Changes in the microbiome of mariculture feed organisms after treatment with a potentially probiotic strain of Phaeobacter inhibens

The Phaeobacter genus has been explored as probiotics in mariculture as a sustainable strategy for prevention of bacterial infections. Its antagonistic effect against common fish pathogens is predominantly due to the production of the antibacterial compound tropodithietic acid (TDA) and TDA-producing strains have repeatedly been isolated from mariculture environments.

Despite many in vitro trials targeting pathogens, little is known about its impact on host-associated microbiomes in mariculture. Hence, the purpose of this study was to investigate how the addition of a TDA-producing P. inhibens affects the microbiomes of live feed organisms and fish larvae. We used 16S rRNA gene sequencing to characterize the bacterial diversity associated with live-feed microalgae (Tetraselmis suecica), live-feed copepod nauplii (Acartia tonsa), and turbot (Scophthalmus maximus) eggs/larvae.

The microbial communities were unique to the three organisms investigated and the addition of the probiotic bacterium had varying effects on the diversity and richness of the microbiomes. The structure of the live-feed microbiomes were significantly changed, while no effect was seen on the community structure associated with turbot larvae.

The changes were highly targeted at particular taxa. The Rhodobacterales order were indigenous to all three microbiomes and decreased in relative abundance when P. inhibens was introduced in the copepod and turbot microbiomes, while they were unaffected in the microalgal microbiome. Altogether, the study demonstrates that addition of P. inhibens in higher concentrations, as part of a probiotic regime, does not appear to cause major imbalances in the microbiome, but the effects are particular towards closely related taxa.Importance This work is an essential part of the risk assessment of the application of roseobacters as probiotics in mariculture.

It provides insights into the impact of TDA-producing Phaeobacter inhibens on the commensal bacteria related to mariculture live-feed and fish larvae. Also, the study provides a sequencing-based characterization of the microbiomes related to mariculture-relevant microalga, copepods, and turbot larvae.