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Microbially Mediated Transformation of Dissolved Nitrogen in Aquatic Environments a Dissertation Submitted to Kent State Univers

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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 ACKNOWLEDGEMENTS……………………………………………………………………..xiv CHAPTER I. General Introduction ………………………………………..…………………………….1 References…………………………….………………..………………………...15 II. The Relative Importance of Anammox and Denitrification in Total N2 Production in Offshore Bottom Seawater of the South Atlantic Bight………………………..…...…..28 Abstract……………………………………………………….…….…………...29 Introduction……………………………………………………….…..…………30 Methods…………………………………………………………....…………….31 Results and Discussion…………………………………………………………..35 Conclusion ………………………………………….…………………………...39 References…………………………….…………………………………………40 III. The Relative Importance of Anammox to Denitrification in Total N2 Production in Lake Erie……………………………………………………………………………………….53 Abstract……………………………………………………….…….……………54 Introduction……………………………………………………….…..…………55 Methods…………………………………………………………....…………….57 Results and Discussion……………………………………………….…...……..59 iii Conclusion…………………………………………….………………………....65 References…………………….…………………………………….....................66 IV. Temporal Dynamics and Depth Variations of Dissolved Free Amino Acids and Polyamines in Coastal Seawater Determined by High-Performance Liquid Chromatography................................................................................................................79 Abstract…………………………………………………………….……………80 Introduction……………………………………………………….…..………….81 Methods…………………………………………………………....……………..82 Results…………………………………………………….……………………...87 Discussion………………………………………………………………………..91 Conclusion……………………………………………………………………….95 References………………………………………………………………………..96 V. Identification of Polyamine-Responsive Bacterioplankton Taxa in the South Atlantic Bight…………………………………………………………………..………………..115 Abstract……………………………………………………….…….…………..116 Introduction……………………………………………………….…..………...117 Methods…………………………………………………………....……………118 Results ……………………………………………….…………………………123 Discussion………………………………………………………………………127 Conclusion……………………………………………………………………...130 References………………………………………………………………………131 VI. Metagenomic and Metatranscriptomic Characterization of Polyamine-Transforming Bacterioplankton in Marine Environments………………………………...……….......148 iv Abstract……………………………………………………….…….…………..149 Introduction……………………………………………………….…..………...150 Methods…………………………………………………………....……………151 Results.……………………………………………….…………………………157 Discussion………………………………………………………………………163 Conclusion……………………………………………………………………...168 References……………………………………………………………………....169 VII. Summary…………………………………………………………...…………………...199 References…………………………………………………...………………….206 v LIST OF FIGURES Figure 1.1. The simplified diagram of N cycle in oxic and suboxic aquatic ecosystems………..25 Figure 1.2. The chemical structure of individual polyamine compounds, including putrescine, cadaverine, norspermidine, spermidine, and spermine…………………………....................26 Figure 1.3. Polyamine degradation pathways and associated genes in bacteria…........................27 Figure 2.1. The sampling sites in the offshore bottom water of the SAB in spring (st1 and st2) and fall (st2, st3, and st4) of 2011…………………………………………………………....45 Figure 2.2. Principal component analysis (PCA) biplot of environmental variables in bottom water of st1and st2 in spring and st2, st3, and st4 in fall in the offshore of the SAB………..46 Figure 2.3. The N2 production rates through anammox and denitrification in offshore bottom water of the SAB in (a) spring and (b) fall, 2011……………………………………………47 Figure S2.1. The depth profiles of oxygen saturation (%) in the water column at offshore SAB sites in (a) spring and (b) fall, 2011…………………………………………….…………....48 15 15 - 15 + Figure S2.2. The production of the N-labeled N2 during (a) NO3 incubation and (b) NH4 15 - 15 + incubation in st1 and (c) NO3 incubation and (d) NH4 incubation in st2 of the offshore bottom water in the SAB in spring, 2011……………………………………………………49 15 15 - 14 + Figure S2.3. The production of the N-labeled N2 during NO3 + NH4 incubations in (a) st1 and (b) st2 in the offshore bottom water of the SAB in spring, 2011………………………..50 15 15 - 15 + Figure S2.4. The production of the N-labeled N2 during (a) NO3 incubation and (b) NH4 15 - 15 + 15 - incubation in st2, (c) NO3 incubation and (d) NH4 incubation in st3, and (e) NO3 15 + incubation and (f) NH4 incubation in st4 of the offshore bottom water in the SAB in fall, 2011…………………………………………………………………………………………..51 vi 15 15 - 14 + Figure S2.5. The production of the N-labeled N2 during NO3 + NH4 incubations in (a) st2, (b) st3, and (c) st4 in the offshore bottom water of the SAB in fall, 2011………….....…….52 Figure 3.1. The sampling sites in SB, SS, CB1, and CB2 of Lake Erie in August of 2010, 2011, and 2012………………………………………………………………………..……………73 Figure 3.2. The N2 production rates through anammox and denitrification in bottom water of SB, SS, CB1, and CB2 in August of (a) 2010, (b) 2011, and (c) 2012 in Lake Erie…………..…74 Figure S3.1. Principal component analysis (PCA) biplot of environmental variables in bottom water of SB, SS, CB1, and CB2 in Lake Erie in August of 2010, 2011, and 2012………….75 15 - 15 + Figure S3.2. The production of the 15N-labeled N2 after incubation with (a) NO3 , (b) NH4 , 15 - 14 + 15 - 15 + 15 - 14 + and (c) NO3 + NH4 in SB, (d) NO3 , (e) NH4 , and (f) NO3 + NH4 in SS, and (g) 15 - 15 + 15 - 14 + NO3 , (h) NH4 , and (i) NO3 + NH4 in CB1 of bottom water in Lake Erie in August, 2010…………………………………………………………………………………………..76 15 15 - Figure S3.3. The production of the N-labeled N2 after incubation with (a) NO3 and (b) 15 + 15 - 15 + 15 - 15 + NH4 in SB, (c) NO3 and (d) NH4 in SS, (e) NO3 and (f) NH4 in CB1, and (g) 15 - 15 + NO3 and (h) NH4 in CB2 of bottom water in Lake Erie in August, 2011………….…...77 15 15 - Figure S3.4. The production of the N-labeled N2 after incubation with (a) NO3 and (b) 15 + 15 - 15 + 15 - 15 + NH4 in SB, (c) NO3 and (d) NH4 in SS, (e) NO3 and (f) NH4 in CB1, and (g) 15 - 15 + NO3 and (h) NH4 in CB2 of bottom water in Lake Erie in August, 2012………………78 Figure 4.1. Depth profiles of temperature and salinity at the GRNMS in (a) spring and (b) fall, 2011………………………………………………………………………………….……...107 Figure 4.2. HPLC chromatograms of (A) a standard mixture and (B) a seawater sample..........108 Figure 4.3. Temporal and depth dynamics of DFAAs and PAs………………………………..109 vii Figure 4.4. The NMDS ordination based on individual DFAA concentrations at the GRNMS in spring and fall, 2011………………………………………………………………………..110 Figure 4.5. Variations in the concentrations of major DFAAs in (a) surface, (b) mid-depth, and (c) bottom water and major PAs in (d) surface, (e) mid-depth, and (f) bottom water within a diurnal cycle at the GRNMS in spring……………………………………………………..111 Figure 4.6. Variations in the concentrations of major individual DFAAs in (a) surface and (b) bottom water and major PAs in (c) surface and (d) bottom water within a diurnal cycle at the GRNMS in fall……………………………………………………………………………..112 Figure S4.1. The NMDS ordination based on individual DFAA relative abundances at the GRNMS in spring and fall, 2011…………………………………………………………...113 Figure S4.2. The NMDS ordination based on individual PA concentrations at the GRNMS in spring and fall, 2011………………………………………………………………………..114 Figure 5.1. Sampling stations of st1 (nearshore), st2 (river-influenced nearshore), st3 (offshore), and st4 (open ocean) in the South Atlantic Bight (SAB) in October, 2011………………...140 Figure 5.2. Principal component analysis (PCA) biplot of environmental variables measured in water samples from st1, st2, st3, and st4……………………………………………………141 Figure 5.3. The relative abundance (%) of major bacterioplankton families in libraries of CTR, PUT, and SPD treatments from (a) st1, (b) st2, (c) st3, and (d) st4………………………...142 Figure 5.4. Changes in putrescine and spemidine concentrations (bar graph; left axis) and cell abundance (line graph; right axis) in the CTR, PUT, and SPD microcosms from (a) st1, (b) st2, (c) st3, and (d) st4 after 48 h incubation………………………………………….…....143 viii Figure 5.5. The non-metric multidimensional scaling
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    Leibniz-Institut für Meereswissenschaften The integration of microalgae photobioreactors in a recirculation system for low water discharge mariculture Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät an der Christian-Albrechts-Universität zu Kiel vorgelegt von Nicole Kube Kiel, 2006 Referentin: Prof. Dr. Karin Lochte Koreferent: Prof. Dr. Dr. h.c. Harald Rosenthal Tag der mündlichen Prüfung: Zum Druck genehmigt: Kiel, den Der Dekan Foreword The manuscripts included in this thesis are prepared for submission to peer- reviewed journals as listed below: Wecker B., Kube N., Bischoff A.A., Waller U. (2006). MARE – Marine Artificial Recirculated Ecosystem: feasibility and modelling of a novel integrated recirculation system. (manuscript) Kube N., Bischoff A.A., Wecker B., Waller U. Cultivation of microalgae using a continuous photobioreactor system based on dissolved nutrients of a recirculation system for low water discharge mariculture (manuscript) Kube N. And Rosenthal H. Ozonation and foam fractionation used for the removal of bacteria and parti- cles in a marine recirculation system for microalgae cultivation (manuscript) Kube N., Bischoff A.A., Blümel M., Wecker B., Waller U. MARE – Marine Artificial Recirulated Ecosystem II: Influence on the nitrogen cycle in a marine recirculation system with low water discharge by cultivat- ing detritivorous organisms and phototrophic microalgae. (manuscript) This thesis has been realised with the help of several collegues. The contributions in particular
  • Functional Characterization of Seven Γ-Glutamylpolyamine Synthetase

    Functional Characterization of Seven Γ-Glutamylpolyamine Synthetase

    JOURNAL OF BACTERIOLOGY, Aug. 2011, p. 3923–3930 Vol. 193, No. 15 0021-9193/11/$12.00 doi:10.1128/JB.05105-11 Copyright © 2011, American Society for Microbiology. All Rights Reserved. Functional Characterization of Seven ␥-Glutamylpolyamine Synthetase Genes and the bauRABCD Locus for Polyamine and ␤-Alanine Utilization in Pseudomonas aeruginosa PAO1ᰔ Xiangyu Yao,1† Weiqing He,1,2† and Chung-Dar Lu1,3* Department of Biology, Georgia State University, Atlanta, Georgia 303031; Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China2; and Department of Medical Laboratory Sciences and Biotechnology, China Medical University, Taichung, Taiwan 404023 Received 16 April 2011/Accepted 13 May 2011 Pseudomonas aeruginosa and many other bacteria can utilize biogenic polyamines, including diaminopropane (DAP), putrescine (Put), cadaverine (Cad), and spermidine (Spd), as carbon and/or nitrogen sources. Tran- scriptome analysis in response to exogenous Put and Spd led to the identification of a list of genes encoding putative enzymes for the catabolism of polyamines. Among them, pauA1 to pauA6, pauB1 to pauB4, pauC, and pauD1 and pauD2 (polyamine utilization) encode enzymes homologous to Escherichia coli PuuABCD of the ␥-glutamylation pathway in converting Put into GABA. A series of unmarked pauA mutants was constructed for growth phenotype analysis. The results revealed that it requires specific combinations of pauA knockouts to abolish utilization of different polyamines and support the importance of ␥-glutamylation for polyamine catabolism in P. aeruginosa. Another finding was that the list of Spd-inducible genes overlaps almost completely with that of Put-inducible ones except the pauA3B2 operon and the bauABCD operon (␤-alanine utilization).
  • Structural, Spectroscopic, and Mechanistic Insights Into the Three Phases of Nitrification Metallobiochemistry

    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 .