Aquaculture Microbiology: The Role and Importance of Microbial Communities in Diversified and Sustainable Aquaculture

Aquaculture has grown at an impressive rate over the past few decades. However, guaranteeing aquaculture sustainability is a huge challenge in terms of maintaining productive output on the one hand and safeguarding natural resources and the environment on the other. Major stumbling blocks include emerging infectious diseases, demand for aquafeed ingredients, as well as the direct environmental impact of aquaculture activities.

Like all vertebrates, fish also harbour complex commensal microbial communities, with potentially important roles in disease, physiology, host immune responses, tissue development and nutrition. The use of omics techniques to study microbes in complex host-associated ecosystems has resulted in the generation of vast quantities of sequencing data, with a particular focus on rRNA genes to understand microbial diversity. However, our ability to understand the complexity of the gut microbiome is often hindered by a lack of standardized protocols, which is often not comparable across studies, for example, differences in DNA extraction methods, PCR protocols, sequencing platforms, normalisation techniques, etc. Furthermore, as with much research focused around microbial community diversity, there is a dearth of aquaculture microbiology studies that are able prove causation, rather than simply correlation, when linking microbiome to host phenotype. In this respect an growing number of germ free models of aquaculture species under development that will provide important insights, and the use existing teleost model systems is becoming increasingly widespread.

As well as understanding the impact of additives, feed ingredients and antibiotics on the microbiome, there is a need to understand the function of the microbiome alongside our understanding the aquaculture environment more broadly. Disease is a major concern. Commensal microbiota are assumed to act as a barrier against pathogenic invasion and establishment. Better understanding of the ecological rules conducting the microbial colonization of larvae, for example, could be important to improve the results at hatchery level where disease has been traditionally counteracted by prophylactic use of antibiotics and desinfectants. Furthermore, antimicrobial resistance emergence and transfer is also a mediated via the aquaculture microbiome, just as it is in terrestrial agriculture. Advances are being made in our understanding of how subtherapeutic antimicrobial pollution as well as prohylactic or growth promoting antimicrobial use impacts microbial communties in aquaculture.

This Research Topic will cover a broad range of questions about these challenges and how they are being addressed using many different experimental approaches based in omics technologies and the use of model organisms. Furthermore, this Research Topic will survey the impact of the application of genomic methodologies in aquaculture research and to attempt to predict where these approaches will lead research in this area in the future.

We welcome authors to contribute original research articles as well as review articles that will illustrate and stimulate the continuing generation of knowledge by the application of omics approaches to solve important problems in aquaculture,

Potential topics include, but are not limited to:

• Functionality of host-microbe interactions in aquaculture systems
• Community assembly in fish and other aquaculture animals, including metagenomics of reared organisms or aquaculture environments
• Integrative approaches applied to microbial ecology including (meta)transcriptomics and (meta)proteomics
• Probiotics and prebiotics and their effect on gut microbial communities in farmed aquatic organisms.
• Antibiotic resistance and resistome in farmed aquatic organisms and aquaculture systems.
• Microbial control in aquaculture
• Genomics of bacterial pathogens impacting aquaculture