I PELAGIC NITROGEN CYCLING. 1 Primary Productivityand PelagicNitrogenCycling... P. M. Glibert

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1 Introduction XXUl T H Blackburn and J S(Jrensen I PELAGIC NITROGEN CYCLING 1 Primary Productivityand PelagicNitrogenCycling P M Glibert 11 Introduction 12 Methodology 121 Tracer techniques 122 Other techniques 13 Nutritional status of phytoplankton 14 Pelagicuptake and mineralizationof nitrogen 141 Rates of ammonium regenerationrelativeto uptake 142 Rates of supplyof 'new' versus'regenerated'nitrogen 15 Conclusions 2 Pelagic Primary Productionin NearshoreWaters E Paasche 21 Introduction 22 Concentrationsofnitrogenin the pelagicenvironment 23 Nitrogen uptake rates and nitrogen primary production 24 Indices of nitrogen nutrition and their use in coastal waters 25 Supplyand utilizationof 'new' nitrogen 251 Open shelfwaters 252 Inshore waters 26 Supply and utilizationof 'regenerated'nitrogen 27 Conclusions ' xv

2 XVI 3 MicrofaunainPelagicFoodChains T F enchel 31 Introduction 32 Distribution patterns and quantitative role 33 Mineralization of C, Nand P II BENTHIC NITROGEN CYCLING 4 Benthic Primary Production and Oxygen Profiles N P Revsbech, J Nielsen and P K Hansen 41 Introduction 42 The chemical microenvironment at the sediment surface 43 The nitrogen cycle in the chemical microenvironment near the sediment surface 44 Factors regulating benthic photosynthesis 45 Summary 5 Benthic Nitrogen Fixation D G Capone 51 Introduction 52 N2 fixation and nitrogenase 53 N2-fixing bacteria 54 Methodology 55 Physiological ecology: regulating factors 551 Oxygen 552 Ammonium and nitrate 553 Organic substrate 554 Inhibitors 56 N2 fixation in benthic marine environments 57 Conclusions 6 Amino Acid and Amine Biogeochemistry in Marine Particulate Material and Sediments C Lee 61 Introduction 62 Methods 621 Preparation of samples for analysis 622 Hydrolysis of bound amino acids and amines 623 Analysis of free amino acids 624 Analysis of free amines 63 Amino nitrogen compounds in particulate matter

3 631 Sources of particulate amino compounds 632 Transformation of amino compounds in particles 633 Decomposition of particulate amino compounds with depth 64 Amino nitrogen compounds in sediments 65 Conclusions XVll Distributions and Metabolism of Quaternary Amines in Marine Sediments " G M King 71 Introduction 72 Quaternary amine chemistry 73 Methods for the analysisof quaternary amines 731 Ion exchangechromatography 732 Spectrophotometry 733 Chromatographicmethods 734 Radiotracer methods 735 Other techniques 74 Distribution of quaternary amines and related compounds 741 Bacteria and cyanobacteria 742 Plants and algae 743 Animals 744 Sediments 75 Physiologyand metabolismof quaternary aminesand related compounds 751 Laboratorystudies 752 In situstudies 76 Conclusions 8 BenthicMineralizationandBacterialProduction T H Blackburn 81 Introduction 82 Rates of nitrogenmineralization 821 Sedimentincubations 822 Sediment 15N-ammoniumincubations 823 Exchangemeasurements 824 Gradient measurements 825 SpecificN-substrate mineralization 83 Rates of nitrogen assimilation 831 Thymidineassimilation 832 Adenosineassimilation 833 Frequencyof dividingcells

4 xviii 834 Incubation and directcounts 835 Phospholipidmeasurements 836 Incorporation of 15N-ammonium 84 Calculationfrom C:N models 85 Conclusions Nitrogenin BenthicFood Chains K R Tenore 91 Introduction 92 The role of nitrogen in nutrition of benthos 93 Nitrogen sourcesavailableto benthos 931 Suspensionfeeders 932 Deposit feedersand detritus-basedfood chains 933 Nitrogen changesin 'aging' detritus 934 Temporal changes in nitrogen resources to detritus food chains Nitrificationin Estuarineand CoastalMarine Sediments 207 K Henriksenand W M Kemp 101 Introduction Methods N-tracers Specificinhibitors Indirectmeasurements Potential activities Counting methods Temporal and spatial patterns Temporal patterns Spatial patterns Physicaland chemicalregulation Temperature Oxygen Ammonium Carbon dioxideand ph Salinity Toxic and stimulatingcompounds Surfaces Biologicaland ecologicalregulation Diatom interactions Macrofaunalinteractions Macrophyteeffects Interaction with ammonificationand denitrification 233

5 107 Nitrification in nitrogen and oxygen budgets 108 Conclusions XIX Nitrate Reduction and Denitrification in Marine Sediments I Koike and J S~rensen 111 Introduction 112 Oxygenand nitrate profilesin marine sediments 113 Assays of nitrate reduction and denitrification in manne sediments Diffusion-advectionmodels Direct estimatesof Nz production Use of 15Nisotope techniques Use of the CzHz inhibition technique 114 Variation of nitrate reduction and denitrificationactivitiesin 259 marine sediments Regionalvariation of denitrification 1142 Seasonalvariation of denitrification Diel variation of denitrification Populations of nitrate-reducing and denitrifyingbacteria in marine sediments Most-probable-number and chemostat enrichment techniques 1152 'Potential' for nitrate reduction and denitrification Conclusions Benthic Fauna and Biogeochemical Processes in Marine Sediments: microbial activities and fluxes E Kristensen 121 Introduction 122 Sedimentreworking 123 Ventilation 124 Properties of burrows 125 Benthicfauna and mineralization 126 Nitrificationand denitrificationin burrows 127 Faecal pelletsand microniches 128 Conclusions BenthicFauna and BiogeochemicalProcessesin Marine Sediments: the role of burrowstructures 301 R C Aller 131 Introduction 301

6 xx 132 Burrow microenvironments 133 Quantification of solute distributions around burrows 134 The average microenvironments and bulk sediment distributions 135 Source-sink models of bulk chemistry of the bioturbated zone 136 Sediment ammonium production rates and fluxes 137 Conclusions III MODELS OF NITROGEN CYCLING 14 Modelling Benthic Nitrogen Cycling in Temperate Coastal Ecosystems C Billen and C Lance/at 141 Introduction Idealized models of seasonal variations of nitrogen cycling Closed system- three compartment model Closed system-seven compartment model Open-system model Kinetics of sedimentary processes Input of organic matter to coastal sediments Sinking of phytoplankton Deposition Nitrogen mineralization in sediments Nitrification and nitrate reduction in sediments Nitrification Nitrate reduction Modelling benthic nitrogen recycling Seasonal variations of denitrification Long-term variations of nitrogen diagenesis Conclusions Nitrogen Models at the Community Level: plant-animal-m:crobe interactions R C Newell C L M%ney, J G Fie/d M I Lucas and T A Probyn 151 Introduction 152 Outline of conceptual model 1421 What substrates do bacteria utilize under natural conditions? What is the flux of materials through bacteria? A simple conceptual model for a macrophyte community The fate of different components of kelp A coupled C:N flow model for a kelp community Evaluation and significance of the model

7 XXI 154 A nitrogen flow model for a pelagic system Presentation of the model Validation of the model Requirements for a better model: Spatial and temporal 'decoupling' ofc and N flow Euphotic zone model Pycnocline zone model Conclusions Nitrogen BiogeochemistryandModellingof CarmarthenBay R F C MantouraN J P OwensandP H Burkill Introduction Carmarthen Bay physiography Field and experimentalmethods Coastal bay mixingand growth limitingnutrients Bay circulationand residencetime Nitrogen reservoirs,speciationand seasonal variation Bay distribution and anomalies Nitrogen assimilationand ammonification Bay fronts Zooplankton excretion Nitrogen budget 1610Conclusions Index 443

Sun. Photosynthesis (performed by plants, algae, and some bacteria) Respiration (performed by all organisms) 6 O 2 6 CO 2.

Sun. Photosynthesis (performed by plants, algae, and some bacteria) Respiration (performed by all organisms) 6 O 2 6 CO 2. Photosynthesis (performed by plants, algae, and some bacteria) Sun 6 O 6 CO 6 H O C 6 H O 6 (glucose) Solar energy + 6 H O + 6 CO C 6 H O 6 + 6 O Energy Respiration (performed by all organisms) 6 O 6 CO