Investigating fish larvae-microbe interactions in the 21st century: Old questions studied with new tools

Abstract

All animals need a mutualistic interaction with their microbiota for proper development and functioning. Also for the fish-microbiota interaction considerable research has been done, and especially for reared fish larvae this interaction is crucial for their viability. However, during the 1980s and 1990s a number of findings revealed at that time current methods were not suitable for studying the total microbial community and that data on composition of microbiota was biased. Several recent methodological revolutions have boosted the possibilities for addressing questions related to fish larvae-microbiota interactions that previously lacked suitable tools for proper evaluation. These methodological achievements include the development of experimental rearing systems including gnotobiotic systems for fish, new visualization tools, and molecular "omics" tools for characterizing the response of the host on a variety of levels and for characterizing both composition and activity of fish microbiota. We present and review these tools and give examples on how they have been used to improve our understanding of fish larvae-microbiota interactions. With respect to understanding, this includes in particular how the microbiota is established and maintained, what the functionality of the microbiota is and how it affects fish health, and finally how we can apply this knowledge for management of a healthy and beneficial microbiota in aquaculture settings.