and coined the term and contained a dense population of cells morphologically resem- “comammox” (complete ammonia oxidizer) to describe such a bling described Nitrospira species13,15 (Extended Data Fig. 1a, b). hypothetical microbe. Conditions selecting for comammox may A second abundant population consisted of rod-shaped cells, but be characterized by slow, substrate-influx-limited growth with a no organism in ENR4 displayed the typical morphologies of known spatial clustering of biomass in microbial aggregates and biofilms7. AOM. Inspection by fluorescence in situ hybridization (FISH) with A prerequisite for the existence of comammox would also be that any nitrifier-specific ribosomal RNA-targeted probes10,22 confirmed that biochemical incompatibilities of ammonia and nitrite oxidation can ENR4 contained Nitrospira (Extended Data Fig. 1c) but no other be overcome by adaptations of enzymes or cellular compartmentali- detectable nitrifiers. Moreover, known bacterial or archaeal genes zation7. Aside from these theoretical considerations, the old question of ammonia monooxygenase (AMO) subunit alpha (amoA) and 16S of whether comammox exists in nature has not been resolved. rRNA genes of AOA were not detected by PCR in ENR4. Considering 1Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. 2Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia. 3Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark. 4Helmholtz-Centre for Environmental Research - UFZ, Department of Proteomics, Permoserstrasse 15, 04318 Leipzig, Germany. 5Helmholtz-Centre for Environmental Research - UFZ, Department of Metabolomics, Permoserstrasse 15, 04318 Leipzig, Germany. 6Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. 7DVGW-Forschungsstelle TUHH, Hamburg University of Technology, Am Schwarzenberg-Campus 3, 21073 Hamburg, Germany. 504 | NATURE | VOL 528 | 24/31 DECEMBER 2015 © 2015 Macmillan Publishers Limited. All rights reserved ARTICLE RESEARCH amo hao s nxr to 36.4) ) ) ) 0 .9 c biogenesi 32. to 67 CcmI (46.6 to 55.7 (57.1 to 67.7 in Ca. Nitrospira Cytochrome Hypothetical Putative transposaseAmoC1AmoA (42.4s clade AmoBto 67.6) A (42.3 (43.3 to OrfMto 60.5) 60.8) (58.4 toCopD 67.2) (27.2CopC to AmoD253.6(28.6AmoD1) to (37.158.7)AmoE1 (31.6 to 47.6) (40.0 to 61.1) toHypothetical 50.3) Hypothetical proteinCycB proteinCycA (53.8HaoB to (40.4 70.6HAO to 47.3 (52.2) prote CcmH ( HypotheticalHypotheticalHypothetical proteins protein proteinPutativePutative transposas transposaseNxrBe NxrA tRNA glycine proteins inopinata MBR Nitrospira bin 1 2 8 3 7 0 3 8 2 93. 82. 85. 53. 95. 85. 98. 87. WWTP VetMed Nitrospira bin 2 8 4 1 9 8 4 0 3 8 3 93. 82. 63. 91. 81. 56. 52. 95. 85. 98. 87. 1 5 0 86. 96. 92. GWW Nitrospira bin 3 5 6 8 3 2 8 3 5 8 2 1 6 3 9 5 7 *55. 59. 84. 80. 55. 73. 73. 61. 69. 60. 90. 82. 99. 93. 40. 49. GWW Nitrospira bin 4 2 7 2 3 6 8 6 0 9 1 0 *55. 61. 82. 80. 55. 72. 68. 59. 64. 98. 98. GWW Nitrospira bin 5 3 3 7 0 2 2 0 6 8 *56. 61. 90. 83. 52. 73. 68. 72. 96. 1 7 90. 80. GWW Nitrospira bin 8 4 9 1 9 9 81. *55. 60. 97. 89. 8 1 8 6 57. 90. 79. 98. GWW Nitrospira bin 9 0 8 3 6 9 2 9 9 8 1 2 3 7 97. 90. 82. 68. 61. 90. 83. 50. 72. 68. 73. 99. 95. 1 99. GWW Nitrospira bin 10 7 1 9 3 1 3 3 0 3 0 88. 81. 66. 63. 89. 84. 51. 73. 99. 97. Figure 1 | Key nitrification gene loci in Ca. N. inopinata and the the predicted gene products compared to Ca. N. inopinata. Asterisks metagenomic Nitrospira population genome bins containing putative mark comammox clade B amoA genes. Wiggly lines indicate ends of comammox Nitrospira. Gene alignments of the amoCAB, hao, and metagenomic contigs. Underlined gene products of Ca. N. inopinata have nxrAB loci with flanking genes are shown. Only two or three of up to homologues in AOB genomes (amino acid identities in per cent to AOB nine syntenic cytochrome c biogenesis genes upstream of the hao loci are are indicated in parentheses), but gene arrangements can differ from displayed. Colours identify homologous genes. Genes without homologues AOB24. Genes and noncoding regions are drawn to scale. Metagenomic in the analysed data set are white if their function is known, otherwise bins are numbered as in Supplementary Table 8. MBR, membrane grey. Transposases are magenta irrespectively of homology. Numbers bioreactor; WWTP, wastewater treatment plant; GWW, groundwater well. below genes represent amino acid sequence identities (in per cent) of the intriguing possibility that the Nitrospira population might be Nitrospira strain as ‘Candidatus Nitrospira inopinata’ (in.o.pi.na'ta. L. responsible for both ammonia and nitrite oxidation, we sequenced fem. adj. inopinata unexpected, surprising). the metagenome of the enrichment (Supplementary Tables 1–7) to identify the ammonia oxidizer. Sequence assembly and differential Discovery of comammox coverage binning23 showed that the ENR4 metagenome was domi- The obtained bacterial genomes were screened for the key functional nated by two organisms (one Nitrospira strain and a betaproteobac- genes of autotrophic nitrification. As expected, Ca. N. inopinata pos- terium affiliated with the family Hydrogenophilaceae) and revealed sesses the key enzyme for nitrite oxidation, nitrite oxidoreductase two additional rare populations (an alphaproteobacterium related to (NXR). Its genome contains the nxrA and nxrB genes coding for the Tepidamorphus gemmatus, family Rhodobiaceae, and an actinobacte- subunits alpha and beta, respectively, of the periplasmic Nitrospira rium affiliated with Thermoleophilum, family Thermoleophilaceae).
Load more

Recommended publications
  • Nitrobacter As an Indicator of Toxicity in Wastewater
    State Water Survey Division WATER QUALITY SECTION AT Illinois Department of PEORIA, ILLINOIS Energy and Natural Resources SWS Contract Report 326 NITROBACTER AS AN INDICATOR OF TOXICITY IN WASTEWATER by Wuncheng Wang and Paula Reed Prepared for and funded by the Illinois Department of Energy and Natural Resources September 1983 CONTENTS PAGE Abstract 1 Introduction 1 Scope of study 3 Acknowledgments 3 Literature review 3 Microbial nitrification 3 Influence of toxicants on nitrification 5 Materials and methods 10 Culture 10 Methods 11 Results 12 Preliminary tests 13 Metal toxicity 13 Organic compounds toxicity 16 Time effect 22 Discussion 22 References 27 NITROBACTER AS AN INDICATOR OF TOXICITY IN WASTEWATER by Wuncheng Wang and Paula Reed ABSTRACT This report presents the results of a study of the use of Nitrobacter as an indicator of toxicity. Nitrobacter are strictly aerobic, autotrophic, and slow growing bacteria. Because they convert nitrite to nitrate, the effects that toxins have on them can be detected easily by monitoring changes in their nitrite consumption rate. The bacterial cultures were obtained from two sources — the Peoria and Princeton (Illinois) wastewater treatment plants — and tests were con• ducted to determine the effects on the cultures of inorganic ions and organic compounds. The inorganic ions included cadmium, copper, lead, and nickel. The organic compounds were phenol, chlorophenol (three derivatives), dichlo- rophenol (two derivatives), and trichlorophenol. The bioassay procedure is relatively simple and the results are repro• ducible . The effects of these chemical compounds on Nitrobacter were not dramatic. For example, of the compounds tested, 2,4,6-trichlorophenol was the most toxic to Nitrobacter.
    [Show full text]
  • CUED Phd and Mphil Thesis Classes
    High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice.
    [Show full text]
  • General Introduction
    Physiological Characteristics and Genomic Properties of Nitrosomonas mobilis Isolated from Nitrifying Granule of Wastewater Treatment Bioreactor December 2016 Soe Myat Thandar ソー ミャット サンダー Physiological Characteristics and Genomic Properties of Nitrosomonas mobilis Isolated from Nitrifying Granule of Wastewater Treatment Bioreactor December 2016 Waseda University Graduate School of Advanced Science and Engineering Department of Life Science and Medical Bioscience Research on Environmental Biotechnology Soe Myat Thandar ソー ミャット サンダー Contents Abbreviations ................................................................................................................... i Chapter 1-General introduction .................................................................................... 1 1.1. Nitrification and wastewater treatment system .......................................................... 3 1.2. Important of Nitrosomonas mobilis ........................................................................... 8 1.3. Objectives and outlines of this study ....................................................................... 12 1.4. Reference.................................................................................................................. 12 Chapter 2- Physiological characteristics of Nitrosomonas mobilis Ms1 ................... 17 2.1. Introduction .............................................................................................................. 19 2.2. Material and methods ..............................................................................................
    [Show full text]
  • Metaproteomics Reveals Differential Modes of Metabolic Coupling Among Ubiquitous Oxygen Minimum Zone Microbes
    Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes Alyse K. Hawleya, Heather M. Brewerb, Angela D. Norbeckb, Ljiljana Paša-Tolicb, and Steven J. Hallama,c,d,1 aDepartment of Microbiology and Immunology, cGraduate Program in Bioinformatics, and dGenome Sciences and Technology Training Program, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; and bBiological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 Edited by Edward F. DeLong, Massachusetts Institute of Technology, Cambridge, MA, and approved June 10, 2014 (received for review November 26, 2013) Marine oxygen minimum zones (OMZs) are intrinsic water column transformations in nonsulfidic OMZs, providing evidence for features arising from respiratory oxygen demand during organic a cryptic sulfur cycle with the potential to drive inorganic carbon matter degradation in stratified waters. Currently OMZs are expand- fixation processes (13). Indeed, many of the key microbial players ing due to global climate change with resulting feedback on marine implicated in nitrogen and sulfur transformations in OMZs, in- ecosystem function. Here we use metaproteomics to chart spatial cluding Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and temporal patterns of gene expression along defined redox and SUP05/ARCTIC96BD-19 Gammaproteobacteria have the gradients in a seasonally stratified fjord to better understand metabolic potential for inorganic carbon fixation (14–19), and
    [Show full text]
  • APP201895 APP201895__Appli
    APPLICATION FORM DETERMINATION Determine if an organism is a new organism under the Hazardous Substances and New Organisms Act 1996 Send by post to: Environmental Protection Authority, Private Bag 63002, Wellington 6140 OR email to: [email protected] Application number APP201895 Applicant Neil Pritchard Key contact NPN Ltd www.epa.govt.nz 2 Application to determine if an organism is a new organism Important This application form is used to determine if an organism is a new organism. If you need help to complete this form, please look at our website (www.epa.govt.nz) or email us at [email protected]. This application form will be made publicly available so any confidential information must be collated in a separate labelled appendix. The fee for this application can be found on our website at www.epa.govt.nz. This form was approved on 1 May 2012. May 2012 EPA0159 3 Application to determine if an organism is a new organism 1. Information about the new organism What is the name of the new organism? Briefly describe the biology of the organism. Is it a genetically modified organism? Pseudomonas monteilii Kingdom: Bacteria Phylum: Proteobacteria Class: Gamma Proteobacteria Order: Pseudomonadales Family: Pseudomonadaceae Genus: Pseudomonas Species: Pseudomonas monteilii Elomari et al., 1997 Binomial name: Pseudomonas monteilii Elomari et al., 1997. Pseudomonas monteilii is a Gram-negative, rod- shaped, motile bacterium isolated from human bronchial aspirate (Elomari et al 1997). They are incapable of liquefing gelatin. They grow at 10°C but not at 41°C, produce fluorescent pigments, catalase, and cytochrome oxidase, and possesse the arginine dihydrolase system.
    [Show full text]
  • Metabolic Versatility of the Nitrite-Oxidizing Bacterium Nitrospira
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185504; this version posted July 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira 2 marina and its proteomic response to oxygen-limited conditions 3 Barbara Bayer1*, Mak A. Saito2, Matthew R. McIlvin2, Sebastian Lücker3, Dawn M. Moran2, 4 Thomas S. Lankiewicz1, Christopher L. Dupont4, and Alyson E. Santoro1* 5 6 1 Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, 7 CA, USA 8 2 Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, 9 Woods Hole, MA, USA 10 3 Department of Microbiology, IWWR, Radboud University, Nijmegen, The Netherlands 11 4 J. Craig Venter Institute, La Jolla, CA, USA 12 13 *Correspondence: 14 Barbara Bayer, Department of Ecology, Evolution and Marine Biology, University of California, 15 Santa Barbara, CA, USA. E-mail: [email protected] 16 Alyson E. Santoro, Department of Ecology, Evolution and Marine Biology, University of 17 California, Santa Barbara, CA, USA. E-mail: [email protected] 18 19 Running title: Genome and proteome of Nitrospira marina 20 21 Competing Interests: The authors declare that they have no conflict of interest. 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185504; this version posted July 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • The Bacterial Communities of Sand-Like Surface Soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Yang Wang
    The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Yang Wang To cite this version: Yang Wang. The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA). Agricultural sciences. Université Paris-Saclay, 2015. English. NNT : 2015SACLS120. tel-01261518 HAL Id: tel-01261518 https://tel.archives-ouvertes.fr/tel-01261518 Submitted on 25 Jan 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. NNT : 2015SACLS120 THESE DE DOCTORAT DE L’UNIVERSITE PARIS-SACLAY, préparée à l’Université Paris-Sud ÉCOLE DOCTORALE N°577 Structure et Dynamique des Systèmes Vivants Spécialité de doctorat : Sciences de la Vie et de la Santé Par Mme Yang WANG The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Thèse présentée et soutenue à Orsay, le 23 Novembre 2015 Composition du Jury : Mme. Marie-Claire Lett , Professeure, Université Strasbourg, Rapporteur Mme. Corinne Cassier-Chauvat , Directeur de Recherche, CEA, Rapporteur M. Armel Guyonvarch, Professeur, Université Paris-Sud, Président du Jury M.
    [Show full text]
  • Wastewater Structure of Nitrifying Bacteria from Concentrations on The
    Effects of pH and Oxygen and Ammonium Concentrations on the Community Structure of Nitrifying Bacteria from Wastewater Alenka Princic, Ivan Mahne, France Megusar, Eldor A. Paul and James M. Tiedje Appl. Environ. Microbiol. 1998, 64(10):3584. Downloaded from Updated information and services can be found at: http://aem.asm.org/content/64/10/3584 http://aem.asm.org/ These include: REFERENCES This article cites 18 articles, 8 of which can be accessed free at: http://aem.asm.org/content/64/10/3584#ref-list-1 CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» on March 17, 2014 by COLARADO STATE UNIV 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, Oct. 1998, p. 3584–3590 Vol. 64, No. 10 0099-2240/98/$04.0010 Copyright © 1998, American Society for Microbiology. All Rights Reserved. Effects of pH and Oxygen and Ammonium Concentrations on the Community Structure of Nitrifying Bacteria from Wastewater ALENKA PRINCˇICˇ,1,2* IVAN MAHNE,1 FRANCE MEGUSˇAR,1 ELDOR A. PAUL,2 2 AND JAMES M. TIEDJE 1 Biotechnical Faculty, University of Ljubljana, Biology Center, 1000 Ljubljana, Slovenia, Downloaded from and Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824-13252 Received 13 February 1998/Accepted 29 June 1998 Shifts in nitrifying community structure and function in response to different ammonium concentrations (50, 500, 1,000, and 3,000 mg of N liter21), pH values (pH 6.0, 7.0, and 8.2), and oxygen concentrations (1, 7, and 21%) were studied in experimental reactors inoculated with nitrifying bacteria from a wastewater treatment plant.
    [Show full text]
  • Being Aquifex Aeolicus: Untangling a Hyperthermophile's Checkered Past
    GBE Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past Robert J.M. Eveleigh1,2, Conor J. Meehan1,2,JohnM.Archibald1, and Robert G. Beiko2,* 1Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada 2Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada *Corresponding author: E-mail: [email protected]. Accepted: November 22, 2013 Abstract Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyper- thermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic analyses focused on Aquifex aeolicus identified Thermotogae and Downloaded from Aquificae either as successive early branches or sisters in a rooted bacterial phylogeny, but many phylogenies and cellular traits have suggested a stronger affiliation with the Epsilonproteobacteria. Different scenarios for the evolution of the Aquificae yield different phylogenetic predictions. Here, we outline these scenarios and consider the fit of the available data, including three sequenced Aquificae genomes, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the Epsilonproteobacteria have the strongest affinities with the three Aquificae analyzed. However, this pattern is shown by only a http://gbe.oxfordjournals.org/ minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: Most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, whereas a wide range of metabolic and cellular processes strongly supported the link between Aquificae and Epsilonproteobacteria.
    [Show full text]
  • Comparison of Physiology and Genome-Wide Expression in Two Nitrosomonas Spp
    Comparison of physiology and genome-wide expression in two Nitrosomonas spp. under batch cultivation By Mohammad Ghashghavi A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science In Microbiology and Biotechnology Department of Biological Sciences University of Alberta © Mohammad Ghashghavi, 2014 Abstract: Ammonia oxidizing bacteria (AOB) play a central role in the nitrogen cycle by oxidizing ammonia to nitrite. Nitrosomonas europaea ATCC 19718 has been the single most studied AOB that has contributed to our understanding of chemolithotrophic ammonia oxidation. As a closely related species, Nitrosomonas eutropha C91 has also been extensively studied. Both of these bacteria are involved in wastewater treatment systems and play a crucial part in major losses of ammonium-based fertilizers globally. Although comparative genome analysis studies have been done before, change in genome-wide expression between closely related organisms are scarce. In this study, we compared these two organisms through physiology and transcriptomic experiments during exponential and early stationary growth phase. We found that under batch cultivation, N. europaea produces more N2O while N. eutropha consumes more nitrite. From transcriptomic analysis, we also found that there are selections of motility genes that are highly expressed in N. eutropha during early stationary growth phase and such observation was completely absent in N. europaea. Lastly, principle homologous genes that have been well studied had different patterns of expression in these strains. This study not only gives us a better understanding regarding physiology and genome-wide expression of these two AOB, it also opens a wide array of opportunities to further our knowledge in understanding other closely related species with regards to their evolution, physiology and niche preference.
    [Show full text]
  • Nitrifying Bacteria
    ® AWT-1AQUARIUM WATER TREATMENT Nitrifying bacteria. 1 WHAT IS IT? AWT-1® It is a solution that contains 9 species of nitrifying bacteria respon- sible for eliminating the ammonia and nitrites present in the water of aqua- riums and ponds. USES AND APPLICATIONS PONDS EXHIBITION, QUARANTINE OR BREEDING FRESH OR TANKS SALT WATER AQUARIUMS 2 LIVENTIA.NET HOW DOES IT WORK? The bacterial AWT-1® complex acts directly on the nitrogen Nitrates accumulate slowly over time and are much less toxic cycle, mainly in converting ammonia to nitrite then nitrate. to the animals. Nitrosomones bacteria feed on inorganic compounds with AWT-1® allows an adequate balance of these microorganisms ammonia as their main source of energy, these bacteria in to achieve the establishment of the nitrogen cycle. turn produce nitrite (NO2). CYCLE OF A NEW TANK (NUMBERS ARE ILLUSTRATIVE) 50 amonia nitrite 40 nitrate 30 TOTAL NITROGEN WATER CHANGE 20 NITROGEN (mg/l) 10 0 0 10 20 30 40 50 time (days) 3 NITROSOMONAS BACTERIA Facultative bacteria reduce 4 LIVENTIA.NET WHAT ARE THE BENEFITS? • Eliminates ammonia and nitrites present • Grown when ordered to insure the greatest bacterial • Generates a more efficient operation of bio-filters viability and longest shelf life. • Reduces water change • Custom made for fresh, brackish or salt water. • Reduces chemical and biological demands for oxygen • Extremely concentrated to insure quick reduction of • Reduces suspended and dissolved solids ammonia and nitrite • Not harmful to aquatic life • Can be custom made for unique environments or • Can be used in fresh or salt water applications. • One application • Complementary blend of Nitrifying bacteria used to seed, control build-up of ammonia and nitrite in aquariums, ponds and aquaculture operations.
    [Show full text]
  • High Functional Diversity Among Nitrospira Populations That Dominate Rotating Biological Contactor Microbial Communities in a Municipal Wastewater Treatment Plant
    The ISME Journal (2020) 14:1857–1872 https://doi.org/10.1038/s41396-020-0650-2 ARTICLE High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant 1 1 1 1 1 2 Emilie Spasov ● Jackson M. Tsuji ● Laura A. Hug ● Andrew C. Doxey ● Laura A. Sauder ● Wayne J. Parker ● Josh D. Neufeld 1 Received: 18 October 2019 / Revised: 3 March 2020 / Accepted: 30 March 2020 / Published online: 24 April 2020 © The Author(s) 2020. This article is published with open access Abstract Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, 1234567890();,: 1234567890();,: Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm.
    [Show full text]