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Recent Submissions

  • Untargeted Metabolomic Profiling and Antioxidant Capacities of Different Solvent Crude Extracts of Ephedra foeminea

    Al-Nemi, Ruba; Makki, Arwa A.; Sawalha, Khaled; Hajjar, Dina A.; Jaremko, Mariusz (Metabolites, MDPI AG, 2022-05-17) [Article]
    Ephedra foeminea is a traditional medicinal plant used in the Eastern Mediterranean region. This study aims to investigate the chemical profiles of different solvent extracts of E. foeminea via an untargeted metabolomics approach, alongside determining their antioxidant capacities. E. foeminea samples collected from Jordan were macerated in solvents of varying polarities; dichloromethane/methanol, methanol, ethanol, ethyl acetate, and acetone. The crude extracts were subjected to comprehensive chemical profiling and metabolomics study using Gas chromatography–Mass spectrometry (GC–MS), Liquid chromatography–Mass spectrometry (LC–MS), and Nuclear Magnetic Resonance (NMR). The obtained data were analyzed using Venn diagrams, Principle Component Analysis (PCA), and Metabolite Enrichment Set Analysis (MESA). ABTS assay was performed to measure the crude extracts’ antioxidant activity. MESA revealed the dominant chemical groups as amino acids, fatty acids, carboxylic acids, and carbohydrates. Results indicated that dichloromethane/methanol and methanolic extracts had the most distinct composition as well as the most unique compounds. The methanolic extract had the most potency (IC50 249.6 µg/mL) in the ABTS assay. However, no significant differences were found. In conclusion, solvents influenced the recovery of metabolites in E. foeminea and the antioxidant activity of the E. foeminea methanolic extract could be correlated to the abundant presence of diverse bioactive compounds.
  • Rootstock–scion combination contributes to shape diversity and composition of microbial communities associated with grapevine root system

    Marasco, Ramona; Alturkey, Hend; Fusi, Marco; Brandi, Michele; Ghiglieno, Isabella; Valenti, Leonardo; Daffonchio, Daniele (Environmental Microbiology, Wiley, 2022-05-17) [Article]
    To alleviate biotic and abiotic stresses and enhance fruit yield, many crops are cultivated in the form of grafted plants, in which the shoot (scion) and root (rootstock) systems of different species are joined together. Because (i) the plant species determines the microbial recruitment from the soil to the root and (ii) both scion and rootstock impact the physiology, morphology and biochemistry of the grafted plant, it can be expected that their different combinations should affect the recruitment and assembly of plant microbiome. To test our hypothesis, we investigated at a field scale the bacterial and fungal communities associated with the root system of seven grapevine rootstock–scion combinations cultivated across 10 different vineyards. Following the soil type, which resulted in the main determinant of the grapevine root microbial community diversity, the rootstock–scion combination resulted more important than the two components taken alone. Notably, the microbiome differences among the rootstock–scion combinations were mainly dictated by the changes in the relative abundance of microbiome members rather than by their presence/absence. These results reveal that the microbiome of grafted grapevine root systems is largely influenced by the combination of rootstock and scion, which affects the microbial diversity uptaken from soil.
  • Nutritional control regulates symbiont proliferation and life history in coral-dinoflagellate symbiosis

    Cui, Guoxin; Liew, Yi Jin; Konciute, Migle K.; Zhan, Ye; Hung, Shiou-Han; Thistle, Jana; Gastoldi, Lucia; Schmidt-Roach, Sebastian; Dekker, Job; Aranda, Manuel (BMC Biology, Springer Science and Business Media LLC, 2022-05-13) [Article]
    Background The coral-Symbiodiniaceae symbiosis is fundamental for the coral reef ecosystem. Corals provide various inorganic nutrients to their algal symbionts in exchange for the photosynthates to meet their metabolic demands. When becoming symbionts, Symbiodiniaceae cells show a reduced proliferation rate and a different life history. While it is generally believed that the animal hosts play critical roles in regulating these processes, far less is known about the molecular underpinnings that allow the corals to induce the changes in their symbionts. Results We tested symbiont cell proliferation and life stage changes in vitro in response to different nutrient-limiting conditions to determine the key nutrients and to compare the respective symbiont transcriptomic profiles to cells in hospite. We then examined the effects of nutrient repletion on symbiont proliferation in coral hosts and quantified life stage transitions in vitro using time-lapse confocal imaging. Here, we show that symbionts in hospite share gene expression and pathway activation profiles with free-living cells under nitrogen-limited conditions, strongly suggesting that symbiont proliferation in symbiosis is limited by nitrogen availability. Conclusions We demonstrate that nitrogen limitation not only suppresses cell proliferation but also life stage transition to maintain symbionts in the immobile coccoid stage. Nutrient repletion experiments in corals further confirmed that nitrogen availability is the major factor limiting symbiont density in hospite. Our study emphasizes the importance of nitrogen in coral-algae interactions and, more importantly, sheds light on the crucial role of nitrogen in symbiont life history regulation.
  • The complete mitochondrial genome of Dendrophyllia minuscula (Cnidaria: Scleractinia) from the NEOM region of the Northern Red Sea

    Terraneo, Tullia Isotta; Arrigoni, Roberto; Marchese, Fabio; Chimienti, Giovanni; Eweida, Ameer Abdulla; Rodrigue, Mattie; Benzoni, Francesca (Mitochondrial DNA Part B, Informa UK Limited, 2022-05-12) [Article]
    The scleractinian coral family Dendrophylliidae is a major component of shallow and deep-water coral ecosystems worldwide, but our knowledge on the evolutionary history of the family remains scarce. Here, we used ezRAD coupled with Illumina sequencing technology and reconstructed the complete mitochondrial genome of Dendrophyllia minuscula (GenBank accession number OL634845), from mesophotic depths in the Red Sea NEOM area. The mitochondrial genome of D. minuscula consisted of 19,054 bp, organized in 13 protein-coding genes, 2 rRNA genes, and 2 tRNA genes, in agreement with the Scleractinia typical mitogenome organization. This complete mitochondrial genome contributes toward a better knowledge of mesophotic and deep-water coral diversity and evolutionary history.
  • Penetration of ultraviolet-B radiation in oligotrophic regions of the oceans during the Malaspina 2010 Expedition

    Overmans, Sebastian; Duarte, Carlos M.; Sobrino, C.; Iuculano, F.; Álvarez-Salgado, X. A.; Agusti, Susana (Journal of Geophysical Research: Oceans, American Geophysical Union (AGU), 2022-05-10) [Article]
    Few studies have investigated ultraviolet (UV) radiation in the open ocean besides its harmful effects on organisms and influence on biogeochemical processes. Here, we assessed UV attenuation, with particular focus on UV-B, across the (sub)tropical ocean during the Malaspina 2010 Circumnavigation. Vertical UV radiometer profiles together with Chl-a concentration, and UV absorption by CDOM (aCDOM(λ)) and by suspended particulate matter (ap(λ)) were measured at 117 stations. At PAR and across UV-A and UV-B wavelengths, the lowest downwelling attenuation coefficients (Kd) during the expedition were recorded in ultra-oligotrophic regions at 5ºS–15ºS (mean Kd(305nm): 0.129 m-1, mean Kd(313nm): 0.107 m-1) in the Indian and South Pacific Oceans. The waters here were comparatively more transparent than at 5ºN–15ºN (mean Kd(305nm): 0.239 m-1, mean Kd(313nm): 0.181 m-1) where Equatorial upwelling occurs. Kd was highest near the Costa Rica Dome (Kd(313nm): 0.226 m-1) and at the confluence of the Benguela and Agulhas currents (Kd(313nm): 0.251 m-1). The contribution of ap(λ) towards non-water absorption (anw(λ)) was significantly lower at 305 nm than at 313 nm and 320 nm, suggesting the contribution of absorption by detritus and phytoplankton particles decreases compared with that of CDOM absorption as UV-B wavelength decreases. Both aCDOM(λ) and ap(λ) at UV-B wavelengths were lowest in the Indian Ocean whereas Kd was lowest in the South Pacific. This finding emphasizes that other factors besides absorption, such as scattering by reflective phytoplankton or inorganic particles, strongly influence UV-B attenuation in open ocean waters.
  • Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark

    Womersley, Freya C.; Humphries, Nicolas E.; Queiroz, Nuno; Vedor, Marisa; da Costa, Ivo; Furtado, Miguel; Tyminski, John P.; Abrantes, Katya; Araujo, Gonzalo; Bach, Steffen S.; Barnett, Adam; Berumen, Michael L.; Bessudo Lion, Sandra; Braun, Camrin D.; Clingham, Elizabeth; Cochran, Jesse; de la Parra, Rafael; Diamant, Stella; Dove, Alistair D. M.; Dudgeon, Christine L.; Erdmann, Mark V.; Espinoza, Eduardo; Fitzpatrick, Richard; Cano, Jaime González; Green, Jonathan R.; Guzman, Hector M.; Hardenstine, Royale; Hasan, Abdi; Hazin, Fábio H. V.; Hearn, Alex R.; Hueter, Robert E.; Jaidah, Mohammed Y.; Labaja, Jessica; Ladino, Felipe; Macena, Bruno C. L.; Morris, John J.; Norman, Bradley M.; Peñaherrera-Palma, Cesar; Pierce, Simon J.; Quintero, Lina M.; Ramírez-Macías, Dení; Reynolds, Samantha D.; Richardson, Anthony J.; Robinson, David P.; Rohner, Christoph A.; Rowat, David R. L.; Sheaves, Marcus; Shivji, Mahmood S.; Sianipar, Abraham B.; Skomal, Gregory B.; Soler, German; Syakurachman, Ismail; Thorrold, Simon R.; Webb, D. Harry; Wetherbee, Bradley M.; White, Timothy D.; Clavelle, Tyler; Kroodsma, David A.; Thums, Michele; Ferreira, Luciana C.; Meekan, Mark; Arrowsmith, Lucy M.; Lester, Emily K.; Meyers, Megan M.; Peel, Lauren R.; Sequeira, Ana M. M.; Eguíluz, V. M.; Duarte, Carlos M.; Sims, David W. (Proceedings of the National Academy of Sciences, 2022-05-09) [Article]
    Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (>300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial “cryptic” lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.
  • Highly diverse and geographically differentiated Symbiodiniaceae communities associated with the hydrocoral Millepora alcicornis in the Atlantic Ocean

    Garrido, Amana Guedes; de Assis Leite, Deborah Catharine; Machado, Laís Feitosa; Peixoto, Raquel S; Zilberberg, Carla (Coral Reefs, Springer Science and Business Media LLC, 2022-05-07) [Article]
    The symbiotic relationship between corals and symbiodiniaceans can favor reef formation, but is easily rupted when these organisms are exposed to thermal anomalies. Here, we assessed the ITS2 rDNA phylotype diversity of dominant Symbiodiniaceae lineages associated with the hydrocoral Millepora alcicornis and investigated host–symbiont distribution patterns in the Atlantic Ocean. This is the first effort to assess the symbiont community of this hydrocoral over nearly its entire distributional range. Millepora alcicornis is highly generalist in the composition of its photosymbiont community. We found 16 ITS2 phylotypes, mainly of the genus Breviolum but also of the genera Symbiodinium and Cladocopium; nine of them are new lineages. The distribution patterns of the M. alcicornis–Symbiodiniaceae associations were explained by differences in primary productivity, photosynthetically active radiation, water turbidity, and temperature. Six geographic sections were identified. Colonies from the Brazilian Northeastern Region showed the most stable associations, with two Breviolum phylotypes, while those from the Brazilian Eastern Region showed the most diverse symbiont community, composed of three genera of Symbiodiniaceae. A new and dominant phylotype of Breviolum was identified in the Brazilian Southern Region. Our results suggest a radiation of Breviolum lineages associated with M. alcicornis through the Atlantic Ocean. The impressive diversity of symbiotic associations observed characterizes an adaptable host–symbiont relationship, which can be key for colonization of new habitats and the resilience of milleporids to environmental changes.
  • Monitoring coastal water flow dynamics using sub-daily high-resolution SkySat satellite and UAV-based imagery

    Johansen, Kasper; Dunne, Aislinn; Tu, Yu-Hsuan; Jones, Burton; McCabe, Matthew (Water Research, Elsevier BV, 2022-05-05) [Article]
    Sub-daily tracking of dynamic features and events using high spatial resolution satellite imagery has only recently become possible, with advanced observational capabilities now available through tasking of satellite constellations. Here, we provide a first of its kind demonstration of using sub-daily 0.50 m resolution SkySat imagery to track coastal water flows, combining these data with object-based detection and a machine-learning approach to map the extent and concentration of two dye plumes. Coincident high-frequency unmanned aerial vehicle (UAV) imagery was also employed for quantitative modeling of dye concentration and evaluation of the sub-daily satellite-based dye tracking. Our results show that sub-daily SkySat imagery can track dye plume extent with low omission (8.73–16.05%) and commission errors (0.32–2.77%) and model dye concentration (coefficient of determination = 0.73; root mean square error = 28.68 ppb) with the assistance of high-frequency UAV data. The results also demonstrate the capabilities of using UAV imagery for scaling between field data and satellite imagery for tracking coastal water flow dynamics. This research has implications for monitoring of water flows and nutrient or pollution exchange, and it also demonstrates the capabilities of higher temporal resolution satellite data for delivering further insights into dynamic processes of coastal systems.
  • Global estimates of the extent and production of macroalgal forests

    Duarte, Carlos M.; Gattuso, Jean-Pierre; Hancke, Kasper; Gundersen, Hege; Filbee-Dexter, Karen; Pedersen, Morten F.; Middelburg, Jack J.; Burrows, Michael T.; Krumhansl, Kira A.; Wernberg, Thomas; Moore, Pippa; Pessarrodona, Albert; Ørberg, Sarah B.; Pinto, Isabel S.; Assis, Jorge; Queirós, Ana M.; Smale, Dan A.; Bekkby, Trine; Serrão, Ester A.; Krause-Jensen, Dorte (Global Ecology and Biogeography, Wiley, 2022-05-05) [Article]
    Aim- Macroalgal habitats are believed to be the most extensive and productive of all coastal vegetated ecosystems. In stark contrast to the growing attention on their contribution to carbon export and sequestration, understanding of their global extent and production is limited and these have remained poorly assessed for decades. Here we report a first data-driven assessment of the global extent and production of macroalgal habitats based on modelled and observed distributions and net primary production (NPP) across habitat types. Location- Global coastal ocean. Time period- Contemporary. Major taxa studied- Macroalgae. Methods- Here we apply a comprehensive niche model to generate an improved global map of potential macroalgal distribution, constrained by incident light on the seafloor and substrate type. We compiled areal net primary production (NPP) rates across macroalgal habitats from the literature and combined this with our estimates of the global extent of these habitats to calculate global macroalgal NPP. Results- We show that macroalgal forests are a major biome with a global area of 6.06–7.22 million km2, dominated by red algae, and NPP of 1.32 Pg C/year, dominated by brown algae. Main conclusions- The global macroalgal biome is comparable, in area and NPP, to the Amazon forest, but is globally distributed as a thin strip around shorelines. Macroalgae are expanding in polar, subpolar and tropical areas, where their potential extent is also largest, likely increasing the overall contribution of algal forests to global carbon sequestration.
  • Polyphasic Analysis Reveals Potential Petroleum Hydrocarbon Degradation and Biosurfactant Production by Rare Biosphere Thermophilic Bacteria From Deception Island, an Active Antarctic Volcano

    Schultz, Junia; Argentino, Isabella Campelo Vilardi; Kallies, René; Nunes da Rocha, Ulisses; Rosado, Alexandre S. (Frontiers in Microbiology, Frontiers Media SA, 2022-05-04) [Article]
    Extreme temperature gradients in polar volcanoes are capable of selecting different types of extremophiles. Deception Island is a marine stratovolcano located in maritime Antarctica. The volcano has pronounced temperature gradients over very short distances, from as high as 100°C in the fumaroles to subzero next to the glaciers. These characteristics make Deception a promising source of a variety of bioproducts for use in different biotechnological areas. In this study, we isolated thermophilic bacteria from sediments in fumaroles at two geothermal sites on Deception Island with temperatures between 50 and 100°C, to evaluate the potential capacity of these bacteria to degrade petroleum hydrocarbons and produce biosurfactants under thermophilic conditions. We isolated 126 thermophilic bacterial strains and identified them molecularly as members of genera Geobacillus, Anoxybacillus, and Brevibacillus (all in phylum Firmicutes). Seventy-six strains grew in a culture medium supplemented with crude oil as the only carbon source, and 30 of them showed particularly good results for oil degradation. Of 50 strains tested for biosurfactant production, 13 showed good results, with an emulsification index of 50% or higher of a petroleum hydrocarbon source (crude oil and diesel), emulsification stability at 100°C, and positive results in drop-collapse, oil spreading, and hemolytic activity tests. Four of these isolates showed great capability of degrade crude oil: FB2_38 (Geobacillus), FB3_54 (Geobacillus), FB4_88 (Anoxybacillus), and WB1_122 (Geobacillus). Genomic analysis of the oil-degrading and biosurfactant-producer strain FB4_88 identified it as Anoxybacillus flavithermus, with a high genetic and functional diversity potential for biotechnological applications. These initial culturomic and genomic data suggest that thermophilic bacteria from this Antarctic volcano have potential applications in the petroleum industry, for bioremediation in extreme environments and for microbial enhanced oil recovery (MEOR) in reservoirs. In addition, recovery of small-subunit rRNA from metagenomes of Deception Island showed that Firmicutes is not among the dominant phyla, indicating that these low-abundance microorganisms may be important for hydrocarbon degradation and biosurfactant production in the Deception Island volcanic sediments.
  • Home sweet home: spatiotemporal distribution and site fidelity of the reef manta ray (Mobula alfredi) in Dungonab Bay, Sudan.

    Knochel, Anna; Hussey, Nigel E; Kessel, Steven T; Braun, Camrin D; Cochran, Jesse E M; Hill, Graham; Klaus, Rebecca; Checkchak, Tarik; Elamin El Hassen, Nasereldin M; Younnis, Mohammed; Berumen, Michael L. (Movement ecology, BioMed Central Ltd, 2022-04-28) [Article]
    Background: Reef manta ray (Mobula alfredi) populations along the Northeastern African coastline are poorly studied. Identifying critical habitats for this species is essential for future research and conservation efforts. Dungonab Bay and Mukkawar Island National Park (DMNP), a component of a UNESCO World Heritage Site in Sudan, hosts the largest known M. alfredi aggregation in the Red Sea. Methods: A total of 19 individuals were tagged using surgically implanted acoustic tags and tracked within DMNP on an array of 15 strategically placed acoustic receivers in addition to two offshore receivers. Two of these acoustically monitored M. alfredi were also equipped with satellite linked archival tags and one individual was fitted with a satellite transmitting tag. Together, these data are used to describe approximately two years of residency and seasonal shifts in habitat use. Results: Tagged individuals were detected within the array on 96% of monitored days and recorded an average residence index of 0.39 across all receivers. Detections were recorded throughout the year, though some individuals were absent from the receiver array for weeks or months at a time, and generalized additive mixed models showed a clear seasonal pattern in presence with the highest probabilities of detection occurring in boreal fall. The models indicated that M. alfredi presence was highly correlated with increasing chlorophyll-a levels and weakly correlated with the full moon. Modeled biological factors, including sex and wingspan, had no influence on animal presence. Despite the high residency suggested by acoustic telemetry, satellite tag data and offshore acoustic detections in Sanganeb Atoll and Suedi Pass recorded individuals moving up to 125 km from the Bay. However, all these individuals were subsequently detected in the Bay, suggesting a strong degree of site fidelity at this location. Conclusions: The current study adds to growing evidence that M. alfredi are highly resident and site-attached to coastal bays and lagoons but display seasonal shifts in habitat use that are likely driven by resource availability. This information can be used to assist in managing and supporting sustainable ecotourism within the DMNP, part of a recently designated UNESCO World Heritage Site.
  • Inducing Polyp Bail-out in Coral Colonies to Obtain Individualized Micropropagates for Laboratory Experimental Use.

    Cardoso, Pedro M; Alsaggaf, Ahmed A; Villela, Helena M; Peixoto, Raquel S (Journal of visualized experiments : JoVE, MyJove Corporation, 2022-04-28) [Article]
    Corals are colonial animals formed by modular units called polyps. Coral polyps are physiologically linked and connected by tissue. The phenomenon of polyp bail-out is a process induced by acute stress, in which coral polyps digest the tissue connecting them to the rest of the colony and ultimately detach from the skeleton to continue living as separate individuals. Coral biologists have acknowledged the process of polyp bail-out for years, but only recently the micropropagates generated by this process have been recognized as a model system for coral biology studies. The use of polyp bail-out can create a high number of clonal units from a single coral fragment. Another benefit is that single polyps or patches of polyps can be easily visualized under a microscope and maintained in highly standardized low-cost environments such as Petri dishes, flasks, and microfluidic chips. The present protocol demonstrates reproducible methods capable of inducing coral micropropagation and different approaches for maintaining the single polyps alive in the long term. This methodology was capable of successfully cultivating polyps of the coral species Pocillopora verrucosa for up to 8 weeks after bail-out, exhibiting the practicality of using individual coral polyps for coral research.
  • Mapping seagrass meadows in coastal China using GEE

    Li, Qi; Jin, Runjie; Ye, Zhanjiang; Gu, Jiali; Li, Dan; He, Junyu; Christakos, George; Agusti, Susana; Duarte, Carlos M.; Wu, Jiaping (Geocarto International, Informa UK Limited, 2022-04-25) [Article]
    Seagrass meadows are virtual blue carbon ecosystems facing a dramatic decline on a global scale. Tracking the status and trends of seagrass meadows, which is still pending on large scales, is an emerging priority for their conservation and restoration. Here, we develop a semi-automatic procedure to identify and map seagrass meadows. Using Sentinel-2 data in Google Earth Engine (GEE) platform, a map is generated, showing a total of 11113.4 ha of seagrass meadows in coastal China in 2020. There exists the largest extent (6450.3 ha) in the coast of the South China Sea, while the second area (3909.5 ha) is in the Yellow Sea-Bohai Sea, and the seagrass meadows in the East China Sea cover about 753.6 ha. Our results provide the baseline data of seagrass meadows distribution in coastal China, and this study can be of reference for mapping seagrass meadows on a broader or even global scale.
  • Novel Hybrid 1,2,4- and 1,2,3-Triazoles Targeting Mycobacterium Tuberculosis Enoyl Acyl Carrier Protein Reductase (InhA): Design, Synthesis, and Molecular Docking

    El Sawy, Maged A.; Elshatanofy, Maram M.; El Kilany, Yeldez; Kandeel, Kamal; Elwakil, Bassma H.; Hagar, Mohamed; Aouad, Mohamed Reda; Albelwi, Fawzia Faleh; Rezki, Nadjet; Jaremko, Mariusz; El Ashry, El Sayed H. (International Journal of Molecular Sciences, MDPI AG, 2022-04-24) [Article]
    Tuberculosis (TB) caused by Mycobacterium tuberculosis is still a serious public health concern around the world. More treatment strategies or more specific molecular targets have been sought by researchers. One of the most important targets is M. tuberculosis’ enoyl-acyl carrier protein reductase InhA which is considered a promising, well-studied target for anti-tuberculosis medication development. Our team has made it a goal to find new lead structures that could be useful in the creation of new antitubercular drugs. In this study, a new class of 1,2,3- and 1,2,4-triazole hybrid compounds was prepared. Click synthesis was used to afford 1,2,3-triazoles scaffold linked to 1,2,4-triazole by fixable mercaptomethylene linker. The new prepared compounds have been characterized by different spectroscopic tools. The designed compounds were tested in vitro against the InhA enzyme. At 10 nM, the inhibitors 5b, 5c, 7c, 7d, 7e, and 7f successfully and totally (100%) inhibited the InhA enzyme. The IC50 values were calculated using different concentrations. With IC50 values of 0.074 and 0.13 nM, 7c and 7e were the most promising InhA inhibitors. Furthermore, a molecular docking investigation was carried out to support antitubercular activity as well as to analyze the binding manner of the screened compounds with the target InhA enzyme’s binding site.
  • Metabolomic Study on Tridacna maxima Giant Clams Reveals Metabolic Fingerprint of Environmental Pollutants

    Almulhim, Fatimah F.; Rossbach, Susann; Emwas, Abdul-Hamid M.; Kharbatia, Najeh M.; Jaremko, Lukasz; Jaremko, Mariusz; Duarte, Carlos M. (Accepted for publication in Frontiers in Marine Science, Frontiers, 2022-04-22) [Article]
    Metabolite profiling of marine invertebrates, such as bivalve mollusks, may not only provide insights into the health state of an individual holobiont, but also the pollution levels of their habitats. Here, we combined 1H nuclear magnetic responance (NMR) spectroscopy and mass spectrometry (MS)-based metabolomics techniques to investigate the tissue-specific metabolomic profiles of Tridacna maxima. Animals were collected from across across-shelf gradient in the Red Sea, from inshore to off-shore. We unequivocally profiled 306 metabolites and observed that the collection location had minimal effects on metabolite composition. However, we observed significant differences in metabolite profiles among different tissues (i.e., gills, mantle tissue, and digestive system). Importantly, in addition to endogenous metabolites, we detected the presence of terephthalic acid and isophthalic acid, which likely originate from marine plastic ingestion. Collectively, our study opens opportunities for a deeper understanding of Tridacna maxima physiology through metabolomics, and illustrates the power of invertebrate metabolite profiling for monitoring plastic-related aquatic pollutants.
  • Preparation, Characterization, and Electrochemical Performance of the Hematite/Oxidized Multi-Walled Carbon Nanotubes Nanocomposite

    Banbela, Hadeel M.; Alharbi, Laila M.; Al-Dahiri, Reema H.; Jaremko, Mariusz; Abdel Salam, Mohamed (Molecules, MDPI AG, 2022-04-22) [Article]
    In this research work, a hematite (α-Fe2O3) nanoparticle was prepared and then mixed with oxidized multi-walled carbon nanotubes (O-MWCNT) to form a stable suspension of an α-Fe2O3/O-MWCNTs nanocomposite. Different characterization techniques were used to explore the chemical and physical properties of the α-Fe2O3/O-MWCNTs nanocomposite, including XRD, FT-IR, UV-Vis, and SEM. The results revealed the successful formation of the α-Fe2O3 nanoparticles, and the oxidation of the MWCNT, as well as the formation of stable α-Fe2O3/O-MWCNTs nanocomposite. The electrochemical behaviour of the α-Fe2O3/O-MWCNTs nanocomposite was investigated using cyclic voltammetry (CV) and linear sweep voltammetry (LSV), and the results revealed that modification of α-Fe2O3 nanoparticles with O-MWCNTs greatly enhanced electrochemical performance and capacitive behaviour, as well as cycling stability.
  • Trade-Offs and Synergies Between Seagrass Ecosystems and Fishing Activities: A Global Literature Review

    Herrera, Mariana; Tubío, Ana; Pita, Pablo; Vázquez, Elsa; Olabarria, Celia; Duarte, Carlos M.; Villasante, Sebastián (Frontiers in Marine Science, Frontiers Media SA, 2022-04-22) [Article]
    Seagrass ecosystems support human well-being by delivering a wide range of ecosystem services. Particularly important is the significant role they play in food provisioning by supporting fisheries worldwide. Despite their socio-economic importance, it is only recently when they have been considered as important social-ecological systems worldwide. Research focused on the interactions between seagrasses and human activities have been understudied and never addressed from a global approach, even though this knowledge is essential to create relevant policy and management plans, and to promote governance systems, which consider fishers’ needs and rights. Thus, we carried out a global systematic review on trade-offs and/or synergies between seagrasses and fishing activities, aiming to analyse the current state of the art on these interactions, to identify potential gaps in knowledge, and to pinpoint key research priorities. We found a total of 94 publications assessing the relationship between seagrass ecosystems and fisheries, which have tripled between 2001-2021, being most of them empirical studies (90%) with ecological scope (a total of 68). Socioeconomic studies (3%) on the subject were identified as a knowledge gap. Most studies (72%) were carried out in northern hemisphere countries, with an underrepresentation of studies in tropical regions. The studies reporting trade-off (a total of 69) interactions almost tripled those reporting synergies (a total of 31) between seagrass ecosystems and fisheries. Mechanical damage to seagrasses by fishing gear is the main source (51%) of trade-offs, followed by overfishing (28%), while aquaculture cages’ emissions (20%) are also a relevant source of trade-offs. Seafood market demand and conflicts of use were the main drivers for trade-offs. When assessing synergistic interactions, most studies (27 out of 31) reported a larger abundance or recruitment of species with commercial interest mediated by seagrass habitat provision. Globally, seagrass ecosystems are mainly affected by industrial and small-scale fisheries, including aquaculture and shellfisheries, and to a lesser extent, by recreational fisheries. Fisheries management system is not specified in more than half (53) of the reviewed publications, which represents a key knowledge gap with implications for sustainable management. Nevertheless, we document a fast increase in studies covering fishery-seagrass interactions, which, if accompanied by better reporting of the nature of the interactions and the socio-economic context of the fishery, would help improve the sustainable management of both systems.
  • Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle

    Pogoreutz, Claudia; Oakley, Clinton A; Rädecker, Nils; Cardenas, Anny; Perna, Gabriela; Xiang, Nan; Peng, Lifeng; Davy, Simon K.; Ngugi, David K.; Voolstra, Christian R. (The ISME Journal, Springer Science and Business Media LLC, 2022-04-20) [Article]
    Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.
  • Rapid evolution of SARS-CoV-2 challenges human defenses.

    Duarte, Carlos M.; Ketcheson, David I.; Eguíluz, Víctor M; Agusti, Susana; Fernández-Gracia, Juan; Jamil, Tahira; Laiolo, Elisa; Gojobori, Takashi; Alam, Intikhab (Scientific reports, Springer Science and Business Media LLC, 2022-04-19) [Article]
    The race between pathogens and their hosts is a major evolutionary driver, where both reshuffle their genomes to overcome and reorganize the defenses for infection, respectively. Evolutionary theory helps formulate predictions on the future evolutionary dynamics of SARS-CoV-2, which can be monitored through unprecedented real-time tracking of SARS-CoV-2 population genomics at the global scale. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein determining infection success. We estimate that the > 820 million people that had been infected by October 5, 2021, produced up to 1021 copies of the virus, with 12 new effective RBD variants appearing, on average, daily. Doubling of the number of RBD variants every 89 days, followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics involving collaborative global sequencing and vaccination
  • Morphological characteristics and abundance of prokaryotes associated with gills in mangrove brachyuran crabs living along a tidal gradient

    Garuglieri, Elisa; Booth, Jenny Marie; Fusi, Marco; Yang, Xinyuan; Marasco, Ramona; Mbobo, Tumeka; Clementi, Emanuela; Sacchi, Luciano; Daffonchio, Daniele (PLOS ONE, Public Library of Science (PLoS), 2022-04-14) [Article]
    Due to the chemico-physical differences between air and water, the transition from aquatic life to the land poses several challenges for animal evolution, necessitating morphological, physiological and behavioural adaptations. Microbial symbiosis is known to have played an important role in eukaryote evolution, favouring host adaptation under changing environmental conditions. We selected mangrove brachyuran crabs as a model group to investigate the prokaryotes associated with the gill of crabs dwelling at different tidal levels (subtidal, intertidal and supratidal). In these animals, the gill undergoes a high selective pressure, finely regulating multiple physiological functions during both animal submersion under and emersion from the periodical tidal events. We hypothesize that similarly to other marine animals, the gills of tidal crabs are consistently colonized by prokaryotes that may quantitatively change along the environmental gradient driven by the tides. Using electron microscopy techniques, we found a thick layer of prokaryotes over the gill surfaces of all of 12 crab species from the mangrove forests of Saudi Arabia, Kenya and South Africa. We consistently observed two distinct morphotypes (rod- and spherical-shaped), positioned horizontally and/or perpendicularly to the gill surface. The presence of replicating cells indicated that the prokaryote layer is actively growing on the gill surface. Quantitative analysis of scanning electron microscopy images and the quantification of the bacterial 16S rRNA gene by qPCR revealed a higher specific abundance of prokaryote cells per gill surface area in the subtidal species than those living in the supratidal zone. Our results revealed a correlation between prokaryote colonization of the gill surfaces and the host lifestyle. This finding indicates a possible role of prokaryote partnership within the crab gills, with potential effects on animal adaptation to different levels of the intertidal gradient present in the mangrove ecosystem.

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