The search for new biological sources of commercial value is a major goal for the sustainable management of natural resources. The huge amount of fishery by-catch or processing by-products continuously produced needs to be managed to avoid environmental problems and keep resource sustainability. Fishery by-products can represent an interesting source of high added value bioactive compounds, such as proteins, carbohydrates, collagen, polyunsaturated fatty acids, chitin, polyphenolic constituents, carotenoids, vitamins, alkaloids, tocopherols, tocotrienols, toxins; nevertheless, their biotechnological potential is still largely underutilized. Depending on their structural and functional characteristics, marine-derived biomolecules can find several applications in food industry, agriculture, biotechnological (chemical, industrial or environmental) fields. Fish internal organs are a rich and underexplored source of bioactive compounds; the fish gut microbiota biosynthesizes essential or short-chain fatty acids, vitamins, minerals or enzymes and is also a source of probiotic candidates, in turn producing bioactive compounds with antibiotic and biosurfactant/bioemulsifier activities. Chemical, enzymatic and/or microbial processing of fishery by-catch or processing by-products allows the production of different valuable bioactive compounds; to date, however, the lack of cost-effective extraction strategies so far has prevented their exploitation on a large scale. Standardization and optimization of extraction procedures are urgently required, as processing conditions can affect the qualitative and quantitative properties of these biomolecules. Valorization routes for such raw materials can provide a great additional value for companies involved in the field of bioprospecting. The present review aims at collecting current knowledge on fishery by-catch or by-products, exploring the valorization of their active biomolecules, in application of the circular economy paradigm applied to the fishery field. It will address specific issues from a biorefinery perspective: (i) fish tissues and organs as potential sources of metabolites, antibiotics and probiotics; (ii) screening for bioactive compounds; (iii) extraction processes and innovative technologies for purification and chemical characterization; (iv) energy production technologies for the exhausted biomass. We provide a general perspective on the techno-economic feasibility and the environmental footprint of the production process, as well as on the definition of legal constraints for the new products production and commercial use.

The marine biosphere represents a yet underexploited natural source of bioactive compounds, mainly of microbial origin. Among them, biosurfactants (BSs) are functional molecules, which are attracting a great interest due to their biocompatibility, versatility, and applications in several biotechnological fields. BSs are surface active amphipathic compounds, containing both a hydrophilic and a hydrophobic moiety, which are grouped in low (glycolipids and lipopeptides) or high molecular weight (polymeric complexes) compounds. A number of environmental factors such as pH, salinity, temperature, and nutrient availability can affect microbial BS production. Marine microorganisms with different phylogenetic affiliations and isolated from several marine habitats (e.g., seawater, sediments, and higher organisms) worldwide (spanning from the Mediterranean Sea to Antarctica) have been reported as surfactant producers. However, most of the marine microbial world remains still unexplored. The present chapter aims at giving a general overview on the recent advances about BSs of marine origin, in order to enhance the knowledge inherent their production, chemical characterization and identification, interesting biological properties, and potential biotechnological applications.

Fish gut represents a peculiar ecological niche where bacteria can transit and reside to play vital roles by producing bio-compounds with nutritional, immunomodulatory and other functions. This complex microbial ecosystem reflects several factors (environment, feeding regimen, fish species, etc.). The objective of the present study was the identification of intestinal microbial strains able to produce molecules called biosurfactants (BSs), which were tested for surface and antibacterial activity in order to select a group of probiotic bacteria for aquaculture use. Forty-two bacterial isolates from the digestive tracts of twenty Mediterranean grey mullets were screened for testing emulsifying (E-24), surface and antibiotic activities. Fifty percent of bacteria, ascribed to Pseudomonas aeruginosa, Pseudomonas sp., P. putida and P. anguilliseptica, P. stutzeri, P. protegens and Enterobacter ludwigii were found to be surfactant producers. Of the tested strains, 26.6% exhibited an antibacterial activity against Staphylococcus aureus (10.0 ± 0.0–14.5 ± 0.7 mm inhibition zone), and among them, 23.3% of isolates also showed inhibitory activity vs. Proteus mirabilis (10.0 ± 0.0–18.5 ± 0.7 mm inhibition zone) and 6.6% vs. Klebsiella pneumoniae (11.5 ± 0.7–17.5 ± 0.7 mm inhibition zone). According to preliminary chemical analysis, the bioactive compounds are suggested to be ascribed to the class of glycolipids. This works indicated that fish gut is a source of bioactive compounds which deserves to be explored.

Fish populations play an active role in the maintenance of aquatic ecosystems biodiversity. Their intestinal microbiota and fillet chemistry depend on abiotic and biotic factors of the water environments that they inhabit. The present study investigated the grey mullets’ gut microbiota from a transitional aquatic ecosystem (Santa Giusta Lagoon, Sardinia, Italy) by a multidisciplinary approach which refers the results of (1) gut cultivable microbiota analyses (MA), (2) the trace metal assessment of fish muscle (TM), (3) the physico-chemical water monitoring (PC). MA detected the greatest number of total aerobic heterotrophic bacteria, Enterobacteriaceae and coliforms in Autumn (mean values 1.3 × 10⁵, 2.4 × 10⁴, 1.1 × 10⁴ cfu g⁻¹, respectively) when the accumulated rain and mean values of nutrients (reactive phosphorous and silica) were the highest. Marine bacteria were more numerous in Summer (mean value 7.4 × 10⁵ cfu g⁻¹) when the highest mean values of water temperature and salinity were registered. The gut bacteria were identified as Pseudomonas spp. (64%), Aeromonas spp. (17%), Ochrobactrum pseudogrignonense (10%), Providencia spp. (5%), Enterobacter ludwigii (2%) and Kocuria tytonicola (2%). TM showed that Ca, Na, B and Ni increased their concentrations in Winter while maxima of P, Zn, Cu and Fe were found in muscles of fish sampled in Summer. This study highlighted that the fish intestinal microbiota and metal composition of the fillet reflected the seasonal aquatic environmental variability.