Portuguese Institute for the Ocean and Atmosphere

Lisbon, Portugal

Portuguese Institute for the Ocean and Atmosphere

Lisbon, Portugal
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Califano G.,University of Algarve | Califano G.,Friedrich - Schiller University of Jena | Castanho S.,Portuguese Institute for the Ocean and Atmosphere | Soares F.,Portuguese Institute for the Ocean and Atmosphere | And 5 more authors.
Frontiers in Microbiology | Year: 2017

As wild fish stocks decline worldwide, land-based fish rearing is likely to be of increasing relevance to feeding future human generations. Little is known about the structure and role of microbial communities in fish aquaculture, particularly at larval developmental stages where the fish microbiome develops and host animals are most susceptible to disease. We employed next-generation sequencing (NGS) of 16S rRNA gene reads amplified from total community DNA to reveal the structure of bacterial communities in a gilthead seabream (Sparus aurata) larviculture system. Early- (2 days after hatching) and late-stage (34 days after hatching) fish larvae presented remarkably divergent bacterial consortia, with the genera Pseudoalteromonas, Marinomonas, Acinetobacter, and Acidocella (besides several unclassified Alphaproteobacteria) dominating the former, and Actinobacillus, Streptococcus, Massilia, Paracoccus, and Pseudomonas being prevalent in the latter. A significant reduction in rearing-water bacterial diversity was observed during the larviculture trial, characterized by higher abundance of the Cryomorphaceae family (Bacteroidetes), known to populate microniches with high organic load, in late-stage rearing water in comparison with early-stage rearing-water. Furthermore, we observed the recruitment, into host tissues, of several bacterial phylotypes-including putative pathogens as well as mutualists-that were detected at negligible densities in rearing-water or in the live feed (i.e., rotifers and artemia). These results suggest that, besides host-driven selective forces, both the live feed and the surrounding rearing environment contribute to shaping the microbiome of farmed gilthead sea-bream larvae, and that a differential establishment of host-associated bacteria takes place during larval development. © 2017 Califano, Castanho, Soares, Ribeiro, Cox, Mata and Costa.


Abrantes F.,Portuguese Institute for the Ocean and Atmosphere | Abrantes F.,University of Algarve | Cermeno P.,CSIC - Institute of Marine Sciences | Lopes C.,Portuguese Institute for the Ocean and Atmosphere | And 8 more authors.
Biogeosciences | Year: 2016

Coastal upwelling systems account for approximately half of global ocean primary production and contribute disproportionately to biologically driven carbon sequestration. Diatoms, silica-precipitating microalgae, constitute the dominant phytoplankton in these productive regions, and their abundance and assemblage composition in the sedimentary record is considered one of the best proxies for primary production. The study of the sedimentary diatom abundance (SDA) and total organic carbon content (TOC) in the five most important coastal upwelling systems of the modern ocean (Iberia-Canary, Benguela, Peru-Humboldt, California, and Somalia-Oman) reveals a global-scale positive relationship between diatom production and organic carbon burial. The analysis of SDA in conjunction with environmental variables of coastal upwelling systems such as upwelling strength, satellite-derived net primary production, and surface water nutrient concentrations shows different relations between SDA and primary production on the regional scale. On the global scale, SDA appears modulated by the capacity of diatoms to take up silicic acid, which ultimately sets an upper limit to global export production in these ocean regions. © 2016 Author(s).


Campos A.,Portuguese Institute for the Ocean and Atmosphere | Fonseca P.,Portuguese Institute for the Ocean and Atmosphere | Pilar-Fonseca T.,Portuguese Institute for the Ocean and Atmosphere | Leocadio A.M.,Center for Fisheries and Aquatic science | Castro M.,University of Algarve
Fisheries Research | Year: 2015

Survival estimates were obtained for the Norway lobster, Nephrops norvegicus, retained and escaping from a standard 70 mm mesh size diamond and a modified 55. mm square mesh codend, on board a commercial vessel in fishing grounds off the Portuguese south coast. Ten hauls were carried out, five with each experimental codend, plus three creel sets for the capture of a control group in an adjacent non-trawled area. A total of 571 lobsters were sampled upon arrival on vessel deck, either captured in the codend or retained in the codend cover. In addition, a total of 25 individuals were caught with creels. They were assessed for physical damage and vitality and subsequently placed in cages which were deployed in the same adjacent area for 48 h. Average survival rates were 0.18 and 0.17 for retained individuals and 0.17 and 0.30, for individuals escaping through diamond and square meshes, respectively, and 0.84 for creeled individuals. A discussion is carried out stressing the difficulty in disentangling the influence of the different factors contributing to condition and mortality of individual lobsters. © 2015 Elsevier B.V.


Garcia A.,Portuguese Institute for the Ocean and Atmosphere | Tserpes G.,Hellenic Center for Marine Research | Santos M.N.,Portuguese Institute for the Ocean and Atmosphere | Santos M.N.,International Commission for the Conservation of Atlantic Tuna ICCAT
Journal of the Marine Biological Association of the United Kingdom | Year: 2016

Swordfish (Xiphias gladius) is heavily exploited in the Atlantic Ocean by several European fleets and age and growth studies are essential for the accomplishment of the stock assessments carried out by ICCAT. The present study aims to validate the periodicity of growth increments on swordfish fin spines and provide first estimates of the growth parameters of South Atlantic swordfish. A total of 502 (231 males and 271 females) spine samples were collected from swordfish specimens onboard commercial longline vessels, from 2006 to 2009. Estimated ages ranged between 0 and 12 years, with age groups 3 and 4 dominating the samples. Marginal increment analysis suggested that growth bands were deposited annually in mid-spring. Fitted standard von Bertalanffy growth parameters (sexes combined) were L ∞ = 317.133, k = 0.085 and t 0 = −2.488. Minor, but insignificant, growth differences were observed between sexes. Copyright © Marine Biological Association of the United Kingdom 2016


Kamermans P.,Wageningen University | Blanco A.,Wageningen University | Joaquim S.,Portuguese Institute for the Ocean and Atmosphere | Matias D.,Portuguese Institute for the Ocean and Atmosphere | And 5 more authors.
Aquaculture International | Year: 2016

In order to increase production of bivalves in hatcheries and nurseries, the development of new technology and its integration into commercial bivalve hatcheries is important. Recirculation aquaculture systems (RASs) have several advantages: high densities of the species can be cultured resulting in a cost-effective production system; optimal temperature maximizes production and allows rapid turnover of the product; stable water quality improves growth rate and minimizes stress and potential loss by diseases. Pilot RAS systems were developed for seed rearing of oysters (Crassostrea gigas), scallops (Pecten maximus), mussels (Mytilus edulis) and clams (Ruditapes decussatus). Optimal feed addition and waste matrix were determined. Based on this, system flow rates were designed. Seed growth in the pilot RAS systems was compared at different renewal rates and with growth in flow-through systems (FTS). All four species can be reared in RAS and showed similar growth in RAS and in FTS or in RAS with a higher renewal rate. RAS can keep O2, nitrogen and pH within the desired range. Temperature was generally higher in RAS than in FTS, probably due to heat induced by the pump circulating the water. The supply of sufficient amount of food in combination with a desire to reduce the renewal rate calls for use of concentrated feed in RAS. © 2016 Springer International Publishing Switzerland


Coelho R.,Portuguese Institute for the Ocean and Atmosphere | Coelho R.,University of Algarve | Fernandez-Carvalho J.,Portuguese Institute for the Ocean and Atmosphere | Fernandez-Carvalho J.,University of Algarve | Santos M.N.,Portuguese Institute for the Ocean and Atmosphere
Marine Environmental Research | Year: 2015

Pelagic longliners targeting swordfish and tunas in oceanic waters regularly capture sharks as bycatch, including currently protected species as the bigeye thresher, Alopias superciliosus. Fifteen bigeye threshers were tagged with pop-up satellite archival tags (PSATs) in 2012-2014 in the tropical northeast Atlantic, with successful transmissions received from 12 tags for a total of 907 tracking days. Marked diel vertical movements were recorded on all specimens, with most of the daytime spent in deeper colder water (mean depth = 353 m, SD = 73; mean temperature = 10.7 °C, SD = 1.8) and nighttime spent in warmer water closer to the surface (mean depth = 72 m, SD = 54; mean temperature = 21.9 °C, SD = 3.7). The operating depth of the pelagic longline gear was measured with Minilog Temperature and Depth Recorders (TDRs), and the overlap with habitat utilization was calculated. Overlap is taking place mainly during the night and is higher for juveniles. The results presented herein can be used as inputs for Ecological Risk Assessments for bigeye threshers captured in oceanic tuna fisheries, and serve as a basis for efficient management and conservation of this vulnerable shark species. © 2015 Elsevier Ltd.


Mendes N.J.,São Paulo State University | Cruz V.P.,São Paulo State University | Ashikaga F.Y.,São Paulo State University | Camargo S.M.,São Paulo State University | And 8 more authors.
PeerJ | Year: 2016

The tiger shark (Galeocerdo cuvier) has a global distribution in tropical and warm temperate seas, and it is caught in numerous fisheries worldwide, mainly as bycatch. It is currently assessed as near threatened by the International Union for Conservation of Nature (IUCN) Red List. In this study, we identified nine microsatellite loci through next generation sequencing (454 pyrosequencing) using 29 samples from the western Atlantic. The genetic diversity of these loci were assessed and revealed a total of 48 alleles ranging from 3 to 7 alleles per locus (average of 5.3 alleles). Cross-species amplification was successful at most loci for other species such as Carcharhinus longimanus, C. acronotus and Alopias superciliosus. Given the potential applicability of genetic markers for biological conservation, these data may contribute to the population assessment of this and other species of sharks worldwide. © 2016 Mendes et al.


PubMed | Portuguese Institute for the Ocean and Atmosphere, University of Florida, São Paulo State University, Florida College and 2 more.
Type: | Journal: PeerJ | Year: 2016

The tiger shark (Galeocerdo cuvier) has a global distribution in tropical and warm temperate seas, and it is caught in numerous fisheries worldwide, mainly as bycatch. It is currently assessed as near threatened by the International Union for Conservation of Nature (IUCN) Red List. In this study, we identified nine microsatellite loci through next generation sequencing (454 pyrosequencing) using 29 samples from the western Atlantic. The genetic diversity of these loci were assessed and revealed a total of 48 alleles ranging from 3 to 7 alleles per locus (average of 5.3 alleles). Cross-species amplification was successful at most loci for other species such as Carcharhinus longimanus, C. acronotus and Alopias superciliosus. Given the potential applicability of genetic markers for biological conservation, these data may contribute to the population assessment of this and other species of sharks worldwide.


PubMed | Portuguese Institute for the Ocean and Atmosphere and University of Algarve
Type: Journal Article | Journal: Marine environmental research | Year: 2015

Pelagic longliners targeting swordfish and tunas in oceanic waters regularly capture sharks as bycatch, including currently protected species as the bigeye thresher, Alopias superciliosus. Fifteen bigeye threshers were tagged with pop-up satellite archival tags (PSATs) in 2012-2014 in the tropical northeast Atlantic, with successful transmissions received from 12 tags for a total of 907 tracking days. Marked diel vertical movements were recorded on all specimens, with most of the daytime spent in deeper colder water (mean depth=353m, SD=73; mean temperature=10.7C, SD=1.8) and nighttime spent in warmer water closer to the surface (mean depth=72m, SD=54; mean temperature=21.9C, SD=3.7). The operating depth of the pelagic longline gear was measured with Minilog Temperature and Depth Recorders (TDRs), and the overlap with habitat utilization was calculated. Overlap is taking place mainly during the night and is higher for juveniles. The results presented herein can be used as inputs for Ecological Risk Assessments for bigeye threshers captured in oceanic tuna fisheries, and serve as a basis for efficient management and conservation of this vulnerable shark species.

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