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- Fish pathology research and diagnosis in aquaculture of farmed fish; a proteomics perspectivePublication . Moreira, Márcio; Schrama, Denise; Farinha, Ana Paula; Cerqueira, Marco; Raposo de Magalhães, Cláudia; Carrilho, Raquel; Rodrigues, PedroOne of the main constraints in aquaculture production is farmed fish vulnerability to diseases due to husbandry practices or external factors like pollution, climate changes, or even the alterations in the dynamic of product transactions in this industry. It is though important to better understand and characterize the intervenients in the process of a disease outbreak as these lead to huge economical losses in aquaculture industries. High-throughput technologies like proteomics can be an important characterization tool especially in pathogen identification and the virulence mechanisms related to host-pathogen interactions on disease research and diagnostics that will help to control, prevent, and treat diseases in farmed fish. Proteomics important role is also maximized by its holistic approach to understanding pathogenesis processes and fish responses to external factors like stress or temperature making it one of the most promising tools for fish pathology research.
- Amyloodiniosis in aquaculture: A reviewPublication . Moreira, Márcio; Costas, Benjamín; Rodrigues, Pedro; Lourenço‐Marques, Cátia; Sousa, Rui; Schrama, Denise; Raposo de Magalhães, Cláudia; Farinha, Ana Paula; Soares, FlorbelaFish ectoparasites are one of the pathogens groups that pose great concern to the aquaculture industry. The dinoflagellate Amyloodinium ocellatum is responsible for amyloodiniosis, a parasitological disease with a strong economic impact in temperate and warm water aquaculture, mainly in earthen pond semi-intensive systems. Amyloodiniosis represents one of the most important bottlenecks for aquaculture and, with the predictable expansion of the area of influence of this parasite to higher latitudes due to global warming it might also be a threat to other aquaculture species that are not yet parasitized by A. ocellatum. This review made a compilation of the existing knowledge about this parasite and the disease associated with it. It was noticed that, except from the life cycle characterisation, detection methods, histopathological analysis, and treatments, there are still a lot of areas that need a further investment in research. Areas like parasite-host interactions, epidemiological models, taxonomy, host physiological responses to parasitism, and genome sequencing, amongst others, can contribute to a better understanding of this disease. These proposed approaches and routes of investigation will enhance and contribute to a more standardised knowledge, creating the opportunity for a better understanding of amyloodiniosis impacts on fish and contributing for the development of new tools against A. ocellatum, that may reduce fish mortality in aquaculture production due to amyloodiniosis outbreaks.
- Understanding the individual role of fish, oyster, phytoplankton and macroalgae in the ecology of integrated production in earthen pondsPublication . Cunha, M. E.; Quental-Ferreira, H.; Parejo, A.; Gamito, Sofia; Ribeiro, L.; Moreira, Márcio; Monteiro, I; Soares, F.; Pousao-Ferreira, P.In order to demonstrate that IMTA can be profitable and a good alternative to regular semi-intensive fish mariculture production in earthen ponds three different production treatments with distinct combinations of trophic levels were designed: (i) a combination of fish, filter feeders, phytoplankton and macroalgae, (ii) fish, filter feeders and phytoplankton and (iii) fish, phytoplankton and macroalgae, to evaluate the role of each trophic level within an Integrated Multi-Trophic Aquaculture system (IMTA). Each treatment was carried out under semi-intensive conditions with two replicates, in a total of 6 earthen ponds of 500 m(2) surface and depth of 1.5 m. The results showed that fish, oyster, phytoplankton and macroalgae integrated aquaculture is a healthy sustainable production system for mariculture in earthen ponds, providing much more fish supply compared with the other two treatments. Ponds with filter feeders had significantly lower turbidity (Nephelometric Formazin unit (FNU) of 13 in the morning and 17 in the afternoon) when compared to ponds without filter feeders (16 FNU in the morning and 20 FNU in the afternoon) with increased light penetration throughout water column (61 and 55 cm transparency in ponds with filter feeders compared to 51 cm in ponds without filter feeders) and consequently higher photosynthetic activity with significantly higher dissolved oxygen (5.4 mg L in the morning and 6.7 mg L-1 in the afternoon in ponds with filter feeders compared to 5.3 mg L-1 in the morning and 6.4 mg L-1 in the afternoon in ponds without filter feeders) and carbon sequestration (0.50 and 0.53 mg L-1 8 h(-1) in ponds with filter feeders and 0.43 mg L-1 8 h(-1) in ponds without filter feeders). In the fish, filter feeder, phytoplanton and macroalgae IMTA treatment, phytoplankton played a crucial role because they increased DO levels, removed the excess of nutrients from animal excretion, and was used as food by the filter feeders. Almost as important is the presence of filter feeders since they control the density of the microalgae and particulate matter in the ponds contributing to a more constant level of DO and higher transparency of the water column. The increased transparency and pond fertilization by oyster excretion, resulted in higher proliferation of phytoplankton (chlorophyll a concentrations of 16.5 mu gL(-1) and 20.2 mu g L-1 in ponds with filter feeder and 13.3 mu g L-1 in ponds without filter feeder) with benefits not only for filter feeders themselves but also for the macroalgae. At the end there was higher water quality and higher savings (14% day(-1)) in the energy costs for pond aeration. Meagre, white seabream and flathead grey mullet enhance their performance in IMTA systems with the presence of filter feeders with food conversion rates (FCR) of 1.52 when compared with 2.46 in the regular semi-intensive system composed by fish, phytoplankton and macroalgae. Meagre grew significantly more in IMTA systems with controlled macroalgae while white seabream and flathead grey mullet enhance their performance in the presence of macroalgae. The results show that the fish, oyster, phytoplankton and macroalgae integrated production in earthen ponds is an improved system compared to the regular semi-intensive fish production. The enhanced water quality in these systems leads to improved fish performance and higher biomass production, and to reduction in the energy power used, contributing to greater profitability.
- A Proteomics and other Omics approach in the context of farmed fish welfare and biomarker discoveryPublication . Raposo de Magalhães, Cláudia; Cerqueira, Marco; Schrama, Denise; Moreira, Márcio; Boonanuntanasarn, Surintorn; Rodrigues, PedroThe rapid and intensive growth of aquaculture over the last decade, poses a tremendous challenge to this industry in order to comply with the latest guidelines, established to minimise its negative effects on the environment, animal welfare and public health. Farmed fish welfare has become one of the main priorities towards sustainable aquaculture production with several initiatives launched by the European Union within the framework of the 2030 agenda. It is clear that an unbiased and reliable way to access farmed fish welfare needs to be implemented due to the lack of reliable indicators and standardised methods that are used at present. In this review, we start by addressing the status quo of animal and fish welfare definition in particular, describing the methods and assays currently used to measure it. We then explain why we believe these methods are unreliable and why there is a need to establish new ones that will promote productivity and consumer's acceptance of farmed fish. The establishment of a new type of welfare biomarkers using cutting-edge technologies like proteomics and other omics technologies is proposed as a solution to this issue. Therefore, we provide a brief description of these new methodologies, describing for each one how they can improve our scientific knowledge and the role they can play in farmed fish welfare biomarker discovery.
- Cytotoxic and hemolytic activities of extracts of the fish parasite dinoflagellate amyloodinium ocellatumPublication . Moreira, Márcio; Soliño, Lucia; Marques, Cátia L.; Laizé, Vincent; Pousão-Ferreira, Pedro; Fidalgo E Costa, Pedro; Soares, FlorbelaThe dinoflagellate Amyloodinium ocellatum is the etiological agent of a parasitic disease named amyloodiniosis. Mortalities of diseased fish are usually attributed to anoxia, osmoregulatory impairment, or opportunistic bacterial infections. Nevertheless, the phylogenetic proximity of A. ocellatum to a group of toxin-producing dinoflagellates from Pfiesteria, Parvodinium and Paulsenella genera suggests that it may produce toxin-like compounds, adding a new dimension to the possible cause of mortalities in A. ocellatum outbreaks. To address this question, extracts prepared from different life stages of the parasite were tested in vitro for cytotoxic effects using two cell lines derived from branchial arches (ABSa15) and the caudal fin (CFSa1) of the gilthead seabream (Sparus aurata), and for hemolytic effects using erythrocytes purified from the blood of gilthead seabream juveniles. Cytotoxicity and a strong hemolytic effect, similar to those observed for Karlodinium toxins, were observed for the less polar extracts of the parasitic stage (trophont). A similar trend was observed for the less polar extracts of the infective stage (dinospores), although cell viability was only affected in the ABSa15 line. These results suggest that A. ocellatum produces tissue-specific toxic compounds that may have a role in the attachment of the dinospores’ and trophonts’ feeding process.
- Seagrass meadows improve inflowing water quality in aquaculture pondsPublication . de los Santos, Carmen B.; Olivé, Irene; Moreira, Márcio; Silva, André; Freitas, Cátia; Araújo Luna, Ravi; Quental-Ferreira, Hugo; Martins, Márcio; Costa, Monya; Silva, João; Cunha, Maria Emilia; Soares, Florbela; Pousão-Ferreira, Pedro; Santos, RuiWater quality is critical for fish health in aquaculture production. In flow-through systems, the inflowing water normally requires quality controls and treatments for being supplied from coastal water bodies that can be polluted by nutrients, suspended solids, and microorganisms. Here we assess how seagrass meadows benefit aquaculture systems through the provision of ecosystem services (water filtration, biological control, and regulation of dissolved gasses) in the water reservoir that supplies earthen ponds in an aquaculture system in southern Portugal. In the 1.45-ha reservoir, seagrasses retained daily an estimate of 0.8–1.8 kg d−1 of nitrogen, 0.04–0.07 kg d−1 of phosphorus in their biomass, and 0.7–1.1 kg dw d−1 of suspended total particulate matter, bringing benefits in terms of nutrient and particle removal from the water column. Diel and spatial variation in faecal coliforms levels (Escherichia coli) in the reservoir suggested that seagrasses, in combination with light exposure, may reduce the levels of this pathogen. Furthermore, the seagrass-dominated system oxygenated the water through photosynthesis at a faster rate than the respiratory oxygen consumption, maintaining the system above the aquaculture minimum oxygen. This study demonstrates that seagrasses can be used as a nature-based solution to overcome water quality challenges in flow-through aquaculture ponds.
- Influence of age on stress responses of White Seabream to AmyloodiniosisPublication . Moreira, Márcio; Cordeiro-Silva, Anaísa; Barata, Marisa; Pousão-Ferreira, Pedro; Soares, FlorbelaAmyloodiniosis is a disease that represents a major bottleneck for semi-intensive aquaculture, especially in Southern Europe. The inefficacy of many of the treatments for this disease on marine fish produced in semi-intensive aquaculture has led to a new welfare approach to amyloodiniosis. There is already some knowledge of several welfare issues that lead to amyloodiniosis as well as the stress, physiological, and immunological responses to the parasite by the host, but no work is available about the influence of fish age on the progression of amyloodiniosis. The objective of this work was to determine if stress, hematological, and histopathological responses are age dependent. For that purpose, we determined the mortality rate, histopathological lesions, hematological indexes, and stress responses (cortisol, glucose, lactate, and total protein) in “Small” (total weight: 50 ± 5.1 g, age: 273 days after eclosion (DAE)) and “Big” (total weight: 101.3 ± 10.4 g, age: 571 DAE) white seabream (Diplodus sargus) subjected to an Amyloodinium ocellatum infestation (8000 dinospores mL−1) during a 24-h period. The results demonstrated a strong stress response to A. ocellatum, with marked differences in histopathological alterations, glucose levels, and some hematological indexes between the fish of the two treatments. This work elucidates the need to take in account the size and age of the fish in the development and establishment of adequate mitigating measures and treatment protocols for amyloodiniosis.
- Report and genetic identification of Amyloodinium ocellatum in a sea bass (Dicentrarchus labrax) broodstock in PortugalPublication . Marques, Cátia L.; Medeiros, Ana; Moreira, Márcio; Quental-Ferreira, Hugo; Mendes, Ana C.; Pousão-Ferreira, Pedro; Soares, FlorbelaIn this paper we report a case of amyloodiniosis in a sea bass (Dicentrarchus labrax) broodstock in Portugal. Microscopic examination of gill filaments showed the presence of trophonts while histological observation revealed gills epithelial hyperplasia, hypertrophy and lamellar fusion of secondary lamellae. The amplification and sequencing of the small subunit ribosomal RNA gene allowed the identification of the parasite as Amyloodinium ocellatum. It was also possible to amplify a partial sequence of ribosomal RNA from a Colpodellid, a predator of protists.
- Effect of amino acid supplementation and stress on expression of molecular markers in meagre (Argyrosomus regius)Publication . Herrera, M.; Matias, A. C.; Soares, F.; Ribeiro, L.; Moreira, Márcio; Salamanca, N.; Jerez-Cepa, I.; Mancera, J. M.; Astola, A.The objectives of this work were: 1) develop of molecular stress biomarkers obtaining sequence data of different transcripts, 2) study the molecular stress response through the expression quantification of key gene involved in it, and 3) assess the effects of dietary amino acid additives on stress response in meagre meagres (Argyrososmus regius). Fish batches were fed two experimental diets with tryptophan (Trp) or aspartate (Asp) added for seven days. Before sampling fish were submitted to confinement/netting stress during 1 h, except control fish. Therefore fish were sampled before and after stress (1 h and 6 h post-stress). The sampling consisted of blood and tissues (brain, hypophysis and liver). Several gene expressions related to the stress response were measured in those tissues, and the cloning of corticotropin-releasing hormone (crh), corticotropin-releasing hormone binding protein (crh-bp), and thyrotropin-releasing hormone (trh) has been reported in meagre for the first time. In fact, fish fed an additional Asp diet did not present any sl, prl and gh expression changes, as for the control group. Contrarily, the Trp diet altered the prl and gh expressions after stress. For crh and crh-bp expressions, no significant differences were detected within the Asp diet hence that amino acid improved the stress response. However, Asp feeding, but not Trp, enhanced pomc-a expression after stress. Hsp70 expression varied for every treatment, including the control feeding, indicating a late response at 6 h post-stress sampling, where both Asp and Trp treatments increased these expressions significantly. Concluding, the response of molecular stress markers to amino acid enriched diets was diverse. The stressor did not change significantly the relative expression of most analyzed genes for control feeding groups, though the Asp supplemented diet was more effective for attenuating molecular markers than the Trp one.
- Thermal and nutritional strategies for managing tenacibaculum maritimum in aquaculture: a welfare-oriented reviewPublication . Carrilho, Raquel Vaz; Moreira, Márcio Júlio Vicente; Farinha, Ana Paula; Schrama, Denise; Soares, Florbela; Rodrigues, Pedro; Cerqueira, MarcoDisease outbreaks pose a significant challenge in aquaculture, leading to substantial economic losses for producers. Tenacibaculosis, a significant ulcerative bacterial disease caused by Tenacibaculum maritimum, affects a wide range of marine fish species globally. Current disease management relies on antibiotics and chemicals, leading to environmental issues, impaired fish and consumer health, and increased antimicrobial-resistant bacteria. This narrative review critically explores welfare-oriented alternatives, specifically examining the potential of temperature modulation and functional diets. Although thermal strategies show promise for warm-water species through behavioural fever mechanisms, their effectiveness remains limited by species-specific thermal tolerances and lack of commercial validation. Nutritional interventions using marine algae, probiotics, and immunostimulants demonstrate broader applicability but suffer from inconsistent methodologies, limited commercial validation, and significant knowledge gaps. We propose that integration of these approaches could theoretically represent a paradigm shift from pathogen-focused to host-centred disease management, pending empirical validation. However, this integration concept requires rigorous validation, as significant knowledge gaps persists regarding optimal implementation protocols, welfare monitoring frameworks, and economic viability assessments. From our perspective, transitioning to welfare-oriented aquaculture demands rigorous evaluation and validation, commercial-scale trials, economic cost–benefit analysis, and the establishment of regulatory frameworks before these theoretical alternatives can be responsibly implemented.