Table of Contents Abstract ............................................................................................................................ 4 Acknowledgments ........................................................................................................... 7 Chapter I - General introduction ..................................................................................... 9 1.1 Ecosystem services ............................................................................................. 9 1.2 Invasive species – one of the main threats to ecosystems .................................. 11 1.3 Potential threats of invasive species .................................................................. 14 1.4 Context-dependency of impacts of invaders ...................................................... 15 1.5 Impacts of invasive ecosystem engineers .......................................................... 18 1.6 Crassostrea gigas as an invasive ecosystem engineer: potential impacts on biodiversity and ecosystem functioning ........................................................................ 19 1.7 Aims of this thesis ............................................................................................. 25 Chapter II: Impacts of non-indigenous oysters on biodiversity and a protected biogenic habtiat in an intertidal boulder-field .............................................................. 26 2.1 Introduction ........................................................................................................ 26 2.2 Materials and methods ...................................................................................... 29 2.2.1 Study site ...................................................................................................... 29 2.2.2 Cover of S. alveolata on boulders with and without C. gigas ......................... 30 2.2.3 Experimental addition of C. gigas onto boulders ............................................ 30 2.2.4 Sampling of experimental boulders ............................................................... 31 2.2.5 Statistical analysis ......................................................................................... 32 2.3 Results .............................................................................................................. 33 2.3.1 Amount of S. alveolata on boulders with or without C. gigas .......................... 33 2.3.2 Experimental addition of C. gigas .................................................................. 34 2.3.3 Effects of C. gigas on biodiversity .................................................................. 34 2.3.4 Effects of C. gigas on community structure .................................................... 35 2.3.5 Effects of C. gigas on the establishment of S. alveolata ................................ 36 2.3.6 Effects of C. gigas on the establishment of Fucus vesiculosus, Ascidia conghilega and Littorina littorea ............................................................................... 36 2.3.7 Effects of the experimental procedure ......................................................... 37 2.4 Discussion ......................................................................................................... 49 Chapter III - Effects of non-indigenous oysters on biodiversity vary with increasing cover and environmental context .............................................................. 55 3.1 Introduction ....................................................................................................... 55 3.2 Materials and methods ..................................................................................... 57 3.2.1 Study sites ..................................................................................................... 57 3.2.2 Experimental set-up ...................................................................................... 58 3.2.3 Sampling methods ........................................................................................ 58 3.2.4 Statistical analysis ......................................................................................... 59 1 3.3 Results .............................................................................................................. 60 3.3.1 Effects of C. gigas on the total number of individuals .................................. 60 3.3.2 Effects on biodiversity after 4 months ......................................................... 61 3.3.3 Effects on biodiversity after 15 months ....................................................... 61 3.3.4 Effects on assemblage structure after 4 months ......................................... 62 3.3.5 Effects on assemblage structure after 15 months ....................................... 63 3.3.6 Effects on β-diversity .................................................................................. 64 3.3.7 Effects on individual taxa after 4 months ..................................................... 64 3.3.8 Effects on individual taxa after 15 months ................................................... 65 3.4 Discussion ........................................................................................................ 77 Chapter IV - Effects of non-indigenous oysters on ecosystem processes of estuarine habitats .......................................................................................................... 83 4.1 Introduction ....................................................................................................... 83 4.2 Materials and methods ...................................................................................... 86 4.2.1 Study site ...................................................................................................... 86 4.2.2 Experimental design ..................................................................................... 87 4.2.3 Organic matter (OM) content and C/N ratios ............................................... 87 4.2.4 Pore-water nutrient concentrations ............................................................. 88 4.2.5 Flux across the sediment-water interface (SWI) .......................................... 89 4.2.6 Community respiration .................................................................................. 89 4.2.7 Biological assemblages ................................................................................. 90 4.2.8 Statistical analysis ......................................................................................... 90 4.3 Results .............................................................................................................. 91 4.3.1 Organic matter (OM) content and C/N ratio ................................................ 91 4.3.2 Pore-water nutrient concentrations ............................................................. 92 4.3.3 Diffusive nutrient fluxes ............................................................................... 92 4.3.4 Inventory and residence time of nutrients ................................................... 93 4.3.5 Community respiration ................................................................................ 93 4.3.6 Relationship between changes in assemblage structure and functional variables .................................................................................................................. 94 4.4 Discussion ........................................................................................................ 110 Chapter V - Effects of non-indigenous oysters on the diversity and functioning of microbial assemblages ................................................................................................ 118 5.1 Introduction ...................................................................................................... 118 5.2 Methods........................................................................................................... 122 5.2.1 Study site and experimental design .......................................................... 122 5.3 Sampling techniques for ecosystem processes ............................................... 122 5.3.1 Gas flux of CO2 and CH4 .......................................................................... 122 5.3.2 Procedural controls for gas fluxes ............................................................. 123 2 5.3.3 Pore-water nutrients .................................................................................... 123 5.3.4 Chlorophyll content of the oxic layer of sediment ...................................... 124 5.3.5 Total organic carbon and total nitrogen in the oxic and anoxic sediment ... 124 5.3.6 Dehydrogenase enzyme activity as an estimate of microbial activity ........ 125 5.4 Microbial diversity ............................................................................................ 125 5.4.1 DNA extraction from the oxic and anoxic sediment ................................... 125 5.4.2 Polymerase chain reactions ...................................................................... 126 5.4.3 Terminal restriction fragment length polymorphism and fragment analysis 127 5.5 Statistical analyses .......................................................................................... 128 5.5.1 Univariate data analyses .......................................................................... 128 5.5.2 Multivariate data analyses .......................................................................