DOCSLIB.ORG

Nitrosomonas Nm143-Like Ammonia Oxidizers and Nitrospira Marina -Like Nitrite Oxidizers Dominate the Nitri¢Er Community in a Marine Aquaculture Bio¢Lm Barbel¨ U

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Nitrosomonas Nm143-Like Ammonia Oxidizers and Nitrospira Marina -Like Nitrite Oxidizers Dominate the Nitri¢Er Community in a Marine Aquaculture Bio¢Lm Barbel¨ U RESEARCH ARTICLE Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina -like nitrite oxidizers dominate the nitri¢er community in a marine aquaculture bio¢lm Barbel¨ U. Foesel1,2, Armin Gieseke3, Carsten Schwermer3, Peter Stief3, Liat Koch4, Eddie Cytryn4,5, Jose´ R. de la Torre´ 6, Jaap van Rijn5, Dror Minz4, Harold L. Drake2 & Andreas Schramm1,2 1Department of Biological Sciences, Microbiology, University of Aarhus, Aarhus, Denmark; 2Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany; 3Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen, Germany; 4The Volcani Center, Institute for Soil, Water and Environmental Sciences, ARO, Bet-Dagan, Israel; 5Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, Israel; and 6Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA Correspondence: Andreas Schramm, Abstract Department of Biological Sciences, Microbiology, University of Aarhus, Ny Zero-discharge marine aquaculture systems are an environmentally friendly Munkegade, Building 1540, DK-8000, alternative to conventional aquaculture. In these systems, water is purified and Aarhus C, Denmark. Tel.: 145 8942 3248; recycled via microbial biofilters. Here, quantitative data on nitrifier community fax: 145 8942 2722; structure of a trickling filter biofilm associated with a recirculating marine e-mail: [email protected] aquaculture system are presented. Repeated rounds of the full-cycle rRNA approach were necessary to optimize DNA extraction and the probe set for FISH Present address: Barbel¨ U. Foesel, Bereich to obtain a reliable and comprehensive picture of the ammonia-oxidizing Mikrobiologie, Department Biologie I Ludwig- community. Analysis of the ammonia monooxygenase gene (amoA) confirmed Maximilians-Universitat¨ Munchen, ¨ Germany. Eddie Cytryn, Department of Soil Water and the results. The most abundant ammonia-oxidizing bacteria (AOB) were members Climate and Biotechnology Institute, of the Nitrosomonas sp. Nm143-lineage (6.7% of the bacterial biovolume), University of Minnesota, Saint Paul, MN, USA. followed by Nitrosomonas marina-like AOB (2.2% of the bacterial biovolume). Both were outnumbered by nitrite-oxidizing bacteria of the Nitrospira marina- Received 26 June 2007; revised 16 October lineage (15.7% of the bacterial biovolume). Although more than eight other 2007; accepted 21 October 2007. nitrifying populations were detected, including Crenarchaeota closely related to the ammonia-oxidizer ‘Nitrosopumilus maritimus’, their collective abundance was DOI:10.1111/j.1574-6941.2007.00418.x below 1% of the total biofilm volume; their contribution to nitrification in the biofilter is therefore likely to be negligible. Editor: Michael Wagner Keywords marine aquaculture; nitrifying biofilm; DNA extraction; Nitrosomonas sp. Nm143; Nitrospira marina. enough to keep ammonia concentrations below toxic levels Introduction (e.g. o 30 mM for juvenile gilthead seabream; Wajsbrot Declining marine fish stocks have induced a rapid growth et al., 1993), and yet dynamic enough to buffer fluctuations in marine aquaculture (FAO, 2004), an industry that can in ammonium production, e.g., caused by changing fish have deleterious effects on local environments via uncon- population size, age, and feeding. This challenge is quite trolled discharge of nutrients and organic matter (Wu, different from nitrification in activated sludge and waste- 1995; Christensen et al., 2000; Holmer et al., 2003). As an water biofilms, where ammonium concentrations are often environmentally friendly alternative, a zero-discharge mar- high and ammonia-oxidizing bacteria (AOB) with a low ine aquaculture system has been developed with integrated substrate affinity but high reaction rates dominate (Wagner microbial biofilters that couple nitrification with sludge et al., 2002; Koops et al., 2003). Marine nitrifying biofilters digestion and denitrification (Cytryn et al., 2003; Gelfand have not been evaluated in detail, and nitrifier diversity has et al., 2003). Nitrification in such a system has to be efficient sometimes been described on the basis of only a few clone FEMS Microbiol Ecol ]] (2007) 1–13 c 2007 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved 2 B.U. Foesel et al. sequences. Such diverse nitrifiers as Nitrosomonas europaea biosensors (Larsen et al., 1997), respectively. Depth-resolved À (Hovanec & Delong, 1996), Nitrosomonas cryotolerans, and NOx production rates were computed from the profiles using the nitrite-oxidizing bacterium (NOB) Nitrospira marina the software PROFILE v.1.0 (Berg et al., 1998). (Tal et al., 2003), Nitrosomonas marina (Grommen et al., 2005), or Nitrosomonas aestuarii and Nitrosomonas sp. DNA extraction Nm143 (Itoi et al., 2006) have been detected in marine DNA was first extracted from 3 cm plastic strip fragments by biofilters. Recently, even a crenarchaeal ammonia oxidizer bead-beating (= DNA extraction method A), based on a (AOA), ‘Nitrosopumilus maritimus’, was isolated from a modified version of the FastDNAs SPIN Kit for soil (Qbio- marine aquarium (Konneke¨ et al., 2005), and subsequently gene Inc., Carlsbad, CA). Extraction tubes contained-acid archaeal ammonia monooxygenase genes (amoA) were washed and baked glass beads (0.36 g with a diameter of detected in marine samples and activated sludge (Francis 106 mm; Sigma-Aldrich, St Louis, MO, and six to eight beads et al., 2005; Park et al., 2006). However, quantitative data on with a diameter of 5 mm; Marienfeld, Lauda-Koenigshofen, the nitrifying community structure of marine biofilters are Germany). Wash buffer was 50 mM NaCl, 10 mM Tris-HCl still lacking, and the importance of the respective species (pH 7.5), 2.5 mM EDTA, and 50% (v/v) ethanol. As this remains unclear. Therefore, the goal of this study was to method proved insufficient for yielding DNA of AOB, the provide a comprehensive and quantitative analysis of the FastDNAs Kit (Qbiogene) was combined with an enzymatic AOB and NOB communities in a marine, nitrifying biofilter. digestion step (Juretschko et al., 1998), hereafter referred to as the DNA extraction method B: biofilm pellet (0.25 g) was Materials and methods resuspended in 300 mL DNA extraction buffer [100 mM Tris- HCl (pH 8.0), 100 mM sodium EDTA (pH 8.0), 100 mM System operation and biofilm sampling sodium phosphate (pH 8.0), 1.5 M NaCl, 1% cetyltrimethy- Biofilm samples originated from the trickling filter of a zero- lammonium bromide], transferred to a Lysis matrix E tube discharge marine aquaculture system (Cytryn et al., 2003; (Qbiogene), and bead-beaten (2 Â 15 s at speed 4.0 and Gelfand et al., 2003) that was stocked with gilthead seabream 1 Â 15 s at speed 4.5) using a FastPreps Instrument (Qbio- (Sparus aurata). The trickling filter consisted of 1 m3 polyvinyl gene). Then, 50 mL of enzyme mixture I [lysozyme (Sigma- chloride (PVC) cross-flow medium with a surface area of Aldrich, Steinheim, Germany), lipase typ7 (from Candida 240 m2 (Jerushalmi Ltd., Ashod, Israel). The top of the filter rugosa, Sigma), pectinase (from Aspergillus niger,Sigma),and was continuously sprinkled with water from the fish pool b-glucuronidase (from Helix pomatia, Sigma), 10 mg LÀ1 (pool volume 2.3 m3)atarateof60LminÀ1 (Æ 20 L minÀ1). each] was added and the biofilm was incubated for 30 min at Normal inlet ammonia concentrations were c.20mMwith 37 1C, followed by addition of 50 mLofenzymemixtureII peaks of up to 100 mM after feeding; outlet concentrations [proteinase K (Roche Diagnostics GmbH, Mannheim, Ger- ranged from 6 to 42 mM(Gelfandet al., 2003), and salinity was many), protease typ9 (from Bacillus polymyxa,Sigma),and kept at c. 20 psu. The system was restarted in spring 2003; for pronase P (from Streptomyces griseus,Sigma),10mgLÀ1 each] sampling of intact biofilm, plastic strips were inserted into the and incubation for 30 min at 37 1C. Finally, the sample was trickling filter. Samples were taken after several months of incubatedwith75mL of 20% dodecyl sulfate for 2 h at 65 1C, stable operation in October 2003 and April/May 2004 by then 800 mL cell-lysis solution (CLS)-TC (Qbiogene) was removing the strips that were either directly frozen (for DNA addedforasecondbead-beatinground(2Â 15satspeed5.0 extraction) or fixed in 4% paraformaldehyde (for FISH; and 1 Â 15 s at speed 5.5), and DNA extraction was continued Amann et al., 1990b). Vertical sections (thickness, 14–30 mm) with the FastDNAs Kit following the manufacturer’s instruc- were prepared from fixed biofilms as described earlier tions. In addition, the DNA extraction protocol described by (Schramm et al., 1996). Additionally, biofilm was scraped off Burrell et al. (2001) was tested, which includes enzymatic the PVC substratum and fixed for qualitative FISH-compar- digestion with lysozyme and proteinase K. ison of the nitrifier community on the original PVC substra- tum and the inserted plastic strips. PCR amplification of 16S rRNA genes and amoA Primer sets GM3/GM4 (Muyzer et al., 1995), 616V (Jur- Microsensor measurements etschko et al., 1998)/NSO1225R (published as probe by Biofilm samples (1–2 cm2 on plastic strips) were incubated in a Mobarry et al., 1996), and NSMR76F (published as probe laminar flow chamber with artificial seawater (20 psu Red Sea by Burrell et al., 2001)/NSO1225R were used for amplifica- salt, Red Sea Fish Pharm, Eilat, Israel) amended with 25 mM tion of bacterial, b-AOB, and Nitrosomonas marina-like 16S 1 À1 NH4
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]
  • 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]
  • Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas
    microorganisms Article Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas 1 1, 1 1 2, 1,3, Huilong Ou , Mingyu Li y, Shufei Wu , Linli Jia , Russell T. Hill * and Jing Zhao * 1 College of Ocean and Earth Science of Xiamen University, Xiamen 361005, China; [email protected] (H.O.); [email protected] (M.L.); [email protected] (S.W.); [email protected] (L.J.) 2 Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA 3 Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration (USER), Xiamen University, Xiamen 361005, China * Correspondence: [email protected] (J.Z.); [email protected] (R.T.H.); Tel.: +86-592-288-0811 (J.Z.); Tel.: +(410)-234-8802 (R.T.H.) The author contributed equally to the work as co-first author. y Received: 24 September 2019; Accepted: 25 December 2019; Published: 30 December 2019 Abstract: Some sponges have been shown to accumulate abundant phosphorus in the form of polyphosphate (polyP) granules even in waters where phosphorus is present at low concentrations. But the polyP accumulation occurring in sponges and their symbiotic bacteria have been little studied. The amounts of polyP exhibited significant differences in twelve sponges from marine environments with high or low dissolved inorganic phosphorus (DIP) concentrations which were quantified by spectral analysis, even though in the same sponge genus, e.g., Mycale sp. or Callyspongia sp. PolyP enrichment rates of sponges in oligotrophic environments were far higher than those in eutrophic environments.
    [Show full text]
  • Characterization of a Microbial Community Capable of Nitrification At
    Bioresource Technology 101 (2010) 491–500 Contents lists available at ScienceDirect Bioresource Technology journal homepage: www.elsevier.com/locate/biortech Characterization of a microbial community capable of nitrification at cold temperature Thomas F. Ducey *, Matias B. Vanotti, Anthony D. Shriner, Ariel A. Szogi, Aprel Q. Ellison Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, USDA, 2611 West Lucas Street, Florence, SC 29501, United States article info abstract Article history: While the oxidation of ammonia is an integral component of advanced aerobic livestock wastewater Received 5 February 2009 treatment, the rate of nitrification by ammonia-oxidizing bacteria is drastically reduced at colder temper- Received in revised form 30 July 2009 atures. In this study we report an acclimated lagoon nitrifying sludge that is capable of high rates of nitri- Accepted 30 July 2009 fication at temperatures from 5 °C (11.2 mg N/g MLVSS/h) to 20 °C (40.4 mg N/g MLVSS/h). The Available online 5 September 2009 composition of the microbial community present in the nitrifying sludge was investigated by partial 16S rRNA gene sequencing. After DNA extraction and the creation of a plasmid library, 153 partial length Keywords: 16S rRNA gene clones were sequenced and analyzed phylogenetically. Over 80% of these clones were Nitrite affiliated with the Proteobacteria, and grouped with the b- (114 clones), - (7 clones), and -classes (2 Ammonia-oxidizing bacteria c a Nitrosomonas clones). The remaining clones were affiliated with the Acidobacteria (1 clone), Actinobacteria (8 clones), Activated sludge Bacteroidetes (16 clones), and Verrucomicrobia (5 clones). The majority of the clones belonged to the genus 16S rRNA gene Nitrosomonas, while other clones affiliated with microorganisms previously identified as having floc forming or psychrotolerance characteristics.
    [Show full text]
  • Nitrification and Nitrifying Bacteria in a Coastal Microbial
    ORIGINAL RESEARCH published: 01 December 2015 doi: 10.3389/fmicb.2015.01367 Nitrification and Nitrifying Bacteria in a Coastal Microbial Mat Haoxin Fan 1, Henk Bolhuis 1 and Lucas J. Stal 1, 2* 1 Department of Marine Microbiology, Royal Netherlands Institute for Sea Research, Yerseke, Netherlands, 2 Department of Aquatic Microbiology, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands The first step of nitrification, the oxidation of ammonia to nitrite, can be performed by ammonia-oxidizing archaea (AOA) or ammonium-oxidizing bacteria (AOB). We investigated the presence of these two groups in three structurally different types of coastal microbial mats that develop along the tidal gradient on the North Sea beach of the Dutch barrier island Schiermonnikoog. The abundance and transcription of amoA, a gene encoding for the alpha subunit of ammonia monooxygenase that is present in both AOA and AOB, were assessed and the potential nitrification rates in these mats were measured. The potential nitrification rates in the three mat types were highest in autumn and lowest in summer. AOB and AOA amoA genes were present in all three mat types. The composition of the AOA and AOB communities in the mats of the tidal and intertidal stations, based on the diversity of amoA, were similar and clustered separately from the supratidal microbial mat. In all three mats AOB amoA genes were significantly more abundant than AOA amoA genes. The abundance of neither AOB nor AOA amoA genes correlated with the potential nitrification rates, but AOB amoA transcripts were Edited by: Hongyue Dang, positively correlated with the potential nitrification rate.
    [Show full text]
  • Nutrient Control Design Manual: State of Technology Review Report,” Were
    United States Office of Research and EPA/600/R‐09/012 Environmental Protection Development January 2009 Agency Washington, DC 20460 Nutrient Control Design Manual State of Technology Review Report EPA/600/R‐09/012 January 2009 Nutrient Control Design Manual State of Technology Review Report by The Cadmus Group, Inc 57 Water Street Watertown, MA 02472 Scientific, Technical, Research, Engineering, and Modeling Support (STREAMS) Task Order 68 Contract No. EP‐C‐05‐058 George T. Moore, Task Order Manager United States Environmental Protection Agency Office of Research and Development / National Risk Management Research Laboratory 26 West Martin Luther King Drive, Mail Code 445 Cincinnati, Ohio, 45268 Notice This document was prepared by The Cadmus Group, Inc. (Cadmus) under EPA Contract No. EP‐C‐ 05‐058, Task Order 68. The Cadmus Team was lead by Patricia Hertzler and Laura Dufresne with Senior Advisors Clifford Randall, Emeritus Professor of Civil and Environmental Engineering at Virginia Tech and Director of the Occoquan Watershed Monitoring Program; James Barnard, Global Practice and Technology Leader at Black & Veatch; David Stensel, Professor of Civil and Environmental Engineering at the University of Washington; and Jeanette Brown, Executive Director of the Stamford Water Pollution Control Authority and Adjunct Professor of Environmental Engineering at Manhattan College. Disclaimer The views expressed in this document are those of the individual authors and do not necessarily, reflect the views and policies of the U.S. Environmental Protection Agency (EPA). Mention of trade names or commercial products does not constitute endorsement or recommendation for use. This document has been reviewed in accordance with EPA’s peer and administrative review policies and approved for publication.
    [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]
  • WWW-VERSION (Without Papers) in This Online Version of the Thesis, Paper I-IV Are Not Included but Can Be Obtained from Electronic Article Databases E.G
    Downloaded from orbit.dtu.dk on: Sep 27, 2021 Discovery and description of complete ammonium oxidizers in groundwater-fed rapid sand filters Palomo, Alejandro Publication date: 2017 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Palomo, A. (2017). Discovery and description of complete ammonium oxidizers in groundwater-fed rapid sand filters. Department of Environmental Engineering, Technical University of Denmark (DTU). General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Discovery and description of complete ammonium oxidizers in groundwater-fed rapid sand filters Alejandro Palomo-González PhD Thesis June 2017 DTU Environment Department of Environmental Engineering Technical University of Denmark Alejandro Palomo-González Discovery and description of complete ammonium oxidizers in ground- water-fed rapid sand filters PhD Thesis, June 2017 The synopsis part of this thesis is available as a pdf-file for download from the DTU research database ORBIT: http://www.orbit.dtu.dk.
    [Show full text]
  • Characterization of Nitrifying Bacteria in Marine Recirculation Aquaculture Systems with Regard to Process Optimization
    Characterization of nitrifying bacteria in marine recirculation aquaculture systems with regard to process optimization Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften im Department Biologie der Universität Hamburg vorgelegt von Sabine Keuter aus Nordhorn Hamburg 2011 LIST OF CONTENTS LIST OF ABBREVIATIONS ……………………………………………………………………………………………………………………………………………………. 2 SUMMARY ………………………………………………………………………………………………………………………………………….………………………………… 3 ZUSAMMENFASSUNG ………………………………………………………………………………………………………………………………………………………… 5 CHAPTER I: Introduction ……………………………………………………………………………………………………………………………………………………………………..… 7 CHAPTER II: Relevance of Nitrospira for nitrite oxidation in a marine recirculation aquaculture system and physiological features of a Nitrospira marina -like isolate ……………………………….. 19 CHAPTER III: Monitoring nitrification potentials and nitrifying populations during the biofilter activation phases of three marine RAS …………………………………………………………………………………….…….……… 37 CHAPTER IV: Substances migrating from plastics impair marine nitrifiers………………………………………………………….…………….….63 CHAPTER V: Effects of high nitrate concentrations and low pH on nitrification in marine RAS ………………………….……….. 72 CHAPTER VI: Residual nitrification potentials after long term storage of biocarriers …………………………………..…………..……… 84 REFERENCES ………………………………………………………………………………………………………………….………………………………………………….. 94 APPENDIX ………………………………………. ……………………………………………………………………………….………..……………………….……………108 LIST OF ABBREVIATIONS AOA ammonia oxidizing archaea AOB ammonia oxidizing
    [Show full text]
  • 270. E. B.: Two Kinds of Lithotrophs Missing in Nature, Zeitschrift Für Allgemeine Mikrobiologie 17 (1977), 491-493
    270. E. B.: Two Kinds of Lithotrophs Missing in Nature, Zeitschrift für Allgemeine Mikrobiologie 17 (1977), 491-493. Zeitschrift für Allg. Mikrobiologie 1977 491-493 (Institut für Physikalische Chemie, Universität Wien) Two kinds of lithotrophs missing in nature E. BRODA (Eingegangen am 14. 9.1976) Two groups of lithotrophic bacteria, the existence of which may be expected on evolutionary and thermodynamical grounds, have not yet been detected: (A) photosynthetic, anaerobic, am- monia bacteria, analogous to coloured sulphur bacteria, and (B) chemosynthetic bacteria that oxidize ammonia to nitrogen with O2 or nitrate as oxidant. The versatility of the prokaryotes in their energy metabolism has long astonished microbiologists. The bacteria have developed processes, i.e., enzymes, for the utili- zation of a wide range indeed of exergonic reactions. Attention is now drawn to further processes in energy metabolism which on the basis of considerations on the evolution of the bioenergetic processes (BRODA I975a) may be expected to have existed, or to exist, but which have not yet been found. Two kinds of "lithotrophic" bacteria with such mechanisms will now be predicted. Lithotrophs are bacteria that use in- organic reductants in their energy metabolism (FROl\fAGEOT and SENEZ 1960); all autotrophs must be lithotrophs, though the reverse need not be true. The two bac- teria here predicted would generate dinitrogen (N2). The nitrifying bacteria make adenosine triphosphate, ATP, through oxidative phos- phorylation coupled to the aerobic oxidation of ammonia, a highly exergonic process. Thus, in nitrification Nitrosomonas produces nitrite, and Nitrobacter makes nitrate. The redox reactions are: NHt + 1.5 O2 = H 20 + NO;- + 2 H+; = - 65 kcal (1) NO;- + 0.5 O2 = NO;-; = - 18 kcal (2) The negativity of the free enthalpy change, is the precondition for the produc- tion of ATP and, consequently, for the endergonic reduction of CO 2 to biomass.
    [Show full text]
  • Nitrification 31
    NITROGEN IN SOILS/Nitrification 31 See also: Eutrophication; Greenhouse Gas Emis- Powlson DS (1993) Understanding the soil nitrogen cycle. sions; Isotopes in Soil and Plant Investigations; Soil Use and Management 9: 86–94. Nitrogen in Soils: Cycle; Nitrification; Plant Uptake; Powlson DS (1999) Fate of nitrogen from manufactured Symbiotic Fixation; Pollution: Groundwater fertilizers in agriculture. In: Wilson WS, Ball AS, and Hinton RH (eds) Managing Risks of Nitrates to Humans Further Reading and the Environment, pp. 42–57. Cambridge: Royal Society of Chemistry. Addiscott TM, Whitmore AP, and Powlson DS (1991) Powlson DS (1997) Integrating agricultural nutrient man- Farming, Fertilizers and the Nitrate Problem. Wallingford: agement with environmental objectives – current state CAB International. and future prospects. Proceedings No. 402. York: The Benjamin N (2000) Nitrates in the human diet – good or Fertiliser Society. bad? Annales de Zootechnologie 49: 207–216. Powlson DS, Hart PBS, Poulton PR, Johnston AE, and Catt JA et al. (1998) Strategies to decrease nitrate leaching Jenkinson DS (1986) Recovery of 15N-labelled fertilizer in the Brimstone Farm experiment, Oxfordshire, UK, applied in autumn to winter wheat at four sites in eastern 1988–1993: the effects of winter cover crops and England. Journal of Agricultural Science, Cambridge unfertilized grass leys. Plant and Soil 203: 57–69. 107: 611–620. Cheney K (1990) Effect of nitrogen fertilizer rate on soil Recous S, Fresnau C, Faurie G, and Mary B (1988) The fate nitrate nitrogen content after harvesting winter wheat. of labelled 15N urea and ammonium nitrate applied to a Journal of Agricultural Science, Cambridge 114: winter wheat crop.
    [Show full text]
  • A Novel Marine Nitrite-Oxidizing Nitrospira Species from Dutch Coastal North Sea Water
    ORIGINAL RESEARCH ARTICLE published: 18 March 2013 doi: 10.3389/fmicb.2013.00060 A novel marine nitrite-oxidizing Nitrospira species from Dutch coastal North Sea water Suzanne C. M. Haaijer1*, Ke Ji 1, Laura van Niftrik1, Alexander Hoischen 2, Daan Speth1, MikeS.M.Jetten1, Jaap S. Sinninghe Damsté3 and Huub J. M. Op den Camp1 1 Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands 2 Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Nijmegen, Nijmegen, Netherlands 3 Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Texel, Netherlands Edited by: Marine microorganisms are important for the global nitrogen cycle, but marine nitrifiers, Boran Kartal, Radboud University, especially aerobic nitrite oxidizers, remain largely unexplored. To increase the number Netherlands of cultured representatives of marine nitrite-oxidizing bacteria (NOB), a bioreactor Reviewed by: cultivation approach was adopted to first enrich nitrifiers and ultimately nitrite oxidizers Eva Spieck, University of Hamburg, Germany from Dutch coastal North Sea water. With solely ammonia as the substrate an active Luis A. Sayavedra-Soto, Oregon State nitrifying community consisting of novel marine Nitrosomonas aerobic ammonia oxidizers University, USA (ammonia-oxidizing bacteria) and Nitrospina and Nitrospira NOB was obtained which *Correspondence: converted a maximum of 2 mmol of ammonia per liter per day. Switching the feed of the Suzanne C. M. Haaijer, Department of culture to nitrite as a sole substrate resulted in a Nitrospira NOB dominated community Microbiology, Institute for Water and Wetland Research, Radboud (approximately 80% of the total microbial community based on fluorescence in situ University Nijmegen, hybridization and metagenomic data) converting a maximum of 3 mmol of nitrite per liter Heyendaalseweg 135, Nijmegen, per day.
    [Show full text]