Stefano Carboni

IMC International Marine Centre

Background Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new h...

In Scotland, bivalves are widely distributed. However, their larvae dispersion is still largely unknown and difficult to assess in situ. And, while Mytilus spp. dominate shellfish production, it is mostly dependent on natural spat recruitment from wild populations. Understanding the larval distribution pattern would safeguard natural resources whil...

While the UK is the fourth largest aquaculture producer in Europe by volume, it is the second largest by value with an annual first sale value of around £1 billion. Over 90% of this value is from Atlantic salmon farmed in Scotland, but other fin-fish and shellfish aquaculture species are important to several UK regions. In this review, we describe...

Novel aquafeed formulation for unconventional farmed fish species

The mussel industry faces challenges such as low and inconsistent levels of larvae settlement and poor-quality spat, leading to variable production. However, mussel farming remains a vital sustainable and environmentally responsible method for producing protein, fostering ecological responsibility in the aquaculture sector. We investigate the popul...

The European flat oyster, Ostrea edulis, once formed extensive reef habitats throughout European seas and estuaries. These reefs are now largely functionally extinct, yet interest and support for their restoration is rapidly growing. A major bottleneck to scaling up oyster reef restoration is the lack of available oysters to supply the growing dema...

Blue mussels (Mytilus sp.) are an economically important species for European aquaculture. Their importance as a food source is expected to increase in the coming net-zero society due to their low environmental footprint; however, their production is affected by anthropogenic stressors and climate change. During reproduction, lipids are key molecul...

Oyster farming is considered a sustainable seafood production with environmental benefits related to water purification, but negative effects on the benthic ecosystem functioning could be caused by the release of feaces and pseudofeaces, collectively called bio-deposits. In this study, we compared the first time the daily bio-deposit production of...

The thinlip grey mullet (Chelon ramada) belongs to the Mugilidae family, it is a low-trophic, euryhaline species adapted to a wide range of environmental conditions. As such, it represent a candidate to diversify aquaculture production toward more sustainable species. Nonetheless, several bottlenecks have to be overcome before production is underta...

Salinity is one of the main factors affecting physiological performances of teleost fish. Its influence on survival and growth rate of juvenile (five months old) Mugil cephalus (25.33 ± 1.01 mm length) was tested under hatchery conditions. After acclimation, fish were reared for three months at two salinities: freshwater (FW, 0 ppt) and saltwater (...

Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality...

Responsible aquaculture, the farming of aquatic organisms, is a sustainable strategic sector for land and coastal communities. It significantly contributes to food security and enhancement of economic development; it provides employment opportunities and often contributes to the ecological services provided by the environment. According to the Food...

Mussels often hybridise to form the Mytilus species complex comprised of M. edulis and M. galloprovincialis as the main species cultivated in Europe and, where their geographical distribution overlaps, the species M. trossulus. It has been suggested that M. trossulus have a weaker shell than the UK native M. edulis and hybridisation reduces farmed...

The world's ever-growing population presents a major challenge in providing sustainable food options and in reducing pressures on the Earth's agricultural land and freshwater resources. Current estimates suggest that agriculture contributes ~30% of global greenhouse gas (GHG) emissions. Additionally, there is an increased demand for animal protein,...

Background Apoptosis is an important process for an organism’s innate immune system to respond to pathogens, while also allowing for cell differentiation and other essential life functions. Caspases are one of the key protease enzymes involved in the apoptotic process, however there is currently a very limited understanding of bivalve caspase diver...

Background Nitric oxide (NO) is presumed to be a regulator of metamorphosis in many invertebrate species, and although NO pathways have been comparatively well-investigated in gastropods, annelids and crustaceans, there has been very limited research on the effects of NO on metamorphosis in bivalve shellfish. Results In this paper, we investigate...

Apoptosis is an important process for an organism’s innate immune system to respond to pathogens, while also allowing for cell differentiation and other essential life functions. Caspases are one of the key protease enzymes involved in the apoptotic process, however there is currently a very limited understanding of bivalve caspase diversity and fu...

Bivalve metamorphosis is a developmental transition from a free-living larva to a benthic juvenile (spat), regulated by a complex interaction of neurotransmitters and neurohormones such as L-DOPA and epinephrine (catecholamine). We recently suggested an N-Methyl-D-aspartate (NMDA) receptor pathway as an additional and previously unknown regulator o...

The maturation and reproduction of Pacific whiteleg shrimp, Penaeus vannamei, through the practice of unilateral eyestalk ablation though common is an animal welfare concern. This study assessed the resilience of offspring from non-ablated P. vannamei when challenged with an isolate of Vibrio parahaemolyticus (Vp) causing acute hepatopancreatic nec...

Background Nitric oxide (NO) is a presumed regulator of metamorphosis in many invertebrate species, and although NO pathways have been comparatively well-investigated in gastropods, annelids and crustaceans, there has been very limited research on the effects of NO on metamorphosis in bivalve shellfish. Results In this paper, we investigate the eff...

Background: Nitric oxide (NO) is presumed to be a regulator of metamorphosis in many invertebrate species, and although NO pathways have been comparatively well-investigated in gastropods, annelids and crustaceans, there has been very limited research on the effects of NO on metamorphosis in bivalve shellfish. Results: In this paper, we investigate...

Mussels close their shell as a protective strategy and the quantification of this behavioral marker may represent an alarm signal when they are exposed to environmental stressors. In the present study, we investigated the ability of the Mediterranean mussel Mytilus galloprovincialis to recover and then the resilience or inertia of valve activity af...

In this study, we have developed an approach to classify the suitability of shallow coastal lagoons for pacific oyster aquaculture as the first step in a site selection process. Historical bio-physical data and local knowledge were combined to produce overall scores for biological and logistical criteria relevant for oyster farming which were then...

Microplastics have been considered to be dangerous for aquatic organisms’ health (Alomar et al. 2017). Indeed, their accumulation by ingestion can lead to increased exposure to pollutants and pathogens, and effects on physiological activities linked to nutrient uptake, growth and survival (Browne et al. 2011; Sussarellu et al. 2016; Fendall and Sew...

Blue mussels (Mytilus edulis L. 1758) are important components of coastal ecosystems and in the economy of rural and coastal areas. The understanding of their physiological processes at key life stages is important both within food production systems and in the management of wild populations. Lipids are crucial molecules for bivalve growth, but the...

Bivalve farming is a major European aquaculture activity, representing 48.5% of total biomass produced. Italy is one of the largest consumers of oysters but local production does not meet the market demand. Italy has approximately 384,000 ha of shallow lagoons in its coastal area, already devoted to extensive aquaculture activities, which could als...

Blue mussels (Mytilus edulis L.) are important components of coastal ecosystems functioning through benthopelagic coupling and ecosystem engineering. At the same time, mussel production is central in the economy of coastal areas. Therefore, understanding their nutritional, physiological and metabolic processes at key life stages is important for th...

In this study, a machine learning approach (RandomForest) was applied to connect the lipidome profile of gonads to their maturation stages analysed via histological and imaging analysis techniques

Numerous United Kingdom and European Union expert panels recommend that the general adult population consumes ~250 mg of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) per day through the consumption of one portion of oily fish per week. The long-chain omega-3 fatty acids EPA and DHA are only found in appreciable amounts in marine organ...

Microplastics debris (<5 mm) are increasingly abundant in the marine environment, therefore, potentially becoming a growing threat for different marine organisms. Through aquatic animals, these can enter in the human food chain, and can be perceived as a risk for consumers’ health. Different studies report the presence of particles in marketable s...

This study evaluated reproductive performance of non-ablated Litopenaeus vannamei and the quality of their offspring under commercial conditions. Five tanks were stocked with non-ablated female and other five with ablated individuals as control. Two different larval rearing trials (Larviculture I and II) have been conducted. Six larviculture tanks...

The development of diagnostic markers has been a long-standing interest of population geneticists as it allows clarification of taxonomic uncertainties. Historically, there has been much debate on the taxonomic status of species belonging to the Mytilus species complex (M. edulis, M. galloprovincialis and M. trossulus), and whether they are discret...

Sample and RAD barcodes. Details each sample used: sample ID, library number, Me15/16 Genotype, RAD barcode (P1 adapter), RAD barcode (P1 adapter), number of raw reads (paired-ended) and number of RAD-tags. (CSV)

KASP assay primer sequences. List of the allele-specific primers and common primer designed for the allele-specific PCR genotyping assay. (CSV)

Details of the RAD and KASP assay results. Genotypes of the 12 assays for 40 development individuals. (CSV)

Details of the Me15/16 genotyping results. Genotypes results for Me15/16 preliminary assay for all 278 samples, summarised Table 2. (CSV)

Details of the KASP genotyping results. Genotypes results for the 12 KASP assays for all 278 samples. (CSV)

Details of the 378 selected SNP markers. N means no SNP reported for the species. To be selected a SNP needs to be present in at least 50% of all samples and to be reported in a species, the SNP needs to be in at least 50% of the samples of this species (see Materials and Methods). (CSV)

Ciliates have been reported as pathogens of many species of economically important bivalves. Mussel protozoan X (MPX), is an uncharacterised intracellular ciliate of mussels and has been widely reported in Mytilus spp. around the world. In order to characterise this ciliate, Mytilus edulis samples were collected from a site on the West coast of Sco...

Sea urchins are broadly recognised as a delicacy and their quality as food for humans is highly influenced by their diet. Lipids in general and the long-chain polyunsaturated fatty acids (LC-PUFA) in particular, are essential nutrients that determine not only the nutritional value of sea urchins but also guarantee normal growth and reproduction in...

Introduction In many European coastal areas, the high market demand for the gonads of sea urchin Paracentrotus lividus (Lamarck, 1816) exposes their natural populations to over fishing, causing a sharp decline in the abundance of wild stocks (Carboni et al., 2012). Scientific research seeks to bridge the gap between supply and demand of aquaculture...

In this study, we present the results of two experiments; in the first one we evaluated the effects of four larval dietary treatments on the survival and growth of the sea urchin Paracentrotus lividus, larvae and post-larvae. In the second experimentwe have measured the effects of two different settlement substrates,combined withthe presence of con...

New research is currently underway to explore the potential of macroalgae for the production of biofuels. Marine biofuels in general and macroalgae in particular, offer a number of advantages over terrestrial biofuels including reduced competition for freshwater resources and for land use. Sugars can be extracted from macroalgae and processed into...

This study compared the growth of sea urchin Paracentrotus lividus larvae cultured using two different rearing methods: a variable method based on a variable amount of feed (microalgae) and seawater exchange (30% or 50%) established according to the phytoplankton concentration in the larval cultures and a fixed method characterized by a fixed amoun...

Scotland is unusual among nations with active research programs into sea urchin cultivation, in that despite having native edible species, there has not been a major fishery for sea urchins in recent times. Sea urchin aquaculture research is conducted by two laboratories in Scotland: since 1995 at the Scottish Association for Marine Science (SAMS)...

Light is a key environmental cue involved in the entrainment and regulation of fish development and physiology. Species specific spectral differences in sensitivity are believed to be an adaptation to the species’ ecological niche and therefore fish larvae are predisposed to perform better under specific light environments. This study investigated...

The effects of formulated feeds on Paracentrotus lividus broodstock performances and carotenoid compositions were investigated. Performance of offspring derived from each dietary treatment was compared to determine whether maternal provisioning of nutrients affected offspring development and survival under commercial culture conditions. At the end...

Light is a key environmental factor that synchronizes all life-stages of fish, from embryo development to sexual maturation. The underwater photo-environment is complex since light characteristics (i.e. intensity, photoperiod and spectrum) depend on the absorbance properties of the water column. The aim of this paper is to review the effects of art...