Stefano Carboni | University of Stirling (original) (raw)

Papers by Stefano Carboni

BMC Genomics, May 2, 2022

Background: Molluscs remain one significantly under-represented taxa amongst available genomic re... more 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 high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia. Results: Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences. Conclusions: The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multidisciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises.

Aquaculture, Mar 1, 2019

Reproductive performance and offspring quality of non-ablated Pacific white shrimp (Litopenaeus v... more Reproductive performance and offspring quality of non-ablated Pacific white shrimp (Litopenaeus vannamei) under intensive commercial scale conditions Simão Zacarias *

PLOS ONE, Jan 4, 2017

Sea urchins are broadly recognised as a delicacy and their quality as food for humans is highly i... more 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 captivity. The contribution of endogenous production (biosynthesis) of LC-PUFA in sea urchins remained unknown. Using Paracentrotus lividus as our model species, we aimed to characterise both molecularly and functionally the repertoire of fatty acyl desaturases (Fads), key enzymes in the biosynthesis of LC-PUFA, in sea urchins. Three Fads, namely FadsA, FadsC1 and FadsC2, were characterised. The phylogenetic analyses suggested that the repertoire of Fads within the Echinodermata phylum varies among classes. On one hand, orthologues of the P. lividus FadsA were found in other echinoderm classes including starfishes, brittle stars and sea cucumbers, thus suggesting that this desaturase is virtually present in all echinoderms. Contrarily, the FadsC appears to be sea urchin-specific desaturase. Finally, a further desaturase termed as FadsB exists in starfishes, brittle stars and sea cucumbers, but appears to be missing in sea urchins. The functional characterisation of the P. lividus Fads confirmed that the FadsA was a Δ5 desaturase with activity towards saturated and polyunsaturated fatty acids (FA). Moreover, our experiments confirmed that FadsA plays a role in the biosynthesis of non-methylene interrupted FA, a group of compounds typically found in marine invertebrates. On the other hand, both FadsC desaturases from P. lividus showed Δ8 activity. The present results demonstrate that P. lividus possesses desaturases that account for all the desaturation reactions required to biosynthesis the physiological essential eicosapentaenoic and arachidonic acids through the so-called "Δ8 pathway".

Springer eBooks, 2020

Microplastics debris (<5 mm) are increasingly abundant in the marine environment, therefore, pote... more 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 shellfish including the world wide commercially grown Pacific oyster Magallana gigas (Thunberg, 1793). The aim of this study is to examine the potential risk of microplastics entering in the human food chain through this shellfish species, investigating the dynamics of the uptake, egestion (faeces) and rejection (pseudofaeces) of microplastics in Pacific oysters under controlled conditions. M. gigas collected from a farm in the San Teodoro lagoon (Italy), were exposed to 60 fluorescent orange polystyrene particles L-1 of known sizes (100, 250 and 500 µm). The uptake of each particle size was 19.4 ± 1.1%, 19.4 ± 2 % and 12.9 ± 2 % respectively. After exposure M. gigas were left to depurate for 72 hrs, during which 84.6 ± 2 % of the particles taken up were released whilst 15.4 ± 2 % were retained inside the shell cavity. No microplastic particles were found in the animals' soft tissues. The results of this study, suggest that depuration is an effective method to reduce presence of large microplastic particles, in the size range 100 to 500 µm, in M. gigas. Importantly, the data suggests that the burden that could theoretically be up taken by consumers from these shellfish is negligible when compared to other routes. Capsule Microplastic of tested sizes were not retained in the tissues but can be retained in the shell cavity; Depuration is an effective method to reduce microplastics in farmed Pacific oysters

PLOS ONE, Feb 21, 2020

Blue mussels (Mytilus edulis L. 1758) are important components of coastal ecosystems and in the e... more 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 their diversity and roles have not been fully characterised. In this study, traditional lipid profiling techniques, such as fatty acid (FA) and lipid class analysis, are combined to untargeted lipidomics to elucidate the lipid metabolism in newly settled spat fed on a range of diets. The evaluated diets included single strains treatments (Cylindrotheca fusiformis CCAP 1017/2-CYL, Isochrysis galbana CCAP 927/1-ISO, Monodopsis subterranean CCAP 848/1-MONO, Nannochloropsis oceanica CCAP 849/10-NANNO) and a commercial algae paste (SP). Spat growth was influenced by the diets, which, according to their efficacy were ranked as follows: ISO>NANNO/CYL>SP>MONO. A higher triacylglycerols (TG) content, ranging from 4.23±0.82 μg mg ashfree Dry weight (DW)-1 at the beginning of the trial (T0) to 51

Reviews in Aquaculture, Mar 29, 2021

While the UK is the fourth largest aquaculture producer in Europe by volume, it is the second lar... more 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 finfish and shellfish aquaculture species are important to several UK regions. In this review, we describe the state of the art in UK aquaculture breeding and stock supply, and how innovation in genetics technologies can help achieve the Scottish Government's ambitious target of doubling its aquaculture industry by 2030. Particular attention is given to the four most important UK aquaculture species: Atlantic salmon, rainbow trout, blue mussel and Pacific oyster, and we contrast the highly variable level of selective breeding and genomics technologies used in these sectors. A major factor in the success of Atlantic salmon farming has been large-scale investment in modern breeding programmes, including family selection programmes and genomic selection. This has proven cost-effective at scale, leading to improved production efficiency and reduction of some infectious diseases. We discuss the feasibility of applying similar technologies to the UK shellfish sectors, to ensure consistent and robust spat supply and begin trait selection. Furthermore, we discuss species-specific application of modern breeding technologies in a global context, and the future potential of genomics and genome editing technologies to improve commercially desirable traits. Increased adoption of modern breeding technologies will assist UK aquaculture industries to meet the challenges for sustainable expansion, and remain competitive in a global market.

PLOS ONE, Jul 12, 2018

The development of diagnostic markers has been a long-standing interest of population geneticists... more 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 discrete species. We analysed reference pure specimens of M. edulis, M. galloprovincialis and M. trossulus, using Restriction site associated DNA (RAD) sequencing and identified over 6,000 SNP markers separating the three species unambiguously. We developed a panel of diagnostic SNP markers for the genotyping of Mytilus species complex as well as the identification of hybrids and interspecies introgression events in Mytilus species. We validated a panel of twelve diagnostic SNP markers which can be used for species genotyping. Being able to accurately identify species and hybrids within the Mytilus species complex is important for the selective mussel stock management, the exclusion of invasive species, basic physiology and biodiversity studies.

Aquaculture, 2016

ABSTRACT

Developmental Biology, 2021

Bivalve metamorphosis is a developmental transition from a free-living larva to a benthic juvenil... more 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 of bivalve metamorphosis. To explore this theory further, we successfully induced metamorphosis in the Pacific oyster, Crassostrea gigas, by exposing competent larvae to L-DOPA, epinephrine, MK-801 and ifenprodil. Subsequently, we cloned three NMDA receptor subunits CgNR1, CgNR2A and CgNR2B, with sequence analysis suggesting successful assembly of functional NMDA receptor complexes and binding to natural occurring agonists and the channel blocker MK-801. NMDA receptor subunits are expressed in competent larvae, during metamorphosis and in spat, but this expression is neither self-regulated nor regulated by catecholamines. In-situ hybridisation of CgNR1 in competent larvae identified NMDA receptor presence in the apical organ/cerebral ganglia area with a potential sensory function, and in the nervous network of the foot indicating an additional putative muscle regulatory function. Furthermore, phylogenetic analyses identified molluscan-specific gene expansions of key enzymes involved in catecholamine biosynthesis. However, exposure to MK-801 did not alter the expression of selected key enzymes, suggesting that NMDA receptors do not regulate the biosynthesis of catecholamines via gene expression.

Journal of Invertebrate Pathology, Mar 1, 2018

Ciliates have been reported as pathogens of many species of economically important bivalves. Muss... more 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 Scotland, and four different fixatives for histological examination were tested. Fresh preparations of mussel digestive glands were also examined by laser scanning confocal microscopy. Intracellular ciliates were prepared by laser capture microdissection and partial sequences of small subunit ribosomal RNA gene and of large subunit ribosomal RNA gene were generated, using Phyllopharyngea primers. Methacarn solution proved to be the best fixative for both histological and molecular characterisation. The morphological and molecular investigations confirmed that this ciliate belongs to the class Phyllopharyngea, order Rhynchodida. However, this organism does not belong to any known family, genus or species, therefore, a new description is necessary, following further morphological analyses. Most mussel samples containing MPX displayed mild to moderate infections, with no signs of necrosis or haemocytic response, although a single sample displayed a severe infection (~10 3 ciliates per section). The localisation of this ciliate in tissues other than the digestive gland, the presence of necrosis in infected tissue of the most severely infected mussel and the binary fission of this ciliate have been observed here for the first time. We also report the first observation of the live ciliate isolated from tissue. Although MPX remains of unknown significance to the mussel industry, tools and protocols described here will be useful in further characterising these and other ciliates (subclass Rhynchodia) known as pathogens for bivalves.

Aquaculture, Nov 1, 2016

New research is currently underway to explore the potential of macroalgae for the production of b... more 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 biofuels by anaerobic digestion and fermentation. This process generates significant waste biomass, which, if used, could improve the economic sustainability of the biorefinery sector. Bivalves' aquaculture relies heavily on the production of unicellular algae to feed juvenile individuals and this can represent a bottleneck for the bivalve industry especially in locations where sunlight is limited. Previous research explored the use of macroalgae derived digestate as alternative or integrative feed for juvenile bivalves, exploiting the notion that organic particulate matter (detritus) is an integral part of this animal class natural diet. The prospect of using waste products from the emerging biorefinery industry to solve a bottleneck for aquaculture businesses and, by so doing, improving profitability of both, is an exciting one. In this paper we describe the main nutritional profiles (Protein, Lipid, Carbohydrates and Fatty acids) of the tested diets and investigate the potential for the use of a biorefinery a by-product as replacement option for bivalves' production, by benchmarking it against aquaculture industry standards (live microalgae and commercially available algae paste) and natural detritus constituted by farmed sea urchin digesta. Both the digestate and the natural detritus supported the survival and growth of bivalve spat, especially when used at 50% inclusion rate, over the course of 4-week preliminary trials. Data *Manuscript Click here to download Manuscript: The use of biorefinery by product as bivalve feed-revised.docx Click here to view linked References suggest that a synergistic effect of the nutritional profiles of the diets employed may underpin the 26 observed results. 27 18:3n-3 12.26±1.43 a 4.19±0.14 d 2.55±0.07 e 2.53±0.05 e 7.43±0.61 c 9.44±1.16 b 18:4n-3 11.32±0.25 a 8.90±0.87 b 1.64±0.06 d 1.05±0.03 e 6.60±0.42 c 8.38±0.22 b 18:5n-3 5.06±0.41 a 0.74±0.09 d nd 0.32±0.04 e 2.67±0.17 c 3.82±0.24 b 20:5n-3 3.12±0.10 b 13.84±1.29 a 1.20±0.03 f 1.72±0.14 e 2.19±0.09 d 2.66±0.013 c 22:6n-3 8.16±0.33 a 5.50±0.63 b nd 0.21±0.02 d 4.29±0.33 c 6.07±0.25 b Total n-3 PUFA 40.62±2.36 a 33.63±3.04 b 5.54±0.15 d 5.97±0.28 d 23.59±1.24 c 29.92±2.43 b 16;2 0.82±0.15 b 2.20±0.08 a 0.23±0.01 d 0.17±0.01 e 0.55±0.05 c 0.65±0.10 bc 16;3 0.33±0.43 c 1.55±1.48 a 1.16±0.04 b 0.47±0.04 d 0.69±0.05 c 0.18±0.02 e 16;4 5.90±0.21 a 0.81±0.15 d nd nd 2.76±0.26 c 3.94±0.19 b 15:0 DMA 0.53±0.03 e 0.79±0.07 d 1.04±0.11 b 1.89±0.65 a 0.84±0.04 c 0.76±0.23 cd 16:0 DMA 1.47±0.08 c 2.18±0.15 b 2.84±0.05 a 2.03±0.03 b 2.18±0.14 b 1.58±0.13 c Total PUFA 53.02±2.88 a 46.62±1.98 b 15.60±0.25 d 11.43±0.38 e 34.75±1.47 c 40.85±1.89 b Total PUFA includes n-6; n-3; 16;2; 16;3 and 16;4. Values below 0.5% for all tested diets are not included in this table. Mean±SD; n=6. nd: not detected.

Aquaculture Research, Aug 24, 2022

Frontiers in Marine Science

In Scotland, bivalves are widely distributed. However, their larvae dispersion is still largely u... more 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 while also ensuring sustainable farming practises. The feasibility of a model that simulates biophysical interactions between larval behaviour and ocean motions was investigated. We employed an unstructured tri-dimensional hydrodynamic model (finite volume coastal ocean model) to drive a particle tracking model, where prediction of larval movement and dispersal at defined locations might aid in population monitoring and spat recruitment. Our findings reveal a strong link between larval distribution and meteorological factors such as wind forces and currents velocity. The model, also, depicts a fast and considerable larval movement, resulting i...

Animal Reproduction Science

Nutrients

The world’s ever-growing population presents a major challenge in providing sustainable food opti... more 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, the production of which is particularly polluting. Therefore, the climate-disrupting potential of feeding the planet is likely to substantially worsen in the future. Due to the nutritional value of animal-based protein, it is not a simple solution to recommend a wholesale reduction in production/consumption of animal proteins. Rather, employing strategies which result in the production of low carbon animal protein may be part of the solution to reduce the GHGs associated with our diets without compromising diet quality. We suggest that farmed mussels may present a partial solution to this dilemma. Mussel production has a relatively low GH...

Aquaculture

Highlights-Non-ablated Penaeus vannamei females produce offspring that are more resilient to comm... more Highlights-Non-ablated Penaeus vannamei females produce offspring that are more resilient to commonly encountered pathogens.-Postlarvae from non-ablated female have a significantly higher resistance to VpAHPND.-Juveniles from non-ablated animals have better survival to WSD than their juvenile counterparts from ablated female.