Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis).

The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed across Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to overexploitation and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was in the low-moderate range, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels was assessed. Genomic prediction accuracies using the full density panel were high (> 0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e., 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relatedness should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

Inclusion of condition in natural capital assessments is critical to the implementation of marine nature-based solutions.

Current approaches to measure ecosystem services (ES) within natural capital (NC) and nature-based solutions (NbS) assessments are generally coarse, often using a single figure for ecosystem services (e.g., nutrient remediation or blue carbon sequestration) applied to the local or national habitat stock, which fails to take account of local ecosystem conditions and regional variability. As such, there is a need for improved understanding of the link between habitat condition and ES provision, using comparable indicators in order to take more informed management decisions. Here the UK, Solent Marine Sites (SEMS) is used as a case study system to demonstrate how Water Framework Directive (WFD) 'ecological status' and other indicators of ecosystem condition (state or quality) can be coupled with habitat extent information to deliver a more precise locally-tailored NC approach for active coastal and marine habitat restoration. Habitat extent and condition data are collected for seven NbS relevant coastal habitats (littoral sediment, mat-forming green macroalgae, subtidal sediment, saltmarsh, seagrass, reedbeds and native oyster beds). The workflow includes: 1) biophysical assessment of regulatory ES; 2) monetary valuation; and 3) compilation of future scenarios of habitat restoration and creation. The results indicate that incorporating classifications by condition indices into local NC extent accounts improved ES benefits by 11-67%. This suggests that omitting condition from NC assessments could lead to undervaluation of ES benefits. Future scenarios of restoration in the SEMS also show that the additional regulatory benefits of reaching 'Good' ecological status are £376 million annually, but could be as much as £1.218 billion if 'High'status and all habitat creation targets were met. This evidence of the potential value of restoration and importance of including condition indices in assessments is highly relevant to consider when investing in water ecosystems conservation and restoration as called for by the UN Decade on Ecosystem Restoration (2021-2030), and more generally in global nutrient neutrality and blue carbon policy strategies.

The increased prevalence of Vibrio species and the first reporting of Vibrio jasicida and Vibrio rotiferianus at UK shellfish sites.

Warming sea-surface temperature has led to an increase in the prevalence of Vibrio species in marine environments. This can be observed particularly in temperate regions where conditions for their growth has become more favourable. The increased prevalence of pathogenic Vibrio species has resulted in a worldwide surge of Vibriosis infections in human and aquatic animals. This study uses sea-surface temperature data around the English and Welsh coastlines to identify locations where conditions for the presence and growth of Vibrio species is favourable. Shellfish samples collected from three locations that were experiencing an increase in sea-surface temperature were found to be positive for the presence of Vibrio species. We identified important aquaculture pathogens Vibrio rotiferianus and Vibrio jasicida from these sites that have not been reported in UK waters. We also isolated human pathogenic Vibrio species including V. parahaemolyticus from these sites. This paper reports the first isolation of V. rotiferianus and V. jasicida from UK shellfish and highlights a growing diversity of Vibrio species inhabiting British waters.

The plastic Trojan horse: Biofilms increase microplastic uptake in marine filter feeders impacting microbial transfer and organism health.

Microplastic pollution has become a major source of concern, with a large body of literature surrounding the impacts of microplastic ingestion by biota. However, many of these studies utilise virgin microbeads, which are not reflective of environmental microplastics that are rapidly colonised with microbial communities (plastisphere) in marine ecosystems. It is a concern therefore that current evidence of the impacts of microplastics on biota are unrepresentative of the environmental microplastic pollution. In this study, uptake and bioaccumulation of both virgin and Escherichia coli coated microplastics, by European native oysters (Ostrea edulis) were compared, and the physiological responses of oysters to the exposure were investigated. The uptake of E. coli coated microplastics was found to be significantly higher than the uptake of virgin microplastics, with average concentrations of 42.3 ± 23.5 no. g-1 and 11.4 ± 0.6 no. g-1 microbeads found in oysters exposed to coated and virgin microplastics, respectively. This suggests that environmental microplastic uptake into the marine trophic web by benthic filter feeders may be greater than previously thought. The oxygen consumption and respiration rate of oysters exposed to E. coli coated microplastics increased significantly over time, whilst virgin microplastics did not produce any measurable significant physiological responses. However, less than 0.5% of the total amount of administered microbeads were retained by all oysters, suggesting a limited residence time within the organisms. Although microplastics did not bioaccumulate in oyster tissues in the short-term, microorganisms assimilated by the ingestion of coated microplastics may be transferred to higher trophic levels. This poses a risk, not only for wildlife, but also for food safety and human health. The capacity to carry pathogens and expose a wide range of organisms to them means microplastics may have an important role as vectors for disease.

Assessing the natural capital value of water quality and climate regulation in temperate marine systems using a EUNIS biotope classification approach.

Using a natural capital framework to inform improvements to water quality and mitigation of climate change requires robust and spatially explicit ecosystem service data. Yet, for coastal habitats this approach is often constrained by a) sufficient and relevant habitat extent data and b) significant variability in baseline assessments used to quantify and value regulatory habitat services. Here, the European Nature Information System (EUNIS) habitat classification scheme is used to map seven key temperate coastal biotopes (littoral sediment, mat-forming green macroalgae, subtidal sediment, saltmarsh, seagrass, reedbeds and native oyster reefs) within the UK's Solent European Marine Site (SEMS). We then estimate the capacity of these biotopes to remove nitrogen (N) and phosphorus (P) and carbon (C), alongside monetary values associated with the resulting benefits. Littoral and sublittoral sediments (including those combined with macroalgae) were the largest contributors to total N, P and C removal, reflecting their large biotope area. However, our results also show considerable differences in relative biotope contributions to nutrient removal depending on how they are analysed and delineated over large spatial scales. When considered at a regional catchment level seagrass meadows, saltmarshes and reedbeds all had considerable N, P and C removal potential. Overall, we estimate that SEMS biotopes provide nutrient reductions and avoided climate damages equivalent to UK £1.1 billion, although this could be nearly £10 billion if water-treatment infrastructure costs and high carbon trading prices are utilised. Despite the variability in the final natural capital evaluations, the substantial regulatory value of N, P and C ecosystem services support a strong rational for restoring temperate coastal biotopes.

Ephemeral detection of Bonamia exitiosa (Haplosporida) in adult and larval European flat oysters Ostrea edulis in the Solent, United Kingdom.

The haplosporidian parasite Bonamia exitiosa was detected using PCR in four adult and six larval brood samples of the European flat oyster Ostrea edulis from the Solent, UK. This represents the second reported detection of this parasite along the south coast of England. Adult oysters were collected and preserved from seabed populations or restoration broodstock cages between 2015 and 2018. The larvae within brooding adults sampled during 2017 and 2018 were also preserved. Molecular analysis of all samples was performed in 2019. The DNA of B. exitiosa was confirmed to be present within the gill tissue of one oyster within the Portsmouth wild fishery seabed population (n = 48), sampled in November 2015; the congeneric parasite Bonamia ostreae was not detected in this individual. This is the earliest record of B. exitiosa in the Solent. Concurrent presence of both B. ostreae and B. exitiosa, determined by DNA presence, was confirmed in the gill and heart tissue of three mature individuals from broodstock cages sampled in October 2017 (n = 99), two from a location on the River Hamble and one from the Camber Dock in Portsmouth Harbour. B. exitiosa was not detected in the November 2018 broodstock populations. A total of six larval broods were positive for B. exitiosa, with five also positive for B. ostreae. None of the brooding adults were positive for B. exitiosa suggesting that horizontal transmission from the surrounding environment to the brooding larvae is occurring. Further sampling of broodstock populations conducted by the Fish Health Inspectorate at the Centre for Environment, Fisheries and Aquaculture Science in June 2019 did not detect infection of O. edulis by B. exitiosa. These findings together suggest that the pathogen has not currently established in the area.

Active management is required to turn the tide for depleted Ostrea edulis stocks from the effects of overfishing, disease and invasive species.

The decline of the European oyster Ostrea edulis across its biogeographic range has been driven largely by over-fishing and anthropogenic habitat destruction, often to the point of functional extinction. However, other negatively interacting factors attributing to this catastrophic decline include disease, invasive species and pollution. In addition, a relatively complex life history characterized by sporadic spawning renders O. edulis biologically vulnerable to overexploitation. As a viviparous species, successful reproduction in O. edulis populations is density dependent to a greater degree than broadcast spawning oviparous species such as the Pacific oyster Crassostrea (Magallana) gigas. Here, we report on the benthic assemblage of O. edulis and the invasive gastropod Crepidula fornicata across three actively managed South coast harbors in one of the few remaining O. edulis fisheries in the UK. Long-term data reveals that numbers of O. edulis sampled within Chichester Harbour have decreased by 96%, in contrast numbers of C. fornicata sampled have increased by 441% over a 19-year period. The recent survey data also recorded extremely low densities of O. edulis, and extremely high densities of C. fornicata, within Portsmouth and Langstone Harbours. The native oyster's failure to recover, despite fishery closures, suggests competitive exclusion by C. fornicata is preventing recovery of O. edulis, which is thought to be due to a lack of habitat heterogeneity or suitable settlement substrate. Large scale population data reveals that mean O. edulis shell length and width has decreased significantly across all years and site groups from 2015 to 2017, with a narrowing demographic structure. An absence of juveniles and lack of multiple cohorts in the remaining population suggests that the limited fishing effort exceeds biological output and recruitment is poor. In the Langstone & Chichester 2017 sample 98% of the population is assigned to a single cohort (modal mean 71.20 ± 8.78 mm, maximum length). There is evidence of small scale (<5 km) geographic population structure between connected harbors; the 2015 Portsmouth and Chichester fishery populations exhibited disparity in the most frequent size class with 36% within 81-90 mm and 33.86% within 61-70 mm, respectively, the data also indicates a narrowing demographic over a short period of time. The prevalence of the disease Bonamiosis was monitored and supports this microgeographic population structure. Infection rates of O. edulis by Bonamia ostreae was 0% in Portsmouth Harbor (n = 48), 4.1% in Langstone (n = 145) and 21.3% in Chichester (n = 48) populations. These data collectively indicate that O. edulis is on the brink of an ecological collapse within the Solent harbors. Without effective intervention to mitigate the benthic dominance by C. fornicata in the form of biologically relevant fishery policy and the management of suitable recruitment substrate these native oyster populations could be lost.

The effects of Mary Rose conservation treatment on iron oxidation processes and microbial communities contributing to acid production in marine archaeological timbers.

The Tudor warship the Mary Rose has reached an important transition point in her conservation. The 19 year long process of spraying with polyethylene glycol (PEG) has been completed (April 29(th) 2013) and the hull is air drying under tightly controlled conditions. Acidophilic bacteria capable of oxidising iron and sulfur have been previously identified and enriched from unpreserved timbers of the Mary Rose, demonstrating that biological pathways of iron and sulfur oxidization existed potentially in this wood, before preservation with PEG. This study was designed to establish if the recycled PEG spray system was a reservoir of microorganisms capable of iron and sulfur oxidization during preservation of the Mary Rose. Microbial enrichments derived from PEG impregnated biofilm collected from underneath the Mary Rose hull, were examined to better understand the processes of cycling of iron. X-ray absorption spectroscopy was utilised to demonstrate the biological contribution to production of sulfuric acid in the wood. Using molecular microbiological techniques to examine these enrichment cultures, PEG was found to mediate a shift in the microbial community from a co-culture of Stenotrophomonas and Brevunidimonas sp, to a co-culture of Stenotrophomonas and the iron oxidising Alicyclobacillus sp. Evidence is presented that PEG is not an inert substance in relation to the redox cycling of iron. This is the first demonstration that solutions of PEG used in the conservation of the Mary Rose are promoting the oxidation of ferrous iron in acidic solutions, in which spontaneous abiotic oxidation does not occur in water. Critically, these results suggest PEG mediated redox cycling of iron between valence states in solutions of 75% PEG 200 and 50% PEG 2000 (v/v) at pH 3.0, with serious implications for the future use of PEG as a conservation material of iron rich wooden archaeological artefacts.

Novel bacterial community associated with 500-year-old unpreserved archaeological wood from King Henry VIII's Tudor Warship the Mary Rose.

A 500-year-old unpreserved Mary Rose sample, historically containing an iron bolt, was analyzed using enrichment cultures and 16S sequencing. The novel community of bacteria present demonstrates a biological pathway of Fe and S oxidation and a range of acid-generating metabolisms, with implications for preservation and biogeochemical cycling.

Phylogenetic relationships elucidate colonization patterns in the intertidal grazers Osilinus Philippi, 1847 and Phorcus Risso, 1826 (Gastropoda: Trochidae) in the northeastern Atlantic Ocean and Mediterranean Sea.

Snails in the closely related trochid genera Phorcus Risso, 1826 and Osilinus Philippi, 1847 are ecologically important algal grazers in the intertidal zone of the northeastern Atlantic Ocean and Mediterranean Sea. Here we present the first complete molecular phylogeny for these genera, based on the nuclear 28S rRNA gene and the mitochondrial 16S rRNA and COI genes, and show that the current classification is erroneous. We recognize nine species in a single genus, Phorcus: estimated by BEAST analysis, this arose 30 (± 10) Ma; it consists of two subgenera, Phorcus and Osilinus, which we estimate diverged 14 (± 4.5) Ma. Osilinus kotschyi, from the Arabian and Red Seas, is not closely related and is tentatively referred to Priotrochus Fischer, 1879. Our phylogeny allows us to address biogeographical questions concerning the origins of the Mediterranean and Macaronesian species of this group. The former appear to have evolved from Atlantic ancestors that invaded the Mediterranean on several occasions after the Zanclean Flood, which ended the Messinian Salinity Crisis 5.3 Ma; whereas the latter arose from several colonizations of mainland Atlantic ancestors within the last 3 (± 1.5) Ma.

Cysteine S-glycosylation, a new post-translational modification found in glycopeptide bacteriocins.

O-Glycosylation is a ubiquitous eukaryotic post-translational modification, whereas early reports of S-linked glycopeptides have never been verified. Prokaryotes also glycosylate proteins, but there are no confirmed examples of sidechain glycosylation in ribosomal antimicrobial polypeptides collectively known as bacteriocins. Here we show that glycocin F, a bacteriocin secreted by Lactobacillus plantarum KW30, is modified by an N-acetylglucosamine ß-O-linked to Ser18, and an N-acetylhexosamine S-linked to C-terminal Cys43. The O-linked N-acetylglucosamine is essential for bacteriostatic activity, and the C-terminus is required for full potency (IC(50) 2 nM). Genomic context analysis identified diverse putative glycopeptide bacteriocins in Firmicutes. One of these, the reputed lantibiotic sublancin, was shown to contain a hexose S-linked to Cys22.