Microbial Communities in Aquaculture Ecosystems

Abstract

This book sheds light on the major functions of microbial communities in aquaculture ecosystems, showing that by recycling nutrients, degrading organic matter and preventing disease outbreaks, a variety of microbes are truly beneficial to a wide range of aquaculture industries. It discusses how deteriorating environmental quality enables some microbial strains to trigger disease, describes the development of highly sustainable tools to improve water quality, and identifies crucial factors that endanger microbial homeostasis in aquaculture ecosystems. The book also covers post-antibiotic approaches for preventing and treating opportunistic microbial infections based on harnessing environmental and fish-associated microbial communities. Furthermore, it explores how manipulating and engineering these complex microbial communities using bio-agents such as probiotics, phages, natural nutritional additives, or with fine-tuned biofilters will open the door for new ways to develop a more sustainable and cost-effective aquaculture industry. Including an accessible presentation of modern high-throughput sequencing technology to identify host-microbial interactions in aquaculture ecosystems, this book is a valuable resource for scientists, aquaculture and fishery experts, sustainability enthusiasts and scholars in the areas of biology and marine agriculture. Intro; Preface; Contents; The Rise and Fall of Antibiotics in Aquaculture; 1 A Brief History of Antibiotics; 1.1 Discovery of Antibiotics; 1.2 First Steps in the Use of Antibiotics in Aquaculture; 2 The Phenomenon of Antibiotic Resistance; 2.1 Why Does a Bacterium Become Resistant?; 2.2 How Does a Bacterium Become Resistant?; 2.3 The Role of Aquaculture in Antibiotic Resistance; 3 Adverse Effects of Antibiotherapy on Fish Microbiota; 3.1 Roles of the Microbiota in Fish Health; 3.2 Collateral Targeting of the Microbiota by Antimicrobial Compounds; 3.3 Over-elicitation of Inflammatory Responses 3.4 Permanent Alteration of the Microbiota3.5 Increased Carrying Capacity for Resistant and/or Pathogenic Bacteria; 4 Aquatic Pathogens Resistant to Antibiotics: The Case of Aeromonas salmonicida; 5 Antibiotic Alternatives and the One Health Perspective; 6 Conclusion; References; Host-Microbiota Interactions and Their Importance in Promoting Growth and Resistance to Opportunistic Diseases in Salmonids; 1 Introduction; 1.1 Salmonid Aquaculture and Related Stressors; 1.2 Host-Microbiota Interactions and Their Involvement in Health; 2 An Overview of Salmonid Microbiomes 2.1 Atlantic Salmon (Salmo salar)2.1.1 Compositional Shifts During Freshwater-Seawater Migration; 2.1.2 Influence of the Diet and Protein Sources; 2.1.3 Antibiotherapy; 2.1.4 Captivity; 2.2 Rainbow Trout (Oncorhynchus mykiss); 2.2.1 Influence of Nutrition; 2.2.2 Diet-Immunity Interactions; 2.2.3 Pathogen Inhibition; 2.3 Brook Charr (Salvelinus fontinalis); 2.3.1 Microbiota Structure and the Stress Response; 2.3.2 Symbiont-Based Therapeutic Tools Against Opportunistic Pathogens; 3 An Overview of High-Throughput Methods and Their Contribution to Microbiota Studies 3.1 Whole-Genome Sequencing (for Specific Microbes)3.2 Metabarcoding (Who Is There?); 3.3 Metagenomics (What Are They Doing?); 4 Future Perspectives for Microbiota Modulation; 4.1 Host-Microbiota Interactions in Light of the One Health Perspective; 4.2 Fine-Grained Modulation Using Dietary Supplements; 4.2.1 Probiotics; 4.2.2 Prebiotics and Synbiotics; 4.2.3 Phage Therapy; 4.3 Coarse-Grained Modulation: The Case of K-Selection; 4.4 Toward Real-Time Microbiota Monitoring; 5 Conclusion; References; Would Bacteriophages Be a New Old Complement to Antibiotics in Aquaculture? 1 The Enemy of My Enemy Is My Friend2 The Biology of Phages; 3 Phagotherapy in the Digital Age: What if We Could Make a Custom Phage?; 4 Phage Therapy in Aquaculture; 5 Toward Phagotherapy to Control Furunculosis; 6 Keep Going Until Efficient Phagotherapy; References; Controlling Factors for Community Assembly in Developing Cod Larvae (Gadus morhua); 1 Introduction; 2 Effect of Live Feed Diets on Cod Larval Microbiota; 2.1 Summary of Research Results; 3 Effect of Water Treatment and Water Microbiota on Microbiota and Gene Expression in Cod Larvae; 3.1 Summary of Research Results