Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets

Abstract

Background Sustainable aquaculture relies on multiple factors, including water quality, fish diets, and farmed fish. Replacing fishmeal (FM) with alternative protein sources is key for improving sustainability in aquaculture and promoting fish health. Indeed, great research efforts have been made to evaluate novel feed formulations, focusing especially on the effects on the fish gut microbiome. Few studies have explored host-environment interactions. In the present study, we evaluated the influence of novel insect-based (Tenebrio molitor) fish diets on the microbiome at the water-fish interface in an engineered rainbow trout (Oncorhynchus mykiss) farming ecosystem. Using 16S rRNA gene metabarcoding, we comprehensively analyzed the microbiomes of water, tank biofilm, fish intestinal mucus, fish cutis, and feed samples. Results Core microbiome analysis revealed the presence of a highly reduced core shared by all sample sources, constituted by Aeromonas spp., in both the control and novel feed test groups. Network analysis showed that samples were clustered based on the sample source, with no significant differences related to the feed formulation tested. Thus, the different diets did not seem to affect the environment (water and tank biofilm) and fish (cutis and intestinal mucus) microbiomes. To disentangle the contribution of feed at a finer scale, we performed a differential abundance analysis and observed differential enrichment/impoverishment in specific taxa, comparing the samples belonging to the control diet group and the insect-based diet group. Conclusions Omic exploration of the water-fish interface exposes patterns that are otherwise undetected. These data demonstrate a link between the environment and fish and show that subtle but significant differences are caused by feed composition. Thus, the research presented here is a step towards positively influencing the aquaculture environment and its microbiome.

The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean

“…It has been found also in the skin core microbiota of farmed Atlantic salmon (Lorgen-Ritchie et al 2022) and as dominant in Sparus aurata farmed larvae(Califano et al 2017), which are more in uenced by the surrounding sea water(Nikouli et al 2019). Despite that Acinetobacter contains putative pathogenic species and strains, their presence is much more common in freshwater sh(Behera et al 2017, Louvado et al 2021, Bruno et al 2023). Our three Acinetobacter-related OTUs are closely related (≥ 99% similarity) with potential freshwater sh gills and skin pathogens Α. johnsonii, Α. lwo i (Kozińska et al 2014)d schindleri(Zhao et al 2022).…”