Development of standards for assessing water quality in marine coastal waters of Bahrain.

Marine coastal waters of Bahrain are under pressure due to human activities and climate change. We used marine monitoring data (2005-2020) from 27 sites to establish baseline conditions and develop standards for assessments of water quality. Five hydrodynamic regions were identified: Oyster Beds, North, West, East, East (Coastal). Data from Oyster Beds sites, likely to be less impacted by human activities, were used to determine baseline conditions. For most parameters, candidate thresholds were based on 50 % and 100 % variation from baseline and 95th percentiles. Comparisons of data against different thresholds showed different outcomes. Overall, results indicate good water quality, with potential concerns in East (Coastal). Trend analyses showed some significant trends in all regions: downward (favourable) for some parameters (e.g. turbidity: North) and upward for others (e.g. nitrate: Oyster Beds, East and East (Coastal)). Future work requires greater understanding around optimum guidelines that protect and mitigate any adverse ecological impacts.

Antibiotic Resistance Mediated by Escherichia coli in Kuwait Marine Environment as Revealed through Genomic Analysis.

Antibiotic-resistance gene elements (ARGEs) such as antibiotic-resistance genes (ARGs), integrons, and plasmids are key to the spread of antimicrobial resistance (AMR) in marine environments. Kuwait's marine area is vulnerable to sewage contaminants introduced by numerous storm outlets and indiscriminate waste disposal near recreational beaches. Therefore, it has become a significant public health issue and warrants immediate investigation. Coliforms, especially Gram-negative Escherichia coli, have been regarded as significant indicators of recent fecal pollution and carriers of ARGEs. In this study, we applied a genome-based approach to identify ARGs' prevalence in E. coli isolated from mollusks and coastal water samples collected in a previous study. In addition, we investigated the plasmids and intl1 (class 1 integron) genes coupled with the ARGs, mediating their spread within the Kuwait marine area. Whole-genome sequencing (WGS) identified genes resistant to the drug classes of beta-lactams (blaCMY-150, blaCMY-42, blaCTX-M-15, blaDHA-1, blaMIR-1, blaOKP-B-15, blaOXA-1, blaOXA-48, blaTEM-1B, blaTEM-35), trimethoprim (dfrA14, dfrA15, dfrA16, dfrA1, dfrA5, dfrA7), fluroquinolone (oqxA, oqxB, qnrB38, qnrB4, qnrS1), aminoglycoside (aadA2, ant(3'')-Ia, aph(3'')-Ib, aph(3')-Ia, aph(6)-Id), fosfomycin (fosA7, fosA_6, fosA, fosB1), sulfonamide (sul1, sul2, sul3), tetracycline (tet-A, tet-B), and macrolide (mph-A). The MFS-type drug efflux gene mdf-A is also quite common in E. coli isolates (80%). The plasmid ColRNAI was also found to be prevalent in E. coli. The integron gene intI1 and gene cassettes (GC) were reported to be in 36% and 33%, respectively, of total E. coli isolates. A positive and significant (p < 0.001) correlation was observed between phenotypic AMR-intl1 (r = 0.311) and phenotypic AMR-GC (r = 0.188). These findings are useful for the surveillance of horizontal gene transfer of AMR in the marine environments of Kuwait.

Expanding ocean protection and peace: a window for science diplomacy in the Gulf.

The ecological state of the Persian or Arabian Gulf (hereafter 'Gulf') is in sharp decline. Calls for comprehensive ecosystem-based management approaches and transboundary conservation have gone largely unanswered, despite mounting marine threats made worse by climate change. The region's long-standing political tensions add additional complexity, especially now as some Gulf countries will soon adopt ambitious goals to protect their marine environments as part of new global environmental commitments. The recent interest in global commitments comes at a time when diplomatic relations among all Gulf countries are improving. There is a window of opportunity for Gulf countries to meet global marine biodiversity conservation commitments, but only if scientists engage in peer-to-peer diplomacy to build trust, share knowledge and strategize marine conservation options across boundaries. The Gulf region needs more ocean diplomacy and coordination; just as critically, it needs actors at its science-policy interface to find better ways of adapting cooperative models to fit its unique marine environment, political context and culture. We propose a practical agenda for scientist-led diplomacy in the short term and lines of research from which to draw (e.g. co-production, knowledge exchange) to better design future science diplomacy practices and processes suited to the Gulf's setting.

Establishing a marine monitoring programme to assess antibiotic resistance: A case study from the Gulf Cooperation Council (GCC) region.

The World Health Organization considers antimicrobial resistance as one of the most pressing global issues which poses a fundamental threat to human health, development, and security. Due to demographic and environmental factors, the marine environment of the Gulf Cooperation Council (GCC) region may be particularly susceptible to the threat of antimicrobial resistance. However, there is currently little information on the presence of AMR in the GCC marine environment to inform the design of appropriate targeted surveillance activities. The objective of this study was to develop, implement and conduct a rapid regional baseline monitoring survey of the presence of AMR in the GCC marine environment, through the analysis of seawater collected from high-risk areas across four GCC states: (Bahrain, Oman, Kuwait, and the United Arab Emirates). 560 Escherichia coli strains were analysed as part of this monitoring programme between December 2018 and May 2019. Multi-drug resistance (resistance to three or more structural classes of antimicrobials) was observed in 32.5% of tested isolates. High levels of reduced susceptibility to ampicillin (29.6%), nalidixic acid (27.9%), tetracycline (27.5%), sulfamethoxazole (22.5%) and trimethoprim (22.5%) were observed. Reduced susceptibility to the high priority critically important antimicrobials: azithromycin (9.3%), ceftazidime (12.7%), cefotaxime (12.7%), ciprofloxacin (44.6%), gentamicin (2.7%) and tigecycline (0.5%), was also noted. A subset of 173 isolates was whole genome sequenced, and high carriage rates of qnrS1 (60/173) and bla CTX-M-15 (45/173) were observed, correlating with reduced susceptibility to the fluoroquinolones and third generation cephalosporins, respectively. This study is important because of the resistance patterns observed, the demonstrated utility in applying genomic-based approaches to routine microbiological monitoring, and the overall establishment of a transnational AMR surveillance framework focussed on coastal and marine environments.

The tropical Pacific Oceanscape: Current issues, solutions and future possibilities.

Marine ecosystems across the world's largest ocean - the Pacific Ocean - are being increasingly affected by stressors such as pollution, overfishing, ocean acidification, coastal development and warming events coupled with rising sea levels and increasing frequency of extreme weather. These anthropogenic-driven stressors, which operate cumulatively at varying spatial and temporal scales, are leading to ongoing and pervasive degradation of many marine ecosystems in the Pacific Island region. The effects of global warming and ocean acidification threaten much of the region and impact on the socio-cultural, environmental, economic and human health components of many Pacific Island nations. Simultaneously, resilience to climate change is being reduced as systems are overburdened by other stressors, such as marine and land-based pollution and unsustainable fishing. Consequently, it is important to understand the vulnerability of this region to future environmental scenarios and determine to what extent management actions can help protect, and rebuild ecosystem resilience and maintain ecosystem service provision. This Special Issue of papers explores many of these pressures through case studies across the Pacific Island region, and the impacts of individual and cumulative pressures on the condition, resilience and survival of ecosystems and the communities that depend on them. The papers represent original work from across the tropical Pacific oceanscape, an area that includes 22 Pacific Island countries and territories plus Hawaii and the Philippines. The 39 papers within provide insights on anthropogenic pressures and habitat responses at local, national, and regional scales. The themes range from coastal water quality and human health, assessment of status and trends for marine habitats (e.g. seagrass and coral reefs), and the interaction of local pressures (pollution, overfishing) with increasing temperatures and climate variability. Studies within the Special Issue highlight how local actions, monitoring, tourism values, management, policy and incentives can encourage adaptation to anthropogenic impacts. Conclusions identify possible solutions to support sustainable and harmonious environment and social systems in the unique Pacific Island oceanscape.

Baseline assessment of coastal water quality, in Vanuatu, South Pacific: Insights gained from in-situ sampling.

Nearshore deterioration of water quality in Pacific coastal waters is a growing problem, associated with increasing urban and industrial sewage discharges, and agricultural runoff. Published water quality studies in the Pacific region are limited in both number and scope, making it difficult to resolve the extent of the issue or quantify the variability of water quality across Pacific islands and countries. This study collected water quality measurements over three years in the coastal waters around the Island of Efate (Vanuatu) with majority of work carried out in Port Vila, its capital. Port Vila is the key urban centre for Vanuatu where the increasing population and pollution inputs are placing substantial pressure on the coastal environment. Highest concentrations of dissolved nutrients and suspended sediments were measured adjacent or near the urban drains that enter the coastal areas along the capital's seafront, highlighting many of the issues around anthropogenic inputs are linked to the increasing urbanisation in Port Vila Bay. We provide baseline data that explores variability of coastal water quality and these types of datasets for Pacific islands are a first step towards facilitating development of long-term monitoring programmes and informing coastal zone management decision making.

Microplastic pollution as a grand challenge in marine research: A closer look at their adverse impacts on the immune and reproductive systems.

Microplastic (MP) pollution of the marine environment is now a growing global concern posing a threat to a variety of species through the ingestion and transfer within food webs. This is considered a potential toxicological threat to marine species due to the chemical additives used to make many plastic products, or the persistent organic pollutants that may accumulate on them while residing in the environment. While the presence of MPs in the marine environment is widely documented, there are no other review articles providing a summary of published effect studies of MPs on the immune and reproductive systems of marine species. This manuscript reviews reproductive and immune-system changes in response to MPs in 7 and 9 species, respectively. Some species such as Mytilus galloprovincialis and oyster Crassostrea gigas were investigated in multiple papers. Most studies have been conducted on invertebrates, and only 3 studies have been performed on vertebrates, with exposure times ranging between 30 min and 60 days. A review of the literature revealed that the most common MPs types studied in relation to adverse impacts on immune system and reproductive success in marine species were polystyrene (PS) and polyethylene (PE). The immune system's responses to MPs exposure varied depending on the species, with altered organismal defense mechanisms and neutrophil function observed in fish and changes in lysosomal membrane stability and apoptotic-like nuclear alterations in phagocytes reported in invertebrate species. Reproductive responses to MPs exposure, varied depending on species, but included significant reduction in gamete and oocyte quality, fecundity, sperm swimming speed, and quality of offspring. The lack of published data means that developing a clear understanding of the impact across taxonomic groups with different feeding and behavioral traits is often difficult. Further work is required to better understand the risk MPs pose to the immune and reproductive systems of marine species in order to fully evaluate the impact these ubiquitous pollutants are having on marine ecosystems and the associated goods and services they provide.

Evidence of microplastics (MP) in gut content of major consumed marine fish species in the State of Kuwait (of the Arabian/Persian Gulf).

Microplastics (MP), the debris that collectively refers to plastic fragments and particles of <5 mm in size within marine environments, has been the subject of interest within the past decade. Evidence of its occurrence and abundance, has been recorded in this communication after examining gastrointestinal specimens of eight commercially available fish species common to the Arabian (Persian) Gulf acquired locally from the State of Kuwait. The species studied belonged to different trophic levels, and the specimens were subjected to Micro Raman and Micro Fourier Infrared Spectroscopy (FTIR) in Attenuated Reflective Mode (ATR) to determine the presence and type of polymer of the MP. The detected MP set a president for the first time in the examined fish species within the State of Kuwait, which are of immense commercial importance. Various particles were detected, and three MP particles (fragments) were detected within the guts of Acanthopagrus latus, Eleutheronemaa tetradactylum and Lutjanus quinquelineatus. Based on the nature and behaviour of these particular fish types which prefer to stay in muddy waters and sheltered lagoons, it is suspected that common primary sources of MP (i.e. waste fragmentation) have led to passive/active intake (e.g. detritus ingestion) of these particles (fragments) by these species of fish in Kuwait.

De novo transcriptome assembly of the Qatari pearl oyster Pinctada imbricata radiata.

The pearl oyster Pinctada imbricata radiata is an iconic species in Qatar, representing an integral part of the nation's cultural heritage and one of the main economic foundations upon which the nation developed. During the early part of the 20th century, nearly half the Qatar population was involved in the pearl oyster industry. However, the fishery has undergone steady decline since the 1930s, and the species is now under threat due to multiple confounding pressures. This manuscript presents the first de novo transcriptome of the Qatari pearl oyster assembled into 30,739 non-redundant coding sequences and with a BUSCO completeness score of 98.4%. Analysis of the transcriptome reveals the close evolutionary distance to the conspecific animal Pinctada imbricata fucata but also highlights differences in immune genes and the presence of distinctive transposon families, suggesting recent adaptive divergence. This data is made available for all to utilise in future studies on the species.

The Comet Assay in Marine Animals.

Comet assay is a quick and versatile technique for assessing DNA damage in individual cells. It allows for the detection of DNA single- and double-strand breaks, as well as the presence of alkali labile sites and cross-links. Here we describe protocols for the single-cell gel electrophoresis (Comet assay) in its alkaline (pH > 13), mild alkaline (pH = 12.1) and neutral (pH = 8) versions when applied in marine animals.

Spatial and temporal analysis of biliary 1-hydroxypyrene, hepatic ethoxyresorufin-O-deethylase and muscle acetylcholinesterase activity in UK flatfish.

Chemical pollution of the marine environment from anthropogenic sources is a global concern due to the potential for long term effects on the ecosystem. Chemical monitoring schemes can detect harmful substances in water, sediment or biota. However, the presence of specific determinants gives no information on how individual species or the ecosystem are impacted. Biological effects techniques are therefore used in environmental monitoring schemes to provide a clearer picture of whether the chemicals present are causing deleterious effects on the species sampled, or whether organisms have been exposed to certain classes of organic contaminants that they may be able to metabolise. Using these techniques, we can provide an assessment of the health of our marine environment (Thain et al., 2008).

Antimicrobial resistance in the Gulf Cooperation Council region: A proposed framework to assess threats, impacts and mitigation measures associated with AMR in the marine and aquatic environment.

It is becoming increasingly clear that the genetic diversity and abundance of antimicrobial resistance (AMR) in non-clinical settings has been underestimated and that the environment plays an integral role in enabling the development of AMR. Due to specific demographic and environmental factors the Gulf Cooperation Council (GCC) region may be particularly susceptible to the threat of AMR, with the marine and aquatic environment potentially playing a specific role in its development and propagation. The demographic factors include rapid population growth, significant international population movements, heavy antibiotic use and insufficient antibiotic stewardship. Environmental factors leading to susceptibility include notable inputs of untreated sewage effluent, high ambient water temperatures, elevated concentrations of heavy metals, and poorly regulated use of antimicrobials in veterinary settings. However, to date there is only a limited understanding of the role that this environment plays in enabling the emergence and propagation AMR in this region. This article provides an overview of the risk associated with AMR in the marine and aquatic environment in the GCC region and proposes a framework for understanding how such environments interact with the wider development and propagation of resistance. It identifies priority actions aligned with the World Health Organisation AMR Global Action Plan and associated national action plans to evaluate the role of marine and aquatic systems relative to the wider factors driving AMR emergence and propagation. The proposed framework and actions to evaluate the role of marine and aquatic environments in driving propagation and emergence of AMR are equally applicable at the regional and national level beyond the GCC.

Role of Marine Snows in Microplastic Fate and Bioavailability.

Microplastics contaminate global oceans and are accumulating in sediments at levels thought sufficient to leave a permanent layer in the fossil record. Despite this, the processes that vertically transport buoyant polymers from surface waters to the benthos are poorly understood. Here we demonstrate that laboratory generated marine snows can transport microplastics of different shapes, sizes, and polymers away from the water surface and enhance their bioavailability to benthic organisms. Sinking rates of all tested microplastics increased when incorporated into snows, with large changes observed for the buoyant polymer polyethylene with an increase in sinking rate of 818 m day-1 and for denser polyamide fragments of 916 m day-1. Incorporation into snows increased microplastic bioavailability for mussels, where uptake increased from zero to 340 microplastics individual-1 for free microplastics to up to 1.6 × 105 microplastics individual-1 when incorporated into snows. We therefore propose that marine snow formation and fate has the potential to play a key role in the biogeochemical processing of microplastic pollution.

An integrated approach to assess the impacts of zinc pyrithione at different levels of biological organization in marine mussels.

The mechanisms of sublethal toxicity of the antifouling biocide, zinc pyrithione (ZnPT), have not been well-studied. This investigation demonstrates that 14-d sublethal exposure to ZnPT (0.2 or 2 µM, alongside inorganic Zn and sea water controls) is genotoxic to mussel haemocytes but suggests that this is not caused by oxidative DNA damage as no significant induction of oxidised purines was detected by Fpg-modified comet assay. More ecologically relevant endpoints, including decreased clearance rate (CR), cessation of attachment and decreased tolerance of stress on stress (SoS), also showed significant response to ZnPT exposure. Our integrated approach was underpinned by molecular analyses (qRT-PCR of stress-related genes, 2D gel electrophoresis of proteins) that indicated ZnPT causes a decrease in phosphoenolpyruvate carboxykinase (PEPCK) expression in mussel digestive glands, and that metallothionein genes are upregulated; PEPCK downregulation suggests that altered energy metabolism may also be related to the effects of ZnPT. Significant relationships were found between % tail DNA (comet assay) and all higher level responses (CR, attachment, SoS) in addition to PEPCK expression. Principal component analyses suggested that expression of selected genes described more variability within groups whereas % tail DNA reflected different ZnPT concentrations.

Baseline screening for the presence of antimicrobial resistance in E. coli isolated from Kuwait's marine environment.

Here we present the findings of a study where 598 isolates of Escherichia coli (351 derived from seawater; 247 derived from the Venus clam, Circenita callipyga) were obtained from Kuwait's marine environment. Isolates were screened for their potential resistance to an array of 23 commonly deployed frontline antibiotics. Results demonstrate the resistant was widespread across all sites with high-levels of resistance (seawater: summer 89-64%; winter 90-57% and biota: summer 77%; winter 88%) observed to at least 1 of the 23 antibiotics tested. Resistance to Ampicillin was by far the most widely observed profile in seawater and biota across both summer and winter seasons, with 55.9 to 70.9% isolates displaying resistance to this antibiotic. This study demonstrates the potential of AMR screening to be used in Kuwait to detect issues related to water quality and the consequences it may pose for human health.

Hepatocellular adenoma in a European flatfish (Limanda limanda): Genetic alterations in laser-capture micro-dissected tissue and global transcriptomic approach.

Liver tumours in flatfish have been diagnosed using histopathology for decades to monitor the impacts of marine pollution. Here we describe the application of specific gene (retinoblastoma, Rb) profiling in laser capture micro-dissected samples, and a suppression subtractive hybridization (SSH) approach to isolate differentially expressed genes in hepatocellular adenoma (HCA) samples from dab, Limanda limanda. The Rb profiles from apparently normal and HCA micro-dissected samples of fish from the North Sea showed no significant difference, and genotypic heterogeneity within defined histological phenotypes was observed. In the SSH, sequences associated with cell signalling, cell cycle, gene expression regulation, protein transport and protein degradation were isolated. These included up-regulation of arrestin domain containing 3 (arrdc3), Rac-1 and tribbles, and down-regulation of ankyrin repeat/sterile alpha-motif domain-containing protein 1B-like (ANKS1B-like), c-fos, CDKN1B and RhoA-like sequences, previously implicated in mammalian HCA. This study offers new candidates involved in fish liver tumour development.

Integration of biological effects, fish histopathology and contaminant measurements for the assessment of fish health: A pilot application in Irish marine waters.

This study investigates the use of a weight of evidence (WOE) approach to evaluate fish health status and biological effects (BEs) of contaminants for assessment of ecosystem health and discusses its potential application in support of the Marine Strategy Framework Directive (MSFD). External fish disease, liver histopathology and several BEs of contaminant exposure including 7-ethoxy resorufin O-de-ethylase (EROD), acetylcholinesterase (AChE), bile metabolites, vitellogenin (VTG) and alkali labile phosphates (ALP) were measured in two flatfish species from four locations in Ireland. Contaminant levels in fish were generally low with PCBs in fish liver below OSPAR environmental assessment criteria (EAC). There were consistencies with low PCB levels, EROD and PAH bile metabolite levels detected in fish. Dab from Cork, Dublin and Shannon had the highest relative prevalence of liver lesions associated with the carcinogenic pathway. An integrated biomarker response (IBR) showed promise to be useful for evaluation of environmental risk, although more contaminant parameters in liver are required for a full assessment with the present study.

Nanosilver inhibits nitrification and reduces ammonia-oxidising bacterial but not archaeal amoA gene abundance in estuarine sediments.

Silver nanoparticles (AgNPs) enter estuaries via wastewater treatment effluents, where they can inhibit microorganisms, because of their antimicrobial properties. Ammonia-oxidising bacteria (AOB) and archaea (AOA) are involved in the first step of nitrification and are important to ecosystem function, especially where effluent discharge results in high nitrogen inputs. Here, we investigated the effect of a pulse addition of AgNPs on AOB and AOA ammonia monooxygenase (amoA) gene abundances and benthic nitrification potential rates (NPR) in low-salinity and mesohaline estuarine sediments. Whilst exposure to 0.5 mg L-1 AgNPs had no significant effect on amoA gene abundances or NPR, 50 mg L-1 AgNPs significantly decreased AOB amoA gene abundance (up to 76% over 14 days), and significantly decreased NPR by 20-fold in low-salinity sediments and by twofold in mesohaline sediments, after one day. AgNP behaviour differed between sites, whereby greater aggregation occurred in mesohaline waters (possibly due to higher salinity), which may have reduced toxicity. In conclusion, AgNPs have the potential to reduce ammonia oxidation in estuarine sediments, particularly where AgNPs accumulate over time and reach high concentrations. This could lead to long-term risks to nitrification, especially in polyhaline estuaries where ammonia-oxidation is largely driven by AOB.

Application of a weight of evidence approach utilising biological effects, histopathology and contaminant levels to assess the health and pollution status of Irish blue mussels (Mytilus edulis).

A weight of evidence (WOE) approach, integrating biological effects, mussel histopathology and tissue contaminant levels is proposed to evaluate mussel health and pollution status. Contaminant levels, histopathology and several biological effects (BEs) including Lysosomal membrane stability (LMS), acetylcholinesterase (AChe), metallothionein proteins (MT) and alkali labile phosphate (ALP), in Mytilus edulis are presented, improving the current knowledge base for these data. Potential links between histopathology, BEs and contaminants and ranking of sites are investigated with an integrated response (IR) indexing technique. Histopathological condition indices (Ih) in mussel digestive gland are used to calculate health indices. A spatial and temporal assessment is conducted at Irish coastal locations. Linear mixed effects modelling revealed effects of confounding factors such as reproductive condition on NRRT (gonad stage (p < 0.001)). Higher prevalence of inflammation, brown cells and epithelial thinning of the digestive gland was evident at Dublin and Wexford and this linked well with the Ih. Levels of contaminants were generally found to be low with few exceptions as were BE responses. Using the IR approach, Dublin was ranked as being most impacted while Shannon ranked the least impacted, this being consistent with the BE ranking.

Dynamics of nuclear receptor gene expression during Pacific oyster development.

BACKGROUND: Nuclear receptors are a highly conserved set of ligand binding transcription factors, with essential roles regulating aspects of vertebrate and invertebrate biology alike. Current understanding of nuclear receptor regulated gene expression in invertebrates remains sparse, limiting our ability to elucidate gene function and the conservation of developmental processes across phyla. Here, we studied nuclear receptor expression in the early life stages of the Pacific oyster, Crassostrea gigas, to identify at which specific key stages nuclear receptors are expressed RESULTS: We used quantitative RT-PCR to determine the expression profiles of 34 nuclear receptors, revealing three developmental key stages, during which nuclear receptor expression is dynamically regulated: embryogenesis, mid development from gastrulation to trochophore larva, and late larval development prior to metamorphosis. Clustering of nuclear receptor expression patterns demonstrated that transcriptional regulation was not directly related to gene phylogeny, suggesting closely related genes may have distinct functions. Expression of gene homologs of vertebrate retinoid receptors suggests participation in organogenesis and shell-formation, as they are highly expressed at the gastrulation and trochophore larval initial shell formation stages. The ecdysone receptor homolog showed high expression just before larval settlement, suggesting a potential role in metamorphosis. CONCLUSION: Throughout early oyster development nuclear receptors exhibited highly dynamic expression profiles, which were not confined by gene phylogeny. These results provide fundamental information on the presence of nuclear receptors during key developmental stages, which aids elucidation of their function in the developmental process. This understanding is essential as ligand sensing nuclear receptors can be disrupted by xenobiotics, a mode of action through which anthropogenic environmental pollutants have been found to mediate effects.