Alexandra Meziti

Inland recirculating aquaculture is a thriving food industry providing sustainable and locally sourced high-quality protein. However, its expansion is accompanied by emerging challenges regarding the spread of pathogens and diseases. Detection and management of pathogens in aquaculture remain underdeveloped compared to other animal farming sectors due to the vast diversity of species involved, the non-domesticated species, and limited knowledge regarding pathogens, host responses, and disease mechanisms. Furthermore, recirculating aquaculture systems are heavily dependent on beneficial bacterial communities for waste product removal and water quality maintenance, with opportunistic pathogens constituting an inherent component of these microbial communities. To enhance the potential of inland aquaculture as a sustainable source of protein, it is imperative to adopt advanced tools for pathogen detection and monitoring and for assessing the overall health of the microbial ecosystem. This paper presents an overview of promising current molecular and technological advancements that offer solutions for pathogen detection and system monitoring in aquaculture. We focus on recently developed point-of-care and on-site detection methods using miniaturized laboratory equipment and robust workflows that operate independently of cold chain logistics. We explore current methodologies for monitoring pathogens in the environment rather than through fish health assessments. Lastly, we discuss techniques from other scientific disciplines in aquaculture, including CRISPR-Cas protocols for pathogen detection and the implementation of "omics" approaches for comprehensive characterization of microbial states. These methods demonstrate considerable potential for pathogen surveillance and, subsequently, early responses in the dynamic aquaculture field. Through a better understanding of available options aquaculture managers and molecular scientist can collaborate and optimize systems. This paper aims to facilitate communication between molecular scientists and aquaculture managers, equipping the aquaculture industry with knowledge to enhance pathogen management techniques in their facilities.

The introduction of the holobiont concept has triggered scientific interest in depicting the structural and functional diversity of animal microbial symbionts, which has resulted in an unprecedented wealth of such cross-domain biological associations. The steadfast technological progress in nucleic acid-based approaches would cause one to expect that scientific works on the microbial symbionts of animals would be balanced at least for the farmed animals of human interest. For some animals, such as ruminants and a few farmed fish species of financial significance, the scientific wealth of the microbial worlds they host is immense and ever growing. The opposite happens for other animals, such as snails, in both the wild and farmed species. Snails are evolutionary old animals, with complex ecophysiological roles, living in rich microbial habitats such as soil and sediments or water. In order to create a stepping stone for future snail microbiome studies, in this literature review, we combined all the available knowledge to date, as documented in scientific papers, on any microbes associated with healthy and diseased terrestrial and aquatic snail species from natural and farmed populations. We conducted a Boolean search in Scopus, Web of Science, and ScienceDirect until June 2024, identifying 137 papers, of which 60 were used for original data on snail bacterial communities in the gastrointestinal tract, hepatopancreas, and feces. We provide a synthesis on how representative this knowledge is towards depicting the possible snail core microbiota, as well as the steps that need to be taken in the immediate future to increase the in-depth and targeted knowledge of the bacterial component in snail holobionts.

As aquaculture is nowadays the major fish‐food production sector, continuous research is undergoing for aquafeeds that could replace conventional fishmeal in order to enhance its environmental and economic sustainability. Fish gut microorganisms might be involved in nutrient assimilation and thus they are crucial for their hosts’ well-being. In this study, the bacterial diversity was investigated by16S rRNA gene metabarcoding in order to investigate changes in midgut (M) and feces (F) microbiota of sea bass Dicentrachus labrax fed with conventional (C) and innovative-low fish meal diet (I), aiming at discovering microbiota that could be associated with the enhancement of host's health and productivity. Our results indicated that Proteobacteria (Pseudomonadota) prevailed in all samples followed by Firmicutes (Bacillota) or Bacteroidota (mostly in feces), while fecal communities were richer. Taxonomic distributions at the operational taxonomic unit level in midgut samples revealed differentially abundant fermentative species that prevailed in individuals fed with the innovative diet. Especially Staphylococcus was more abundant in MI samples implying enhancement from ingredients present only in the innovative diet and implying that this feed shapes rather favorable microbiota, which could support the digestion and good growth performance in aquaculture.

Background-Aim: Protistan communities have a major contribution to biochemical processes and food webs in coastal ecosystems. However, related studies are scarce and usually limited in specific groups and/or sites. The present study examined the spatial structure of the entire protistan community in seven different gulfs and three different depths in a regional Mediterranean Sea, aiming to define taxa that are important for differences detected in the marine microbial network across the different gulfs studied as well as their trophic interactions. Methods: Protistan community structure analysis was based on the diversity of the V2–V3 hypervariable region of the 18S rRNA gene. Operational taxonomic units (OTUs) were identified using a 97% sequence identity threshold and were characterized based on their taxonomy, trophic role, abundance and niche specialization level. The differentially abundant, between gulfs, OTUs were considered for all depths and interactions amongst them were calculated, with statistic and network analysis. Results: It was shown that Dinophyceae, Bacillariophyta and Syndiniales were the most abundant groups, prevalent in all sites and depths. Gulfs separation was more striking at surface corroborating with changes in environmental factors, while it was less pronounced in higher depths. The study of differentially abundant, between gulfs, OTUs revealed that the strongest biotic interactions in all depths occurred between parasite species (mainly Syndiniales) and other trophic groups. Most of these species were generalists but not abundant highlighting the importance of rare species in protistan community assemblage. Conclusion: Overall this study revealed the emergence of parasites as important contributors in protistan network regulation regardless of depth.