The potential of rice protein concentrate (RPC) to substitute fishmeal (FM) protein in the diet of Oreochromis niloticus was assessed in a five-month-long feeding trial. Fishmeal protein was replaced by RPC at rates of 0% (control), 25%, 50%, and 75% (RPC0, RPC25, RPC50, and RPC75, respectively). RPC25 had no significant effect on antioxidant capacity (total antioxidant capacity; superoxide dismutase, catalase, and glutathione peroxidase activities) and immune indices (lysozyme, nitric oxide, antiprotease, and bactericidal activities) after one, two, and five months of feeding, while the values for these parameters were significantly lower in the RPC75 group compared to those in the RPC0 group. The RPC25 group showed higher mRNA levels of the intestinal cytokines IL-1β, IL-10β, TGF-β, and TNF-α than the control group. In fish affected by Aeromonas veronii, the highest significant cumulative mortality was recorded in the RPC75 group, followed by the RPC50, RPC25, and control groups. Gut microbiome analyses showed a reduction in microbial diversity in response to the addition of RPC, regardless of the RPC content, and the composition of the community of the RPC samples differed from that of the control. RPC-enriched diets resulted in higher relative abundances of Bacteroidetes and Fusobacteria in the gut compared to that in the gut of the control fish. In summary, RPC can be used to replace up to 25% of the FM protein in the diet of O. niloticus, while improving the antioxidant capacity, immunocompetence, and disease resistance of the fish.

Fish farm deposition, resulting in organic matter accumulation on bottom sediments, has been identified as among the main phenomena causing negative environmental impacts in aquaculture. An in situ bioremediation treatment was carried out in order to reduce the organic matter accumulation in the fish farm sediments by promoting the natural microbial biodegradation processes. To assess the effect of the treatment, the concentration of organic matter in the sediment and its microbial degradation, as well as the response of the benthic prokaryotic community, were investigated. The results showed a significant effect of the treatment in stimulating microbial degradation rates, and the consequent decrease in the concentration of biochemical components beneath the cages during the treatment. During the bioremediation process, the prokaryotic community in the fish farm sediment responded to the overall improvement of the sediment conditions by showing the decrease of certain anaerobic taxa (e.g. Clostridiales, Acidaminobacteraceae and Caldilinaceae). This suggested that the bioactivator was effective in promoting a shift from an anaerobic to an aerobic metabolism in the prokaryotic community. However, the larger importance of Lachnospiraceae (members of the gut and faecal microbiota of the farmed fishes) in treated compared to non-treated sediments suggested that the bioactivator was not efficient in reducing the accumulation of faecal bacteria from the farmed fishes. Our results indicate that bioremediation is a promising tool to mitigate the aquaculture impact in fish farm sediments, and that further research needs to be oriented to identifying more successful interventions able to specifically target also fish-faeces related microbes.

Gilthead seabream is among the most important farmed fish species in the Mediterranean Sea. Several approaches are currently applied to assure a lower impact of diseases and higher productivity, including the exploration of the fish microbiome and its manipulation as a sustainable alternative to improve aquaculture practices. Here, using 16S rRNA gene high-throughput sequencing, we explored the microbiome of farmed seabream to assess similarities and differences among microbial assemblages associated to different tissues and compare them with those in the surrounding environment. Seabream had distinct associated microbiomes according to the tissue and compared to the marine environment. The gut hosted the most diverse microbiome; different sets of dominant ASVs characterized the environmental and fish samples. The similarity between fish and environmental microbiomes was higher in seawater than sediment (up to 7.8 times), and the highest similarity (3.9%) was observed between gill and seawater, suggesting that gills are more closely interacting with the environment. We finally analyzed the potential connections occurring among microbiomes. These connections were relatively low among the host’s tissues and, in particular, between the gut and the others fish-related microbiomes; other tissues, including skin and gills, were found to be the most connected microbiomes. Our results suggest that, in mariculture, seabream microbiomes reflect only partially those in their surrounding environment and that the host is the primary driver shaping the seabream microbiome. These data provide a step forward to understand the role of the microbiome in farmed fish and farming environments, useful to enhance disease control, fish health, and environmental sustainability.

Aquaculture plays a major role in the coastal economy of the Mediterranean Sea. This raises the issue of the impact of fish cages on the surrounding environment. Here, we explore the impact of aquaculture on the composition of the digestive gland microbiome of a representative locally dwelling wild holobiont, the grazer gastropod Patella caerulea, at an aquaculture facility located in Southern Sicily, Italy. The microbiome was assessed in individuals collected on sea bream aquaculture cages and on a rocky coastal tract located about 1.2 km from the cages, as the control site. Patella caerulea microbiome variations were explained in the broad marine metacommunity context, assessing the water and sediment microbiome composition at both sites, and characterizing the microbiome associated with the farmed sea bream. The P. caerulea digestive gland microbiome at the aquaculture site was characterized by a lower diversity, the loss of microorganisms sensitive to heavy metal contamination, and by the acquisition of fish pathogens and parasites. However, we also observed possible adaptive responses of the P. caerulea digestive gland microbiome at the aquaculture site, including the acquisition of putative bacteria able to deal with metal and sulfide accumulation, highlighting the inherent microbiome potential to drive the host acclimation to stressful conditions.