Centre for Marine and Environmental Research

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Gilthead seabream liver integrative proteomics and metabolomics analysis reveals regulation by different prosurvival pathways in the metabolic adaptation to stress

Publication . Raposo de Magalhães, Cláudia; Farinha, Ana Paula; Blackburn, Gavin; Whitfield, Phillip D.; Carrilho, Raquel; Schrama, Denise; Cerqueira, Marco; Rodrigues, Pedro

The study of the molecular mechanisms of stress appraisal on farmed fish is paramount to ensuring a sustainable aquaculture. Stress exposure can either culminate in the organism’s adaptation or aggravate into a metabolic shutdown, characterized by irreversible cellular damage and deleterious effects on fish performance, welfare, and survival. Multiomics can improve our understanding of the complex stressed phenotype in fish and the molecular mediators that regulate the underlying processes of the molecular stress response. We profiled the stress proteome and metabolome of Sparus aurata responding to different challenges common to aquaculture production, characterizing the disturbed pathways in the fish liver, i.e., the central organ in mounting the stress response. Label-free shotgun proteomics and untargeted metabolomics analyses identified 1738 proteins and 120 metabolites, separately. Mass spectrometry data have been made fully accessible via ProteomeXchange, with the identifier PXD036392, and via MetaboLights, with the identifier MTBLS5940. Integrative multivariate statistical analysis, performed with data integration analysis for biomarker discovery using latent components (DIABLO), depicted the 10 most-relevant features. Functional analysis of these selected features revealed an intricate network of regulatory components, modulating different signaling pathways related to cellular stress, e.g., the mTORC1 pathway, the unfolded protein response, endocytosis, and autophagy to different extents according to the stress nature. These results shed light on the dynamics and extent of this species’ metabolic reprogramming under chronic stress, supporting future studies on stress markers’ discovery and fish welfare research.

2022-12-06Journal article

Open Access

Time-lagged correlation analysis of Shellfish toxicity reveals predictive links to adjacent areas, species, and environmental conditions

Publication . Patrício, André; Lopes, Marta B.; Reis Costa, Pedro; Costa, Rafael S.; Henriques, Rui; Vinga, Susana

Diarrhetic Shellfish Poisoning (DSP) is an acute intoxication caused by the consumption of contaminated shellfish, which is common in many regions of the world. To safeguard human health, most countries implement programs focused on the surveillance of toxic phytoplankton abundance and shellfish toxicity levels, an effort that can be complemented by a deeper understanding of the underlying phenomena. In this work, we identify patterns of seasonality in shellfish toxicity across the Portuguese coast and analyse time-lagged correlations between this toxicity and various potential risk factors. We extend the understanding of these relations through the introduction of temporal lags, allowing the analysis of time series at different points in time and the study of the predictive power of the tested variables. This study confirms previous findings about toxicity seasonality patterns on the Portuguese coast and provides further quantitative data about the relations between shellfish toxicity and geographical location, shellfish species, toxic phytoplankton abundances, and environmental conditions. Furthermore, multiple pairs of areas and shellfish species are identified as having correlations high enough to allow for a predictive analysis. These results represent the first step towards understanding the dynamics of DSP toxicity in Portuguese shellfish producing areas, such as temporal and spatial variability, and towards the development of a shellfish safety forecasting system.

2022-09-30Journal article

Open Access

Gene-associated markers as a genomic and transcriptomic resource for a highly migratory and apex predator shark (Isurus oxyrinchus)

Publication . Domingues, Rodrigo R.; Mastrochirico-Filho, Vito Antonio; Mendes, Natalia J.; Hashimoto, Diogo T.; Coelho, Rui; Antunes, Agostinho; Foresti, Fausto; Mendonça, Fernando F.

The shortfin mako, Isurus oxyrinchus, is an oceanic pelagic shark species found worldwide in tropical and subtropical waters. It is frequently caught by pelagic longline fisheries, but despite its commercial importance and ecological significance, little is still known about its biology and ecology at the molecular level. Therefore, we combined two massive parallel sequencing approaches, double digest restriction site-associated DNA sequencing (ddRAD) and RNA sequencing (RNAseq), for single nucleotide polymorphism (SNP) discovery in the shortfin mako. The ddRAD yielded a total of 82,676 putative SNPs. For RNAseq, a total of 129,663 putative SNPs were found. After the stricter filtering procedure, 405 SNPs from ddRAD and 1165 SNPs from RNAseq were retained and suitable for further analysis. Annotation analysis of SNPs from ddRAD revealed a total of 55 gene associated SNP markers, of which 32 SNPs (58.2%) are associated with diseases and defense responses, 9 SNPs (16.4%) are associated with developmental process, and 3 SNPs (5.4%) are present in genes involved in the reproductive function. For RNAseq, 739 SNPs were annotated and associated to relevant functions amongst which 10 SNPs (0.53%) were related with reproduction, 6 SNPs (0.32%) with growth, and 9 (0.48%) with locomotion. Overall, the genotyping of the SNPs was followed by the validation of 255 SNPs from ddRAD and 646 for RNAseq in 31 individuals from the Atlantic and Indian oceans. Our results provide valuable sequence resources for future population genomics analysis, comparative genomics, phylogenomics, and molecular evolution of the globally endangered shortfin mako shark.

2022Journal article

Restricted

Global dataset of soil organic carbon in tidal marshes

Publication . Maxwell, Tania L.; Rovai, André S.; Adame, Maria Fernanda; Adams, Janine B.; Álvarez-Rogel, José; Austin, William E. N.; Beasy, Kim; Boscutti, Francesco; Böttcher, Michael E.; Bouma, Tjeerd J.; Bulmer, Richard H.; Burden, Annette; Burke, Shannon A.; Camacho, Saritta; Chaudhary, Doongar R.; Chmura, Gail L.; Copertino, Margareth; Cott, Grace M.; Craft, Christopher; Day, John; de los Santos, Carmen B.; Denis, Lionel; Ding, Weixin; Ellison, Joanna C.; Ewers Lewis, Carolyn J.; Giani, Luise; Gispert, Maria; Gontharet, Swanne; González-Pérez, José A.; González-Alcaraz, M. Nazaret; Gorham, Connor; Graversen, Anna Elizabeth L.; Grey, Anthony; Guerra, Roberta; He, Qiang; Holmquist, James R.; Jones, Alice R.; Juanes, José A.; Kelleher, Brian P.; Kohfeld, Karen E.; Krause-Jensen, Dorte; Lafratta, Anna; Lavery, Paul S.; Laws, Edward A.; Leiva-Dueñas, Carmen; Loh, Pei Sun; Lovelock, Catherine E.; Lundquist, Carolyn J.; Macreadie, Peter I.; Mazarrasa, Inés; Megonigal, J. Patrick; Neto, Joao M.; Nogueira, Juliana; Osland, Michael J.; Pagès, Jordi F.; Perera, Nipuni; Pfeiffer, Eva-Maria; Pollmann, Thomas; Raw, Jacqueline L.; Recio, María; Ruiz-Fernández, Ana Carolina; Russell, Sophie K.; Rybczyk, John M.; Sammul, Marek; Sanders, Christian; Santos, Rui; Serrano, Oscar; Siewert, Matthias; Smeaton, Craig; Song, Zhaoliang; Trasar-Cepeda, Carmen; Twilley, Robert R.; Van de Broek, Marijn; Vitti, Stefano; Antisari, Livia Vittori; Voltz, Baptiste; Wails, Christy N.; Ward, Raymond D.; Ward, Melissa; Wolfe, Jaxine; Yang, Renmin; Zubrzycki, Sebastian; Landis, Emily; Smart, Lindsey; Spalding, Mark; Worthington, Thomas A.

Tidal marshes store large amounts of organic carbon in their soils. Field data quantifying soil organic carbon (SOC) stocks provide an important resource for researchers, natural resource managers, and policy-makers working towards the protection, restoration, and valuation of these ecosystems. We collated a global dataset of tidal marsh soil organic carbon (MarSOC) from 99 studies that includes location, soil depth, site name, dry bulk density, SOC, and/or soil organic matter (SOM). The MarSOC dataset includes 17,454 data points from 2,329 unique locations, and 29 countries. We generated a general transfer function for the conversion of SOM to SOC. Using this data we estimated a median (+/- median absolute deviation) value of 79.2 +/- 38.1 Mg SOC ha-1 in the top 30 cm and 231 +/- 134 Mg SOC ha-1 in the top 1 m of tidal marsh soils globally. This data can serve as a basis for future work, and may contribute to incorporation of tidal marsh ecosystems into climate change mitigation and adaptation strategies and policies.

2023Journal article

Open Access

Effects of dietary curcumin in growth performance, oxidative status and gut morphometry and function of gilthead seabream postlarvae

Publication . Xavier, Maria João; Navarro-Guillén, Carmen; Lopes, André; Colen, R.; Teodósio, Rita; Mendes, Rodrigo; Oliveira, Beatriz; Valente, Luisa M.P.; Conceição, Luís E.C.; Engrola, Sofia

An imbalance in the production and detoxification of reactive oxygen species and other oxidants can disrupt a l l types of cellular compounds, and lead to a state of oxidative stress. Preventing this state is essential to improve growth and health in animal production. Therefore, the aim of this work was to assess i f the dieta r y supple-mentation of curcumin cou l d improve the antioxidant status and intestine structu r e and functionalit y of gilthead seabream postlarvae, with the global objective of improving fish growth performance and robustness. Two experimental diets supplemented with different doses of curcumin (LOW and HIGH diets), and a commercial diet were fed to quadruplicate groups of postlarvae, for 20 days. At the end of the feeding trial fish fed the supple-mented diets significantly improved their antioxidant status compared to CTRL fed fish. LOW and HIGH fed fish presented lower protein oxidative damage (P < 0.05) and higher total antioxidant capacity (P < 0.05). Moreover, postlarvae fed curcumin supplemented diets also presented an upregulation of nuclear factor erythroid 2 - related factor 2 (nrf2) and glutathione-disulfide reductase (gr) in HIGH (P < 0.05) and heat shock protein 70 (hsp70) in LOW treatments (P < 0.05). No differences were observed in growth performance, intestine morphome t r y , and digestive enzymes activities among treatments (P > 0.05). In conclusion, dieta r y curcumin supplementation was able to enhance gilthead seabream postlarvae robustness through a modulation of the oxidative status, increasing total antioxidant capacity and decreasing protein oxidative damage. This data pro-vide evidence that curcumin can be a suitable feed additive to promote heath status and robustness of fish at early stages of development, therefore contributing for the development and sustainabilit y of marine fish hatchery production.

2022Journal article

Open Access