Composizione biochimica di diverse specie microalgali e prove di feeding su Ruditapes philippinarum

L'utilizzo di diete a base di microalghe per l'allevamento di novellame di molluschi bivalvi sta ottenendo sempre maggiore interesse data la crescente domanda di mercato nel settore dell'acquacoltura. Le dimensioni cellulari, la composizione biochimica e la digeribilità della parete cellulare delle microalghe sono fattori fondamentali per la loro applicabilità nell'alimentazione dei bivalvi; anche il contenuto di acidi grassi essenziali quali EPA e DHA ha un ruolo rilevante poiché influenza il tasso di crescita e di sviluppo degli animali. Nel presente studio sono stati utilizzati due ceppi autoctoni della Sacca di Goro del genere Thalassiosira, Pheaodactylum tricornutum, l'alga verde Tetraselmis chui e l'aptofita T-Iso, quest’ultima ampiamente utilizzata nell'alimentazione di diverse specie di molluschi bivalvi. Gli esperimenti condotti hanno permesso di (1) caratterizzare la crescita e la composizione biochimica delle 5 specie microalgali e (2) di analizzare l'applicabilità delle stesse tramite prove di alimentazione su larve e novellame di Ruditapes philippinarum, al fine di ottimizzarne la produzione. I risultati migliori, per numero di sopravvissuti e taglia raggiunta, sono stati ottenuti con larve alimentate con dieta plurispecifica a base di T-Iso e Thalassiosira ceppo A in rapporto 2:1; Thalassiosira ceppo A e P. tricornutum, in diete monospecifiche, sono state identificate come le più appetibili e assimilabili dal novellame, il quale mostra buoni valori del tasso massimo di clearance (2,17±0,25 e 2,27±0,15 L h-1, rispettivamente) e di efficienza di assorbimento del cibo (67 e 46%). Si è trattato di uno studio preliminare volto a verificare eventuali miglioramenti legati all’utilizzo di diete diversificate rispetto a quelle standardizzate di solito impiego; la ricerca di nuove specie algali e ulteriori analisi sulle attuali specie disponibili e sulla loro applicabilità potranno essere utili alla crescita sostenibile del settore dell’acquacoltura.

Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing

The Manila clam (Ruditapes philippinarum) is a worldwide cultured bivalve species with important commercial value. Diseases affecting this species can result in large economic losses. Because knowledge of the molecular mechanisms of the immune response in bivalves, especially clams, is scarce and fragmentary, we sequenced RNA from immune-stimulated R. philippinarum hemocytes by 454-pyrosequencing to identify genes involved in their immune defense against infectious diseases.

Seawater acidification affects the physiological energetics and spawning capacity of the Manila clam Ruditapes philippinarum during gonadal maturation

Ocean acidification is predicted to have widespread implications for marine bivalve mollusks. While our understanding of its impact on their physiological and behavioral responses is increasing, little is known about their reproductive responses under future scenarios of anthropogenic climate change. In this study, we examined the physiological energetics of the Manila clam Ruditapes philippinarum exposed to CO2-induced seawater acidification during gonadal maturation. Three recirculating systems filled with 600 L of seawater were manipulated to three pH levels (8.0, 7.7, and 7.4) corresponding to control and projected pH levels for 2100 and 2300. In each system, temperature was gradually increased ca. 0.3 °C per day from 10 to 20 °C for 30 days and maintained at 20 °C for the following 40 days. Irrespective of seawater pH levels, clearance rate (CR), respiration rate (RR), ammonia excretion rate (ER), and scope for growth (SFG) increased after a 30-day stepwise warming protocol. When seawater pH was reduced, CR, ratio of oxygen to nitrogen, and SFG significantly decreased concurrently, whereas ammonia ER increased. RR was virtually unaffected under acidified conditions. Neither temperature nor acidification showed a significant effect on food absorption efficiency. Our findings indicate that energy is allocated away from reproduction under reduced seawater pH, potentially resulting in an impaired or suppressed reproductive function. This interpretation is based on the fact that spawning was induced in only 56% of the clams grown at pH 7.4. Seawater acidification can therefore potentially impair the physiological energetics and spawning capacity of R. philippinarum.

Why is Asari (= Manila) clam Ruditapes philippinarum fitness poor in Arcachon Bay: a meta-analysis to answer?

Asari (= Manila) clam, Ruditapes philippinarum, is the second bivalve mollusc in terms of production in the world and, in many coastal areas, can beget important socio-economic issues. In Europe, this species was introduced after 1973. In Arcachon Bay, after a decade of aquaculture attempt, Asari clam rapidly constituted neo-naturalized population which is now fished. However, recent studies emphasized the decline of population and individual performances. In the framework of a national project (REPAMEP), some elements of fitness, stressors and responses in Arcachon bay were measured and compared to international data (41 publications, 9 countries). The condition index (CI=flesh weight/shell weight) was the lowest among all compared sites. Variation in average Chla concentration explained 30% of variation of CI among different areas. Among potential diseases, perkinsosis was particularly prevalent in Arcachon Bay, with high abundance, and Asari clams underwent Brown Muscle Disease, a pathology strictly restricted to this lagoon. Overall element contamination was relatively low, although arsenic, cobalt, nickel and chromium displayed higher values than in other ecosystems where Asari clam is exploited. Finally, total hemocyte count (THC) of Asari clam in Arcachon Bay, related to the immune system activity, exhibited values that were also under what is generally observed elsewhere. In conclusion, this study, with all reserves due to heterogeneity of available data, suggest that the particularly low fitness of Asari clam in Arcachon Bay is due to poor trophic condition, high prevalence and intensity of a disease (perkinsosis), moderate inorganic contamination, and poor efficiency of the immune system.

Benthic nematodes biodiversity patterns along the gradient of the Tagus estuary (Western Coast of Portugal): Link with abundances distribution pattern of the nonindigenous bivalve Ruditapes philippinarum

The non-indigenous bivalve Ruditapes philippinarum is native to the western Pacific Ocean and it has been one of the most widely introduced species for aquaculture purposes in Europe. In Portugal its presence is known in several estuaries for more than two decades and its populations have increased greatly along the last years1. Currently it’s one of the dominant benthic species in some areas of the Tagus estuary (264,1±470,8 ind./30s tow). Studies on the impacts of invasive bivalves on meiofaunal communities are scarce and restricted to the harvesting effect. Meiofauna of the Tagus estuary is poorly known and possible impacts of the introduction of R. philippinarum were never assessed.

Bioconcentration of selected personal care products in Ruditapes philippinarum (Manila clam)

The Bioconcentration Factor (BCF) is the principal source of information used to assess and regulate the potential hazard and risk for a chemical that has the potential to bioaccumulate in the marine environment, according to the Marine Strategy Framework Directive (MSFD). The main objective of this thesis was to estimate the BCFs of two different emerging contaminants in Ruditapes philippinarum (Manila clam) under controlled laboratory conditions: the UV filter 4-methylbenzylidene camphor (4-MBC) commonly used in skincare products, and the artificial sweetener Acesulfame potassium (ACE-K) used as a food additive. Ruditapes philippinarum organisms were exposed directly to 4-MBC and ACE-K nominal concentration of 1, 10 and 100 μg L-1 during 10 days. Bioconcentration factors (BCFs) were estimated according to 3 different models for both compounds. The 4-MBC estimated BCFs fall in range of 61553 - 539143 L Kg-1, showing that this compound is very bioaccumulative and could also undergo biomagnification in the marine food chain. On the contrary, estimated ACE-K BCF is consistently lower, in order of 7 L Kg-1 for the nominal exposure concentration of 100 μg L-1. The low ACE-K BCF could be explained by its high solubility in water and thus a rapid metabolization by clams during the experiments. In summary, future research focusing on the marine environment is needed on these two emerging compounds.

Moluscos bivalves em Portugal: composição química e metais contaminantes

Dissertação para obtenção do Grau de Mestre em Tecnologia e Segurança Alimentar

Ultrastructural data on the life cycle of the parasite, Perkinsus atlanticus (Apicomplexa), on the clam, Ruditapes phillipinarum, in the Mediterranean

An Apicomplexan Perkinsus species has been found parasitizing the clam Ruditapes philippinarum (= Tapes semidecussatus) collected on the Mediterranean coast in the region of the Ebro Delta (Tarragona, Spain). Light and transmission electron microscopy were used to study different stages of this parasite during zoosporulation induced by incubation in thioglycollate medium and seawater. During incubation the trophozoites began zoosporulation, which originated prezoosporangia and zoosporangia at different developmental stages. Successive cytokinesis and nucleokinesis gave rise to prezoospores, which became elongate and differentiated in biflagellated zoospores. The latter presented large mitochondria and an apical complex formed by a conoid, polar ring, micronemes, rhophtries and subpellicular microtubules. The zoosporangium wall showed some typical lamosomes and a discharge tube developed in early phases of incubation. Ultrastructural data were compared with the only four species of the genus Perkinsus previously described. The morphological data, the host and the geographic proximity suggest that the species located on the Mediterranean coast was Perkinsus atlanticus.

mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host -parasite interaction

Background The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis. Results A database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed. Conclusions This study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.

Microbiological responses to depuration and transport of native and exotic clams at optimal and stressful temperatures

The microbiological responses of two bivalves species from Tagus estuary, Venerupis pullastra (native clam) and Ruditapes philippinarum (exotic clam) were investigated during 48h of depuration and subsequent simulated transport in semi-dry conditions at two temperatures (4 and 22°C) until reaching 50% lethal time (LT50). Regardless of temperature and species, the maintenance of clams in water for 48h (depuration period) did not affect LT50 during transport. R.philippinarum showed higher survival rates than V.pullastra, always reaching LT50 later, especially at 4°C. Significant differences between clams' species were found in almost all microbiological parameters. This can be related with clams' biological activity and habitat environmental conditions since both clams do not coexist in Tagus estuary. Depuration was efficient to reduce the bacterial load, particularly Escherichia coli, but not efficient to remove Vibrio spp. In both species, the growth of Vibrio spp. was inhibited at 4°C, whereas exponential growth occurred at 22°C. Total viable counts significantly increased in most treatments, while E.coli counts significantly decreased to undetected levels, except for non-depurated R.philippinarum simulated transported at 4°C. Thus, this study highlights the importance of clams depuration for at least 24h in polluted estuarine areas, followed by transport at low temperatures (4°C). © 2013 Elsevier Ltd.

Mitochondrial inheritance and germ line determination in a bivalve species with Doubly Uniparental Inheritance (DUI)

Mitochondria are inherited maternally in most metazoans. However, in some bivalves, two mitochondrial lineages are present: one transmitted through eggs (F), the other through sperm (M). This is called Doubly Uniparental Inheritance (DUI). During male embryo development, spermatozoon mitochondria aggregate and end up in the primordial germ cells, while they are dispersed in female embryos. The molecular mechanisms of segregation patterns are still unknown. In the DUI species Ruditapes philippinarum, I examined sperm mitochondria distribution by MitoTracker, microtubule staining and TEM, and I localized germ line determinants with immunocytochemical analysis. I also analyzed the gonad transcriptome, searching for genes involved in reproduction and sex determination. Moreover, I analyzed an M-type specific open reading frame that could be responsible for maintenance/degradation of M mitochondria during embryo development. These transcripts were also localized in tissues using in situ hybridization. As in Mytilus, two distribution patterns of M mitochondria were detected in R. philippinarum, supporting that they are related to DUI. Moreover, the first division midbody concurs in positioning aggregated M mitochondria on the animal-vegetal axis of the male embryo: in organisms with spiral segmentation this zone is not involved in further cleavages, so aggregation is maintained. Moreover, sperm mitochondria reach the same embryonic area where germ plasm is transferred, suggesting their contribution in male germ line formation. The finding of reproduction and ubiquitination transcripts led to formulate a model in which ubiquitination genes stored in female oocytes during gametogenesis would activate sex-gene expression in the early embryonic developmental stages (preformation). Only gametogenetic cells were labeled by in situ hybridization, proving their specific transcription in developing gametes. Other than having a role in sex determination, some ubiquination factors could also be involved in mitochondrial inheritance, and their differential expression could be responsible for the different fate of sperm mitochondria in the two sexes.

Characterization of mitochondrial genomes in bivalve species with doubly uniparental inheritance of mitochondria

Many bivalve species possess two distinct mtDNA lineages, called F and M, respectively inherited maternally and paternally: this system is called doubly uniparental inheritance (DUI). The main experimental project of my PhD was the quantification of the two mtDNAs during the development of the DUI species Ruditapes philippinarum, from early embryos to sub-adults, using Real-Time qPCR. I identified the time interval in which M mtDNA is lost from female individuals, while it is retained in males (which are heteroplasmic through all of their life cycle). The results also suggested absence of mtDNA replication during early embryogenesis, a process constituting a bottleneck that highly reduces the copy number of mtDNA molecules in cells of developing larvae. In males this bottleneck may produce cells homoplasmic for M mtDNA, and could be considered as a first step of the segregation of M in the male germ line. Another finding was the characterization, in young clams approaching the first reproductive season, of a significant boost in copy number of F mtDNA in females and of M in males. Given the age of animals in which this mtDNA-specific growth was observed, the finding could probably be the outcome of the first round of gonads and gametes production. Other lines of research included the characterization of the unassigned regions in mt genomes of DUI bivalves. These regions can harbor signals involved in the control of replication and/or transcription of the mtDNA molecule, as well as additional open reading frames (ORFs) not related to oxidative phosphorylation. These features in DUI species could be associated to the maintenance of separate inheritance routes for the two mtDNAs. Additional ORFs are also found in other animal mt genomes: I summarized the presence of gene duplications as a co-author in a review focusing on animal mt genomes with unusual gene content.

Evaluation of the threat of marine CO2 leakage-associated acidification on the toxicity of sediment metals to juvenile bivalves

The effects of the acidification associated with CO2 leakage from sub-seabed geological storage was studied by the evaluation of the short-term effects of CO2-induced acidification on juveniles of the bivalve Ruditapes philippinarum. Laboratory scale experiments were performed using a CO2-bubbling system designed to conduct ecotoxicological assays. The organisms were exposed for 10 days to elutriates of sediments collected in different littoral areas that were subjected to various pH treatments (pH 7.1; pH 6.6; pH 6.1). The acute pH-associated effects on the bivalves were observed, and the dissolved metals in the elutriates were measured. The median toxic effect pH was calculated, which ranged from 6.33 and 6.45. The amount of dissolved Zn in the sediment elutriates increased in parallel with the pH reductions and was correlated with the proton concentrations. The pH, the pCO2 and the dissolved metal concentrations (Zn and Fe) were linked with the mortality of the exposed bivalves.

Multifactorial analysis and food safety issues of edible marine gastropods intended for human consumption

The present thesis aims to evaluate a method to assess the viability; estimate the bacterial and viral (Hepatitis A and Norovirus) contamination; describe how some parameters change during a week in refrigerated condition and after 24 hours of immersion; estimate indole-producing bacteria and biogenic amines; evaluate the presence of saxitoxin and tetrodotoxin. The method to assess the viability using sea salt is easy to apply. Marine gastropods did not accumulate fecal contaminants, but vibrios due to their feeding. The Vibrio spp. load was even higher than the one registered on Ruditapes philippinarum belonging to the same area For what to concern the evaluation during a week in refrigerated condition and after 24 hours of immersion, non-re-immersed gastropods exceeded the acceptable mortality (10%) after three days in refrigerated conditions, but the Vibrio spp. load did not show a significant increase within three days. The TVC was already high from the beginning and its major part consisted of SSOs, which could be explained by gastropods’ feed, such as the Pseudomonas spp. load and the abundance of IPB. The BAs amount was also correlated with viability and had a statistically significant difference within a week on refrigerated conditions, principally because putrescine, tyramine, spermidine, and cadaverine rise in non-re-immersed samples. It also should be noted that the BAs amount was higher on average than the recommendation of literature. Moreover, re-immersed batches showed acceptable viability even after 3 days, and the Vibrio spp. load, TVC, SSOs, and biogenic amines remained almost constant within a week contrary to non-re-immersed samples. Finally, T. mutabilis and B. brandaris did not accumulate NoVs and TTX. We obtained only one positivity of the HAV sample and traces of STX (not at levels toxic to humans). Our results contribute to identifying food-borne hazards for T. mutabilis and B. brandaris.

Mitochondrial Inheritance, Mito-nuclear Coevolution, and Sex-associated Genes in Bivalve Molluscs: Transcriptomics and Molecular Evolution

Bivalvia represents an ancient taxon including around 25,000 living species that have adapted to a wide range of environmental conditions, and show a great diversity in body size, shell shapes, and anatomic structure. Bivalves are characterized by highly variable genome sizes and extremely high levels of heterozygosity, which obstacle complete and accurate genome assemblies and hinder further genomic studies. Moreover, some bivalve species presented a stable evolutionary exception to the strictly maternal inheritance of mitochondria, namely doubly uniparental inheritance (DUI), making these species a precious model to study mitochondrial biology. During my PhD, I focused on a DUI species, the Manila clam Ruditapes philippinarum, and my work was two-folded. First, taking advantage of a newly assembled draft genome and a large RNA-seq dataset from different tissues of both sexes, I investigated 1) the role of gene expression and alternative splicing in tissue differentiation; 2) the relationship across tissue specificity, regulatory network connectivity, and sequence evolution; 3) sexual contrasting genetic markers potentially associated with sexual differentiation. The detailed information for this part is in Chapter 2. Second, using the same RNA-seq data, I investigated how nuclear oxidative phosphorylation (OXPHOS) genes coordinate with two divergent mitochondrial genomes in DUI species (mito-nuclear coordination and coevolution). To address this question, I compared transcription, polymorphism, and synonymous codon usage in the mitochondrial and nuclear OXPHOS genes of R. philippinarum in Chapter 3. To my knowledge, this thesis represents the first study exploring the role of alternative splicing in tissue differentiation, and the first study analyzing both transcriptional regulation and sequence evolution to investigate the coordination of OXPHOS genes in bivalves.