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There is a growing consensus that future technological developments of aquaculture systems should account for the structure and function of microbial communities in the whole system and not only in fish guts. In this study, we aimed to investigate the composition of bacterioplankton communities of a hatchery recirculating aquaculture system (RAS) used for the production of Senegalese sole (Solea senegalensis) juveniles. To this end, we used a 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses to characterize the bacterioplankton communities of the RAS and its water supply. Overall, the most abundant orders were Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales, Flavobacteriales, Lactobacillales, Thiotrichales, Burkholderiales and Bdellovibrionales. Although we found a clear distinction between the RAS and the water supply bacterioplankton communities, most of the abundant OTUs ([greater than or equal to]50 sequences) in the hatchery RAS were also present in the water supply. These included OTUs related to Pseudoalteromonas genus and the Roseobacter clade, which are known to comprise bacterial members with activity against Vibrio fish pathogens. Overall, in contrast to previous findings for sole grow-out RAS, our results suggest that the water supply may influence the bacterioplankton community structure of sole hatchery RAS. Further studies are needed to investigate the effect of aquaculture practices on RAS bacterioplankton communities and identification of the key drivers of their structure and diversity.

There is a growing consensus that future technological developments of aquaculture systems should account for the structure and function of microbial communities in the whole system and not only in fish guts. In this study, we aimed to investigate the composition of bacterioplankton communities of a hatchery recirculating aquaculture system (RAS) used for the production of Senegalese sole (Solea senegalensis) juveniles. To this end, we used a 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses to characterize the bacterioplankton communities of the RAS and its water supply. Overall, the most abundant orders were Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales, Flavobacteriales, Lactobacillales, Thiotrichales, Burkholderiales and Bdellovibrionales. Although we found a clear distinction between the RAS and the water supply bacterioplankton communities, most of the abundant OTUs ([greater than or equal to]50 sequences) in the hatchery RAS were also present in the water supply. These included OTUs related to Pseudoalteromonas genus and the Roseobacter clade, which are known to comprise bacterial members with activity against Vibrio fish pathogens. Overall, in contrast to previous findings for sole grow-out RAS, our results suggest that the water supply may influence the bacterioplankton community structure of sole hatchery RAS. Further studies are needed to investigate the effect of aquaculture practices on RAS bacterioplankton communities and identification of the key drivers of their structure and diversity.

Knowing the factors responsible for sex determination in a species has significant theoretical and practical implications; the dmrt1 gene (Doublesex and Mab-3 (DM)-related Transcription factor 1) plays this role in diverse animal species. Solea senegalensis is a commercially important flat fish in which females grow 30% faster than males. It has 2n = 42 chromosomes and an XX / XY chromosome system for sex determination, without heteromorph chromosomes but with sex proto-chromosome. In the present study, we are providing the genomic structure and nucleotide sequence of dmrt1 gene obtained from cDNA from male and female adult gonads. A cDNA of 2027 containing an open-reading frame (ORF) of 1206 bp and encoding a 402 aa protein it is described for dmrt1 gene of S. senegalensis. Multiple mRNA isoforms indicating a high variable system of alternative splicing in the expression of dmrt1 of the sole in gonads were studied. None isoforms could be related to sex of individuals. The genomic structure of the dmrt1 of S. senegalensis showed a gene of 31400 bp composed of 7 exons and 6 introns. It contains an unexpected duplication of more than 10399 bp, involving part of the exon I, exons II and III and a SINE element found in the sequence that it is proposed as responsible for the duplication. A mature miRNA of 21 bp in length was localized at 336 bp from exon V. Protein-protein interacting networks of the dmrt1 gene showed matches with dmrt1 protein from Cynoglossus semilaevis and a protein interaction network with 11 nodes (dmrt1 plus 10 other proteins). The phylogenetic relationship of the dmrt1 gene in S. senegalensis is consistent with the evolutionary position of its species. The molecular characterization of this gene will enhance its functional analysis and the understanding of sex differentiation in Solea senegalensis and other flatfish.

Knowing the factors responsible for sex determination in a species has significant theoretical and practical implications; the dmrt1 gene (Doublesex and Mab-3 (DM)-related Transcription factor 1) plays this role in diverse animal species. Solea senegalensis is a commercially important flat fish in which females grow 30% faster than males. It has 2n = 42 chromosomes and an XX / XY chromosome system for sex determination, without heteromorph chromosomes but with sex proto-chromosome. In the present study, we are providing the genomic structure and nucleotide sequence of dmrt1 gene obtained from cDNA from male and female adult gonads. A cDNA of 2027 containing an open-reading frame (ORF) of 1206 bp and encoding a 402 aa protein it is described for dmrt1 gene of S. senegalensis. Multiple mRNA isoforms indicating a high variable system of alternative splicing in the expression of dmrt1 of the sole in gonads were studied. None isoforms could be related to sex of individuals. The genomic structure of the dmrt1 of S. senegalensis showed a gene of 31400 bp composed of 7 exons and 6 introns. It contains an unexpected duplication of more than 10399 bp, involving part of the exon I, exons II and III and a SINE element found in the sequence that it is proposed as responsible for the duplication. A mature miRNA of 21 bp in length was localized at 336 bp from exon V. Protein-protein interacting networks of the dmrt1 gene showed matches with dmrt1 protein from Cynoglossus semilaevis and a protein interaction network with 11 nodes (dmrt1 plus 10 other proteins). The phylogenetic relationship of the dmrt1 gene in S. senegalensis is consistent with the evolutionary position of its species. The molecular characterization of this gene will enhance its functional analysis and the understanding of sex differentiation in Solea senegalensis and other flatfish.

Background Solea senegalensis (Kaup, 1858) is a commercially important flatfish species, belonging to the Pleuronectiformes order. The taxonomy of this group has long been controversial, and the karyotype of the order presents a high degree of variability in diploid number, derived from chromosomal rearrangements such as Robertsonian fusions. Previously it has been proposed that the large metacentric chromosome of S. senegalensis arises from this kind of chromosome rearrangement and that this is a proto-sex chromosome. Results In this work, the Robertsonian origin of the large metacentric chromosome of S. senegalensis has been tested by the Zoo-FISH technique applied to two species of the Soleidae family ( Dicologlossa cuneata and Dagetichthys lusitanica) , and by comparative genome analysis with Cynoglossus semilaevis . From the karyotypic analysis we were able to determine a chromosome complement comprising 2n = 50 (FN = 54) in D. cuneata and 2n = 42 (FN = 50) in D. lusitanica. The large metacentric painting probe gave consistent signals in four acrocentric chromosomes of the two Soleidae species; and the genome analysis proved a common origin with four chromosome pairs of C. semilaevis . As a result of the genomic analysis, up to 61 genes were annotated within the thirteen Bacterial Artificial Chromosome clones analysed. Conclusions These results confirm that the large metacentric chromosome of S. senegalensis originated from a Robertsonian fusion and provide new data about the chromosome evolution of S. senegalensis in particular, and of Pleuronectiformes in general.

Background Organophosphate pesticides-OP-, like malathion, can alter the normal functioning of neuro-endocrine systems (e.g., hypothalamus-pituitary-thyroid-HPT- axis), and to interfere on the thyroidal homeostasis. Through direct interactions with thyroid receptors, an/or indirectly via up-stream signalling pathways, from the HPT axis (i.e., negative feedback regulation), malathion possess the ability to affect integrity of thyroidal follicular tissue, and it can also block or delay its hormonal functioning. This insecticide can alter the majority of the ontogenetic processes, inducing several deformities, and also provoking decreases in the growth and survival patterns. The present study has been performed to determine the sublethal effects of malathion during the first month of life of the Senegalese sole, Solea senegalensis , and it is mainly focused on the metamorphosis phase. Different transcript expression levels (i.e. thyroid receptors, matrix and bone -Gla-proteins) and immunohistochemical patterns (i.e. thyroid hormones, osteocalcin, cell proliferation) have been analysed during the most critical phases of the flatfish metamorphosis, that is, through differentiation of thyroid system and skeletal development, migration of the eye, and further adaptation to benthic behaviours. Results In early life stages of the Senegalese sole, the exposure to the highest concentration of malathion (6.25 μg/L) affected to the growth patterns, showing the exposed individuals, a reduction around 60 and 92% of the total length and the dry weigth, respectively. In paralell, a significant reduction of the thyroid follicles (i.e., size and number) it was also been recorded, in a dose-dependent way. Abnormal phenotypes induced in the exposed larvae, did not complete the process of metamorphosis, and displayed several morphological abnormalities and developmental disorders, which were mainly associated with the eye migration process, and with thyroidal and skeletal disorders (i.e., transcriptional and protein changes of thyroid hormones and receptors, and of matrix and bone Gla proteins distribution), that conduced to an inadequate adaptation to the benthic life. Conclusions In the Senegalese sole, the majority of the ontogenetic alterations induced by the exposure to malathion were mainly associated to the metamorphosis period, which is a thyroid-driven proccess. In fact, most crucial and transitional ontogenic events, appeared notably disturbed, for e.g., thyroid gland differentiation and functioning, migration of eye, skeletal development and benthonic behaviors.

For several decades, both concerted evolution and non-concerted evolution of rRNA genes have been discovered in a wide variety of species. To explore the evolutionary patterns and to evaluate the variability at the intra-individual and interspecific levels in Soleidae, a total of 233 complete 18S-ITS1-5.8S rDNA sequences from 11 representative species were generated. The results indicated that six species had little variation, suggesting a concerted evolutionary pattern. However, in the other five species, much variation was observed. Two or three types of 18S and ITS1-5.8S, or even the entire 18S-ITS1-5.8S rDNA sequence, were identified, suggesting a non-concerted evolutionary pattern. According to the pseudogene identification criteria, Type B and C in the five species that underwent non-concerted evolution were postulated as pseudogenes. The phylogenetic analysis based on these rDNA sequences showed that some of the pseudogenes diverged from the corresponding species or even clustered with other species, and the potential causes for this are discussed. Further analyses of the pseudogenes revealed that they could also provide particular evolutionary information, suggesting that pseudogenes should be taken into consideration rather than being discarded arbitrarily. Moreover, the results provided molecular support for the inclusion of Pseudaesopia japonica in the genus Pseudaesopia, and not in Zebrias or other genera.

Otolith geochemistry is used increasingly as a natural tag to retrospectively determine habitat use in marine fishes. It is necessary to first conduct a thorough assessment of spatio-temporal variability before attempting to use the approach to determine estuarine residency or natal origins. In particular, knowledge of temporal variation at different scales is important when such variability may confound spatial discrimination. We assayed elements and calculated the elemental ratios to Ca (Li:Ca, Mg:Ca, Mn:Ca, Cu:Ca, Sr:Ca, Ba:Ca, Pb:Ca) in otoliths of juvenile Solea solea and Solea senegalensis, collected over several months in 2006 and 2009 in Portuguese estuaries, using laser ablation inductively coupled plasma mass spectrometry (LA ICP-MS). The elemental compositions of the otoliths varied significantly between and within years in both of the species, although the within-year variability did not interfere in spatial discrimination. The overall classification accuracy of juveniles to their estuaries of origin varied among the years and species, ranging from 71.0 to 80.1%. Established elemental signatures constitute the baseline data for future assessments of connectivity between juvenile and adult populations of the 2 sole species.

A single specimen of Indian Zebra Sole, Zebrias synapturoides (Jenkins, 1910) was trawled off Al–Qunfudhah, which is being reported herein as a new record for the Red Sea. This species is characterized by (1) the presence of three bars on head and by the (2) dorsal and anal fins joined to the basal portion of the caudal fin. Zebrias synapturoides is widely distributed in the Indian Ocean and the paucity of its record in the Red Sea could be attributed to the inadequate sampling efforts in the shallow sandy habitats.

The estimation of fractional trophic levels(TROPHs) is essential for the management offisheries resources as well as for quantifyingthe ecosystem effects of fishing. We gatheredall available information concerning thefeeding habits of 332 fish stocks, belonging to146 species, 59 families and 21 orders,throughout the Mediterranean Sea, and estimatedtheir TROPH values. The latter ranged from 2.0to 4.5 and the following functional trophicgroups were identified: (a) pure herbivores (TROPH = 2.0–2.1, mean = 2.02, SD = 0.03),which were very rare and represented by Siganus luridus, Siganus rivulatus andSarpa salpa, all of which feed on red,brown, green and blue-green algae; (b)omnivores with a preference for vegetablematerial (2.1 < TROPH < 2.9, mean = 2.5,SD = 0.12), but feeding on other prey, such assponges, hydrozoans, anthozoans, polychaetes,ostracods, isopods, amphipods and copepods. This type of omnivore was very rare among thecases reviewed; (c) omnivores with a preferencefor animal material (2.9 < TROPH < 3.7,mean = 3.4, SD = 0.19) feeding on a wide variety ofprey (e.g., algae, foraminifera, brachyurans,balanoids, ascidians, amphipods,appendicularians, annelids, isopods,gastropods, cnidarians, ophiurids, polychaetes,cladocerans, mysids, euphausids, fish larvae,cephalopods). They were the most numerous andwere mainly represented by species of thefamilies Blenniidae, Bothidae, Centracanthidae,Gobiidae, Labridae, Lotidae, Macrouridae,Mullidae, Ophidiidae, Soleidae, Triglidaeand Engraulidae; and (d) carnivores witha preference for large decapods, cephalopodsand fish (3.7 < TROPH < 4.5). They werethe next most abundant group among the casesreviewed. They were mainly represented byspecies of the families Dalatiidae, Lophiidae,Scombridae, Scyliorhinidae, Synodontidae,Torpedinidae, Merlucciidae, Xiphiidae andZeidae. This group was divided into twosubgroups: one exhibiting a preference fordecapods and fish (3.7 < TROPH < 4.0,mean = 3.85, SD = 0.09) and another one exhibitinga preference for fish and cephalopods (4.0

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