DOCSLIB.ORG

How Biology Handles Nitrite Luisa B

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
How Biology Handles Nitrite Luisa B This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. Review pubs.acs.org/CR How Biology Handles Nitrite Luisa B. Maia and JoséJ. G. Moura* REQUIMTE/CQFB, Departamento de Química, Faculdade de Cienciaŝ e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal Biographies 5328 Acknowledgments 5329 Abbreviations 5329 References 5329 Note Added in Proof 5357 1. INTRODUCTION Nitrite is one of the players in the broad nitrogen biogeochemical cycle. This nitrogen oxo-anion is involved in key pathways crucial to life on Earth and to the planetary “recycling” of nitrogen. From a human perspective, nitrite (and CONTENTS nitrate) is an important food preservative that has been used for the last five millennia.1 This successful nitrite utilization was, 1. Introduction 5273 however, overshadowed in the 1970s, when it was suggested 2. Biological Fate of Nitrite 5274 that nitrite might increase the incidence of cancer, through the 2.1. Biological Fate of Nitrite − Nitrite in the − formation of N-nitrosamines.2 8 Recently, another twist took Nitrogen Cycle 5274 place, and nitrite is now being rediscovered as a beneficial 2.1.1. Classic and New Pathways 5274 molecule, endogenously formed or therapeutically added, 2.1.2. Nitrite and Nitrogen “Recycling” 5277 involved in cell survival during hypoxic events, as will be here 2.2. Biological Fate of Nitrite − Nitrite in Signal- discussed. ing Pathways 5277 In this Review, we will review the physiological role of nitrite 2.2.1. Nitrite in Signaling Pathways in Mam- in the biochemical cycle of nitrogen (section 2.1) and in mals 5277 mammalian and plant signaling pathways (sections 2.2.1 and 2.2.2. Nitrite in Signaling (and Other) Path- 2.2.2). A very brief description of potential bacterial signaling ways in Plants 5297 (section 2.2.3) will also be included. In the “Nitrite in the 2.2.3. Nitrite in Signaling (and Other) Path- Nitrogen Cycle” section, the main, well-established, pathways ways in Bacteria 5303 will be briefly described, with emphasis on the nitrite-mediated 3. Biological Mechanistic Strategies To Handle reactions. In the “Nitrite in Signaling Pathways” section, the Nitrite 5305 nitrite-mediated reactions will be discussed with a deeper detail: 3.1. Nitrite Reduction to Ammonium 5306 the nitrite-mediated signaling and damaging pathways are a 3.1.1. Dissimilatory Nitrite Reduction to Am- (comparatively) recent and controversial area, and the Review monium 5307 will be oriented to discuss the feasibility of these novel 3.1.2. Assimilatory Nitrite Reduction to Am- pathways mainly from the chemical point of view. As will be monium 5312 described in section 2, the living organisms use nitrite for 3.1.3. Nitrite Reduction to Ammonium by remarkably different purposes, oxidizing and reducing it. Other Enzymes 5313 Subsequently (section 3), several key reaction mechanisms 3.2. Nitrite Reduction to Nitric Oxide 5314 will be analyzed at a molecular level of detail, and structure/ 3.2.1. Dissimilatory Nitrite Reduction to Nitric activity relationships will be, as much as possible, systematically Oxide by an Iron-Dependent Enzyme 5315 explored to discuss the mechanistic strategies that biology 3.2.2. Dissimilatory Nitrite Reduction to Nitric developed to reduce and oxidize nitrite. Oxide by a Copper-Dependent Enzyme 5319 The global aim is to review the present functional, structural, 3.2.3. Signaling Nitrite Reduction to Nitric and mechanistic knowledge of nitrite reduction/oxidation, to Oxide by a Molybdenum-Dependent assess in what extent we understand how nitrite is handled by Enzyme 5322 living organisms. Nitrite formation is outside the scope of this 3.3. Nitrite Oxidation to Nitrate 5326 Review. This knowledge is essential for the comprehension of 3.3.1. Dissimilatory Nitrite Oxidation to Nitrate 5326 the global nitrogen biochemical cycle and, consequently, for the 4. Outlook 5327 comprehension of the impressive changes the human activities Author Information 5328 Corresponding Author 5328 Notes 5328 Received: September 20, 2013 Published: April 2, 2014 © 2014 American Chemical Society 5273 dx.doi.org/10.1021/cr400518y | Chem. Rev. 2014, 114, 5273−5357 Chemical Reviews Review are introducing in the cycle. Furthermore, the wealth of environmentally (soils, oceans, and crust) available ammonium information gathered and discussed enables one to further and nitrate/nitrite. The nitrate assimilation is dependent on evaluate the feasibility and physiological significance of the two sequential reactions (assimilatory ammonification, Figure presently accepted “avenues” of NO formation in humans and 1, orange arrows): first, the reduction of nitrate to nitrite, plants and to foresee new potential pathways. catalyzed by molybdenum-dependent nitrate reductases (NaR; described in refs 1667,1679), and then the reduction of nitrite 2. BIOLOGICAL FATE OF NITRITE to ammonium, catalyzed by sirohaem-containing nitrite 34−41 2.1. Biological Fate of Nitrite − Nitrite in the Nitrogen Cycle reductases (CSNiR; described in section 3.1.2). The electron source to carry out the nitrite reduction to ammonium Nitrogen is absolutely essential for life, being the fourth most is (i) the photosynthetically reduced ferredoxin, in photo- abundant element in living organisms (behind hydrogen, synthetic organisms (e.g., cyanobacteria and chloroplasts of 9 oxygen, and carbon). Nitrogen is used by all organisms for photosynthetic eukaryotes36,39,42), or (ii) the reduced pyridine the biosynthesis of amino acids, nucleosides, and other nucleotide pool, in most heterotrophs, but also in some fundamental compounds, and two nitrogen assimilatory phototrophs (e.g., nonphotosynthetic tissues of higher plants42 pathways were developed to provide the necessary reduced and Rhodobacter capsulatus,43,44 respectively). For that reason, “ ” “ nitrogen. This is then recycled in a universal organic there are two types of assimilatory CSNiR: ferredoxin- ” nitrogen pool . In addition, some organisms also use nitrogen dependent and NAD(P)H-dependent enzymes. Within each “ ” compounds as substrates for respiration , and for that purpose type, the enzymes share sequence and structural similarity, several nitrogen dissimilatory pathways have also evolved. The regardless of their prokaryotic or eukaryotic origin. Both types nitrogen biochemical cycle (Figure 1, Table 1) keeps this hold a sirohaem, where the nitrite reduction takes place, and an iron−sulfur center (Fe/S). Yet NAD(P)H-dependent enzymes contain an additional FAD domain that is involved in the − NAD(P)H binding and oxidation.34 44 Ammonium then enters the “organic nitrogen pool” (Figure 1, pink arrows) in the form of two amino acids, glutamine and glutamate, through the concerted action of glutamine synthase (eq 1) and glutamate synthase (eq 2) of bacteria, fungi, and plants. Ammonium can also be directly incorporated into glutamate through the glutamate dehydrogenase enzyme present in all forms of life (eq 3). However, under most physiological conditions, glutamate dehydrogenase catalyzes instead the reverse reaction, yielding ammonium in amino acid catabolism. Hence, the key enzyme that controls the entrance of the “organic nitrogen pool” is the glutamine synthase, not surprisingly one of the most complex regulatory enzymes. Besides this crucial role, glutamine synthase is also of main importance in animals, where it is responsible for the removal of toxic ammonium. Figure 1. Biochemical cycle of nitrogen. Dinitrogen fixation, yellow arrow; assimilatory ammonification, orange arrows; “organic nitrogen pool”, pink arrows; denitrification, blue arrows; dissimilatory nitrate reduction to ammonium (DNRA), green arrows; nitrification, black arrows; anaerobic ammonium oxidation (AnAmmOx), gray arrows; “denitrification/intra-aerobic methane oxidation”, violet arrows. element in forms available to support live on Earth, “starting” with fixation from the atmosphere (the largest nitrogen source) − and “recycling” it through the dissimilatory pathways.10 17 2.1.1. Classic and New Pathways. Two nitrogen The organic nitrogen, in the form of amino and amide assimilatory pathways provide the reduced nitrogen (ammo- groups, can now be transferred to other amino acids and several nium) essential for biosynthetic purposes (Figure 1, yellow and other nitrogen-containing biomolecules, supporting the vital orange arrows, Table 1). The organisms capable of dinitrogen biosynthetic needs. The organic nitrogen is then “recycled” fixation (some free-living archea and bacteria, e.g., Azotobacter, between all living organism, through chain foods, waste and symbiotic bacteria, e.g., Rhizobium) possess a unique products, and organic decay. Eventually, the organic nitrogen pathway, where the atmospheric dinitrogen is directly reduced is converted back to ammonium and returned to the to ammonium, in a reaction catalyzed by molybdenum/iron- environment, in a process called mineralization, thus closing − dependent nitrogenases18 (Figure 1, yellow arrow).22 33 All of the “organic” part of the nitrogen cycle ((Figure 1, pink the other organisms, prokaryotic and eukaryotic, depend on arrows). 5274 dx.doi.org/10.1021/cr400518y | Chem. Rev. 2014, 114, 5273−5357 Chemical Reviews Review Table 1. Main Pathways of the Biochemical Cycle of Nitrogen aFigures where the reaction and/or enzyme is represented. bSections where the reaction and/or enzyme is discussed. − The biochemical cycle of nitrogen continues
Load more

Recommended publications
  • Novel Copper-Containing Membrane Monooxygenases (Cummos) Encoded by Alkane- Utilizing Betaproteobacteria
    Lawrence Berkeley National Laboratory Recent Work Title Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane- utilizing Betaproteobacteria. Permalink https://escholarship.org/uc/item/8z48x96q Journal The ISME journal, 14(3) ISSN 1751-7362 Authors Rochman, Fauziah F Kwon, Miye Khadka, Roshan et al. Publication Date 2020-03-01 DOI 10.1038/s41396-019-0561-2 Peer reviewed eScholarship.org Powered by the California Digital Library University of California 1 1 2 1Novel copper-containing membrane monooxygenases 2(CuMMOs) encoded by alkane-utilizing Betaproteobacteria 3 4Running title: Novel CuMMOs in Betaproteobacteria 5 6Fauziah F. Rochman1, Miye Kwon2, Roshan Khadka1, Ivica Tamas1,3, Azriel 7Abraham Lopez-Jauregui1,4, Andriy Sheremet1, Angela Smirnova1, Rex R. 8Malmstrom5, Sukhwan Yoon2, Tanja Woyke5, Peter F. Dunfield1*, Tobin J. 9Verbeke1 10 111 Department of Biological Sciences, University of Calgary, 2500 University 12Dr. NW Calgary AB Canada T2N 1N4 132 Department of Civil and Environmental Engineering, Korea Advanced 14Institute of Science and Technology, Daejeon, Korea 153Department of Biology and Ecology, University of Novi Sad Novi Sad, Serbia 164 Instituto Tecnologico y de Estudios Superiores de Monterrey, Chihuahua, 17Mexico 185 Department of Energy Joint Genome Institute, Walnut Creek, California, 19USA. 20 21*Corresponding author: [email protected]; 403-220-2469 22 3 2 4 23Competing interests: The authors declare that they have no competing 24interests. 5 3 6 25Abstract 26Copper-containing membrane monooxygenases (CuMMOs) are encoded by 27xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, 28or some short chain alkanes and alkenes. In a metagenome constructed from 29an oilsands tailings pond we detected an xmoCABD gene cluster with <59% 30derived amino acid identity to genes from known bacteria.
    [Show full text]
  • Structural, Spectroscopic, and Mechanistic Insights Into the Three Phases of Nitrification Metallobiochemistry
    STRUCTURAL, SPECTROSCOPIC, AND MECHANISTIC INSIGHTS INTO THE THREE PHASES OF NITRIFICATION METALLOBIOCHEMISTRY A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy | Chemistry and Chemical Biology By Meghan Anne Smith August 2018 © 2018 Meghan Anne Smith STRUCTURAL, SPECTROSCOPIC, AND MECHANISTIC INSIGHTS INTO THE THREE PHASES OF NITRIFICATION METALLOBIOCHEMISTRY Meghan Anne Smith, Ph. D. Cornell University 2018 Biological ammonia (NH3) oxidation, referred to as nitrification, is a critical part of the biogeochemical nitrogen cycle. Nitrification is mediated by both bacteria and – archaea to ultimately oxidize NH3 to nitrite (NO 2 ), though there are also complete NH3-oxidizing (comammox) bacteria capable of oxidizing NH3 completely to nitrate – (NO3 ). In addition to these products, nitrification is also a major source of the by- products and environmental pollutants nitric oxide (NO), nitrous oxide (N2O) and nitrogen dioxide (NO2). Many steps of biological nitrification, including those leading to the production of these harmful products, are not currently clear; however, the work presented in this dissertation describes recent efforts and discoveries towards a complete understanding of the nitrification pathway. This process begins in both bacteria and archaea with the enzyme ammonia monooxygenase (AMO), which oxidizes NH3 to hydroxylamine (NH2OH). There exist two metal-binding sites in AMO of interest as these are highly conserved in AMOs and related enzymes. The true active site of this enzyme remains in debate, but here we show that both sites must remain intact for effective catalysis. In bacteria, the formed NH2OH is further oxidized to NO by the enzyme NH2OH oxidoreductase (HAO), though prior convention stated – that HAO was able to oxidize NH2OH fully to NO2 .
    [Show full text]
  • Metagenome-Scale Analysis Yields Insights Into the Structure And
    Zhang et al. BMC Genetics (2016) 17:21 DOI 10.1186/s12863-016-0330-4 RESEARCH ARTICLE Open Access Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap Xian Zhang1,2, Jiaojiao Niu1,2, Yili Liang1,2, Xueduan Liu1,2 and Huaqun Yin1,2* Abstract Background: Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China. A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap. Results: Taxonomic analysis revealed unexpectedly high microbial biodiversity of this extremely acidic environment, as most sequences were phylogenetically assigned to Proteobacteria,whileEuryarchaeota-related sequences occupied little proportion in this system, assuming that Archaea probably played little role in the bioleaching systems. At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A. ferrivorans-like and A. ferrooxidans-like groups. In addition, Caudovirales were the dominant viral type observed in this extremely environment. Functional analysis illustrated that the principal participants related to the key metabolic pathways (carbon fixation, nitrogen metabolism, Fe(II) oxidation and sulfur metabolism) were mainly identified to be Acidithiobacillus-like, Thiobacillus-like and Leptospirillum-like microorganisms, indicating their vital roles. Also, microbial community harbored certain adaptive mechanisms (heavy metal resistance, low pH adaption, organic solvents tolerance and detoxification of hydroxyl radicals) as they performed their functions in the bioleaching system.
    [Show full text]
  • Maximum Likelihood Placement of Environmental DNA Sequence Reads Into Curated Reference Phylogenies
    Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2011 MLTreeMap - maximum likelihood placement of environmental DNA sequence reads into curated reference phylogenies Stark, Manuel Abstract: Bei der Erforschung von mikrobiellen Gemeinschaften in situ stösst die traditionelle Mikrobi- ologie an ihre Grenzen, weil nur ein verschwindend kleiner Teil der Mikroben in Reinkultur gezu! chtet werden kann. Die Idee diesen Engpass zu umgehen, indem man DNA direkt aus aus der Umwelt extrahiert und daraufhin sequenziert, fu! hrte zur Entstehung eines neuen Forschungsfeldes, der Metagenomik. Mit Hilfe des metagenomischen Ansatzes ist es möglich, objektive Informationen u! ber alle in einer Probe präsenten Mikroben zu erhalten. Ein gewichtiger Nachteil ist allerdings, dass die gewonnenen Sequenz- daten nur fragmentiert vorliegen. MLTreeMap, das in dieser Dissertation vorgestellt wird, ist ein Soft- warepaket, welches in der Metagenomik Anwendung findet. Es wurde entwickelt, um Einblicke indie phylogenetischen und funktionellen Eigenschaften von Metagenomen und den ihnen zugrundeliegenden mikrobiellen Gemeinschaften zu gewinnen. Hierfür werden die zur Diskussion stehenden DNA Sequenzen auf eine Reihe von relevanten Markergenen hin durchsucht und deren wahrscheinlichste phylogenetische Herkunft ermittelt. Zu diesen Genen gehören proteinkodierende phylogenetische Marker, 16S und 18S rRNA Gene und Marker für wichtige Stoffwechselwege. Beispiele für letztere sind die Gene der Schlüsse- lenzyme der Photosynthese, Stickstofffixierung, Methanfixierung und Ammoniakoxidation. MLTreeMap kann entweder direkt über das Web benutzt werden (http://mltreemap.org) oder aber auf einem lokalen Computer installiert werden. Wir veröffentlichten MLTreeMap im Jahr 2010 im Journal BMC Genomics. Traditional microbiology has proven to be insufficient for studying entire microbial communities in situ, because only a small fraction of microbes can be grown in pure culture.
    [Show full text]
  • Dissertation
    DISSERTATION Titel der Dissertation The ecophysiology of nitrite-oxidizing bacteria in the genus Nitrospira: Novel aspects and unique features angestrebter akademischer Grad Doktor der Naturwissenschaften (Dr. rer. nat.) Verfasser: Frank Michael Maixner Matrikel-Nummer: 0409617 Dissertationsgebiet (lt. 444 Ökologie Studienblatt): Betreuer: Univ.-Prof. Dr. Michael Wagner Wien, am 13. April 2009 meiner Familie Contents Chapter I General Introduction and Outline 1 Chapter II Nitrite concentration influences the population structure of Nitrospira-like bacteria 27 Chapter III Environmental genomics reveals a functional chlorite dismutase in the nitrite-oxidizing bacterium ‘Candidatus Nitrospira defluvii’ 39 Chapter IV Nitrite oxidoreductase (Nxr) - the metabolic key enzyme of nitrite-oxidizing Nitrospira: Characterization of an unusual Nxr and its application as a novel functional and phylogenetic marker gene 67 Chapter V Summary/Zusammenfassung 123 Appendix 131 Supplement chapter I – paper 1 Selective enrichment and molecular characterization of a previously uncultured Nitrospira-like bacterium from activated sludge 133 Supplement chapter I – paper 2 Physiological and phylogenetic characterization of a novel lithoautotrophic nitrite-oxidizing bacterium, ‘Candidatus Nitrospira bockiana’ 145 Supplement chapter I – figure 1 155 Supplement chapter I – table 1 161 List of publications 163 List of oral & poster presentations 165 Danksagung 169 Curriculum vitae 171 Abbreviations A adenine AmoA ammonia monooxygenase subunit A ARB Arbor (software package comprising various tools for sequence and phylogenetic analysis) AOA ammonia-oxidizing archaea AOB ammonia-oxidizing bacteria C cytosin CLD chlorite dismutase CLSM confocal laser scanning microscope; confocal laser scanning miocroscopy DNA deoxyribonucleic acid et al. et alii Fig. figure FISH fluorescence in situ hybridization G guanine Hao hydroxylamine oxidoreductase N nitrogen N.
    [Show full text]
  • MOLECULAR METHODS to DETECT REGULATORY GENES in ANAEROBIC AMMONIA OXIDIZING BACTERIA by TREVAR LYTLE Bachelor of Science in Mi
    MOLECULAR METHODS TO DETECT REGULATORY GENES IN ANAEROBIC AMMONIA OXIDIZING BACTERIA By TREVAR LYTLE Bachelor of Science in Microbiology, Cell, and Molecular Biology Oklahoma State University Stillwater, Ok. 2018 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of MASTER OF SCIENCE May 2020 MOLECULAR METHODS TO DETECT REGULATORY GENES IN ANAEROBIC AMMONIA OXIDIZING BACTERIA Thesis Approved: Dr. Mark Krzmarzick Thesis Adviser Dr. Greg Wilber Dr. Wouter Hoff ii ACKNOWLEDGEMENTS This project is a collaborative effort between the University of Arizona, Oklahoma State University, and Pima County Reginal Wastewater Reclamation Department (PCRWRD). Through the help of Drs. Mark Krzmarzick, Brian Couger, (Oklahoma State University) and James Field (University of Arizona), this study was made possible. iii Acknowledgements reflect the views of the author and are not endorsed by committee members or Oklahoma State University. Name: Trevar Lytle Date of Degree: MAY 2020 Title of Study: MOLECULAR METHODS TO DETECT REGULATORY GENES IN ANAEROBIC AMMONIA OXIDIZING BACTERIA Major Field: Civil and Environmental Engineering Abstract: Anaerobic ammonia oxidizing bacteria (anammox) are a group of bacteria capable - + of using nitrite (NO 2 ) as their electron acceptor and ammonium (NH 4 ) as their electron donor to produce Nitrogen gas (N 2) in anaerobic environments. This is the ANAMMOX reaction. In this process, there is a 50-60% reduction in energy requirements, less sludge production, and does not require BOD compared to traditional nitrogen removal processes. The ANAMMOX discovery is credited to the work of Dr. Arnold Mulder who found that decreasing ammonium and nitrite concentrations were coupled with the release of N 2.
    [Show full text]
  • Warming Exacerbates the Impact of Nutrient Enrichment on Microbial Functional
    1 Warming exacerbates the impact of nutrient enrichment on microbial functional 2 potentials important to the nutrient cycling in shallow lake mesocosms 3 4 Lijuan Ren 1, Yuanyuan Liu 1, Torben L Lauridsen 2, 3, Martin Søndergaard 2, 3, 5 Boping Han 1, Jianjun Wang 4, Erik Jeppesen 2, 3, 5, 6*, Jizhong Zhou 7, 8,9, and 6 Qinglong L. Wu 2, 4, * 7 8 1 Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 9 China 10 2 Sino-Danish Centre for Education and Research, University of Chinese Academy of 11 Sciences, Beijing, China 12 3 Department of Bioscience, Aarhus University, Silkeborg, Denmark 13 4 State Key Laboratory of Lake Science and Environment, Nanjing Institute of 14 Geography and Limnology, Chinese Academy of Sciences, Nanjing, China 15 5 Limnology Laboratory, Department of Biological Sciences and Centre for 16 Ecosystem Research and Implementation, Middle East Technical University, Ankara, 17 Turkey 18 6 Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey 19 7 Institute for Environmental Genomics and Department of Microbiology and Plant 20 Biology, School of Civil Engineering and Environmental Sciences, University of 21 Oklahoma, Norman, OK, USA 22 8 Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, 23 Berkeley, CA, USA 24 9 State Key Joint Laboratory of Environment Simulation and Pollution Control, 25 School of Environment, Tsinghua University, Beijing, China 1 26 Corresponding authors: Qinglong L. Wu, Email: [email protected]; or Erik 27 Jeppesen, Email: [email protected]. 28 29 Keywords: warming, eutrophication, shallow lake, microbial functional potentials, 30 nutrient cycling 31 32 Running title: Microbial functional response to warming 2 33 Table S1 Full names of the abbreviated enzymes/proteins/genes in the main text.
    [Show full text]
  • Phylogenetic and Functional Marker Genes to Study Ammonia-Oxidizing Microorganisms (AOM) in the Environment
    Appl Microbiol Biotechnol (2010) 85:425–440 DOI 10.1007/s00253-009-2228-9 MINI-REVIEW Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment Pilar Junier & Verónica Molina & Cristina Dorador & Ora Hadas & Ok-Sun Kim & Thomas Junier & Karl-Paul Witzel & Johannes F. Imhoff Received: 10 June 2009 /Revised: 28 August 2009 /Accepted: 28 August 2009 /Published online: 24 September 2009 # The Author(s) 2009. This article is published with open access at Springerlink.com Abstract The oxidation of ammonia plays a significant role able lag phases, and sensitivity to certain organic compounds. in the transformation of fixed nitrogen in the global nitrogen Culture-independent approaches have contributed importantly cycle. Autotrophic ammonia oxidation is known in three to our understanding of the diversity and distribution of these groups of microorganisms. Aerobic ammonia-oxidizing microorganisms in the environment. In this review, we present bacteria and archaea convert ammonia into nitrite during an overview of approaches that have been used for the nitrification. Anaerobic ammonia-oxidizing bacteria (anam- molecular study of ammonia oxidizers and discuss their mox) oxidize ammonia using nitrite as electron acceptor and application in different environments. producing atmospheric dinitrogen. The isolation and cultiva- tion of all three groups in the laboratory are quite problematic Keywords AOB . AOA . Anammox . Functional marker . due to their slow growth rates, poor growth yields, unpredict- Phylogenetic marker P. Junier O.-S. Kim Laboratory of Microbial Ecology, University of Neuchatel, School of Biological Sciences and Institute of Microbiology, 2009 Neuchatel, Switzerland Seoul National University, 56-1 Shillim-dong, Kwanak-gu, P.
    [Show full text]
  • Microbially Mediated Transformation of Dissolved Nitrogen in Aquatic Environments a Dissertation Submitted to Kent State Univers
    Microbially Mediated Transformation of Dissolved Nitrogen in Aquatic Environments A dissertation submitted to Kent State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy by Xinxin Lu (Lucy) May 2015 © Copyright All rights reserved Except for previously published material Dissertation written by Xinxin Lu (Lucy) B.S., Jimei University, 2005 M.S., Ocean University of China, 2008 Ph.D., Kent State University, 2015 Approved by _______________________________________________________________ Xiaozhen Mou, Associate Professor, Ph.D., Department of Biological Sciences _______________________________________________________________ Laura G. Leff, Professor, Ph.D., Department of Biological Sciences _______________________________________________________________ Darren L. Bade, Assistant Professor, Ph.D., Department of Biological Sciences _______________________________________________________________ Joseph D. Ortiz, Professor, Ph.D., Department of Geology _______________________________________________________________ Scott Sheridan, Professor, Ph.D., Department of Geography Accepted by _______________________________________________________________ Laura G. Leff, Professor, Ph.D., Chair, Department of Biological Sciences _______________________________________________________________ James L. Blank, Professor, Ph.D., Dean, College of Arts and Sciences TABLE OF CONTENTS TABLE OF CONTENTS………………………………………………………………………...iii LIST OF FIGURES……………………………………………………………………………....vi LIST OF TABLES………………………………………………………………………………..xi
    [Show full text]
  • Contribution of Microbe-Mediated Processes in Nitrogen Cycle to Attain 13 Environmental Equilibrium
    Contribution of Microbe-Mediated Processes in Nitrogen Cycle to Attain 13 Environmental Equilibrium Humera Quadriya, Mohammed Imran Mir, K. Surekha, S. Gopalkrishnan, M. Yahya Khan, Sushil K. Sharma, and Hameeda Bee Abstract Nitrogen (N), the most important element, is required by all living organisms for the synthesis of complex organic molecules like amino acids, proteins, lipids etc. Nitrogen cycle is considered to be the most complex yet arguably important cycle next to carbon cycle. Nitrogen cycle includes oxic and anoxic reactions like organic N mineralization, ammonia assimilation, nitrification denitrification, anaerobic ammonium oxidation (anammox), dissimilatory nitrate reduction to ammonium (DNRA), comammox, codenitrification etc. Nitrogen cycling is one of the most crucial processes required for the recycling of essential chemical requirements on the planet. Soil microorganisms not only improve N-cycle balance but also pave the way for sustainable agricultural practices, leading to improved soil properties and crop productivity as most plants are opportunistic in the uptake of soluble or available forms of N from soil. Microbial N transformations are influenced by plants to improve their nutrition and vice versa. Diverse microorganisms, versatile metabolic activities, and varied biotic H. Quadriya · H. Bee (*) Department of Microbiology, Osmania University, Hyderabad, Telangana, India M. I. Mir Department of Botany, Osmania University, Hyderabad, Telangana, India K. Surekha ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana, India S. Gopalkrishnan ICRISAT-International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India M. Yahya Khan Kalam Biotech Private Limited, Hyderabad, Telangana, India S. K. Sharma ICAR-National Institute of Biotic Stress Management (ICAR-NIBSM), Raipur, Chhattisgarh, India # Springer Nature Singapore Pte Ltd.
    [Show full text]
  • Anammoxosome in Anaerobic Ammonium-Oxidizing Bacteria – Was It Originated from Endosymbiosis？
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Ivy Union Publishing (E-Journals) American Journal of American Journal of Current Microbiology http://ivyunion.org/index.php/ajcmicrob Hong YG et al. American Journal of Current Microbiology 2014, 2:18-40 Page 1 of 13 Current Microbiology Vo1. 2, Article ID 201400350, 13 pages Review Article Anammoxosome in Anaerobic Ammonium-oxidizing Bacteria – was It Originated from Endosymbiosis？ Yiguo Hong1,2, Huiluo Cao2,3, Meng Li2,4 and Ji-Dong Gu2* 1State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanography, Chinese Academy of Sciences, 164 Xingang Road West, Guangzhou 510301, China 2Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China 3Division of Biological Sciences, Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China 4Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA Abstract The anammoxosome is a single membrane-bounded compartment with ATP-generation capability residing in the yet-to-be purely cultured anammox bacteria, which are responsible for the unique biochemical reaction called anaerobic ammonium oxidation (anammox). In this paper, a plausible mechanism for the origin of anammoxosome is proposed, in which anaerobic archaea with capability of metabolizing ammonium and nitrite are thought to gain advantages for survival with reciprocal metabolisms and eventually established as stable endosymbiont under the given environmental conditions by invading into a bacterial cell. Over the long-time specialization and lateral gene transfer during the endosymbiosis establishment, the original archaea might further devolve into the present anammoxosome inside the host to form the structure of anammox bacteria today.
    [Show full text]
  • Lower Soil Carbon Loss Due to Persistent Microbial Adaptation to Climate Warming
    Lower Soil Carbon Loss Due to Persistent Microbial Adaptation to Climate Warming Supplementary Figures and Tables Fig. S1. Warming effects on plant and soil variables. (a) Effects of warming on aboveground - + plant biomass from C 3, C 4 and total species; ( b) Soil pH; (c) Soil nitrate (NO 3 ), ammonia (NH 4 ), total N (TN) and total organic carbon (TOC) across 7 years. Error bars represent standard error of the mean (n = 28). The differences between warming and the control were tested by repeated- measures ANOVA, indicated by *** when p < 0.01, ** when p < 0.05. Fig. S2. Temporal change of soil respiration (R t), heterotrophic respiration (R h) and autotrophic respiration (R a) from 2010 to 2016 . The respiration values were displayed as mean ± standard error ( n = 4). Fig. S3. Flowcharts of ecosystem models. (a) Microbial-ENzyme Decomposition (MEND) model. Soil organic matter (SOM) pools include: particulate organic matter (POM) (e.g., POM decomposed by oxidative and hydrolytic enzymes, denoted by P1 and P2 in the governing equations, respectively), mineral-associated organic matter (MOM, denoted by M), dissolved organic matter (DOM, D), adsorbed phase of DOM (QOM, Q), active and dormant microbes (MBA and MBD, denoted by BA & BD ), POM-degraded enzymes (e.g., EP 1 and EP 2 that break down P1 and P2, respectively), and MOM-degraded enzymes ( EM ). (b) Terrestrial ECOsystem (TECO) model. Fig. S4. A scatterplot of BIOLOG metabolic profiles under warming and control in 2016. Values close to the reference line (red) are in good agreement with the control values. Values above the reference line have an enhanced ability to utilize that carbon source in the warmed plots, value below have an inhibited ability in the warmed plots.
    [Show full text]