Identifying the microbes of interest

Beneath the surface of every aquaculture environment lies an invisible world of microscopic life, composed of tiny residents that directly influence water quality, nutrient cycling and the health of the livestock with whom they share space.

The way these organisms interact with the livestock ranges from acutely pathogenic to recognisably beneficial, thus within this large community reside Microbes of Interest (MOIs), which can be either good/essential or bad/pathogenic. Developing an understanding of this microbial metropolis is crucial to sustainable stock management at each stage of production.

At the hatchery stage, for example, a number of bacterial species have been identified as a requirement for robust egg development, leading to improved survival. Additionally, in RAS (recirculating aquaculture systems) aquaculture, biofilter communities that makeup the microbiome should be balanced for optimal ammonia and nitrite oxidation. Whereas, in open net pen farming in the sea, a watching brief on the composition of plankton communities is now a routine part of biological monitoring. At all stages, in all systems, looking out for pathogens is vital.

Traditional molecular investigations have been confined to PCR, a targeted and very nuanced tool, often deployed when suspicion requires confirmation. An alternative is a metagenomic approach, which provides a “catch-all” output by sequencing every DNA molecule, disclosing the identity of all its “reads” with forensic detail. In this way, hundreds of MOIs relevant to the environment from which they have been collected are captured, named, and their potential relevance to that environment and the stock within it, described.

Uniquely, this approach allows for the capture of the entire microbial fingerprint of a single sample. If that sample is taken from a single fish, then the MOIs in that animal can be described. However, the real power comes from sampling the environment which that animal shares with its cohabitants. So, for example, a sample taken from anaesthetic water through which a number of fish have passed will capture all the microbes associated with those individuals. This provides the farmer with a “microbial heads-up” with regard to the stock and their environment.

This is achieved through the Esox Biologics “Detect™” service, which focuses on a single sample taken from water that has been used to anaesthetise a number of individuals. This number ranges from about 20 fish in circumstances where marine fish are undergoing lice and gill checks, to many thousands if it were to be used in freshwater vaccination operations. All the animals passing through the anaesthetic bath contribute to the bath’s microbial fingerprint, which can then be “read” through metagenomic analysis.