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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 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 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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