Use of recent practical molecular tools for confirmation of beneficial microbes in aquaculture

In very complex and bio-diverse environments, such as Aquaculture grow-out tanks, raceways and spawning facilities, the discovery and impact of introduced beneficial microbes can be difficult to accurately evaluate with traditional microbiological methods.  Rapid assessment of microbial dynamics and individual strain presence are becoming invaluable in choosing effective beneficial probiotic organisms.  With the advent of full genomic bacterial sequencing and practical digital search strategies, strain-specific DNA segments for specific benefical bacteria can often be readily found.  Enumeration of the introduced probiotic strain (qPCR), the target pathogens, even the full microbial community dynamics (Metagenomics) are becoming reasonably obtainable.   Also, the combination of highly directed quantitative PCR (SS-qPCR) with a recent advanced method in FISH technologies, Recognition of Individual Gene-FISH (RING-FISH),  have given further visual insight on the dynamics of biocontrol organisms. A specific example will be discussed that demonstrates the value of these tools in a longer-term study on Tilapia using a direct-fed Bacillus subtilis strain identified by these assessment methods.