Opportunities for microbiome research to enhance farmed freshwater fish quality and production

Abstract

Freshwater fish farming is the largest sub-sector of the global aquaculture industry, with its continued success dependent on the industry's ability to be productive and sustainable. In recent years, microorganisms have been increasingly recognised for their role in the health and overall performance of aquatic organisms, providing the aquaculture industry with a promising avenue for further success. Here, we review the literature on freshwater fish microbiology to evaluate the potential for microbial research to enhance freshwater aquaculture. A systematic review revealed that the existing freshwater fish microbiology literature incorporates <1% of freshwater fish species, with most studies focussed on Cyprinidae, Salmonidae and to a lesser extent Cichlidae. Using social network analyses, this review identified 25 key research areas commonly addressed in the existing literature highlighting the narrow focus of existing studies. Microbial community structure was the most frequently researched area, followed by environment and diet. These studies often evaluated microbiota changes associated with diadromous migrations, new technologies and advancements in feed formulations. However, research areas, such as the role of microorganisms in fish fecundity, omega-3 content, sustainability and palatability, were underrepresented in the literature despite their influence on aquaculture success. These underrepresented research areas are examples of where additional investments in microbial research are needed to ensure the continued expansion and success of freshwater aquaculture.

The Occurrence of Microplastics and the Formation of Biofilms by Pathogenic and Opportunistic Bacteria as Threats in Aquaculture

“…About 90% of the global demand for farmed fish and crustaceans-mainly tilapia and shrimp-is supplied from this area [1]. It is the fastest growing food production sector in the world, with an approximately 60% share of freshwater fish [2].…”

“…The latter has been recently connected with the problem of microbiome in farmed animals, including fish and shellfish. Attention has been paid to the crucial role that the microbiome plays in animal health and productivity [2,5]. Water is one of the most important habitats for microorganisms on Earth; at the same time, it is the main way that they spread in the environment [6][7][8].…”

A large-scale, multi-year microbial community survey of a freshwater trout aquaculture facility

“…Aquaculture has grown extensively over the past three decades, but disease caused by microbes poses one of the greatest threats to the continued growth of this industry (1). While the microbiomes of many farmed fish have been studied (2,3), the microbial communities existing within the built environments of these animals, including raceway surfaces, have garnered less attention. These biomes are important as they offer potential insight into the distributions and abundances of specific pathogens.…”

Gut Microbes Reveal Pseudomonas Medicates Ingestion Preference via Protein Utilization and Cellular Homeostasis Under Feed Domestication in Freshwater Drum, Aplodinotus grunniens

“…In recent years, microorganisms have been increasingly recognized for their role in the health and overall performance of aquatic organisms (Parata et al, 2021). Gut microbiota refers to the entire population of microorganisms that colonize the intestine, and investigations on microbiota associated with a fish gut have deepened our knowledge about the complex interactions that occur between microbes and host fish (Talwar et al, 2018).…”