Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW-DNA extraction protocols

Marine habitats are Earth's largest aquatic ecosystems, yet little is known about marine organism's genomes. Molecular studies can unravel their genetics print, thus shedding light on specie's adaptation and speciation with precise authentication. However, extracting high molecular weight DNA from marine organisms and subsequent DNA library preparation for whole genome sequencing is challenging. The challenges can be explained by excessive metabolites secretion that co-precipitates with DNA and barricades their sequencing. In this work, we sought to resolve this issue by describing an optimized isolation method and comparing its performance with the most commonly reported protocols or commercial kits: SDS/phenol–chloroform method, Qiagen Genomic Tips kit, Qiagen DNeasy Plant mini kit, a modified protocol of Qiagen DNeasy Plant kit, Qiagen DNeasy Blood and Tissue kit, and Qiagen Qiamp DNA Stool mini kit. Our method proved to work significantly better for different marine species regardless of their shape, consistency, and sample preservation, improving Oxford Nanopore Technologies sequencing yield by 39 folds for Spirobranchus sp. and enabling generation of almost 10 GB data per flow cell/run for Chrysaora sp. and Palaemon sp. samples

Molecular investigation of waterborne protozoan contamination using marine Demospongiae

Sponges play important role within aquatic ecosystems due to their diverse abilities including filter-based feeding mechanisms. Hence, this study evaluated the potential use of sponges as ecological biomonitors for water safety surveillance, especially in the presence of Waterborne protozoan pathogens WBPP. Sponge specimens were collected from different Qatari marine ecosystems and subjected to gDNA extraction and real-time PCR using specific primer sets for the most common WBPP. Two sponges from the coastal marine ecosystems were found to be positive for Blastocystis sp., and one sponge was positive for Dientamoeba fragilis within offshore site. No Cryptosporidium spp., Giardia duodenalis, nor Toxoplasma gondii were detected. Further genotyping analysis revealed that the Blastocystis sp. positive samples were subtype ST3 (allele 34), which matched local clinical isolates and D. fragilis specimen was unambiguously clustering with Genotype 2. In conclusion, this study demonstrates the role of marine sponges as ecological biomonitors for WBPP screening and provide insights into these pathogens widespread and their potential transmission to marine and terrestrial organisms including human

Deep behavioral impairment in the pearl oyster Pinctada radiata exposed to anthropogenic noise and light stress

The pearl oyster Pinctada radiata is an iconic species in the Arabian Gulf, which is one of the ecosystems most at risk in the world because of the multiple sources of pollution it faces. Alongside chemical pollution, the Gulf is ranked first with regard to noise and light pollution, and pearl oyster populations are at risk. The impact of these latter types of pollution on marine invertebrates is still poorly known. We used the difference in noise and brightness that can exist between a very quiet room without artificial lighting and a standard laboratory room equipped with a standard aquarium as a testbed to explore the possible impact of noise and light pollution on the behavioral and biological traits of Pinctada radiata without added chemical exposure. During an experiment that lasted 2.5 months, we analyzed their grouping behavior, valve activity, biological rhythm, growth rate and spawning activity. In the standard aquarium kept in the laboratory room, the oysters dispersed instead of regrouping as in their natural environment, regrouping which was observed in the quiet room. They stayed closed longer, the opening amplitude of their valves was systematically lower, and in the closed position, they squeezed their valves more tightly when subjected to noise and light pollution. Their daily opening rhythm was strongly structured by switching the electric light on and off, and females showed significantly less egg-laying behavior. In conclusion, seemingly innocuous human activities can lead to very significant alterations in pearl oyster behavior. We propose that it could have significant effects on populations and ecosystems

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.We acknowledge support from the Smithson Fellowship (C.M.F.)

Composition and spatial distribution of subtidal decapoda on the "Reef Coast", northeastern Brazil, evaluated through a low-impact visual census technique

This study investigated the composition and spatial distribution of the sublittoral decapods on the reefs of Porto de Galinhas Beach, southern coast of Pernambuco, Brazil, through the Underwater Visual Census technique. Data were collected monthly, at night during full-moon tides in low tide periods from June 2004 to May 2005, using SCUBA diving and a visual census with a fixed belt transect (20 m long). Three sampling areas were defined: Confined Waters (low hydrodynamics) with shallow sites (up to 2.5 m deep); Semi-open Water (3 to 6 m deep), influenced by waves and tidal currents (moderate hydrodynamics); and Open Water (7 to 10 m deep), in the breaker zone (high hydrodynamics). A total of 6,287 individuals of 34 species belonging to the infraorders Brachyura (19 species), Achelata and Anomura (5 species each), Caridea (3 species), and Stenopodidea and Astacidea (1 species each) were collected. Two decapod assemblages were distinguished: in a habitat with low hydrodynamics and shallow (Confined) water; and in a habitat with moderate to high hydrodynamics and depths of 3 to 10 m (Semi-open and Open water). At the sites with high hydrodynamics, i.e., the Open-water Area in the breaker zone, decapod diversity was significantly lower than in the other, protected areas on the reef bench. These results suggest that the distribution of subtidal decapods on coastal reefs is influenced by depth and exposure to water stress caused by waves and currents (hydrodynamics). The visual census technique with SCUBA proved to be suitable for ecological studies on subtidal decapods

Confirmation of the presence of Janicea antiguensis (Chace, 1972) (Decapoda: Barbouriidae) in northeastern and eastern Brazil

The barbouriid shrimp Janicea antiguesis (Chace, 1972) is reported from Porto de Galinhas and Tamandaré in Pernambuco and Guarapari in Espírito Santo, Brazil. These records confirm the presence of J. antiguensis in northeastern and eastern Brazil, considerably extending its Brazilian range from Fernando de Noronha to southern Espírito Santo and also representing the first record of this species from mainland coastal reefs. In Brazil, J. antiguensis occurs in or near marine reef caves, typically at depths between 5 and 15 m, and can be most easily observed while scuba diving at night. Colour photographs of J. antiguensis from various Atlantic localities are provided and its colour pattern is compared to that of the closely related Indo-West Pacific barbouriid shrimp, Parhippolyte misticia (Clark, 1989). Some in situ observations are provided for the Porto de Galinhas population of J. antiguensis. Multiple observations of pairs with both individuals brooding embryos at different developmental stages suggest protandric simultaneous hermaphroditism in J. antiguensis

Optimized DNA Extracting Method for Oxford Nanopore- Long reads Sequencing from Marine samples

Sustaining social and economic growth is impossible without a holistic environmental vision that places environmental preservation for Qatar's future generations at the forefront. According to the ministry of development and panning and statistics, the Qatar National Vision (QNV) 2030 aims to direct Qatar towards a balance between developmental needs and the protection of its natural environment, whether land, sea or air. As such, the QNV 2030 includes an emphasis on establishing an environmental institutions that can serve as the guardians of Qatar's environmental heritage. The QNV 2030 also emphasizes the importance of increasing citizens' awareness of their role in protecting the country's environment for their children and the nation's future generations. The State of Qatar has chosen to pursue the path of sustainable development, making it the focus of the Qatar National Development Strategy. Given the large-scale industrialization and the limited land availability, the urban environment will be crucial in maintaining native species. The presence of heavy petrochemical firms in Qatar necessitate stressing on researches related to biomonitoring of environmental ecosystem with the aim to understand and provide impactful solution for different environmental challenges affecting Qatari health, and damages local ecosystem. Due to the extreme temperatures and salinities in the gulf region, the national biodiversity has adapted to survive under extreme conditions. Furthermore, the barriers that isolates the ARABIAN GULF HAS CREATED AN ENVIRONMENT THAT IS RICH WITH ENDEMIC SPECIES THAT ARE SPECIFIC TO THE REGION. As such this project aimed to cover the gap in the genomic analysis of Qatar's rich environment. The goal was to decipher the genetic background of different animal species, marine and environmental species specific to the Qatari environmental landscape that has been previously been described by Qatar University's environmental science center. The study also deciphered the microflora in marine environment that is an important building block of the environment and an indicator of its richness. The outcomes from this study is to help in preservation of important species in Qatar and will guide the establishment of a national genomic habitat platform in Qatar

Diplomacy for the world's hottest sea

Countries that border the Persian or Arabian Gulf [hereafter, “Gulf ”] are adopting ambitious global commitments to protect their marine environments. The United Arab Emirates (UAE) has committed to protecting 30% of its lands and waters by 2030, with other Gulf states expected to soon join. Gulf countries will not meaningfully meet these and other global commitments (such as the post-2020 biodiversity framework) without rebuilding trust, exchanging knowledge, and jumpstarting conservation coordination across their maritime boundaries. Gulf scientists have an overlooked role in this work