Development and Diversity of Epibiont Assemblages on Cultivated Sugar Kelp (Saccharina latissima) in Relation to Farming Schedules and Harvesting Techniques.

Seaweed farming in Europe is growing and may provide environmental benefits, including habitat provisioning, coastal protection, and bioremediation. Habitat provisioning by seaweed farms remains largely unquantified, with previous research focused primarily on the detrimental effects of epibionts, rather than their roles in ecological functioning and ecosystem service provision. We monitored the development and diversity of epibiont assemblages on cultivated sugar kelp (Saccharina latissima) at a farm in Cornwall, southwest UK, and compared the effects of different harvesting techniques on epibiont assemblage structure. Increases in epibiont abundance (PERMANOVA, F4,25 = 100.56, p < 0.001) and diversity (PERMANOVA, F4,25 = 27.25, p < 0.001) were found on cultivated kelps over and beyond the growing season, reaching an average abundance of >6000 individuals per kelp plant with a taxonomic richness of ~9 phyla per kelp by late summer (August). Assemblages were dominated by crustaceans (mainly amphipods), molluscs (principally bivalves) and bryozoans, which provide important ecological roles, despite reducing crop quality. Partial harvesting techniques maintained, or increased, epibiont abundance and diversity beyond the farming season; however, these kelp plants were significantly fouled and would not be commercially viable in most markets. This paper improves understanding of epibiont assemblage development at European kelp farms, which can inform sustainable, ecosystem-based approaches to aquaculture.

Ageing European lobsters (Homarus gammarus) using DNA methylation of evolutionarily conserved ribosomal DNA.

Crustaceans are notoriously difficult to age because of their indeterminate growth and the moulting of their exoskeleton throughout life. The poor knowledge of population age structure in crustaceans therefore hampers accurate assessment of population dynamics and consequently sustainable fisheries management. Quantification of DNA methylation of the evolutionarily conserved ribosomal DNA (rDNA) may allow for age prediction across diverse species. However, the rDNA epigenetic clock remains to be tested in crustaceans, despite its potential to inform both ecological and evolutionary understanding, as well as conservation and management practices. Here, patterns of rDNA methylation with age were measured across 5154 bp of rDNA corresponding to 355 quality-filtered loci in the economically important European lobster (Homarus gammarus). Across 0- to 51-month-old lobsters (n = 155), there was a significant linear relationship between age and percentage rDNA methylation in claw tissue at 60% of quality-filtered loci (n = 214). An Elastic Net regression model using 46 loci allowed for the accurate and precise age estimation of individuals (R 2 = 0.98; standard deviation = 1.6 months). Applying this ageing model to antennal DNA from wild lobsters of unknown age (n = 38) resulted in predicted ages that are concordant with estimates of minimum size at age in the wild (mean estimated age = 40.1 months; range 32.8-55.7 months). Overall, the rDNA epigenetic clock shows potential as a novel, nonlethal ageing technique for European lobsters. However, further validation is required across a wider range of known-age individuals and tissue types before the model can be used in fisheries management.

Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus).

Microbial communities within the gut can markedly impact host health and fitness. To what extent environmental influences affect the differential distribution of these microbial populations may therefore significantly impact the successful farming of the host. Using a sea-based container culture (SBCC) system for the on-growing of European lobster (Homarus gammarus), we tracked the bacterial gut microbiota over a 1-year period. We compared these communities with lobsters of the same cohort, retained in a land-based culture (LBC) system to assess the effects of the culture environment on gut bacterial assemblage and describe the phylogenetic structure of the microbiota to compare deterministic and stochastic assembly across both environments. Bacterial gut communities from SBCCs were generally more phylogenetically clustered, and therefore deterministically assembled, compared to those reared in land-based systems. Lobsters in SBCCs displayed significantly more species-rich and species-diverse gut microbiota compared to those retained in LBC. A reduction in the bacterial diversity of the gut was also associated with higher infection prevalence of the enteric viral pathogen Homarus gammarus nudivirus (HgNV). SBCCs may therefore benefit the overall health of the host by promoting the assembly of a more diverse gut bacterial community and reducing the susceptibility to disease.

The first clawed lobster virus Homarus gammarus nudivirus (HgNV n. sp.) expands the diversity of the Nudiviridae.

Viral diseases of crustaceans are increasingly recognised as challenges to shellfish farms and fisheries. Here we describe the first naturally-occurring virus reported in any clawed lobster species. Hypertrophied nuclei with emarginated chromatin, characteristic histopathological lesions of DNA virus infection, were observed within the hepatopancreatic epithelial cells of juvenile European lobsters (Homarus gammarus). Transmission electron microscopy revealed infection with a bacilliform virus containing a rod shaped nucleocapsid enveloped in an elliptical membrane. Assembly of PCR-free shotgun metagenomic sequencing produced a circular genome of 107,063 bp containing 97 open reading frames, the majority of which share sequence similarity with a virus infecting the black tiger shrimp: Penaeus monodon nudivirus (PmNV). Multiple phylogenetic analyses confirm the new virus to be a novel member of the Nudiviridae: Homarus gammarus nudivirus (HgNV). Evidence of occlusion body formation, characteristic of PmNV and its closest relatives, was not observed, questioning the horizontal transmission strategy of HgNV outside of the host. We discuss the potential impacts of HgNV on juvenile lobster growth and mortality and present HgNV-specific primers to serve as a diagnostic tool for monitoring the virus in wild and farmed lobster stocks.

Halioticida noduliformans infection in eggs of lobster (Homarus gammarus) reveals its generalist parasitic strategy in marine invertebrates.

A parasite exhibiting Oomycete-like morphology and pathogenesis was isolated from discoloured eggs of the European lobster (Homarus gammarus) and later found in gill tissues of adults. Group-specific Oomycete primers were designed to amplify the 18S ribosomal small subunit (SSU), which initially identified the organism as the same as the 'Haliphthoros' sp. NJM 0034 strain (AB178865.1) previously isolated from abalone (imported from South Australia to Japan). However, in accordance with other published SSU-based phylogenies, the NJM 0034 isolate did not group with other known Haliphthoros species in our Maximum Likelihood and Bayesian phylogenies. Instead, the strain formed an orphan lineage, diverging before the separation of the Saprolegniales and Pythiales. Based upon 28S large subunit (LSU) phylogeny, our own isolate and the previously unidentified 0034 strain are both identical to the abalone pathogen Halioticida noduliformans. The genus shares morphological similarities with Haliphthoros and Halocrusticida and forms a clade with these in LSU phylogenies. Here, we confirm the first recorded occurrence of H. noduliformans in European lobsters and associate its presence with pathology of the egg mass, likely leading to reduced fecundity.

Framework for evaluating external and internal parameters associated with Sea Based Container Culture (SBCC): Towards understanding rearing success in European lobsters (Homarus gammarus).

Sea Based Container Culture (SBCC) is a mariculture technique that relies on the natural maintenance of environmental conditions, such as Dissolved Oxygen (DO) concentration and feed availability. This paper discusses a framework to evaluate the rearing success of European Lobsters (Homarus gammarus) in SBCC based on temporal and spatial variations of external parameters, including current velocity, wave velocity, turbulent fluctuations and dissolved oxygen concentrations. The temporal variations considered annual changes to the environment and the effect of biofouling growth, and the spatial variations considered the geographical location (case study of Falmouth bay, Cornwall) and vertical position in the water column. The internal parameters of the containers were modelled using transfer functions derived from previous experimental data. The internal parameters were compared to rearing limitations selected from available literature, which included foraging and mobility behaviours, and DO consumption. The time that internal parameters exceeded the rearing limitations was quantified, allowing rearing success to be predicted. This paper uses a case study of external parameters measured in Cornish waters, UK, to demonstrate the framework methodology. The framework showed that in situ measurements of current, wave and turbulence could be used to predict the internal parameters of SBCC containers, which can be used to predict theoretical rearing success based on rearing limitations. The framework indicated that DO concentrations within the containers should not affect rearing success; however, the foraging and mobility limits were exceeded by 0 to 30% of the time (depending on vertical position in the water column and assessment method). The paper aims to demonstrate the generic framework methodology and understands its limitations in predicting rearing success. The framework provides a tool to optimise the SBCC design for spatial and temporal varying conditions related to a geographical location or (vice versa) identify suitable mariculture sites based on SBCC design and environmental conditions. Additionally, the framework can optimise the vertical position of the SBCC in the water column and identify, from parameters considered, those that are most likely to affect rearing success.

Microbial manipulations to improve fish health and production--a Mediterranean perspective.

The interactions between the endogenous gut microbiota and the fish host are integral in mediating the development, maintenance and effective functionality of the intestinal mucosa and gut associated lymphoid tissues (GALTs). These microbial populations also provide a level of protection against pathogenic visitors to the gastrointestinal (GI) tract and aid host digestive function via the production of exogenous digestive enzymes and vitamins. Manipulation of these endogenous populations may provide an alternative method to antibiotics to control disease and promote health management. Applications of probiotics for Mediterranean teleosts can stimulate immune responses, enhance growth performance, feed utilisation, digestive enzyme activities, antioxidant enzyme activities, gene expression, disease resistance, larval survival, gut morphology, modulate GI microbiota and mediate stress responses. Although considerably less information is available regarding prebiotic applications for Mediterranean teleosts, prebiotics also offer benefits with regards to improving immune status and fish production. Despite the promising potential benefits demonstrated in current literature, obtaining consistent and reliable results is often difficult due to our incomplete understanding of indigenous fish GI microbiota and their subsequent host interactions which mediate and drive both localised and systemic host immunological responses. Additionally, the probiotic and prebiotic (biotics) mechanisms which mediate host benefits at the mucosal interface are poorly understood. Future studies focused on these interactions utilising gnotobiotic techniques should provide a better understanding of how to extract the full potential of biotic applications to promote immune function of Mediterranean teleosts.